HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.

CD4+ T cell responses are exquisitely antigen specific and directed toward peptide epitopes displayed by human leukocyte antigen class II (HLA-II) on antigen-presenting cells. Underrepresentation of diverse alleles in ligand databases and an incomplete understanding of factors affecting antigen presentation in vivo have limited progress in defining principles of peptide immunogenicity. Here, we employed monoallelic immunopeptidomics to identify 358,024 HLA-II binders, with a particular focus on HLA-DQ and HLA-DP. We uncovered peptide-binding patterns across a spectrum of binding affinities and enrichment of structural antigen features. These aspects underpinned the development of context-aware predictor of T cell antigens (CAPTAn), a deep learning model that predicts peptide antigens based on their affinity to HLA-II and full sequence of their source proteins. CAPTAn was instrumental in discovering prevalent T cell epitopes from bacteria in the human microbiome and a pan-variant epitope from SARS-CoV-2. Together CAPTAn and associated datasets present a resource for antigen discovery and the unraveling genetic associations of HLA alleles with immunopathologies.

Dual-Site Chemosensor for Visualizing •OH-GSH Redox and Tracking Ferroptosis-Inducing Pathways In Vivo.

Oxidative stress, characterized by an imbalance between oxidative and antioxidant processes, results in excessive accumulation of intracellular reactive oxygen species. Among these responses, the regulation of intracellular hydroxyl radicals (•OH) and glutathione (GSH) is vital for physiological processes. Real-time in situ monitoring these two opposing bioactive species and their redox interactions is essential for understanding physiological balance and imbalance. In this study, we developed a dual-site fluorescence chemosensor OG-3, which can independently image both exogenous and endogenous •OH and GSH in separate channels both within cells and in vivo, eliminating issues of spatiotemporal inhomogeneous distribution and cross-interference. With its imaging capabilities of monitoring •OH-GSH redox, OG-3 elucidated two different pathways for ferroptosis induction: (i) inhibition of system xc- to block cystine uptake (extrinsic pathway) and (ii) GPX4 inactivation, leading to the loss of antioxidant defense (intrinsic pathway). Moreover, we assessed the antiferroptotic function and effects of ferroptosis inhibitors by monitoring •OH and GSH fluctuations during ferroptosis. This method provides a reliable platform for identifying potential ferroptosis inhibitors, contributing to our understanding of relevant metabolic and physiological mechanisms. It shows potential for elucidating the regulation of ferroptosis mechanisms and investigating further strategies for therapeutic applications.

Ablative margin quantification using deformable versus rigid image registration in colorectal liver metastasis thermal ablation: a retrospective single-center study.

PURPOSE: To investigate the correlation of minimal ablative margin (MAM) quantification using biomechanical deformable (DIR) versus intensity-based rigid image registration (RIR) with local outcomes following colorectal liver metastasis (CLM) thermal ablation. METHODS: This retrospective single-institution study included consecutive patients undergoing thermal ablation between May 2016 and October 2021. Patients who did not have intraprocedural pre- and post-ablation contrast-enhanced CT images for MAM quantification or follow-up period less than 1 year without residual tumor or local tumor progression (LTP) were excluded. DIR and RIR methods were used to quantify the MAM. The registration accuracy was compared using Dice similarity coefficient (DSC). Area under the receiver operating characteristic curve (AUC) was used to test MAM in predicting local tumor outcomes. RESULTS: A total of 72 patients (mean age 57; 44 men) with 139 tumors (mean diameter 1.5 cm ± 0.8 (SD)) were included. During a median follow-up of 29.4 months, there was one residual unablated tumor and the LTP rate was 17% (24/138). The ranges of DSC were 0.96-0.98 and 0.67-0.98 for DIR and RIR, respectively (p < 0.001). When using DIR, 27 (19%) tumors were partially or totally registered outside the liver, compared to 46 (33%) with RIR. Using DIR versus RIR, the corresponding median MAM was 4.7 mm versus 4.0 mm, respectively (p = 0.5). The AUC in predicting residual tumor and 1-year LTP for DIR versus RIR was 0.89 versus 0.72, respectively (p < 0.001). CONCLUSION: Ablative margin quantified on intra-procedural CT imaging using DIR method outperformed RIR for predicting local outcomes of CLM thermal ablation. CLINICAL RELEVANCE STATEMENT: The study supports the role of biomechanical deformable image registration as the preferred image registration method over rigid image registration for quantifying minimal ablative margins using intraprocedural contrast-enhanced CT images. KEY POINTS: • Accurate and reproducible image registration is a prerequisite for clinical application of image-based ablation confirmation methods. • When compared to intensity-based rigid image registration, biomechanical deformable image registration for minimal ablative margin quantification was more accurate for liver registration using intraprocedural contrast-enhanced CT images. • Biomechanical deformable image registration outperformed intensity-based rigid image registration for predicting local tumor outcomes following colorectal liver metastasis thermal ablation.

