Synovial fluid research based on SERS and SERRS for enhanced detection of biomarkers in staged osteoarthritis.

Surface-enhanced (resonance) Raman scattering (SER(R)S) can extremely enhance Raman intensity of samples, which is helpful for detecting synovial fluid (SF) that does not show Raman activity under normal conditions. In this study, SER(R)S spectra of SF from three different osteoarthritis (OA) stages were collected and analyzed for OA progress, finding that the content of collagen increased throughout the disease, while non-collagen proteins and polysaccharides decreased sharply at advanced OA stage accompanied by the increase of phospholipid. The spectral features and differences were enhanced by salting-out and centrifugation. Much more information on biomolecules at different OA stages was disclosed by using SERRS for the first time, these main trace components (ß-carotene, collagen, hyaluronic acid, nucleotide, and phospholipid) can be used as potential biomarkers. It indicates that SERRS has a more comprehensive ability to assist SERS in seeking micro(trace) biomolecules as biomarkers and facilitating accurate and efficient diagnosis and mechanism research of OA.

Predicting prognosis and immunotherapy response in colorectal cancer by pericytes insights from single-cell RNA sequencing.

Immunotherapy has revolutionized the treatment of tumors, but there are still a large number of patients who do not benefit from immunotherapy. Pericytes play an important role in remodeling the immune microenvironment. However, how pericytes affect the prognosis and treatment resistance of tumors is still unknown. This study jointly analyzed single-cell RNA sequencing (scRNA-seq) data and bulk RNA sequencing data of multiple cancers to reveal pericyte function in the colorectal cancer microenvironment. Analyzing over 800 000 cells, it was found that colorectal cancer had more pericyte enrichment in tumor tissues than other cancers. We then combined the TCGA database with multiple public datasets and enrolled more than 1000 samples, finding that pericyte may be closely related to poor prognosis due to the higher epithelial-mesenchymal transition (EMT) and hypoxic characteristics. At the same time, patients with more pericytes have higher immune checkpoint molecule expressions and lower immune cell infiltration. Finally, the contributions of pericyte in poor treatment response have been demonstrated in multiple immunotherapy datasets (n = 453). All of these observations suggest that pericyte can be used as a potential biomarker to predict patient disease progression and immunotherapy response.

Development of a Small-Footprint 50 MHz Linear Array: Fabrication and Micro-Ultrasound Imaging Demonstration.

Compact high-frequency arrays are of interest for clinical and preclinical applications in which a small-footprint or endoscopic device is needed to reach the target anatomy. However, the fabrication of compact arrays entails the connection of several dozens of small elements to the imaging system through a combination of flexible printed circuit boards at the array end and micro-coaxial cabling to the imaging system. The methods currently used, such as wire bonding, conductive adhesives, or a dry connection to a flexible circuit, considerably increase the array footprint. Here, we propose an interconnection method that uses vacuum-deposited metals, laser patterning, and electroplating to achieve a right-angle, compact, reliable connection between array elements and flexible-circuit traces. The array elements are thickened at the edges using patterned copper traces, which increases their cross-sectional area and facilitates the connection. We fabricated a 2.3 mm by 1.7 mm, 64-element linear array with elements at a 36 µm pitch connected to a 4 cm long flexible circuit, where the interconnect adds only 100 µm to each side of the array. Pulse-echo measurements yielded an average center frequency of 55 MHz and a -6 dB bandwidth of 41%. We measured an imaging resolution of 35 µm in the axial direction and 114 µm in the lateral direction and demonstrated the ex vivo imaging of porcine esophageal tissue and the in vivo imaging of avian embryonic vasculature.

Gradient Interphase Engineering Enabled by Anionic Redox for High-Voltage and Long-Life Li-Ion Batteries.

