paper2repo: GitHub Repository Recommendation for Academic Papers

GitHub has become a popular social application platform, where a large number of users post their open source projects. In particular, an increasing number of researchers release repositories of source code related to their research papers in order to attract more people to follow their work. Motivated by this trend, we describe a novel item-item cross-platform recommender system, $\textit{paper2repo}$, that recommends relevant repositories on GitHub that match a given paper in an academic search system such as Microsoft Academic. The key challenge is to identify the similarity between an input paper and its related repositories across the two platforms, $\textit{without the benefit of human labeling}$. Towards that end, paper2repo integrates text encoding and constrained graph convolutional networks (GCN) to automatically learn and map the embeddings of papers and repositories into the same space, where proximity offers the basis for recommendation. To make our method more practical in real life systems, labels used for model training are computed automatically from features of user actions on GitHub. In machine learning, such automatic labeling is often called {\em distant supervision\/}. To the authors' knowledge, this is the first distant-supervised cross-platform (paper to repository) matching system. We evaluate the performance of paper2repo on real-world data sets collected from GitHub and Microsoft Academic. Results demonstrate that it outperforms other state of the art recommendation methods

Transient high glucose causes persistent epigenetic changes and altered gene expression during subsequent normoglycemia

The current goal of diabetes therapy is to reduce time-averaged mean levels of glycemia, measured as HbA1c, to prevent diabetic complications. However, HbA1c only explains <25% of the variation in risk of developing complications. Because HbA1c does not correlate with glycemic variability when adjusted for mean blood glucose, we hypothesized that transient spikes of hyperglycemia may be an HbA1c–independent risk factor for diabetic complications. We show that transient hyperglycemia induces long-lasting activating epigenetic changes in the promoter of the nuclear factor κB (NF-κB) subunit p65 in aortic endothelial cells both in vitro and in nondiabetic mice, which cause increased p65 gene expression. Both the epigenetic changes and the gene expression changes persist for at least 6 d of subsequent normal glycemia, as do NF-κB–induced increases in monocyte chemoattractant protein 1 and vascular cell adhesion molecule 1 expression. Hyperglycemia-induced epigenetic changes and increased p65 expression are prevented by reducing mitochondrial superoxide production or superoxide-induced α-oxoaldehydes. These results highlight the dramatic and long-lasting effects that short-term hyperglycemic spikes can have on vascular cells and suggest that transient spikes of hyperglycemia may be an HbA1c–independent risk factor for diabetic complications

Membrane sampler for interference-free flow injection NO determination in biological fluids with chemiluminescence detection

Abstract The development of a chemiluminescence (CL) method based on the perm-selective properties of a Nafion-cellulose acetate (CA) composite membrane for the monitoring of nitric oxide (NO) in biological fluids is described. Horseradish peroxidase (HRP) was used as NO trapping solution, forming the stable compound HRP-NO. The HRP was denatured and the trapped NO was released and detected by using the luminol-H 2 O 2 system. Using a mixed (size-exclusion and polar-based) transport control, the interference effects of various compounds were minimized. The method was used for NO monitoring in simulated samples, by using a blood specimen as sample matrix. The 3σ detection limit is 0.9 × 10 −6 mol and linear semi-log calibration plot in the range 1.8 × 10 −6 to 2.7 × 10 −3 mol NO was constructed. The applied methodology was further used to prolong the NO lifetime in order to increase the sensitivity of its determination. This was based on the increase of the response in the presence of certain reductive species, which act as NO preservatives in biological fluid samples

High glucose increases angiopoietin-2 transcription in microvascular endothelial cells through methylglyoxal modification of mSin3A

Methylglyoxal is a highly reactive dicarbonyl degradation product formed from triose phosphates during glycolysis. Methylglyoxal forms stable adducts primarily with arginine residues of intracellular proteins. The biologic role of this covalent modification in regulating cell function is not known. Here we report that in mouse kidney endothelial cells, high glucose causes increased methylglyoxal modification of the corepressor mSin3A. Methylglyoxal modification of mSin3A results in increased recruitment of O-GlcNAc-transferase, with consequent increased modification of Sp3 by O-linked N-acetylglucosamine. This modification of Sp3 causes decreased binding to a glucose-responsive GC-box in the angiopoietin-2 (Ang-2) promoter, resulting in increased Ang-2 expression. Increased Ang-2 expression induced by high glucose increased expression of intracellular adhesion molecule 1 and vascular cell adhesion molecule 1 in cells and in kidneys from diabetic mice and sensitized microvascular endothelial cells to the proinflammatory effects of tumor necrosis factor alpha. This novel mechanism for regulating gene expression may play a role in the pathobiology of diabetic vascular disease

Estradiol improves cardiovascular function through up-regulation of SOD2 on vascular wall

Epidemiological studies have shown that estrogens have protective effects in cardiovascular diseases, even though the results from human clinical trials remain controversial, while most of the animal experiments confirmed this effect, but the detailed mechanism remains unclear. In this study, we found that estradiol (E2) treatment significantly increases the expression of mitochondrial superoxide dismutase (SOD2) in mice and in vitro in human aorta endothelial cells. Further investigation shows that E2 up-regulates SOD2 through tethering of estrogen receptor (ER) to Sp1 and the increased binding of Sp1 to GC-box on the SOD2 promoter, where ERα responses E2-mediated gene activation, and ERβ maintains basal gene expression level. The E2/ER-mediated SOD2 up-regulation results in minimized ROS generation, which highly favors healthy cardiovascular function. Gene therapy through lentivirus-carried endothelium-specific delivery to the vascular wall in high-fat diet (HFT) mice shows that the SOD2 expression in endothelial cells normalizes E2 deficiency-induced ROS generation with ameliorated mitochondrial dysfunction and vascular damage, while SOD2 knockdown worsens the problem despite the presence of E2, indicating that E2-induced SOD2 expression plays an important vasculoprotective role. To our knowledge, this is the first report for the mechanism by which E2 improves cardiovascular function through up-regulation of SOD2 in endothelial cells. In turn, this suggests a novel gene therapy through lentivirus-carried gene delivery to vascular wall for E2 deficiency-induced cardiovascular damage in postmenopausal women