Adaptive Preconditioned Gradient Descent with Energy

We propose an adaptive time step with energy for a large class of preconditioned gradient descent methods, mainly applied to constrained optimization problems. Our strategy relies on representing the usual descent direction by the product of an energy variable and a transformed gradient, with a preconditioning matrix, for example, to reflect the natural gradient induced by the underlying metric in parameter space or to endow a projection operator when linear equality constraints are present. We present theoretical results on both unconditional stability and convergence rates for three respective classes of objective functions. In addition, our numerical results shed light on the excellent performance of the proposed method on several benchmark optimization problems.Comment: 32 pages, 3 figure

Automatic Robot Hand-Eye Calibration Enabled by Learning-Based 3D Vision

Hand-eye calibration, as a fundamental task in vision-based robotic systems, aims to estimate the transformation matrix between the coordinate frame of the camera and the robot flange. Most approaches to hand-eye calibration rely on external markers or human assistance. We proposed Look at Robot Base Once (LRBO), a novel methodology that addresses the hand-eye calibration problem without external calibration objects or human support, but with the robot base. Using point clouds of the robot base, a transformation matrix from the coordinate frame of the camera to the robot base is established as I=AXB. To this end, we exploit learning-based 3D detection and registration algorithms to estimate the location and orientation of the robot base. The robustness and accuracy of the method are quantified by ground-truth-based evaluation, and the accuracy result is compared with other 3D vision-based calibration methods. To assess the feasibility of our methodology, we carried out experiments utilizing a low-cost structured light scanner across varying joint configurations and groups of experiments. The proposed hand-eye calibration method achieved a translation deviation of 0.930 mm and a rotation deviation of 0.265 degrees according to the experimental results. Additionally, the 3D reconstruction experiments demonstrated a rotation error of 0.994 degrees and a position error of 1.697 mm. Moreover, our method offers the potential to be completed in 1 second, which is the fastest compared to other 3D hand-eye calibration methods. Code is released at github.com/leihui6/LRBO.Comment: 17 pages, 19 figures, 6 tables, submitted to MSS

Retinal pigment epithelial cells secrete neurotrophic factors and synthesize dopamine: possible contribution to therapeutic effects of RPE cell transplantation in Parkinson's disease

<p>Abstract</p> <p>Background</p> <p>New strategies for the treatment of Parkinson's disease (PD) are shifted from dopamine (DA) replacement to regeneration or restoration of the nigro-striatal system. A cell therapy using human retinal pigment epithelial (RPE) cells as substitution for degenerated dopaminergic (DAergic) neurons has been developed and showed promising prospect in clinical treatment of PD, but the exact mechanism underlying this therapy is not fully elucidated. In the present study, we investigated whether the beneficial effects of this therapy are related to the trophic properties of RPE cells and their ability to synthesize DA.</p> <p>Methods</p> <p>We evaluated the protective effects of conditioned medium (CM) from cultured RPE cells on the DAergic cells against 6-hydroxydopamine (6-OHDA)- and rotenone-induced neurotoxicity and determined the levels of glial cell derived neurotrophic factor (GDNF) and brain derived neurotrophic factor (BDNF) released by RPE cells. We also measured the DA synthesis and release. Finally we transplanted microcarriers-RPE cells into 6-OHDA lesioned rats and observed the improvement in apomorphine-induced rotations (AIR).</p> <p>Results</p> <p>We report here: (1) CM from RPE cells can secret trophic factors GDNF and BDNF, and protect DAergic neurons against the 6-OHDA- and rotenone-induced cell injury; (2) cultured RPE cells express L-dopa decarboxylase (DDC) and synthesize DA; (3) RPE cells attached to microcarriers can survive in the host striatum and improve the AIR in 6-OHDA-lesioned animal model of PD; (4) GDNF and BDNF levels are found significantly higher in the RPE cell-grafted tissues.</p> <p>Conclusion</p> <p>These findings indicate the RPE cells have the ability to secret GDNF and BDNF, and synthesize DA, which probably contribute to the therapeutic effects of RPE cell transplantation in PD.</p

Nurr1 regulates Top IIβ and functions in axon genesis of mesencephalic dopaminergic neurons

