Variability of fuel consumption and CO2 emissions of a gasoline passenger car under multiple in-laboratory and on-road testing conditions.

An increasing divergence regarding fuel consumption (and/or CO2 emissions) between real-world and type-approval values for light-duty gasoline vehicles (LDGVs) has posed severe challenges to mitigating greenhouse gases (GHGs) and achieving carbon emissions peak and neutrality. To address this divergence issue, laboratory test cycles with more real-featured and transient traffic patterns have been developed recently, for example, the China Light-duty Vehicle Test Cycle for Passenger cars (CLTC-P). We collected fuel consumption and CO2 emissions data of a LDGV under various conditions based on laboratory chassis dynamometer and on-road tests. Laboratory results showed that both standard test cycles and setting methods of road load affected fuel consumption slightly, with variations of less than 4%. Compared to the type-approval value, laboratory and on-road fuel consumption of the tested LDGV over the CLTC-P increased by 9% and 34% under the reference condition (i.e., air conditioning off, automatic stop and start (STT) on and two passengers). On-road measurement results indicated that fuel consumption under the low-speed phase of the CLTC-P increased by 12% due to the STT off, although only a 4% increase on average over the entire cycle. More fuel consumption increases (52%) were attributed to air conditioning usage and full passenger capacity. Strong correlations (R2 > 0.9) between relative fuel consumption and average speed were also identified. Under traffic congestion (average speed below 25 km/hr), fuel consumption was highly sensitive to changes in vehicle speed. Thus, we suggest that real-world driving conditions cannot be ignored when evaluating the fuel economy and GHGs reduction of LDGVs.

Important role of mechanical microenvironment on macrophage dysfunction during keloid pathogenesis.

Keloid is considered as a tumor-like skin disease with multiple aetiologies including immunological factors and mechanical microenvironment. Macrophages are plastic and diverse immune cells that play a critical role in maintaining tissue homeostasis by removing dead cells, debris, pathogens and repairing tissues after inflammation. The imbalance of M1/M2 macrophages and disturbances in macrophage functions can steer the progression of chronic inflammation and lead to the development of pathological fibrosis in keloid disease. Recently, it has been shown that macrophages are sensitive to mechanical signals, especially stretching tension and tissue stiffness, which can determine macrophage polarization and functions. Higher stretching tension is known to be an important pathogenic factor of keloid, and the formation of keloid will lead to an increase in tissue stiffness. As little is known about the underlying reasons of macrophages dysfunction in keloid, an understanding of how the mechanical microenvironment interacting with macrophages and affecting their behaviours may help provide mechanism insights into keloid pathogenesis. We thus hypothesize that the synergistic effect of stretching tension and matrix stiffness may contribute to the major pathophysiological niche attributes of macrophages' in vivo mechanical microenvironment in keloids. These mechanism insights of how macrophages sense and respond to their mechanical microenvironment would propel the development of novel strategies for keloid treatment.

Gleevec and Rapamycin Synergistically Reduce Cell Viability and Inhibit Proliferation and Angiogenic Function of Mouse Bone Marrow-Derived Endothelial Progenitor Cells.

