Prioritization of cancer driver gene with prize-collecting steiner tree by introducing an edge weighted strategy in the personalized gene interaction network.

BACKGROUND: Cancer is a heterogeneous disease in which tumor genes cooperate as well as adapt and evolve to the changing conditions for individual patients. It is a meaningful task to discover the personalized cancer driver genes that can provide diagnosis and target drug for individual patients. However, most of existing methods mainly ranks potential personalized cancer driver genes by considering the patient-specific nodes information on the gene/protein interaction network. These methods ignore the personalized edge weight information in gene interaction network, leading to false positive results. RESULTS: In this work, we presented a novel algorithm (called PDGPCS) to predict the Personalized cancer Driver Genes based on the Prize-Collecting Steiner tree model by considering the personalized edge weight information. PDGPCS first constructs the personalized weighted gene interaction network by integrating the personalized gene expression data and prior known gene/protein interaction network knowledge. Then the gene mutation data and pathway data are integrated to quantify the impact of each mutant gene on every dysregulated pathway with the prize-collecting Steiner tree model. Finally, according to the mutant gene's aggregated impact score on all dysregulated pathways, the mutant genes are ranked for prioritizing the personalized cancer driver genes. Experimental results on four TCGA cancer datasets show that PDGPCS has better performance than other personalized driver gene prediction methods. In addition, we verified that the personalized edge weight of gene interaction network can improve the prediction performance. CONCLUSIONS: PDGPCS can more accurately identify the personalized driver genes and takes a step further toward personalized medicine and treatment. The source code of PDGPCS can be freely downloaded from https://github.com/NWPU-903PR/PDGPCS .

Sesquiterpenoids and furan derivatives from the Orychophragmus violaceus (L.) O.E. Schulz endophytic fungus Irpex lacteus OV38.

Nine undescribed compounds, including six tremulane-type sesquiterpenoids, irpexolaceus A-F, one phenolic bisabolane-type sesquiterpenoid, irpexolaceus G, and two furan derivatives, irpexonjust A-B, as well as eight known analogs, were isolated from an endophytic fungus (Irpex lacteus OV38) of Orychophragmus violaceus (L.) O.E. Schulz, a Chinese medicinal and edible plant. The structures of these natural compounds were elucidated based on NMR, HRESIMS, single-crystal X-ray diffraction, and ECD spectroscopic data. Among the tested isolates (50 µg/mL), the inhibitory effects of irpexolaceus A, C, D, F, and G, irpexonjust B, and irpexlacte B against NO release from LPS-induced RAW 264.7 cells were higher than 45%, while irpexlacte C (42.6%), irpexolaceus B (39.6%), irpexonjust A (43.7%), and irpexolaceus E (33.6%) exhibited weaker inhibitory effects on the release of NO.

Selenium Attenuates S. aureus-Induced Inflammation by Regulation TLR2 Signaling Pathway and NLRP3 Inflammasome in RAW 264.7 Macrophages.

This study aimed to investigate the effects of selenium (Se) on the expression of Toll-like receptor (TLR) 2 and pyrin domain-containing protein (NLRP)3 inflammasome in macrophages infected by Staphylococcus aureus (S. aureus). RAW 264.7 macrophages were treated with 2 µmol/L Na2SeO3 for 12 h before infection with S. aureus for 2 h. Through Western blot, qRT-PCR, and ELISA analysis, the core molecules of TLR2 signaling pathway and NLRP3 inflammasome in RAW 264.7 macrophages were detected. Results showed that Se significantly reduced the elevated mRNA expression of TLR2, myeloid differentiation factor-88 (Myd88), NLRP3, Caspase-recruitment domain (ASC), and Caspase-1 induced by S. aureus. Furthermore, compared with I group, the protein expression of TLR2, Myd88, NLRP3, ASC, and Caspase-1 were suppressed in T group. In addition, the mRNA and protein expression of interleukin-1 beta (IL-1ß) induced by S. aureus were also decreased after Se treatment. In conclusion, Se inhibits S. aureus-induced inflammation by suppressing the activation of the TLR2 signaling pathway and NLRP3 inflammasome in RAW 264.7 macrophages.

Short Communication: Effects of Dietary Selenium Supplementation on Selenium Deposition and Antioxidant Status in Postpartum Mice.

This study aimed to investigate the effects of dietary selenium during pregnancy on the selenium deposition and antioxidant enzymes in postpartum mouse serum, liver, and mammary gland. Eighty BALB/c pregnant mice were randomly divided into four groups: CG (Se-deficient basal diet, n = 20), LG (0.05 mg/kg Se-supplemented diet, n = 20), MG (0.1 mg/kg Se-supplemented diet, n = 20), and HG (0.2 mg/kg Se-supplemented diet, n = 20). Four days after parturition, all mice were euthanized. The selenium deposition and antioxidants enzymes in serum, liver, and mammary gland were detected. Results show that with increasing selenium supplementation, the selenium deposition and activation of T-AOC, T-SOD, and GSH-Px increased, meanwhile the concentration of MDA decreased in serum, liver, and mammary gland. Therefore, this study suggested selenium was mainly deposited in the liver, and dietary selenium during pregnancy might improve the antioxidant status in postpartum animals.

[Raman Signal Enhancement for Gas Detection Using a Near Concentric Cavity].

