Gastric mucosal samples were procured and underwent the sequencing of 16S ribosomal RNA (16S rRNA) via Illumina high-throughput sequencing technology to explore the impact of
(
) infection on the ...composition of gastric flora in chronic gastritis (CG) patients. In the results, the operational taxonomic unit (OTU) analysis revealed an overlap of 5706 OTUs shared between the two groups. The top 5 abundance ranking (TOP5) phyla comprised Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Epsilonbacteraeota, while the TOP5 genus was
,
,
,
, and
. In the metabolic pathways at the Kyoto Encyclopedia of Genes and Genomes (KEGG)_L3 level, conspicuous variations across seven functions were observed between the
-positive (HP_Pos) and
-negative (HP_Neg) groups. Subsequently, functional gene enrichment in KEGG pathways was further validated through animal experimentation. In contrast to the mice in the HP_Neg group, those infected with
manifested an infiltration of inflammatory cells, an augmentation in gastric acid secretion, and conspicuously elevated scores regarding gastric activity, along with heightened levels of malondialdehyde. In conclusion, CG patients infected with
displayed a disorder in gastric flora, furnishing a theoretical basis for the prophylaxis of
infection and its associated pathogenic ramifications.
To investigate how the aquatic bacterial community of a stratified reservoir drives the evolution of water parameters, the microbial community structure and network characteristics of bacteria in a ...stratified reservoir were investigated using Illumina MiSeq sequencing technology. A total of 42 phyla and 689 distinct genera were identified, which showed significant seasonal variation. Additionally, stratified variations in the bacterial community strongly reflected the vertical gradient and seasonal changes in water temperature, dissolved oxygen, and nutrition concentration. Furthermore, principal coordinate analysis indicated that most microorganisms were likely influenced by changes in water stratification conditions, exhibiting significant differences during the stratification period and mixing period based on Adonis, MRPP, and Anosim. Compared to the stratification period, 123 enhanced operational taxonomic units (OTUs; 29%) and 226 depleted OTUs (52%) were identified during the mixing period. Linear discriminant analysis effect size results showed that 15 major genera were enriched in the mixing period and 10 major genera were enriched in the stratification period. Importantly, network analysis revealed that the keystone species belonged to hgcI_clade, CL500-29, Acidibacter, Paucimonas, Flavobacterium, Prochlorothrix, Xanthomonadales, Chloroflexia, Burkholderiales, OPB56, KI89A_clade, Synechococcus, Caulobacter or were unclassified. Redundancy analysis showed that temperature, dissolved oxygen, pH, chlorophyll-α, total phosphorus, nitrate, and ammonia were important factors influencing the water bacterial community and function composition, which were consistent with the results of the Mantel test analysis. Furthermore, random forest analysis showed that temperature, dissolved oxygen, ammonia, and total dissolved phosphorous were the most important variables predicting water bacterial community and function community α- and β-diversity (P < 0.05). Overall, these results provide insight into the interactions between the microbial community and water quality evolution mechanism in Zhoucun reservoir.
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•The bacterial community exhibited significant seasonal difference in Zhoucun Reservoir.•T, DO, pH, EC, TDP, NO3−, and NH4+ significantly influenced the water bacterial community and function community.
This research is a development research that aims to produce learning media products in the form of a science encyclopedia book based on Contextual Teaching & Learning (CTL) on energy material and ...its changes for third grade elementary school students and to determine the quality of learning media based on aspects of validity and feasibility aspects. This research refers to the 4D model (Define, Design, Development, Disseminate). The population subjects in this study were third grade students at SD Negeri Sukasari 7, Tangerang City. The instruments used to measure the quality of the learning media developed in this study were the validity aspect assessment sheet by media experts and material experts, the feasibility aspect assessment sheet by the classroom teacher, and student response questionnaires. an average score of 3.95 which indicates "valid" learning media with good criteria, the assessment of material experts who get an average score of 4.00 and 4.15 which indicates "valid" learning media with good criteria, the assessment of class teachers who get an average an average score of 4.26 which indicates the learning media is "very feasible" to be used, and based on student questionnaires, an average score of 4.6 is obtained for small-scale trials and an average score of 4.7 for large-scale trials which show media This learning has a quality that is "very feasible" to be used by students.
Data-independent acquisition (DIA) mass spectrometry–based proteomics generates reproducible proteome data. The complex processing of the DIA data has led to the development of multiple data analysis ...tools. In this study, we assessed the performance of five tools (OpenSWATH, EncyclopeDIA, Skyline, DIA-NN, and Spectronaut) using six DIA datasets obtained from TripleTOF, Orbitrap, and TimsTOF Pro instruments. By comparing identification and quantification metrics and examining shared and unique cross-tool identifications, we evaluated both library-based and library-free approaches. Our findings indicate that library-free approaches outperformed library-based methods when the spectral library had limited comprehensiveness. However, our results also suggest that constructing a comprehensive library still offers benefits for most DIA analyses. This study provides comprehensive guidance for DIA data analysis tools, benefiting both experienced and novice users of DIA-mass spectrometry technology.
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•Reproducible data-independent acquisition proteome data analysis workflows.•Library-based versus library-free approaches for DIA searches.•Comparison of identification and quantification metrics.•Guidance for DIA data analysis.
A guideline study for choosing DIA software tools for both experienced and novice users. Evaluation of 5 DIA tools (OpenSWATH, EncyclopeDIA, Skyline, DIA-NN, Spectronaut) in 6 different data sets, with 12 libraries for 34 conditions. The library-free approach excels when the spectral library size is limited, yet building a comprehensive library remains advantageous for most DIA analyses.