Dual-Site Chemosensor for Monitoring ·OH-Cysteine Redox in Cells and In Vivo.

The reaction between hydroxyl radical (·OH) and cysteine (Cys) plays an important role in the redox balance of living cells. A deeper insight into this intracellular reaction modulation and process is necessary and draws great interest. A highly effective technique consists of the real-time visualization of the two bioactive species and the perception of their respective changes by using a fluorescent probe. In this study, a dual-site chemosensor SPI based on phenothiazine-cyanine was developed, which realized quantitative detection and real-time imaging of ·OH and Cys at their own fluorescence channels (·OH: λex = 485 nm, λem = 608 nm; Cys: λex = 426 nm, λem = 538 nm) without spectral crosstalk. The fluorescent sensor showed excellent anti-interference and selectivity for common biological substances, apart from the successful imaging of exogenous and endogenous ·OH and Cys. We further visualized the redox dynamic reaction and explored the correlation of ·OH and Cys generated by different inhibitors (sulfasalazine and (1S, 3R)-RSL3). Notably, the chemosensor also possesses the capacity to clearly monitor ·OH and Cys in living mice and zebrafish. This study reports on the first chemosensor to investigate the process of intracellular redox modulation and control between ·OH and Cys, which show potential to further explore some metabolic and physiological mechanisms.

Targeted exome-based predictors of patterns of progression of colorectal liver metastasis after percutaneous thermal ablation.

BACKGROUND: Percutaneous thermal ablation is a curative-intent locoregional therapy (LRT) for selected patients with unresectable colorectal liver metastasis (CLM). Several factors have been identified that contribute to local tumour control after ablation. However, factors contributing to disease progression outside the ablation zone after ablation are poorly understood. METHODS: In this retrospective study, using next-generation sequencing, we identified genetic biomarkers associated with different patterns of progression following thermal ablation of CLM. RESULTS: A total of 191 ablation naïve patients between January 2011 and March 2020 were included in the analysis, and 101 had genomic profiling available. Alterations in the TGFß pathway were associated with increased risk of development of new intrahepatic tumours (hazard ratio [HR], 2.75, 95% confidence interval [95% CI] 1.39-5.45, P = 0.004); and alterations in the Wnt pathway were associated with increased probability of receiving salvage LRT for any intrahepatic progression (HR, 5.8, 95% CI 1.94-19.5, P = 0.003). CONCLUSIONS: Our findings indicate that genomic alterations in cancer-related signalling pathways can predict different progression patterns and the likelihood of receiving salvage LRT following percutaneous thermal ablation of CLM.

Liquid Metal-Doped Conductive Hydrogel for Construction of Multifunctional Sensors.

