Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix.

Cell type specific (CTS) analysis is essential to reveal biological insights obscured in bulk tissue data. However, single-cell (sc) or single-nuclei (sn) resolution data are still cost-prohibitive for large-scale samples. Thus, computational methods to perform deconvolution from bulk tissue data are highly valuable. We here present EPIC-unmix, a novel two-step empirical Bayesian method integrating reference sc/sn RNA-seq data and bulk RNA-seq data from target samples to enhance the accuracy of CTS inference. We demonstrate through comprehensive simulations across three tissues that EPIC-unmix achieved 4.6% - 109.8% higher accuracy compared to alternative methods. By applying EPIC-unmix to human bulk brain RNA-seq data from the ROSMAP and MSBB cohorts, we identified multiple genes differentially expressed between Alzheimer's disease (AD) cases versus controls in a CTS manner, including 57.4% novel genes not identified using similar sample size sc/snRNA-seq data, indicating the power of our in-silico approach. Among the 6-69% overlapping, 83%-100% are in consistent direction with those from sc/snRNA-seq data, supporting the reliability of our findings. EPIC-unmix inferred CTS expression profiles similarly empowers CTS eQTL analysis. Among the novel eQTLs, we highlight a microglia eQTL for AD risk gene AP3B2, obscured in bulk and missed by sc/snRNA-seq based eQTL analysis. The variant resides in a microglia-specific cCRE, forming chromatin loop with AP3B2 promoter region in microglia. Taken together, we believe EPIC-unmix will be a valuable tool to enable more powerful CTS analysis.

The impact of previous abdominal surgery on colorectal cancer patients undergoing laparoscopic surgery.

The current study aimed to investigate whether previous abdominal surgery (PAS) could affect the outcomes of colorectal cancer (CRC) surgery. We conducted the search strategy in three databases (PubMed, Embase, and the Cochrane Library) from inception to May 26, 2022. The short-term and long-term outcomes were compared between the PAS group and the non-PAS group. Odds ratios (ORs) and 95% confidence intervals (CIs) were pooled up. Stata (V.16.0) software was used for data analysis. We included 34,827 patients from 14 studies in the current study. After pooling up all the data, we found that there were higher proportions of overall complications (OR = 1.12, I2 = 4.65%, 95% CI 1.03 to 1.23, P = 0.01), ileus (OR = 1.96, I2 = 59.74%, 95% CI 1.12 to 3.44, P = 0.02) and mortality (OR = 1.26, I2 = 0.00%, 95% CI 1.11 to 1.42, P = 0.00) in the PAS group than the non-PAS group. Patients with a history of PAS had higher risks of overall complications and death following CRC surgery. However, it did not appear to significantly affect the short-term outcomes apart from ileus. Surgeons should raise awareness of patients with a history of PAS, and take steps to reduce postoperative complications and mortality.

A new strategy to generate nanobodies for the coumaphos based on the synthesized nanobody libraries.

To break through the bottleneck in preparation of nanobody (Nb) for chemical contaminants induced by the difficulties in the synthesis of immunogen, complexity and unexpectable efficiency of immunization, a novel strategy to generate Nbs based on the designed synthetic Nb libraries with final size up to 109 cfu/mL was adopted and succeeded in selection of anti-coumaphos Nb A4. Furthermore, an affinity-matured mutant Nb 3G was obtained from the secondary library. Finally, an ic-ELISA was established with the limit of detection for coumaphos low to 1.90 ng/mL, 6.4-fold improved than the parent Nb A4, and the detection range from 3.06 to 15.77 ng/mL. Meanwhile, the recovery rate of vegetable samples was from 89.9% to 98.5%. Finally, the accuracy was testified by the standard UPLC-MS/MS method with R2 up to 0.99. Overall, fully synthetic Nb libraries constructed in this work provided an alternative possibility to generate the specific Nbs for chemical contaminants.

Molecular engineering of PETase for efficient PET biodegradation.

