Exploratory study on the metabolic similarity of denitrifying carbon sources.

Mixed carbon sources have been developed for denitrification to eliminate the "carbon dependency" problem of single carbon. The metabolic correlation between different carbon sources is significant as guidance for the development of novel mixed carbon sources. In this study, to explore the metabolic similarity of denitrifying carbon sources, we selected alcohols (methanol, ethanol, and glycerol) and saccharide carbon sources (glucose, sucrose, and starch). Batch denitrification experiments revealed that methanol-acclimated sludge improved the denitrification rate of both methanol (14.42 mg-N/gMLVSS*h) and ethanol (9.65 mg-N/gMLVSS*h), whereas ethanol-acclimated sludge improved the denitrification rate of both methanol (7.80 mg-N/gMLVSS*h) and ethanol (22.23 mg-N/gMLVSS*h). In addition, the glucose-acclimated sludge and sucrose-acclimated sludge possibly improved the denitrification rate of glucose and sucrose, and the glycerol-acclimated sludge improved the denitrification rate of volatile fatty acids (VFAs), alcohols, and saccharide carbon sources. Functional gene analysis revealed that methanol, ethanol, and glycerol exhibited active alcohol oxidation and glyoxylate metabolism, and glycerol, glucose, and sucrose exhibited active glycolysis metabolism. This indicated that the similarity in the denitrification metabolism of these carbon sources was based on functional gene similarity, and glycerol-acclimated sludge exhibited the most diverse metabolism, which ensured its good denitrification effect with other carbon sources.

Neurosurgical application of pineal region tumor resection with 3D 4K exoscopy via infratentorial approach: a retrospective cohort study.

BACKGROUND: The pineal region tumors are challenging for neurosurgeons and can lead to secondary hydrocephalus. The introduction of the exoscope has provided clinical interventions with high image quality and an ergonomic system for pineal region tumor operations. In this study, the authors describe the exoscopic approach used to facilitate the surgical resection of pineal region tumors and relieve hydrocephalus. MATERIALS AND METHODS: In this retrospective cohort study, we consecutively reviewed the clinical and radiological data of 25 patients with pineal region lesions who underwent three-dimensional exoscopic tumor resection at a single center. RESULTS: The patient cohort consisted of 16 males and 9 females, with an average age of 34.6 years (range, 6-62 years; 8 cases aged ≤18). Pathological examination confirmed eight pineal gland tumors, four gliomas, nine germ cell neoplasms, two ependymomas, and two metastatic tumors. Preoperative hydrocephalus was present in 23 patients. Prior to tumor resection, external ventricular drainage (EVD) with Ommaya reservoir implantation was performed in 17 patients. Two patients received preoperative endoscopic third ventriculostomy (ETV), and five patients received a ventriculoperitoneal (VP) shunt, including one who received both procedures. Gross total resection was achieved in 19 patients (76%) in the 'head-up' park bench position using the exoscope. Eight patients (31.6%) with third ventricle invasion received subtotal resection, mainly in glioma cases, which was higher than those without invasion (0%), but not statistically significant ( P =0.278, Fisher's exact test). No new neurological dysfunction was observed after surgery. Two patients (8%) developed intracranial and pulmonary infections, and two patients (8%) suffered from pneumothorax. Hydrocephalus was significantly relieved in all patients postoperatively, and four patients with relapse hydrocephalus were cured during the long-term follow-up. Postoperative adjuvant management was recommended for indicated patients, and a mean follow-up of 24.8±14.3 months showed a satisfied outcome. CONCLUSIONS: The exoscope is a useful tool for pineal region tumor resection and hydrocephalus relief, particularly with posterior third ventricle invasion, as total resection could be achieved without obvious complication. The special superiority of the exoscope for the indicated pineal region tumors should be highlighted.

Distinct aneuploid evolution of astrocytoma and glioblastoma during recurrence.

