Retraction of: Hua Liu, Jing Cheng, Heng Xu and Zhenzhen Wan. Lidocaine has antitumor effect on hepatocellular carcinoma via the circ_DYNC1H1/miR-520a-3p/USP14 axis. Open Life Sciences. Volume 16, Issue 1, doi: 10.1515/biol-2021-0072.https://doi.org/10.1515/biol-2021-0072) has been retracted due to the previously undisclosed conflict of interest between the authors. Authors apologize to the entire scientific community and Editorial team for any issues ensuant from this action.“Lidocaine has antitumor effect on hepatocellular carcinoma via the circ_DYNC1H1/miR-520a-3p/USP14 axis” (


Pandemic coronavirus causes respiratory, enteric and sometimes neurological diseases. Proteome data of individual coronavirus strains were already reported. Here we investigated of SARS-CoV-2 ssRNA and protein of spike, envelope and membrane to determine stress adaptation profile. Thermodynamic properties, Physicochemical behaviour and, amino acid composition along with their RMSD value was analysed. Thermodynamic index of SARS-CoV2 spike, envelope and membrane ssRNA is unstable in higher temperature. Presence of higher proportion of polar with positive and negative charged amino acid residues into spike (S), envelope (E) and membrane (M) protein indicate the lower stress adaptability pattern. Our study represented several unstable pockets into S, E and M proteins of SARS-CoV-2 against different abiotic stresses, specifically higher in spike protein. Contact with heat through solvent may denature the architectural network of SARS-CoV-2 spike, envelope and membrane ssRNA and structural protein. The stress instability index of SARS-CoV-2 and the interactome profile of its transmembrane proteins may help to reveal novel factors for inhibiting SARS-CoV-2 growth. Zoonotic beta coronaviruses can lead to severe acute respiratory syndrome or mild pneumonia . Coronav. The envelope (E) protein of SARS-CoV-2 contains 76 to 109 amino acids with a small (7-12 amino acids) integral hydrophilic tail in C- terminal side; whereas the transmembrane portion having a large N-terminal domain with α helical nature [Coronavirus structural proteins include the spike (S)protein, envelope (E)protein, membrane (M)protein, and nucleocapsid (N)protein , 7. The l nature , 22 The l nature . The M pl nature , 24, 25.SARS-CoV-2 assemble promotes by spike protein which may influence by the expression of envelope and membrane proteins. Additionally D814 to G814 mutation into spike protein of SARS-CoV-2 increases the attachment with host which results enhancing infectivity , 27. A LStudy design: Our study's objective to evaluate and build up stress stability and instability of SARS-CoV-2 based on the ssRNA along with extracellular and transmembrane protein. SARS-CoV-2 Spike ssRNA Sequence were primarily obtained from GENBANK Database. Accession number of SARS-CoV-2 Wuhan: MT079854.1, Alpha: MZ314997, Beta: MZ314998.1, Delta: OK091006.1, Gama: MZ315141.1 and Omicron: OL672836.1 were retrieve for analysis. We focused on the physicochemical and structural properties of these three (the spike (S) protein, envelope (E) protein, membrane (M) protein) protein structures available on the PDB database 6CRV, 5X29 and 3I6G accordingly.Stability index of SARS-CoV-2 ssRNA Secondary Structures: Vienna RNA Web Services (http://rna.tbi.univie.ac.at/) predicted the secondary structure of the RNAs of SARs-Cov-2 [Rs-Cov-2 , 33. In Rs-Cov-2 .Structural Simulation with diversity: Variant of concerns (VOCs) were reported by CDC i.e alpha, beta, gamma, delta, and omicron from the five most heavily affected countries  also represented by “Nextstrain / ncov / open / global / 6m”. The corresponding amino acid sequences were taken and modelled [0 with a single point charge (SPC) water model TIP3P with periodic boundary condition (PBC). Each protein was modeled using OPLS3e force where Na+ and Cl- ions were added to neutralize the charge. The system was energy minimized 2000 steps before a production run of 50 ns. RMSD and RMSF values of the backbone atoms of proteins were calculated for determining equilibrium parameters [modelled  by usingmodelled . Using trameters . The RMSrameters .Amino acid frequency and structural elements: We computed the frequencies of amino acid residues in the protein sequences of the SARS-CoV-2 proteome by using MEGA [ing MEGA . Three mBased on the genomic organization, thermodynamics stability indexes of the SARS-CoV2 was analysed . Virus sThe thermodynamic parameters for the SARS-CoV2 single-stranded RNA are as follows: N-terminal domain (NTD), Receptor binding domain (RBD), Fusion protein (FP), Heptapeptide Repeat 1 (HR1), Heptapeptide Repeat 2 (HR2), Transmembrane region (TM), Cytoplasmic domain (CD), Envelope (E) and Membrane (M) the melting temperature were resulted 70.5 °C, 72.7°C, 87.8°C, 70.9°C, 72.6°C, 70.5°C, 70.9°C, 74.6°C, 73.3°C; whereas the Gibbs free energy were tabulated -196.46 kcal/mol,-113.8 kcal/mol,-11.2 kcal/mol, -42.8 kcal/mol, -29.3 kcal/mol, -19.8 kcal/mol, -28.1 kcal/mol, -54.7 kcal/mol and, -180.4 kcal/mol; similarly enthalpy were studied -2011.7 kcal/mol, -1101.5 kcal/mol, -79.5 kcal/mol, -433.7 kcal/mol, -248.5 kcal/mol, -202.9 kcal/mol, -284.5 kcal/mol, -531 kcal/mol and, -1720.8 kcal/mol; the entropy were resulted -5852.7 cal/mol, -3184.5 cal/mol, -220.2 cal/mol, -1260.3 cal/mol, -822.8 cal/mol, -590.3 cal/mol, -826.6 cal/mol, -1535.7 cal/mol and, -4966.6 cal/mol. These parameters indicate that the SARS-CoV2 ssRNA is unstable accordingly .Amino acid usage patterns are influenced by natural selection pressure at the protein structural stability level; we have compared the amino acids robustness in the chosen proteome which are the most dominant factor in determining stability. Structural comparisons reveal that S, M & E of all the VOC’s are similar. RMSD value of Spike, Membrane and Envelope 0.022±0.01, 0.068 and 0.055 accordingly. Furthermore, some of the propensities of non polar amino acids  with polar amino acids ( i.e Thr and Ser) were higher in the case of S protein; whereas, the opposite was noticssed in E and M protein (Supplementary Table S2). The polar, non-polar, positive and negative charge amino acids distribution were plotted and displayed into the peptide of spike , envelop).The spike protein interface exhibits five thermo-unstable cavity that buries residues 155, 247, 248 250, 254 and 258 in pocket1, pocket2  and pocket3  represented turn structure whereas pocket4  and pocket5  exhibited sheet structure . Thermo-Fig. 3FE-protein represented several stress unstable and stable complexes. The heat unstable complex, pocket1  and pocket2  both have helix structure . WhereasM-protein interface cavity consistently contained cavities, few of them was stress unstable with stable pockets. The heat unstable complex; pocket1  showed sheet structure whereas pocket2  displayed helix structure . ThermosBiothermodynamics is the exploration of the forces and processes that cause biological occurrence Gibbs energy is the driving force behind all natural processes. The Gibbs free energy in growth is influenced by the chemical constitution of the organism and also depends on the environment, especially intermolecular interactions between reaction participants. By taking over the host translation machinery , virusesSTn) pockets and two stable (PST) pockets against heat, two unstable (PSALn) and four stable (PSAL) pockets against alkali, two unstable (PSAn) and stable (PSA) pockets against acidic conditions (ETn) pockets and one stable (PET) pocket against heat, one unstable  and two stable  pockets against alkali with an acidic condition  pockets and one stable  pocket against heat and acidic conditions; similarly it also represented one unstable (PMALn) and stable (PMAL) pocket against alkaline conditions  in the interaction site of human ACE2 with SARS-CoV-2 spike protein (Supplementary Table S3), which may be considered for further studies for the development of a new efficient anti-corona drug [Spike protein of SARS-CoV-2 binds significantly to human ACE2, TMPRSS2 and CD26 are already reported through several amino acid residual interactions. We found a heat unstable pocket (Pona drug , 48. Theona drug , 50. OurWe thank the Oriental Institute of Science and Technology, India for supporting our work.The authors declare that they have no conflict of interest.Supplementary Material 1Supplementary Material 2