The widespread utilization of polyethylene terephthalate (PET) has caused a variety of environmental and health problems. Compared with traditional thermomechanical or chemical PET cycling, the biodegradation of PET may offer a more feasible solution. Though the PETase from Ideonalla sakaiensis (IsPETase) displays interesting PET degrading performance under mild conditions; the relatively low thermal stability of IsPETase limits its practical application. In this study, enzyme-catalysed PET degradation was investigated with the promising IsPETase mutant HotPETase (HP). On this basis, a carbohydrate-binding module from Bacillus anthracis (BaCBM) was fused to the C-terminus of HP to construct the PETase mutant (HLCB) for increased PET degradation. Furthermore, to effectively improve PET accessibility and PET-degrading activity, the truncated outer membrane hybrid protein (FadL) was used to expose PETase and BaCBM on the surface of E. coli (BL21with) to develop regenerable whole-cell biocatalysts (D-HLCB). Results showed that, among the tested small-molecular weight ester compounds (p-nitrophenyl phosphate (pNPP), p-Nitrophenyl acetate (pNPA), 4-Nitrophenyl butyrate (pNPB)), PETase displayed the highest hydrolysing activity against pNPP. HP displayed the highest catalytic activity (1.94 µM(p-NP)/min) at 50 °C and increased longevity at 40 °C. The fused BaCBM could clearly improve the catalytic performance of PETase by increasing the optimal reaction temperature and improving the thermostability. When HLCB was used for PET degradation, the yield of monomeric products (255.7 µM) was ∼25.5 % greater than that obtained after 50 h of HP-catalysed PET degradation. Moreover, the highest yield of monomeric products from the D-HLCB-mediated system reached 1.03 mM. The whole-cell catalyst D-HLCB displayed good reusability and stability and could maintain more than 54.6 % of its initial activity for nine cycles. Finally, molecular docking simulations were utilized to investigate the binding mechanism and the reaction mechanism of HLCB, which may provide theoretical evidence to further increase the PET-degrading activities of PETases through rational design. The proposed strategy and developed variants show potential for achieving complete biodegradation of PET under mild conditions.

Correlation between the triglyceride-glucose index and chronic kidney disease among adults with metabolic-associated fatty liver disease: fourteen-year follow-up.

Background and aims: According to previous studies, triglyceride-glucose (TyG) is related to chronic kidney disease (CKD), but no studies have explored the correlation between TyG and CKD among adults with metabolic dysfunction-associated fatty liver disease (MAFLD). We aimed to explore the associations of the TyG index with CKD among adults with MAFLD. Methods: In this retrospective observational cohort study, data from 11,860 participants who underwent a minimum of three health assessments between 2008 and 2015 were retrospectively collected. Participants were followed up until the final medical visit or health examination. CKD refers to an eGFR < 60 mL/min per 1·73 m2 or the occurrence of two or more incidents of proteinuria. Results: Within a median 10·02-year follow-up period, 2005 (16·9%) participants reported developing CKD. Multivariate Cox regression models indicated a noticeable correlation between the TyG index and CKD incidence (HR per unit increase, 1.19; 95% CI: 1.09-1.29) and between the TyG index and CKD incidence (HR per SD increase, 1.12; 95% CI: 1.06-1.18). The CKD incidence increased by 1.8 times in participants in the highest TyG index quartile relative to patients in the lowest quartile of the TyG index quartile (HR 1·18, 95% CI: 1.01-1.38, P = 0.007). According to subgroup analysis, an elevated TyG index is likely to become more harmful to participants younger than 60 years (P for interaction = 0.035). Conclusion: An elevated TyG index may increase CKD incidence among MAFLD adults, particularly among younger people. Early intervention may help reduce the incidence of CKD.

Biomechanical comparison of a new undercut thread design versus the V-shape thread design for pedicle screws.