Astrocytoma and glioblastoma (GB) are reclassified subtypes of adult diffuse gliomas based on distinct isocitrate dehydrogenase (IDH) mutation in the fifth edition of the WHO Classification of Tumors of the Central Nervous System. The recurrence of gliomas is a common and inevitable challenge, and analyzing the distinct genomic alterations in astrocytoma and GB could provide insights into their progression. This study conducted a longitudinal investigation, utilizing whole-exome sequencing, on 65 paired primary/recurrent gliomas. It examined chromosome arm aneuploidies, copy number variations (CNVs) of cancer-related genes and pathway enrichments during the relapse. The veracity of these findings was verified through the integration of our data with multiple public resources and by corroborative immunohistochemistry (IHC). The results revealed a greater prevalence of aneuploidy changes and acquired CNVs in recurrent lower grade astrocytoma than in relapsed grade 4 astrocytoma and GB. Larger aneuploidy changes were predictive of an unfavorable prognosis in lower grade astrocytoma (P < 0.05). Further, patients with acquired gains of 1q, 6p or loss of 13q at recurrence had a shorter overall survival in lower grade astrocytoma (P < 0.05); however, these prognostic effects were confined in grade 4 astrocytoma and GB. Moreover, acquired gains of 12 genes (including VEGFA) on 6p during relapse were associated with unfavorable prognosis for lower grade astrocytoma patients. Notably, elevated VEGFA expression during recurrence corresponded to poorer survival, validated through IHC and CGGA data. To summarize, these findings offer valuable insights into the progression of gliomas and have implications for guiding therapeutic approaches during recurrence.

A new approach to optimizing aeration using XGB-Bi-LSTM via the online monitoring of oxygen transfer efficiency and oxygen uptake rate.

In wastewater treatment plants (WWTPs), aeration is vital for microbial oxygen needs. To achieve carbon neutrality, optimizing aeration for energy and emissions reduction is imperative. Machine learning (ML) is used in wastewater treatment to reveal complex rules in large data sets has become a trend. In this vein, the present paper proposes an aeration optimization approach based on the extreme gradient boosting-bidirectional long short-term memory (XGB-Bi-LSTM) model via the online monitoring of oxygen transfer efficiency (OTE) and oxygen uptake rate (OUR), thus allowing WWTPs to conserve energy and reduce indirect carbon emissions. The approach uses gain algorithm of XGB to calculate the importance of features and identify important parameters, and then uses Bi-LSTM to predict the target with important parameters as features. Operational data from a WWTP in Suzhou, China, is employed to train and test the approach, the performance of which is compared with ML models suitable for regression prediction tasks (XGB, random forest, light gradient boosting machine, gradient boosting and LSTM). Experimental results show the approach requires only a small number of input parameters to achieve good performance and outperforms other machine-learning models. When OTE and dissolved oxygen (DO) are used as features to predict the alpha factor (αF; since diffusers were used, multiply by the pollution factor F), the R-squared (R2) is 0.9977, the root mean square error (RMSE) is 0.0043, the mean absolute percentage error (MAPE) is 0.0069 and the median absolute error (MedAE) is 0.0032. When the predicted αF and the OUR are used as features to predict the air flow rate of an aeration unit, the R2 is 0.9901, the RMSE is 3.6150, the MAPE is 0.0209 and the MedAE is 1.5472. Using our optimized aeration approach, the energy consumption can be reduced by 23%.

Use of Bevacizumab in recurrent glioblastoma: a scoping review and evidence map.

BACKGROUND: Glioblastoma (GBM) is the most malignant primary tumor in the brain, with poor prognosis and limited effective therapies. Although Bevacizumab (BEV) has shown promise in extending progression-free survival (PFS) treating GBM, there is no evidence for its ability to prolong overall survival (OS). Given the uncertainty surrounding BEV treatment strategies, we aimed to provide an evidence map associated with BEV therapy for recurrent GBM (rGBM). METHODS: PubMed, Embase, and the Cochrane Library were searched for the period from January 1, 1970, to March 1, 2022, for studies reporting the prognoses of patients with rGBM receiving BEV. The primary endpoints were overall survival (OS) and quality of life (QoL). The secondary endpoints were PFS, steroid use reduction, and risk of adverse effects. A scoping review and an evidence map were conducted to explore the optimal BEV treatment (including combination regimen, dosage, and window of opportunity). RESULTS: Patients with rGBM could gain benefits in PFS, palliative, and cognitive advantages from BEV treatment, although the OS benefits could not be verified with high-quality evidence. Furthermore, BEV combined therapy (especially with lomustine and radiotherapy) showed higher efficacy than BEV monotherapy in the survival of patients with rGBM. Specific molecular alterations (IDH mutation status) and clinical features (large tumor burden and double-positive sign) could predict better responses to BEV administration. A low dosage of BEV showed equal efficacy to the recommended dose, but the optimal opportunity window for BEV administration remains unclear. CONCLUSIONS: Although OS benefits from BEV-containing regimens could not be verified in this scoping review, the PFS benefits and side effects control supported BEV application in rGBM. Combining BEV with novel treatments like tumor-treating field (TTF) and administration at first recurrence may optimize the therapeutic efficacy. rGBM with a low apparent diffusion coefficient (ADCL), large tumor burden, or IDH mutation is more likely to benefit from BEV treatment. High-quality studies are warranted to explore the combination modality and identify BEV-response subpopulations to maximize benefits.

