Identification of the CD8+ T-cell Related Signature for Predicting the Prognosis of Gastric Cancer Based on Integrated Analysis of Bulk and Single-cell RNA Sequencing Data.

The infiltration of CD8+ T cells in the tumor microenvironment is associated with better survival and immunotherapy response. However, their roles in gastric cancer have not been explored so far. In here, the profiles of GC gene expression were collected from The Cancer Genome Atlas database. Single-cell transcriptomic data originated from GSE134520. Cell clustering, annotation, and CD8+ T-cell differential genes were from the TISCH database. We determined 896 CD8+ T-cell differential genes by scRNA-seq analysis. After integrating immune-related genes, 174 overlapping genes were obtained and a novel risk model was subsequently built. The performance of CD8+ T-cell-associated gene signature was assessed in the training and external validation sets. The gene signature showed independent risk factors of overall survival for GC. A quantitative nomogram was built to enhance the clinical efficacy of this signature. Furthermore, low-risk individuals showed higher mutation status, higher immune checkpoint expression, low Tumour Immune Dysfunction and Exclusion (TIDE) scores, and higher IPS-PD-1 combined IPS-CTLA4 scores, indicating a greater response to immunotherapy. In addition, analysis of IMvigor210 immunotherapy cohort demonstrated that low-risk individuals had a favorable response to prognosis and immunotherapy. In conclusion, we generated a CD8+ T-cell-related signature that can serve as a promising tool for personalized prognosis prediction and guiding decisions regarding immunotherapy in GC patients.

Dermoscopy-based Radiomics Help Distinguish Basal Cell Carcinoma and Actinic Keratosis: A Large-scale Real-world Study Based on a 207-combination Machine Learning Computational Framework.

This study has used machine learning algorithms to develop a predictive model for differentiating between dermoscopic images of basal cell carcinoma (BCC) and actinic keratosis (AK). We compiled a total of 904 dermoscopic images from two sources - the public dataset (HAM10000) and our proprietary dataset from the First Affiliated Hospital of Dalian Medical University (DAYISET 1) - and subsequently categorised these images into four distinct cohorts. The study developed a deep learning model for quantitative analysis of image features and integrated 15 machine learning algorithms, generating 207 algorithmic combinations through random combinations and cross-validation. The final predictive model, formed by integrating XGBoost with Lasso regression, exhibited effective performance in the differential diagnosis of BCC and AK. The model demonstrated high sensitivity in the training set and maintained stable performance in three validation sets. The area under the curve (AUC) value reached 1.000 in the training set and an average of 0.695 in the validation sets. The study concludes that the constructed discriminative diagnostic model based on machine learning algorithms has excellent predictive capabilities that could enhance clinical decision-making efficiency, reduce unnecessary biopsies, and provide valuable guidance for further treatment.

Energy-guided diffusion model for CBCT-to-CT synthesis.

Cone Beam Computed Tomography (CBCT) plays a crucial role in Image-Guided Radiation Therapy (IGRT), providing essential assurance of accuracy in radiation treatment by monitoring changes in anatomical structures during the treatment process. However, CBCT images often face interference from scatter noise and artifacts, posing a significant challenge when relying solely on CBCT for precise dose calculation and accurate tissue localization. There is an urgent need to enhance the quality of CBCT images, enabling a more practical application in IGRT. This study introduces EGDiff, a novel framework based on the diffusion model, designed to address the challenges posed by scatter noise and artifacts in CBCT images. In our approach, we employ a forward diffusion process by adding Gaussian noise to CT images, followed by a reverse denoising process using ResUNet with an attention mechanism to predict noise intensity, ultimately synthesizing CBCT-to-CT images. Additionally, we design an energy-guided function to retain domain-independent features and discard domain-specific features during the denoising process, enhancing the effectiveness of CBCT-CT generation. We conduct numerous experiments on the thorax dataset and pancreas dataset. The results demonstrate that EGDiff performs better on the thoracic tumor dataset with SSIM of 0.850, MAE of 26.87 HU, PSNR of 19.83 dB, and NCC of 0.874. EGDiff outperforms SoTA CBCT-to-CT synthesis methods on the pancreas dataset with SSIM of 0.754, MAE of 32.19 HU, PSNR of 19.35 dB, and NCC of 0.846. By improving the accuracy and reliability of CBCT images, EGDiff can enhance the precision of radiation therapy, minimize radiation exposure to healthy tissues, and ultimately contribute to more effective and personalized cancer treatment strategies.

