Phononic transport in 1T prime-MoTe2: anisotropic structure with an isotropic lattice thermal conductivity

Molybdenum ditelluride (MoTe2) is an unique transition metal dichalcogenide owing to its energetically comparable 1H and 1T prime phases. This implies a high chance of coexistence of 1H-1T prime heterostructures which poses great complexity in the measurement of the intrinsic lattice thermal conductivities (kappa). In this work, via first-principles calculations, we examine the lattice-wave propagation and thermal conduction in this highly structurally anisotropic 1T prime MoTe2. Our calculation shows that the 1T prime phase has a sound velocity of 2.13 km/s (longitudinal acoustic wave), much lower than that of the 1H phase (4.05 km /s), indicating a staggered transmission of lattice waves across the boundary from 1H to 1T prime phase. Interestingly, the highly anisotropic 1T prime MoTe2 shows nearly isotropic and limited kappa_L of 13.02 W/mK, owing to a large Gruneisen parameter of acoustic flexural mode, heavy masses of Mo and Te elements and a low phonon group velocity. Accumulative kappa_L as a function of mean free path (MFP) indicates phonons with MFP less than ~300 nm contribute 80% of kappa_L and an inflection point at ~600 nm. Our results will be critical for understanding of the size dependent kappa_L of nanostructured 1T prime MoTe2

Promoted Electronic Coupling of Acoustic Phonon Modes in Doped Semimetallic MoTe2

As a prototype of the Weyl superconductor, layered molybdenum telluride (MoTe2) encompasses two semimetallic phases (1T_prime and Td) which differentiate from each other via a slight tilting of the out-of-plane lattice. Both phases are subjected to serious phase mixing which complicates the analysis of its origin of superconductivity. Herein, we explore the electron-phonon coupling (EPC) of the monolayer semimetallic MoTe2, without phase ambiguity under this thickness limit. Apart from the hardening or softening of phonon modes, the strength of the EPC can be strongly modulated by doping. Specifically, longitudinal and out-of-plane acoustic modes are significantly activated for electron doped MoTe2. This is ascribed to the presence of rich valley states and equispaced nesting bands which are dynamically populated under charge doping. Through comparing the monolayer and bilayer MoTe2, the strength of EPC is found to be less likely to depend on thickness for neutral samples but clearly promoted for thinner samples with electron doping, while for hole doping, the strength alters more significantly with the thickness than doping. Our work explains the puzzling issue of the doping sensitivity of the superconductivity in semimetallic MoTe2 and establishes the critical role of activating acoustic phonons in such low-dimensional materials

Acoustic transmission enhancement through a periodically-structured stiff plate without any opening

We report both experimentally and theoretically that the enhanced acoustic transmission can occur in the subwavelength region through a thin but stiff structured-plate without any opening. This exotic acoustic phenomenon is essentially distinct from the previous related studies originated from, either collectively or individually, the interaction of the incident wave with openings in previous structures. It is attributed to the structure-induced resonant excitation of the non-leaky Lamb modes that exist intrinsically in the uniform elastic plate. Our finding should have impact on ultrasonic applications.Comment: 11 pages, 4 figure

CRIT:Identifying RNA-binding protein regulator in circRNA life cycle via non-negative matrix factorization

Circular RNAs (circRNAs) are endogenous non-coding RNAs that regulate gene expression and participate in carcinogenesis. However, the RNA-binding proteins (RBPs) involved in circRNAs biogenesis and modulation remain largely unclear. We developed the circRNA regulator identification tool (CRIT), a non-negative matrix-factorization-based pipeline to identify regulating RBPs in cancers. CRIT uncovered 73 novel regulators across thousands of samples by effectively leveraging genomics data and functional annotations. We demonstrated that known RBPs involved in circRNA control are significantly enriched in these predictions. Analysis of circRNA-RBP interactions using two large cross-linking immunoprecipitation (CLIP) databases, we validated the consistency between CRIT prediction and the CLIP experiments. Furthermore, newly discovered RBPs are functionally connected with authentic circRNA regulators by various biological associations, such as physical interaction, similar binding motifs, common transcription factor modulation, and co-expression. When analyzing RNA sequencing (RNA-seq) datasets after short hairpin RNA (shRNA)/small interfering RNA (siRNA) knockdown, we found several novel RBPs that can affect global circRNA expression, which strengthens their role in the circRNA life cycle. The above evidence provided independent confirmation that CRIT is a useful tool to capture RBPs in circRNA processing. Finally, we show that authentic regulators are more likely the core splicing proteins and peripheral factors and usually harbor more alterations in the vast majority of cancers

A Systems Analysis of the Relationships Between Anemia and Ischemic Stroke Rehabilitation Based on RNA-Seq Data