There are limited data on the prevalence of doravirine (DOR)-associated drug resistance mutations in people with HIV (PWH) in Botswana. This cross-sectional, retrospective study aimed to explore the prevalence of DOR-associated resistance mutations among ART-naïve and -experienced PWH in Botswana enrolled in the population-based Botswana Combination Prevention Project (BCPP).pol sequences were analysed for DOR-associated resistance mutations using the Stanford HIV drug resistance database, and their levels were predicted according to the Stanford DRM penalty scores and resistance interpretation. Virologic failure was defined as HIV-1 RNA load (VL) >400 copies/mL.A total of 6078 HIV-1C P < 0.01). Intermediate DOR-associated resistance mutations were observed in 106/1261 (7.8% [95% CI: 6.9–10.1]) in ART-naïve individuals and 29/212 (13.7% [95% CI: 9.4–8.5]) among ART-experienced participants (P < 0.01). High-level DOR-associated resistance mutations were observed in 33/1261 (2.6% [95% CI: 1.8–3.7]) among ART-naïve and 13/212 (6.1% [95% CI: 3.6–10.8]) among ART-failing PWH (P < 0.01). PWH failing ART with at least one EFV/NVP-associated resistance mutation had high prevalence 13/67 (19.4%) of high-level DOR-associated resistance mutations.Among 6078 PWH, 5999 (99%) had known ART status, and 4529/5999 (79%) were on ART at time of sampling. The suppression rate among ART-experienced was 4517/4729 (96%). The overall prevalence of any DOR-associated resistance mutations was 181/1473 ; by ART status: 42/212 (19.8% [95% CI: 14.7–25.4]) among ART-failing individuals (VL ≥400 copies/mL) and 139/1261 (11.0% [95% CI: 9.3–12.9]) among ART-naïve individuals (DOR-associated mutations were rare (11.0%) among ART-naive PWH but present in 62.7% of Botswana individuals who failed NNRTI-based ART with at least one EFV/NVP-associated resistance mutation. Testing for HIV drug resistance should underpin the use of DOR in PWH who have taken first-generation NNRTIs. The avaA newly approved third-generation NNRTI, doravirine (DOR), has been shown to be more potent, with distinct resistance patterns compared to the earlier-generation NNRTIs 22.1PWH aged 16–64 years in 30 communities in northern, central and southern parts of Botswana participated in the Botswana Combination Prevention Project (BCPP) between 2013 and 2018 2.2In this analysis, we included PWH who were either ART-naïve or ART-experienced, who had HIV-1 viral load (VL) measurement at the first BCPP study visit and had available HIV-1 sequence. HIV-1 VL of participants was quantified using Abbott m2000sp/rt assay  with a range of 40–10 000 000 copies/mL 2.3https://genome.med.harvard.edu/) and through collaboration with PANGEA HIV consortium www.sanger.ac.uk/) with high-sequencing coverage using Illumina platforms MiSeq and HiSeq Both HIV-1 proviral DNA sequences and viral RNA sequences were generated by a long-range HIV genotyping protocol described elsewhere ,23. The 2.4Generated near full-length HIV-1 sequences were subtyped by online tools REGA version 3 2.5https://hivdb.stanford.edu/hivdb/by-sequences/). The level of DOR resistance was predicted according to the Stanford HIV DRM penalty scores and resistance interpretation . Only intermediate and high-level specific DOR-associated resistance mutations were reported. The list of mutations assessed are shown in DOR-associated resistance mutations were identified according to the lists of surveillance drug resistance mutations and major drug resistance mutations (DRMs) in the Stanford University HIV Drug Resistance Database algorithm 9.1  overall; (ii) ART-naïve individuals; (iii) virologic failure (VF) on ART; and (iv) viral suppression (HIV-1 RNA ≤400 copies/mL) on ART. The DOR prevalence was compared between groups (ii) and (iii), as well as between groups (iii) and (iv). The prevalence of specific DOR-associated resistance mutations was estimated within each group and compared among groups. We also assessed the presence of DOR-associated resistance mutations in a subset of participants on NNRTI-based regimens with at least one major efavirenz (EFV)/nevirapine (NVP)-associated resistance mutation .2.6http://www.hiv.lanl.gov/) pol gene. The adjustment for hypermutations was performed before the drug resistance analysis, as a part of quality control. HIV DRMs identified as hypermutations were not included in the prevalence of DOR resistance in this study.Guanine-to-adenine transitions (G-to-A) apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC)-induced hypermutations were screened in the viral sequences using the Hypermut program available in Los Alamos National Laboratory HIV Database tools  in NNRTI-failing individuals with at least one EFV/NVP-associated resistance mutation for detection of DOR-associated resistance mutations. A P value <0.05 was considered statistically significant. All the statistical analysis was done using STATA version 14 software.Patient demographics between ART-naïve and individuals on ART experiencing VF were compared using Wilcoxon rank-sum test for continuous variables such as plasma log2.8The BCPP study was approved by the Institutional Review Board (IRB) at the U.S. Centers for Disease Control and Prevention and the Botswana IRB (HRDC), and it is registered at ClinicalTrials.gov (NCT01965470). All recruited participants provided written informed consent for participation.33.110 copies/mL) was similar to the median HIV-1 VL among individuals experiencing VF on ART . The study entry demographics of BCPP participants stratified by HIV-1 VL groups are in The median age at enrolment of the participants included in this analysis was 34 years , and study participants were mostly women (66%). Among 6078 participants, 5999 (99%) had known ART status (either ‘on ART’ or ‘ART-naive’). The majority of these participants, 4738 (79%), were on ART, whereas 1261 (21%) were ART-naïve at the time of sampling. Among 4738 participants, a total of 4729 had HIV-1 VL data; 4517 (96%) were virally suppressed (HIV-1 VL ≤400 copies/mL). The median HIV-1 VL among ART-naïve individuals . A majority of the participants harboured intermediate DOR-associated resistance mutations with a lower prevalence of 106/1261 (7.8% [95% CI: 6.9–10.1]) in ART-naïve individuals and 29/212 (13.7% [95% CI: 9.4-19.1]) among ART-experienced participants (P < 0.01). The prevalence of high-level DOR-associated resistance mutations was 33/1261 (2.6% [95% CI: 1.8–3.7]) among ART-naïve individuals and 13/212 (6.1% [95% CI: 3.6–10.8]) among individuals experiencing VF on ART (P < 0.01). Of the two intermediate DOR-associated mutations reported in the study (V106M and Y188F), V106M was the most predominant mutation, 12/1473 (0.8%), and was common among individuals experiencing VF on ART 7/212 (3.3%) (P < 0.01). Seven high-level DOR-associated mutations predicted were V106A, Y188L, F227L and M230L, which occurred in 2/1473 (0.14%) participants, F227C and Y318F in 1/1473 (0.07%) each and the G190E 33/1473 (2.2%), which was the most predominant mutation. The prevalence of specific DOR-associated resistance mutations stratified by ART groups are summarized in A total of 1473 participants with viremia were analysed for DOR-associated resistance mutations. Of these, 1261 were ART-naïve, whereas 212 were individuals experiencing VF on ART with HIV-1 VL >400 copies/mL. The overall prevalence of participants with DOR-associated resistance mutations was 181/1473 (12.3% [95% CI: 10.7–14.1]). Higher overall prevalence of DOR-associated resistance mutations was reported among individuals experiencing VF on ART, which was 42/212 (19.8% [95% CI: 14.7–25.4]) compared to 139/1261 (11.0% [95% CI: 9.3–12.9]) in the ART-naïve population  were failing ART with at least one EFV/NVP-associated resistance mutation. A total of 42/67 (62.7% [95% CI: 50.0–74.2]) had a combination of DOR- and EFV/NVP-associated resistance mutations. The overall prevalence of intermediate DOR-associated resistance mutations was 29/67 (43.3% [95% CI: 31.2–56.0]) in this group, whereas the high-level DOR resistance was reported in 13/67 (19.4% [95% CI: 10.8–30.9]). Mutation V106M (7/67:10.4%) was the most predominant intermediate mutation, followed by Y188F. In the high-level resistance group, G190E was the most prevalent at 3/67 (4.5%), followed by equal proportions of V106A and M230L mutations at 2/67 (3.0%), and, lastly, F227C, F227L and Y318F, all occurring at a prevalence of 1/67 (1.4%) each. Individuals without EFV/NVP-associated resistance mutations had no DOR-associated resistance. Among 67 participants with at least one major EFV/NVP-associated resistance mutation, 38 had dual resistance with at least one major NRTI-associated resistance mutation. The prevalence of DOR-associated resistance mutations was higher in this group: 29/38 (76%) overall prevalence, 21 (55%) intermediate and 8 (21.1%) high-level resistance.3.410 copies/mL were not associated with DOR-associated resistance mutations in a small population of 67 participants . The prevalence of intermediate DOR resistance was 735/4517 (16.3% [95% CI: 15.2–17.4]) among individuals with viral suppression on ART vs 29/212 (13.7% [95% CI:9.4–19.1]) among individuals with VF on ART (P = 0.32) and high-level DOR resistance was 175/4517 (3.9% [95% CI: 3.3–4.5]) and 13/212 (6.1% [95% CI: 3.3–10.3]) among individuals with viral suppression and those experiencing VF on ART, respectively (P = 0.11), were not statistically different in the ART-experienced population. Mutations reported in the two groups were G190E (161/4729:3.4%), V106M (21/4729:0.4%), F227L (7/4729: 0.15%), Y188L (6/4729: 0.13%), Y318F (5/4729: 0.11%), V106A and M230L were 4/4729 (0.08%) each and F227C (4/4729: 0.04%). The prevalence of DOR-associated mutations is stratified by individuals with viral suppression and VF on ART in Supplementary Table S1.We also compared the prevalence of HIV-DRMs associated with DOR resistance among individuals with viral suppression on ART (HIV-1 VL ≤400 copies/mL) compared to individuals experiencing VF on ART. The overall prevalence of mutations associated with DOR resistance was similar among individuals with viral suppression on ART, 910/4517 (20.1% [95% CI: 19.0–21.3]), compared to 42/212 (19.8% [95% CI: 14.7–25.8]) among those experiencing VF on ART (P < 0.01).Of all the 1091 participants with DOR-associated resistance, 230 (21.1% [95% CI: 18.7–23.6]) are likely to have specific DOR-associated resistance mutations and 861 (78.9% [95% CI: 76.4–81.3]) with nonspecific DOR-associated resistance mutations. Among 861 with nonspecific DOR-associated resistance mutations, 850 (98.7% [95% CI: 97.7–99.4]) and 11 (1.3% [95% CI: 0.6–2.3]) had intermediate and high-level DOR-associated resistance, respectively , confirming the opportunity for the use of DOR-containing regimens among PWH who are ART-naïve in Botswana. However, the prevalence of DOR-associated resistance among ART-naïve individuals (11.0%: 139/1261) in this study was statistically higher than the 2.9% prevalence of other NNRTI (first-generation)-associated resistance mutations previously reported in the BCPP study P < 0.01). Some studies reported higher resistance to other NNRTI-containing regimens when compared to DOR. A study from Greece, Italy and France reported a lower prevalence of DOR-associated resistance (1.4%) compared to first-generation NNRTI-associated resistance , with no association between HIV-1 subtype and presence of DOR-associated resistance mutations A significantly lower overall prevalence of DOR-associated resistance was reported among ART-naïve compared to individuals experiencing VF on ART  of DOR-associated resistance mutations was among participants failing NNRTI-based therapy in our findings, this was lower when compared to 84.8% reported in a South African study The high-level DOR-associated resistance mutations G190E, F227L and Y318F all showed a similar prevalence among the three groups: ART-naive, individuals with VF, and individuals on ART with viral suppression. The similar prevalence of these mutations across the three groups highlights the importance of gaining a better understanding of their mechanisms, particularly in ART-naïve and ART-suppressed individuals. It was difficult to determine if the presence of these mutations in ART-naïve individuals was due to undisclosed ART use in the BCPP cohort EFV has been associated with an increased risk of developing high-level DOR-associated resistance mutations Because our study had a small number of participants on DTG-based ART, our findings cannot reveal whether DOR can be used as an alternative drug for DTG-failing participants with multi-resistance mutations. As a result, future studies should investigate DOR-associated resistance mutations in DTG-failing participants with multi-drug resistance.In conclusion, the prevalence of intermediate and high-level DOR-associated resistance mutations was low among ART-naïve and ART-failing individuals, with the ART-failing group showing a statistically higher prevalence compared to the ART-naïve group. Specifically, a higher prevalence was observed among PWH with EFV/NVP-associated resistance experiencing VF. Our results support the use of DOR among ART-naïve patients in Botswana; however, we highly recommend HIV drug resistance testing among NNRTI-failing individuals before DOR-based regimen initiation.None declared.