BACKGROUND CONTEXT: Thread shape is regarded as an important factor influencing the fixation strength and osseointegration of bone screws. However, commercial pedicle screws with a V-shaped thread are prone to generating stress concentration at the bone-screw interface, thereby increasing the risk of screw loosening. Thus, modification of the pedicle-screw thread is imperative. PURPOSE: This study aimed to investigate the fixation stability of pedicle screws with the new undercut thread design in comparison to pedicle screws with a V-shaped thread. STUDY DESIGN: In vitro cadaveric biomechanical test and finite element analysis (FEA). METHODS: Pedicle screws with the undercut thread (characterized by a flat crest feature and a tip-facing undercut feature) were custom-manufactured, whereas those with the V-shaped thread were procured from a commercial supplier. Fixation stability was assessed by the cyclic non-pullout compressive biomechanical testing on cadaveric female osteoporotic vertebrae. The vertical displacement and rotation angle of the two types of pedicle screws were calculated every 100 cycles to evaluate their resistance to migration and rotation. FEA was conducted to investigate the stress distribution and bone damage at the bone-screw interface for both types of pedicle screws. RESULTS: Biomechanical testing revealed that the pedicle screws with the undercut thread exhibited significantly lower vertical displacement and rotation angles than the pedicle screws with the V-shape thread (P < 0.05). FEA results demonstrated a more uniform stress distribution in the bone surrounding the thread in the undercut design than in the V-shape design. Additionally, bone damage resulting from the pedicle screw was lower in the undercut design than in the V-shape design. CONCLUSIONS: Pedicle screws with an undercut thread are less prone to migration and rotation and thus more stable in the bone than those with a V-shape thread. CLINICAL SIGNIFICANCE: The undercut thread design may reduce the incidence of pedicle-screw loosening.

BRAF-V600E mutations in plasma and peripheral blood mononuclear cells correlate with prognosis of pediatric Langerhans cell histiocytosis treated with first-line therapy.

BACKGROUND: The clinical relevance of BRAF-V600E alleles in peripheral blood mononuclear cells (PBMCs) and the prognostic impact of the mutants in cell-free (cf) and PBMC DNAs of Langerhans cell histiocytosis (LCH) have not been fully clarified in pediatric LCH. METHODS: We retrospectively determined the levels of BRAF-V600E mutation in paired plasma and PBMC samples at the time of diagnosis of LCH. Subsequently, we performed a separate or combined analysis of the clinical and prognostic impact of the mutants. RESULTS: We assessed BRAF-V600E mutation in peripheral blood from 94 patients of childhood LCH. Our data showed that cfBRAF-V600E was related to young age, multiple-system (MS) disease, involvements of organs with high risk, increased risk of relapse, and worse progression-free survival (PFS) of patients. We also observed that the presence of BRAF-V600E in PBMCs at baseline was significantly associated with MS LCH with risk organ involvement, younger age, and disease progression or relapse. The coexisting of plasma(+)/PBMC(+) identified 36.2% of the patients with the worst outcome, and the hazard ratio was more significant than either of the two alone or neither, indicating that combined analysis of the mutation in plasma and PBMCs was more accurate to predict relapse than evaluation of either one. CONCLUSIONS: Concurrent assessment of BRAF-V600E mutation in plasma and PBMCs significantly impacted the prognosis of children with LCH. Further prospective studies with larger cohorts need to validate the results of this study.

Silica nanoparticles containing nano-silver and chlorhexidine to suppress Porphyromonas gingivalis biofilm and modulate multispecies biofilms toward healthy tendency.

Objectives: This research first investigated the effect of mesoporous silica nanoparticles (nMS) carrying chlorhexidine and silver (nMS-nAg-Chx) on periodontitis-related biofilms. This study aimed to investigate (1) the antibacterial activity on Porphyromonas gingivalis (P. gingivalis) biofilm; (2) the suppressing effect on virulence of P. gingivalis biofilm; (3) the regulating effect on periodontitis-related multispecies biofilm. Methods: Silver nanoparticles (nAg) and chlorhexidine (Chx) were co-loaded into nMS to form nMS-nAg-Chx. Inhibitory zone test and minimum inhibitory concentration (MIC) against P. gingivalis were tested. Growth curves, crystal violet (CV) staining, live/dead staining and scanning electron microscopy (SEM) observation were performed. Biofilm virulence was assessed. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and Quantitative Real Time-PCR (qPCR) were performed to validate the activity and composition changes of multispecies biofilm (P. gingivalis, Streptococcus gordonii and Streptococcus sanguinis). Results: nMS-nAg-Chx inhibited P. gingivalis biofilm dose-dependently (p<0.05), with MIC of 18.75 µg/mL. There were fewer live bacteria, less biomass and less virulence in nMS-nAg-Chx groups (p<0.05). nMS-nAg-Chx inhibited and modified periodontitis-related biofilms. The proportion of pathogenic bacteria decreased from 16.08 to 1.07% and that of helpful bacteria increased from 82.65 to 94.31% in 25 µg/mL nMS-nAg-Chx group for 72 h. Conclusions: nMS-nAg-Chx inhibited P. gingivalis growth, decreased biofilm virulence and modulated periodontitis-related multispecies biofilms toward healthy tendency. pH-sensitive nMS-nAg-Chx inhibit the pathogens and regulate oral microecology, showing great potential in periodontitis adjunctive therapy.

