Abstract
Motivation
The Cancer Genome Atlas (TCGA) program has produced huge amounts of cancer genomics data providing unprecedented opportunities for research. In 2014, we developed TCGA-Assembler, ...a software pipeline for retrieval and processing of public TCGA data. In 2016, TCGA data were transferred from the TCGA data portal to the Genomic Data Commons (GDCs), which is supported by a different set of data storage and retrieval mechanisms. In addition, new proteomics data of TCGA samples have been generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, which were not available for downloading through TCGA-Assembler. It is desirable to acquire and integrate data from both GDC and CPTAC.
Results
We develop TCGA-assembler 2 (TA2) to automatically download and integrate data from GDC and CPTAC. We make substantial improvement on the functionality of TA2 to enhance user experience and software performance. TA2 together with its previous version have helped more than 2000 researchers from 64 countries to access and utilize TCGA and CPTAC data in their research. Availability of TA2 will continue to allow existing and new users to conduct reproducible research based on TCGA and CPTAC data.
Availability and implementation
http://www.compgenome.org/TCGA-Assembler/ or https://github.com/compgenome365/TCGA-Assembler-2
Supplementary information
Supplementary data are available at Bioinformatics online.
Parameter estimation of photovoltaic (PV) models from experimental current versus voltage (I-V) characteristic curves acts a pivotal part in the modeling a PV system and optimizing its performance. ...Although many methods have been proposed for solving this PV model parameter estimation problem, it is still challenging to determine highly accurate and reliable solutions. In this paper, this problem is firstly transformed into an optimization problem, and an objective function (OF) is formulated to quantify the overall difference between the experimental and simulated current data. And then, to enhance the performance of original cuckoo search algorithm (CSA), a novel improved cuckoo search algorithm (ImCSA) is proposed, by combining three strategies with CSA. In ImCSA, a quasi-opposition based learning (QOBL) scheme is employed in the population initialization step of CSA. Moreover, a dynamic adaptation strategy is developed and introduced for the step size without Lévy flight step in original CSA. A dynamic adjustment mechanism for the fraction probability (Pa) is proposed to achieve better tradeoff between the exploration and exploitation to increase searching ability. Afterwards, the proposed ImCSA is used for solving the problem of estimating parameters of PV models based on experimental I-V data. Finally, the proposed ImCSA has been demonstrated on the parameter identification of various PV models, i.e., single diode model (SDM), double diode model (DDM) and PV module model (PMM). Experimental results indicate that the proposed ImCSA outperforms the original CSA and its superior performance in comparison with other state-of-the-art algorithms, and they also show that our proposed ImCSA is capable of finding the best values of parameters for the PV models in such effective way for giving the best possible approximation to the experimental I-V data of real PV cells and modules. Therefore, the proposed ImCSA can be considered as a promising alternative to accurately and reliably estimate parameters of PV models.
The prevalence of metabolic diseases, including obesity, dyslipidemia, type 2 diabetes mellitus (T2DM), and non-alcoholic fatty liver disease (NAFLD), is a severe burden in human society owing to the ...ensuing high morbidity and mortality. Various factors linked to metabolic disorders, particularly environmental factors (such as diet and gut microbiota) and epigenetic modifications, contribute to the progression of metabolic diseases. Dietary components and habits regulate alterations in gut microbiota; in turn, microbiota-derived metabolites, such as short-chain fatty acids (SCFAs), are influenced by diet. Interestingly, diet-derived microbial metabolites appear to produce substrates and enzymatic regulators for epigenetic modifications (such as DNA methylation, histone modifications, and non-coding RNA expression). Epigenetic changes mediated by microbial metabolites participate in metabolic disorders via alterations in intestinal permeability, immune responses, inflammatory reactions, and insulin resistance. In addition, microbial metabolites can trigger inflammatory immune responses and microbiota dysbiosis by directly binding to G-protein-coupled receptors (GPCRs). Hence, diet-gut microbiota-epigenetics may play a role in metabolic diseases. However, their complex relationships with metabolic diseases remain largely unknown and require further investigation. This review aimed to elaborate on the interactions among diet, gut microbiota, and epigenetics to uncover the mechanisms and therapeutics of metabolic diseases.
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•Diet-gut microbiota-epigenetics: a mechanism of metabolic diseases.•Gut microbiota is influenced by diet and epigenetics•Therapeutics targeting diets, gut microbiota dysbiosis and epigenetic.
