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Background Artificial duplicates from pyrosequencing reads may lead to incorrect interpretation of the abundance of species and genes in metagenomic studies. Duplicated reads were filtered out in many metagenomic projects. However, since the duplicated reads observed in a pyrosequencing run also include natural (non-artificial) duplicates, simply removing all duplicates may also cause underestimation of abundance associated with natural duplicates. Results We implemented a method for identification of exact and nearly identical duplicates from pyrosequencing reads. This method performs an all-against-all sequence comparison and clusters the duplicates into groups using an algorithm modified from our previous sequence clustering method cd-hit. This method can process a typical dataset in ~10 minutes; it also provides a consensus sequence for each group of duplicates. We applied this method to the underlying raw reads of 39 genomic projects and 10 metagenomic projects that utilized pyrosequencing technique. We compared the occurrences of the duplicates identified by our method and the natural duplicates made by independent simulations. We observed that the duplicates, including both artificial and natural duplicates, make up 4-44% of reads. The number of natural duplicates highly correlates with the samples' read density (number of reads divided by genome size). For high-complexity metagenomic samples lacking dominant species, natural duplicates only make up <1% of all duplicates. But for some other samples like transcriptomic samples, majority of the observed duplicates might be natural duplicates. Conclusions Our method is available from http://cd-hit.org as a downloadable program and a web server. It is important not only to identify the duplicates from metagenomic datasets but also to distinguish whether they are artificial or natural duplicates. We provide a tool to estimate the number of natural duplicates according to user-defined sample types, so users can decide whether to retain or remove duplicates in their projects.

Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.

Purpose Ubiquitination is one of the important epigenetic modifications, influencing the development of various diseases. The objective of this study is to investigate the ubiquitination related genes in chronic obstructive pulmonary disease (COPD). Methods The gene microarray dataset from COPD patients and ubiquitination related genes were analyzed. Venn diagram analysis was used to intersect differentially expressed genes and ubiquitination related genes. The functional enrichment analysis of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) were performed on differentially expressed ubiquitination related genes. Finally, we confirmed the expression of hub genes through qPCR and western blot experiments in clinical COPD patients and cell lines. Results We identified 2,932 differentially expressed genes and 96 differentially expressed ubiquitination related genes. GO analysis indicated that the differentially expressed ubiquitination related genes were mainly enriched in post-translational protein modification and ubiquitin ligase complex. KEGG analysis showed that ubiquitination related genes were mainly involved in ubiquitin mediated proteolysis and TNF signaling pathway. GSEA analysis suggested that some hub genes are involved in allograft rejection, IL6/JAK/STAT3 signaling and inflammatory response. Our qPCR and western blot experimental results indicate that the expression of USP15 and CUL2 is higher in COPD group compared to the control group, consistent with the bioinformatics analysis. Conclusion Our bioinformatics analysis and experimental results suggest that USP15 and CUL2 may contribute to the progression of COPD through ubiquitination modification. To our knowledge, this is the first study to demonstrate the involvement of USP15 and CUL2 in COPD. Our results may provide new insights into the diagnosis and treatment of COPD.

