Identification of differentially expressed subnetworks based on multivariate ANOVA

<p>Abstract</p> <p>Background</p> <p>Since high-throughput protein-protein interaction (PPI) data has recently become available for humans, there has been a growing interest in combining PPI data with other genome-wide data. In particular, the identification of phenotype-related PPI subnetworks using gene expression data has been of great concern. Successful integration for the identification of significant subnetworks requires the use of a search algorithm with a proper scoring method. Here we propose a multivariate analysis of variance (MANOVA)-based scoring method with a greedy search for identifying differentially expressed PPI subnetworks.</p> <p>Results</p> <p>Given the MANOVA-based scoring method, we performed a greedy search to identify the subnetworks with the maximum scores in the PPI network. Our approach was successfully applied to human microarray datasets. Each identified subnetwork was annotated with the Gene Ontology (GO) term, resulting in the phenotype-related functional pathway or complex. We also compared these results with those of other scoring methods such as <it>t </it>statistic- and mutual information-based scoring methods. The MANOVA-based method produced subnetworks with a larger number of proteins than the other methods. Furthermore, the subnetworks identified by the MANOVA-based method tended to consist of highly correlated proteins.</p> <p>Conclusion</p> <p>This article proposes a MANOVA-based scoring method to combine PPI data with expression data using a greedy search. This method is recommended for the highly sensitive detection of large subnetworks.</p

Enhanced optical response of hybridized VO2/graphene films

Application of graphene as transparent electrodes is an active research area due to its excellent electrical and optical properties. Vanadium dioxide (VO2) is an attractive material since it is a thermochromic material that undergoes a structural phase transition when heat is applied. The phase transition results in the change of electrical and optical characteristics. We report optical characteristics of hybrid materials of graphene and VO2. We observed a 12% improvement in infrared transmittance with VO2 films deposited on graphene sapphire substrates compared to that of bare sapphire substrates. We also found that the phase transition temperature decreases as the number of graphene layers on the substrates increases. In the case of VO2 films on the substrate that was coated with four layers of graphene, the mean phase transition temperature was lowered to similar to 56 degrees C.close4

PINK1 deficiency impairs osteoblast differentiation through aberrant mitochondrial homeostasis

Background PTEN-induced kinase 1 (PINK1) is a serine/threonine-protein kinase in mitochondria that is critical for mitochondrial quality control. PINK1 triggers mitophagy, a selective autophagy of mitochondria, and is involved in mitochondrial regeneration. Although increments of mitochondrial biogenesis and activity are known to be crucial during differentiation, data regarding the specific role of PINK1 in osteogenic maturation and bone remodeling are limited. Methods We adopted an ovariectomy model in female wildtype and Pink1−/− mice. Ovariectomized mice were analyzed using micro-CT, H&E staining, Masson’s trichrome staining. RT-PCR, western blot, immunofluorescence, alkaline phosphatase, and alizarin red staining were performed to assess the expression of PINK1 and osteogenic markers in silencing of PINK1 MC3T3-E1 cells. Clinical relevance of PINK1 expression levels was determined via qRT-PCR analysis in normal and osteoporosis patients. Results A significant decrease in bone mass and collagen deposition was observed in the femurs of Pink1−/− mice after ovariectomy. Ex vivo, differentiation of osteoblasts was inhibited upon Pink1 downregulation, accompanied by impaired mitochondrial homeostasis, increased mitochondrial reactive oxygen species production, and defects in mitochondrial calcium handling. Furthermore, PINK1 expression was reduced in bones from patients with osteoporosis, which supports the practical role of PINK1 in human bone disease. Conclusions In this study, we demonstrated that activation of PINK1 is a requisite in osteoblasts during differentiation, which is related to mitochondrial quality control and low reactive oxygen species production. Enhancing PINK1 activity might be a possible treatment target in bone diseases as it can promote a healthy pool of functional mitochondria in osteoblasts.So-Young Lee received National Research Foundation Grant of Korea (NRF2019R1A2C4070492), funded by the Korean government (https://www.nrf.re.kr) for this work. Soonchul Lee received National Research Foundation Grant of Korea (NRF-2019R1C1C1004017), funded by the Korean government (https://www.nrf.re.kr) for this work

Relationship between time of emergency department admission and adherence to the Surviving Sepsis Campaign bundle in patients with septic shock

