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Background: Three-dimensional (3D) chromatin architecture frequently altered in cancer. However, its changes during the pathogenesis of hepatocellular carcinoma (HCC) remained elusive. Methods: Hi-C and RNA-seq were applied to study the 3D chromatin landscapes and gene expression of HCC and ANHT. Hi-C Pro was used to generate genome-wide raw interaction matrices, which were normalized via iterative correction (ICE). Moreover, the chromosomes were divided into different compartments according to the first principal component (E1). Furthermore, topologically associated domains (TADs) were visualized via WashU Epigenome Browser. Furthermore, differential expression analysis of ANHT and HCC was performed using the DESeq2 R package. Additionally, dysregulated genes associated with 3D genome architecture altered were confirmed using TCGA, qRT-PCR, immunohistochemistry (IHC), etc. Results: First, the intrachromosomal interactions of chr1, chr2, chr5, and chr11 were significantly different, and the interchromosomal interactions of chr4–chr10, chr13–chr21, chr15–chr22, and chr16–chr19 are remarkably different between ANHT and HCC, which resulted in the up-regulation of TP53I3 and ZNF738 and the down-regulation of APOC3 and APOA5 in HCC. Second, 49 compartment regions on 18 chromosomes have significantly switched (A–B or B–A) during HCC tumorigenesis, contributing to up-regulation of RAP2A. Finally, a tumor-specific TAD boundary located on chr5: 6271000–6478000 and enhancer hijacking were identified in HCC tissues, potentially associated with the elevated expression of MED10, whose expression were associated with poor prognosis of HCC patients. Conclusion: This study demonstrates the crucial role of chromosomal structure variation in HCC oncogenesis and potential novel biomarkers of HCC, laying a foundation for cancer precision medicine development. [ABSTRACT FROM AUTHOR]

We isolated a K47-type Klebsiella pneumoniae phage from untreated hospital sewage: vB_KpnP_IME305 (GenBank no. OK149215). Next-generation sequencing (NGS) demonstrated that IME305 has a double-stranded DNA genome of 38,641 bp with 50.9% GC content. According to BLASTn comparisons, the IME305 genome sequence shares similarity with that of Klebsiella phage 6998 (97.37% identity and 95% coverage). IME305 contains 45 open reading frames (ORFs) and no rRNA, tRNA, or virulence-related gene sequences. Bioinformatic analysis showed that IME305 belongs to the phage subfamily Studiervirinae and genus Teetrevirus. [ABSTRACT FROM AUTHOR]

A Klebsiella pneumoniae bacteriophage (vB_KpnM_IME346) was isolated from a hospital sewage sample. This bacteriophage specifically infects a clinical K. pneumoniae strain with a K63 capsular polysaccharide structure. The phage genome was evaluated by next-generation sequencing, which revealed a linear double-stranded DNA genome consisting of 49,482 base pairs with a G+C content of 49.1%. The latent period of vB_KpnM_IME346 was shown to be 20 min, and the burst size was 25–30 pfu (plaque-forming units)/infected cell. Transmission electron microscopy and phylogenetic analysis showed that the JD001-like phage belongs to the genus Jedunavirus of the family Myoviridae. The newly isolated vB_KpnM_IME346 shows infectivity in the clinical host K. pneumoniae KP576 strain, indicating that it is a promising alternative to antibacterial agents for removing K. pneumoniae from patients. [ABSTRACT FROM AUTHOR]

A novel virulent phage, vB_KpnP_IME337, isolated from a hospital sewage in Beijing, China, that infects carbapenem-resistant Klebsiella pneumoniae KN2 capsular type was identified and characterized. Next-generation sequencing and genome analysis revealed that vB_KpnP_IME337 had a linear double-stranded genome with a length of 44,266 base pairs and G+C content of 53.7%. Fifty-two putative open reading frames were identified, and no transfer RNA-encoding genes were detected. BLASTn analysis revealed that phage vB_KpnP_IME337 had the highest sequence similarity with Klebsiella phage phiBO1E, with genome coverage of 79%. Based on morphology, phage vB_KpnP_IME337 was determined to belong to the family Podoviridae of the order Caudovirales. It was shown that phage vB_KpnP_IME337 had an infection duration of ~ 90 min and 10 min latent period, and a highly specific to host strain. In conclusion, phage vB_KpnP_IME337 may be a promising alternative candidate to antibiotic treatment for controlling diseases caused by drug-resistant K. pneumoniae. [ABSTRACT FROM AUTHOR]