Interest in wearable and stretchable multifunctional sensors has grown rapidly in recent years. The sensing elements must accurately detect external stimuli to expand their applicability as sensors. However, the sensor's self-healing and adhesion to a target object have been major challenges in developing such practical and versatile devices. In this study, we prepared a hydrogel (LM-SA-PAA) composed of liquid metal (LM), sodium alginate (SA), and poly(acrylic acid) (PAA) with ultrastretchable, excellent self-healing, self-adhesive, and high-sensitivity sensing capabilities that enable the conformal contact between the sensor and skin even during dynamic movements. The excellent self-healing performance of the hydrogel stems from its double cross-linked networks, including physical and chemical cross-linked networks. The physical cross-link formed by the ionic interaction between the carboxyl groups of PAA and gallium ions provide the hydrogel with reversible autonomous repair properties, whereas the covalent bond provides the hydrogel with a stable and strong chemical network. Alginate forms a microgel shell around LM nanoparticles via the coordination of its carboxyl groups with Ga ions. In addition to offering exceptional colloidal stability, the alginate shell has sufficient polar groups, ensuring that the hydrogel adheres to diverse substrates. Based on the efficient electrical pathway provided by the LM, the hydrogel exhibited strain sensitivity and enabled the detection of various human motions and electrocardiographic monitoring. The preparation method is simple and versatile and can be used for the low-cost fabrication of multifunctional sensors, which have broad application prospects in human-machine interface compatibility and medical monitoring.

Ablative Margins of Colorectal Liver Metastases Using Deformable CT Image Registration and Autosegmentation.

Background Confirming ablation completeness with sufficient ablative margin is critical for local tumor control following colorectal liver metastasis (CLM) ablation. An image-based confirmation method considering patient- and ablation-related biomechanical deformation is an unmet need. Purpose To evaluate a biomechanical deformable image registration (DIR) method for three-dimensional (3D) minimal ablative margin (MAM) quantification and the association with local disease progression following CT-guided CLM ablation. Materials and Methods This single-institution retrospective study included patients with CLM treated with CT-guided microwave or radiofrequency ablation from October 2015 to March 2020. A biomechanical DIR method with AI-based autosegmentation of liver, tumors, and ablation zones on CT images was applied for MAM quantification retrospectively. The per-tumor incidence of local disease progression was defined as residual tumor or local tumor progression. Factors associated with local disease progression were evaluated using the multivariable Fine-Gray subdistribution hazard model. Local disease progression sites were spatially localized with the tissue at risk for tumor progression (<5 mm) using a 3D ray-tracing method. Results Overall, 213 ablated CLMs (mean diameter, 1.4 cm) in 124 consecutive patients (mean age, 57 years ± 12 [SD]; 69 women) were evaluated, with a median follow-up interval of 25.8 months. In ablated CLMs, an MAM of 0 mm was depicted in 14.6% (31 of 213), from greater than 0 to less than 5 mm in 40.4% (86 of 213), and greater than or equal to 5 mm in 45.1% (96 of 213). The 2-year cumulative incidence of local disease progression was 72% for 0 mm and 12% for greater than 0 to less than 5 mm. No local disease progression was observed for an MAM greater than or equal to 5 mm. Among 117 tumors with an MAM less than 5 mm, 36 had local disease progression and 30 were spatially localized within the tissue at risk for tumor progression. On multivariable analysis, an MAM of 0 mm (subdistribution hazard ratio, 23.3; 95% CI: 10.8, 50.5; P < .001) was independently associated with local disease progression. Conclusion Biomechanical deformable image registration and autosegmentation on CT images enabled identification and spatial localization of colorectal liver metastases at risk for local disease progression following ablation, with a minimal ablative margin greater than or equal to 5 mm as the optimal end point. © RSNA, 2023 Supplemental material is available for this article. See also the editorial by Sofocleous in this issue.

Bayesian parametric models for survival prediction in medical applications.

