A unified framework for finding differentially expressed genes from microarray experiments

<p>Abstract</p> <p>Background</p> <p>This paper presents a unified framework for finding differentially expressed genes (DEGs) from the microarray data. The proposed framework has three interrelated modules: (i) gene ranking, ii) significance analysis of genes and (iii) validation. The first module uses two gene selection algorithms, namely, a) two-way clustering and b) combined adaptive ranking to rank the genes. The second module converts the gene ranks into p-values using an R-test and fuses the two sets of p-values using the Fisher's omnibus criterion. The DEGs are selected using the FDR analysis. The third module performs three fold validations of the obtained DEGs. The robustness of the proposed unified framework in gene selection is first illustrated using false discovery rate analysis. In addition, the clustering-based validation of the DEGs is performed by employing an adaptive subspace-based clustering algorithm on the training and the test datasets. Finally, a projection-based visualization is performed to validate the DEGs obtained using the unified framework.</p> <p>Results</p> <p>The performance of the unified framework is compared with well-known ranking algorithms such as t-statistics, Significance Analysis of Microarrays (SAM), Adaptive Ranking, Combined Adaptive Ranking and Two-way Clustering. The performance curves obtained using 50 simulated microarray datasets each following two different distributions indicate the superiority of the unified framework over the other reported algorithms. Further analyses on 3 real cancer datasets and 3 Parkinson's datasets show the similar improvement in performance. First, a 3 fold validation process is provided for the two-sample cancer datasets. In addition, the analysis on 3 sets of Parkinson's data is performed to demonstrate the scalability of the proposed method to multi-sample microarray datasets.</p> <p>Conclusion</p> <p>This paper presents a unified framework for the robust selection of genes from the two-sample as well as multi-sample microarray experiments. Two different ranking methods used in module 1 bring diversity in the selection of genes. The conversion of ranks to p-values, the fusion of p-values and FDR analysis aid in the identification of significant genes which cannot be judged based on gene ranking alone. The 3 fold validation, namely, robustness in selection of genes using FDR analysis, clustering, and visualization demonstrate the relevance of the DEGs. Empirical analyses on 50 artificial datasets and 6 real microarray datasets illustrate the efficacy of the proposed approach. The analyses on 3 cancer datasets demonstrate the utility of the proposed approach on microarray datasets with two classes of samples. The scalability of the proposed unified approach to multi-sample (more than two sample classes) microarray datasets is addressed using three sets of Parkinson's Data. Empirical analyses show that the unified framework outperformed other gene selection methods in selecting differentially expressed genes from microarray data.</p

Influence of Milling Process Parameters on Machined Surface Quality of Carbon Fibre Reinforced Polymer (CFRP) Composites Using Taguchi Analysis And Grey Relational Analysis

The article presents the milled surface quality of Uni-Directional Carbon Fibre Reinforced Polymer (UD-CFRP) composites from Taguchi’s and grey relational analysis. The novelty is demonstrating the possibility of detecting the surface defects in polymer composites during milling using SEM analysis. The material used for this study is UD-CFRP composite laminates and made by hand-layup process. All the milling operations were carried out using a solid tungsten carbide end milling tool and experiments conducted on CNC milling machine. Taguchi L9, 3-level orthogonal array was considered for experimentation. Analysis of Variance (ANOVA) was conducted to explore the significance of each individual input process parameters on multiple performance characteristics. Optimal process parameters are thoroughly validated by grey relational grade achieved by the grey relational analysis for multi performance characteristics. Finally, experimental results were correlated and analyzed with scanning electron micrographs using Scanning Electron Microscope (SEM)

Computational analysis of low velocity impacts on Empty Fruit Bunch (EFB) composite