Cell Cycle-Related FAM64A Could be Activated by TGF-ß Signaling to Promote Glioma Progression.

Gliomas are aggressive brain tumors characterized by uncontrolled cell proliferation. FAM64A, a cell cycle-related gene, has been found to promote cell proliferation in various tumors, including gliomas. However, the regulatory mechanism and clinical significance of FAM64A in gliomas remain unclear. In this study, we investigated FAM64A expression in gliomas with different grades and constructed FAM64A silenced cell lines to study its functions. Our results demonstrated that FAM64A was highly expressed in glioblastoma (P < 0.001) and associated with a poor prognosis (P < 0.001). Expression profiles at the single-cell resolution indicated FAM64A could play a role in a cell-cycle-dependent way to promote glioma cell proliferation. We further observed that FAM64A silencing in glioma cells resulted in disrupted proliferation and migration ability, and increased cell accumulation in the G2/M phase (P = 0.034). Additionally, TGF-ß signaling upregulates FAM64A expression, and SMAD4 and FAM64A co-localize in high-grade glioma tissues. We found FAM64A knockdown inhibited TGF-ß-induced epithelial-mesenchymal transition in glioma. Our findings suggest that FAM64A could serve as a diagnostic and therapeutic target in gliomas.

Pure endoscopic resection of pineal region tumors through supracerebellar infratentorial approach with 'head-up' park-bench position.

OBJECTIVE: Neuroendoscopic resection via supracerebellar infratentorial (SCIT) approach is adequate for some indicated pineal region tumors with the natural infratentorial corridor. We described this full endoscopic approach through a modified 'head-up' park-bench position to facilitate the procedure. METHODS: We reviewed the clinical and radiological data of four patients with pineal region lesions who underwent pure endoscopic tumor resection through the SCIT approach with this modified position. The related literature concerning fully endoscopic pineal region tumor resection was also reviewed. RESULTS: This cohort included four patients with pineal region tumors. External ventricular drainage (Ommaya reservoir) was performed in three patients with hydrocephalus in advance. The average tumor volume was 19.2 ± 17.2 cm3. Pathological examination confirmed two mixed germinomas, one glioblastoma multiforme, and one hemangioblastoma. Gross total resection (GTR) was achieved in all patients, and all patients recovered well without neurological deficits or surgical complications. Hydrocephalus was relieved among all patients. CONCLUSIONS: The pure endoscopic SCIT approach could enable safe and effective resection of pineal region tumors, even for relatively large lesions. The endoscope could provide a panoramic view and illumination of the deep-seated structures. Compared with the sitting position, this modified ergonomic position could be implemented easily.

Optimization on structure and operation parameters of biofilter for decentralized sewage treatment.

Aiming for treating decentralized domestic wastewater in rural China, this study evaluates the effects of ceramsite size and structure, and water recirculation parameters, upon the performance of recirculating biofilter (RBF). RBF shows stable capability of chemical oxygen demand (COD) remediation and ammonia nitrification. In addition, the microbial flora and structures of the various layers in the system are analyzed via high-throughput sequencing in order to study the microbial diversity. The results indicate that while the ceramic particle size has no significant influence on the COD remediation capacity, the ceramics with smaller particle sizes exhibit better ammonia nitrogen (NH4+-N) removal ability, with a first-order linear relationship between the influent ammonia nitrogen load and the effluent NH4+-N concentration in RBF (R2 > 0.64). An increased hydraulic load and intermittent operation are shown to deteriorate the water quality with respect to NH4+-N, while an increased recirculation ratio increases the removal rate of NH4+-N from the effluent. Further, the water distribution time has a stronger effect upon the NH4+-N concentration in the effluent than does the recirculation ratio. Moreover, the microbial structure of the multi-layer recirculating trickle biofilter varies significantly during the process. The results indicate that a high recirculation ratio, long water distribution time, and multi-layer structure will be beneficial for improving the pollutant treatment capacity of RBF.