BACKGROUND: Evidence-based treatment decisions in medicine are made founded on population-level evidence obtained during randomized clinical trials. In an era of personalized medicine, these decisions should be based on the predicted benefit of a treatment on a patient-level. Survival prediction models play a central role as they incorporate the time-to-event and censoring. In medical applications uncertainty is critical especially when treatments differ in their side effect profiles or costs. Additionally, models must be adapted to local populations without diminishing performance and often without the original training data available due to privacy concern. Both points are supported by Bayesian models-yet they are rarely used. The aim of this work is to evaluate Bayesian parametric survival models on public datasets including cardiology, infectious diseases, and oncology. MATERIALS AND METHODS: Bayesian parametric survival models based on the Exponential and Weibull distribution were implemented as a Python package. A linear combination and a neural network were used for predicting the parameters of the distributions. A superiority design was used to assess whether Bayesian models are better than commonly used models such as Cox Proportional Hazards, Random Survival Forest, and Neural Network-based Cox Proportional Hazards. In a secondary analysis, overfitting was compared between these models. An equivalence design was used to assess whether the prediction performance of Bayesian models after model updating using Bayes rule is equivalent to retraining on the full dataset. RESULTS: In this study, we found that Bayesian parametric survival models perform as good as state-of-the art models while requiring less hyperparameters to be tuned and providing a measure of the uncertainty of the predictions. In addition, these models were less prone to overfitting. Furthermore, we show that updating these models using Bayes rule yields equivalent performance compared to models trained on combined original and new datasets. CONCLUSIONS: Bayesian parametric survival models are non-inferior to conventional survival models while requiring less hyperparameter tuning, being less prone to overfitting, and allowing model updating using Bayes rule. Further, the Bayesian models provide a measure of the uncertainty on the statistical inference, and, in particular, on the prediction.

A highly selective and sensitive CdS fluorescent quantum dot for the simultaneous detection of multiple pesticides.

The abuse of pesticides has introduced a large number of residues in soil and drinking water, which can then enter the food chain and the human body. Monitoring pesticide residues and developing simple and fast detection systems for pesticide residues is urgently needed. In this study, we presented one-pot prepared CdS fluorescent quantum dots (QDs) and explored their sensing application for organic pesticides. The CdS QDs can sensitively and selectively detect three different pesticides, dichlorvos (DDVP), paraquat, and glufosinate-ammonium, through different fluorescence responses. Paraquat can effectively quench the fluorescence of the QDs and DDVP can cause remarkable fluorescent enhancement. Glufosinate-ammonium can induce both 150 nm fluorescent blueshifting and 30-fold fluorescent enhancement. The probe exhibited low detection limits for the three pesticides: 1.44 µM for paraquat, 0.23 mM for DDVP, and 49.8 µM for glufosinate-ammonium. Furthermore, based on the results, we utilized the powerful functions of smartphones to establish a concentration-gray value standard curve through RGB values and gray values to realize the qualitative detection and quantitative analysis of DDVP. It is believed that this work presents a new platform for the simultaneous detection of multiple pesticides using a single QDs probe. The present on-site method using a smartphone is of great potential for water monitoring in rural areas.

Contemporary evidence on colorectal liver metastases ablation: toward a paradigm shift in locoregional treatment.

Image-guided percutaneous ablation techniques represent an attractive local therapy for the treatment of colorectal liver metastases (CLM) given its low risk of severe complications, which allows for early initiation of adjuvant therapies and spare functional liver parenchyma, allowing repeated treatments at the time of recurrence. However, ablation does not consistently achieve similar oncological outcomes to surgery, with the latter being currently considered the first-line local treatment modality in international guidelines. Recent application of computer-assisted ablation planning, guidance, and intra-procedural response assessment has improved percutaneous ablation outcomes. In addition, the evolving understanding of tumor molecular profiling has brought to light several biological factors associated with oncological outcomes following local therapies. The standardization of ablation procedures, the understanding of previously unknown biological factors affecting ablation outcomes, and the evidence by ongoing prospective clinical trials are poised to change the current perspective and indications on the use of ablation for CLM.

Iodination/Amidation of the N-Alkyl (Iso)quinolinium Salts.

