NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition.

Dietary habits have been proven to have an impact on the microbial composition and health of the human gut. Over the past decade, researchers have discovered that gut microbiota can use nutrients to produce metabolites that have major implications for human physiology. However, there is no comprehensive system that specifically focuses on identifying nutrient deficiencies based on gut microbiota, making it difficult to interpret and compare gut microbiome data in the literature. This study proposes an analytical platform, NURECON, that can predict nutrient deficiency information in individuals by comparing their metagenomic information to a reference baseline. NURECON integrates a next-generation bacterial 16S rRNA analytical pipeline (QIIME2), metabolic pathway prediction tools (PICRUSt2 and KEGG), and a food compound database (FooDB) to enable the identification of missing nutrients and provide personalized dietary suggestions. Metagenomic information from total number of 287 healthy subjects was used to establish baseline microbial composition and metabolic profiles. The uploaded data is analyzed and compared to the baseline for nutrient deficiency assessment. Visualization results include gut microbial composition, related enzymes, pathways, and nutrient abundance. NURECON is a user-friendly online platform that provides nutritional advice to support dietitians' research or menu design.

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.

Incidental Ring-hyperenhancing Liver Micronodules at CT Hepatic Arteriography-guided Percutaneous Thermal Ablation of Colorectal Liver Metastases.

CT during hepatic arteriography (CTHA) is a highly sensitive imaging method for detecting colorectal liver metastases (CLMs), which supports its use during percutaneous thermal liver ablation. In contrast to its high sensitivity, its specificity for incidental small CLMs not detected at preablation cross-sectional imaging is believed to be low given the absence of specific imaging signatures and the common presence of pseudolesions. In this retrospective study of 22 patients (mean age, 55 years ± 10.6 [SD]; 63.6% male, 36.4% female) with CLMs undergoing CTHA-guided microwave percutaneous thermal ablation between November 2017 and October 2022, the authors provided a definition of incidental ring-hyperenhancing liver micronodules (RHLMs) and investigated whether there is a correlation of RHLMs with histologic analysis or intrahepatic tumor progression at imaging follow-up after applying a biomechanical deformable image registration method. The analysis revealed 25 incidental RHLMs in 41.7% (10 of 24) of the CTHA images from the respective guided ablation sessions. Of those, four RHLMs were ablated. Among the remaining 21 RHLMs, 71.4% (15 of 21) were confirmed to be CLM with either histology (n = 3) or imaging follow-up (n = 12). The remaining 28.6% (six of 21) of RHLMs were not observed at follow-up imaging. This suggests that RHLMs at CTHA may be an early indicator of incidental small CLMs. Keywords: Colorectal Neoplasms, Liver, Angiography, CT, Incidental Findings, Ablation Supplemental material is available for this article. © RSNA, 2024.

Application of neoadjuvant chemoradiotherapy and neoadjuvant chemotherapy in curative surgery for esophageal cancer: A meta-analysis.

BACKGROUND: The effectiveness of neoadjuvant therapy in esophageal cancer (EC) treatment is still a subject of debate. AIM: To compare the clinical efficacy and toxic side effects between neoadjuvant chemoradiotherapy (nCRT) and neoadjuvant chemotherapy (nCT) for locally advanced EC (LAEC). METHODS: A comprehensive search was conducted using multiple databases, including PubMed, EMBASE, MEDLINE, Science Direct, The Cochrane Library, China National Knowledge Infrastructure, Wanfang Database, Chinese Science and Technology Journal Database, and Chinese Biomedical Literature Database Article. Studies up to December 2022 comparing nCRT and nCT in patients with EC were selected. RESULTS: The analysis revealed significant differences between nCRT and nCT in terms of disease-free survival. The results indicated that nCRT provided better outcomes in terms of the 3-year overall survival rate (OSR) [odds ratio (OR) = 0.95], complete response rate (OR = 3.15), and R0 clearance rate (CR) (OR = 2.25). However, nCT demonstrated a better 5-year OSR (OR = 1.02) than nCRT. Moreover, when compared to nCRT, nCT showed reduced risks of cardiac complications (OR = 1.15) and pulmonary complications (OR = 1.30). CONCLUSION: Overall, both nCRT and nCT were effective in terms of survival outcomes for LAEC. However, nCT exhibited better performance in terms of postoperative complications.

MdBT2 regulates nitrogen-mediated cuticular wax biosynthesis via a MdMYB106-MdCER2L1 signalling pathway in apple.