An immune-related gene prognostic prediction risk model for neoadjuvant chemoradiotherapy in rectal cancer using artificial intelligence.

Background: This study aimed to establish and validate a prognostic model based on immune-related genes (IRGPM) for predicting disease-free survival (DFS) in patients with locally advanced rectal cancer (LARC) undergoing neoadjuvant chemoradiotherapy, and to elucidate the immune profiles associated with different prognostic outcomes. Methods: Transcriptomic and clinical data were sourced from the Gene Expression Omnibus (GEO) database and the West China Hospital database. We focused on genes from the RNA immune-oncology panel. The elastic net approach was employed to pinpoint immune-related genes significantly impacting DFS. We developed the IRGPM for rectal cancer using the random forest technique. Based on the IRGPM, we calculated prognostic risk scores to categorize patients into high-risk and low-risk groups. Comparative analysis of immune characteristics between these groups was conducted. Results: In this study, 407 LARC samples were analyzed. The elastic net identified a signature of 20 immune-related genes, forming the basis of the IRGPM. Kaplan-Meier survival analysis revealed a lower 5-year DFS in the high-risk group compared to the low-risk group. The receiver operating characteristic (ROC) curve affirmed the model's robust predictive capability. Validation of the model was performed in the GSE190826 cohort and our institution's cohort. Gene expression differences between high-risk and low-risk groups predominantly related to cytokine-cytokine receptor interactions. Notably, the low-risk group exhibited higher immune scores. Further analysis indicated a greater presence of activated B cells, activated CD8 T cells, central memory CD8 T cells, macrophages, T follicular helper cells, and type 2 helper cells in the low-risk group. Additionally, immune checkpoint analysis revealed elevated PDCD1 expression in the low-risk group. Conclusions: The IRGPM, developed through random forest and elastic net methodologies, demonstrates potential in distinguishing DFS among LARC patients receiving standard treatment. Notably, the low-risk group, as defined by the IRGPM, showed enhanced activation of adaptive immune responses within the tumor microenvironment.

A SwinTransformer-Based Segmentation Framework With Self-Supervised Strategy for Post-Operative Prostate Cancer Radiotherapy.

Radical prostatectomy (prostate removal) is a standard treatment for clinically localized prostate cancer and is often followed by postoperative radiotherapy. Postoperative radiotherapy requires accurate delineation of the clinical target volume (CTV) and lymph node drainage area (LNA) on computed tomography (CT) images. However, the CTV contour cannot be determined by the simple prostate expansion after resection of the prostate in the CT image. Constrained by this factor, the manual delineation process in postoperative radiotherapy is more time-consuming and challenging than in radical radiotherapy. In addition, CTV and LNA have no boundaries that can be distinguished by pixel values in CT images, and existing automatic segmentation models cannot get satisfactory results. Radiation oncologists generally determine CTV and LNA profiles according to clinical consensus and guidelines regarding surrounding organs at risk (OARs). In this work, we design a cascade segmentation block to explicitly establish correlations between CTV, LNA, and OARs, leveraging OARs features to guide CTV and LNA segmentation. Furthermore, inspired by the success of the self-attention mechanism and self-supervised learning, we adopt SwinTransformer as our backbone and propose a pure SwinTransformer-based segmentation network with self-supervised learning strategies. We performed extensive quantitative and qualitative evaluations of the proposed method. Compared to other competitive segmentation models, our model shows higher dice scores with minor standard deviations, and the detailed visualization results are more consistent with the ground truth. We believe this work can provide a feasible solution to this problem, making the postoperative radiotherapy process more efficient.