Scientific Reportshttps://doi.org/10.1038/s41598-022-10197-w, published online 15 April 2022Correction to: The original version of this Article contained an error in the References. The authors omitted the below Reference, which is listed below as Reference 50.et al. Adsorptive purification of CO2/H2 gas mixtures of spent disposable wooden chopstick-derived activated carbon: Optimal synthesis condition. Sep. Purif. Technol.291, 120948 (2022).50. Phadungbut, P. As a result, in the caption of Figure 1 (a),“Representative SEM images (left) and HRTEM images (right) of the (a) biochar, (b) AC7-2 and (c) AC9-2 samples.”now reads:50, (b) AC7-2 and (c) AC9-2 samples.”“Representative SEM images (left) and HRTEM images (right) of the (a) biocharAs a result of the changes, the References have been renumbered.The original Article has been corrected.


The SARS-CoV-2 Omicron variant has been rapidly spreading worldwide. We aimed to characterize Omicron severity by assessing in-hospital deaths and intensive care admissions in a large healthcare system in South Florida during an Omicron predominant surge.Laboratory-confirmed COVID-19 adult patients hospitalized during January 1—14, 2022 were retrospectively reviewed. Risks of in-hospital mortality and intensive care admission were estimated using logistic regression models. Analyses were stratified by age ≥ 65 years and vaccination status, and further adjusted for sex, comorbidities, and history of a previous COVID-19 infection.p< 0.001), with the median time from hospital admission to death being 13 days  . Patients aged ≥ 65 years had 2.6 times higher rates for in-hospital mortality  than those aged < 65 years, but were comparable for ICU admission . Past vaccination offered no protection against in-hospital mortality  or ICU admission  . In multivariable-adjusted models, patients aged ≥ 65 years had a higher in-hospital mortality than those aged < 65 years .500 consecutively hospitalized COVID-19 Omicron patients were included. The median age was 69  years, and 271 (54.2%) were women. The most common comorbidities were hypertension (65.5%), diabetes (32%), and chronic kidney disease (24%). 260 (52%) patients were fully vaccinated (defined as a patient who received 2-dose vaccines), and 32 (6.4%) were previously infected with COVID-19. 252 (50.4%) patients required supplemental oxygen, 54 (10.8%) required intensive care unit (ICU) admission, and 44 (8.8%) patients required mechanical ventilation. At study closeout of March 7, 2022, case fatality rates among patients aged 18–29 years, 30–39 years, 40-49 years, 50-59 years, 60-69 years, 70-79 years, and ≥ 80 years were 0%, 2.2%, 6.4%, 5.3%, 8.0%, 5.7%, and 15.4% respectively (This case series provides characteristics and outcomes of hospitalized adult patients with COVID-19 Omicron variant. Past COVID-19 vaccination did not impact ICU admission rate nor in-hospital mortality.All Authors: No reported disclosures.