Intelligent utilization of the anionic redox reaction (ARR) in Li-rich cathodes is an advanced strategy for the practical implementation of next-generation high-energy-density rechargeable batteries. However, due to the intrinsic complexity of ARR (e.g., nucleophilic attacks), the instability of the cathode-electrolyte interphase (CEI) on a Li-rich cathode presents more challenges than typical high-voltage cathodes. Here, we manipulate CEI interfacial engineering by introducing an all-fluorinated electrolyte and exploiting its interaction with the nucleophilic attack to construct a gradient CEI containing a pair of fluorinated layers on a Li-rich cathode, delivering enhanced interfacial stability. Negative/detrimental nucleophilic electrolyte decomposition has been efficiently evolved to further reinforce CEI fabrication, resulting in the construction of LiF-based indurated outer shield and fluorinated polymer-based flexible inner sheaths. Gradient interphase engineering dramatically improved the capacity retention of the Li-rich cathode from 43 to 71% after 800 cycles and achieved superior cycling stability in anode-free and pouch-type full cells (98.8% capacity retention, 220 cycles), respectively.

Characterizing immune variation and diagnostic indicators of preeclampsia by single-cell RNA sequencing and machine learning.

Preeclampsia is a multifactorial and heterogeneous complication of pregnancy. Here, we utilize single-cell RNA sequencing to dissect the involvement of circulating immune cells in preeclampsia. Our findings reveal downregulation of immune response in lymphocyte subsets in preeclampsia, such as reduction in natural killer cells and cytotoxic genes expression, and expansion of regulatory T cells. But the activation of naïve T cell and monocyte subsets, as well as increased MHC-II-mediated pathway in antigen-presenting cells were still observed in preeclampsia. Notably, we identified key monocyte subsets in preeclampsia, with significantly increased expression of angiogenesis pathways and pro-inflammatory S100 family genes in VCAN+ monocytes and IFN+ non-classical monocytes. Furthermore, four cell-type-specific machine-learning models have been developed to identify potential diagnostic indicators of preeclampsia. Collectively, our study demonstrates transcriptomic alternations of circulating immune cells and identifies immune components that could be involved in pathophysiology of preeclampsia.

Biosynthetic mechanism of the yellow pigments in the marine bacterium Pseudoalteromonas sp. strain T1lg65.

The Pseudoalteromonas genus marine bacteria have attracted increasing interest because of their abilities to produce bioactive metabolites. The pigmented Pseudoalteromonas group encodes more secondary metabolite biosynthetic gene clusters (BGCs) than the non-pigmented group. Here, we report a yellow pigmented bacterium Pseudoalteromonas sp. strain T1lg65, which was isolated from a mangrove forest sediment. We showed that the yellow pigments of T1lg65 belong to the group of lipopeptide alterochromides. Further genetic analyses of the alterochromide BGC revealed that the yellow pigments are biosynthesized by aryl-polyene synthases and nonribosomal peptide synthases. Within the gene cluster, altA encodes a tyrosine ammonia acid lyase, which catalyzes synthesis of the precursor 4-hydroxycinnamic acid (4-HCA) from tyrosine in the alterochromide biosynthetic pathway. In addition, altN, encoding a putative flavin-dependent halogenase, was proven to be responsible for the bromination of alterochromides based on gene deletion, molecular docking, and site mutagenesis analyses. In summary, the biosynthetic pathway, precursor synthesis, and bromination mechanism of the lipopeptide alterochromides were studied in-depth. Our results expand the knowledge on biosynthesis of Pseudoalteromonas pigments and could promote the development of active pigments in the future.IMPORTANCEThe marine bacteria Pseudoalteromonas spp. are important biological resources because they are producers of bioactive natural products, including antibiotics, pigments, enzymes, and antimicrobial peptides. One group of the microbial pigments, alterochromides, holds a great value for their novel lipopeptide structures and antimicrobial activities. Previous studies were limited to the structural characterization of alterochromides and genome mining for the alterochromide biosynthesis. This work focused on the biosynthetic mechanism for alterochromide production, especially revealing functions of two key genes within the gene cluster for the alterochromide biosynthesis. On the one hand, our study provides a target for metabolic engineering of the alterochromide biosynthesis; on the other hand, the 4-HCA synthase AltA and brominase AltN show potential in the biocatalyst industry.

Pan-cancer scRNA-seq analysis reveals immunological and diagnostic significance of the peripheral blood mononuclear cells.

Peripheral blood mononuclear cells (PBMCs) reflect systemic immune response during cancer progression. However, a comprehensive understanding of the composition and function of PBMCs in cancer patients is lacking, and the potential of these features to assist cancer diagnosis is also unclear. Here, the compositional and status differences between cancer patients and healthy donors in PBMCs were investigated by single-cell RNA sequencing (scRNA-seq), involving 262,025 PBMCs from 68 cancer samples and 14 healthy samples. We observed an enhanced activation and differentiation of most immune subsets in cancer patients, along with reduction of naïve T cells, expansion of macrophages, impairment of NK cells and myeloid cells, as well as tumor promotion and immunosuppression. Based on characteristics including differential cell type abundances and/or hub genes identified from weight gene co-expression network analysis (WGCNA) modules of each major cell type, we applied logistic regression to construct cancer diagnosis models. Furthermore, we found that the above models can distinguish cancer patients and healthy donors with high sensitivity. Our study provided new insights into using the features of PBMCs in non-invasive cancer diagnosis.

Implanting Transition Metal into Li2 O-Based Cathode Prelithiation Agent for High-Energy-Density and Long-Life Li-Ion Batteries.

Compensating the irreversible loss of limited active lithium (Li) is essentially important for improving the energy-density and cycle-life of practical Li-ion battery full-cell, especially after employing high-capacity but low initial coulombic efficiency anode candidates. Introducing prelithiation agent can provide additional Li source for such compensation. Herein, we precisely implant trace Co (extracted from transition metal oxide) into the Li site of Li2 O, obtaining (Li0.66 Co0.11 □0.23 )2 O (CLO) cathode prelithiation agent. The synergistic formation of Li vacancies and Co-derived catalysis efficiently enhance the inherent conductivity and weaken the Li-O interaction of Li2 O, which facilitates its anionic oxidation to peroxo/superoxo species and gaseous O2 , achieving 1642.7 mAh/g~Li2O prelithiation capacity (≈980 mAh/g for prelithiation agent). Coupled 6.5 wt % CLO-based prelithiation agent with LiCoO2 cathode, substantial additional Li source stored within CLO is efficiently released to compensate the Li consumption on the SiO/C anode, achieving 270 Wh/kg pouch-type full-cell with 92 % capacity retention after 1000 cycles.

Self-Training Boosted Multi-Factor Matching Network for Composed Image Retrieval.

The composed image retrieval (CIR) task aims to retrieve the desired target image for a given multimodal query, i.e., a reference image with its corresponding modification text. The key limitations encountered by existing efforts are two aspects: 1) ignoring the multiple query-target matching factors; 2) ignoring the potential unlabeled reference-target image pairs in existing benchmark datasets. To address these two limitations is non-trivial due to the following challenges: 1) how to effectively model the multiple matching factors in a latent way without direct supervision signals; 2) how to fully utilize the potential unlabeled reference-target image pairs to improve the generalization ability of the CIR model. To address these challenges, in this work, we first propose a CLIP-Transformer based muLtI-factor Matching Network (LIMN), which consists of three key modules: disentanglement-based latent factor tokens mining, dual aggregation-based matching token learning, and dual query-target matching modeling. Thereafter, we design an iterative dual self-training paradigm to further enhance the performance of LIMN by fully utilizing the potential unlabeled reference-target image pairs in a weakly-supervised manner. Specifically, we denote the iterative dual self-training paradigm enhanced LIMN as LIMN+. Extensive experiments on four datasets, including FashionIQ, Shoes, CIRR, and Fashion200 K, show that our proposed LIMN and LIMN+ significantly surpass the state-of-the-art baselines.

Lattice Engineering on Li2CO3-Based Sacrificial Cathode Prelithiation Agent for Improving the Energy Density of Li-Ion Battery Full-Cell.

