MIClique: An Algorithm to Identify Differentially Coexpressed Disease Gene Subset from Microarray Data

Computational analysis of microarray data has provided an effective way to identify disease-related genes. Traditional disease gene selection methods from microarray data such as statistical test always focus on differentially expressed genes in different samples by individual gene prioritization. These traditional methods might miss differentially coexpressed (DCE) gene subsets because they ignore the interaction between genes. In this paper, MIClique algorithm is proposed to identify DEC gene subsets based on mutual information and clique analysis. Mutual information is used to measure the coexpression relationship between each pair of genes in two different kinds of samples. Clique analysis is a commonly used method in biological network, which generally represents biological module of similar function. By applying the MIClique algorithm to real gene expression data, some DEC gene subsets which correlated under one experimental condition but uncorrelated under another condition are detected from the graph of colon dataset and leukemia dataset

Oxidation-Resistant, Solution-Processed Plasmonic Ni Nanochain-SiO\u3csub\u3ex\u3c/sub\u3e (x \u3c 2) Selective Solar Thermal Absorbers

Metal oxidation at high temperatures has long been a challenge in cermet solar thermal absorbers, which impedes the development of atmospherically stable, high-temperature, high-performance concentrated solar power (CSP) systems. In this work, we demonstrate solution-processed Ni nanochain-SiOx (x \u3c 2) and Ni nanochain-SiO2 selective solar thermal absorbers that exhibit a strong anti-oxidation behavior up to 600 °C in air. The thermal stability is far superior to previously reported Ni nanoparticle-Al2O3 selective solar thermal absorbers, which readily oxidize at 450 °C. The SiOx (x \u3c 2) and SiO2 matrices are derived from hydrogen silsesquioxane and tetraethyl orthosilicate precursors, respectively, which comprise Si-O cage-like structures and Si-O networks. Fourier transform infrared spectroscopy shows that the dissociation of Si-O cage-like structures and Si-O networks at high temperatures have enabled the formation of new bonds at the Ni/SiOx interface to passivate the surface of Ni nanoparticles and prevent oxidation. X-ray photoelectron spectroscopy and Raman spectroscopy demonstrate that the excess Si in the SiOx (x \u3c 2) matrices reacts with Ni nanostructures to form silicides at the interfaces, which further improves the anti-oxidation properties. As a result, Ni-SiOx (x \u3c 2) systems demonstrate better anti-oxidation performance than Ni-SiO2 systems. This oxidation-resistant Ni nanochain-SiOx (x \u3c 2) cermet coating also exhibits excellent high-temperature optical performance, with a high solar absorptance of ∼90% and a low emittance ∼18% measured at 300 °C. These results open the door towards atmospheric stable, high temperature, high-performance solar selective absorber coatings processed by low-cost solution-chemical methods for future generations of CSP systems

The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development

It has long been known that trypanosomes regulate mitochondrial biogenesis during the life cycle of the parasite; however, the mitochondrial protein inventory (MitoCarta) and its regulation remain unknown. We present a novel computational method for genome-wide prediction of mitochondrial proteins using a support vector machine-based classifier with ∼90% prediction accuracy. Using this method, we predicted the mitochondrial localization of 468 proteins with high confidence and have experimentally verified the localization of a subset of these proteins. We then applied a recently developed parallel sequencing technology to determine the expression profiles and the splicing patterns of a total of 1065 predicted MitoCarta transcripts during the development of the parasite, and showed that 435 of the transcripts significantly changed their expressions while 630 remain unchanged in any of the three life stages analyzed. Furthermore, we identified 298 alternatively splicing events, a small subset of which could lead to dual localization of the corresponding protein

The Trypanosoma \u3ci\u3ebrucei\u3c/i\u3e MitoCarta and its regulation and splicing pattern during development