The NaIO4-mediated sequential iodination/amidation reaction of N-alkyl quinolinium iodide salts has been first developed. This cascade process provides an efficient way to rapidly synthesize 3-iodo-N-alkyl quinolinones with high regioselectivity and good functional group tolerance. This protocol was also amenable to the isoquinolinium salts, thus providing a complementary method for preparing the 4-iodo-N-alkyl isoquinolinones.

Isolation and molecular characterization of bovine herpesvirus 4 from cattle in mainland China.

Bovine herpesvirus 4 (BoHV-4) is one of the most important of the known viral respiratory and reproductive pathogens of both young and adult cattle. However, BoHV-4 has not been isolated or detected in mainland China prior to this study. In 2019, BoHV-4 strain 512 was isolated from cattle in Heilongjiang Province, China, using MDBK cells, and characterized by PCR, nucleotide sequence analysis, and transmission electron microscopy. Two other unknown herpesvirus strains, BL6010 and J4034, which were isolated from cattle in 2009 in China and stored at -70℃, were also propagated in MDBK cells and identified as BoHV-4 by PCR. Phylogenetic analysis based on partial nucleotide sequences of the thymidine kinase (TK) gene and glycoprotein B (gB) gene for the three isolates indicated that these three Chinese strains belong to BoHV-4 genotype 1. A preliminary virus neutralization test revealed that 64% of the 70 bovine sera (45/70) collected from Inner Mongolia Autonomous Region, China, had anti-BoHV-4 antibodies and that natural BoHV-4 infection occurred in cattle in China. Here, we report for the first time the isolation and molecular characterization of BoHV-4 from cattle in mainland China.

Tumor Biomarkers and Interventional Oncology: Impact on Local Outcomes for Liver and Lung Malignancy.

PURPOSE OF REVIEW: Interventional oncology (IO) loco-regional treatments are widely utilized in clinical practice. However, local tumor control rates are still widely variable. There is a need to identify and develop novel biomarkers prognosticators following IO therapies. Here, we review the current literature on molecular tumor biomarkers in IO, mainly focusing on patients with liver and lung cancers. RECENT FINDINGS: RAS mutation is a prognosticator for patients with colorectal liver metastases. Several promising serum metabolites, gene signatures, circulating tumor nucleotides, and peptides are being evaluated for patients with hepatocellular carcinoma. Ki-67 and RAS mutation are independent risk factors for local tumor progression in the ablation of lung cancer. The relevant interplay between specific tumor biomarkers and IO loco-regional therapies outcomes has brought a new vision in the management of cancer. Further evolution of personalized interventional oncology accordingly to tumor biomarkers should improve oncologic outcomes for patients receiving IO therapies.

Palladium-Catalyzed Direct Arylation of Alkylpyridine via Activated N-Methylpyridinium Salts.

An efficient Pd-catalyzed arylation of alkylpyridine based on the pyridinium activation strategy has been developed for synthesis of mixed aryl alkylpyridines. It was found that (1) the N-methyl group in the pyridinium salts acted as a transient activator and could be automatically departed after the reaction, (2) CuBr was an indispensable additive for achieving the C6-selective arylation, (3) the α-branched alkyl chain on the alkylpyridine greatly increased the yield of the product. Deuterium labelling experiment revealed that in the case of the α-branched alkylpyridine, the presence of CuBr completely inhibited the H/D exchange at the benzylic position and thus enabled the selective arylation at the C6 position. This protocol demonstrates a broad substrate scope, and with respect to both the aryl iodides and the α-branched alkylpyridine, the desired mixed aryl alkylpyridines were obtained in generally good to excellent yields.

Identification and verification of differentially expressed genes in yak mammary tissue during the lactation cycle.