This article is a review of the latest edition of the Encyclopedia of Russian Philosophy (Moscow, 2020), the result of the work of a team of Russian specialists in philosophy and human sciences, ...edited by M. A. Maslin, professor of History of Russian Philosophy at Moscow University. However, it is also intended to be an assessment of the conditions that legitimate the denomination ‘Russian philosophy’, and a reflection on the character and orientations of Russian thought, especially in the period before and after the Revolution of 1917.
This study aims to determine the effectiveness of the Biodiversity on Mount Ungaran electronic encyclopedia in learning Biology in the Covid-19 Pandemic Era. The research design used was one group ...pretest-posttest design. The instrument used was about thinking skills. The sample in this study was 34 public school students in Central Java. The instrument used was a test of learning outcomes with 35 questions. Data were analyzed using the N-Gain test and Paired Sample t-test. The percentage analysis was used to see students’ responses to the e-encyclopedia used during the learning process. Google classroom and google meet were used in the learning process. The data analysis showed that the N-Gain result was 0.625 with a classical completeness value of 94.11%. The t-test results showed a significant difference in the pretest and post-test data with a significant value of <0.05. In addition, the response of students tested on a small scale obtained 76.90% in the high category. Therefore, the effectiveness of the electronic encyclopedia of biodiversity on Mount Ungaran was moderate.
Abstract
Charles Richardson’s New Dictionary of the English Language is a work of great importance for the history of lexicography, but the dates of its first serial publication from 1818 onwards ...among the 59 instalments of the Encyclopaedia Metropolitana appear never to have been ascertained. They are worked out here, together with the alphabetical ranges of many instalments, from announcements in contemporary periodicals such as the Athenaeum, the Morning Chronicle, and The Times, and are followed by extracts from the first reviews of the dictionary in the same periodicals.
•Cell lines and tissues express a limited proportion of the matrisome in unstimulated/healthy conditions.•Matrisome expression can be used to discriminate cell-types/tissues and disease ...subtypes.•Essential/common matrisome is comprised of 167 genes that are well expressed in cell lines and tissues.•The dark/uncommon matrisome is 431 genes, many of which are involved in inflammatory pathways.•59 members of the matrisome display discordant expression in cell lines versus tissues.
Extracellular matrix remodeling is a hallmark of tissue development, homeostasis, and disease. The processes that mediate remodeling, and the consequences of such, are the topic of extensive focus in biomedical research. Cell culture methods represent a crucial tool utilized by those interested in matrisome function, the easiest of which are implemented with immortalized/cancer cell lines. These cell lines often form the foundations of a research proposal, or serve as vehicles of validation for other model systems. For these reasons, it is important to understand the complement of matrisome genes that are expressed when identifying appropriate cell culture models for hypothesis testing. To this end, we harvested bulk RNA sequencing data from the Cancer Cell Line Encyclopedia (CCLE) to assess matrisome gene expression in 1019 human cell lines. Our examination reveals that a large proportion of the matrisome is poorly represented in human cancer cell lines, with approximately 10% not expressed above threshold in any of the cell lines assayed. Conversely, we identify clusters of essential/common matrisome genes that are abundantly expressed in cell lines. To validate these observations against tissue data, we compared our findings with bulk RNA sequencing data from the Genotype-Tissue Expression (GTEx) portal and The Cancer Genome Atlas (TCGA) program. This comparison demonstrates general agreement between the “essential/common” and “dark/uncommon” matrisome across the three datasets, albeit with discordance observed in 59 matrisome genes between cell lines and tissues. Notably, all of the discordant genes are essential/common in tissues yet minimally expressed in cell lines, underscoring critical considerations for matrix biology researchers employing immortalized cell lines for their investigations.
Despite advances in early diagnosis and treatment, cancer still remains the major reason of mortality worldwide. The forkhead box A (FOXA) family is reported to participate in diverse human diseases. ...However, little is known about their expression and prognostic values in human lung cancer. Herein, we conducted a detailed cancer vs. normal analysis. The mRNA expression levels of FOXA family in numerous kind of cancers, including lung cancer, were analyzed using the Oncomine and GEPIA database. We observed that the mRNA expression levels of FOXA1, and FOXA3 were all increased while FOXA2 were decreased in most cancers compared with normal tissues, especially in lung cancer. Moreover, the expression levels of FOXA1, and FOXA3 are also highly expressed, while FOXA2 were decreased in almost all cancer cell lines, particularly in lung cancer cell lines, analyzing by Cancer Cell Line Encyclopedia (CCLE) and EMBL-EBI databases. Furthermore, the LinkedOmics database was used to evaluate the prognostic values, indicating that higher expression of FOXA1, FOXA3 indicated a poor overall survival (OS), while increased FOXA2 revealed a better OS in lung cancer. To conclusion, FOXA family showed significant expression differences between cancer and normal tissues, especially lung cancer, and FOXA1, FOXA3 could be promising prognostic biomarkers for lung cancer.
•Increased expression of FOXA1 and FOXA3 in LC tissues might play an important role in LC oncogenesis;•High FOXA1 and FOXA3 expression could also serve as a molecular marker to identify high-risk subgroups of patients with LC;•Transcriptional FOXA3 was a total novel prognostic markers for the improvement of lung cancer survival and prognostic accuracy.
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