VisANT: an online visualization and analysis tool for biological interaction data

BACKGROUND: New techniques for determining relationships between biomolecules of all types – genes, proteins, noncoding DNA, metabolites and small molecules – are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems. RESULTS: We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology. CONCLUSION: VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at

Gluon penguin enhancements to inclusive charmless decays of b quark in the 2HDM with flavor changing couplings

We calculate the enhancements to the inclusive charmless decays of b quark, $b \to s g, s q\bar{q}, sgg$, from gluon penguin diagrams induced by the charged and neutral Higgs bosons $(H^{\pm}, h^0, H^0$, and A^0) in the Two-Higgs-Doublet Model with flavor-changing couplings. Within the considered parameter space, the new contributions from charged Higgs boson are dominant. After including the new contributions, the branching ratio $BR(b \to sg)$ (q^2 =0) can be increased form $\sim 0.2$ in the standard model to 4.4% and 2.6% in the two-Higgs-doublet model for $m_{H^+}=100$ and 200 GeV, respectively. The new contribution to the decay mode $b \to s q \bar{q}$ with q=(u,d,s) is, however, numerically small and peaked at the lower q^2 region. The new contribution to $b \to s gg$ can also be neglected.Comment: Latex file, 14 pages with 6 PS or EPS figures. corrected some typos, added new reference

Spatial Self-Distillation for Object Detection with Inaccurate Bounding Boxes

Object detection via inaccurate bounding boxes supervision has boosted a broad interest due to the expensive high-quality annotation data or the occasional inevitability of low annotation quality (\eg tiny objects). The previous works usually utilize multiple instance learning (MIL), which highly depends on category information, to select and refine a low-quality box. Those methods suffer from object drift, group prediction and part domination problems without exploring spatial information. In this paper, we heuristically propose a \textbf{Spatial Self-Distillation based Object Detector (SSD-Det)} to mine spatial information to refine the inaccurate box in a self-distillation fashion. SSD-Det utilizes a Spatial Position Self-Distillation \textbf{(SPSD)} module to exploit spatial information and an interactive structure to combine spatial information and category information, thus constructing a high-quality proposal bag. To further improve the selection procedure, a Spatial Identity Self-Distillation \textbf{(SISD)} module is introduced in SSD-Det to obtain spatial confidence to help select the best proposals. Experiments on MS-COCO and VOC datasets with noisy box annotation verify our method's effectiveness and achieve state-of-the-art performance. The code is available at https://github.com/ucas-vg/PointTinyBenchmark/tree/SSD-Det.Comment: accepted by ICCV 202

VisANT: data-integrating visual framework for biological networks and modules

VisANT is a web-based software framework for visualizing and analyzing many types of networks of biological interactions and associations. Networks are a useful computational tool for representing many types of biological data, such as biomolecular interactions, cellular pathways and functional modules. Given user-defined sets of interactions or groupings between genes or proteins, VisANT provides: (i) a visual interface for combining and annotating network data, (ii) supporting function and annotation data for different genomes from the Gene Ontology and KEGG databases and (iii) the statistical and analytical tools needed for extracting topological properties of the user-defined networks. Users can customize, modify, save and share network views with other users, and import basic network data representations from their own data sources, and from standard exchange formats such as PSI-MI and BioPAX. The software framework we employ also supports the development of more sophisticated visualization and analysis functions through its open API for Java-based plug-ins. VisANT is distributed freely via the web at and can also be downloaded for individual use

VisANT: data-integrating visual framework for biological networks and modules

VisANT is a web-based software framework for visualizing and analyzing many types of networks of biological interactions and associations. Networks are a useful computational tool for representing many types of biological data, such as biomolecular interactions, cellular pathways and functional modules. Given user-defined sets of interactions or groupings between genes or proteins, VisANT provides: (i) a visual interface for combining and annotating network data, (ii) supporting function and annotation data for different genomes from the Gene Ontology and KEGG databases and (iii) the statistical and analytical tools needed for extracting topological properties of the user-defined networks. Users can customize, modify, save and share network views with other users, and import basic network data representations from their own data sources, and from standard exchange formats such as PSI-MI and BioPAX. The software framework we employ also supports the development of more sophisticated visualization and analysis functions through its open API for Java-based plug-ins. VisANT is distributed freely via the web at and can also be downloaded for individual use

