Assessment of Fungal Diversity in Minqin County, a Typical Arid Region in Northwestern China.

Minqin County is located in the Shiyang River Basin. As a typical arid area, it is eroded by the Badain Jaran and Tengger Desert all year round, and knowledge of the fungal diversity in this area is limited. Therefore, fungal community structure and distribution in the soil of the artificial forest, desert transition zone, farmland, and desert were investigated using amplicon sequencing of the fungal ITS gene. Ten fungal phyla and 23 classes were identified, including 1131 fungi OTUs, Sordariomycetes, Dothideomycetes, Pezizomycetes, and Agaricomycetes were the most abundant classes. Although most OTUs are shared among habitats, fungal community composition among samples was highly variable, which may influence the design of restoration practices in this area.

Genome-wide interaction analysis of quantitative traits in outbred mice.

With a large number of quantitative trait loci being identified in genome-wide association studies, researchers have become more interested in detecting interactions among genes or single nucleotide polymorphisms (SNPs). In this research, we carried out a two-stage model selection procedure to detect interacting gene pairs or SNP pairs associated with four important traits of outbred mice, including glucose, high-density lipoprotein cholesterol, diastolic blood pressure and triglyceride. In the first stage, a variance heterogeneity test was used to screen for candidate SNPs. In the second stage, the Lasso method and single pair analysis were used to select two-way interactions. Moreover, the shared Gene Ontology information about the selected interacting gene pairs was considered to study the interactions auxiliarily. Based on this method, we not only replicated the identification of important SNPs associated with each trait of outbred mice, but also found some SNP pairs and gene pairs with significant interaction effects on each trait. Simulation studies were also conducted to evaluate the performance of the two-stage method in different situations.

A case of malignant gastric glomus tumor and literature review: A case report.

RATIONALE: Malignant gastric glomus tumor (GGT) is an extremely rare malignant tumor of mesenchymal origin, it affects the patient's health and even threatens life. Malignant GGT with vascular invasion is even more rarely reported in the available literature without a prognostic study. So, in this case, we report a malignant GGT with vascular invasion and performed a 5-year postoperative follow-up. To the best of our knowledge, we report the first case of malignant GGT with vascular invasion without recurrence 5 years after surgery. This provides examples and lessons for the treatment of malignant GGT with vascular invasion. PATIENT CONCERNS: A 49-year-old male was admitted to the hospital with gallbladder stones found on health check. After completing abdominal CT and ultrasound gastroscopy, a mass in the gastric antrum was found. DIAGNOSES: The diagnosis of malignant GGT was confirmed by combination of postoperative pathology with positive immunohistochemistry for SMA, vimentin, synaptophysin, H-caldesmon, and calponin, mitosis > 10/50 HPF and moderate-to-severe nuclear atypia. INTERVENTIONS: On the 6th day of hospitalization, the patient underwent laparoscopic distal gastrectomy and cholecystectomy. OUTCOMES: The patient was discharged successfully 1 week after surgery and was followed up for 5 years without recurrence. CONCLUSION: Malignant GGT can be asymptomatic. For malignant GGT without distant metastasis, despite the presence of vascular invasion, negative margin surgery can still be the standard surgical radical treatment.

Exploration and validation of the Ki67, Her-2, and mutant P53 protein-based risk model, nomogram and lymph node metastasis model for predicting colorectal cancer progression and prognosis.