Purpose Ubiquitination plays a crucial role in various diseases. This study aims to explore the potential ubiquitination related genes in IPF. Methods The gene microarray dataset GSE24206 was obtained from GEO database. Subsequently, through differential expression analysis and molecular signatures database, we obtained 1734 differentially expressed genes and 742 ubiquitination related genes. Through the venn diagram analysis, we obtained 53 differentially expressed ubiquitination related genes. Then, gene-ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, protein-protein interactions (PPI) and gene set enrichment analysis (GSEA) were applied for the differentially expressed ubiquitination related genes. Finally, the expression of CDC20 and ITCH in IPF patients and cells were validated by qPCR and western blot assay. Results A total of 53 differentially expressed ubiquitination related genes (36 up-regulated genes and 17 down-regulated genes) were identified between 17 IPF patients and 6 healthy controls. GO and KEGG enrichment analysis of ubiquitination related genes mainly involved in regulation of protein ubiquitination, regulation of post-translational protein modification and ubiquitin mediated proteolysis. The PPI results demonstrated that these ubiquitination related genes interacted with each other. The GSEA analysis results for some of the hub genes mainly involved epithelial mesenchymal transition, inflammatory response, hypoxia, and apoptosis. The experiment expression level of CDC20 and ITCH in IPF patients and IPF cells were consistent with the bioinformatics analysis results. Conclusion We identified 53 potential ubiquitination related genes of IPF through bioinformatics analysis. CDC20 and ITCH and other ubiquitination related genes may influence the development of IPF through epithelial mesenchymal transition and inflammatory response. Our research findings provide insights into the mechanisms of fibrosis and may provide evidence for potential therapeutic targets for fibrosis.

Safe street crossing relies on effective pedestrian-vehicle interaction; a delay in drivers’ recognition of pedestrian intentions can critically increase the risk of collision. Nevertheless, existing research lacks a contrasting exploration of driving behaviour at unsignalized streets for real pedestrians and pedestrian dummies. In this study, we develop a pedestrian crossing intention judgment system to quantify subjective driver assessments of pedestrian crossing intentions, focusing on how drivers adjust their behaviour to real pedestrians and pedestrian dummies. Specifically, we establish a naturalistic driving and pedestrian dummy experimental platform based on the campus unsignalized streets. Then, six different experimental scenarios of pedestrians crossing the street are designed. In addition, a subjective judgment of pedestrians’ crossing intentions ( SJPCI ) ranging from 0% to 100% is introduced to quantify drivers’ assessments of pedestrian crossing intentions. The proposed system is validated using 123 effective interactions extracted from 1923 natural driving events. Meanwhile, we designed the same dummy experiment based on the 123-group naturalistic driving scenarios. The results show that naturalistic driving experiments have relatively higher SJPCI values, gentler acceleration, and longer time-to-collision ( TTC ) compared with pedestrian dummy experiments. Effective communication with pedestrians allows drivers to better judge crossing intentions. Our finding is that real crossing pedestrians are significantly less able to have ambiguous intentions, which enhances understandability for drivers.

One of the major challenges for autonomous vehicles (AVs) is how to drive in shared pedestrian environments. AVs cannot make their decisions and behaviour human-like or natural when they encounter pedestrians with different crossing intentions. The main reasons for this are the lack of natural driving data and the unclear rationale of the human-driven vehicle and pedestrian interaction. This paper aims to understand the underlying behaviour mechanisms using data of pedestrian–vehicle interactions from a naturalistic driving study (NDS). A naturalistic driving test platform was established to collect motion data of human-driven vehicles and pedestrians. A manual pedestrian intention judgment system was first developed to judge the pedestrian crossing intention at every moment in the interaction process. A total of 98 single pedestrian crossing events of interest were screened from 1274 pedestrian–vehicle interaction events under naturalistic driving conditions. Several performance metrics with quantitative data, including TTC, subjective judgment on pedestrian crossing intention (SJPCI), pedestrian position and crossing direction, and vehicle speed and deceleration were analyzed and applied to evaluate human-driven vehicles’ yielding behaviour towards pedestrians. The results show how vehicles avoid pedestrians in different interaction scenarios, which are classified based on vehicle deceleration. The behaviour and intention results are needed by future AVs, to enable AVs to avoid pedestrians more naturally, safely, and smoothly.

