The biochemical methane potential test is a standard method to determine the biodegradability of lignocellulosic wastes (LWs) during anaerobic digestion (AD) with disadvantages of long experiment duration and high operating expense. This paper developed a machine learning model to predict the cumulative methane yield (CMY) using the data of 157 LWs regarding physicochemical characteristics, digestion condition and methane yield, with the coefficient of determination equal to 0.869. Model interpretability analyses underscored lignin content, organic loading, and nitrogen content as pivotal attributes for CMY prediction. For the feedstocks with a cellulose content exceeding about 50%, the CMY in the early AD stage would be relatively lower than those with low cellulose content, but prolonging digestion time could promote methane production. Besides, lignin content in feedstock surpassing 15% would significantly inhibit methane production. This work contributes to valuable guidance for feedstock selection and operation optimization for AD plants.

Antioxidants are widely used in the fields of food, medicine, nutraceuticals, and cosmetics. Given their important roles in promoting and maintaining human health, a large number of antioxidants have been reported. Some antioxidant-related databases have been developed; however, the annotation of antioxidants and related information stored in existing databases is incomplete and requires more efficient retrieval methods. This study aimed to develop a manually curated comprehensive antioxidant database (AODB). Currently, it stores 56,666 small molecules tested for antioxidant activity, 1480 antioxidant peptides, and 998 antioxidant proteins, including their structures, names, antioxidant assay records, computable physicochemical and ADMET properties, and sources. AODB supports text search and mining, 2D and 3D chemical structure search, and BLAST-based protein sequence search, enabling users to retrieve antioxidant data quickly and easily. AODB, as a one-stop antioxidant database, can facilitate the exploration of antioxidants and potential applications. AODB is publicly available and updated annually at https://aodb.idruglab.cn/.

BACKGROUND: Procollagen-lysine, 2-oxoglutarate 5-dioxygenases (PLODs) are a group of enzymes that can mediate the hydroxylation of lysyl to hydroxylysine and participate in the formation of stabilized collagen. Evidence has demonstrated that PLODs are involved in the steps of tumor progression, including proliferation, invasion, and metastasis. However, limited information is available on the function of PLOD1/2/3 in lung cancer. In this study, we investigated the expression patterns and prognostic values of PLODs in patients with lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC).
METHODS: The Oncomine database and UALCAN were used to analyze the mRNA expression levels of PLOD family members in non-small cell lung cancer (NSCLC). The prognostic values of PLODs were investigated by the Kaplan-Meier Plotter database. We collected 33 patients with lung cancer to further verify the expression profiles and prognostic values of PLODs. The Kaplan-Meier method was used to perform survival curves, and the log-rank test was performed to evaluate the differences in survival. According to the GSE31210 databset, univariate and multivariate analyses were performed to identify whether PLODs were independent prognostic indicators for survival. Meanwhile, we investigated the mutations, potential biological functions and immune relevance of PLODs on the basis of the cBioPortal, Metascape and TIMER databases respectively.
RESULTS: We found that the mRNA and protein expression levels of PLODs in NSCLC tissues were higher than those in normal lung tissues. High PLOD1/2/3 expression had significant relevance to poor survival in LUAD but not in LUSC. In addition, the GSE31210 dataset showed that PLOD1 and PLOD3 were independent risk factors for relapse-free survival and overall survival (OS) in LUAD. We observed a high alteration rate of PLODs in LUSC patients, and the genetic alterations of PLODs had significant relevance to favorable OS. Furthermore, we observed that PLODs were significantly associated with tumor immunity in lung cancer. The enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway showed that the functions of the PLODs focused on cell cycle, DNA replication, and glycolysis/gluconeogenesis in LUAD.
CONCLUSIONS: These results indicated that PLODs were highly expressed in lung cancer and may be suitable prognostic markers.

Recently, immune checkpoint inhibitors (ICIs) have been successfully used for treating melanoma. Unfortunately, many breast cancer (BC) patients show low response to ICIs due to the lack of infiltrating immune cells. Previous studies revealed that chemokine-CXC receptors (CXCRs) play a crucial role in leukocyte infiltration and promote cancer cell proliferation, migration, metastasis, and angiogenesis. However, the underlying functions of CXCRs in cancer-immunity cycle remain unclear. In this study, we firstly found that in comparison to normal tissues, BC tissues, especially basal-like BC, showed increased mRNA levels of CXCR3/4/5/6/8, but decreased CXCR1/2/7 expression using UALCAN and TIMER database. Interestingly, it\'s was found that the mRNA levels of CXCR3/4/5/6 were decreased in lymphocyte depleted of the BC immune subtype. Subsequently, functional enrichment analysis of distinct CXCRs indicated that CXCR3/4/5/6 were strongly associated to immune-related biological functions. Therefore, further analysis using TIMER and TISIDB database suggested that CXCR3/4/5/6 expression were strongly correlated with tumor-infiltrating lymphocytes (TILs) and immune checkpoints in BC. Finally, Kaplan-Meier Plotter analysis indicated that high mRNA expression of CXCR4 predicted worse relapse-free survival (RFS), whereas CXCR3/5/6 indicated better RFS in BC patients. These findings suggest a therapeutic value for CXCR3/4/5/6 in combination with ICIs for the treatment of BC.

Cardiovascular disease is characterized by its highest morbidity and mortality. One of the main pathological basis of this disease is the dysregulation of gene expression. Non-coding RNA (ncRNA) is a kind of functional RNA, which is transcript from DNA but not translated into proteins. More and more studies have established the important roles of ncRNAs, including transcription, RNA maturation, translation, protein degradation, and their involvement in the pathogenesis of diseases such as cancer and cardiovascular diseases. This chapter will focus on the biological functions of ncRNAs and their advances in cardiovascular disease. With the development of sequencing and computer technology, more and more databases can be easily obtained on the internet. In another part of this chapter, we will summarize some commonly used non-coding RNA databases, which can be easily and quickly used for relevant research.