With the rapid development of industrial internet of thing (IIoT), the distributed topology of IIoT and resource constraints of edge computing conduct new challenges to traditional data storage, ...transmission, and security protection. A distributed trust and allocated ledger of blockchain technology are suitable for the distributed IIoT, which also becomes an effective method for edge computing applications. This paper proposes a resource constrained Layered Lightweight Blockchain Framework (LLBF) and implementation mechanism. The framework consists of a resource constrained layer (RCL) and a resource extended layer (REL) blockchain used in IIoT. We redesign the block structure and size to suit to IIoT edge computing devices. A lightweight consensus algorithm and a dynamic trust right algorithm is developed to improve the throughput of blockchain and reduce the number of transactions validated in new blocks respectively. Through a high throughput management to guarantee the transaction load balance of blockchain. Finally, we conducted kinds of blockchain simulation and performance experiments, the outcome indicated that the method have a good performance in IIoT edge application.
Cardiovascular disease (CVD) is the leading cause of death worldwide, especially in developed countries, and atherosclerosis (AS) is the common pathological basis of many cardiovascular diseases ...(CVDs) such as coronary heart disease (CHD). The role of the gut microbiota in AS has begun to be appreciated in recent years. Trimethylamine N-oxide (TMAO), an important gut microbe-dependent metabolite, is generated from dietary choline, betaine, and L-carnitine. Multiple studies have suggested a correlation between plasma TMAO levels and the risk of AS. However, the mechanism underlying this relationship is still unclear. In this review, we discuss the TMAO-involved mechanisms of atherosclerotic CVD from the perspective of inflammation, inflammation-related immunity, cholesterol metabolism, and atherothrombosis. We also summarize available clinical studies on the role of TMAO in predicting prognostic outcomes, including major adverse cardiovascular events (MACE), in patients presenting with AS. Finally, since TMAO may be a novel therapeutic target for AS, several therapeutic strategies including drugs, dietary, etc. to lower TMAO levels that are currently being explored are also discussed.
Atherosclerosis and its associated cardiovascular diseases (CVDs) are serious threats to human health and have been reported to be associated with the gut microbiota. Recently, the role of berberine ...(BBR) in atherosclerosis and gut microbiota has begun to be appreciated. The purposes of this study were to observe the effects of high or low doses of BBR on atherosclerosis and gut microbiota modulation, and to explore their correlation in ApoE
mice fed a high-fat diet. A significant decrease in atherosclerotic lesions was observed after treatment with BBR, with the effect of the high dose being more obvious. Both BBR treatments significantly reduced total cholesterol, APOB100, and very low-density lipoprotein cholesterol levels but levels of high/low-density lipoprotein cholesterol and lipoprotein (a) were only reduced by high-dose BBR. Decreased pro-inflammatory cytokines tumor necrosis factor-alpha, interleukin (IL)-1β, IL-6 and increased anti-inflammatory IL-10 and adiponectin levels were observed in the high-dose BBR group, but no decrease in IL-6 or increase in IL-10 was evident using the low-dose of BBR. 16S rRNA sequencing showed that BBR significantly altered the community compositional structure of gut microbiota. Specifically, BBR enriched the abundance of
,
,
,
, and
, and changed the abundance of
. These microbiota displayed good anti-inflammatory effects related to the production of short-chain fatty acids (SCFAs) and were related to glucolipid metabolism.
and
were significantly enriched in high-dose BBR group while
and
were more enriched in low-dose, and
was enriched in both BBR doses. Metagenomic analysis further showed an elevated potential for lipid and glycan metabolism and synthesis of SCFAs, as well as reduced potential of TMAO production after BBR treatment. The findings demonstrate that both high and low-dose BBR can improve serum lipid and systemic inflammation levels, and alleviate atherosclerosis induced by high-fat diet in ApoE
mice. The effects are more pronounced for the high dose. This anti-atherosclerotic effect of BBR may be partly attributed to changes in composition and functions of gut microbiota which may be associated with anti-inflammatory and metabolism of glucose and lipid. Notably, gut microbiota alterations showed different sensitivity to BBR dose.