OBJECTIVE: This study investigates the synergistic effects of Gleevec (imatinib) and rapamycin on the proliferative and angiogenic properties of mouse bone marrow-derived endothelial progenitor cells (EPCs). MATERIALS AND METHODS: EPCs were isolated from mouse bone marrow and treated with different concentrations of Gleevec or rapamycin individually or in combination. The cell viability and proliferation were examined using the MTT assay. An analysis of cell cycle and apoptosis was performed using flow cytometry. Formation of capillary-like tubes was examined in vitro, and the protein expression of cell differentiation markers was determined using Western blot analysis. RESULTS: Gleevec significantly reduced cell viability, cell proliferation, and induced cell apoptosis in EPCs. Rapamycin had similar effects on EPCs, but it did not induce cell apoptosis. The combination of Gleevec and rapamycin reduced the cell proliferation but increased cell apoptosis. Although rapamycin had no demonstratable effect on tube formation, the combined therapy of Gleevec and rapamycin significantly reduced tube formation when compared with Gleevec alone. Mechanistically, Gleevec, but not rapamycin, induced a significant elevation in caspase-3 activity in EPCs, and it attenuated the expression of the endothelial protein marker platelet-derived growth factor receptor α. Functionally, rapamycin, but not Gleevec, significantly enhanced the expression of endothelial differentiation marker proteins, while attenuating the expression of mammalian target of rapamycin signaling-related proteins. CONCLUSIONS: Gleevec and rapamycin synergistically suppress cell proliferation and tube formation of EPCs by inducing cell apoptosis and endothelial differentiation. Mechanistically, it is likely that rapamycin enhances the proapoptotic and antiangiogenic effects of Gleevec by promoting the endothelial differentiation of EPCs. Given that EPCs are involved in the pathogenesis of some cardiovascular diseases and critical to angiogenesis, pharmacological inhibition of EPC proliferation by combined Gleevec and rapamycin therapy may be a promising approach for suppressing cardiovascular disease pathologies associated with angiogenesis.

Impaired collagen fibril assembly in keloids with enhanced expression of lumican and collagen V.

Keloids are characterized by fibroblast activation and altered architecture of extracellular matrix (ECM). Excessive deposition of ECM molecules and irregular organization of collagen fibers have been observed in keloids. However, the ultrastructural alteration of collagen has not been fully investigated. In this study, the differences in tissue structure, collagen ultrastructure, matrix components, mechanical properties and collagen assembling molecules between keloids and their extra-lesional skins (ELSs) were explored using histology, transmission electron microscope (TEM), qPCR, Western blot, immunohistochemistry and bioinformatics. Histological evaluation showed thinner fibers in keloids with increased contents of collagen III and proteoglycans, which were supported by TEM findings of thinner collagen fibrils and less developed D-band periodicity in keloids than in ELSs (p < 0.05). In addition, total collagen and water contents were significantly increased (p < 0.05) along with richer proteoglycan production in keloids vs ELSs, which also led to increased stiffness and decreased maximal load in keloids compared with ELSs. Mechanism study showed that multiple molecules related to matrix assembly were significantly upregulated in keloids (p < 0.05). In particular, lumican and collagen V showed high degrees in co-expression analysis and their upregulation levels were revealed from microarray data, which were also verified in keloids at both gene and protein levels (p < 0.05). Nevertheless, siRNA knockdown of lumican failed to affect in vitro collagen assembly, but caused upregulated collagen V expression along with the upregulation of focal adhesion kinase, TGF-ß1, TGF-ß3 and PDGF, among which some are known for capable of enhancing collagen V expression. In conclusion, this study demonstrates impaired collagen assembly along with enhanced expression of lumican and collagen V, both are known for interfering with collagen fibril assembly.

Exogenous application of melatonin to plants, algae, and harvested products to sustain agricultural productivity and enhance nutritional and nutraceutical value: A meta-analysis.

Melatonin is produced by plants, algae, and animals. Worldwide studies show diverse positive effects of exogenous melatonin on plants, edible plant products, and algae, but the potential of melatonin to enhance food and feed systems through these positive effects remains largely unexplored. Through a meta-analysis of about 25,000 observations, we show for the first time that exogenous application of melatonin significantly increases crop productivity and yields, and enhances the nutritional and nutraceutical value of edible plant products and algae by regulating diverse biological functions. We demonstrate that melatonin can improve plants, edible plant products, and algae under various current climate change scenarios, environmental pollution factors, and other stresses by about 7% to nearly 30%, on average, depending on the stressor. We also analyze various technical/methodological factors influencing the desired outcomes and identify conditions that offer optimal enhancement. We show that the positive effect of melatonin on plants and edible plant products varies among species, genera, and families, and strongly depends on the concentration of melatonin and treatment duration. The effect of melatonin is slightly lower on the monocot clade Commelinids than on the eudicot clades Asterids and Rosids. We also show that its stimulatory effect on plants depends on cultivation system, with a larger effect obtained in hydroponic systems. However, it does not depend on application stage (seed or vegetative), application route (foliage, roots, or seed), and whether the cultivation system is ex vivo or in vivo. This is the first meta-analysis examining the effects of melatonin on plants, edible plant products, and algae, and offers a scientific and technical roadmap facilitating sustainable food and feed production through the application of exogenous melatonin.

