Topic-based integrator matching for pull request

Pull Request (PR) is the main method for code contributions from the external contributors in GitHub. PR review is an essential part of open source software developments to maintain the quality of software. Matching a new PR for an appropriate integrator will make the PR reviewing more effective. However, PR and integrator matching are now organized manually in GitHub. To make this process more efficient, we propose a Topic-based Integrator Matching Algorithm (TIMA) to predict highly relevant collaborators(the core developers) as the integrator to incoming PRs . TIMA takes full advantage of the textual semantics of PRs. To define the relationships between topics and collaborators, TIMA builds a relation matrix about topic and collaborators. According to the relevance between topics and collaborators, TIMA matches the suitable collaborators as the PR integrator

Bipartite Consensus for a Class of Nonlinear Multi-agent Systems Under Switching Topologies:A Disturbance Observer-Based Approach

This paper considers the leader-following bipartite consensus for a class of nonlinear multi-agent systems (MASs) subject to exogenous disturbances under directed fixed and switching topologies, respectively. Firstly, two new output feedback control protocols involving signs of link weights are introduced based on relative output measurements of neighboring agents. In order to estimate the disturbances produced by an exogenous system, a disturbance observer-based approach is developed. Then, sufficient conditions for leader-following bipartite consensus with directed fixed topologies are derived. Furthermore, by assuming that each switching topology contains a directed spanning tree, it is proved that the leader-following bipartite consensus can be realized with the designed output feedback control protocol if the dwell time is larger than a non-negative threshold. Finally, numerical simulations inspired by a real-world DC motors are provided to illustrate the effectiveness of the proposed controllers

Rescue of Retinal Degeneration in rd1 Mice by Intravitreally Injected Metformin

Retinitis pigmentosa (RP) is a progressive hereditary retinal degenerative disease in which photoreceptor cells undergo degeneration and apoptosis, eventually resulting in irreversible loss of visual function. Currently, no effective treatment exists for this disease. Neuroprotection and inflammation suppression have been reported to delay the development of RP. Metformin is a well-tested drug used to treat type 2 diabetes, and it has been reported to exert beneficial effects in neurodegenerative diseases, such as Parkinson’s disease and Alzheimer’s disease. In the present study, we used immunofluorescence staining, electroretinogram (ERG) recordings and RNA-Seq to explore the effects of metformin on photoreceptor degeneration and its mechanism in rd1 mice. We found that metformin significantly reduced apoptosis in photoreceptors and delayed the degeneration of photoreceptors and rod bipolar cells in rd1 mice, thus markedly improving the visual function of rd1 mice at P14, P18, and P22 when tested with a light/dark transition test and ERG. Microglial activation in the outer nuclear layer (ONL) of the retina of rd1 mice was significantly suppressed by metformin. RNA-Seq showed that metformin markedly downregulated inflammatory genes and upregulated the expression of crystallin proteins, which have been demonstrated to be important neuroprotective molecules in the retina, revealing the therapeutic potential of metformin for RP treatment. αA-crystallin proteins were further confirmed to be involved in the neuroprotective effects of metformin in a Ca2+ ionophore-damaged 661W photoreceptor-like cell line. These data suggest that metformin exerts a protective effect in rd1 mice via both immunoregulatory and new neuroprotective mechanisms

Metatranscriptomics Reveals the Functions and Enzyme Profiles of the Microbial Community in Chinese Nong-Flavor Liquor Starter

Chinese liquor is one of the world's best-known distilled spirits and is the largest spirit category by sales. The unique and traditional solid-state fermentation technology used to produce Chinese liquor has been in continuous use for several thousand years. The diverse and dynamic microbial community in a liquor starter is the main contributor to liquor brewing. However, little is known about the ecological distribution and functional importance of these community members. In this study, metatranscriptomics was used to comprehensively explore the active microbial community members and key transcripts with significant functions in the liquor starter production process. Fungi were found to be the most abundant and active community members. A total of 932 carbohydrate-active enzymes, including highly expressed auxiliary activity family 9 and 10 proteins, were identified at 62°C under aerobic conditions. Some potential thermostable enzymes were identified at 50, 62, and 25°C (mature stage). Increased content and overexpressed key enzymes involved in glycolysis and starch, pyruvate and ethanol metabolism were detected at 50 and 62°C. The key enzymes of the citrate cycle were up-regulated at 62°C, and their abundant derivatives are crucial for flavor generation. Here, the metabolism and functional enzymes of the active microbial communities in NF liquor starter were studied, which could pave the way to initiate improvements in liquor quality and to discover microbes that produce novel enzymes or high-value added products