Ischemic stroke (IS) is one of the main causes of morbidity and disability worldwide due to its complex mechanism. Anemia was characterized as a risk factor of IS because the direct connection between central nervous system, blood supply, and tissue oxygen delivery. As the key oxygen-carrying molecule in the blood, hemoglobin (Hb) may be decisive in the destiny of penumbral area or influence the brain recovery and neurologic function, which could finally affect the outcome of IS. However, more detailed information on the expression levels of Hb related genes were still lacking possibly because the concentration of Hb was determined by the genes’ expression several hours ago, which may make the research more difficult to perform. This time gap between gene expressions and protein concentration could make these genes predictive bio-markers for IS outcome. In this study, we choose 28 IS patients, of which 12 were suffering from anemia. Statistical analysis results showed that the outcomes of the patients were different when dividing them into two groups characterized by Hb concentration. 2 sex and age matched patients were first chosen to perform RNA-seq analysis on, on two occasions at two different time points, after which the Hb counts were tested at least 24 h after sequencing. Results showed that the outcome of anemia patients was poor compared with non-anemia patients. Two other patients were then chosen for analysis which excluded the coincidence of other factors. The results showed that the low value of Hb under 13 g/dL in men were closely related to the poor outcome of IS patients. Differently expressed Hb related genes were tested and six genes were shown to be positively correlated with the recovery degree of IS patients: ELANE, FGF23, HBB, PIEZO1, RASA4, and PRTN3. Gene CPM was shown to be negatively correlated with clinical outcomes. All of the seven genes were validated to be related to strokes using real-time PCR or literature searches. Taken together, these genes could be considered as new predictors for the recovery of IS patients

Bioinformatic and systems biology approach revealing the shared genes and molecular mechanisms between COVID-19 and non-alcoholic hepatitis

Introduction: Coronavirus disease 2019 (COVID-19) has become a global pandemic and poses a serious threat to human health. Many studies have shown that pre-existing nonalcoholic steatohepatitis (NASH) can worsen the clinical symptoms in patients suffering from COVID-19. However, the potential molecular mechanisms between NASH and COVID-19 remain unclear. To this end, key molecules and pathways between COVID-19 and NASH were herein explored by bioinformatic analysis.Methods: The common differentially expressed genes (DEGs) between NASH and COVID-19 were obtained by differential gene analysis. Enrichment analysis and protein-protein interaction (PPI) network analysis were carried out using the obtained common DEGs. The key modules and hub genes in PPI network were obtained by using the plug-in of Cytoscape software. Subsequently, the hub genes were verified using datasets of NASH (GSE180882) and COVID-19 (GSE150316), and further evaluated by principal component analysis (PCA) and receiver operating characteristic (ROC). Finally, the verified hub genes were analyzed by single-sample gene set enrichment analysis (ssGSEA) and NetworkAnalyst was used for the analysis of transcription factor (TF)-gene interactions, TF-microRNAs (miRNA) coregulatory network, and Protein-chemical Interactions.Results: A total of 120 DEGs between NASH and COVID-19 datasets were obtained, and the PPI network was constructed. Two key modules were obtained via the PPI network, and enrichment analysis of the key modules revealed the common association between NASH and COVID-19. In total, 16 hub genes were obtained by five algorithms, and six of them, namely, Kruppel-like factor 6 (KLF6), early growth response 1 (EGR1), growth arrest and DNA-damage-inducible 45 beta (GADD45B), JUNB, FOS, and FOS-like antigen 1 (FOSL1) were confirmed to be closely related to NASH and COVID-19. Finally, the relationship between hub genes and related pathways was analyzed, and the interaction network of six hub genes was constructed with TFs, miRNAs, and compounds.Conclusion: This study identified six hub genes related to COVID-19 and NASH, providing a new perspective for disease diagnosis and drug development

Enhancement of Canonical Wnt/β-Catenin Signaling Activity by HCV Core Protein Promotes Cell Growth of Hepatocellular Carcinoma Cells

BACKGROUND: The Hepatitis C virus (HCV) core protein has been implicated as a potential oncogene or a cofactor in HCV-related hepatocellular carcinoma (HCC), but the underlying mechanisms are unknown. Overactivation of the Wnt/β-catenin signaling is a major factor in oncogenesis of HCC. However, the pathogenesis of HCV core-associated Wnt/β-catenin activation remains to be further characterized. Therefore, we attempted to determine whether HCV core protein plays an important role in regulating Wnt/β-catenin signaling in HCC cells. METHODOLOGY: Wnt/β-catenin signaling activity was investigated in core-expressing hepatoma cells. Protein and gene expression were examined by Western blot, immunofluorescence staining, RT-qPCR, and reporter assay. PRINCIPAL FINDINGS: HCV core protein significantly enhances Tcf-dependent transcriptional activity induced by Wnt3A in HCC cell lines. Additionally, core protein increases and stabilizes β-catenin levels in hepatoma cell line Huh7 through inactivation of GSK-3β, which contributes to the up-regulation of downstream target genes, such as c-Myc, cyclin D1, WISP2 and CTGF. Also, core protein increases cell proliferation rate and promotes Wnt3A-induced tumor growth in the xenograft tumor model of human HCC. CONCLUSIONS/SIGNIFICANCE: HCV core protein enhances Wnt/β-catenin signaling activity, hence playing an important role in HCV-associated carcinogenesis

Co-activation of STAT3 and YES-Associated Protein 1 (YAP1) Pathway in EGFR-Mutant NSCLC

Background: The efficacy of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) in EGFR-mutant non–small cell lung cancer (NSCLC) is limited by adaptive activation of cell survival signals. We hypothesized that both signal transducer and activator of transcription 3 (STAT3) and Src-YES-associated protein 1 (YAP1) signaling are dually activated during EGFR TKI treatment to limit therapeutic response. Methods: We used MTT and clonogenic assays, immunoblotting, and quantitative polymerase chain reaction to evaluate the efficacy of EGFR TKI alone and in combination with STAT3 and Src inhibition in three EGFR-mutant NSCLC cell lines. The Chou-Talalay method was used for the quantitative determination of drug interaction. We examined tumor growth inhibition in one EGFR-mutant NSCLC xenograft model (n = 4 mice per group). STAT3 and YAP1 expression was evaluated in tumors from 119 EGFR-mutant NSCLC patients (64 in an initial cohort and 55 in a validation cohort) by quantitative polymerase chain reaction. Kaplan-Meier and Cox regression analyses were used to assess the correlation between survival and gene expression. All statistical tests were two-sided. Results: We discovered that lung cancer cells survive initial EGFR inhibitor treatment through activation of not only STAT3 but also Src-YAP1 signaling. Cotargeting EGFR, STAT3, and Src was synergistic in two EGFR-mutant NSCLC cell lines with a combination index of 0.59 (95% confidence interval [CI] = 0.54 to 0.63) for the PC-9 and 0.59 (95% CI = 0.54 to 0.63) for the H1975 cell line. High expression of STAT3 or YAP1 predicted worse progression-free survival (hazard ratio [HR] = 3.02, 95% CI = 1.54 to 5.93, P = .001, and HR = 2.57, 95% CI = 1.30 to 5.09, P = .007, respectively) in an initial cohort of 64 EGFR-mutant NSCLC patients treated with firstline EGFR TKIs. Similar results were observed in a validation cohort. Conclusions: Our study uncovers a coordinated signaling network centered on both STAT3 and Src-YAP signaling that limits targeted therapy response in lung cancer and identifies an unforeseen rational upfront polytherapy strategy to minimize residual disease and enhance clinical outcomes

Comorbid depressive symptoms can aggravate the functional changes of the pain matrix in patients with chronic back pain: A resting-state fMRI study

ObjectiveThe purposes of this study are to explore (1) whether comorbid depressive symptoms in patients with chronic back pain (CBP) affect the pain matrix. And (2) whether the interaction of depression and CBP exacerbates impaired brain function.MethodsThirty-two patients with CBP without comorbid depressive symptoms and thirty patients with CBP with comorbid depressive symptoms were recruited. All subjects underwent functional magnetic resonance imaging (fMRI) scans. The graph theory analysis, mediation analysis, and functional connectivity (FC) analysis were included in this study. All subjects received the detection of clinical depressive symptoms and pain-related manifestations.ResultCompared with the CBP group, subjects in the CBP with comorbid depressive symptoms (CBP-D) group had significantly increased FC in the left medial prefrontal cortex and several parietal cortical regions. The results of the graph theory analyses showed that the area under the curve of small-world property (t = −2.175, p = 0.034), gamma (t = −2.332, p = 0.023), and local efficiency (t = −2.461, p = 0.017) in the CBP-D group were significantly lower. The nodal efficiency in the ventral posterior insula (VPI) (t = −3.581, p = 0.0007), and the network efficiency values (t = −2.758, p = 0.008) in the pain matrix were significantly lower in the CBP-D group. Both the topological properties and the FC values of these brain regions were significantly correlated with self-rating depression scale (SDS) scores (all FDR corrected) but not with pain intensity. Further mediation analyses demonstrated that pain intensity had a mediating effect on the relationship between SDS scores and Pain Disability Index scores. Likewise, the SDS scores mediated the relationship between pain intensity and PDI scores.ConclusionOur study found that comorbid depressive symptoms can aggravate the impairment of pain matrix function of CBP, but this impairment cannot directly lead to the increase of pain intensity, which may be because some brain regions of the pain matrix are the common neural basis of depression and CBP