Developing sacrificial cathode prelithiation technology to compensate for active lithium loss is vital for improving the energy density of lithium-ion battery full-cells. Li2CO3 owns high theoretical specific capacity, superior air stability, but poor conductivity as an insulator, acting as a promising but challenging prelithiation agent candidate. Herein, extracting a trace amount of Co from LiCoO2 (LCO), a lattice engineering is developed through substituting Li sites with Co and inducing Li defects to obtain a composite structure consisting of (Li0.906Co0.043▫0.051)2CO2.934 and ball milled LiCoO2 (Co-Li2CO3@LCO). Notably, both the bandgap and Li─O bond strength have essentially declined in this structure. Benefiting from the synergistic effect of Li defects and bulk phase catalytic regulation of Co, the potential of Li2CO3 deep decomposition significantly decreases from typical >4.7 to ≈4.25 V versus Li/Li+, presenting >600 mAh g-1 compensation capacity. Impressively, coupling 5 wt% Co-Li2CO3@LCO within NCM-811 cathode, 235 Wh kg-1 pouch-type full-cell is achieved, performing 88% capacity retention after 1000 cycles.

Manipulated Fluoro-Ether Derived Nucleophilic Decomposition Products for Mitigating Polarization-Induced Capacity Loss in Li-Rich Layered Cathode.

Electrolyte engineering is a fascinating choice to improve the performance of Li-rich layered oxide cathodes (LRLO) for high-energy lithium-ion batteries. However, many existing electrolyte designs and adjustment principles tend to overlook the unique challenges posed by LRLO, particularly the nucleophilic attack. Here, we introduce an electrolyte modification by locally replacing carbonate solvents in traditional electrolytes with a fluoro-ether. By benefit of the decomposition of fluoro-ether under nucleophilic O-related attacks, which delivers an excellent passivation layer with LiF and polymers, possessing rigidity and flexibility on the LRLO surface. More importantly, the fluoro-ether acts as "sutures", ensuring the integrity and stability of both interfacial and bulk structures, which contributed to suppressing severe polarization and enhancing the cycling capacity retention from 39 % to 78 % after 300 cycles for the 4.8 V-class LRLO. This key electrolyte strategy with comprehensive analysis, provides new insights into addressing nucleophilic challenge for high-energy anionic redox related cathode systems.

The efficacy and safety of different systemic combination therapies on advanced hepatocellular carcinoma: a systematic review and meta-analysis.

Background and aims: Systemic combinations have recently brought significant therapeutic benefits for advanced hepatocellular carcinoma (aHCC). To design the most effective combination regimens, a systematic review (PROSPERO ID: CRD42022321949) was conducted to evaluate the efficacy and safety of systemic combinations on aHCC. Methods: We retrieved all the studies from PubMed, Embase, the Cochrane Central Register of Controlled Trials (CENTRAL), and China National Knowledge Infrastructure (CNKI) using the Medical Subject Headings (MeSH) terms until December 21, 2022. The effect indicators (hazard ratio [HR], relative risk [RR], and median) were pooled by a fixed- or random-effects model. A subgroup analysis was conducted according to types and specific therapies. Results: In total, 88 eligible studies were selected from 7249 potential records. Each kind of combination treatment (chemotherapy plus chemotherapy, targeted plus immune checkpoint inhibitor (ICI) therapy, targeted plus chemotherapy, and targeted plus targeted therapy) had a better objective response rate (ORR) in patients with aHCC, compared to the monotherapy mostly with sorafenib (RR: 1.57 [1.44-1.71]; I 2 = 30%). Of those, targeted plus ICI therapy showed better therapeutic efficiency in overall survival (median: 15.02 [12.67-17.38]), progression-free survival (median: 7.08 [6.42-7.74]), and ORR (RR: 1.81 [1.55-2.13]), compared to the monotherapy. Specifically, Atezo plus Beva showed all those benefits. Our pooled result showed all the combinations had increased ≥3 Grade treatment-related adverse events (TrAEs), with an RR of 1.25 [95% CI: 1.15-1.36], compared to the monotherapy. Conclusion: The systemic combinations, especially targeted plus ICI therapy, including Atezo plus Beva, significantly improve clinical outcomes but increase side effects in patients with aHCC. Future trials should concentrate on improvement in therapeutic efficiency and reduction of toxicity of targeted plus ICI therapy. Systematic review registration: https://www.crd.york.ac.uk/prospero, identifier CRD42022321949.

Superharmonic and Microultrasound Imaging With Plane Wave Beamforming Techniques.

Superharmonic contrast imaging (SpHI) suppresses tissue clutter and allows high-contrast visualization of the vasculature. An array-based dual-frequency (DF) probe has been developed for SpHI, integrating a 21-MHz, 256-element microultrasound imaging array with a 2-MHz, 32-element array to take advantage of the broadband nonlinear responses from microbubble (MB) contrast agents. In this work, ultrafast imaging with plane waves was implemented for SpHI to increase the acquisition frame rate. Ultrafast imaging was also implemented for microultrasound B-mode imaging (HFPW B-mode) to enable high-resolution visualization of the tissue structure. Coherent compounding was demonstrated in vitro and in vivo in both imaging modes. Acquisition frame rates of 4.5 kHz and 187 Hz in HFPW B-mode imaging were achieved for imaging up to 21 mm with one and 25 angles, respectively, and 3.5 kHz and 396 Hz in the SpHI mode with one and nine coherently compounded angles, respectively. SpHI images showed suppression of tissue clutter prior to and after the introduction of MBs in vitro and in vivo. The nine-angle coherently compounded 2-D SpHI images of contrast-filled flow channel showed a contrast-to-tissue ratio (CTR) of 26.0 dB, a 2.5-dB improvement relative to images reconstructed from 0° steering. Consistent with in vitro imaging, the nine-angle compounded 2-D SpHI of a Lewis lung cancer tumor showed a 2.6-dB improvement in contrast enhancement, relative to 0° steering, and additionally revealed a region of nonviable tissue. The 3-D display of the volumetric SpHI data acquired from a xenograft mouse tumor using both 0° steering and nine-angle compounding allowed the visualization of the tumor vasculature. A small vessel visible in the compounded SpHI image, measuring around [Formula: see text], is not visualized in the 0° steering SpHI image, demonstrating the superiority of the latter in detecting fine structures within the tumor.

Mechanism of HBx carcinogenesis interaction with non-coding RNA in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is an extremely malignant tumor that affects individuals throughout the world. One of the main causes of HCC is hepatitis B virus (HBV). Therefore, it is crucial to understand the mechanisms underlying HBV carcinogenesis. Increasing evidence suggests that the HBV X protein (HBx), which is encoded by HBV, plays a significant role in cell apoptosis, DNA damage repair, and cell cycle regulation. This ultimately leads to the development of HCC. Additionally, recent studies have shown that non-coding RNA (ncRNA) also contributes to the carcinogenesis and pathogenesis of different of tumors. ncRNA plays a significant role in the formation of HCC by regulating the inflammatory signaling pathway, activating immune cells, and modifying epigenetics. However, it remains unclear whether ncRNA is involved in the regulation of the carcinogenic mechanisms of HBx. This article reviews the carcinogenic mechanism of HBx and its interaction with ncRNA, providing a novel strategy for the clinical diagnosis and treatment of HCC.

Semantic-Aware Modular Capsule Routing for Visual Question Answering.

Visual Question Answering (VQA) is fundamentally compositional in nature, and many questions are simply answered by decomposing them into modular sub-problems. The recent proposed Neural Module Network (NMN) employ this strategy to question answering, whereas heavily rest with off-the-shelf layout parser or additional expert policy regarding the network architecture design instead of learning from the data. These strategies result in the unsatisfactory adaptability to the semantically-complicated variance of the inputs, thereby hindering the representational capacity and generalizability of the model. To tackle this problem, we propose a Semantic-aware modUlar caPsulE Routing framework, termed as SUPER, to better capture the instance-specific vision-semantic characteristics and refine the discriminative representations for prediction. Particularly, five powerful specialized modules as well as dynamic routers are tailored in each layer of the SUPER network, and the compact routing spaces are constructed such that a variety of customizable routes can be sufficiently exploited and the vision-semantic representations can be explicitly calibrated. We comparatively justify the effectiveness and generalization ability of our proposed SUPER scheme over five benchmark datasets, as well as the parametric-efficient advantage. It is worth emphasizing that this work is not to pursue the state-of-the-art results in VQA. Instead, we expect that our model is responsible to provide a novel perspective towards architecture learning and representation calibration for VQA.

From Li to Na: Exploratory Analysis of Fe-Based Phosphates Polyanion-Type Cathode Materials by Mn Substitution.