This paper is to investigate the impact response on peak force behavior of the material at low velocity impact EFB composite. This is because impact damage on EFB composite is not well-known using quasi-static indentation. Series of quasi-static indentation was conducted in experiment to obtain the impact result. However, more experimental results are required to gain an accurate result. Simulation is useful to predict results at a reduced cost and time. Mesh has been created to simulate EFB composite rectangular panel using LS-Dyna. Material properties of EFB composite obtained from three point bending test experiment using Instron 3367. Mesh density on EFB composite rectangular panel is differed, which are 0.5mm, 1mm, 1.5mm, 2mm, and 2.5 mm, and results from the simulation is compared to the experimental results which show the same pattern as the simulation result. From the study, the result proved that the simulation is in good agreement and has the same trend as the experimental result

Nano-refrigerants and nano-lubricants in refrigeration : synthesis, mechanisms, applications, and challenges

Addressing global energy security and environmental concerns, the utilization of nano-refrigerants and nano-lubricants has emerged as an innovative path for enhancing heat transfer. This research focuses on enhancing the thermophysical properties, heat transfer efficiency, and tribological characteristics of nanofluids—nanoparticles dispersed in refrigerants or lubricants. These nanofluids have demonstrated significant potential in applications such as cooling, air conditioning systems, and heat transfer equipment including pumps and pipes. A comprehensive understanding of parameters like thermal conductivity, viscosity, pressure drop, pumping power, and energy performance is delivered, with the aim of enhancing the overall efficiency of refrigeration systems, particularly the coefficient of performance (COP). Additionally, the review covers existing research on flow and pool boiling heat transfer, nano-lubricant tribological enhancement, and nano-refrigerant condensation. The study also addresses the challenges associated with the use of nano-refrigerants and nano-lubricants and offers a prospective outlook for their usage. These novel nanofluids are anticipated to emerge as effective solutions for increasing the COP and reducing energy consumption in the industrial sector, thus extending beyond the scope of previous efforts in this field. This review could serve as a valuable resource for a broad audience interested in this novel approach to energy efficiency

Endodontic Microbiology: A Bibliometric Analysis of the Top 50 Classics

Background: Citation analysis has emerged to play a significant role in recognition of the most useful areas of research. Endodontic microbiology has been a topic of interest for endodontists as well as periodontists and oral surgeons. This bibliometric analysis is aimed at identifying and reporting the characteristics of the top 50 cited articles on endodontic microbiology. Methods: The articles were identified through a search on Web of Science (WoS), property of Clarivate Analytics database published on endodontic microbiology. The citation information of the selected articles was recorded. The Journal of Endodontics, International Endodontic Journal, Oral Surgery Oral Medicine Oral Pathology Oral Radiology and Endodontology, Dental Traumatology, and Australian Endodontic Journal were searched in the search title. Descriptive and bivariate analyses were performed using a statistical software package SPSS. Statistical analysis was performed using Shapiro-Wilk, Kruskal-Wallis, Post hoc, Mann-Kendall trend, and Spearman-rank tests. Results: The 50 most cited articles were published from 1965 to 2012 with citation count varying from 1065 to 103 times. The total citation counts of articles recorded were 11,525 (WoS), 12,602 (Elseviers' Scopus), and 28,871 (Google Scholar). The most prolific years in terms of publications were 2001, 2002, and 2003, with five publications each, followed by 2005 with four. The year with most citations was 1998, with 1,330 citations, followed by 1965 and 2001, with 1,065 and 1,015 citations, respectively. A total of 136 authors contributed to the top 50 most cited articles with 27 corresponding institutions from 12 different countries. The most common methodological design was in vitro study, followed by clinic-laboratory study, literature review, systematic review and meta-analysis, and animal study. Conclusions: The present study provided a detailed list of the top 50 most cited and classic articles on microbiology in endodontics. This will help researchers, students, and clinicians in the field of endodontics as an impressive source of information

Glycoprotein Ib activation by thrombin stimulates the energy metabolism in human platelets

