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Abstract Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. We develop a methodology, TRND, that integrates a preliminary TRN, microarray data, gene ontology and phylogenic similarity to accurately discover TRNs and apply the method to E. coli K12. The approach can easily be extended to include other methodologies. Although gene ontology and phylogenic similarity have been used in the context of gene-gene networks, we show that more information can be extracted when gene-gene scores are transformed to gene-transcription factor (TF) scores using a preliminary TRN. This seems to be preferable over the construction of gene-gene interaction networks in light of the observed fact that gene expression and activity of a TF made of a component encoded by that gene is often out of phase. TRND multi-method integration is found to be facilitated by the use of a Bayesian framework for each method derived from its individual scoring measure and a training set of gene/TF regulatory interactions. The TRNs we construct are in better agreement with microarray data. The number of gene/TF interactions we discover is actually double that of existing networks.

Under laboratory conditions, nitrogen adsorption from the coking wax oil was studied respectively by D72 and D001-CC cationic activation resins as adsorbents in a continuous fixed bed reactor. Micro reaction system of fluid catalytic cracking unit was used to study the catalytic racking reaction performance of coking wax oil after denitrification. Adsorption properties of two kinds of activation resin were compared by studing the adsorption breakthrough curve in the fixed bed, the dynamic adsorption properties of alkaline nitrogen compounds in the coking wax oil and the affect of the adsorption temperature on the removal rate of basic nitrogen compounds. Catalytic cracking performances of coking wax oil before and after denitrification were finally compared with catalytic cracking experiments. Results of experiments showed that the optimum adsorption temperature of D001-CC activation resin was 70 °C, the adsorption capacity was saturated 6 hours later, and the saturated adsorption capacity is 19. 35 mg/g. The optimum adsorption temperature of D72 activation resin was 60 °C,the adsorption capacity was saturated 5 hours after, and the saturated adsorption capacity was 7. 75 mg/g. The degree of catalytic cracking of coking wax oil deepened and the conversion rate improved after dealing with the resin denitrification. When the reaction temperature was 400 °C, the conversion rate of coking wax oil without denitrification was 44%. The conversion rate of coking wax oil reached 81. 5% after 30 minute's adsorption denitrification treatment. The influences of alkaline nitrogen content on catalyst activity were more sensitive at higher reaction temperature. The more substantially decrease of alkaline nitrogen content in the coking wax oil, the more significantly increases of catalytic cracking conversion rates. [ABSTRACT FROM AUTHOR]

Transcriptional regulatory network (TRN) discovery using information from a single source does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. A methodology, TRND, that integrates a preliminary TRN, gene expression data and gene ontology is developed to discover TRNs. The method is applied to a comprehensive set of expression data on B cell and a preliminary TRN that included 1,335 genes, 443 transcription factors (TFs) and 4032 gene/TF interactions. Predictions were obtained for 443 TFs and 9,589 genes. 14,616 of 4,247,927 possible gene/TF interactions scored higher than the imposed threshold. Results for three TFs, E2F-4, p130 and c-Myc, were examined in more detail to assess the accuracy of the integrated methodology. Although the training sets for E2F-4 and p130 were rather limited, the activities of these two TFs were found to be highly correlated and a large set of coregulated genes is predicted. These predictions were confirmed with published experimental results not used in the training set. A similar test was run for the c-Myc TF using the comprehensive resource www.myccancergene.org. In addition, correlations between expression of genes that encode TFs and TF activities were calculated and showed that the assumption of TF activity correlates with encoding gene expression might be misleading. The constructed B cell TRN, and scores for individual methodologies and the integrated approach are available at systemsbiology.indiana.edu/trndresults. [ABSTRACT FROM AUTHOR]

Hydrothermal process was successfully used to synthesize Fe3O4 powder using ferrous chloride (FeCl2) and diamine hydrate (H4N2·H2O) as starting materials by carefully controlling the reaction conditions. The as-prepared Fe3O4 sample was characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM), and its magnetic properties were evaluated on a vibrating sample magnetometer (VSM). The nanoscale (40 nm) Fe3O4 powder obtained at 140 °C for 6 h possessed a saturation magnetization of 85.8 emu/g, a little lower than that of the correspondent bulk Fe3O4 (92 emu/g). It is suggested that the well-crystallized Fe3O4 grains formed under appropriate hydrothermal conditions should be responsible for the increased saturation magnetization in nanosized Fe3O4. [Copyright &y& Elsevier]

Protein tyrosine kinase 7 (PTK7) is a catalytically inactive receptor tyrosine kinase that is involved in development and tumorigenesis. PTK7 expression and its functional roles have been investigated in several human cancers, although controversial results have been obtained. In this study, we investigated the expression of PTK7 protein in invasive ductal breast cancer tissues, and analyzed its relationship with clinicopathologic parameters. Seventy-nine consecutive invasive breast cancer tissues were included in the study, and PTK7 protein was detected in invasive ductal breast cancers and normal breast epithelial cells by immunohistochemistry. Positive staining was noted in all normal breast epithelial cells and differential expression was observed in breast carcinomas. Thirty-eight of 79 samples (48.1%) were negative or stained weakly for PTK7 (-), 19 (24.1%) showed moderate staining (+), and 22 (27.8%) were strongly stained (++). PTK7 expression was negatively associated with tumor grade ( P =0.025, r =-0.251), tumor-node-metastasis stage ( P =0.004, r =-0.317), lymph node metastasis ( P =0.002, r =-0.351), human epidermal growth factor receptor 2 expression ( P =0.029, r =-0.245), and Ki67 expression ( P =0.004, r =-0.317), and positively associated with estrogen receptor (ER) expression ( P =0.037, r =0.235). No significant relationship was found between PTK7 expression and patient age or progesterone receptor (PR) expression. Our data indicated that PTK7 protein was down-regulated in breast cancer cells compared with healthy epithelial cells, and that PTK7 may be a tumor suppressor gene in breast cancer. Future studies should explore the molecular mechanisms underlying the down-regulation and functional roles of PTK7 in breast cancer., Competing Interests: None., (IJCEP Copyright © 2019.)

Objective: To investigate the impact of the regeneration of interstitial cell of Cajal (ICC) on the conduction of slow wave and gastric emptying in rats undergoing Roux-en-Y gastrojejunostomy., Methods: Twenty male SD rats were randomly divided into experimental group and control group. The experimental group consisted of ten rats undergoing Roux-en-Y gastrojejunostomy. The control group only underwent pyloric transection and anastomosis. Gastric scintigraphy was performed in the two groups respectively to measure the half time of gastric emptying (t1/2) at sixteen weeks after the surgical manipulations, and then the myoelectrical activities near the gastrojejunal anastomosis were recorded. The study also observed the regeneration of ICC by the electron microscopy. The data of the 2 groups was compared by t test., Results: In the sixteenth postoperative week, the t1/2 was (23.5 ± 4.5) minutes for rats in the Roux-en-Y group and (10.2 ± 2.3) minutes for those in the control group, indicating delayed gastric emptying in the Roux-en-Y group (t=7.978, P=0.000), accompanied with the abnormal myoelectrical activities near the gastrojejunal anastomosis. The morphological detection showed that ICC near the gastrojejunal anastomosis regenerated and reconstructed their network in the rats of the experimental group., Conclusion: The abnormal myoelectrical activities near the gastrojejunal anastomosis, basing on the regeneration and reconstruction of ICC, may make a significant delay on the gastric emptying.