Inactivation of mitochondrial MUL1 E3 ubiquitin ligase deregulates mitophagy and prevents diet-induced obesity in mice.

Obesity is a growing epidemic affecting millions of people worldwide and a major risk factor for a multitude of chronic diseases and premature mortality. Accumulating evidence suggests that mitochondria have a profound role in diet-induced obesity and the associated metabolic changes, but the molecular mechanisms linking mitochondria to obesity remain poorly understood. Our studies have identified a new function for mitochondrial MUL1 E3 ubiquitin ligase, a protein known to regulate mitochondrial dynamics and mitophagy, in the control of energy metabolism and lipogenesis. Genetic deletion of Mul1 in mice impedes mitophagy and presents a metabolic phenotype that is resistant to high-fat diet (HFD)-induced obesity and metabolic syndrome. Several metabolic and lipidomic pathways are perturbed in the liver and white adipose tissue (WAT) of Mul1(-/-) animals on HFD, including the one driven by Stearoyl-CoA Desaturase 1 (SCD1), a pivotal regulator of lipid metabolism and obesity. In addition, key enzymes crucial for lipogenesis and fatty acid oxidation such as ACC1, FASN, AMPK, and CPT1 are also modulated in the absence of MUL1. The concerted action of these enzymes, in the absence of MUL1, results in diminished fat storage and heightened fatty acid oxidation. Our findings underscore the significance of MUL1-mediated mitophagy in regulating lipogenesis and adiposity, particularly in the context of HFD. Consequently, our data advocate the potential of MUL1 as a therapeutic target for drug development in the treatment of obesity, insulin resistance, NAFLD, and cardiometabolic diseases.

Identification of molecular subtypes based on chromatin regulator-related genes and experimental verification of the role of ASCL1 in conferring chemotherapy resistance to breast cancer.

Objective: The aim of this study was to identify the molecular subtypes of breast cancer based on chromatin regulator-related genes. Methods: The RNA sequencing data of The Cancer Genome Atlas-Breast Cancer cohort were obtained from the official website, while the single-cell data were downloaded from the Gene Expression Omnibus database (GSE176078). Validation was performed using the Molecular Taxonomy of Breast Cancer International Consortium dataset. Furthermore, the immune characteristics, tumor stemness, heterogeneity, and clinical characteristics of these molecular subtypes were analyzed. The correlation between chromatin regulators and chemotherapy resistance was examined in vitro using the quantitative real-time polymerase chain reaction (qRT-PCR) and Cell Counting Kit-8 (CCK8) assays. Results: This study identified three stable molecular subtypes with different prognostic and pathological features. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction analyses revealed that the differentially expressed genes were associated with disease processes, such as mitotic nuclear division, chromosome segregation, condensed chromosome, and specific chromosome region. The T stage and subtypes were correlated with the clinical features. Tumor heterogeneity (mutant-allele tumor heterogeneity, tumor mutational burden, purity, and homologous recombination deficiency) and tumor stemness (RNA expression-based stemness score, epigenetically regulated RNA expression-based stemness score, DNA methylation-based stemness score, and epigenetically regulated DNA methylation-based stemness score) significantly varied between the three subtypes. Furthermore, Western blotting, qRT-PCR, and CCK8 assays demonstrated that the expression of ASCL1 was positively correlated with chemotherapy resistance in breast cancer. Conclusion: This study identified the subtypes of breast cancer based on chromatin regulators and analyzed their clinical features, gene mutation status, immunophenotype, and drug sensitivity. The results of this study provide effective strategies for assessing clinical prognosis and developing personalized treatment strategies.