Molecular mechanisms through which different carbon sources affect denitrification by Thauera linaloolentis: Electron generation, transfer, and competition.

Characterizing the molecular mechanism through which different carbon sources affect the denitrification process would provide a basis for the proper selection of carbon sources, thus avoiding excessive carbon source dosing and secondary pollution while also improving denitrification efficiency. Here, we selected Thauera linaloolentis as a model organism of denitrification, whose genomic information was elucidated by draft genome sequencing and KEGG annotations, to investigate the growth kinetics, denitrification performances and characteristics of metabolic pathways under diverse carbon source conditions. We reconstructed a metabolic network of Thauera linaloolentis based on genomic analysis to help develop a systematic method of researching electron pathways. Our findings indicated that carbon sources with simple metabolic pathways (e.g., ethanol and sodium acetate) promoted the reproduction of Thauera linaloolentis, and its maximum growth density reached OD600 = 0.36 and maximum specific growth rate reached 0.145 h-1. These carbon sources also accelerated the denitrification process without the accumulation of intermediates. Nitrate could be reduced completely under any carbon source condition; but in the "glucose group", the maximum accumulation of nitrite was 117.00 mg/L (1.51 times more than that in the "ethanol group", which was 77.41 mg/L), the maximum accumulation of nitric oxide was 363.02 µg/L (7.35 times more than that in the "ethanol group", which was 49.40 µg/L), and the maximum accumulation of nitrous oxide was 22.58 mg/L (26.56 times more than that in the "ethanol group", which was 0.85 mg/L). Molecular biological analyses demonstrated that diverse types of carbon sources directly induced different carbon metabolic activities, resulting in variations in electron generation efficiency. Furthermore, the activities of the electron transport system were positively correlated with different carbon metabolic activities. Finally, these differences were reflected in the phenomenon of electronic competition between denitrifying reductases. Thus we concluded that this was the main molecular mechanism through which the carbon source type affected the denitrification process. In brief, carbon sources with simple metabolic pathways induced higher efficiency of electron generation, transfer, and competition, which promoted rapid proliferation and complete denitrification; otherwise Thauera linaloolentis would grow slowly and intermediate products would accumulate seriously. Our study established a method to evaluate and optimize carbon source utilization efficiency based on confirmed molecular mechanisms.

Proposed new prognostic model using the systemic immune-inflammation index for primary central nervous system lymphoma: A prospective-retrospective multicohort analysis.

Purpose: The systemic immune-inflammation index (SII) has been considered a novel prognostic biomarker in several types of lymphoma. Our aims were to determine the best statistical relationship between pretreatment SII and survival and to combination of SII and the Memorial Sloan Kettering Cancer Center model (MSKCC) to derive the best prognostic mode in primary central nervous system lymphoma (PCNSL). Methods: Pretreatment SII and clinical data in 174 newly diagnosed PCNSL patients were included from two retrospective discovery cohorts (n = 128) and one prospective validation cohort (n = 46). A generalized additive model, Kaplan-Meier curve, and Cox analysis were performed. The high risk versus low risk of SII-MSKCC for the PCNSL cutoff point (0-1 vs. 2-4) was determined by the minimum P-value approach. Results: The SII showed a U-shaped relationship with the risk of overall survival (OS; P = 0.006). The patients with low SII or high SII had poorer OS and progression-free survival (PFS) than those with median SII. For PFS and OS, SII-MSKCC was a better predictor than MSKCC alone. The area under the receiver operating characteristic curve of the SII-MSKCC score was 0.84 for OS and 0.78 for PFS in the discovery cohorts. The predictive value of the SII-MSKCC score (OS, 0.88; PFS, 0.95) was verified through the validation cohort. Multivariable Cox analysis and Kaplan-Meier curve showed excellent performance for SII-MSKCC, with significant separation of two groups and better performance than MSKCC alone. Conclusions: We propose a new prognostic model using SII, age, and Karnofsky score that outperforms MSKCC alone and enables individualized estimates of patient outcome.

Insights into the relationship between denitrification and organic carbon release of solid-phase denitrification systems: Mechanism and microbial characteristics.