Introductions: Identifying biological markers of colorectal cancer (CRC) development and prognosis and exploring the intrinsic connection between these molecular markers and CRC progression is underway. However, a single molecular tumor marker is often difficult to assess and predict the progression and prognosis of CRC. Consequently, a combination of tumor-related markers is much needed. Ki67, Her-2, and mutant P53 (MutP53) proteins play pivotal roles in CRC occurrence, progression and prognosis. Methods: Based on the expressions by immunochemistry, we developed a risk model, nomogram and lymph node metastasis model by R software and Pythons to explore the value of these proteins in predicting CRC progression, prognosis, and examined the relationship of these proteins with the CRC clinicopathological features from 755 (training set) and 211 CRC (validation set) patients collected from the hospital. Results: We found that Ki67 expression was significantly correlated with T-stage, N-stage, TNM-stage, vascular invasion, organization differentiation, and adenoma carcinogenesis. Moreover, Her-2 expression was significantly correlated with T-stage, N-stage, TNM-stage, vascular and nerve invasion, pMMR/dMMR, signet ring cell carcinoma, and organization differentiation. MutP53 expression was significantly correlated with T-stage, N-stage, TNM-stage, vascular and nerve invasion, adenoma carcinogenesis, signet ring cell carcinoma, organization differentiation, and pMMR/dMMR. Increased expression of each of the protein indicated a poor prognosis. The established risk model based on the three key proteins showed high predictive value for determining the pathological characteristics and prognosis of CRC and was an independent influencer for prognosis. The nomogram prediction model, which was based on the risk model, after sufficient evaluation, showed more premium clinical value for predicting prognosis. Independent cohort of 211 CRC patients screened from the hospital verified the strong predictive efficacy of these models. The utilization of the XGBoost algorithm in a lymph node metastasis model, which incorporates three crucial proteins, demonstrated a robust predictive capacity for lymph node metastasis. Discussion: The risk model, nomogram and lymph node metastasis model have all provided valuable insights into the involvement of these three key proteins in the progression and prognosis of CRC. Our study provides a theoretical basis for further screening of effective models that utilize biological markers of CRC.

Diet-derived antioxidants and osteoporosis: A Mendelian randomization study.

BACKGROUND: Antioxidants can prevent osteoporosis, but the association between serum antioxidants and the cause of osteoporosis remains unknown. We aimed to utilize Mendelian randomization (MR) to determine whether genetically predicted serum levels of diet-derived antioxidants can affect the risk of osteoporosis, to determine the effect of dietary supplementation of antioxidants. METHODS: Genetic variants associated with diet-derived antioxidants were selected from the genome-wide association studies. A total of 12,946 osteoporosis cases and 506,624 healthy controls were obtained from UK Biobank (UKB) and Genetic Factors of Osteoporosis (GEFOS) consortia. We implemented a two-sample MR design and performed several sensitivity analyses to evaluate the causal relationship. RESULTS: In UKB, the genetically predicted higher ß-carotene (OR = 0.863, p = 7.37 × 10-6, power = 100%) and γ-tocopherol (OR = 0.701, p = 0.021, power = 5%) had an inverse relationship with osteoporosis. However, only the association of serum ß-carotene passed FDR correction. In GEFOS, there were no significant diet-derived antioxidants. The direction of the association of ß-carotene with osteoporosis (OR = 0.844, p = 0.106, power = 87%) was consistent with that in the UKB dataset. A fixed-effects meta-analysis confirmed that ß-carotene (OR = 0.862, p = 2.21 × 10-6) and γ-tocopherol (OR = 0.701, p = 2.31 × 10-2) could decrease the risk of osteoporosis. To reduce exclusion limit bias, we used total body bone mineral density, lumbar spine bone mineral density and femoral neck bone mineral density as surrogates and found that the genetically elevated circulating ß-carotene level could increase total body BMD (beta = 0.043, p-value = 8.26 x 10-5, power = 100%), lumbar spine BMD (beta = 0.226, p-value = 0.001, power = 100%) and femoral neck BMD(beta = 0.118, p-value = 0.016, power = 100%). CONCLUSIONS: We observed that genetically predicted serum ß-carotene could elevate BMD and prevent osteoporosis.

Association of clinical outcomes and the predictive value of T lymphocyte subsets within colorectal cancer patients.