Background Paraneoplastic pemphigus is a rare autoimmune mucocutaneous disease often associated with neoplasms. When complicated with bronchiolitis obliterans, it can lead to irreversible pulmonary dysfunction and carries a high risk of mortality. We report a case of pulmonary small lymphocytic lymphoma combined with paraneoplastic pemphigus and bronchiolitis obliterans, aiming to increase clinical awareness of this condition and promote early diagnosis and treatment. Case presentation We report the case of a 69-year-old male who initially presented with oral lichen planus and developed cough and dyspnea on exertion three months later. Blood gas analysis revealed hypoxemia, and pulmonary function tests showed extremely severe mixed ventilatory dysfunction. Chest imaging demonstrated thickened walls of peripheral bronchioles, centrilobular nodules, and partial bronchiectasis in both lower lobes. Laboratory tests were positive for anti-desmoglein 3 antibodies. Ultimately, a mediastinal biopsy confirmed the diagnosis of pulmonary small lymphocytic lymphoma. The patient received two cycles of treatment with Orelabrutinib combined with Obinutuzumab, after which his oral lichen planus and dyspnea improved. Conclusions Clinicians should be alert to the possibility of paraneoplastic pemphigus in patients presenting with refractory oral mucosal lesions. Especially when accompanied by unexplained pulmonary imaging abnormalities and dyspnea, bronchiolitis obliterans should be considered. Recognizing the early predictive value of oral lesions is crucial for avoiding misdiagnosis or delayed diagnosis, enabling timely intervention and improved patient outcomes.

The 5-year survival rate is less than 30%. [...]it is necessary to explore the pathological process of IPF from the perspective of cell biology, and these explorations can provide a basis for the treatment of IPF. [...]the mechanism of autophagy in different respiratory diseases including IPF remains unclear. [...]investigations are required to better explain the detailed mechanisms of autophagy. [...]due to the lack of patient survival information in the GSE24206 dataset, we did not analyze the impact of these genes on the prognosis of patients with IPF. [...]we identified 20 differentially expressed autophagy-related genes (11 up-regulated genes and nine down-regulated genes) that may be involved in the development of IPF.

Autophagy plays essential roles in the development of COPD. We aim to identify and validate the potential autophagy-related genes of COPD through bioinformatics analysis and experiment validation. The mRNA expression profile dataset GSE38974 was obtained from GEO database. The potential differentially expressed autophagy-related genes of COPD were screened by R software. Then, protein-protein interactions (PPI), correlation analysis, gene-ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied for the differentially expressed autophagy-related genes. Finally, RNA expression of top five differentially expressed autophagy-related genes was validated in blood samples from COPD patients and healthy controls by qRT-PCR. A total of 40 differentially expressed autophagy-related genes (14 up-regulated genes and 26 down-regulated genes) were identified between 23 COPD patients and 9 healthy controls. The PPI results demonstrated that these autophagy-related genes interacted with each other. The GO and KEGG enrichment analysis of differentially expressed autophagy-related genes indicated several enriched terms related to autophagy and mitophagy. The results of qRT-PCR showed that the expression levels of and in COPD patients and healthy controls were consistent with the bioinformatics analysis results from mRNA microarray. We identified 40 potential autophagy-related genes of COPD through bioinformatics analysis. and may affect the development of COPD by regulating autophagy. These results may expand our understanding of COPD and might be useful in the treatment of COPD.

Through room-temperature tensile testing, microstructural observation, and comparative analysis of dislocation configurations, this study investigates the deformation and damage behavior of a high-concentration Re/Ru single-crystal alloy. The results show that the alloy possesses excellent mechanical properties at room temperature, with a tensile strength of 875 MPa and a yield strength of 847 MPa. During tensile deformation, plastic strain primarily occurs through dislocation slip within the γ matrix and dislocation shear into the γ′ phase. Dislocations sheared into the γ′ phase exhibit distinct decomposition patterns. Microcracks initiate at γ′/γ interfaces where two slip systems intersect. As tensile loading continues, these microcracks coalesce, leading to increased local stress and unstable crack propagation along the γ/γ′ interfaces, ultimately resulting in fracture. This process constitutes the deformation and damage mechanism of the alloy during room-temperature tensile deformation. These findings suggest that high Re/Ru concentrations fundamentally alter low-temperature deformation pathways, which may improve resistance to brittle fracture during cold start or handling conditions.