Yaks (Bos grunniens) live primarily in the Qinghai-Tibetan plateau (altitude: 2000-5000 m). Their milk presents unusual characteristics, containing large amounts of solids including fat and protein, and it is, therefore, important to understand the genetic makeup of the yak. To identify potentially critical genes playing a role in yak mammary tissue from colostrum to mature milk phase of lactogenesis, the early lactation (colostrum) stage (ELS; day 1 after parturition) and mature lactation (milk) stage (MLS; day 15) were chosen for comparison. An ELS-specific cDNA library was established by suppression subtractive hybridization and 25 expressed sequence tags at ELS were identified by sequencing and alignment. To further confirm our results the expression levels of 21 genes during the lactation cycle were measured using quantitative real-time RT-PCR (qRT-PCR). The qRT-PCR results confirmed 9 significantly up-regulated genes at ELS vs. MLS in yak mammary tissue, in which the l-amino acid oxidase 1 (LAO1) and collagen, type I, alpha I (COL1A1) were the most significantly up-regulated. During the lactation cycle, the highest expression of some milk fat genes (i.e., XDH and FABP3) in yak mammary tissue appears earlier than that in dairy cow. Our data also indicate MYC potentially playing a central role through putative regulation of COL1A1, CD44, SPARC, FASN and GPAM.

Iridium-Catalyzed Alkylation of Amine and Nitrobenzene with Alcohol to Tertiary Amine under Base- and Solvent-Free Conditions.

Herein, an efficient and green method for the selective synthesis of tertiary amines has been developed that involves iridium-catalyzed alkylation of various primary amines with aromatic or aliphatic alcohols. Notably, the catalytic protocol enables this transformation in the absence of additional base and solvent. Furthermore, the alkylation of nitrobenzene with primary alcohol to tertiary amine has also been achieved by the same catalytic system. Deuterium-labeling experiments and a series of control experiments were conducted, and the results suggested that an intermolecular borrowing hydrogen pathway might exist in the alkylation process.

Di-(2-picolyl)-N-(2-quinolinylmethyl)amine-Functionalized Triarylboron: Lewis Acidity Enhancement and Fluorogenic Discrimination Between Fluoride and Cyanide in Aqueous Solution.

Triarylboron-based Lewis acids as fluoride sensors face a stimulating academic challenge because of the high hydration enthalpy of fluoride, and are usually influenced by a competing response for cyanide ion. Herein, we present a new triarylborane functionalized by a metal-ion ligand, di-(2-picolyl)-N-(2-quinolinylmethyl)amine, with subsequent metalation. In aqueous solution, this triarylborane (QB) can capture fluoride and cyanide anions through chelation induced by the synergy of boron and metal ions. Moreover, this triarylborane moiety acts as a fluorescent reporter of the binding, allowing for discrimination between fluoride and cyanide anions through dual-channel fluorescence changes. The different chelation models and fluorogenic responses of this sensor toward F- and CN- were verified by the single-crystal structures of 2-to-2 adduct for KCN and 1-to-1 for KF.

Palladium-Catalyzed Domino Reaction for Stereoselective Synthesis of Multisubstituted Olefins: Construction of Blue Luminogens.

The first Pd-catalyzed multicomponent reaction of aryl iodides, alkenyl bromides, and strained alkenes has been developed, which allowed us to synthesize a variety of multisubsituted olefins in yields of 45-96% with excellent stereoselectivity. The configuration of the product was controlled by the configuration of the alkenyl bromides. Moreover, this practical methodology employing readily available substrates was found to be tolerant to a wide range of functional groups. Fifty six examples of highly stereoselective tri- or tetrasubstituted olefins have been successfully synthesized via this methodology. Most of the synthesized tetrasubstituted olefins are good aggregation-induced emission (AIE) luminogens.

A TBET-based ratiometric probe for Au(3+) and its application in living cells.

In this paper, we designed and synthesized a novel TBET-based ratiometric fluorescent chemodosimeter, RH-Au, for Au(3+). It was found that the probe RH-Au displayed highly selective, sensitive and naked-eye detection upon the addition of Au(3+). The probe RH-Au can be used in the pH range 6.0-7.5 and the detection limit was determined to be as low as 2.91 nM (0.57 ppb). We also demonstrated a successful application of imaging Au(3+) in living cells using RH-Au.