Cuticular waxes play important roles in plant development and the interaction between plants and their environment. Researches on wax biosynthetic pathways have been reported in several plant species. Also, wax formation is closely related to environmental condition. However, the regulatory mechanism between wax and environmental factors, especially essential mineral elements, is less studied. Here we found that nitrogen (N) played a negative role in the regulation of wax synthesis in apple. We therefore analysed wax content, composition and crystals in BTB-TAZ domain protein 2 (MdBT2) overexpressing and antisense transgenic apple seedlings and found that MdBT2 could downregulate wax biosynthesis. Furthermore, R2R3-MYB transcription factor 16-like protein (MdMYB106) interacted with MdBT2, and MdBT2 mediated its ubiquitination and degradation through the 26S proteasome pathway. Finally, HXXXD-type acyl-transferase ECERIFERUM 2-like1 (MdCER2L1) was confirmed as a downstream target gene of MdMYB106. Our findings reveal an N-mediated apple wax biosynthesis pathway and lay a foundation for further study of the environmental factors associated with wax regulatory networks in apple.

Intraprocedural Versus Initial Follow-up Minimal Ablative Margin Assessment After Colorectal Liver Metastasis Thermal Ablation: Which One Better Predicts Local Outcomes?

OBJECTIVES: The aim of this study was to investigate the prognostic value of 3-dimensional minimal ablative margin (MAM) quantified by intraprocedural versus initial follow-up computed tomography (CT) in predicting local tumor progression (LTP) after colorectal liver metastasis (CLM) thermal ablation. MATERIALS AND METHODS: This single-institution, patient-clustered, tumor-based retrospective study included patients undergoing microwave and radiofrequency ablation between 2016 and 2021. Patients without intraprocedural and initial follow-up contrast-enhanced CT, residual tumors, or with follow-up less than 1 year without LTP were excluded. Minimal ablative margin was quantified by a biomechanical deformable image registration method with segmentations of CLMs on intraprocedural preablation CT and ablation zones on intraprocedural postablation and initial follow-up CT. Prognostic value of MAM to predict LTP was tested using area under the curve and competing-risk regression model. RESULTS: A total of 68 patients (mean age ± standard deviation, 57 ± 12 years; 43 men) with 133 CLMs were included. During a median follow-up of 30.3 months, LTP rate was 17% (22/133). The median volume of ablation zone was 27 mL and 16 mL segmented on intraprocedural and initial follow-up CT, respectively ( P < 0.001), with corresponding median MAM of 4.7 mm and 0 mm, respectively ( P < 0.001). The area under the curve was higher for MAM quantified on intraprocedural CT (0.89; 95% confidence interval [CI], 0.83-0.94) compared with initial follow-up CT (0.66; 95% CI, 0.54-0.76) in predicting 1-year LTP ( P < 0.001). An MAM of 0 mm on intraprocedural CT was an independent predictor of LTP with a subdistribution hazards ratio of 11.9 (95% CI, 4.9-28.9; P < 0.001), compared with 2.4 (95% CI, 0.9-6.0; P = 0.07) on initial follow-up CT. CONCLUSIONS: Ablative margin quantified on intraprocedural CT significantly outperformed initial follow-up CT in predicting LTP and should be used for ablation endpoint assessment.

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.

Study Protocol STEREOLAB: Stereotactic Liver Ablation Assisted with Intra-Arterial CT Hepatic Arteriography and Ablation Confirmation Software Assessment.

PURPOSE: This study aims to evaluate the technical efficacy and local tumor progression-free survival (LTPFS) of a standardized workflow for thermal ablation of colorectal liver metastases (CRLM) consisting of CT during hepatic arteriography (CTHA)-based imaging analysis, stereotactic thermal ablation, and computer-based software assessment of ablation margins. MATERIALS AND METHODS: This investigator initiated, single-center, single-arm prospective trial will enroll up to 50 patients (≤ 5 CRLM, Measuring ≤ 5 cm). Procedures will be performed in an angio-CT suite under general anesthesia. The primary objective is to estimate LTPFS with a follow-up of up to 2 years and secondary objectives are analysis of the impact of minimal ablative margins on LTPFS, adverse events, contrast media utilization and radiation exposure, overall oncological outcomes, and anesthesia/procedural time. Adverse events (AE) will be recorded by CTCAE (Common Toxicity Criteria for Adverse Events), and Bayesian optimal phase-2 design will be applied for major intraprocedural AE stop boundaries. The institutional CRLM ablation registry will be used as benchmark for comparative analysis with the historical cohort. DISCUSSION: The STEREOLAB trial will introduce a high-precision and standardized thermal ablation workflow for CRLM consisting of CT during hepatic arteriography imaging, stereotactic guidance, and ablation confirmation. Trial Registration ClinicalTrials.gov identifier: (NCT05361551).

