Guest editorial special issue on pulsed power science and technology

This special issue of the IEEE TRANSACTIONS ON PLASMA SCIENCE (TPS) mainly contains works presented at the 21st IEEE International Pulsed Power Conference (PPC) held in Brighton, U.K., between June 18–22, 2017 ( http://ece-events.unm.edu/ppc2017/ ). This conference marks an important step, as it was located outside of the USA for the first time. The PPC is well known for serving the Pulsed Power and Plasma Science communities as the principal forum for the professionals worldwide, where the most important technical presentations and discussions are taking place; the Brighton conference was no exception. The 21st PPC was extremely successful, with 470 quality papers submitted as equal contributions from the Americas, Europe, and Asia

Analysis on Relationship between Code Quality and Code Coverage in an XP Environment: a Case Study on the SWURV Project

The thesis used hypothesis testing and correlation analysis methods to explore the relationship between structural code coverage and the quality of software developed in an eXtreme Programming (XP) environment, via a case study of a commercial software product. We find that improving code coverage is helpful to detect residual defects, but it is not enough, and we also need other testing, like acceptance testing, in the process of XP software development to provide good quality software products. In addition, in order to investigate why the strength of association between code coverage and residual defect density is not as strong as that presented in prior work, a detailed defect root cause analysis is performed, showing that over 96% of bugs cannot be detected by improving code coverage. Based on the defect categories and distribution of defect root cause, six improvement actions are proposed for future XP projects

Visualization 1.mp4

The video demonstrates the feedback length dependence of the inter-mode beatnote signal of a terahertz quantum cascade laser frequency comb under optical feedback

Table_4_Prognostic and Predictive Models for Left- and Right- Colorectal Cancer Patients: A Bioinformatics Analysis Based on Ferroptosis-Related Genes.docx

BackgroundLeft- and right-sided colorectal cancer (LCRC, RCRC) are significantly different in epidemiology and clinical manifestations and have altered outcomes. However, as a hot tumor prognostic marker, the role of ferroptosis-related genes (FRGs) in LCRC and RCRC is unknown.MethodsFrom The Cancer Genome Atlas (TCGA) database, we downloaded the expression profiles of CRC patients. A “DESeq2” package was performed to compare the differentially expressed genes (DEGs) of LCRC and RCRC. FRGs were identified using the FerrDb. The prognostic value of differentially expressed FRG (DE-FRG) in left- and right-CRC was assessed separately by Cox regression analysis. Subsequently, functional enrichment analysis, ESTIMATE, and single sample Gene Set Enrichment Analysis (ssGSEA) were performed based on LCRC and RCRC samples to reveal the potential function of FRGs-related risk signatures. The differential expression of FRGs in tumor tissues and adjacent normal tissues were verified by Western blot. The differential expression and prognosis in LCC and RCC were verified by immunohistochemistry.ResultsBased on the identified 14 DE-FRGs, the LCRC prognostic model consisted of NOS2 and IFNG; NOS2 and ALOXE established the prognostic signature that could distinguish RCRC outcomes. In the functional analysis, the DEGs (high risk vs. low risk) of the LCRC and RCRC were significantly enriched in the immune- and lipid-related terms and pathways. ESTIMATE and ssGSEA suggested that these FRGs-related risk signatures were affiliated with the infiltration of immune cell subtypes. Western blotting results showed that NOS2 and ALOXE3 were significantly highly expressed in cancer, and the difference was statistically significant (P ConclusionThis study constructed a potential prognostic model of LCRC and RCRC, respectively. We also identified the crucial pathways that contribute to elucidating the pathogenesis of CRC.</p

Table_5_Prognostic and Predictive Models for Left- and Right- Colorectal Cancer Patients: A Bioinformatics Analysis Based on Ferroptosis-Related Genes.docx