Solid-phase denitrification is a promising alternative denitrification technology when facing a shortage of carbon sources. Nevertheless, it is still unclear whether there is a certain interaction between the denitrification process and the carbon release process in a solid-phase denitrification system. In this study, the concept of "Self-adaptation" was proposed for the relationship between denitrification and carbon release. At various influent nitrate loads, the PCL-supported denitrification system achieved an average nitrate removal rate of over 90.59 ± 7.01 % and a maximum denitrification rate of 0.67 ± 0.06 gN/(L·d). Microorganisms can spontaneously regulate the carbon release rate of PCL in response to changes in influent nitrate load, demonstrating "self-adaptation" of the PCL-supported solid-phase denitrification system. Regulation of carbon release rate via the "Self-adaptation" was achieved by changes in extracellular depolymerase activity. Acidovorax_sp. played a key role in "Self-adaptation", for its function of both denitrification and PCL degradation.

Prognostic significance of pretreatment red blood cell distribution width in primary diffuse large B-cell lymphoma of the central nervous system for 3P medical approaches in multiple cohorts.

Background/aims: Predicting the clinical outcomes of primary diffuse large B-cell lymphoma of the central nervous system (PCNS-DLBCL) to methotrexate-based combination immunochemotherapy treatment in advance and therefore administering the tailored treatment to the individual is consistent with the principle of predictive, preventive, and personalized medicine (PPPM/3PM). The red blood cell distribution width (RDW) has been reported to be associated with the clinical outcomes of multiple cancer. However, its prognostic role in PCNS-DLBCL is yet to be evaluated. Therefore, we aimed to effectively stratify PCNS-DLBCL patients with different prognosis in advance and early identify the patients who were appropriate to methotrexate-based combination immunochemotherapy based on the pretreatment level of RDW and a clinical prognostic model. Methods: A prospective-retrospective, multi-cohort study was conducted from 2010 to 2020. We evaluated RDW in 179 patients (retrospective discovery cohorts of Huashan Center and Renji Center and prospective validation cohort of Cancer Center) with PCNS-DLBCL treated with methotrexate-based combination immunochemotherapy. A generalized additive model with locally estimated scatterplot smoothing was used to identify the relationship between pretreatment RDW levels and clinical outcomes. The high vs low risk of RDW combined with MSKCC score was determined by a minimal P-value approach. The clinical outcomes in different groups were then investigated. Results: The pretreatment RDW showed a U-shaped relationship with the risk of overall survival (OS, P = 0.047). The low RDW (< 12.6) and high RDW (> 13.4) groups showed significantly worse OS (P < 0.05) and progression-free survival (PFS; P < 0.05) than the median group (13.4 > RDW > 12.6) in the discovery and validation cohort, respectively. RDW could predict the clinical outcomes successfully. In the discovery cohort, RDW achieved the area under the receiver operating characteristic curve (AUC) of 0.9206 in predicting the clinical outcomes, and the predictive value (AUC = 0.7177) of RDW was verified in the validation cohort. In addition, RDW combined with MSKCC predictive model can distinguish clinical outcomes with the AUC of 0.8348 for OS and 0.8125 for PFS. Compared with the RDW and MSKCC prognosis variables, the RDW combined with MSKCC scores better identified a subgroup of patients with favorable long-term survival in the validation cohort (P < 0.001). RDW combined MSKCC score remained to be independently associated with clinical outcomes by multivariable analysis. Conclusions: Based on the pretreatment RDW and MSKCC scores, a novel predictive tool was established to stratify PCNS-DLBCL patients with different prognosis effectively. The predictive model developed accordingly is promising to judge the response of PCNS-DLBCL to methotrexate-based combination immunochemotherapy treatment. Thus, hematologists and oncologists could tailor and adjust therapeutic modalities by monitoring RDW in a prospective rather than the reactive manner, which could save medical expenditures and is a key concept in 3PM. In brief, RDW combined with MSKCC model could serve as an important tool for predicting the response to different treatment and the clinical outcomes for PCNS-DLBCL, which could conform with the principles of predictive, preventive, and personalized medicine. Supplementary Information: The online version contains supplementary material available at 10.1007/s13167-022-00290-5.

The Anti-Glioma Effect of Juglone Derivatives through ROS Generation.