Copper-Mediated and Palladium-Catalyzed Cross-Coupling of Indoles and N-Methylpyridinium Salts: A Practical Way to Prepare 3-(Pyridin-2-yl)indoles.

Herein, a Pd/Cu bimetallic-catalyzed direct C-H heteroarylation of pyridines via the traceless protecting group strategy is described. A series of N-methyl-activated pyridines and 1-methylindoles are coupled with high regioselectivity to produce the corresponding 3-(pyridin-2-yl)indoles in moderate to good yields, wherein related electron-rich heterocycles (e.g., indole, 1-methylpyrrole, benzofuran, benzo[b]thiophene) are also applicable. Streamlined operation, good functional group tolerance, and late-stage modifications make this twofold C-H activation protocol an attractive route for the synthesis of 3-(pyridin-2-yl)indole derivatives.

A radio pulsar phase from SGR J1935+2154 provides clues to the magnetar FRB mechanism.

The megajansky radio burst, FRB 20200428, and other bright radio bursts detected from the Galactic source SGR J1935+2154 suggest that magnetars can make fast radio bursts (FRBs), but the emission site and mechanism of FRB-like bursts are still unidentified. Here, we report the emergence of a radio pulsar phase of the magnetar 5 months after FRB 20200428. Pulses were detected in 16.5 hours over 13 days using the Five-hundred-meter Aperture Spherical radio Telescope, with luminosities of about eight decades fainter than FRB 20200428. The pulses were emitted in a narrow phase window anti-aligned with the x-ray pulsation profile observed using the x-ray telescopes. The bursts, conversely, appear in random phases. This dichotomy suggests that radio pulses originate from a fixed region within the magnetosphere, but bursts occur in random locations and are possibly associated with explosive events in a dynamically evolving magnetosphere. This picture reconciles the lack of periodicity in cosmological repeating FRBs within the magnetar engine model.

Salvage Locoregional Therapy Following Progression After Radiotherapy for Hepatocellular Carcinoma Is Associated with Improved Outcomes.

PURPOSE: To evaluate the impact of salvage locoregional therapy (salvage-LT) on survival of hepatocellular carcinoma (HCC) patients presenting with intrahepatic tumor progression following radiotherapy. METHODS: This single-institution retrospective analysis included consecutive HCC patients having intrahepatic tumor progression following radiotherapy during 2015-2019. Overall survival (OS) was calculated from the date of intrahepatic tumor progression after initial radiotherapy by using the Kaplan-Meier method. Log-rank tests and Cox regression models were used for univariable and multivariable analyses. An inverse probability weighting was used to estimate treatment effect of salvage-LT considering confounding factors. RESULTS: A total of 123 patients (mean age ± SD, 70 years ± 10; 97 men) were evaluated. Among those, 35 patients underwent 59 sessions of salvage-LT, including transarterial embolization/chemoembolization (n = 33), ablation (n = 11), selective internal radiotherapy (n = 7), and external beam radiotherapy (n = 8). At a median follow-up of 15.1 months (range, 3.4-54.5 months), the median OS was 23.3 months in patients who received salvage-LT and 6.6 months who did not. At multivariate analysis, ECOG performance status, Child-Pugh class, albumin-bilirubin grade, extrahepatic disease, and lack of salvage-LT were independent predictors of worse OS. After inverse probability weighting, salvage-LT was associated with a survival benefit of 8.9 months (95% CI: 1.1, 16.7 months; p = 0.03). CONCLUSIONS: Salvage locoregional therapy is associated with increased survival in HCC patients suffering from intrahepatic tumor progression following initial radiotherapy.

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.

[Direct determination of five xanthic acids in water by ultra performance liquid chromatography-tandem mass spectrometry].