The detection of dissolved gases in seawater plays an important role in ocean observation and exploration. Raman spectroscopy has a great advantage in simultaneous multiple species detection and is thus regarded as a favorable choice for ocean application. However, its sensitivity remains insufficient, and a demand in enhancements is called! for before putting Raman spectroscopy to actual use in marine studies In this work, we developed a near-concentric cavity, in which laser beam could be trapped and reflected back and forth, for the purpose of intensifying Raman signals. The factors that would influence Raman signals were taken into account. The result show that the smaller angle between collection direction and optical axis of reflection mirror, the stronger the signal and signal to noise ratio (SNR) is. With a collection angle of 30 degrees, our Near-concentric Cavity System managed to raise the SNR to a figure about 16 times larger than that of common methods applying 90 degrees. Moreover, the alignment pattern in our system made it possible to excel concentric cavity with a 3 times larger SNR. Compared with the single-pass Raman signal, the signal intensity of our near-concentric cavity was up to 70 times enhanced. According to the obtained results of CO2 measurement, it can be seen that the new system provides a limit of detection(LOD) for CO2 about 0.19 mg x L(-1) using 3-σ criterion standard, and the LOD of 11.5 µg x L(-1) for CH4 was evaluated with the theoretical cross section values of CO2 and CH4.

[Time-resolved evaluation of self-absorption in laser induced plasma from nickel sample].

Laser induced breakdown spectroscopy (LIBS) has been shown to be a promising technique for element analysis. However, self-absorption effect deeply influences the LIBS measurements. In the present paper, a Q-switched Nd:YAG laser operated at 1 064 nm was used to generate nickel plasmas in air. Four atomic lines Ni I 341.476/351.034/351.505/352.454 nm which belong to the same electronic configuration (3d9 (2D)4p-3d9 (2D)4s) of Ni were chosen for self-absorption investigation. Self-absorption of Ni I 351. 034 nm corresponding to the highest energy level 3D1 of 3d(9) (2D)4s was not observed in the plasma emission investigated. While for the other three lines, a strong self-absorption appeared at the prophase of the plasma and tended to weaken. The self-absorption at Ni I 352.454 nm was the most serious and still visible at the delay of 1100 ns, compared with the lines of Ni I 341.476/351.505 nm whose self-absorption duration is 900 and 500 ns respectively. It was also found that the self-absorption effect had power dependence and decreased with the increase in laser pulse energy. The obtained results suggest that the self-absorption effect could be alleviated by suitable atomic line selection, operating at a higher pulse energy and detecting with a longer delay. The possible reasons for the self-absorption duration difference for different lines were also discussed.

Influence of Shenqing Recipe on morphology and quantity of colonic interstitial cells of Cajal in trinitrobenzene sulfonic acid induced rat colitis.

OBJECTIVE: To observe the influence of Shenqing Recipe (SQR), a kind of Traditional Chinese Medicine, on the morphology and quantity of colonic interstitial cells of Cajal (ICC) in trinitrobenzene sulfonic acid (TNBS)-induced rat colitis, and to investigate the possible mechanism of SQR in regulating intestinal dynamics. METHODS: Sixty rats were randomly divided into normal control, model 1, model 2, mesalazine, and high-dose, and low-dose SQR groups with 10 rats in each group. TNBS (10 mg) dissolved in 50% ethanol was instilled into the lumen of the rat colon of the latter five groups to induce colitis. On the 4th day after administration of TNBS, each treatment group was administered one of the following formulations by enteroclysis gavage once a day for 7 days: 600 mg•kg⁻¹â€¢d⁻¹ mesalazine, 2.4 g•kg⁻¹â€¢d⁻¹ SQR, and 1.2 g•kg⁻¹â€¢d⁻¹ SQR. Model 2 rats received normal saline solution. After 7 days colonic samples were collected. While the colonic samples of model 1 group were collected on the 3rd day after TNBS administered. Ultrastructure of ICC in the damaged colonic tissues was observed with transmission electron microscope. Expression of c-kit protein in colonic tissue was determined by immunohistochemical staining and Western blot. RESULTS: The ultrastructure of colonic ICC in the rat model of TNBS-induced colitis showed a severe injury, and administration of SQR or mesalazine reduced the severity of injury. Similarly, the expression of c-kit protein of TNBS-induced colitis rat model was significantly decreased compared with the normal control group (P < 0.05). Treatment with SQR or mesalazine significantly increased the expression of c-kit protein compared with the administration of control formulations (P < 0.05), especially the high-dose SQR group. CONCLUSION: SQR could alleviate and repair the injured ICC, and improve its quantity, which might be involved in regulating intestinal motility.

[Efficacy of concurrent radio-chemotherapy and chemotherapy alone in the treatment of locally advanced non-small-cell lung cancer].

OBJECTIVE: To evaluate the effect and acute toxicity of concurrent radio-chemotherapy, by NVB and DDP, plus concurrent radiotherapy in comparison with chemotherapy alone in the treatment of inoperable locally advanced non-small-cell lung cancer (LANSCLC). METHODS: Sixty-four patients with inoperable LANSCLC were randomly divided by envelope method into two groups: concurrent radio-chemotherapy group (n = 33) and conventional chemotherapy group (n = 31). The patients in conventional chemotherapy group were treated by NP regimen (NVB + DDP): NVB 25 mg/m(2), d1, 8 and DDP 25-30 mg/m(2) d1-3. In the radio-chemotherapy group by NP regimen plus conventional radiotherapy by (60)Co: 64-68 Gy/2 Gy x 5/w x 6-7w. RESULTS: All patients completed the treatment schedule. The overall response rate (CR + PR) in the radio-chemotherapy group was significantly higher than that in the conventional chemotherapy group: 81.8% vs 45.2%, (P < 0.01) with 1- and 2-year survival rates of 69.7% vs 38.7% (P < 0.05) and 39.4% vs 16.1% (P < 0.05). without any significant difference in the acute toxicity between two groups (P > 0.05). CONCLUSION: Compared with conventional chemotherapy (NVP and DDP), concurrent radio-chemotherapy (NVP and DDP plus concurrent radiotherapy) is more effective and tolerable for the inoperable locally advanced non-small-cell lung cancer.