To explore why these standard treatments fail for some patients, we evaluated whether the variation in HPV oncoprotein levels among HPV+ OPSCCs affects mitochondrial metabolism, a source of antioxidant capacity. In cell line and patient-derived xenograft models, levels of HPV full-length E6 (fl-E6) inversely correlated with oxidative phosphorylation, antioxidant capacity, and therapy resistance, and fl-E6 was the only HPV oncoprotein to display such correlations. Ectopically expressing fl-E6 in models with low baseline levels reduced mitochondrial mass, depleted antioxidant capacity, and sensitized to therapy. In this setting, fl-E6 repressed the peroxisome proliferator–activated receptor gamma co-activator 1α/estrogen-related receptor α (PGC-1α/ERRα) pathway for mitochondrial biogenesis by reducing p53-dependent PGC-1α transcription. Concordant observations were made in 3 clinical cohorts, where expression of mitochondrial components was higher in tumors of patients with reduced survival. These tumors contained the lowest fl-E6 levels, the highest p53 target gene expression, and an activated PGC-1α/ERRα pathway. Our findings demonstrate that E6 can potentiate treatment responses by depleting mitochondrial antioxidant capacity and provide evidence for low E6 negatively affecting patient survival. E6’s interaction with the PGC-1α/ERRα axis has implications for predicting and targeting treatment resistance in OPSCC.Therapy with radiation plus cisplatin kills HPV  PGC-1α (PGC-1α) . Our fin+ OPSCCs with survival outcomes annotation. In The Cancer Genome Atlas (TCGA), RNA-Seq data are available from 53 OPSCCs that express high-risk HPV transcripts  and intermediate tertiles (P = 0.043) (+ OPSCC cohort (n = 47) into tertiles by the identical methodology used for TCGA cases (P = 0.048). Wide variation in therapy was apparent from characteristics of the JHU and TCGA cohorts (https://doi.org/10.1172/jci.insight.159600DS1), making the relationship between survival and response to radiation plus chemotherapy unclear. Thus, we examined a subcohort of patients within the broader VU HPV+ OPSCC cohort (n = 37). Despite small sample size, dividing these cases into tertiles revealed better 3-year OS (P = 0.041) in the lowest versus the highest tertile  . This fiC cohort . DividinGA cases  showed bC cohort  who rece tertile . This as+ OPSCC PDX models previously established by us from treatment-naive patients  mice showed a positive linear correlation with mitochondrial mass defined by MT-CO1/B2M ratio  using the Cell Mito Stress Test on the Seahorse XF platform. A strong positive correlation was shown between mitochondrial mass and basal OCR in the cell lines  and cell line models for prediction of increased mitochondrial mass, mitochondrial function, and cisplatin response. RNA-Seq was performed for the 7 HPVpatients . Upregulrd curve    . The hig E6, E7) . This as E6, E7) . No othe E6, E7) . Althougial mass , whereasial mass . Similarll lines , whereasll lines . These f+ head and neck cancer lines with highest mitochondrial mass and lowest fl-E6 (SDHB (complex II), UQCRC2 (complex III), MTCO2P12 (complex IV), ATP5F1A (complex V), ACADM (acyl-CoA dehydrogenase medium chain-1), and MDH1   were reduced by fl-E6 overexpression (tert/1 keratinocytes expressing E7 (N-tert/E7 keratinocytes)  , and theenase-1) . Similarpression . To detenocytes) . Three bnocytes) , F and Gnocytes) , H and I-CO1/B2M  and basa-CO1/B2M . Increas and Broad GDAC Firebrowse repository. A total of 53 HPVpression . RNA-Seqescribed . RNA-SeqU cohort .n = 53) were aligned to HPV genomes using Bowtie2 and samples with alignment selected and identified as containing HPV 16, HPV 33, HPV 35, or HPV 56 genomes. Gene expression values were represented by the normalized reads of reads per kilobase of transcript per million mapped reads. HPV genome sequences and annotations with gene coordinates were obtained from RefSeq (https://www.ncbi.nlm.nih.gov/refseq/). Reads with mapped coordinates corresponding to regions specific for each gene were counted. Fl-E6 expression was quantitated in a region nonoverlapping with E6*. The probe region specific to E6* overlaps fl-E6 and thus represents total E6. E6* is calculated by subtracting fl-E6 from total E6. HPV 16 gene expression analysis used GenBank K02718.1, with the following gene coordinates for quantitation: E6: 227-408, total E6: 83-226, E7: 562-858, E2: 2814-3331, E4: 3332-3619, and E5: 3863-4099. HPV 33 gene expression analysis used GenBank M12732.1, with the following gene coordinates for quantitation: E6: 232-413, total E6: 109-230, E7: 573-866, E2: 2814-3325, E4: 3326-3577, and E5: 3854-4081. HPV 35 gene expression analysis used GenBank X74477.1, with the following gene coordinates for quantitation: E6: 233-414, total E6: 110-231, E7: 562-861, E1: 868-2713, E2: 2882-3293, E4: 3294-3584, and E5: 3814-4065. HPV 56 gene expression analysis used GenBank: X74483.1, with the following gene coordinates for quantitation: E6: 234-415, total E6: 102-232, E7: 572-889, E2: 2806-3221, E4: 3222-3577, and E5: 3854-4081.RNA-Seq reads within FastQ files for each TCGA OPSCC sample . Ribosomal RNA depletion was performed with Ribo-zero rRNA Removal Kit, HMR (Illumina Inc.). Library preparation was performed with the NEBNext Ultra II Non-directional Synthesis Module (New England Biolabs). Samples were sequenced on Illumina NextSeq High Output sequencer and aligned to combined genome from hg38 (human), mm10 (mouse), and the high-risk HPV genomes — 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 — using STAR with default parameters. HPV sequences in all samples mapped to HPV 16 exclusively. After STAR first-pass alignment, reads mapped to mm10 were removed, and reads aligned to human genome (hg38) and HPV genomes were retained. Raw counts for each viral transcript  were obtained from reads mapped to each gene based on the alignment file. Fl-E6 was computed as the ratio of the average coverage level in the first intron (approximate full-length E6 level) divided by the average coverage level in the first exon . RnaSTAR was used to identify the first introns for E6*, which are, in the format of donor-acceptor, 227-408 for HPV 16. The average coverage of read pairs within the intron  was divided by the average coverage of read pairs within exon1 , where coverage was computed by dividing the number of reads by the feature width. RNA-Seq data reported here were submitted to National Center for Biotechnology Information Gene Expression Omnibus (GSE193388).The 7 treatment-naive HPVNSG mice . The PDX–/– (RRID:CVCL_HD97) cells are from ATCC. UM-SCC047 (RRID:CVCL_7759) and UMSCC104 (RRID:CVCL_7712) are from Sigma-Aldrich. UDSCC2 (RRID:CVCL_E325) and 93VU147T (RRID:CVCL_L895) cell lines were gifts from Silvio Gutkind  and Hans Joenje , respectively. Cell lines were authenticated using the Identify Mapping Kit (Coriell). They were cultured in DMEM-F12 (Gibco), 10% heat-inactivated FBS, 1% penicillin-streptomycin, and 1% nonessential amino acids. N/tert-1/E7 cells were cultured in keratinocyte serum-free medium (Thermo Fisher Scientific).SCC090 (RRID:CVCL_1899), SCC152 (RRID:CVCL_0113), SCC154 (RRID:CVCL_2230), HEK293(RRID:CVCL_0045), HCT116 (RRID:CVCL_0291), and HCT116 p53Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN). DNase I  was used to remove genomic DNA from RNA samples. Reverse transcription was performed with oligo-dT plus random decamer primers using Superscript II (Thermo Fisher Scientific). QRT-PCR was performed with SYBR green master mix (Thermo Fisher Scientific) using Step-one Plus Real-Time PCR. Primers are in Fl-E6 was expressed transiently using the pLentiN-16E6no* plasmid (RRID:Addgene_37445) and its pLentiN vector control (RRID:Addgene_37444). Transient PGC-1α overexpression was achieved with the pcDNA4 PGC-1α plasmid (RRID:Addgene_10974). A total of 4 μg of each plasmid was delivered per well in 6-well plates using Lipofectamine 2000 (Thermo Fisher Scientific) and incubated for 72 hours. SiRNA silencing of PGC-1α was performed using the mix of the 3 validated targeting siRNAs and scrambled negative control included in the PPARGC1A TriFECTa DsiRNA Kit (IDT) per supplier instructions. SiRNA was delivered at 50 nM concentration per well in 6-well plates using Lipofectamine RNAiMax (Thermo Fisher Scientific) and incubated for 72 hours.tert-E7 cells were similarly infected with the control and E6 viruses before blasticidin selection, propagation, and analysis of bulk cultures.The pLentiN-16E6no* plasmid containing full-length E6 and its pLentiN vector backbone control were used for stable fl-E6 expression. Lentiviral preparation and transduction were performed as described . BrieflyHPV 16 E6 mutant constructs 16E6, 16E6 (V42L), 16E6-8S9A10T, 16E6-I128T, and 16E6* are previously described . The pGLp-trifluoro-methoxyphenyl hydrazone, and 2 μM each of antimycin and rotenone (Sigma-Aldrich). Total protein per well was determined afterward with the Pierce BCA Protein Assay Kit (Thermo Fisher Scientific). Results were analyzed using XFe Wave software (Seahorse Bioscience), and 1 × 105 cells were used to measure NADPH and NADP+ levels using an NADP+/NADPH colorimetric quantitation kit (Sigma-Aldrich).Mitochondrial DNA content was determined by qPCR as described . OCR wasCell viability after 72-hour treatment with cisplatin, DMNQ, MnTMPyP, and/or MitoTEMPO (Sigma-Aldrich) was determined by WST-1 and/or BrdU assays (Sigma-Aldrich). Cisplatin dissolved in saline was administered intraperitoneally in vivo at 2 mg/kg. For irradiation, cells were harvested during exponential growth and plated at 2,000 cells/mL in 60 mm dishes containing 2 mL media. After 12 hours, they received 2, 4, or 6 Gy using a Gammacell 40 irradiator (Best Theratronics). Media were changed postirradiation. Colonies were stained with crystal violet (Thermo Fisher Scientific) and counted 10 days later.t tests. Pearson correlation coefficients were based on analyzing the means. Two-way ANOVA was used when comparing xenograft growth curves. Log-rank tests were used for Kaplan-Meier analyses. P values were calculated for multiple comparisons using a 1-way ANOVA corrected with Dunnett’s or Holm-Šidák procedure. Tests used are indicated in figure legends. Analyses were performed using Prism (GraphPad Software). A P value less than 0.05 was considered significant.When comparing 2 groups for cell viability or gene expression, significance was calculated using 2-tailed unpaired Mouse experiments were performed under Wistar Institute IACUC protocols 201166 and 201178 . PDXs were previously established under University of Pennsylvania IRB-approved protocol 417200 “Head and Neck Cancer Specimen Bank”  by signing a combined informed consent and HIPAA form for use of tissue for research. All clinical data shown are obtained from deidentified, publicly available data sets.MKS and DB conceived the study. DB, MKS, EAW, IMM, and BEW wrote and edited the manuscript and/or designed figures and tables. MKS, PR, LL, and VS performed experiments. PAG, PR, MKS, XW, XL, and BEW performed bioinformatic and/or statistical analyses. DB, EAW, PAG, DPK, and HN supervised the study and data analysis. DB, JBJ, RMB, XW, and XL analyzed clinical and/or pathologic data. All authors read and approved the final manuscript.