Nintedanib inhibits keloid fibroblast functions by blocking the phosphorylation of multiple kinases and enhancing receptor internalization.

Keloid is a benign skin tumor characterized by its cell hyperproliferative activity, invasion into normal skin, uncontrolled growth, overproduction and deposition of extracellular matrices and high recurrence rate after various therapies. Nintedanib is a receptor tyrosine kinase inhibitor targeting VEGF, PDGF, FGF, and TGF-ß receptors with proved efficacy in anti-angiogenesis and in treating various types of cancers. In this study, we investigated the effects of nintedanib on keloid fibroblasts in both in vitro and ex vivo models. Keloid fibroblasts were prepared from 54 keloid scar samples in active stages collected from 49 patients. We found that nintedanib (1-4 µM) dose-dependently suppressed cell proliferation, induced G0/G1 cell cycle arrest, and inhibited migration and invasion of keloid fibroblasts. The drug also significantly inhibited the gene and protein expression of collagen I (COL-1) and III (COL-3), fibronectin (FN), and connective growth factor (CTGF), as well as the gene expression of other pathological factors, such as alpha smooth muscle actin (α-SMA), plasminogen activator inhibitor-1 (PAI-1), FK506-binding protein 10 (FKBP10), and heat shock protein 47 (HSP47) in keloid fibroblasts. Furthermore, nintedanib treatment significantly suppressed the phosphorylation of p38, JNK, ERK, STAT3, and Smad, enhanced endocytosis of various growth factor receptors. Using an ex vivo tissue explant model, we showed that nintedanib significantly suppressed cell proliferation, migration, and collagen production. The drug also significantly disrupted microvessel structure ex vivo. In summary, our results demonstrate that nintedanib is likely to become a potential targeted drug for keloid systemic therapy.

[Effects of stereoscopic cultivation on photosynthetic characteristics and growth of Tulipa edulis].

The effect of stereoscopic cultivation on the growth, photosynthetic characteristics and yield of Tulipa edulis was studied to explore the feasibility of stereoscopic cultivation on efficient cultivation of T.edulis. Total leaf area and photosynthetic parameters of T.edulis under stereoscopic cultivation (the upper, middle and the lower layers ) and the control were measured using LI-3100 leaf area meter and LI-6400XT photosynthesis system in the growing peak period of T.edulis.Plant biomass and biomass allocation were also determined.In addition, the bulb regeneration and yield of T.edulis were measured in the harvesting time.The results indicated that in the middle layer of stereoscopic cultivation, leaf biomass proportion was the highest, but total bulb fresh and dry weight and output growth (fresh weight) were the lowest among the treatments.And total bulb fresh weight in the middle of stereoscopic cultivation reduced significantly, by 22.84%, compared with the control.Light intensity in the lower layer of stereoscopic cultivation was moderate, in which T.edulis net photosynthetic rate and water use efficiency were higher than those of the other layers of stereoscopic cultivation, and bulb biomass proportion was the highest in all the treatments.No significant difference was detected in the total bulb fresh weight, dry weight and output growth (fresh weight) between the middle layer of stereoscopic cultivation and the control.In general, there was no significant difference in the growth status of T.edulis between stereoscopic cultivation and the control.Stereoscopic cultivation increased the yield of T.edulis by 161.66% in fresh weight and 141.35% in dry weight compared with the control in the condition of the same land area, respectively.In conclusion, stereoscopic cultivation can improve space utilization, increase the production, and achieve the high density cultivation of T.edulis.

Mechanical loading on cell-free polymer composite scaffold enhances in situ regeneration of fully functional Achilles tendon in a rabbit model.

Traditional tendon engineering using cell-loaded scaffold has limited application potential due to the need of autologous cells. We hypothesize that potent mechanical loading can efficiently induce in situ Achilles tendon regeneration in a rabbit model by using a cell-free porous composite scaffold. In this study, melt-spinning was used to fabricate PGA (polyglycolic acid) and PLA (polylactic acid) filament fibers as well as non-woven PGA fibers. The PLA/PGA (4:2) filament fibers were further braided into a hybrid yarn，which was knitted into a PLA/PGA tubular mesh with potent mechanical property for sustaining natural tendon strain. The results showed that a complete cross-section of Achilles tendon created a model of full mechanical loading on the bridging scaffold, which could efficiently induce in situ tendon regeneration by promoting host cell infiltration, matrix production and tissue remodeling. Histologically, mechanical loading assisted in forming parallel aligned collagen fibers and tenocytes in a fashion similar to those of native tendon. Transmission electron microscope further demonstrated that mechanical strain induced collagen fibril development by increasing fibril diameter and forming bipolar structure, which resulted in enhanced mechanical properties. Interestingly, the synergistic effect between mechanical loading and hyaluronic acid modification was also observed on the induced tenogenic differentiation of infiltrated host fibroblasts. In conclusion, potent mechanical loading is the key inductive microenvironment for in situ tendon regeneration for this polymer-based composite scaffold with proper matrix modification, which may serve as a universal scaffold product for tendon regeneration.

Step-wise CAG@PLys@PDA-Cu2+ modification on micropatterned nanofibers for programmed endothelial healing.

Native-like endothelium regeneration is a prerequisite for material-guided small-diameter vascular regeneration. In this study, a novel strategy is proposed to achieve phase-adjusted endothelial healing by step-wise modification of parallel-microgroove-patterned (i.e., micropatterned) nanofibers with polydopamine-copper ion (PDA-Cu2+) complexes, polylysine (PLys) molecules, and Cys-Ala-Gly (CAG) peptides (CAG@PLys@PDA-Cu2+). Using electrospun poly(l-lactide-co-caprolactone) random nanofibers as the demonstrating biomaterial, step-wise modification of CAG@PLys@PDA-Cu2+ significantly enhanced substrate wettability and protein adsorption, exhibited an excellent antithrombotic surface and outstanding phase-adjusted capacity of endothelium regeneration involving cell adhesion, endothelial monolayer formation, and the regenerated endothelium maturation. Upon in vivo implantation for segmental replacement of rabbit carotid arteries, CAG@PLys@PDA-Cu2+ modified grafts (2 mm inner diameter) with micropatterns on inner surface effectively accelerated native-like endothelium regeneration within 1 week, with less platelet aggregates and inflammatory response compared to those on non-modified grafts. Prolonged observations at 6- and 12-weeks post-implantation demonstrated a positive vascular remodeling with almost fully covered endothelium and mature smooth muscle layer in the modified vascular grafts, accompanied with well-organized extracellular matrix. By contrast, non-modified vascular grafts induced a disorganized tissue formation with a high risk of thrombogenesis. In summary, step-wise modification of CAG@PLys@PDA-Cu2+ on micropatterned nanofibers can significantly promote endothelial healing without inflicting thrombosis, thus confirming a novel strategy for developing functional vascular grafts or other blood-contacting materials/devices.

Type I collagen and fibromodulin enhance the tenogenic phenotype of hASCs and their potential for tendon regeneration.

Our previous work demonstrated the tendon-derived extracellular matrix (ECM) extracts as vital niches to specifically direct mesenchymal stem cells towards tenogenic differentiation. This study aims to further define the effective ECM molecules capable of teno-lineage induction on human adipose-derived stem cells (hASCs) and test their function for tendon engineering. By detecting the teno-markers expression levels in hASCs exposed to various substrate coatings, collagen I (COL1) and fibromodulin (FMOD) were identified to be the key molecules as a combination and further employed to the modification of poly(L-lactide-co-ε-caprolactone) electrospun nanoyarns, which showed advantages in inducting seeded hASCs for teno-lineage specific differentiation. Under dynamic mechanical loading, modified scaffold seeded with hASCs formed neo-tendon in vitro at the histological level and formed better tendon tissue in vivo with mature histology and enhanced mechanical properties. Primary mechanistic investigation with RNA sequencing demonstrated that the inductive mechanism of these two molecules for hASCs tenogenic differentiation was directly correlated with positive regulation of peptidase activity, regulation of cell-substrate adhesion and regulation of cytoskeletal organization. These biological processes were potentially affected by LOC101929398/has-miR-197-3p/TENM4 ceRNA regulation axis. In summary, COL1 and FMOD in combination are the major bioactive molecules in tendon ECM for likely directing tenogenic phenotype of hASCs and certainly valuable for hASCs-based tendon engineering.