A novel Vibrio alginolyticus phage, VAP7, was isolated from seawater collected from Sanya, Hainan province, China. Whole-genome sequencing analysis revealed that phage VAP7 has a linear, double-stranded DNA genome of 144,685 bp with an average G+C content of 41.9% and a high degree of sequence similarity to Vibrio phage VP-1. Annotation results identified 193 open reading frames and one transfer RNA-encoding gene in the phage genome. The morphology and the results of phylogenetic analysis suggest that VAP7 should be classified as a new member of the family Ackermannviridae. Moreover, phage VAP7 grew over a wide pH (5.0-10.0) and temperature (4-40 °C) range. Host-range experiments revealed that VAP7 could infect 31 Vibrio alginolyticus strains. Thus, VAP7 infecting Vibrio alginolyticus strains represents a potential new candidate for use in phage therapy. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa (P. aeruginosa) infection has imposed a great threat to patients with cystic fibrosis. With the emergence of multidrug-resistant P. aeruginosa, developing an alternative anti-microbial strategy is indispensable and more urgent than ever. In this study, a lytic P. aeruginosa phage was isolated from the sewage of a hospital, and one protein was predicted as the depolymerase-like protein by genomic sequence analysis, it includes two catalytic regions, the Pectate lyase_3 super family and Glycosyl hydrolase_28 super family. Further analysis demonstrated that recombinant depolymerase-like protein degraded P. aeruginosa exopolysaccharide and enhanced bactericidal activity mediated by serum in vitro. Additionally, this protein disrupted host bacterial biofilms. All of these results showed that the phage-derived depolymerase-like protein has the potential to be developed into an anti-microbial agent that targets P. aeruginosa. [ABSTRACT FROM AUTHOR]

Purpose: Randomness of fluid and structure properties inherently exists in actual pipes. The waves of parameters may play a significant role in the pipeline dynamic characteristics. However, the vibration analysis of pipe-conveying fluid is usually done by considering the deterministic parameters. To overcome the limitation, a stochastic dynamic model is proposed for the dynamic characteristics analysis of pipe-conveying fluid. Methods: Considering the uncertain fluid and structure properties described as one-dimensional stochastic field function, a stochastic dynamic pipeline model based on the stochastic finite element is presented for three-dimensional dynamic characteristics analysis in this paper. A stochastic analytical formula is deduced to obtain the statistical results of the structural dynamic characteristics and responses of pipeline with random properties. Results: The statistics obtained from the presented model are compared with the prior experimental data and Monte Carlo simulation so as to validate the presented model and analysis method, and good agreement is obtained. Effects of structure and fluid randomness are studied in linear and nonlinear pipeline systems, respectively. Conclusion: It is found that the effects of random properties on pipeline eigenvalue and dynamic response are significant, especially the influences of the random elastic modulus, density and flow velocity. [ABSTRACT FROM AUTHOR]

Random properties and random loads are highly important in rotor dynamic analysis because they cause system dynamic responses to behave randomly. In this paper, a stochastical finite element of rotating shaft based on Timosheko beam theory is proposed for rotor system modeling, in which material and geometric random properties are considered one-dimensional stochastic field functions. A random response analytical method is developed to determine the statistics of the dynamic responses of stochastical rotor systems under random loads. The numerically obtained whirl speed of a turbopump rotor system is compared with the test data to validate the proposed model, and good agreement is observed. Linear and nonlinear turbopump rotor systems are employed to compare the results obtained from the proposed model and the Monte Carlo simulation. The numerically predicted results, which coincide well with Monte Carlo simulation data, demonstrate the feasibility and efficiency of the proposed stochastic model and method for actual rotor system analysis and design. [ABSTRACT FROM AUTHOR]

OBJECTIVE: This study aimed to assess the efficacy, safety and tolerability of oral moxifloxacin in patients with respiratory tract infections (RTIs) treated by attending physicians in routine clinical practice in China. METHODS: This was an open-label, prospective, uncontrolled, post-marketing surveillance study that was undertaken between November 2002 and July 2003. Altogether, 855 patients with RTIs were treated with moxifloxacin. Data were collected by 257 physicians throughout China. Symptoms of RTI (fever, cough, purulent sputum, dyspnoea, thoracic pain, nasal obstruction, nasal secretion and headache), together with auscultatory findings, were assessed at baseline and at follow-up visits, and classified as ‘absent’, ‘mild’ or ‘severe’ by the attending physician. RESULTS: Moxifloxacin produced significant improvements in 70.7% of patients after only 3 days of treatment. In 91.7% of patients, symptoms were improved after 5 days of treatment; 76.1% of patients recovered after 7 days and 84.7% recovered after 10 days of treatment. The mean ± SD time until recovery was 5.1 ± 2.6 days. Assessment of treatment efficacy by the physicians was ‘good’ or ‘very good’ for 89.2% of patients. In 87.3% of cases, physicians rated patients’ acceptance of therapy with moxifloxacin as ‘good’ or ‘very good’. The tolerability of moxifloxacin therapy was rated as ‘good’ or ‘very good’ for 88.8% of patients. Very few adverse events (4.1% of patients) were reported with moxifloxacin; most of them involved mild CNS disorders and gastrointestinal disturbances. CONCLUSIONS: Moxifloxacin was shown to be an effective and well tolerated treatment for this group of patients with RTIs and was highly rated by both physicians and patients because of rapid symptom improvement and good tolerability. [ABSTRACT FROM AUTHOR]