PO-132 Exogenous VD3 alleviates chronic fatigue syndrome by activating MEKs/ERKs-SIRT1 signaling pathway in skeletal muscle

Objective To investigate the effects of exogenous VD3 on exercise-induced chronic fatigue syndrome (CFS) and its mechanism. Methods 80 male mice were randomly divided into 5 groups（n=16）. One group was named as quiet control group (C) while the other four were used to build CFS model by forced swimming. Among the four groups, three were selected for feeding VD3 1 h before exercise (bVD), 15 min after starting exercise (mVD) and 1 h after exercise (aVD) respectively, and the group without VD3 feeding was CFS model group (CFS). The behavior and condition of mice was observed during the whole process. After the training was completed totally, the tail suspension test and the forced swimming test were implemented, and then the blood and quadriceps were dissected. Serum testosterone and corticosterone content, as well as the antioxidant system indexes in the quadriceps, including malondialdehyde (MDA), total antioxidant capacity (T-AOC), glutathione peroxidase (GSH-PX) and total superoxide dismutase (T-SOD), were measured. Routine western blotting experimentation was used to measure signal pathway indicators, containing SIRT1, SIRT3, ERK1/2, p-ERK1/2 and MEK1/2. Results Compared with C group, CFS group appeared serious damage caused by fighting, and the concentration of serum testosterone decreased significantly (p<0.01 or p<0.05) while cortisol concentration increased significantly (p<0.01 or p<0.05). Regarding antioxidant stress system indexes, the expression of MDA, T-SOD and GSH-PX significantly increased (p<0.05). The concentration of MEK and SIRT3 decreased significantly (p<0.01 or p<0.05). Compared with CFS group, VD intervention group (bVD, mVD and aVD) showed less damage caused by fighting and significantly lighter body weight (p<0.05), and the concentration of serum testosterone increased significantly (p<0.05) while that of cortisol decreased significantly (p<0.01 or p<0.05). The expression of MDA decreased significantly (p<0.05), on the countrary, T-AOC, T-SOD and GSH-PX increased significantly (p<0.05). The expressions of MEK, p-ERK/ERK, SIRT1 and SIRT3 were significantly upregulated (p<0.01 or p<0.05). Conclusions Exogenous VD3 could alleviate CFS, which probably related to activate the MEKs/ERKs-SIRT1 signal transduction axis and hence regulate the expression of SIRT3

Structures and Stabilities of Carbon Chain Clusters Influenced by Atomic Antimony

The C-C bond lengths of the linear magnetic neutral CnSb, CnSb+ cations and CnSb− anions are within 1.255–1.336 Å, which is typical for cumulene structures with moderately strong double-bonds. In this report, we found that the adiabatic ionization energy (IE) of CnSb decreased with n. When comparing the IE~n relationship of CnSb with that of pure Cn, we found that the latter exhibited a stair-step pattern (n ≥ 6), but the IE~n relationship of CnSb chains took the shape of a flat curve. The IEs of CnSb were lower than those of corresponding pure carbon chains. Different from pure carbon chains, the adiabatic electron affinity of CnSb does not exhibit a parity effect. There is an even-odd alternation for the incremental binding energies of the open chain CnSb (for n = 1–16) and CnSb+ (n = 1–10, when n > 10, the incremental binding energies of odd (n) chain of CnSb+ are larger than adjacent clusters). The difference in the incremental binding energies between the even and odd chains of both CnSb and pure Cn diminishes with the increase in n. The incremental binding energies for CnSb- anions do not exhibit a parity effect. For carbon chain clusters, the most favorable binding site of atomic antimony is the terminal carbon of the carbon cluster because the terminal carbon with a large spin density bonds in an unsaturated way. The C-Sb bond is a double bond with Wiberg bond index (WBI) between 1.41 and 2.13, which is obviously stronger for a carbon chain cluster with odd-number carbon atoms. The WBI of all C-C bonds was determined to be between 1.63 and 2.01, indicating the cumulene character of the carbon chain. Generally, the alteration of WBI and, in particular, the carbon chain cluster is consistent with the bond length alteration. However, the shorter C-C distance did not indicate a larger WBI. Rather than relying on the empirical comparison of bond distance, the WBI is a meaningful quantitative indicator for predicting the bonding strength in the carbon chain