Hormesis Research in China Is More Prevalent than Previously Thought.

An analysis of China's domestic publications revealed that China's hormesis-related research was enormously underestimated. China's documented hormesis-related research spans at least four decades, covers a broad spectrum of research areas, and is more abundant than previously thought. These findings should be considered in historical assessments of the concept of hormesis. Moreover, similar to the international literature, different terms have been used to describe the same phenomenon (hormesis), which hampers communication, generalization of findings and accumulation of knowledge. Hence, we advocate that 'hormesis' should be cited as a keyword in all the relevant publications written in Chinese language.

Synergistic effects of mechanical stimulation and crimped topography to stimulate natural collagen development for tendon engineering.

Suitable scaffold structures and mechanical loading are essential for functional tendon engineering. However, the bipolar fibril structure of native tendon collagen is yet to be recaptured in engineered tendons. This study compared the development of Achilles tendons of postnatal rats with and without (via surgical section) mechanical loading to define the mechanism of mechanical stimulation-mediated tendon development. The results demonstrated that the severed tendons weakened mechanically and exhibited disorganization without a bipolar fibril superstructure. Proteomic analysis revealed differentially expressed key regulatory molecules related to the collagen assembly process, including decreased fibromodulin, keratocan, fibroblast growth factor-1, and increased lumican and collagen5a1 in the severed tendons with immunohistochemical verification. Additionally, a complex regulatory network of mechanical stimulation-mediated collagen assembly in a spatiotemporal manner was also revealed using bioinformatics analysis, wherein PI3K-Akt and HDAC4 may be the predominant signaling pathways. A wavy microgrooved surface (Y = 5.47sin(0.015x)) that biomimics tendon topography was observed to enhance the expression of collagen assembly molecules under mechanical loading, and the aforementioned pathways are particularly involved and verified with their respective inhibitors of LY-294002 and LMK-235. Furthermore, an electrospun crimped nanofiber scaffold (approximately 2 µm fiber diameter and 0.12 crimpness) was fabricated to biomimic the tenogenic niche environment; this was observed to be more effective on enhancing collagen production and assembly under mechanical stimulation. In conclusion, the synergistic effect between topographical niche and mechanical stimulation was observed to be essential for collagen assembly and maturation and should be applied to functional tendon engineering in the future. STATEMENT OF SIGNIFICANCE: In biomaterial-mediated tendon regeneration, mechanical stimulation is essential for tendon collagen assembly. However, the underlying mechanisms remain not fully defined, leading to the failure of the native-like collagen regeneration. In this study, a mechanical stimulation deprivation model of rat tendon was established to reveal the mechanisms in tendon development and define the key regulatory molecules including small leucine-rich proteoglycans, lysyl oxidase and collagen V. After ensuring the importance of biomimetic structure in tendon remodeling, crimped nanofibers were developed to verify these regulatory molecules, and demonstrated that mechanical stimulation significantly enhanced collagen assembly via PIK3 and HDAC4 pathways in biomaterial-regulated tendon regeneration. This study provides more insightful perspectives in the physiologically remodeling progression of tendon collagen and design of tendon scaffolds.

Mechanisms of cerium-induced stress in plants: A meta-analysis.

A comprehensive evaluation of the effects of cerium on plants is lacking even though cerium is extensively applied to the environment. Here, the effects of cerium on plants were meta-analyzed using a newly developed database consisting of approximately 8500 entries of published data. Cerium affects plants by acting as oxidative stressor causing hormesis, with positive effects at low concentrations and adverse effects at high doses. Production of reactive oxygen species and its linked induction of antioxidant enzymes (e.g. catalase and superoxide dismutase) and non-enzymatic antioxidants (e.g. glutathione) are major mechanisms driving plant response mechanisms. Cerium also affects redox signaling, as indicated by altered GSH/GSSG redox pair, and electrolyte leakage, Ca2+, K+, and K+/Na+, indicating an important role of K+ and Na+ homeostasis in cerium-induced stress and altered mineral (ion) balance. The responses of the plants to cerium are further extended to photosynthesis rate (A), stomatal conductance (gs), photosynthetic efficiency of PSII, electron transport rate, and quantum yield of PSII. However, photosynthesis response is regulated not only by physiological controls (e.g. gs), but also by biochemical controls, such as via changed Hill reaction and RuBisCO carboxylation. Cerium concentrations <0.1-25 mg L-1 commonly enhance chlorophyll a and b, gs, A, and plant biomass, whereas concentrations >50 mg L-1 suppress such fitness-critical traits at trait-specific concentrations. There was no evidence that cerium enhances yields. Observations were lacking for yield response to low concentrations of cerium, whereas concentrations >50 mg Kg-1 suppress yields, in line with the response of chlorophyll a and b. Cerium affects the uptake and tissue concentrations of several micro- and macro-nutrients, including heavy metals. This study enlightens the understanding of some mechanisms underlying plant responses to cerium and provides critical information that can pave the way to reducing the cerium load in the environment and its associated ecological and human health risks.

A Systematic Review of the Efficacy and Safety of Aspirin When Delivered at Different Medication Times for the Primary and Secondary Prevention of Cardiovascular and Cerebrovascular Diseases.

PURPOSE: Effective antiplatelet therapy can significantly reduce the incidence and mortality rate of cardiovascular and cerebrovascular diseases. Aspirin is widely used in the secondary prevention of cardiovascular and cerebrovascular diseases; however, there is widespread debate as to when patients should take an enteric-coated aspirin tablet on a daily basis. In the present study, we evaluated the efficacy and safety of different aspirin medication times (morning or before bedtime) in terms of the primary and secondary prevention of cardiovascular and cerebrovascular diseases using meta-analysis. METHODS: Studies with randomized control trials (RCT) or crossover trials regarding to the usage of aspirin (morning or before bedtime) for the primary or secondary prevention of cardiovascular and cerebrovascular diseases were searched in Medline, EMbase, Cochrane Library, CNKI, Wanfang Data, VIP Database and CBM. Review Manager 5 (RevMan 5, v5.3), a Cochrane systematic reviews software, was used to perform meta-analysis based on the recommendation of the Cochrane Handbook for risk assessment tools. RESULTS: Meta-analysis showed that taking low-dose aspirin tablets before bed reduced systolic and diastolic blood pressure compared with taking it in the morning. At the same time, the number of studies on platelet aggregation rate, C-reactive protein (CRP), serum nitric oxide (NO) or thromboxane B2 (TXB2) is too small to be reliable. However, there was a large heterogeneity across the studies. The quality of some studies was not high enough. CONCLUSION: Additional blood pressure benefits can be achieved by taking aspirin before bedtime, but it does not affect its antiplatelet effect and does not pose a higher risk of bleeding.

Uncovering the Complexity Mechanism of Different Formulas Treatment for Rheumatoid Arthritis Based on a Novel Network Pharmacology Model.

