The cumulative of genes carrying mutations is vital for the establishment and development of cancer. However, this driver gene exploring research line has selected and used types of tools and models ...of analysis unsystematically and discretely. Also, the previous studies may have neglected low-frequency drivers and seldom predicted subgroup specificities of identified driver genes. In this study, we presented an improved driver gene identification and analysis pipeline that comprises the four most widely focused analyses for driver genes: enrichment analysis, clinical feature association with expression profiles of identified driver genes as well as with their functional modules, and patient stratification by existing advanced computational tools integrating multi-omics data. The improved pipeline's general usability was demonstrated straightforwardly for breast cancer, validated by some independent databases. Accordingly, 31 validated driver genes, including four novel ones, were discovered. Subsequently, we detected cancer-related significantly enriched gene ontology terms and pathways, probable drug targets, two co-expressed modules associated significantly with several clinical features, such as number of positive lymph nodes, Nottingham prognostic index, and tumor stage, and two biologically distinct groups of BRCA patients. Data and source code of the case study can be downloaded at https://github.com/hauldhut/drivergene .
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Ginsenosides are major bioactive compounds present in the
species. Ginsenosides exhibit various pharmaceutical properties, including anticancer, anti-inflammatory, antimetastatic, hypertension, and ...neurodegenerative disorder activities. Although several commercial products have been presented on the market, most of the current chemical processes have an unfriendly environment and a high cost of downstream processing. Compared to plant extraction, microbial production exhibits high efficiency, high selectivity, and saves time for the manufacturing of industrial products. To reach the full potential of the pharmaceutical resource of ginsenoside, a suitable microorganism has been developed as a novel approach. In this review, cell biological mechanisms in anticancer activities and the present state of research on the production of ginsenosides are summarized. Microbial hosts, including native endophytes and engineered microbes, have been used as novel and promising approaches. Furthermore, the present challenges and perspectives of using microbial hosts to produce ginsenosides have been discussed.
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Memetic algorithms (MAs) represent one of the recent growing areas in evolutionary algorithm (EA) research. The term MAs is now widely used as a synergy of evolutionary or any population-based ...approach with separate individual learning or local improvement procedures for problem search. Quite often, MAs are also referred to in the literature as Baldwinian EAs, Lamarckian EAs, cultural algorithms, or genetic local searches. In the last decade, MAs have been demonstrated to converge to high-quality solutions more efficiently than their conventional counterparts on a wide range of real-world problems. Despite the success and surge in interests on MAs, many of the successful MAs reported have been crafted to suit problems in very specific domains. Given the restricted theoretical knowledge available in the field of MAs and the limited progress made on formal MA frameworks, we present a novel probabilistic memetic framework that models MAs as a process involving the decision of embracing the separate actions of evolution or individual learning and analyzing the probability of each process in locating the global optimum. Further, the framework balances evolution and individual learning by governing the learning intensity of each individual according to the theoretical upper bound derived while the search progresses. Theoretical and empirical studies on representative benchmark problems commonly used in the literature are presented to demonstrate the characteristics and efficacies of the probabilistic memetic framework. Further, comparisons to recent state-of-the-art evolutionary algorithms, memetic algorithms, and hybrid evolutionary-local search demonstrate that the proposed framework yields robust and improved search performance.
Computation offloading has emerged as one of the promising approaches to address the issues of restricted resources, leading to poor user experiences on smartphones in terms of battery life and ...performance when executing CPU intensive tasks. Meanwhile, an entire research domain has been initiated around this topic and several concepts have been studied touching both the smartphone and the cloud side. In this paper, we develop a categorization of fundamental aspects regarding computation offloading in heterogeneous cloud computing from the perspective of smartphone applications. We refer to heterogeneity in terms of the multitude of smartphone applications, the various uplink channels, and the variety of cloud solutions. We also survey state-of-the-art solutions for the identified categories. Finally, we conclude with a summary of the most important research challenges in making computation offloading reality.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Phosphor-converted white light-emitting diodes (WLEDs) have received significant attention; however, the leaked light from their blue InGaN chips has an undesirable effect on human health. Hence, it ...is necessary to develop red, green, and blue-emitting phosphors, which can be excited by an NUV chip instead of a blue chip. Herein, green-emitting ZnO:Cu2+ phosphors have been successfully synthesized by a simple and facile thermal diffusion method. The obtained powder shows a broad emission band peaking at 525 nm and a strong absorption peak at 377 nm. The ZnO:5%Cu2+ phosphor annealed at 800 °C in 2 hours revealed a lifetime of 0.57 ms, an activation energy of 0.212 eV, and the highest emission intensity with (x, y) CIE colour coordinates (0.3130, 0.5253). A WLED prototype has been fabricated by coating the ZnO:5%Cu2+ phosphor on an NUV 375 nm LED chip, where this coated phosphor shows a high quantum efficiency (QE) of 56.6%. This is, so far, the highest reported QE value for ZnO-based phosphors. These results suggest that the ZnO:Cu2+ phosphor could be an excellent candidate for NUV-pumped phosphor-converted WLED applications.