It has long been known that trypanosomes regulate mitochondrial biogenesis during the life cycle of the parasite; however, the mitochondrial protein inventory (MitoCarta) and its regulation remain unknown. We present a novel computational method for genome-wide prediction of mitochondrial proteins using a support vector machine-based classifier with ~90% prediction accuracy. Using this method, we predicted the mitochondrial localization of 468 proteins with high confidence and have experimentally verified the localization of a subset of these proteins. We then applied a recently developed parallel sequencing technology to determine the expression profiles and the splicing patterns of a total of 1065 predicted MitoCarta transcripts during the development of the parasite, and showed that 435 of the transcripts significantly changed their expressions while 630 remain unchanged in any of the three life stages analyzed. Furthermore, we identified 298 alternatively splicing events, a small subset of which could lead to dual localization of the corresponding proteins

Application of relay puncture technique in treating patients with complicated lower extremity arterial diseases

Objective This study aimed to introduce and evaluate the safety and efficacy of the relay puncture technique in patients with complicated lower extremity arterial diseases. Methods A total of 21 patients (16 male and five female patients; median age: 68.5 years old), who had suffered from lower extremity arterial diseases between December 2014 and July 2017, were retrospectively collected. For all patients, the contralateral femoral artery was not available for puncture access, and the length of the devices was too short for the brachial artery approach. Therefore, the relay puncture technique, in which the first puncture was performed on the brachial artery, followed by an antegrade puncture on the femoral artery, was used to accomplish the endovascular therapy. Percutaneous transluminal angioplasty and/or percutaneous transluminal stenting were/was used to assess the efficacy of the relay puncture technique. The ankle–brachial index (ABI) and Rutherford clinical classification were used to evaluate the improvement of symptoms after treatment. Patients were followed up for 1, 3, 6, and 12 months, and annually (mean: 16.6 months) after discharge. Results The relay puncture treatment had a 100% technical success rate, and immediately decreased the ischemic symptoms of patients after the procedure. The ABI significantly increased from 0.33 ± 0.18 to 0.75 ± 0.21 at the 1-year follow-up time point (P < 0.05). No serious complications occurred during the follow-up period. The 1-year primary patency rate was 71.43%. Conclusion The relay puncture technique is a feasible technique in the hands of experienced and skilled equipment operators for the treatment of lower extremity arterial diseases, when the contralateral femoral artery is not available for puncture, and the length of the device is too short to treat the distal lesion of the femoral artery and popliteal artery through the brachial artery approach

A Modified Electrochemical Model to Account for Mechanical Effects Due to Lithium Intercalation and External Pressure

For a battery cell, both the porosity of the electrodes/separator and the transport distance of charged species can evolve due to mechanical deformation arising from either lithium intercalation-induced swelling and contraction of the active particles or externally applied mechanical loading. To describe accurately the coupling between mechanical deformation and the cell\u27s electrochemical response, we extend Newman\u27s DualFoil model to allow variable, non-uniform porosities in both electrodes and the separator, which are dynamically updated based on the electrochemical and mechanical states of the battery cell. In addition, the finite deformation theory from continuum mechanics is used to modify the electrochemical transport equations to account for the change of the charged species transport distance. The proposed coupled electrochemomechanical model is tested with a parameterized commercial cell. Our simulation results confirm that mass conservation is satisfied with the new formulation. We further show that mechanical effects have a significant impact on the cell\u27s electrochemical response at high charge/discharge rates

Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early Drosophila embryonic development

The linker histone H1 is critical to maintenance of higher-order chromatin structures and to gene expression regulation. However, H1 dynamics and its functions in embryonic development remain unresolved. Here, we profiled gene expression, nucleosome positions, and H1 locations in early Drosophila embryos. The results show that H1 binding is positively correlated with the stability of beads-on-a-string nucleosome organization likely through stabilizing nucleosome positioning and maintaining nucleosome spacing. Strikingly, nucleosomes with H1 placement deviating to the left or the right relative to the dyad shift to the left or the right, respectively, during early Drosophila embryonic development. H1 occupancy on genic nucleosomes is inversely correlated with nucleosome distance to the transcription start sites. This inverse correlation reduces as gene transcription levels decrease. Additionally, H1 occupancy is lower at the 5\u27 border of genic nucleosomes than that at the 3\u27 border. This asymmetrical pattern of H1 occupancy on genic nucleosomes diminishes as gene transcription levels decrease. These findings shed new lights into how H1 placement dynamics correlates with nucleosome positioning and gene transcription during early Drosophila embryonic development