Redox Neutral Radical-Relay Nickel-Catalyzed Remote Carbonylation.

A novel and efficient method for the catalytic installation of a carbonyl group via remote radical coupling is disclosed. The nickel-catalyzed reaction proceeds to undergo a sequential single-electron transfer, 1,5-hydrogen atom transfer, and carbonyl insertion, thus providing the α-substituted ketone. Further, this reaction could be carried out smoothly under normal pressure and redox-neutral conditions, and demonstrated functional-group compatibility and excellent site-selectivity.

Discovery of novel hydroxyamidine based indoleamine 2,3-dioxygenase 1 (IDO1) and thioredoxin reductase 1 (TrxR1) dual inhibitors.

In order to take advantage of both immunotherapeutic and metabolic antitumor agents, novel dual indoleamine 2,3- dioxygenase 1 (IDO1) and thioredoxin reductase 1 (TrxR1) inhibitors were designed. Thioredoxin reductase 1 (TrxR1) is a main ROS modulator within CRC cells. Indoleamine 2,3-dioxygenase (IDO1) is crucial controller for tryptophan (Trp) metabolism that is also important for CRC immunotherapy. Herein, ten compounds 12a-j containing hydroxyamidine scaffold were designed, synthesized and evaluated for inhibitory activities against IDO1/TrxR1 enzyme and CRC cells. Among these compounds, the most active compound 12d (ZC0109) showed excellent and balanced activity against both IDO1 (IC50 = 0.05 µM) and TrxR1 (IC50 = 3.00 ± 0.25 µM) were selected for further evaluation. Compound ZC0109 exhibited good dual inhibition against IDO1 and TrxR1 both in vitro and in vivo. Further mechanistic studies reveal that, through IDO1 and TrxR1 inhibition by ZC0109 treatment, accumulated ROS effectively induced apoptosis and G1/S cell cycle arrest in cancer cells. In vivo evaluation demonstrated excellent anti-tumor effect of ZC0109 with the notable ability of promoting ROS-induced apoptosis, reducing kynurenine level in plasma and restoring anti-tumor immune response. Thus, ZC0109 represents a potential CRC therapy agent for further development.

The anti-TMV potency of the tobacco-derived fungus Aspergillus versicolor and its active alkaloids, as anti-TMV activity inhibitors.

Nicotiana tabacum (tobacco) has attracted interest as one of the most economically important industrial crops widely cultivated in China, whose dried leaves are popularly consumed medicinally and recreationally by human societies. In this study, five undescribed alkaloids derivatives, isoaspergillines A-E, together with eight known alkaloids, notoamide D, (1R,4S)-4-benzyl-1-isopropyl-2,4-dihydro-1H-pyrazino-[2,1-b]quinazoline-3,6-dione, protuboxepin K, notoamide C, notoamide M, deoxybrevianamide E, cyclo (D-Pro-L-Trp), and versicolamide B, were obtained from the culture of the Nicotiana tabacum-derived fungus Aspergillus versicolor. Their structures were mainly elucidated through comprehensive analyses of spectroscopic data. Bioactivity evaluation of all isolated compounds revealed that isoaspergilline A and notoamide M exhibited anti-TMV activities with IC50 values of 20.0 and 22.8 µM, respectively. Molecular docking suggested that isoaspergilline A and notoamide M were well located into the active site of anti-TMV by interacting with SER138, SER143, and ASN73 residues. This study enlightens the therapeutic potential of the endophytic fungus A. versicolor and it is helpful to find undescribed anti-TMV activity inhibitors, as well as searching for new anti-TMV candidates from natural sources.

Integrated analysis of senescence-associated genes in pancreatic ductal adenocarcinoma.