Juglone has been extensively reported as a natural antitumor pigment. However, it is easy to be oxidized due to active hydroxy in the quinone. Here, we designed some new juglone derivatives, as the hydroxy was replaced by methyl (D1), allyl (D2), butyl (D3), and benzyl (D4) groups. Nuclear magnetic resonance spectra and mass spectrometry were applied to confirm the derivatives and oxidative products of juglone. U87 and U251 cell lines were used for tests in vitro, and primary human glioblastoma cells were applied for in vivo experiments. The CCK8 and EdU assay demonstrated the anti-tumor effect of the four derivatives, and IC50 for U87 was 3.99, 3.28, 7.60, and 11.84 µM, respectively. In U251, IC50 was 7.00, 5.43, 8.64, and 18.05 µM, respectively. D2 and D3 were further selected, and flow cytometry showed that apoptosis rates were increased after D2 or D3 treatment via ROS generation. Potential targets were predicted by network pharmacology analysis, most of which were associated with apoptosis, cell cycle, and metabolism pathway. CDC25B and DUSP1 were two of the most likely candidates for targets. The orthotopic glioblastoma model was established to evaluate the anti-glioma effect and side-effect of juglone derivatives, and the in vivo experiments confirmed the anti-glioma effects of juglone derivatives. In conclusion, new derivatives of juglone were created via chemical group substitution and could inhibit glioma cell viability and proliferation and induce apoptosis rate via ROS generation.

Identification of Four Metabolic Subtypes of Glioma Based on Glycolysis-Cholesterol Synthesis Genes.

Based on alterations in gene expression associated with the production of glycolysis and cholesterol, this research classified glioma into prognostic metabolic subgroups. In this study, data from the CGGA325 and The Cancer Genome Atlas (TCGA) datasets were utilized to extract single nucleotide variants (SNVs), RNA-seq expression data, copy number variation data, short insertions and deletions (InDel) mutation data, and clinical follow-up information from glioma patients. Glioma metabolic subtypes were classified using the ConsensusClusterPlus algorithm. This study determined four metabolic subgroups (glycolytic, cholesterogenic, quiescent, and mixed). Cholesterogenic patients had a higher survival chance. Genome-wide investigation revealed that inappropriate amplification of MYC and TERT was associated with improper cholesterol anabolic metabolism. In glioma metabolic subtypes, the mRNA levels of mitochondrial pyruvate carriers 1 and 2 (MPC1/2) presented deletion and amplification, respectively. Differentially upregulated genes in the glycolysis group were related to pathways, including IL-17, HIF-1, and TNF signaling pathways and carbon metabolism. Downregulated genes in the glycolysis group were enriched in terpenoid backbone biosynthesis, nitrogen metabolism, butanoate metabolism, and fatty acid metabolism pathway. Cox analysis of univariate and multivariate survival showed that risks of glycolysis subtypes were significantly higher than other subtypes. Those results were validated in the CGGA325 dataset. The current findings greatly contribute to a comprehensive understanding of glioma and personalized treatment.

Regional discrepancy of microbial community structure in activated sludge system from Chinese WWTPs based on high-throughput 16S rDNA sequencing.

Overall understanding of microbial community structure in activated sludge (AS) system at regional level is of great significance for operation regulation of wastewater treatment plants (WWTPs). In this study, 110 AS samples from 21 cities in different Chinese regions were analyzed based on high-throughput 16S ribosomal DNA (rDNA) sequencing to explore effects of different regions on microbial community structure. Results showed that the regions with different characteristics (south and north, coastal and inland, high GDP and low GDP) had great impact on AS bacterial community in China. Core bacterial communities (101 OTUs) in south China were more abundant than those in north China (49 OTUs), and many core species in south China were associated with nutrient removal. Coastal WWTPs possessed unique bacterial communities due to the influence of marine bacteria. Phyla Chloroflexi and Acidobacteria were observed to be main biomarkers in coastal WWTPs. Compared with low GDP regions, more diverse microbial community and effective wastewater treatment were discovered in high GDP regions, and environmental factor analysis suggested that they were mainly correlated with high capacity and influent TP in the WWTPs. ß nearest taxon index (ßNTI) analysis showed that microbial community assembly in the analyzed AS samples was dominated by deterministic factors (70.67%) and influent quality was observed to be main factor.