BackgroundLeft- and right-sided colorectal cancer (LCRC, RCRC) are significantly different in epidemiology and clinical manifestations and have altered outcomes. However, as a hot tumor prognostic marker, the role of ferroptosis-related genes (FRGs) in LCRC and RCRC is unknown.MethodsFrom The Cancer Genome Atlas (TCGA) database, we downloaded the expression profiles of CRC patients. A “DESeq2” package was performed to compare the differentially expressed genes (DEGs) of LCRC and RCRC. FRGs were identified using the FerrDb. The prognostic value of differentially expressed FRG (DE-FRG) in left- and right-CRC was assessed separately by Cox regression analysis. Subsequently, functional enrichment analysis, ESTIMATE, and single sample Gene Set Enrichment Analysis (ssGSEA) were performed based on LCRC and RCRC samples to reveal the potential function of FRGs-related risk signatures. The differential expression of FRGs in tumor tissues and adjacent normal tissues were verified by Western blot. The differential expression and prognosis in LCC and RCC were verified by immunohistochemistry.ResultsBased on the identified 14 DE-FRGs, the LCRC prognostic model consisted of NOS2 and IFNG; NOS2 and ALOXE established the prognostic signature that could distinguish RCRC outcomes. In the functional analysis, the DEGs (high risk vs. low risk) of the LCRC and RCRC were significantly enriched in the immune- and lipid-related terms and pathways. ESTIMATE and ssGSEA suggested that these FRGs-related risk signatures were affiliated with the infiltration of immune cell subtypes. Western blotting results showed that NOS2 and ALOXE3 were significantly highly expressed in cancer, and the difference was statistically significant (P ConclusionThis study constructed a potential prognostic model of LCRC and RCRC, respectively. We also identified the crucial pathways that contribute to elucidating the pathogenesis of CRC.</p

Table_1_Prognostic and Predictive Models for Left- and Right- Colorectal Cancer Patients: A Bioinformatics Analysis Based on Ferroptosis-Related Genes.docx

BackgroundLeft- and right-sided colorectal cancer (LCRC, RCRC) are significantly different in epidemiology and clinical manifestations and have altered outcomes. However, as a hot tumor prognostic marker, the role of ferroptosis-related genes (FRGs) in LCRC and RCRC is unknown.MethodsFrom The Cancer Genome Atlas (TCGA) database, we downloaded the expression profiles of CRC patients. A “DESeq2” package was performed to compare the differentially expressed genes (DEGs) of LCRC and RCRC. FRGs were identified using the FerrDb. The prognostic value of differentially expressed FRG (DE-FRG) in left- and right-CRC was assessed separately by Cox regression analysis. Subsequently, functional enrichment analysis, ESTIMATE, and single sample Gene Set Enrichment Analysis (ssGSEA) were performed based on LCRC and RCRC samples to reveal the potential function of FRGs-related risk signatures. The differential expression of FRGs in tumor tissues and adjacent normal tissues were verified by Western blot. The differential expression and prognosis in LCC and RCC were verified by immunohistochemistry.ResultsBased on the identified 14 DE-FRGs, the LCRC prognostic model consisted of NOS2 and IFNG; NOS2 and ALOXE established the prognostic signature that could distinguish RCRC outcomes. In the functional analysis, the DEGs (high risk vs. low risk) of the LCRC and RCRC were significantly enriched in the immune- and lipid-related terms and pathways. ESTIMATE and ssGSEA suggested that these FRGs-related risk signatures were affiliated with the infiltration of immune cell subtypes. Western blotting results showed that NOS2 and ALOXE3 were significantly highly expressed in cancer, and the difference was statistically significant (P ConclusionThis study constructed a potential prognostic model of LCRC and RCRC, respectively. We also identified the crucial pathways that contribute to elucidating the pathogenesis of CRC.</p

The expression of angiogenesis and glycolysis related genes in comparing with common groups.