H)-one represents a new template for AKA inhibitors, with antiproliferative activity against cancer cells. A quinazolin-4(3H)-one derivative was further designed and synthesized in order to improve the pharmacokinetic properties and antiproliferation activity against NSCLC cell lines. The derivative, BIQO-19 (Ethyl 6-(4-oxo-3-(pyrimidin-2-ylmethyl)-3,4-dihydroquinazolin-6-yl)imidazo pyridine-2-carboxylate), exhibited improved solubility and antiproliferative activity in NSCLC cells, including epidermal growth factor receptor–tyrosine kinase inhibitor (EGFR-TKI)-resistant NSCLC cells. BIQO-19 effectively inhibited the growth of the EGFR-TKI-resistant H1975 NSCLC cells, with the suppression of activated AKA (p-AKA) expression in these cells. The inhibition of AKA by BIQO-19 significantly induced G2/M phase arrest and subsequently evoked apoptosis in H1975 cells. In addition, the combination of gefitinib and BIQO-19 exhibited synergistic antiproliferative activity in NSCLC cells. These findings suggest the potential of BIQO-19 as a novel therapeutic agent for restoring the sensitivity of gefitinib in EGFR-TKI-resistant NSCLC cells.Non-small cell lung cancer (NSCLC) is the most common lung cancer subtype. Although chemotherapy and targeted therapy are used for the treatment of patients with NSCLC, the survival rate remains very low. Recent findings suggested that aurora kinase A (AKA), a cell cycle regulator, is a potential target for NSCLC therapy. Previously, we reported that a chemical entity of quinazolin-4(3 Lung cancer is the leading cause of death from cancer, and constitutes almost 25% of all cancer-related deaths . Lung caAurora kinase is a serine/threonine kinase which plays an important role in cell cycle regulation . The higH)-one is a well-known core heterocycle pharmacophore used in medicinal chemistry that exhibits a variety of biological activities, including sedative, antiviral, antibacterial, anti-inflammatory, and anticancer effects pyridine-2-carboxylate) as an FL-4 derivative (H)-one derivative FL-4 +. Compound 5, 6-(6-aminopyridin-3-yl)-3-(pyrimidin-2-ylmethyl)quinazolin-4(3H)-one, was obtained as a white solid, yield 83.4%, ESI-MS: m/z 331.1 [M + H]+. BIQO-19 was separated as white crystals, yield 87.4%, m.p. 284–286 °C. 1H-NMR  δ 8.68 , 8.49 , 8.41 , 8.24 , 8.21 , 7.96 , 7.86 , 7.76 , 7.57 , 7.23 , 5.45 , 4.46 , 1.44 . 13C-NMR  δ 164.50, 163.17, 161.06, 157.58, 148.15, 147.78, 144.54, 137.61, 135.54, 132.70, 128.76, 126.98, 126.59, 125.0, 123.8, 122.9, 120.2, 119.3, 117.6, 61.4, 51.7, 14.5. HRMS (ESI-QTOF) m/z Calcd. For C23H19O3N6 [M + Na]+ m/z: 449.1333, found: 449.1324. NMR and high resolution mass spectras are shown in The synthesis of the compound BIQO-19 is summarized in Culture media, fetal bovine serum, antibiotic-antimycotic solution , and trypsin-EDTA solution (1×) were purchased from Gibco . Gefitinib (CAS No. HY-50895) was purchased from MedChemExpress . Trichloroacetic acid (TCA), sulforhodamine B (SRB), crystal violet solution, and bovine serum albumin (BSA) were purchased from Sigma-Aldrich . Anti-aurora kinase A (#14475), anti-p-aurora kinase A (T288) (#3079), anti-p21 Waf1/Cip1 (#2947), anti-cdc2 (#9116), anti-cdc25C (#4688), anti-PARP (#9532), anti-Cleaved PARP (D214) (#5625), anti-Caspase-8 (#9746), and anti-Cleaved Caspase-8 (D374) (#9496) antibodies were obtained from Cell Signaling Technology .The ADMET properties of the FL-4 and BIQO-19 compounds were calculated with the ADMET descriptors of Discovery Studio 3.0. The ADMET descriptors parameter was set as the default. Each of the ADMET profile levels were categorized by following the criteria. ADMET_Solubility_Level: 0  < −8.0), 1  < −6.0), 2  < −4.1), 3  < −2.0), 4  ≤ 0.0), 5 ), 6 (warning: molecules with one or more unknown AlogP98 types). ADMET_BBB_Level: 0 , 1 , 2 , 3 , 4 (undefined).2.The human non-small lung cancer cell lines A549, NCI-H1975, NCI-H1299, and NCI-H1993 were purchased from the American Type Culture Collection . The human non-small cell lung cancer cell lines HCC827, PC9, HCC827-gef and PC9-gef were a kind gift from Dr. Jae Cheol Lee and Dr. Jin Kyung Rho . HCC827-gef and PC9-gef cells were subcultured in the presence of 1 µM gefitinib. All cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic. Cells were incubated at 37 °C in a humidified atmosphere with 5% COw/v) SRB in 1% acetic acid for 2 h at room temperature. The stained proteins were dissolved in 10 mM Tris solution (pH 10) and measured the absorbance at 515 nm with a VersaMax ELISA microplate reader .Cell viability was measured using the SRB method as described previously . BrieflyCells (500 cells/well) were seeded and cultured overnight. The compounds were treated for 48 h, the cells were washed with phosphate buffered saline (PBS), and continued incubation. Culture medium was replaced every three days for ten days. Cells were fixed with 4% paraformaldehyde solution and stained with 0.1% crystal violet.http://www.kmplot.com/lung, accessed on 6 April 2022). A total of 1925 lung cancer patient gene expression values and survival data were analyzed using multiple microarray datasets [The OS of patients with lung cancer and adenocarcinoma with different expression levels of Aurora Kinase A was analyzed through a Web-based meta-analysis Kaplan–Meier plotter . Recombinant human aurora A protein (Active) (ab271368) and Recombinant human aurora B protein (Active) (ab51435) were purchased from Abcam . Myelin basic protein was selected as a substrate and staurosporine was used as a positive control. The ADP-Glo The cells were collected and lysed in sample loading buffer . Total protein concentrations were quantified using a BCA Protein Assay Kit . Quantified proteins were loaded onto SDS-polyacrylamide gels and separated by molecular weight via electrophoresis (PAGE). Then, proteins were transferred to polyvinylidene fluoride membranes ; 5% BSA in Tris-buffered saline containing 0.1% Tween-20 (TBST) was used for blocking. The membranes were blocked for 30 min at room temperature with mild shaking, then incubated with antibodies diluted in 2.5% BSA in TBST overnight at 4 °C with mild shaking. Following secondary antibody incubation and washing with TBST, the chemiluminescence signals were detected using the WEST-Queen detection system  and LAS-4000 .A molecular simulation was carried out using the Molecular Operating Environment . BIQO-19 was built in MOE using the Builder program and energy-minimized for docking simulation. The 3D structure of aurora A (PDB ID: 6C2T) was obtain from the PDB databank and optimized, 3-D protonated, and energy-minimized using the default parameters of MOE. The docking site was defined by the Site Finder application, including the residues within 10 Å of the cocrystallization ligand. The docking results were analyzed using Accelrys Discovery Studio Visualizer 4.5.TM Pro version 6.0 software .Cells were seeded and starved in serum-free medium overnight. After starvation, the cells were treated with compounds for the indicated times. After incubation, cells were harvested, washed with PBS, and fixed with 70% ethanol in PBS overnight at −20 °C. The fixed cells were washed with PBS, resuspended in 100 µg/mL of RNase A for 30 min at room temperature, and stained with 50 µg/mL PI. Fluorescence intensity was analyzed using a FACSCalibur flow cytometer  and BD CellQuestTM Pro version 6.0 software .Cells were treated with samples for 72 h and stained with an Annexin V-FITC apoptosis detection kit  according to the manufacturer’s instructions. Briefly, cells were collected after 72 h treatment, washed with PBS, resuspended in 1× binding buffer, and stained with Annexin V-FITC and PI in the dark for 15 min. After incubation, the cells were diluted with 1× binding buffer and analyzed using an FACSCalibur flow cytometer  and BD CellQuestp < 0.05, ** p < 0.01, *** p < 0.001) was calculated using one-way analysis of variance coupled with Dunnett’s t-test or Student’s t-test.Data were obtained from three independent experiments, and are shown as the means ± standard deviation. Statistical significance -one derivative, BIQO-19, which is an aurora kinase A inhibitor that exhibits an improved ADMET profile and antiproliferative activity in NSCLC cells. The mechanisms of action for the antiproliferative activities of BIQO-19 in EGFR-TKI-resistant NSCLC H1975 cells involve aurora kinase A-mediated arrest at the G2/M phase of the cell cycle and the induction of apoptosis. Combined treatment with BIQO-19 and gefitinib exhibits synergetic activity with respect to inhibiting proliferation and inducing apoptosis in H1975 cells. Therefore, targeting aurora kinase A using a new class of inhibitors in combination with EGFR-TKIs represents a potential therapeutic strategy for treating patients with EGFR-TKI-resistant NSCLC.