<div><p>Thrombin-induced platelet activation requires substantial amounts of ATP. However, the specific contribution of each ATP-generating pathway <i>i</i>.<i>e</i>., oxidative phosphorylation (OxPhos) versus glycolysis and the biochemical mechanisms involved in the thrombin-induced activation of energy metabolism remain unclear. Here we report an integral analysis on the role of both energy pathways in human platelets activated by several agonists, and the signal transducing mechanisms associated with such activation. We found that thrombin, Trap-6, arachidonic acid, collagen, A23187, epinephrine and ADP significantly increased glycolytic flux (3–38 times <i>vs</i>. non-activated platelets) whereas ristocetin was ineffective. OxPhos (33 times) and mitochondrial transmembrane potential (88%) were increased only by thrombin. OxPhos was the main source of ATP in thrombin-activated platelets, whereas in platelets activated by any of the other agonists, glycolysis was the principal ATP supplier. In order to establish the biochemical mechanisms involved in the thrombin-induced OxPhos activation in platelets, several signaling pathways associated with mitochondrial activation were analyzed. Wortmannin and LY294002 (PI3K/Akt pathway inhibitors), ristocetin and heparin (GPIb inhibitors) as well as resveratrol, ATP (calcium-release inhibitors) and PP1 (Tyr-phosphorylation inhibitor) prevented the thrombin-induced platelet activation. These results suggest that thrombin activates OxPhos and glycolysis through GPIb-dependent signaling involving PI3K and Akt activation, calcium mobilization and protein phosphorylation.</p></div

Developments in Nanoparticles Enhanced Biofuels and Solar Energy in Malaysian Perspective: A Review of State of the Art

The rapid rise in global oil prices, the scarcity of petroleum sources, and environmental concerns have all created severe issues. As a result of the country's rapid expansion and financial affluence, Malaysia's energy consumption has skyrocketed. Biodiesel and solar power are currently two of the most popular alternatives to fossil fuels in Malaysia. These two types of renewable energy sources appear to be viable options because of their abundant availability together with environmental and performance competence to highly polluting and fast depleting fossil fuels. The purpose of adopting renewable technology is to expand the nation's accessibility to a reliable and secure power supply. The current review article investigates nonconventional energy sources added with nanosized metal particles called as nanomaterials including biodiesel and solar, as well as readily available renewable energy options. Concerning the nation's energy policy agenda, the sources of energy demand are also investigated. The article evaluates Malaysia's existing position in renewable energy industries, such as biodiesel and solar, as well as the impact of nanomaterials. This review article discusses biodiesel production, applications, and government policies in Malaysia, as well as biodiesel consumption and recent developments in the bioenergy sector, such as biodiesel property modifications utilizing nanoparticle additions. In addition, the current review study examines the scope of solar energy, different photovoltaic concentrators, types of solar energy harvesting systems, photovoltaic electricity potential in Malaysia, and the experimental setup of solar flat plate collectors (FPC) with nanotechnology

Strain-Engineering Mott-Insulating La2_2CuO4_4

The transition temperature $T_\textrm{c}$ of unconventional superconductivity is often tunable. For a monolayer of FeSe, for example, the sweet spot is uniquely bound to titanium-oxide substrates. By contrast for La$_{2-\mathrm{x}}$Sr$_\mathrm{x}$CuO$_4$ thin films, such substrates are sub-optimal and the highest $T_\textrm{c}$ is instead obtained using LaSrAlO$_4$. An outstanding challenge is thus to understand the optimal conditions for superconductivity in thin films: which microscopic parameters drive the change in $T_\mathrm{c}$ and how can we tune them? Here we demonstrate, by a combination of x-ray absorption and resonant inelastic x-ray scattering spectroscopy, how the Coulomb and magnetic-exchange interaction of La$_2$CuO$_4$ thin films can be enhanced by compressive strain. Our experiments and theoretical calculations establish that the substrate producing the largest $T_\textrm{c}$ under doping also generates the largest nearest neighbour hopping integral, Coulomb and magnetic-exchange interaction. We hence suggest optimising the parent Mott state as a strategy for enhancing the superconducting transition temperature in cuprates.Comment: 15 pages, 7 figures and 2 tables (including Supplementary Information