Zn promoted GaZrOx ternary solid solution oxide combined with SAPO-34 effectively converts CO2 to light olefins with low CO selectivity.

We proposed a new strategy for CO2 hydrogenation to prepare light olefins by introducing Zn into GaZrOx to construct ZnGaZrOx ternary oxides, which was combined with SAPO-34 to prepare a high-performance ZnGaZrOx/SAPO-34 tandem catalyst for CO2 hydrogenation to light olefins. By optimizing the Zn doping content, the ratio and mode of the two-phase composite, and the process conditions, the 3.5%ZnGaZrOx/SAPO-34 tandem catalyst showed excellent catalytic performance and good high-temperature inhibition of the reverse water-gas shift (RWGS) reaction. The catalyst achieved 26.6% CO2 conversion, 82.1% C2=-C4= selectivity and 11.8% light olefins yield. The ZnGaZrOx formed by introducing an appropriate amount of Zn into GaZrOx significantly enhanced the spillover H2 effect and also induced the generation of abundant oxygen vacancies to effectively promote the activation of CO2. Importantly, the RWGS reaction was also significantly suppressed at high temperatures, with the CO selectivity being only 46.1% at 390°C.

Efficacy and safety of CO2 fractional laser versus Er:YAG fractional laser in the treatment of atrophic acne scar: A meta-analysis and systematic review.

BACKGROUND: To date, a consensus on the relative efficacy and safety of CO2 fractional laser versus erbium-doped yttrium aluminum garnet (Er:YAG) fractional laser treatments for atrophic acne scars has not been reached. This meta-analysis aims to systematically assess and compare their effectiveness and safety in clinical practice. METHODS: For this meta-analysis, we conducted comprehensive searches in Pubmed, Embase, and Cochrane databases, covering publications from their inception up to August 2023. Our focus was on studies comparing fractional CO2 laser with Er:YAG fractional laser treatments for atrophic acne scars. We excluded duplicate publications, research lacking full-text access, incomplete data, or cases where data extraction was not feasible. Additionally, animal experiments, reviews, and systematic reviews were not considered. Data analysis was performed using STATA 15.1. RESULTS: Eight studies (seven randomized controlled trials (RCTs) and a retrospective study) were included in this meta-analysis. The sample size ranged from 28 to 106 with a total of 418 patients, including 210 in the CO2 fractional group and 208 in Er:YAG fractional group. The pooled results showed that the effective rate of CO2 fractional laser in treating atrophic acne scar was significantly higher than that of Er:YAG fractional laser (OR = 1.81, 95% CI: 1.08-3.01) and the downtime of CO2 fractional laser in treating atrophic acne scar was significantly shorter than that of Er:YAG fractional laser (Weighted Mean Difference (WMD) = -2.11, 95% CI: -3.11 to -1.10). In addition, VAS of CO2 fractional laser in treating atrophic acne scar was significantly higher than that of Er:YAG fractional laser (WMD = 1.77, 95% CI: 1.32-2.21) and the duration of erythema of CO2 fractional laser in treating atrophic acne scar was significantly longer than that of Er:YAG fractional laser (WMD = 1.85, 95% CI: 1.63-2.07). However, there was no significant difference in the duration of pain and incidence of PIHbetween CO2 fractional laser and of Er:YAG fractional laser. CONCLUSION: When it comes to treating atrophic acne scars, CO2 fractional laser demonstrates superior efficacy and leads to shorter downtime. However, it is important to note that CO2 fractional laser treatments tend to result in higher pain intensity and may carry a higher risk of post-treatment pigmentation compared to Er:YAG fractional laser procedures.

Establishment of a real-time fluorescent quantitative PCR detection method and phylogenetic analysis of BoAHV-1.

BACKGROUND: Infectious bovine rhinotracheitis (IBR), caused by Bovine alphaherpesvirus-1 (BoAHV-1), is an acute, highly contagious disease primarily characterized by respiratory tract lesions in infected cattle. Due to its severe pathological damage and extensive transmission, it results in significant economic losses in the cattle industry. Accurate detection of BoAHV-1 is of paramount importance. In this study, we developed a real-time fluorescent quantitative PCR detection method for detecting BoAHV-1 infections. Utilizing this method, we tested clinical samples and successfully identified and isolated a strain of BoAHV-1.1 from positive samples. Subsequently, we conducted a genetic evolution analysis on the isolate strain's gC, TK, gG, gD, and gE genes. RESULTS: The study developed a real-time quantitative PCR detection method using SYBR Green II, achieving a detection limit of 7.8 × 101 DNA copies/µL. Specificity and repeatability analyses demonstrated no cross-reactivity with other related pathogens, highlighting excellent repeatability. Using this method, 15 out of 86 clinical nasal swab samples from cattle were found to be positive (17.44%), which was higher than the results obtained from conventional PCR detection (13.95%, 12/86). The homology analysis and phylogenetic tree analysis of the gC, TK, gG, gD, and gE genes of the isolated strain indicate that the JL5 strain shares high homology with the BoAHV-1.1 reference strains. Amino acid sequence analysis revealed that gC, gE, and gG each had two amino acid mutations, while the TK gene had one synonymous mutation and one H to Y mutation, with no amino acid mutations observed in the gD gene. Phylogenetic tree analysis indicated that the JL5 strain belongs to the BoAHV-1.1 genotype and is closely related to American strains such as C33, C14, and C28. CONCLUSIONS: The established real-time fluorescent quantitative PCR detection method exhibits good repeatability, specificity, and sensitivity. Furthermore, genetic evolution analysis of the isolated BoAHV-1 JL-5 strain indicates that it belongs to the BoAHV-1.1 subtype. These findings provide a foundation and data for the detection, prevention, and control Infectious Bovine Rhinotracheitis.

Impact of Health Education Based on Protective Motivation Theory on the Mood State, Cancer-Related Fatigue, and Hope Level of Gastric Cancer Patients.

Background: Gastric cancer patients often feel physically tired and weak, lacking confidence and enthusiasm for relevant treatments. We aimed to explore the impacts of health education based on the theory of protective motivation on the emotional state, cancer-related fatigue, and hope levels of gastric cancer patients. Methods: A total of 160 gastric cancer patients admitted to the Sanmenxia Central Hospital, Henan, China, from May 2019 to March 2022 were selected as subjects. The control group (n=80) received routine health education, while the observation group (n=80) received health education based on the theory of protective motivation. Intervention evaluations included the Morisky medication compliance score, Plain Mood State Scale (POMS), Cancer Fatigue Scale (CFS), Herth Hope Scale (HHI), and Simple Health Survey Scale (SF-36). Results: After intervention, both groups showed an improvement in Morisky's medication compliance score, HHI scale score, and SF-36 scale score (all P<0.05). Additionally, the observation group exhibited greater improvement than the control group (P<0.05). There were no significant differences in POMS scale score and CFS scale score between the two groups before and after intervention. However, after intervention, both groups experienced a decrease in POMS scale score and CFS scale score (both P<0.05), with the observation group showing a more significant decrease compared to the control group (P<0.05). Conclusion: Health education based on the theory of protective motivation effectively enhances the mood state, reduces cancer-related fatigue, and increases hope levels among gastric cancer patients, thereby improving their medication compliance and overall quality of life.

BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning.

Transcription factors (TFs) are proteins essential for regulating genetic transcriptions by binding to transcription factor binding sites (TFBSs) in DNA sequences. Accurate predictions of TFBSs can contribute to the design and construction of metabolic regulatory systems based on TFs. Although various deep-learning algorithms have been developed for predicting TFBSs, the prediction performance needs to be improved. This paper proposes a bidirectional encoder representations from transformers (BERT)-based model, called BERT-TFBS, to predict TFBSs solely based on DNA sequences. The model consists of a pre-trained BERT module (DNABERT-2), a convolutional neural network (CNN) module, a convolutional block attention module (CBAM) and an output module. The BERT-TFBS model utilizes the pre-trained DNABERT-2 module to acquire the complex long-term dependencies in DNA sequences through a transfer learning approach, and applies the CNN module and the CBAM to extract high-order local features. The proposed model is trained and tested based on 165 ENCODE ChIP-seq datasets. We conducted experiments with model variants, cross-cell-line validations and comparisons with other models. The experimental results demonstrate the effectiveness and generalization capability of BERT-TFBS in predicting TFBSs, and they show that the proposed model outperforms other deep-learning models. The source code for BERT-TFBS is available at https://github.com/ZX1998-12/BERT-TFBS.

Unraveling the important role of comammox Nitrospira to nitrification in the coastal aquaculture system.

Increasing nitrogen (N) input to coastal ecosystems poses a serious environmental threat. It is important to understand the responses and feedback of N removal microbial communities, particularly nitrifiers including the newly recognized complete ammonia-oxidizers (comammox), to improve aquaculture sustainability. In this study, we conducted a holistic evaluation of the functional communities responsible for nitrification by quantifying and sequencing the key functional genes of comammox Nitrospira-amoA, AOA-amoA, AOB-amoA and Nitrospira-nxrB in fish ponds with different fish feeding levels and evaluated the contribution of nitrifiers in the nitrification process through experiments of mixing pure cultures. We found that higher fish feeding dramatically increased N-related concentration, affecting the nitrifying communities. Compared to AOA and AOB, comammox Nitrospira and NOB were more sensitive to environmental changes. Unexpectedly, we detected an equivalent abundance of comammox Nitrospira and AOB and observed an increase in the proportion of clade A in comammox Nitrospira with the increase in fish feeding. Furthermore, a simplified network and shift of keystone species from NOB to comammox Nitrospira were observed in higher fish-feeding ponds. Random forest analysis suggested that the comammox Nitrospira community played a critical role in the nitrification of eutrophic aquaculture ponds (40-70 µM). Through the additional experiment of mixing nitrifying pure cultures, we found that comammox Nitrospira is the primary contributor to the nitrification process at 200 µM ammonium. These results advance our understanding of nitrifying communities and highlight the importance of comammox Nitrospira in driving nitrification in eutrophic aquaculture systems.

Integrative analyses of bulk and single-cell transcriptomics reveals the infiltration and crosstalk of cancer-associated fibroblasts as a novel predictor for prognosis and microenvironment remodeling in intrahepatic cholangiocarcinoma.

BACKGROUND: Intrahepatic cholangiocarcinoma (ICC) is a highly malignant neoplasm and characterized by desmoplastic matrix. The heterogeneity and crosstalk of tumor microenvironment remain incompletely understood. METHODS: To address this gap, we performed Weighted Gene Co-expression Network Analysis (WGCNA) to identify and construct a cancer associated fibroblasts (CAFs) infiltration biomarker. We also depicted the intercellular communication network and important receptor-ligand complexes using the single-cell transcriptomics analysis of tumor and Adjacent normal tissue. RESULTS: Through the intersection of TCGA DEGs and WGCNA module genes, 784 differential genes related to CAFs infiltration were obtained. After a series of regression analyses, the CAFs score was generated by integrating the expressions of EVA1A, APBA2, LRRTM4, GOLGA8M, BPIFB2, and their corresponding coefficients. In the TCGA-CHOL, GSE89748, and 107,943 cohorts, the high CAFs score group showed unfavorable survival prognosis (p < 0.001, p = 0.0074, p = 0.028, respectively). Additionally, a series of drugs have been predicted to be more sensitive to the high-risk group (p < 0.05). Subsequent to dimension reduction and clustering, thirteen clusters were identified to construct the single-cell atlas. Cell-cell interaction analysis unveiled significant enhancement of signal transduction in tumor tissues, particularly from fibroblasts to malignant cells via diverse pathways. Moreover, SCENIC analysis indicated that HOXA5, WT1, and LHX2 are fibroblast specific motifs. CONCLUSIONS: This study reveals the key role of fibroblasts - oncocytes interaction in the remodeling of the immunosuppressive microenvironment in intrahepatic cholangiocarcinoma. Subsequently, it may trigger cascade activation of downstream signaling pathways such as PI3K-AKT and Notch in tumor, thus initiating tumorigenesis. Targeted drugs aimed at disrupting fibroblasts-tumor cell interaction, along with associated enrichment pathways, show potential in mitigating the immunosuppressive microenvironment that facilitates tumor progression.