The geometric mean end-point titer (GMT) of anti-RBD-IgG in PLWH was also reduced, especially in patients with CD4 counts <200 cells/µL, regardless of age, gender, or HIV viral load. GMTs of anti-RBD-IgG in both PLWH and healthy controls declined gradually over time. Similar results were also observed in the anti-spike-IgG response. The frequency of RBD-specific MBCs in PLWH decreased (p<0.05), and then remained stable over time. Lastly, through multivariate analysis, we found the factors that predicted a less robust response to inactivated vaccines in PLWH were a low CD4 count and long time interval after vaccination. In conclusion, inactivated vaccines are well-tolerated in PLWH but with low immunogenicity. Therefore, SARS-CoV-2 vaccines and booster doses should be given priority in PLWH, especially in patients with low CD4 counts.It is important to know the safety and efficacy of vaccination in immunocompromised people living with HIV (PLWH), but currently, there is limited data on the inactivated SARS-CoV-2 vaccines’ safety and immune responses in PLWH. In this prospective observational study, 139 PLWH and 120 healthy controls were enrolled and monitored for 21–105 days after a two-dose vaccination. The safety, anti-receptor binding domain IgG (anti-RBD-IgG) and anti-spike-IgG responses, and RBD-specific memory B cell (MBC) responses were evaluated. The overall adverse events within seven days were reported in 12.9% (18/139) of PLWH and 13.3% (16/120) of healthy controls. No serious adverse events occurred in both groups. Overall, the seroprevalence of anti-RBD-IgG in PLWH was significantly decreased (87.1% vs. 99.2%; Trial registration:ClinicalTrials.gov identifier: NCT05043129.. The coronavirus disease 2019 (COVID-19) epidemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in 2019 and has continued to rage worldwide, bringing a heavy burden to global public health . Even th+ T cell loss after receiving an inactivated COVID-19 vaccine in a treatment-naïve HIV-positive patient was reported by a recent study  vs. 278.6 [95% CI: 204.1–380.4], p<0.05; 3 months: 93.3 [95% CI: 68.66–126.8] vs. 150.8 [95% CI: 109.9–206.8], p<0.05; 2 AU/mL, IQR [1.67–2.90 log2 AU/mL] vs. 2.64 log2 AU/mL, IQR [2.07–3.94 log2 AU/mL], p<0.01; 2 months: 1.42 log2 AU/mL, IQR [1.23–4.63 log2 AU/mL] vs. 2.17 log2 AU/mL, IQR [1.88–2.86 log2 AU/mL], p = 0.169; 3 months: 1.65 log2 AU/mL, IQR [1.38–2.01 log2 AU/mL] vs. 1.78 log2 AU/mL, IQR [1.21–2.29 log2 AU/mL], p = 0.786; To better understand the variation of humoral immune responses with passing time, we stratified three groups by time interval after full-course vaccination in the cross-sectional analysis. As expected, GMTs of anti-RBD-IgG gradually decreased over time in both PLWH and healthy controls. However, GMTs of anti-RBD-IgG in PLWH were sharply lower than that of healthy controls at every time point (1 month: 155.3 [95% CI: 128.3–188.1] vs. 441.6 [95% CI: 355–549.5], In summary, the weakened antibody response in PLWH kept on falling over time, whereas the impaired MBC response did not change over time.p<0.001; 2 AU/mL, IQR [1.72–2.98 log2 AU/mL] vs. 1.61 log2 AU/mL, IQR [1.41–2.03 log2 AU/mL]; p<0.001; To further explore the dynamic changes of antibody levels in PLWH, a longitudinal analysis was conducted in PLWH. Of the 96 PLWH observed after 1 month, 52 were followed up to the 6th month. As expected, GMTs of anti-RBD-IgG showed a clear downward trend in the 6th month compared with the 1st month (219.6 [95% CI: 179.3–268.8] vs. 97.37 [95% CI: 83.99–112.9]; Lastly, we wanted to investigate the risk factors related to inferior response to anti-RBD-IgG in PLWH. As shown in In this prospective study, we evaluated the safety, antibody responses, and RBD-specific MBC responses of inactivated SARS-CoV-2 vaccines in PLWH and healthy controls. Our results showed that inactivated vaccines were safe and well-tolerated in PLWH. The antibody and MBC responses waned in PLWH, especially in PLWH with CD4 counts <200 cells/µL. Therefore, PLWH should be vaccinated ahead of the healthy population.PLWH with SARS-CoV-2 have poor clinical outcomes, especially those who are immunosuppressed or do not receive ART ,19. HoweOur results showed that PLWH had lower anti-RBD-IgG and anti-spike-IgG titers than healthy controls 21–105 days after vaccination, which is consistent with previous studies showing that PLWH had lower immune responses to the vaccine than healthy individuals . Previou+ T cells and a series of immune abnormalities [The level of immunosuppression is usually reflected by the CD4 cell counts . Usuallymalities . Howevermalities . In thismalities ,11. Thismalities . Of notemalities , hence, The MBCs produced during primary infection are quickly reactivated after a secondary infection, thus, preventing severe disease or death ,15. HencThere are some limitations in this study. First, few subjects participated in the follow-up until month 6 after full vaccination because the sporadic localized outbreaks of COVID-19 partially impeded travel. Second, the early stages of B and T cell responses were not evaluated, as we were mainly focusing on the significance of durable humoral immune responses. Therefore, further studies about the early stages of B and T cell responses in PLWH are needed. Third, the best correlation of antibody titers and vaccine efficacy in PLWH is currently unknown, and more large-scale population studies are needed. Nonetheless, we believe our results are particularly important and meaningful to clinicians.In conclusion, the inactivated SARS-CoV-2 vaccines are safe and well-tolerated in people living with HIV, with no serious adverse events reported. However, the antibody response and RBD-specific MBC response were weak, especially in PLWH with a low CD4 count. Therefore, SARS-CoV-2 vaccines and booster doses should be prioritized for this special population.Click here for additional data file.


Trichoderma strains isolated from forest species of the Cerrado-Caatinga ecotone as biological control agents of crop pathogenic fungi. Nineteen Trichoderma strains were used to assess the antagonistic activity by in vitro bioassays against the plant pathogens Colletotrichum truncatum, Lasiodiplodia theobromae, Macrophomina phaseolina, and Sclerotium delphinii isolated from soybean, cacao, fava bean, and black pepper crops, respectively. All Trichoderma strains demonstrated inhibitory activity on pathogen mycelial growth, with maximum percent inhibition of 70% against C. truncatum, 78% against L. theobromae, 78% against M. phaseolina, and 69% against S. delphinii. Crude methanol extracts (0.5 to 2.0 mg mL-1) of Trichoderma strains were able to inhibit the growth of C. truncatum, except Trichoderma sp. T3 (UFPIT06) and T. orientale (UFPIT09 and UFPIT17) at 0.5 mg mL-1, indicating that the endophytes employ a biocontrol mechanism related to antibiosis, together with multiple mechanisms. Discriminant metabolites of Trichoderma extracts were unveiled by liquid chromatography-tandem mass spectrometry-based metabolomics combined with principal component analysis (PCA), which included antifungal metabolites and molecules with other bioactivities. These results highlight the biocontrol potential of Trichoderma strains isolated from the Cerrado-Caatinga ecotone against crop pathogenic fungi, providing support for ongoing research on disease control in agriculture.The indiscriminate use of chemical pesticides increasingly harms the health of living beings and the environment. Thus, biological control carried out by microorganisms has gained prominence, since it consists of an environmentally friendly alternative to the use of pesticides for controlling plant diseases. Herein, we evaluated the potential role of endophytic  Diseases caused by fungi are among the most harmful to plants due to their rapid spread and the ability to adapt to various environmental conditions . The mosResearch on alternative methods of controlling fungal diseases has been widely developed, often requiring the integrated implementation of several methods, known as integrated disease management (IDM) , 4. AmonA promising alternative method for plant pathogen control is based on the use of antagonistic microorganisms, such as endophytic fungi, capable of protecting their hosts from the action of pathogens , 9. ThesRecent research has revealed that although endophytic microorganisms have received global interest, there are still several gaps in knowledge, such as the different biomes explored . ConsideThe Cerrado and Caatinga biomes are recognized for their great importance. The Cerrado, also known as the Brazilian savanna, is one of the 25 biodiversity hotspots for conservation priorities in the world , 17, andTrichoderma species have been tried as BCA and used as an alternative to synthetic pesticides to control a variety of plant diseases + was identified as trigonelline (T. longibrachiatum (UFPIT02), Trichoderma sp. T2 (UFPIT05), T. koningiopsis (UFPIT07), Trichoderma sp. T5 (UFPIT11), Trichoderma sp. T6 (UFPIT13), and T. koningiopsis (UFPIT19) isolates. The MS/MS spectrum was characterized by the fragment of m/z 92.0496 [__HCOOH]+, referring to the carboxylic acid group +, identified as phomalone , T. longibrachiatum (UFPIT02), and T. orientale  isolates was identified as columbianetin  and Trichoderma sp. T6 (UFPIT13) isolates. The metabolite of m/z 419.1713 detected in T. orientale (UFPIT01), T. longibrachiatum (UFPIT02), Trichoderma sp. T6 (UFPIT13), and T. orientale  isolates were identified as syringaresinol , was identified as brefeldin-A (BFA) . The metabolite of m/z 453.1914 was identified as physodic acid , was identified as HT-2 toxin  and T. longibrachiatum (UFPIT02) isolates. The metabolite of m/z 163.0393 detected in all Trichoderma spp. was identified as 4-hydroxycoumarin , L. theobromae (B), M. phaseolina COUFPI 10 and COUFPI 11 (C), and S. delphinii COUFPI 209 and COUFPI 249 (D) paired with Trichoderma strains. Means followed by the same letter do not differ from each other by the Scott–Knott test at the 5% probability level. The coefficients of variation (CVs) were 20.51% for L. theobromae, 15.99% for M. phaseolina COUFPI 10, 19.13% for M. phaseolina COUFPI 11, 10.68% for S. delphinii COUFPI 209, and 9.54% for S. delphinii COUFPI 249. Different lowercase letters indicate a significant difference between Trichoderma spp. Different capital letters indicate a significant difference between Trichoderma spp.Mycelial growth rate index (MGRI) of (TIF)Click here for additional data file.S2 Fig(TIF)Click here for additional data file.S3 Fig(TIF)Click here for additional data file.S4 Fig(TIF)Click here for additional data file.S5 Fig(TIF)Click here for additional data file.S6 Fig(TIF)Click here for additional data file.S7 Fig(TIF)Click here for additional data file.S8 Fig-1, 8.45% for 1.0 mg mL-1 and 9.36% for 2.0 mg mL-1.The coefficients of variation (CVs) were 4.65% for the concentration of 0.5 mg mL(TIF)Click here for additional data file.S9 FigTrichoderma spp. cultures generated using MetaboAnalyst. Con = Control, UFPIT01 = T1, UFPIT02 = T2, UFPIT03 = T3, UFPIT04 = T4, UFPIT05 = T5, UFPIT06 = T6, UFPIT07 = T7, UFPIT08 = T8, UFPIT09 = T9, UFPIT10 = T10, UFPIT11 = T11, UFPIT12 = T12, UFPIT13 = T13, UFPIT14 = T14, UFPIT15 = T15, UFPIT16 = T16, UFPIT17 = T17, UFPIT18 = T18, and UFPIT19 = T19.PC1 x PC2 (A) and PC1 x PC3 (B) loading plots of metabolic fingerprints of (TIF)Click here for additional data file.S10 Fig(TIF)Click here for additional data file.S11 Fig(TIF)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.