Background: Cellular senescence plays a critical role in the occurrence and development, and immune modulation of cancer. This research primarily investigated the role of senescence-associated genes (SAGs) in the survival and tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC). Methods: From the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) database, the gene expression profiles and clinical data of PDAC samples were downloaded. SAGs in the TCGA cohort were used to build a novel prognostic model and validated in the ICGC cohort. The relationship of signature with the immune landscape, tumor mutational burden (TMB), as well as the sensitivity of different therapies, was explored. Moreover, a nomogram was developed to predict the overall survival of PDAC patients. Results: A prognostic signature was constructed on basis of three SAGs, and patients in the low-risk score group had a longer survival time. The accuracy of the signature to distinguish different score groups was confirmed through principal component analysis (PCA) and the Receiver operator curves curve. The mRNA expression of the three signature genes was also verified in normal pancreatic and PDAC cell lines by RT-qPCR. The signature could independently predict the prognosis of PDAC patients and had broad applicability. Meanwhile, the nomogram predicted that 1- and 3-years survival rates were in good agreement with the observed overall survival rates. Low-risk patients had lower tumor mutational burden, and low-TMB patients had a better prognosis. Low- and high-risk patients exhibit distinct immune cell infiltration and immune checkpoint changes. By further analyzing the risk score, patients in the low-risk group were more responsive to immunotherapy and a variety of commonly used chemotherapeutic drugs. Conclusion: The prognostic signature can well predict the prognosis and assess the possibility of immunotherapy in personalized PDAC treatment.

Regioselective Synthetic Approach to Higher Alkenes from Lower Alkenes with Sulfoxides in the Fe3+/H2O2 System via Direct Alkylation or Arylation of the Csp2-H Bond on the C═C Bond of Alkenes.

The regioselective synthetic approach to higher alkenes from lower alkenes by using sulfoxides as alkyl or aryl reagents in the Fe3+/H2O2 system has been developed. This reaction realized direct alkylation or arylation of alkenes. In this reaction, sulfoxides afforded one Csp3 or Csp2 atom to the C═C bond of alkenes; one new Csp2-Csp3 bond or Csp2-Csp2 bond was formed. Nearly 40 products including di-, tri-, and tetra-substituted products were regioselectively synthesized. Both aliphatic and aromatic alkenes could participate in this reaction. Moreover, not only dimethyl sulfoxide but also three other sulfoxides can be applied to this reaction, including diethyl, dibenzyl, and diphenyl sulfoxide. The mechanism studies showed that this reaction may experience a coupling process via radical addition-elimination and the Fe3+/H2O2 system made the sulfoxides offered one alkyl or aryl radical to the C═C bond of alkenes.

Ecology of Middle East respiratory syndrome coronavirus, 2012-2020: A machine learning modelling analysis.

The ongoing enzootic circulation of the Middle East respiratory syndrome coronavirus (MERS-CoV) in the Middle East and North Africa is increasingly raising the concern about the possibility of its recombination with other human-adapted coronaviruses, particularly the pandemic SARS-CoV-2. We aim to provide an updated picture about ecological niches of MERS-CoV and associated socio-environmental drivers. Based on 356 confirmed MERS cases with animal contact reported to the WHO and 63 records of animal infections collected from the literature as of 30 May 2020, we assessed ecological niches of MERS-CoV using an ensemble model integrating three machine learning algorithms. With a high predictive accuracy (area under receiver operating characteristic curve = 91.66% in test data), the ensemble model estimated that ecologically suitable areas span over the Middle East, South Asia and the whole North Africa, much wider than the range of reported locally infected MERS cases and test-positive animal samples. Ecological suitability for MERS-CoV was significantly associated with high levels of bareland coverage (relative contribution = 30.06%), population density (7.28%), average temperature (6.48%) and camel density (6.20%). Future surveillance and intervention programs should target the high-risk populations and regions informed by updated quantitative analyses.

[3+1+1+1] Annulation to the Pyridine Structure in Quinoline Molecules Based on DMSO as a Nonadjacent Dual-Methine Synthon: Simple Synthesis of 3-Arylquinolines from Arylaldehydes, Arylamines, and DMSO.

