Marked TGF-β-regulated miRNA expression changes in both COPD and control lung fibroblasts

© 2019, The Author(s). COPD is associated with disturbed tissue repair, possibly due to TGF-β-regulated miRNA changes in fibroblasts. Our aim was to identify TGF-β-regulated miRNAs and their differential regulation and expression in COPD compared to control fibroblasts. Small RNA sequencing was performed on TGF-β-stimulated and unstimulated lung fibroblasts from 15 COPD patients and 15 controls. Linear regression was used to identify TGF-β-regulated and COPD-associated miRNAs. Interaction analysis was performed to compare miRNAs that responded differently to TGF-β in COPD and control. Re-analysis of previously generated Ago2-IP data and Enrichr were used to identify presence and function of potential target genes in the miRNA-targetome of lung fibroblasts. In total, 46 TGF-β-regulated miRNAs were identified in COPD and 86 in control fibroblasts (FDR < 0.05). MiR-27a-5p was the most significantly upregulated miRNA. MiR-148b-3p, miR-589-5p and miR-376b-3p responded differently to TGF-β in COPD compared to control (FDR < 0.25). MiR-660-5p was significantly upregulated in COPD compared to control (FDR < 0.05). Several predicted targets of miR-27a-5p, miR-148b-3p and miR-660-5p were present in the miRNA-targetome, and were mainly involved in the regulation of gene transcription. In conclusion, altered TGF-β-induced miRNA regulation and differential expression of miR-660-5p in COPD fibroblasts, may represent one of the mechanisms underlying aberrant tissue repair and remodelling in COPD

Loss of PINK1 Increases the Heart's Vulnerability to Ischemia-Reperfusion Injury.

Mutations in PTEN inducible kinase-1 (PINK1) induce mitochondrial dysfunction in dopaminergic neurons resulting in an inherited form of Parkinson's disease. Although PINK1 is present in the heart its exact role there is unclear. We hypothesized that PINK1 protects the heart against acute ischemia reperfusion injury (IRI) by preventing mitochondrial dysfunction

Performance and Emission Parameters of Homogeneous Charge Compression Ignition (HCCI) Engine: A Review

Strict emission regulations and demand for better fuel economy are driving forces for finding advanced engines that will be able to replace the conventional internal combustion engines in the near future. Homogeneous charge compression ignition (HCCI) engines use a different combustion technique; there are no spark plugs or injectors to assist the combustion. Instead, when the mixtures reach chemical activation energy, combustion auto-ignites in multiple spots. The main objective of this review paper is to study the engine performance and emission characteristics of HCCI engines operating in various conditions. Additionally, the impact of different fuels and additives on HCCI engine performance is also evaluated. The study also introduces a potential guideline to improve engine performance and emission characteristics. Compared to conventional compression ignition and spark ignition combustion methods, the HCCI combustion mode is noticeably faster and also provides better thermal efficiency. Although a wide range of fuels including alternative and renewable fuels can be used in the HCCI mode, there are some limitation/challenges, such as combustion limited operating range, phase control, high level of noise, cold start, preparation of homogeneous charge, etc. In conclusion, the HCCI combustion mode can be achieved in existing spark ignition (SI) engines with minor adjustments, and it results in lower oxides of nitrogen (NOx) and soot emissions, with practically a similar performance as that of SI combustion. Further improvements are required to permit extensive use of the HCCI mode in future.</p

Read-Right: a "web app" that improves reading speeds in patients with hemianopia

Effective behavioral therapies exist for patients with brain injury. The main issue is one of access. Can the internet be used as a resource so that suitable patients can build up enough practice to improve? We tested this hypothesis using a web-based application for patients with a right-sided hemianopia causing slow text reading. We studied 33 patients aged 26-81 years who fitted the entry criteria and accessed the therapy website between May 2010 and December 2011, in a longitudinal cohort study. The therapy consisted of reading animated, laterally scrolling text whose content and form was selected by the patients. Reading speeds on static text (main outcome) were assessed after every 5-h period of practice had been accrued. Statistical analysis was carried out using a repeated measures ANOVA. Read-Right therapy produced significant improvements in text reading speeds at all time points with a clear dose effect: 10 % at 5 h, 20 % at 10 h, 39 % at 15 h and 46 % at 20 h. Sub-analyses demonstrated that this was unlikely to be due to either multiple exposure to the testing materials (familiarity) or to the simple passage of time. This is the first example of a clinically proven therapy being delivered effectively to stroke patients over the internet. As therapists' time is more limited than patients' capacity to improve, carefully designed, web-based resources like Read-Right represent a realistic way of delivering a sufficient therapy dose to patients so they can obtain clinically meaningful improvements