Xanthates with different alkyl groups, such as ethyl, propyl, butyl, and amyl groups, are widely used in large quantities in the mining flotation of metallic minerals. Xanthates enter environmental waters through mineral processing wastewater discharge and are ionized or hydrolyzed into ions or molecules of xanthic acids (XAs) in water. XAs endanger aquatic plants and animals, as well as human health. To the best of our knowledge, XA analysis is mainly limited to butyl xanthate. Moreover, the isomers and congeners of XAs cannot be determined separately using the existing methods. Herein, a novel method based on ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was established to separate and analyze five XAs, namely, ethyl-, isopropyl-, n-butyl-, isobutyl-, and amyl-XAs, in water. Water samples were filtered through a 0.22 µm hydrophilic polytetrafluoroethylene (PTFE) membrane and directly injected into the UPLC-MS/MS instrument. Separation was performed using a Waters Acquity UPLC BEH C18 column (100 mm×2.1 mm, 1.7 µm) with ammonia solution (pH 11)-acetonitrile (9∶1, v/v) as the mobile phase for isocratic elution. The five XAs were detected in the negative electrospray ionization (ESI-) and multiple reaction monitoring (MRM) modes. An internal standard method was used for quantification. The pretreatment and UPLC-MS/MS conditions were comprehensively optimized to achieve the separation and analysis of the five XAs via direct injection. The XAs showed negligible adsorption on hydrophobic PTFE, hydrophilic PTFE, hydrophilic polypropylene, and polypropylene membranes during filtration. However, the amyl-XA showed obvious adsorption on nylon and polyether sulfone membranes. The five XAs mainly formed [M-H]- parent ions in the ESI- mode and the main daughter ions obtained following collisional fragmentation depended on the alkyl groups of the XAs. Increasing the pH of the ammonia solution in the mobile phase to 11 led to the isomeric separation of n-butyl- and isobutyl-XAs. The optimized mobile phase inhibited the tailing of the chromatographic peak of amyl-XA and effectively improved all the chromatographic peak shapes of XAs. The BEH C18 column was selected as the chromatographic column owing to its better compatibility with high-pH solutions compared with the T3 C18 column. Preservation experiments conducted over 8 d showed that the concentration of all five XAs decreased over time at room temperature; among the XAs analyzed, the concentration of ethyl-XA revealed the most significant decrease. However, the recoveries of the five XAs at 4 and -20 ℃ remained high, ranging from 101% to 105% and from 100% to 106%, respectively, on the 8th day. The preservation observed with a high concentration of XAs was similar to that found with a low concentration. The preservation time was extended to 8 days at pH 11 and 4 ℃ away from the light. No significant matrix effects were observed for the five XA samples in surface water and groundwater, but industrial sewage exerted obvious matrix inhibitory effects on ethyl- and isopropyl-XAs. Owing to the short retention times of ethyl- and isopropyl-XAs, the co-fluxed interferents in the industrial sewage depressed the MS signals. The five XAs showed good linearity in the range of 0.25-100 µg/L, with correlation coefficients greater than 0.9996. The method detection limits were as low as 0.03-0.04 µg/L, and the intra- and inter-day precisions were 1.3%-2.1% and 3.3%-4.1%, respectively. The recoveries obtained under low, medium, and high spiked levels (1.00, 20.0, 80.0 µg/L) were 96.9%-133%, 100%-107%, and 104%-112%, respectively. The corresponding RSDs were 2.1%-3.0%, 0.4%-1.9%, and 0.4%-1.6%, respectively. The optimized method was successfully applied to the analysis of XAs in surface water, groundwater, and industrial sewage. The method could separate and detect various congeners and isomers of XAs without the need for cumbersome pretreatment processes, and its advantages include smaller sample requirements, simpler operation, higher sensitivity, and longer preservation time. The proposed technique presents excellent application potential in XA environmental monitoring and water evaluation, and mineral flotation studies.

Comprehensive mapping of antigenic linear B-cell epitopes on K205R protein of African swine fever virus with monoclonal antibodies.

African swine fever virus causes an acute, highly contagious swine disease with high mortality, leading to enormous losses in the pig industry. The K205R, a nonstructural protein of African swine fever virus, is abundantly expressed in the cytoplasm of infected cells at the early stage of infection and induces a strong immune response. However, to date, the antigenic epitopes of this immunodeterminant have not been characterized. In the present study, the K205R protein was expressed in a mammalian cell line and purified using Ni-affinity chromatography. Furthermore, three monoclonal antibodies (mAbs; 5D6, 7A8, and 7H10) against K205R were generated. Indirect immunofluorescence assay and western blot results showed that all three mAbs recognized native and denatured K205R in African swine fever virus (ASFV)-infected cells. To identify the epitopes of the mAbs, a series of overlapping short peptides were designed and expressed as fusion proteins with maltose-binding protein. Subsequently, the peptide fusion proteins were probed with monoclonal antibodies using western blot and enzyme-linked immunosorbent assay. The three target epitopes were fine-mapped; the core sequences of recognized by the mAbs 5D6, 7A8, and 7H10 were identified as 157FLTPEIQAILDE168, 154REKFLTP160, and 136PTNAMFFTRSEWA148, respectively. Probing with sera from ASFV-infected pigs in a dot blot assay demonstrated that epitope 7H10 was the immunodominant epitope of K205R. Sequence alignment showed that all epitopes were conserved across ASFV strains and genotypes. To our knowledge, this is the first study to characterize the epitopes of the antigenic K205R protein of ASFV. These findings may serve as a basis for the development of serological diagnostic methods and subunit vaccines.

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.