Q2 and Q4 of non-HDL-C were associated with increased odds of SICH  compared to Q3. Q1 and Q2 of LDL-C was associated with increased odds of mortality  compared to Q3. In AIS patients who received IV tPA, low LDL-C was associated with increased odds of mortality while HDL-C may be protective against poor functional outcome.Contradicting evidence exists regarding the role of lipids in outcomes following intravenous (IV) thrombolysis with tissue plasminogen activator (tPA). Restricted cubic spline curves and adjusted logistic regression were used to evaluate associations of low-density lipoprotein cholesterol (LDL-C), non-high-density lipoprotein cholesterol (non-HDL-C), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and LDL-C/HDL-C ratio with poor functional outcome, symptomatic intracranial hemorrhage (SICH) and 90-day mortality, among 1004 acute ischemic stroke (AIS) patients who received IV tPA in a comprehensive stroke center. Quartile (Q) 1, Q2 and Q3 of HDL-C were associated with increased odds of poor functional outcome (adjusted odds ratio (adjOR) 1.66, 95% CI 1.06–2.60,  Stroke incidence and stroke-related mortality increased substantially from 1990 to 2019, and the stroke burden will continue to increase globally, especially in underdeveloped countries ,4, with In this study, we included consecutive patients who received IV tPA from September 2006 to June 2018. All these patients had no contraindications to IV tPA use. The study obtained ethics approval from the National Healthcare Group-Domain Specific Review Board (NHG DSRB Ref: 2010/00509). Patients were assessed by a neurologist for eligibility to receive intravenous thrombolysis according to institutional protocol and American Heart Association/American Stroke Association guidelines at a standard dose of 0.9 mg/kg body weight [LDL-C was calculated by the Friedewald equation (TC-HDL-C-TG/5) , while sThe primary outcome measured was poor functional outcome  of 3–6). Secondary outcomes measured were symptomatic intracranial hemorrhage (SICH) and 90-day all-cause mortality. SICH was based on the European Cooperative Acute Stroke Study (ECASS) II definition . The 90-p < 0.05.Analyses were performed using SPSS for Windows version 27.0  and R version 4.0.5. Restricted cubic splines with 5 knots were plotted to visually assess the univariate associations between the lipid parameters and the three outcomes. These served qualitative and descriptive purposes only. Since non-linear (U-shaped/inverse U-shaped/J-shaped/reverse tick) associations were found, lipid parameters were divided into quartiles for analysis. Descriptive statistics for continuous variables were presented as mean (SD) when normality and homogeneity assumptions were satisfied, otherwise as median (interquartile range) (IQR), and n (%) for categorical variables. Differences in continuous variables were assessed using 2 sample t-test when normality and homogeneity assumptions were satisfied; otherwise, Mann-Whitney U test was used where data was not distributed normally. Chi-square or Fisher’s exact test was used for categorical variables. Covariates that were selected a priori for variable adjustment were gender, age, hypertension, atrial fibrillation, large vessel occlusion, diabetes mellitus, admitting NIHSS and admitting SBP. Logistic regression assessed the associations between lipid levels and outcomes, and with LAA. Results were presented as adjusted odds ratio (adjOR) with 95% confidence interval (CI). Statistical significance was set at two-sided This section may be divided by subheadings. It should provide a concise and precise description of the experimental results, their interpretation, as well as the experimental conclusions that can be drawn.1265 consecutive patients with ischemic stroke treated with IV tPA were analyzed and 1004 patients with valid lipid assessments were included in this study. Of 1004 patients, 589/986 (59.7%) were male, 586/883 (66.4%) were of Chinese ethnicity, 596/916 (65.1%) experienced a LVO and 190/1004 (18.9%) had AF. There were 657/1004 (65.4%) patients with history of with hypertension, 526/1004 (52.4%) with hyperlipidemia, and 306/1004 (30.5%) with diabetes mellitus. Median age was 66 (IQR 56–77) years while median admitting NIHSS was 15 (IQR 8–21). Median LDL-C, non-HDL-C, TC, HDL-C and LDL-C/HDL-C were 2.86 (IQR 2.18–3.50) mmol/L, 3.43 (IQR 2.70–4.19) mmol/L, 4.62 (IQR 3.86–5.36) mmol/L, 1.12 (IQR 0.95–1.32) mmol/L and 2.49 (IQR 1.84–3.30) respectively. In accordance with the TOAST classification, 322/975 (33.0%) had LAA stroke, 341/975 (35.0%) had cardioembolic (CE) stroke, 168/975 (17.2%) had small vessel occlusion (SVO), 10/975 (1.0%) had stroke of other determined etiology and 134/975 (13.7%) had cryptogenic stroke .p = 0.024) compared to Q1. Q2 and Q4 of non-HDL-C was significantly associated with increased odds of LAA  compared to Q1. Q3 of HDL-C was associated with increased odds of LAA  compared to Q4. Lastly, Q3 and Q4 of LDL-C/HDL-C were associated with increased odds of LAA  compared to Q1  count, neutrophils, platelets, admitting NIHSS and presence of LVO were significantly higher in the LAA compared to non-LAA group . Regardied to Q1 .Of 1004 patients, 479/995 (48.1%) experienced poor functional outcomes (mRS 3–6), 48/1003 (4.8%) suffered SICH and 117/990 (11.8%) died.  There waWhen evaluating the following relationships between lipid parameters and outcomes measured, variables adjusted for in the multivariate model include gender, age, hypertension, atrial fibrillation, large vessel occlusion, diabetes mellitus, admitting NIHSS and admitting SBP. Restricted cubic spline curves showed a ‘reverse tick’ relationship between LDL-C, non-HDL-C and TC with poor functional outcome .p = 0.028, adjOR 1.63, 95% CI 1.05–2.53, p = 0.027 and OR 1.56, 95% CI 1.01–2.44, p = 0.048 respectively) when compared to Q4. Q2 and Q4 of LDL-C/HDL-C ratio were associated increased odds of poor functional outcome  when compared to Q3  when compared to Q3. Similarly, Q2 and Q4 of TC were significantly associated with increased odds SICH  when compared to Q3. Q2 of HDL-C remained significantly associated with increased odds of SICH  when compared to Q1  when compared to Q3. Q2 of LDL-C/HDL-C was associated with increased odds of mortality  when compared to Q3. No significant associations were found to relate non-HDL-C, TC and HDL-C with mortality on multivariate analysis  compared to previous thrombolysis studies. However, this study was a single institution retrospective cohort study that solely evaluated intravenous thrombolysis patients. This may limit the generalisability of results to other cohorts, warranting more prospective studies on lipid parameters and ischemic stroke outcomes. We would like to acknowledge the possibility of Type I error in the multivariate analyses in which significant associations may no longer hold true after Bonferroni correction. Excessive correction of statistical level of significance may also increase the likelihood of Type II error as a trade-off to reduce Type I error, which may increase false negatives. The multivariate relationship between HDL-C and poor functional outcome is to be interpreted with caution as no significant relationship was found on univariate analysis, in which the possible reasons can be explained statistically by Lo et al. and Wang et al. ,39. HencIn AIS patients who received IV tPA, low LDL-C was associated with increased odds of mortality while HDL-C may be protective against poor functional outcome.