Abstract Background Nighttime hospital admission is often associated with increased mortality risk in various diseases. This study investigated compliance rates with the Surviving Sepsis Campaign (SSC) 3-h bundle for daytime and nighttime emergency department (ED) admissions and the clinical impact of compliance on mortality in patients with septic shock. Methods We conducted an observational study using data from a prospective, multicenter registry for septic shock provided by the Korean Shock Society from 11 institutions from November 2015 to December 2017. The outcome was the compliance rate with the SSC 3-h bundle according to the time of arrival in the ED. Results A total of 2049 patients were enrolled. Compared with daytime admission, nighttime admission was associated with higher compliance with the administration of antibiotics within 3 h (adjusted odds ratio (adjOR), 1.326; 95% confidence interval (95% CI), 1.088–1.617, p = 0.005) and with the complete SSC bundle (adjOR, 1.368; 95% CI, 1.115–1.678; p = 0.003), likely to result from the increased volume of all patients and sepsis patients admitted during daytime hours. The hazard ratios of the completion of SSC bundle for 28-day mortality and in-hospital mortality were 0.750 (95% CI 0.590–0.952, p = 0.018) and 0.714 (95% CI 0.564–0.904, p = 0.005), respectively. Conclusion Septic shock patients admitted to the ED during the daytime exhibited lower sepsis bundle compliance than those admitted at night. Both the higher number of admitted patients and the higher patients to medical staff ratio during daytime may be factors that are responsible for lowering the compliance

Applications of Hodograph Transformation to Hydrodynamic Problems Influenced by Gravitation

138 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 1980.The hydrodynamic problems influenced by gravitation have been examined through hodograph transformations. It has been found that even with strong influence of the gravitational field, the stream function can be solved in the hodograph plane through numerical calculations. The velocity function of free streamlines must be determined through iterations and it has been also found that this iterative process is rapidly convergent. Favorable agreement of the results with the experimental data substantiates the fact that this method is effective in dealing with flow problems strongly influenced by gravitation. The idea of subdividing the hodograph and matching their boundary values along the cut can be extended to problems with more complicated configurations.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Analysis of social welfare impact of crop pest and disease damages due to climate change: a case study of dried red peppers

Abstract Climate change can affect agricultural production both directly and indirectly. The direct impact is through climate change itself while the indirect impact is through the outbreak of pests and diseases (P&D) affected by climate change. We measured the difference in social welfare change of dried red peppers in monetary values between these two effects based on constructed three models. In the P&D damage model, the effects of climatic factors on P&D damages were analyzed. In the yield model, the direct and indirect effects of climatic factors on the dried red pepper yields were analyzed. Lastly, the effect of rising temperatures on the social welfare of dried red peppers was measured in monetary values using the equilibrium displacement model (EDM). As a key result, although these rising temperatures increase the yields and social welfare, there are differences in social welfare change between with and without P&D damages, and the difference increases over time. This implies that global climate change can affect agricultural production around the world, which can affect food security around the world beyond changes in crop prices and social welfare. So rigorous pest control and damage predictions are needed

Thermal sensation and comfort models for non-uniform and transient environments: Part I: local sensation of individual body parts

A three-part series presents the development of models for predicting the local thermal sensation (Part I) and local comfort (Part II) of different parts of the human body, and also the whole-body sensation and comfort responses (Part III). The models predict these subjective responses to the environment from thermophysiological measurements or predictions (skin and core temperatures). The models apply to a range of environments: uniform and non-uniform, transient and stable. They are based on diverse results from the literature and from body-part-specific human subject tests in a climate chamber. They were validated against a test of passengers in automobiles. This series is intended to present the rationale, structure, and coefficients for these models so that others can test and develop them further as additional empirical data becomes available. The experimental methods and some measured results from the climate chamber tests have been published previously. Part I describes thermal sensation models representing 19 individual local body parts. The models’ structure and coefficients were derived by regression of skin and core temperatures against thermal sensation votes obtained in the chamber experiments. The sensation for each local body part is predicted by a logistic function with four inputs: local skin temperature, mean skin temperature presenting the whole body thermal state, and the time derivatives of skin and core temperatures representing the response to transients. These inputs can be obtained from thermophysiological computer programs that treat the body as multiple segments