Unraveling the Contribution of High Temperature Stage to Jiang-Flavor Daqu, a Liquor Starter for Production of Chinese Jiang-Flavor Baijiu, With Special Reference to Metatranscriptomics

Jiang-flavor (JF) daqu is a liquor starter used for production of JF baijiu, a well-known distilled liquor in China. Although a high temperature stage (70°C) is necessary for qualifying JF daqu, little is known regarding its active microbial community and functional enzymes, along with its role in generating flavor precursors for JF baijiu aroma. In this investigation, based on metatranscriptomics, fungi, such as Aspergillus and Penicillium, were identified as the most active microbial members and 230 carbohydrate-active enzymes were identified as potential saccharifying enzymes at 70°C of JF daqu. Notably, most of enzymes in identified carbohydrate and energy pathways showed lower expression levels at 70°C of JF daqu than those at the high temperature stage (62°C) of Nong-flavor (NF) daqu, indicating lowering capacities of saccharification and fermentation by high temperature stage. Moreover, many enzymes, especially those related to the degradation of aromatic compounds, were only detected with low expression levels at 70°C of JF daqu albeit not at 62°C of NF daqu, indicating enhancing capacities of generating special trace aroma compounds in JF daqu by high temperature stage. Additionally, most of enzymes related to those capacities were highly expressed at 70°C by fungal genus of Aspergillus, Coccidioides, Paracoccidioides, Penicillium, and Rasamsonia. Therefore, this study not only sheds light on the crucial functions of high temperature stage but also paves the way to improve the quality of JF baijiu and provide active community and functional enzymes for other fermentation industries

Algorithms for Graph Drawing Problems

A graph G is called planar if it can be drawn on the plan such that no two distinct edges intersect each other but at common endpoints. Such drawing is called a plane embedding of G. A plane graph is a graph with a fixed embedding. A straight-line drawing G of a graph G = (V, E) is a drawing where each vertex of V is drawn as a distinct point on the plane and each edge of G is drawn as a line segment connecting two end vertices. In this thesis, we study a set of planar graph drawing problems. First, we consider the problem of monotone drawing: A path P in a straight line drawing Γ is monotone if there exists a line l such that the orthogonal projections of the vertices of P on l appear along l in the order they appear in P. We call l a monotone line (or monotone direction) of P. G is called a monotone drawing of G if it contains at least one monotone path Puw between every pair of vertices u,w of G. Monotone drawings were recently introduced by Angelini et al. and represent a new visualization paradigm, and is also closely related to several other important graph drawing problems. As in many graph drawing problems, one of the main concerns of this research is to reduce the drawing size, which is the size of the smallest integer grid such that every graph in the graph class can be drawn in such a grid. We present two approaches for the problem of monotone drawings of trees. Our first approach show that every n-vertex tree T admits a monotone drawing on a grid of size O(n1.205) × O( n1.205) grid. Our second approach further reduces the size of drawing to 12n × 12n, which is asymptotically optimal. Both of our two drawings can be constructed in O(n) time. We also consider monotone drawings of 3-connected plane graphs. We prove that the classical Schnyder drawing of 3-connected plane graphs is a monotone drawing on a f × f grid, which can be constructed in O(n) time. Second, we consider the problem of orthogonal drawing. An orthogonal drawing of a plane graph G is a planar drawing of G such that each vertex of G is drawn as a point on the plane, and each edge is drawn as a sequence of horizontal and vertical line segments with no crossings. Orthogonal drawing has attracted much attention due to its various applications in circuit schematics, relationship diagrams, data flow diagrams etc. . Rahman et al. gave a necessary and sufficient condition for a plane graph G of maximum degree 3 to have an orthogonal drawing without bends. An orthogonal drawing D(G) is orthogonally convex if all faces of D(G) are orthogonally convex polygons. Chang et al. gave a necessary and sufficient condition (which strengthens the conditions in the previous result) for a plane graph G of maximum degree 3 to have an orthogonal convex drawing without bends. We further strengthen the results such that if G satisfies the same conditions as in previous papers, it not only has an orthogonally convex drawing, but also a stronger star-shaped orthogonal drawing