Both LiFePO4 (LFP) and NaFePO4 (NFP) are phosphate polyanion-type cathode materials, which have received much attention due to their low cost and high theoretical capacity. Substitution of manganese (Mn) elements for LFP/NFP materials can improve the electrochemical properties, but the connection between local structural changes and electrochemical behaviors after Mn substitution is still not clear. This study not only achieves improvements in energy density of LFP and cyclic stability of NFP through Mn substitution, but also provides an in-depth analysis of the structural evolutions induced by the substitution. Among them, the substitution of Mn enables LiFe0.5 Mn0.5 PO4 to achieve a high energy density of 535.3 Wh kg-1 , while NaFe0.7 Mn0.3 PO4 exhibits outstanding cyclability with 89.6% capacity retention after 250 cycles. Specifically, Mn substitution broadens the ion-transport channels, improving the ion diffusion coefficient. Moreover, LiFe0.5 Mn0.5 PO4 maintains a more stable single-phase transition during the charge/discharge process. The transition of NaFe0.7 Mn0.3 PO4 to the amorphous phase is avoided, which can maintain structural stability and achieve better electrochemical performance. With systematic analysis, this research provides valuable guidance for the subsequent design of high-performance polyanion-type cathodes.

Smoke and Spike: Benzo[a]pyrene Enhances SARS-CoV-2 Infection by Boosting NR4A2-Induced ACE2 and TMPRSS2 Expression.

Cigarette smoke aggravates severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, the underlying mechanisms remain unclear. Here, they show that benzo[a]pyrene in cigarette smoke extract facilitates SARS-CoV-2 infection via upregulating angiotensin-converting enzyme 2 (ACE2) and transmembrane protease serine 2 (TMPRSS2). Benzo[a]pyrene trans-activates the promoters of ACE2 and TMPRSS2 by upregulating nuclear receptor subfamily 4 A number 2 (NR4A2) and promoting its binding of NR4A2 to their promoters, which is independent of functional genetic polymorphisms in ACE2 and TMPRSS2. Benzo[a]pyrene increases the susceptibility of lung epithelial cells to SARS-CoV-2 pseudoviruses and facilitates the infection of authentic Omicron BA.5 in primary human alveolar type II cells, lung organoids, and lung and testis of hamsters. Increased expression of Nr4a2, Ace2, and Tmprss2, as well as decreased methylation of CpG islands at the Nr4a2 promoter are observed in aged mice compared to their younger counterparts. NR4A2 knockdown or interferon-λ2/λ3 stimulation downregulates the expression of NR4A2, ACE2, and TMPRSS2, thereby inhibiting the infection. In conclusion, benzo[a]pyrene enhances SARS-CoV-2 infection by boosting NR4A2-induced ACE2 and TMPRSS2 expression. This study elucidates the mechanisms underlying the detrimental effects of cigarette smoking on SARS-CoV-2 infection and provides prophylactic options for coronavirus disease 2019, particularly for the elderly population.

The tumor immune microenvironment of nasopharyngeal carcinoma after gemcitabine plus cisplatin treatment.

Gemcitabine plus cisplatin (GP) chemotherapy is the standard of care for nasopharyngeal carcinoma (NPC). However, the mechanisms underpinning its clinical activity are unclear. Here, using single-cell RNA sequencing and T cell and B cell receptor sequencing of matched, treatment-naive and post-GP chemotherapy NPC samples (n = 15 pairs), we show that GP chemotherapy activated an innate-like B cell (ILB)-dominant antitumor immune response. DNA fragments induced by chemotherapy activated the STING type-I-interferon-dependent pathway to increase major histocompatibility complex class I expression in cancer cells, and simultaneously induced ILB via Toll-like receptor 9 signaling. ILB further expanded follicular helper and helper type 1 T cells via the ICOSL-ICOS axis and subsequently enhanced cytotoxic T cells in tertiary lymphoid organ-like structures after chemotherapy that were deficient for germinal centers. ILB frequency was positively associated with overall and disease-free survival in a phase 3 trial of patients with NPC receiving GP chemotherapy ( NCT01872962 , n = 139). It also served as a predictor for favorable outcomes in patients with NPC treated with GP and immunotherapy combined treatment (n = 380). Collectively, our study provides a high-resolution map of the tumor immune microenvironment after GP chemotherapy and uncovers a role for B cell-centered antitumor immunity. We also identify and validate ILB as a potential biomarker for GP-based treatment in NPC, which could improve patient management.