(A) The expression levels of angiogenesis-related genes in MCF7 cells that treated by Narciclasine. (B) The expression levels of angiogenesis-related genes in MCF7 cells that treated by Bruceine D. (C) The expression levels of glycolysis-related genes in MCF7 cells that treated by Narciclasine and Bruceine D. (D) Venn plot of angiogenesis-related genes in Narciclasine and Bruceine D treatment groups. (E) Venn plot of glycolysis-related genes in Narciclasine and Bruceine D treatment groups. *p < 0.05, ***p < 0.001, ****p < 0.0001. The vertical axis in Fig C and D means the expression level of genes, where the red square represents high expression, and the blue square represents low expression.</p

Image_3_Prognostic and Predictive Models for Left- and Right- Colorectal Cancer Patients: A Bioinformatics Analysis Based on Ferroptosis-Related Genes.tif

BackgroundLeft- and right-sided colorectal cancer (LCRC, RCRC) are significantly different in epidemiology and clinical manifestations and have altered outcomes. However, as a hot tumor prognostic marker, the role of ferroptosis-related genes (FRGs) in LCRC and RCRC is unknown.MethodsFrom The Cancer Genome Atlas (TCGA) database, we downloaded the expression profiles of CRC patients. A “DESeq2” package was performed to compare the differentially expressed genes (DEGs) of LCRC and RCRC. FRGs were identified using the FerrDb. The prognostic value of differentially expressed FRG (DE-FRG) in left- and right-CRC was assessed separately by Cox regression analysis. Subsequently, functional enrichment analysis, ESTIMATE, and single sample Gene Set Enrichment Analysis (ssGSEA) were performed based on LCRC and RCRC samples to reveal the potential function of FRGs-related risk signatures. The differential expression of FRGs in tumor tissues and adjacent normal tissues were verified by Western blot. The differential expression and prognosis in LCC and RCC were verified by immunohistochemistry.ResultsBased on the identified 14 DE-FRGs, the LCRC prognostic model consisted of NOS2 and IFNG; NOS2 and ALOXE established the prognostic signature that could distinguish RCRC outcomes. In the functional analysis, the DEGs (high risk vs. low risk) of the LCRC and RCRC were significantly enriched in the immune- and lipid-related terms and pathways. ESTIMATE and ssGSEA suggested that these FRGs-related risk signatures were affiliated with the infiltration of immune cell subtypes. Western blotting results showed that NOS2 and ALOXE3 were significantly highly expressed in cancer, and the difference was statistically significant (P ConclusionThis study constructed a potential prognostic model of LCRC and RCRC, respectively. We also identified the crucial pathways that contribute to elucidating the pathogenesis of CRC.</p

Fluorine-19 NMR Studies on the Acid State of the Intestinal Fatty Acid Binding Protein^†

The intestinal fatty acid binding protein (IFABP) is composed of two β-sheets with a large hydrophobic cavity into which ligands bind. After eight 4-19F-phenylalanines were incorporated into the protein, the acid state of both apo- and holo-IFABP (at pH 2.8 and 2.3) was characterized by means of 1H NMR diffusion measurements, circular dichroism, and 19F NMR. Diffusion measurements show a moderately increased hydrodynamic radius while near- and far-UV CD measurements suggest that the acid state has substantial secondary structure as well as persistent tertiary interactions. At pH 2.8, these tertiary interactions have been further characterized by 19F NMR and show an NOE cross-peak between residues that are located on different β-strands. Side chain conformational heterogeneity on the millisecond time scale was captured by phase-sensitive 19F−19F NOESY. At pH 2.3, native NMR peaks are mostly gone, but the protein can still bind fatty acid to form the holoprotein. An exchange cross-peak of one phenylalanine in the holoprotein is attributed to increased motional freedom of the fatty acid backbone caused by the slight opening of the binding pocket at pH 2.8. In the acid environment Phe128 and Phe17 show dramatic line broadening and chemical shift changes, reflecting greater degrees of motion around these residues. We propose that there is a separation of specific regions of the protein that gives rise to the larger radius of hydration. Temperature and urea unfolding studies indicate that persistent hydrophobic clusters are nativelike and may account for the ability of ligand to bind and induce nativelike structure, even at pH 2.3

PPI analysis of 5 cell cycle related genes.

(A) PPI network analysis of key cell cycle genes. (B) The position of some hub genes in cell cycle process.</p