Non-small cell lung cancer (NSCLC) is a highly malignant type of cancer with a poor 5-year survival rate. The development of prognostic biomarkers and novel drug targets are required in order to improve the survival for NSCLC patients. Signal transducer and activator of transcription (STAT) proteins are cytoplasmic transcription factors known to play key roles in many cellular biological processes. However, the roles of STAT family members in the development and progression of NSCLC have not yet been apparently determined. Our study investigated the roles of STATs in the prognosis of NSCLC using cBioPortal, Human Protein Atlas, ONCOMINE, and Kaplan-Meier Plotter databases. High mutation rate of STATs existed in both lung adenocarcinoma (ADE) patients and squamous cell carcinoma (SCC) patients. High mRNA expression of STAT2 was significantly associated with shorter overall survival (OS) in NSCLC patients, while increased STAT5 and STAT6 were associated with better OS in NSCLC patients. We further found that increased mRNA expressions of STAT2 and STAT3 predicted unfavorable overall survival (OS) while high mRNA expression of STAT5B and STAT6 related to favorable OS for lung ADE patients. However, no significant correlation was identified for lung SCC patients. In stratified survival analysis, high expression of STAT2 predicted poor prognosis in stage II NSLCC patients, surgical margins negative patients and female patients. Taken together, our results illustrated that STAT5B and STAT6 could be effective prognostic biomarkers for survivals of NSCLC patients. And STAT2 might be a promising therapeutic target for the treatment of NSCLC as well as ADE.

UNASSIGNED: Nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (NOX) are frequently deregulated in several human malignancies, including gastric cancer (GC). NOX-derived reactive oxygen species have been reported to contribute to gastric carcinogenesis and cancer progression. However, the expression and prognostic role of individual NOX in GC patients remain elusive.
UNASSIGNED: We investigated genetic alteration and mRNA expression of NOX family in GC patients via the cBioPortal, Human Protein Atlas, and Oncomine databases. Furthermore, we evaluated prognostic value of distinct NOX in GC patients through \"The Kaplan-Meier plotter\" database.
UNASSIGNED: Our analysis demonstrated that mRNA deregulation of NOX genes was common alteration in GC patients. Compared with normal tissues, NOX1/2/4 mRNA expression levels in GC tissues were higher, while NOX5 and DUOX1/2 expression levels were lower. Importantly, our results indicated that high mRNA expression of NOX2 was associated with better overall survival whereas NOX4 and DUOX1 were correlated with worse overall survival in all GC patients, particularly in intestinal-type GC patients. In addition, our data also shed light on the diverse roles of individual NOX members in GC patients with different clinicopathological features, including human epidermal growth factor receptor 2 status, clinical stages, pathological grades, and different choices of treatments of GC patients.
UNASSIGNED: These findings suggest that individual NOX family genes, especially NOX2/4, and DUOX1, are potential prognostic markers in GC and implicate that the use of NOX inhibitor targeting NOX4 and DUOX1 may be an effective strategy for GC therapy.

It has been reported previously that a dopamine receptor D2 (DRD2) antagonist was able to induce cancer cell apoptosis and that DRD2 was expressed at high levels in pituitary adenomas. However, the expression of DRD2 in gastric cancer and its correlation with the prognosis of patients with gastric cancer remain to be elucidated. In the present study, the expression of DRD2 in 84 paired gastric cancer tissues and respective adjacent non-cancerous tissues were detected using an immunohistochemical assay. The correlation between the expression of DRD2 and the with survival durations of the patients with gastric cancer was analyzed using Kaplan-Meier analysis. In addition, online resources were utilized to further analyze the correlation between the mRNA expression level of DRD2 and prognosis. The effect of the DRD2 antagonist, thioridazine, on the proliferation of the AGS gastric cancer cells was determined. The results of the present study showed that the percentage of gastric cancer cases with a high expression level of DRD2 (51.2%) was higher, compared with that of cases with a low expression level of DRD2 (39.3%). Patients with a higher expression of DRD2 had shorter survival durations. The online database analysis revealed that the expression of DRD2 was also inversely correlated with the prognosis of patients with gastric cancer. Furthermore, the DRD2 antagonist, thioridazine, inhibited the growth of AGS gastric cancer cells. In conclusion, as the expression of DRD2 was negatively correlated with survival durations in patients with gastric cancer, it may be considered as a prognosis marker in the future. Developing DRD2 antagonists may assist in increasing the efficiency of cancer therapy.

The covalent modification of intrinsically nucleophilic cysteine in proteins is crucial for diverse biochemical events. Bioinformatics approaches may prove useful in the design and discovery of covalent molecules targeting the cysteine in proteins to tune their functions and activities. Herein, we describe the Cysteinome, the first online database that provides a rich resource for the display, search and analysis of structure, function and related annotation for proteins with targetable cysteine as well as their covalent modulators. To this end, Cysteinome compiles 462 proteins with targetable cysteine from 122 different species along with 1217 covalent modulators curated from existing literatures. Proteins are annotated with a detailed description of protein families, biological process and related diseases. In addition, covalent modulators are carefully annotated with chemical name, chemical structure, binding affinity, physicochemical properties, molecule type and related diseases etc. The Cysteinome database may serve as a useful platform for the identification of crucial proteins with targetable cysteine in certain cellular context. Furthermore, it may help biologists and chemists for the design and discovery of covalent chemical probes or inhibitors homing at functional cysteine of critical protein targets implicated in various physiological or disease process. The Cysteinome database is freely available to public at http://www.cysteinome.org/.

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