A [3+1+1+1] annulation of arylamines, arylaldehydes, and dimethyl sulfoxide (DMSO) to the pyridine structure in quinolines using DMSO as a nonadjacent dual-methine (═CH-) synthon is disclosed. In this annulation, arylamines provide two carbon atoms and one nitrogen atom, arylaldehydes furnish one carbon atom, and DMSO provides two nonadjacent methines (═CH-) to the pyridine ring in quinoline molecules. This annulation provides a simple approach for the synthesis of 3-arylquinolines from readily available substrates in useful yields. On the basis of the control experiments and the literature, a plausible mechanism is proposed.

Spatiotemporal coherent modulation imaging for dynamic quantitative phase and amplitude microscopy.

The single-shot capability of coherent modulation imaging (CMI) makes it have great potential in the investigation of dynamic processes. Its main disadvantage is the relatively low signal-to-noise ratio (SNR) which affects the spatial resolution and reconstruction accuracy. Here, we propose the improvement of a general spatiotemporal CMI method for imaging of dynamic processes. By making use of the redundant information in time-series reconstructions, the spatiotemporal CMI can achieve robust and fast reconstruction with higher SNR and spatial resolution. The method is validated by numerical simulations and optical experiments. We combine the CMI module with an optical microscope to achieve quantitative phase and amplitude reconstruction of dynamic biological processes. With the reconstructed complex field, we also demonstrate the 3D digital refocusing ability of the CMI microscope. With further development, we expect the spatiotemporal CMI method can be applied to study a range of dynamic phenomena.

Unexpected Annulation between 2-Aminobenzyl Alcohols and Benzaldehydes in the Presence of DMSO: Regioselective Synthesis of Substituted Quinolines.

An unexpected annulation among 2-aminobenzyl alcohols, benzaldehydes, and DMSO to quinolines has been disclosed. For the reported annulation between 2-aminobenzyl alcohols and benzaldehydes, the change of the solvent from toluene to DMSO led to the change of the product from the diheteroatomic cyclic benzoxazines to monoheteroatomic cyclic quinolines. This annulation can be used to synthesize regioselectively different substituted quinolines by the choice of different 2-amino alcohols, aldehydes, and sulfoxides as substrates. Interestingly, introducing substituent groups to the α-position of sulfoxides resulted in the interchange of the positions between benzaldehydes and sulfoxides in the product quinolines. On the basis of the control experiments and literatures, a plausible mechanism for this annulation was proposed.

Two C═C Bond Participation in Annulation to Pyridines Based on DMF as the Nonadjacent N and C Atom Donors.

Two C═C bond participation in annulation to pyridines using N,N-dimethylformamide (DMF) as the N1 and C4 synthons has been carried out. In this reaction, DMF contributed one N atom and one C atom to two disconnected positions of pyridine ring, with no need for an additional nitrogen source. Two C═C bonds in two molecules of substituted styrenes offered four carbon atoms in the presence of iodine and persulfate. With the optimized conditions in hand, both symmetric and unsymmetric diaryl-substituted pyridines were obtained in useful yields. On the basis of relevant literature and a series of control experimental results, a possible mechanism was proposed in this work, which may demonstrate how DMF provides both N1 and C4 sources.

Epidemiology and evolution of Middle East respiratory syndrome coronavirus, 2012-2020.

