Microbial characterization based on multifractal analysis of metagenomes

IntroductionThe species diversity of microbiomes is a cutting-edge concept in metagenomic research. In this study, we propose a multifractal analysis for metagenomic research.Method and ResultsFirstly, we visualized the chaotic game representation (CGR) of simulated metagenomes and real metagenomes. We find that metagenomes are visualized with self-similarity. Then we defined and calculated the multifractal dimension for the visualized plot of simulated and real metagenomes, respectively. By analyzing the Pearson correlation coefficients between the multifractal dimension and the traditional species diversity index, we obtain that the correlation coefficients between the multifractal dimension and the species richness index and Shannon diversity index reached the maximum value when q = 0, 1, and the correlation coefficient between the multifractal dimension and the Simpson diversity index reached the maximum value when q = 5. Finally, we apply our method to real metagenomes of the gut microbiota of 100 infants who are newborn and 4 and 12 months old. The results show that the multifractal dimensions of an infant's gut microbiomes can distinguish age differences.Conclusion and DiscussionThere is self-similarity among the CGRs of WGS of metagenomes, and the multifractal spectrum is an important characteristic for metagenomes. The traditional diversity indicators can be unified under the framework of multifractal analysis. These results coincided with similar results in macrobial ecology. The multifractal spectrum of infants’ gut microbiomes are related to the development of the infants

Cross-Utterance Conditioned VAE for Non-Autoregressive Text-to-Speech

Modelling prosody variation is critical for synthesizing natural and expressive speech in end-to-end text-to-speech (TTS) systems. In this paper, a cross-utterance conditional VAE (CUC-VAE) is proposed to estimate a posterior probability distribution of the latent prosody features for each phoneme by conditioning on acoustic features, speaker information, and text features obtained from both past and future sentences. At inference time, instead of the standard Gaussian distribution used by VAE, CUC-VAE allows sampling from an utterance-specific prior distribution conditioned on cross-utterance information, which allows the prosody features generated by the TTS system to be related to the context and is more similar to how humans naturally produce prosody. The performance of CUC-VAE is evaluated via a qualitative listening test for naturalness, intelligibility and quantitative measurements, including word error rates and the standard deviation of prosody attributes. Experimental results on LJ-Speech and LibriTTS data show that the proposed CUC-VAE TTS system improves naturalness and prosody diversity with clear margins

Coulomb effects on the formation of proton halo nuclei

The exotic structures in the 2s_{1/2} states of five pairs of mirror nuclei ^{17}O-^{17}F, ^{26}Na-^{26}P, ^{27}Mg-^{27}P, ^{28}Al-^{28}P and ^{29}Si-^{29}P are investigated with the relativistic mean-field (RMF) theory and the single-particle model (SPM) to explore the role of the Coulomb effects on the proton halo formation. The present RMF calculations show that the exotic structure of the valence proton is more obvious than that of the valence neutron of its mirror nucleus, the difference of exotic size between each mirror nuclei becomes smaller with the increase of mass number A of the mirror nuclei and the ratios of the valence proton and valence neutron root-mean-square (RMS) radius to the matter radius in each pair of mirror nuclei all decrease linearly with the increase of A. In order to interpret these results, we analyze two opposite effects of Coulomb interaction on the exotic structure formation with SPM and find that the contribution of the energy level shift is more important than that of the Coulomb barrier for light nuclei. However, the hindrance of the Coulomb barrier becomes more obvious with the increase of A. When A is larger than 34, Coulomb effects on the exotic structure formation will almost become zero because its two effects counteract with each other.Comment: 9 pages, 6 figures. One colum

CT Findings of an Ectopic Pancreas in the Anterior Mediastinum

We report here on a rare case of an ectopic pancreatic tissue in the anterior mediastinum. A 32-year-old woman without any symptoms was transferred to our hospital because of an abnormal large mediastinal shadow on her chest radiograph during a checkup. The computed tomography (CT) scan revealed a giant cystic-solid mass that measured 16 × 13 × 8 cm and it was located in the center of the anterior mediastinum and it symmetrically grew to two sides. On enhanced CT scans, the solid component of the mass showed marked enhancement. We performed total surgical resection of the mass and complete pancreatic tissues were verified on the pathological examination

Role of exosomes in non-small cell lung cancer and EGFR-mutated lung cancer

As an important mediator of information transfer between cells, exosomes play a unique role in regulating tumor growth, supporting vascular proliferation, tumor invasion, and metastasis. Exosomes are widely present in various body fluids, and therefore they can be used as a potential tool for non-invasive liquid biopsy. The present study reviews the role of exosomes in liquid biopsy, tumor microenvironment formation, and epithelial-mesenchymal transition in non-small cell lung cancer (NSCLC). By targeting epidermal growth factor receptor (EGFR) therapy as a first-line treatment for patients with NSCLC, this study also briefly describes the occurrence of EGRF+ exosomes and the role of exosomes and their contents in non-invasive detection and potential therapeutic targets in EGFR-mutated lung cancer

Expression Signature and Role of miR-30d-5p in Non-Small Cell Lung Cancer: a Comprehensive Study Based on in Silico Analysis of Public Databases and in Vitro Experiments

Background/Aims: The purpose of this study was to probe the clinico-pathological significance and the underlying mechanism of miR-30d-5p expression in non-small cell lung cancer (NSCLC). Methods: We initially examined the level of miR-30d-5p expression in NSCLC and non-cancer tissues using RT-qPCR. Then, a series of validation analyses including a meta-analysis of data from microarray chips in Gene Expression Omnibus (GEO), data mining of the cancer genome atlas (TCGA) and an integrated meta-analysis incorporating GEO microarray chips, TCGA data, in-house RT-qPCR and literature studies were performed to examine the clinico-pathological value of miR-30d-5p expression in NSCLC. In vitro experiments were further conducted to investigate the impact of miR-30d-5p on NSCLC cell growth. The molecular mechanism by which miR-30d-5p regulates the pathogenesis of NSCLC was probed through a bioinformatics analysis of its target genes. Moreover, dual luciferase reporter assay was conducted to verify the targeting regulatory relationship between miR-30d-5p and CCNE2. Results: Based on results from RT-qPCR, GEO meta-analysis, TCGA data mining and the integrated meta-analysis incorporating GEO microarray chips, TCGA data, in-house RT-qPCR and literature studies, miR-30d-5p expression was decreased in NSCLC tissues, and patients with NSCLC who presented with lower miR-30d-5p expression tended to display an advanced clinical progression. Significant pathways including the Mucin type O-glycan biosynthesis pathway, cell cycle pathway and cysteine and methionine metabolism pathway (all P< 0.05) revealed potential roles of the target genes of miR-30d-5p in the oncogenesis of NSCLC. Results from in vitro experiments indicated that miR-30d-5p could attenuate proliferation and viability of NSCLC cells. Among the 12 identified hub genes, nine genes including E2F3, CCNE2, SKP2, CDK6, TFDP1, LDHA, GOT2, DNMT3B and ST6GALNAC1 were validated by Pearson’s correlation test and the human protein atlas (HPA) database as targets of miR-30d-5p with higher probability. Specifically, dual luciferase reporter assay confirmed that CCNE2 was directly targeted by miR-30d-5p. Conclusion: In summary, miR-30d-5p expression is decreased in NSCLC, and it might play the role as tumor suppressor in NSCLC by regulating target genes