The BSS (battery swapping station) is a newly proposed mode of supplying power to the EV (electric vehicle). Different from the BCS (battery charging station), the BSS prepares the batteries for EVs ...in advance and could complete the battery swapping in a short time. The operations designed for the BCS are not appropriate for BSS anymore and the researches about BSS are at the early stage. In this paper, we propose a dynamic operation model of BSS in electricity market. The new model is based on the short-term battery management and includes the mathematical formulation and market strategy. We have tested the model in a 24-hour simulation. The result shows clearly that the BSS makes decisions in market environment through tracing the number of batteries in different kinds of states and acquires additional revenue by responding actively to the price fluctuation in electricity market. The feasibility and the practicability of the model are confirmed.
Purpose TRIMP and sRPE are both representative indicators of training load(TL), and the correlation between two has been widely demonstrated across various sports. The aim of this study was to ...investigate the reliability of sRPE-TRIMP correlation across different intensities/duration of training in cross-country skiing, and whether sRPE can serve as an validity supplement to TRIMP data in cases of lost heart rate data. Method 10 athletes were used as the experimental objects. The intensity, duration and RPE of 273 different types of training sessions were collected, and statistical methods were used for data analysis. Results 1. There was a significant correlation between sRPE and TRIMP ( r = 0.68, p < 0.05), but the correlation differs among the LIT, MIT and HIT groups ( r = 0.70, 0.46, r = 0.31, p < 0.05) 2. sRPE-TRIMP correlation among three different time duration in the LIT group (0-60 min, 60-120 min and 120-180 min), are all highly significant ( r = 0.70, 0.67, 0.69, p < 0.05) and the LRsRPE-TRIMP of 3 duration have no significant differences (chow test, p > 0.05). 3. The difference in actual training duration between samples was the main reason for the difference in the application effect of sRPE, because the actual training duration ratio of LIT was 89.7 ± 16.4%; MIT, 98.5 ± 6.2%; and HIT, 94.4 ± 13.5%. Conclusion 1. The linear relationship between sRPE and TRIMP (LRsRPE-TRIMP) is more significant in LIT compared to that in MIT and HIT. 2. Variations in the duration of LIT sessions do not affect the consistency of the relationship between sRPE and TRIMP. 3. Discrepancies between actual and planned training durations directly impact the significance of the LRsRPE-TRIMP.
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•Polydatin is a monocrystal-line compound purified from Polygonum cuspidatum.•Polydatin has effects on multiple systems, especially the cardiovascular system.•Polydatin treats AS ...mainly from anti-inflammatory, and anti-oxidative stress.•Polydatin can act in the entire process of reverse cholesterol transport.•This review also covers the toxicology and pharmacokinetics of polydatin.
With the advancement of science and technology, the living standards of human beings have continuously improved, but the incidence and mortality from atherosclerosis worldwide have also increased by year. Although interventional surgery and the continuous development of new drugs have significant therapeutic effects, their side effects cannot be ignored. Polydatin, an active ingredient isolated from the natural medicine Polygonum cuspidatum, has been shown to have a prominent role in the treatment of cardiovascular diseases. Polydatin treats atherosclerosis mainly from three aspects: anti-inflammatory, regulating lipid metabolism and anti-oxidative stress. This article will review the pharmacological mechanism of polydatin in anti-atherosclerosis, the biological characteristics of Polygonum cuspidatum, the toxicology and pharmacokinetics of polydatin and will provide ideas for further research.
Atherosclerosis (AS), especially atherosclerotic cardiovascular diseases (ASCVDs), and metabolic diseases (such as diabetes, obesity, dyslipidemia, and nonalcoholic fatty liver disease) are major ...public health issues worldwide that seriously threaten human health. Exploring effective natural product-based drugs is a promising strategy for the treatment of AS and metabolic diseases. Berberine (BBR), an important isoquinoline alkaloid found in various medicinal plants, has been shown to have multiple pharmacological effects and therapeutic applications. In view of its low bioavailability, increasing evidence indicates that the gut microbiota may serve as a target for the multifunctional effects of BBR. Under the pathological conditions of AS and metabolic diseases, BBR improves intestinal barrier function and reduces inflammation induced by gut microbiota-derived lipopolysaccharide (LPS). Moreover, BBR reverses or induces structural and compositional alterations in the gut microbiota and regulates gut microbe-dependent metabolites as well as related downstream pathways; this improves glucose and lipid metabolism and energy homeostasis. These findings at least partly explain the effect of BBR on AS and metabolic diseases. In this review, we elaborate on the research progress of BBR and its mechanisms of action in the treatment of AS and metabolic diseases from the perspective of gut microbiota, to reveal the potential contribution of gut microbiota to the multifunctional biological effects of BBR.
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