Traditional Chinese medicine (TCM) with the characteristics of "multi-component-multi-target-multi-pathway" has obvious advantages in the prevention and treatment of complex diseases, especially in the aspects of "treating the same disease with different treatments". However, there are still some problems such as unclear substance basis and molecular mechanism of the effectiveness of formula. Network pharmacology is a new strategy based on system biology and poly-pharmacology, which could observe the intervention of drugs on disease networks at systematical and comprehensive level, and especially suitable for study of complex TCM systems. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease, causing articular and extra articular dysfunctions among patients, it could lead to irreversible joint damage or disability if left untreated. TCM formulas, Danggui-Sini-decoction (DSD), Guizhi-Fuzi-decoction (GFD), and Huangqi-Guizhi-Wuwu-Decoction (HGWD), et al., have been found successful in controlling RA in clinical applications. Here, a network pharmacology-based approach was established. With this model, key gene network motif with significant (KNMS) of three formulas were predicted, and the molecular mechanism of different formula in the treatment of rheumatoid arthritis (RA) was inferred based on these KNMSs. The results show that the KNMSs predicted by the model kept a high consistency with the corresponding C-T network in coverage of RA pathogenic genes, coverage of functional pathways and cumulative contribution of key nodes, which confirmed the reliability and accuracy of our proposed KNMS prediction strategy. All validated KNMSs of each RA therapy-related formula were employed to decode the mechanisms of different formulas treat the same disease. Finally, the key components in KNMSs of each formula were evaluated by in vitro experiments. Our proposed KNMS prediction and validation strategy provides methodological reference for interpreting the optimization of core components group and inference of molecular mechanism of formula in the treatment of complex diseases in TCM.

A Novel Network Pharmacology Strategy to Decode Mechanism of Lang Chuang Wan in Treating Systemic Lupus Erythematosus.

Complex disease is a cascade process which is associated with functional abnormalities in multiple proteins and protein-protein interaction (PPI) networks. One drug one target has not been able to perfectly intervene complex diseases. Increasing evidences show that Chinese herb formula usually treats complex diseases in the form of multi-components and multi-targets. The key step to elucidate the underlying mechanism of formula in traditional Chinese medicine (TCM) is to optimize and capture the important components in the formula. At present, there are several formula optimization models based on network pharmacology has been proposed. Most of these models focus on the 2D/3D similarity of chemical structure of drug components and ignore the functional optimization space based on relationship between pathogenetic genes and drug targets. How to select the key group of effective components (KGEC) from the formula of TCM based on the optimal space which link pathogenic genes and drug targets is a bottleneck problem in network pharmacology. To address this issue, we designed a novel network pharmacological model, which takes Lang Chuang Wan (LCW) treatment of systemic lupus erythematosus (SLE) as the case. We used the weighted gene regulatory network and active components targets network to construct disease-targets-components network, after filtering through the network attribute degree, the optimization space and effective proteins were obtained. And then the KGEC was selected by using contribution index (CI) model based on knapsack algorithm. The results show that the enriched pathways of effective proteins we selected can cover 96% of the pathogenetic genes enriched pathways. After reverse analysis of effective proteins and optimization with CI index model, KGEC with 82 components were obtained, and 105 enriched pathways of KGEC targets were consistent with enriched pathways of pathogenic genes (80.15%). Finally, the key components in KGEC of LCW were evaluated by in vitro experiments. These results indicate that the proposed model with good accuracy in screening the KGEC in the formula of TCM, which provides reference for the optimization and mechanism analysis of the formula in TCM.

Identification of Cooperative Gene Regulation Among Transcription Factors, LncRNAs, and MicroRNAs in Diabetic Nephropathy Progression.

The pathogenesis of diabetic nephropathy (DN) is accompanied by alterations in biological function and signaling pathways regulated through complex molecular mechanisms. A number of regulatory factors, including transcription factors (TFs) and non-coding RNAs (ncRNAs, including lncRNAs and miRNAs), have been implicated in DN; however, it is unclear how the interactions among these regulatory factors contribute to the development of DN pathogenesis. In this study, we developed a network-based analysis to decipher interplays between TFs and ncRNAs regulating progression of DN by combining omics data with regulatory factor-target information. To accomplish this, we identified differential expression programs of mRNAs and miRNAs during early DN (EDN) and established DN. We then uncovered putative interactive connections among miRNA-mRNA, lncRNA-miRNA, and lncRNA-mRNA implicated in transcriptional control. This led to the identification of two lncRNAs (MALAT1 and NEAT1) and the three TFs (NF-κB, NFE2L2, and PPARG) that likely cooperate with a set of miRNAs to modulate EDN and DN target genes. The results highlight how crosstalk among TFs, lncRNAs, and miRNAs regulate the expression of genes both transcriptionally and post-transcriptionally, and our findings provide new insights into the molecular basis and pathogenesis of progressive DN.