Effect of freezing-thawing on the quality changes of large yellow croaker treated by low-salt soaking during frozen storage.

Introduction: The production of the large yellow croaker has seasonal and regional characteristics, which is typically preserved on ice, possibly leading to its deterioration in a short time. Therefore, in this study, we focused on the effect of temperature fluctuation on the quality changes of the large yellow croaker during frozen storage. Methods: In this experiment, the large yellow croaker was soaked in a low-salt solution, and physical and chemical properties, water-holding capacity, color, and protein characteristics of the muscle were investigated after repeated freeze-thaw (F-T) cycles and frozen storage. Results and discussion: The results show the deterioration of muscle quality of large yellow croaker after low-salt treatment was lower than that of the salt-free soaking group. The salting treatment significantly (P < 0.05) enhanced the yield of large yellow croaker, which was 24.3% greater than the salt-free soaking group after 6 weeks of frozen storage. The microstructure of the salted muscle was more stable and maintained its cellular structure after F-T cycles and frozen storage. The b* value of the salt-free soaking group increased from b* value of the low-salt soaking group decreased from acceptable range. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis indicates the content of 17 kDa peptide decreased in the low-salt soaking group, and the peptides at 21 and 24 kDa increased during frozen storage. The results of the present study provide guidance for the optimal processing, transport, and storage of large yellow croaker, but the effect of salting on lipid oxidation and protein oxidation requires further study.

Gene clusters based on OLIG2 and CD276 could distinguish molecular profiling in glioblastoma.

BACKGROUND: The molecular profiling of glioblastoma (GBM) based on transcriptomic analysis could provide precise treatment and prognosis. However, current subtyping (classic, mesenchymal, neural, proneural) is time-consuming and cost-intensive hindering its clinical application. A simple and efficient method for classification was imperative. METHODS: In this study, to simplify GBM subtyping more efficiently, we applied a random forest algorithm to conduct 26 genes as a cluster featured with hub genes, OLIG2 and CD276. Functional enrichment analysis and Protein-protein interaction were performed using the genes in this gene cluster. The classification efficiency of the gene cluster was validated by WGCNA and LASSO algorithms, and tested in GSE84010 and Gravandeel's GBM datasets. RESULTS: The gene cluster (n = 26) could distinguish mesenchymal and proneural excellently (AUC = 0.92), which could be validated by multiple algorithms (WGCNA, LASSO) and datasets (GSE84010 and Gravandeel's GBM dataset). The gene cluster could be functionally enriched in DNA elements and T cell associated pathways. Additionally, five genes in the signature could predict the prognosis well (p = 0.0051 for training cohort, p = 0.065 for test cohort). CONCLUSIONS: Our study proved the accuracy and efficiency of random forest classifier for GBM subtyping, which could provide a convenient and efficient method for subtyping Proneural and Mesenchymal GBM.

DDX60 Is Associated With Glioma Malignancy and Serves as a Potential Immunotherapy Biomarker.

DDX60, an interferon (IFN)-inducible gene, plays a promotional role in many tumors. However, its function in glioma remains unknown. In this study, bioinformatic analysis (TCGA, CGGA, Rembrandt) illustrated the upregulation and prognostic value of DDX60 in gliomas. Immunohistochemical staining of clinical samples (n = 49) validated the DDX60 expression is higher in gliomas than in normal tissue (n = 20, P < 0.0001). It also could be included in nomogram as a parameter to predict the 3- and 5-year survival risk (C-index = 0.86). The biological process of DDX60 in glioma was mainly enriched in the inflammatory and immune response by GSEA and GO analysis. DDX60 expression had a positive association with most inflammatory-related functions, such as hematopoietic cell kinase (HCK) (R = 0.31), interferon (R = 0.72), STAT1 (R = 54), and a negative correlation with IgG (R = -0.24). Furthermore, DDX60 expression tends to be positively related to multiple infiltrating immune cells, while negatively related to CD56 dim nature killer cell in glioma. Some important immune checkpoints, like CTLA-4, PD-L1, EGF, CD96, and CD226, were all positively related with DDX60 (all Pearson correlation R > 0.26). The expression and correlation between DDX60, EGF, and PD-L1 were confirmed by western blot in clinical samples (n = 14, P < 0.0001) and GBM cells. These results indicated that DDX60 might have important clinical significance in glioma and could serve as a potential immune therapeutic target.