Experimental study on the uniaxial compressive behaviour of a fibre reinforced polymer standing support

Laboratory tests were conducted to investigate the behaviour of an innovative fibre reinforced polymer (FRP) standing support subject to uniaxial compression. The FRP standing support consisted of two major components: 1) the internal cylindrical concrete column made of coal rejects and a cementitious grout, and 2) the external FRP jacket. A total of ten specimens with different water-to-cementitious grout (w/c) ratios and various layers of FRP confinement were prepared and tested. As expected, an increased w/c ratio adversely affected the compressive strength of the internal cylindrical column. The compressive strength of the column decreased from 15.9 MPa to 13.4 MPa when the w/c ratio increased from 1 to 1.2. Test results also indicated that the columns became much stronger and more deformable when confined with an FRP jacket. In contrast to the unconfined control specimens, the columns confined with two layers of FRP experienced an increase of approximately 150% in maximum compressive strength at approximately 500% higher axial deformation. A further growth in strength and deformability was also observed when the columns were confined with four layers of FRP. The maximum strength and deformability achieved were up to 49.6 MPa and 7.2% respectively

Optimization of urban mini-bus stop spacing: a case study of Shanghai (China)

U posljednjih se nekoliko godina služba mini-autobusa brzo razvija, a odgovarajući razmak između stajališta značajno poboljšava učinkovitost putovanja stanovnika. Kako bi mini-bus stajališta bila praktično locirana, u ovom se radu najprije predlaže matematički model temeljen na Voronoi dijagramima u svrhu smanjenja ukupnog vremena putovanja putnika. Za rješenje tog modela primijenjena je poboljšana tehnika Wilson-Han-Powell sekvencionalno kvadratno programiranje (SQP). Na temelju geografskih informacijskih sustava (GIS) korišten je Kartezijanski koordinatni sustav za izračunavanje pješačke udaljenosti između mini-bus stanica i početnih ili odredišta, koja se ne mogu izravno izmjeriti. Drugo, u skladu sa stvarnim stanjem, u radu se predlažu metode modifikacije za podešavanje stajališta mini-autobusa. Valjanost i korisnost metodologije ispitana je njenom primjenom na stvarnom slučaju u Šangaju (Kina). Rezultati proračuna pokazuje da se modelom dobro rješava problem određivanja razmaka između stajališta mini autobusa.In recent years, the mini-bus service has gained a rapid development, while the reasonable stop spacing is significant to improve residents’ travel efficiency. In order to locate the mini-bus stops practically, this paper firstly proposes a mathematical model based on Voronoi Diagrams to minimize residents’ total travel time. Improved Wilson-Han-Powell Sequential Quadratic Programming (SQP) technique is employed to solve the model. Based on Geographic Information Systems (GIS), the Cartesian coordinate system is used to calculate the walking distance between mini-bus stops and origins or destinations, which cannot be directly measured. Secondly, based on the actual situation, this paper proposes modification methods for adjusting mini-bus stops. The validity and usefulness of the methodology is tested through applying it to a real case in Shanghai (China). The calculation results suggest that the model deals well with the mini-bus stop spacing problem