Since it was first discovered, thousands of years ago, silkworm silk has been known to be an abundant biopolymer with a vast range of attractive properties. The utilization of silk fibroin (SF), the ...main protein of silkworm silk, has not been limited to the textile industry but has been further extended to various high-tech application areas, including biomaterials for drug delivery systems and tissue engineering. The outstanding mechanical properties of SF, including its facile processability, superior biocompatibility, controllable biodegradation, and versatile functionalization have allowed its use for innovative applications. In this review, we describe the structure, composition, general properties, and structure-properties relationship of SF. In addition, the methods used for the fabrication and modification of various materials are briefly addressed. Lastly, recent applications of SF-based materials for small molecule drug delivery, biological drug delivery, gene therapy, wound healing, and bone regeneration are reviewed and our perspectives on future development of these favorable materials are also shared.
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When it comes to the co-expressed gene module detection, its typical challenges consist of overlap between identified modules and local co-expression in a subset of biological samples. The nature of ...module detection is the use of unsupervised clustering approaches and algorithms. Those methods are advanced undoubtedly, but the selection of a certain clustering method for sample- and gene-clustering tasks is separate, in which the latter task is often more complicated.
This study presented an R-package, Overlapping CoExpressed gene Module (oCEM), armed with the decomposition methods to solve the challenges above. We also developed a novel auxiliary statistical approach to select the optimal number of principal components using a permutation procedure. We showed that oCEM outperformed state-of-the-art techniques in the ability to detect biologically relevant modules additionally.
oCEM helped non-technical users easily perform complicated statistical analyses and then gain robust results. oCEM and its applications, along with example data, were freely provided at https://github.com/huynguyen250896/oCEM .
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Japanese encephalitis (JE) is the major cause of viral encephalitis (VE) in most Asian-Pacific countries. In Vietnam, there is no nationwide surveillance system for JE due to lack of medical ...facilities and diagnoses. Culex tritaeniorhynchus, Culex vishnui, and Culex quinquefasciatus have been identified as the major JE vectors in Vietnam. The main objective of this study was to forecast a risk map of Culex mosquitoes in Hanoi, which is one of the most densely populated cities in Vietnam. A total of 10,775 female adult Culex mosquitoes were collected from 513 trapping locations. We collected temperature and precipitation information during the study period and its preceding month. In addition, the other predictor variables (e.g., normalized difference vegetation index NDVI, land use/land cover and human population density), were collected for our analysis. The final model selected for estimating the Culex mosquito abundance included centered rainfall, quadratic term rainfall, rice cover ratio, forest cover ratio, and human population density variables. The estimated spatial distribution of Culex mosquito abundance ranged from 0 to more than 150 mosquitoes per 900m.sup.2 . Our model estimated that 87% of the Hanoi area had an abundance of mosquitoes from 0 to 50, whereas approximately 1.2% of the area showed more than 100 mosquitoes, which was mostly in the rural/peri-urban districts. Our findings provide better insight into understanding the spatial distribution of Culex mosquitoes and its associated environmental risk factors. Such information can assist local clinicians and public health policymakers to identify potential areas of risk for JE virus. Risk maps can be an efficient way of raising public awareness about the virus and further preventive measures need to be considered in order to prevent outbreaks and onwards transmission of JE virus.
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The paper examines the impact of changes in the exchange rate on Vietnam's trade balance with Japan based on the employment of both aggregate and industry-level data in a set of linear and nonlinear ...autoregressive distributed lag models. The results from the models indicate a degree of bias in regression when using aggregate data and a linear ARDL approach. Among the 19 industries under consideration, the NARDL model presents different responses to exchange rate movements from 16 industries, which account for 46% of imports and 63% of exports between Vietnam and Japan. Using aggregate data, the model shows that the exchange rate positively affects the Vietnam-Japan trade balance in the case of currency depreciation, whereas currency appreciation has no impact on the trade balance. Thus, it is concluded that the exchange rate is an effective tool to stimulate exports and improve the trade balance between Vietnam and Japan.
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Multi-drug resistance to antibiotics represents a growing challenge in treating infectious diseases. Outside the hospital, bacteria with the multi-drug resistance (MDR) phenotype have an increased ...prevalence in anthropized environments, thus implying that chemical stresses, such as metals, hydrocarbons, organic compounds, etc., are the source of such resistance. There is a developing hypothesis regarding the role of metal contamination in terrestrial and aquatic environments as a selective agent in the proliferation of antibiotic resistance caused by the co-selection of antibiotic and metal resistance genes carried by transmissible plasmids and/or associated with transposons. Efflux pumps are also known to be involved in either antibiotic or metal resistance. In order to deal with these situations, microorganisms use an effective strategy that includes a range of expressions based on biochemical and genetic mechanisms. The data from numerous studies suggest that heavy metal contamination could affect the dissemination of antibiotic-resistant genes. Environmental pollution caused by anthropogenic activities could lead to mutagenesis based on the synergy between antibiotic efficacy and the acquired resistance mechanism under stressors. Moreover, the acquired resistance includes plasmid-encoded specific efflux pumps. Soil microbiomes have been reported as reservoirs of resistance genes that are available for exchange with pathogenic bacteria. Importantly, metal-contaminated soil is a selective agent that proliferates antibiotic resistance through efflux pumps. Thus, the use of multi-drug efflux pump inhibitors (EPIs) originating from natural plants or synthetic compounds is a promising approach for restoring the efficacy of existing antibiotics, even though they face a lot of challenges.
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