Age-related gene and miRNA expression changes in airways of healthy individuals

© 2019, The Author(s). Knowledge on age-related miRNA changes in healthy individuals and their interaction with mRNAs is lacking. We studied age-related mRNA and miRNA expression changes and their interactions in normal airways. RNA and small RNA sequencing was performed on bronchial biopsies of 86 healthy individuals (age: 18–73) to determine age-related expression changes. Per age-related miRNA we determined the enrichment of age-related predicted targets and their correlation. We identified 285 age-related genes and 27 age-related miRNAs. Pathway enrichment showed that genes higher expressed with age were involved in synapse-related processes. Genes lower expressed with age were involved in cell cycle regulation, the immune system and DNA damage/repair. MiR-146a-5p, miR-146b-5p and miR-142-5p were lower expressed with increasing age and we found a significant enrichment for predicted targets of these miRNAs among genes that were higher expressed with age. The expression levels of the enriched predicted targets RIMS2 and IGSF1 were negatively correlated with both miR-146a-5p and miR-146b-5p. RIMS2 was present in the enriched process, i.e. positive regulation of synaptic transmission. In conclusion, genes decreased with ageing are involved in several of the ageing hallmarks. Genes higher expressed with ageing were involved in synapse-related processes, of which RIMS2 is potentially regulated by two age-related miRNAs

The AFLOW Fleet for Materials Discovery

The traditional paradigm for materials discovery has been recently expanded to incorporate substantial data driven research. With the intent to accelerate the development and the deployment of new technologies, the AFLOW Fleet for computational materials design automates high-throughput first principles calculations, and provides tools for data verification and dissemination for a broad community of users. AFLOW incorporates different computational modules to robustly determine thermodynamic stability, electronic band structures, vibrational dispersions, thermo-mechanical properties and more. The AFLOW data repository is publicly accessible online at aflow.org, with more than 1.7 million materials entries and a panoply of queryable computed properties. Tools to programmatically search and process the data, as well as to perform online machine learning predictions, are also available.Comment: 14 pages, 8 figure

State-of-the-Art of Establishing Test Procedures for Real Driving Gaseous Emissions from Light- and Heavy-Duty Vehicles

Air pollution caused by vehicle emissions has raised serious public health concerns. Vehicle emissions generally depend on many factors, such as the nature of the vehicle, driving style, traffic conditions, emission control technologies, and operational conditions. Concerns about the certification cycles used by various regulatory authorities are growing due to the difference in emission during certification procedure and Real Driving Emissions (RDE). Under laboratory conditions, certification tests are performed in a ‘chassis dynamometer’ for light-duty vehicles (LDVs) and an ‘engine dynamometer’ for heavy-duty vehicles (HDVs). As a result, the test drive cycles used to measure the automotive emissions do not correctly reflect the vehicle’s real-world driving pattern. Consequently, the RDE regulation is being phased in to reduce the disparity between type approval and vehicle’s real-world emissions. According to this review, different variables such as traffic signals, driving dynamics, congestions, altitude, ambient temperature, and so on have a major influence on actual driving pollution. Aside from that, cold-start and hot-start have been shown to have an effect on on-road pollution. Contrary to common opinion, new technology such as start-stop systems boost automotive emissions rather than decreasing them owing to unfavourable conditions from the point of view of exhaust emissions and exhaust after-treatment systems. In addition, the driving dynamics are not represented in the current laboratory-based test procedures. As a result, it is critical to establish an on-road testing protocol to obtain a true representation of vehicular emissions and reduce emissions to a standard level. The incorporation of RDE clauses into certification procedures would have a positive impact on global air quality

Polyunsaturated fatty acids and risk of melanoma: A Mendelian randomisation analysis

Melanoma is the deadliest form of skin cancer, mainly affecting populations of European ancestry. Some observational studies suggest that particular diets reduce melanoma risk, putatively through an increase in polyunsaturated fatty acid (PUFA) consumption. However, interpretation of these observational findings is difficult due to residual confounding or reverse causality. To date, a randomized controlled trial has not been carried out to examine the relationship between PUFAs and melanoma. Hence, we performed a Mendelian randomisation (MR) study to evaluate the link between PUFAs and melanoma. To perform MR, we used summary results from the largest risk genome‐wide association study (GWAS) meta‐analysis of melanoma, consisting of 12,874 cases and 23,203 controls. As instrumental variables we selected SNPs associated with PUFA levels from a GWAS meta‐analysis of PUFA levels, from the CHARGE consortium. We used the inverse variance weighted method to estimate a causal odds ratio. To aid interpretation, we established a benchmark “large” predicted change in PUFAs in which, for example, an increase in docosahexaenoic acid (DPA) of 0.17 units (equal to 1 standard deviation) moves a person from the 17th percentile to the median. Raising PUFA levels by a large amount (increasing DPA by 0.17 units) only negligibly changed melanoma risk: odds ratio [OR] = 1.03 (95% confidence interval [CI] = 0.96–1.10). Other PUFAs yielded similar results as DPA. Our MR analysis suggests that the effect of PUFA levels on melanoma risk is either zero or very small

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes