Pan-cancer analysis of super enhancer-induced PRR7-AS1 as a potential prognostic and immunological biomarker

Introduction: Systematic pan-cancer analysis of the roles and regulatory mechanisms for PRR7-AS1 is currently not available.Methods: In the present study, a comprehensive bioinformatic approach was used to mine the underlying oncogenic effects of PRR7-AS1, including expression status, prognostic value and immune characteristics.Results: We discovered that PRR7-AS1 expression was remarkably upregulated in most cancer types and exhibited a negative correlation with the prognosis. Furthermore, PRR7-AS1 expression was inversely connected with the majority of tumor-infiltrating immune cells, immune scores and immune checkpoint gene expression in pancancer. There was also a significant correlation between PRR7-AS1 expression status and tumor mutational burden, microsatellite instability, and neoantigens in certain tumors. PRR7-AS1 had the best predictive power for immune checkpoint blockade efficacy compared to other well-recognized biomarkers. PRR7-AS1 overexpression could affect cytotoxic T cells-mediated antitumor responses. Functional enrichment analysis revealed that PRR7-AS1 might be involved in the metabolic pathways. Super enhancer activity might have participated in the regulation of PRR7-AS1 expression. And we constructed the competitive endogenous RNA networks for PRR7-AS1.Discussion: In general, PRR7-AS1 had the potential to be a diagnostic, prognostic and immune biomarker for pan cancer. PRR7-AS1 was correlated with an immunosuppressive microenvironment and was a new potential target for immunotherapy. Epigenetic factors were the driving forces for PRR7-AS1 overexpression in tumors

Titanium Phosphate Nanoplates Modified With AgBr@Ag Nanoparticles: A Novel Heterostructured Photocatalyst With Significantly Enhanced Visible Light Responsive Activity

AgBr@Ag modified titanium phosphate composites were fabricated through a two-step approach. The prepared samples were characterized by X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. The optical properties of the composites were characterized by using UV-vis diffuse reflectance spectroscopy. The photocatalytic activities of the composites were investigated on the degradation of Rhodamine B and ciprofloxacin under visible light irradiation. AgBr@Ag/titanium phosphate was determined to exhibit considerably higher photocatalytic activity than the corresponding individual components. The mechanism on the enhancement of the photocatalytic activity was proposed based on the results of photoluminescence spectra and photocurrent measurements. Furthermore, the possible photocatalytic mechanisms of organic compounds degradation were also proposed

Oscillation-specific nodal alterations in early to middle stages Parkinsons disease.

Background: Different oscillations of brain networks could carry different dimensions of brain integration. We aimed to investigate oscillation-specific nodal alterations in patients with Parkinsons disease (PD) across early stage to middle stage by using graph theory-based analysis. Methods: Eighty-eight PD patients including 39 PD patients in the early stage (EPD) and 49 patients in the middle stage (MPD) and 36 controls were recruited in the present study. Graph theory-based network analyses from three oscillation frequencies (slow-5: 0.01-0.027 Hz; slow-4: 0.027-0.073 Hz; slow-3: 0.073-0.198 Hz) were analyzed. Nodal metrics (e.g. nodal degree centrality, betweenness centrality and nodal efficiency) were calculated. Results: Our results showed that (1) a divergent effect of oscillation frequencies on nodal metrics, especially on nodal degree centrality and nodal efficiency, that the anteroventral neocortex and subcortex had high nodal metrics within low oscillation frequencies while the posterolateral neocortex had high values within the relative high oscillation frequency was observed, which visually showed that network was perturbed in PD; (2) PD patients in early stage relatively preserved nodal properties while MPD patients showed widespread abnormalities, which was consistently detected within all three oscillation frequencies; (3) the involvement of basal ganglia could be specifically observed within slow-5 oscillation frequency in MPD patients; (4) logistic regression and receiver operating characteristic curve analyses demonstrated that some of those oscillation-specific nodal alterations had the ability to well discriminate PD patients from controls or MPD from EPD patients at the individual level; (5) occipital disruption within high frequency (slow-3) made a significant influence on motor impairment which was dominated by akinesia and rigidity. Conclusions: Coupling various oscillations could provide potentially useful information for large-scale network and progressive oscillation-specific nodal alterations were observed in PD patients across early to middle stages

Data from: Resilience of self-organised and top-down planned cities—a case study on London and Beijing street networks

The success or failure of the street network depends on its reliability. In this article, using resilience analysis, the author studies how the shape and appearance of street networks in self-organised and top-down planned cities influences urban transport. Considering London and Beijing as proxies for self-organised and top-down planned cities, the structural properties of London and Beijing networks first are investigated based on their primal and dual representations of planar graphs. The robustness of street networks then is evaluated in primal space and dual space by deactivating road links under random and intentional attack scenarios. The results show that the reliability of London street network differs from that of Beijing, which seems to rely more on its architecture and connectivity. It is found that top-down planned Beijing with its higher average degree in the dual space and assortativity in the primal space is more robust than self-organised London using the measures of maximum and second largest cluster size and network efficiency. The article offers an insight, from a network perspective, into the reliability of street patterns in self-organised and top-down planned city systems

Image-based patient-specific computational biomechanical analysis of the interaction between blood flow and atherosclerosis

This research focuses on the development of a biomechanical strategy for risk assessment of atherosclerotic plaque rupture, which is a leading cause of acute cardiovascular events, such as heart attack and stroke. Image-based three-dimensional coronary and carotid arterial models were developed, and computational biomechanical analysis was performed to evaluate the mechanical interaction between blood flow and atherosclerosis. This study uncovered the biomechanical risk factors that are associated with high-risk atherosclerosis and provided a biomechanical tool for detecting high-risk plaques. It will help with future clinical diagnosis and treatment of cardiovascular diseases

dataset

This zip file includes the raw datasets (Beijing and London street networks) and graphs created in the primal and dual space for Beijing, London, ERPG, and GRID. The raw datasets are ArcGIS shapefile format and the graphs are ‘pajek’ format

Maximum cluster size and second largest cluster size as a function of proportion of edges removed in the primal space under the random attack scenario.

<p>Gray dot is maximum cluster size; Blue dot is maximum cluster size averaged over one hundred realisations with error bar; Dark dot is second largest cluster size; Red dot is second largest cluster size averaged over one hundred realisations with error bar. Upper left panel: ERPG; Upper right panel: GRID; Bottom left panel: London; Bottom right panel: Beijing.</p

Boxplot of critical points over one hundred realisations under the random and intentional attack scenarios in the primal and dual space for each net.

<p>Left panel: primal space. Right panel: dual space. Dashed red lines within the boxes are the critical points calculated by second largest cluster size averaged over one hundred realisations shown in Table A in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141736#pone.0141736.s001" target="_blank">S1 Appendix</a>.</p

A Survey on Personal Data Cloud

Personal data represent the e-history of a person and are of great significance to the person, but they are essentially produced and governed by various distributed services and there lacks a global and centralized view. In recent years, researchers pay attention to Personal Data Cloud (PDC) which aggregates the heterogeneous personal data scattered in different clouds into one cloud, so that a person could effectively store, acquire, and share their data. This paper makes a short survey on PDC research by summarizing related papers published in recent years. The concept, classification, and significance of personal data are elaborately introduced and then the semantics correlation and semantics representation of personal data are discussed. A multilayer reference architecture of PDC, including its core components and a real-world operational scenario showing how the reference architecture works, is introduced in detail. Existing commercial PDC products/prototypes are listed and compared from several perspectives. Five open issues to improve the shortcomings of current PDC research are put forward