BACKGROUND: The ongoing transmission of the Middle East respiratory syndrome coronavirus (MERS-CoV) in the Middle East and its expansion to other regions are raising concerns of a potential pandemic. An in-depth analysis about both population and molecular epidemiology of this pathogen is needed. METHODS: MERS cases reported globally as of June 2020 were collected mainly from World Health Organization official reports, supplemented by other reliable sources. Determinants for case fatality and spatial diffusion of MERS were assessed with Logistic regressions and Cox proportional hazard models, respectively. Phylogenetic and phylogeographic analyses were performed to examine the evolution and migration history of MERS-CoV. RESULTS: A total of 2562 confirmed MERS cases with 150 case clusters were reported with a case fatality rate of 32.7% (95% CI: 30.9‒34.6%). Saudi Arabia accounted for 83.6% of the cases. Age of ≥ 65 years old, underlying conditions and ≥ 5 days delay in diagnosis were independent risk factors for death. However, a history of animal contact was associated with a higher risk (adjusted OR = 2.97, 95% CI: 1.10-7.98) among female cases < 65 years but with a lower risk (adjusted OR = 0.31, 95% CI: 0.18-0.51) among male cases ≥ 65 years old. Diffusion of the disease was fastest from its origin in Saudi Arabia to the east, and was primarily driven by the transportation network. The most recent sub-clade C5.1 (since 2013) was associated with non-synonymous mutations and a higher mortality rate. Phylogeographic analyses pointed to Riyadh of Saudi Arabia and Abu Dhabi of the United Arab Emirates as the hubs for both local and international spread of MERS-CoV. CONCLUSIONS: MERS-CoV remains primarily locally transmitted in the Middle East, with opportunistic exportation to other continents and a potential of causing transmission clusters of human cases. Animal contact is associated with a higher risk of death, but the association differs by age and sex. Transportation network is the leading driver for the spatial diffusion of the disease. These findings how this pathogen spread are helpful for targeting public health surveillance and interventions to control endemics and to prevent a potential pandemic.

Cedrol from Ginger Ameliorates Rheumatoid Arthritis via Reducing Inflammation and Selectively Inhibiting JAK3 Phosphorylation.

Ginger, as a food spice, is widely applied due to its extensive effects. Cedrol (CE) found in ginger is a sesquiterpene with anti-inflammatory activity. The objective of this research is to discuss the efficacy of CE on ameliorating rheumatoid arthritis (RA). CE inhibited chronic inflammation and pain in a dose-dependent manner accompanied by rapid onset and long duration. Besides, CE treatment effectively ameliorated the paw edema volume and arthritis score with no significant effect on body weight. Organ index, T-cell and B-cell proliferation, histopathology, and immunohistochemistry demonstrated that CE had immunological enhancement and attenuated RA effects. Remarkably, inhibition of phosphorylated-JAK3 protein, thereby abating the secretion of pro-inflammatory cytokines and inflammation-related mediators, was involved in the potential mechanism of CE efficiency through forming a hydrogen bond with ARG953 and ILE955 in the JAK3 active pocket. At the same time, the pharmacokinetic results showed that the absolute bioavailability of CE at 20, 40, and 80 mg/kg was 30.30, 23.68, and 16.11%, respectively. The current results offered clues for mastering the ameliorated RA of CE and further perfected the effective substance basis on the anti-inflammatory effect of ginger, which was beneficial for further applications.

Epidemiology and Ecology of Severe Fever With Thrombocytopenia Syndrome in China, 2010‒2018.

BACKGROUND: The growing epidemics of severe fever with thrombocytopenia syndrome (SFTS), an emerging tick-borne disease in East Asia, and its high case fatality rate have raised serious public health concerns. METHODS: Surveillance data on laboratory-confirmed SFTS cases in China were collected. The spatiotemporal dynamics and epidemiological features were explored. The socioeconomic and environmental drivers were identified for SFTS diffusion using survival analysis and for SFTS persistence using a two-stage generalized boosted regression tree model. RESULTS: During 2010‒2018, a total of 7721 laboratory-confirmed SFTS cases were reported in China, with an overall case fatality rate (CFR) of 10.5%. The average annual incidence increased >20 times and endemic areas expanded from 27 to 1574 townships, whereas the CFR declined from 19% to 10% during this period. Four geographical clusters-the Changbai Mountain area, the Jiaodong Peninsula, the Taishan Mountain area, and the Huaiyangshan Mountain area-were identified. Diffusion and persistence of the disease were both driven by elevation, high coverages of woods, crops, and shrubs, and the vicinity of habitats of migratory birds but had different meteorological drivers. Residents ≥60 years old in rural areas with crop fields and tea farms were at increased risk to SFTS. CONCLUSIONS: Surveillance of SFTS and intervention programs need to be targeted at areas ecologically suitability for vector ticks and in the vicinity of migratory birds to curb the growing epidemic.