Introduction: Tumor immunity is a hot topic in tumor research today, and human immunity is closely related to tumor progression. T lymphocyte is an important component of human immune system, and the changes in their subsets may influence the progression of colorectal cancer (CRC) to some extent. This clinical study systematically describes and analyzes the association of CD4+ and CD8+ T-lymphocyte content and CD4+/CD8+ T-lymphocyte ratio with CRC differentiation, clinical pathological stage, Ki67 expression, T-stage, N-stage, carcinoembryonic antigen (CEA) content, nerve and vascular infiltration, and other clinical features, as well as preoperative and postoperative trends. Furthermore, a predictive model is constructed to evaluate the predictive value of T-lymphocyte subsets for CRC clinical features. Methods: Strict inclusion and exclusion criterion were formulated to screen patients, preoperative and postoperative flow cytometry and postoperative pathology reports from standard laparoscopic surgery were assessed. PASS and SPSS software, R packages were invoked to calculate and analyze. Results: We found that a high CD4+ T-lymphocyte content in peripheral blood and a high CD4+/CD8+ ratio were associated with better tumor differentiation, an earlier clinical pathological stage, lower Ki67 expression, shallower tumor infiltration, a smaller number of lymph node metastases, a lower CEA content, and a lower likelihood of nerve or vascular infiltration (P < 0.05). However, a high CD8+ T-lymphocyte content indicated an unpromising clinical profile. After effective surgical treatment, the CD4+ T-lymphocyte content and CD4+/CD8+ ratio increased significantly (P < 0.05), while the CD8+ T-lymphocyte content decreased significantly (P < 0.05). Further, we comprehensively compared the merits of CD4+ T-lymphocyte content, CD8+ T-lymphocyte content, and CD4+/CD8+ ratio in predicting the clinical features of CRC. We then combined the CD4+ and CD8+ T-lymphocyte content to build models and predict major clinical characteristics. We compared these models with the CD4+/CD8+ ratio to explore their advantages and disadvantages in predicting the clinical features of CRC. Discussion: Our results provide a theoretical basis for the future screening of effective markers in reflecting and predicting the progression of CRC. Changes in T lymphocyte subsets affect the progression of CRC to a certain extent, while their changes also reflect variations in the human immune system.

Genomic analysis of matrix metalloproteinases affecting the prognosis and immunogenic profile of gastric cancer.

This study systematically and comprehensively analyzed the characteristics of matrix metalloproteinases (MMPs) in gastric cancer (GC) and revealed the relationship between MMPs and prognoses, clinicopathological features, tumor microenvironment, gene mutations, and drug therapy response in patients with GC. Based on the mRNA expression profiles of 45 MMP-related genes in GC, we established a model that classified GC patients into three groups based on cluster analysis of the mRNA expression profiles. The 3 groups of GC patients showed significantly different prognoses as well as tumor microenvironmental characteristics. Next, we used Boruta's algorithm and PCA method to establish an MMP scoring system and found that lower MMP scores were associated with better prognoses, lower clinical stages, better immune cell infiltration, lower degrees of immune dysfunction and rejection, and more genetic mutations. Whereas a high MMP score was the opposite. These observations were further validated with data from other datasets, showing the robustness of our MMP scoring system. Overall, MMP could be involved in the tumor microenvironment (TME), clinical features, and prognosis of GC. An in-depth study of MMP patterns can better understand the indispensable role of MMP in the development of GC and reasonably assess the survival prognosis, clinicopathological features, and drug efficacy of different patients, thus providing clinicians with a broader vision of GC progression and treatment.

Simultaneous estimation of QTL effects and positions when using genotype data with errors.

Accurate genetic data are important prerequisite of performing genetic linkage test or association test. Currently, most analytical methods assume that the observed genotypes are correct. However, due to the constraint at the technical level, most of the genetic data that people used so far contain errors. In this paper, we considered the problem of QTL mapping based on biological data with genotyping errors. By analysing all possible genotypes of each individual in framework of multipleinterval mapping, we proposed an algorithm of inferring all model parameters through the expectation-maximization (EM) algorithm and discussed the hypothesis testing of the existence of QTL. We carried out extensive simulation studies to assess the proposed method. Simulation results showed that the new method outperforms the method that does not take the genotyping errors into account, and therefore it can decrease the impact of genotyping errors on QTL mapping. The proposed method was also applied to analyse a real barley dataset.