A comprehensive evaluation of full-spectrum cell-free RNAs highlights cell-free RNA fragments for early-stage hepatocellular carcinoma detection.

BACKGROUND: Various studies have reported cell-free RNAs (cfRNAs) as noninvasive biomarkers for detecting hepatocellular carcinoma (HCC). However, they have not been independently validated, and some results are contradictory. We provided a comprehensive evaluation of various types of cfRNA biomarkers and a full mining of the biomarker potential of new features of cfRNA. METHODS: We first systematically reviewed reported cfRNA biomarkers and calculated dysregulated post-transcriptional events and cfRNA fragments. In 3 independent multicentre cohorts, we further selected 6 cfRNAs using RT-qPCR, built a panel called HCCMDP with AFP using machine learning, and internally and externally validated HCCMDP's performance. FINDINGS: We identified 23 cfRNA biomarker candidates from a systematic review and analysis of 5 cfRNA-seq datasets. Notably, we defined the cfRNA domain to describe cfRNA fragments systematically. In the verification cohort (n = 183), cfRNA fragments were more likely to be verified, while circRNA and chimeric RNA candidates were neither abundant nor stable as qPCR-based biomarkers. In the algorithm development cohort (n = 287), we build and test the panel HCCMDP with 6 cfRNA markers and AFP. In the independent validation cohort (n = 171), HCCMDP can distinguish HCC patients from control groups (all: AUC = 0.925; CHB: AUC = 0.909; LC: AUC = 0.916), and performs well in distinguishing early-stage HCC patients (all: AUC = 0.936; CHB: AUC = 0.917; LC: AUC = 0.928). INTERPRETATION: This study comprehensively evaluated full-spectrum cfRNA biomarker types for HCC detection, highlighted the cfRNA fragment as a promising biomarker type in HCC detection, and provided a panel HCCMDP. FUNDING: National Natural Science Foundation of China, and The National Key Basic Research Program (973 program).

A FadR-Type Regulator Activates the Biodegradation of Polycyclic Aromatic Hydrocarbons by Mediating Quorum Sensing in Croceicoccus naphthovorans Strain PQ-2.

Bacteria employ multiple transcriptional regulators to orchestrate cellular responses to adapt to constantly varying environments. The bacterial biodegradation of polycyclic aromatic hydrocarbons (PAHs) has been extensively described, and yet, the PAH-related transcriptional regulators remain elusive. In this report, we identified an FadR-type transcriptional regulator that controls phenanthrene biodegradation in Croceicoccus naphthovorans strain PQ-2. The expression of fadR in C. naphthovorans PQ-2 was induced by phenanthrene, and its deletion significantly impaired both the biodegradation of phenanthrene and the synthesis of acyl-homoserine lactones (AHLs). In the fadR deletion strain, the biodegradation of phenanthrene could be recovered by supplying either AHLs or fatty acids. Notably, FadR simultaneously activated the fatty acid biosynthesis pathway and repressed the fatty acid degradation pathway. As intracellular AHLs are synthesized with fatty acids as substrates, boosting the fatty acid supply could enhance AHL synthesis. Collectively, these findings demonstrate that FadR in C. naphthovorans PQ-2 positively regulates PAH biodegradation by controlling the formation of AHLs, which is mediated by the metabolism of fatty acids. IMPORTANCE Master transcriptional regulation of carbon catabolites is extremely important for the survival of bacteria that face changes in carbon sources. Polycyclic aromatic hydrocarbons (PAHs) can be utilized as carbon sources by some bacteria. FadR is a well-known transcriptional regulator involved in fatty acid metabolism; however, the connection between FadR regulation and PAH utilization in bacteria remains unknown. This study revealed that a FadR-type regulator in Croceicoccus naphthovorans PQ-2 stimulated PAH biodegradation by controlling the biosynthesis of the acyl-homoserine lactone quorum-sensing signals that belong to fatty acid-derived compounds. These results provide a unique perspective for understanding bacterial adaptation to PAH-containing environments.