The Application of 2d Mxene Nanosheet -Based Thermosensitive Gel Delivery System Loaded with Cisplatin and Imiquimod for Lung Cancer.

Introduction: Lung cancer's high incidence and dismal prognosis with traditional treatments like surgery and radiotherapy necessitate innovative approaches. Despite advancements in nanotherapy, the limitations of single-treatment modalities and significant side effects persist. To tackle lung cancer effectively, we devised a temperature-sensitive hydrogel-based local injection system with near-infrared triggered drug release. Utilizing 2D MXene nanosheets as carriers loaded with R837 and cisplatin (DDP), encapsulated within a temperature-sensitive hydrogel-forming PEG-MXene@DDP@R837@SHDS (MDR@SHDS), we administered in situ injections of MDR@SHDS into tumor tissues combined with photothermal therapy (PTT). The immune adjuvant R837 enhances dendritic cell (DC) maturation and tumor cell phagocytosis, while PTT induces tumor cell apoptosis and necrosis by converting light energy into heat energy. Methods: Material characterization employed transmission electron microscopy, X-ray photoelectron spectroscopy, phase transition temperature, and near-infrared thermography. In vitro experiments assessed Lewis cell proliferation and apoptosis using CCK-8, Edu, and TUNEL assays. In vivo experiments on C57 mouse Lewis transplant tumors evaluated the photothermal effect via near-infrared thermography and assessed DC maturation and CD4+/CD8+ T cell ratios using flow cytometry. The in vivo anti-tumor efficacy of MDR@SHDS was confirmed by tumor growth curve recording and HE and TUNEL staining of tumor sections. Results: The hydrogel exhibited excellent temperature sensitivity, controlled release properties, and high biocompatibility. In vitro experiments revealed that MDR@SHDS combined with PTT had a greater inhibitory effect on tumor cell proliferation compared to MDR@SHD alone. Combining local immunotherapy, chemotherapy, and PTT yielded superior anti-tumor effects than individual treatments. Conclusion: MDR@SHDS, with its simplicity, biocompatibility, and enhanced anti-tumor effects in combination with PTT, presents a promising therapeutic approach for lung cancer treatment, offering potential clinical utility.

Morphological Changes of the Temporomandibular Joint and Masseter Muscle After Mandibular Angle Osteotomy.

Mandibular angle osteotomy with outer cortex grinding is an effective cosmetic procedure for correcting square faces. However, morphological changes in the mandible may also cause temporomandibular joint (TMJ) disorders. This retrospective study aimed to investigate the morphological stabilization of the TMJ and changes in masseter muscle thickness after mandibular angle osteotomy to evaluate the safety of the procedure. Data from patients who underwent mandibular angle osteotomy with outer cortex grinding between January 2016 and January 2019 were retrospectively reviewed. Preoperative and long-term follow-up (~1 y) computed tomography data were collected from these patients, and morphological changes in the TMJ and masseter muscle were analyzed. The results from the computed tomography data showed that the condylar length and condylar height were significantly reduced 1 year after the operation (P < 0.05). In addition, the morphology of the TMJ was stable, and the distance between the mandibular condyle and the glenoid fossa did not change significantly. No significant difference was observed in masseter muscle thickness before and after the operation. After mandibular angle osteotomy with outer cortex grinding, the length and height of the mandibular condyle were functionally restored without any disorders of the TMJ. Moreover, the masseter muscle exhibited stable function. In conclusion, the procedure is safe for occlusal function and suitable for popularization.