Microbacterium foliorum NRRL B-24224. The genome has a length of 17,453 bp and contains 25 total protein-coding genes, 20 of which were assigned functions. Based on gene content, Burgy was assigned to actinobacteriophage cluster EE.Burgy is a siphovirus that was isolated from compost soil near Fremont Township, Iowa, using  Actinobacteria have been identified throughout aquatic, soil, and animal microbiomes  , using standard methods ( plating . Transmi (n = 4) .M. foliorum (68.7%) (DNA was isolated from Burgy using the Promega Wizard DNA cleanup kit. The genome was sequenced using an Illumina MiSeq sequencer (v3 reagents) after the library was prepared using the NEBNext Ultra II FS kit, yielding 640,328 single-end 150-bp reads, which constituted ~5,500-fold coverage. Raw reads were assembled and checked for completeness using Newbler v2.9 with default parameters and Consed v29, respectively, as described previously (iorum 68.% (7). Buhttp://cobamide2.bio.pitt.edu/computer.htm), PECAAN (https://blog.kbrinsgd.org/), HHPRED (http://phages.wustl.edu/starterator), TMHMM v2.0  accession no. SRX14443487.The sequencing results for Burgy are available in GenBank with accession no.


Clostridium botulinum is responsible for botulism, a potentially lethal foodborne intoxication. Here, we report the draft genome sequences of C. botulinum group II strains 202F (serotype F) and Hazen (serotype E). The genomes share many similarities, including multiple mobile genetic elements. Clostridium botulinum is an anaerobic, Gram-positive, spore-forming bacterium that produces the neurotoxin that causes botulism (C. botulinum strains are divided into four groups (I to IV)  , with moI to IV) , 5. HereC. botulinum strains 202F and Hazen were originally isolated from marine sediments in California, USA, in 1965  (Francisella sp. strain MA067296 plasmid (CP016929.1) was identified in 202F. Another plasmid  with 99% sequence homology to C. botulinum pCBI (CP006904.1)  indicative of a putative phage-like plasmid.Sequencing of strain 202F yielded 845,112 raw reads and 34 contigs with 30× median coverage, while 629,334 raw reads and 80 contigs with 25× median coverage were obtained for strain Hazen. The 202F and Hazen genomes comprise 3,829,425 bp and 3,821,401 bp, respectively, and both have 27.2% G+C content. Strain 202F contained 3,496 protein-coding sequences and 121 RNAs, while Hazen had 3,422 protein-coding sequences and 120 RNAs. A comparative analysis between the previously sequenced 202F genome (GenBank accession number C. botulinum strains 202F and Hazen have been deposited in DDBJ/ENA/GenBank under accession numbers NPMX00000000.1 and NPMY00000000.1 for the contigs and SRA accession numbers SRR17916278 and SRR17916277 for the raw reads, respectively.The genome sequences of


Residents and staff of continuing care retirement communities (CCRC) experienced many challenges during the COVID-19 pandemic including loss, social isolation, and staff turnover. This study examined factors that contribute to resilience in staff during the late stage of the pandemic using the Connor-Davidson Resilience Scale. Resilience scores ranged from 0 (low) to 100 (high). A total of 96 staff  were enrolled, and average age was 48.41 years (SD = 16.16). Average resilience in staff was 75.16 (SD = 11.81). Those under 35 years of age reported lower resilience scores (M = 67.38) compared to those 35-49 years of age (M = 76.65), 50-64 (M = 75.83), and 65 years and older (M = 82.71), p <.05. Staff who were married scored higher than those who were not (M = 76.63 vs 69.05), p < .05. Findings can inform professional development programs aimed at increasing coping skills in staff.


Correction to: BMC Psychiatry 22, 106 (2022)https://doi.org/10.1186/s12888-022-03764-yFollowing publication of the original article , the aut5. Mangolian Shahrbabaki P, Dehghan M, Maazallahi M, Asadi N. Fear and anxiety in girls aged 7 to 11 years old and related factors during the coronavirus pandemic. Clin Child Psychol Psychiatry. 2022;27(1):259-68.The original article  has been


We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong during November 2021–February 2022. In addition to Omicron and Delta variants, we detected a BA.1/BA.2 recombinant with a breakpoint near the 5′ end of the spike gene in 2 epidemiologically linked case-patients. Continued surveillance for SARS-CoV-2 recombinants is needed. We previously demonstrated the feasibility of testing incoming travelers for SARS-CoV-2 genomic surveillance (The SARS-CoV-2 Omicron variant (Pango lineage B.1.1.529) emerged in November 2021. Within a few weeks, subvariants BA.1, BA.1.1, and BA.2 were detected in varying proportions on different continents, but BA.1 initially was dominant (>100). Deduced genomes predominantly were Delta (n = 58) and Omicron  variants (Using our previously described next-generation sequencing method  Table 1.https://www.pfizer.com); patient 1 received the second dose on November 1, 2021, and patient 2 received the second dose on June 22, 2021.In our phylogenetic analysis, 2 additional nearly identical sequences formed a distinct branch in the Omicron clade  Figure 2https://www.medrxiv.org/content/10.1101/2022.03.03.22271812v2; T. Peacock, unpub. data, https://github.com/cov-lineages/pango-designation/issues/441).The distinct topology of viral sequences from these patients suggested that they were infected by a recombinant virus. To test that hypothesis, we used previously reported BA.1- and BA.2-defining single-nucleotide polymorphisms (SNPs) to analyze the genomes . We founWe further examined our sequence data to exclude the possibility of coinfection or contamination , panel AWe found no similar BA.1/BA.2 recombinant sequences in GISIAD or GenBank , suggesting a novel recombinant. The BA.1 region of this recombinant virus is genetically close to 3 BA.1 sequences detected in Europe and the United States , panel Bhttps://doi.org/10.1101/2020.08.05.238386; P. Colson et al., unpub. data; T. Peacock, unpub. data). The high transmissibility of Omicron (Emerging Omicron subvariants could allow vaccine breakthrough and widespread reinfection. Previous studies reported detection of SARS-CoV-2 interlineage recombinants at the same time as different SARS-CoV-2 lineages were cocirculating (Additional information recombinant BA.1/BA.2 SARS-CoV-2 virus in arriving travelers, Hong Kong, China, February 2022.


S-gene) amplification (SGTF) in real-time reversetranscription–polymerase chain reaction (RT-PCR) was used as a proxy indicator ofinfection with likely BA.5-related sublineages and S-gene targetpresence (SGTP) of infection with likely XBB/XBB.1.5-related sublineages . Specimenswith missing Ct values for N or ORF1ab were excluded.SARS-CoV-2–positive specimens with either null or reduced amplification of thespike S-gene  were considered tohave SGTF  or SGTP (XBB/XBB.1.5-related); control-patients werethose who received a negative NAAT result. Tests among persons fulfilling any offollowing criteria were excluded from analyses: 1) presence of an immunocompromisingconditionAs of January 16, 2023, genomic sequencing data were available for a random subset ofICATT specimens with SGTP and collection dates through January 2, showing an increase inXBB.1.5 prevalence over time. During December 1, 2022–January 2, 2023, XBB.1.5comprised 33% (495) of specimens exhibiting SGTP. During the interval December11–January 2, XBB.1.5 accounted for 38% of sequenced ICATT specimens with SGTP(377), and during the interval December 18–January 2, XBB.1.5 accounted for 43%of sequenced ICATT specimens with SGTP (252) were positive for SARS-CoV-2, including 10,596(78%) with SGTF (BA.5-related) and 3,052 (22%) with SGTP (XBB/XBB.1.5-related) . More coAcross age groups, VE was generally similar against BA.5-related infections andXBB/XBB.1.5-related infections. VE against symptomatic BA.5-related infection was 52%among persons aged 18–49 years, 43% among persons aged 50–64, and 37%among those aged ≥65 years . VEagaiThis report provides the first estimates of bivalent mRNA COVID-19 VE againstsymptomatic SARS-CoV-2 infection with XBB-related sublineages. These preliminaryestimates from national pharmacy testing conducted during December 1,2022–January 13, 2023, showed relative bivalent booster dose VE  to be similar for XBB/XBB.1.5sublineage–related infections and BA.5 sublineage–related infections.VE estimates for both sublineages included in this analysis were similar toestimates from the same ICATT network published during a period of Omicron BA.5,BQ.1, and BQ.1.1 sublineage circulation in fall 2022 -gene target presence as a proxy for BA.2sublineages, including XBB and XBB.1.5, during December 2022–January2023, the results showed that a bivalent mRNA booster dose providedadditional protection against symptomatic XBB/XBB.1.5 infection for at leastthe first 3 months after vaccination in persons who had previously received2–4 monovalent vaccine doses.Using spike (As new SARS-CoV-2 variants emerge, continued vaccine effectiveness monitoringis important. All persons should stay up to date with recommend COVID-19vaccines, including receiving a bivalent booster dose when eligible.