<p>Abstract</p> <p>Background</p> <p>NURR1 (also named as NR4A2) is a member of the steroid/thyroid hormone receptor family, which can bind to DNA and modulate expression of target genes. Previous studies have shown that NURR1 is essential for the nigral dopaminergic neuron phenotype and function maintenance, and the defects of the gene are possibly associated with Parkinson's disease (PD).</p> <p>Results</p> <p>In this study, we used new born <it>Nurr1 </it>knock-out mice combined with Affymetrix genechip technology and real time polymerase chain reaction (PCR) to identify <it>Nurr1 </it>regulated genes, which led to the discovery of several transcripts differentially expressed in the nigro-striatal pathway of <it>Nurr1 </it>knock-out mice. We found that an axon genesis gene called <it>Topoisomerase IIβ </it>(<it>Top IIβ</it>) was down-regulated in <it>Nurr1 </it>knock-out mice and we identified two functional NURR1 binding sites in the proximal <it>Top IIβ </it>promoter. While in <it>Top IIβ </it>null mice, we saw a significant loss of dopaminergic neurons in the substantial nigra and lack of neurites along the nigro-striatal pathway. Using specific TOP II antagonist ICRF-193 or <it>Top IIβ </it>siRNA in the primary cultures of ventral mesencephalic (VM) neurons, we documented that suppression of TOP IIβ expression resulted in VM neurites shortening and growth cones collapsing. Furthermore, microinjection of ICRF-193 into the mouse medial forebrain bundle (MFB) led to the loss of nigro-striatal projection.</p> <p>Conclusion</p> <p>Taken together, our findings suggest that <it>Top IIβ </it>might be a down-stream target of <it>Nurr1</it>, which might influence the processes of axon genesis in dopaminergic neurons via the regulation of TOP IIβ expression. The <it>Nurr1-Top IIβ </it>interaction may shed light on the pathologic role of <it>Nurr1 </it>defect in the nigro-striatal pathway deficiency associated with PD.</p

A Compact Dielectric Resonator Antenna Excited by a Planar Monopole Patch for Wideband Applications

A compact dielectric resonator antenna (DRA) suitable for wideband applications is presented in this paper. The proposed antenna is mainly composed by a notched cylindrical dielectric resonator (DR) coated with a metal surface on the top and a finite ground plane where the presented DR is placed. This antenna is very simple in structure and has a very low overall height of 0.14λmin at its lowest operation frequency. A comprehensive parametric study is carried out based on Ansoft HFSS to optimize the bandwidth. The proposed antenna has been successfully simulated, optimized, fabricated, and measured. The measurement results demonstrate that the proposed design produces an impedance bandwidth of more than 75%, ranging from 2.9 GHz to 6.7 GHz for the reflection coefficient less than −10 dB. In particular, consistent broadside radiation patterns, stable gain, and high radiation efficiency are also obtained within the operation frequency band

Overlapping Structures Detection in Protein-Protein Interaction Networks Using Community Detection Algorithm Based on Neighbor Clustering Coefficient

With the rapid development of bioinformatics, researchers have applied community detection algorithms to detect functional modules in protein-protein interaction (PPI) networks that can predict the function of unknown proteins at the molecular level and further reveal the regularity of cell activity. Clusters in a PPI network may overlap where a protein is involved in multiple functional modules. To identify overlapping structures in protein functional modules, this paper proposes a novel overlapping community detection algorithm based on the neighboring local clustering coefficient (NLC). The contributions of the NLC algorithm are threefold: (i) Combine the edge-based community detection method with local expansion in seed selection and the local clustering coefficient of neighboring nodes to improve the accuracy of seed selection; (ii) A method of measuring the distance between edges is improved to make the result of community division more accurate; (iii) A community optimization strategy for the excessive overlapping nodes makes the overlapping structure more reasonable. The experimental results on standard networks, Lancichinetti-Fortunato-Radicchi (LFR) benchmark networks and PPI networks show that the NLC algorithm can improve the Extended modularity (EQ) value and Normalized Mutual Information (NMI) value of the community division, which verifies that the algorithm can not only detect reasonable communities but also identify overlapping structures in networks

Conjugation polymer nanobelts: a novel fluorescent sensing platform for nucleic acid detection†

In this article, we report on the facile and rapid synthesis of conjugation polymer poly(p-phenylenediamine) nanobelts (PNs) via room temperature chemical oxidation polymerization of p-phenylenediamine monomers by ammonium persulfate in aqueous medium. We further demonstrate the proof-of-concept that PNs can be used as an effective fluorescent sensing platform for nucleic acid detection for the first time. The general concept used in this approach lies in the facts that the adsorption of the fluorescently labeled single-stranded DNA probe by PN leads to substantial fluorescence quenching, followed by specific hybridization with the complementary region of the target DNA sequence. This results in desorption of the hybridized complex from PN surface and subsequent recovery of fluorescence. We also show that the sensing platform described herein can be used for multiplexing detection of nucleic acid sequences

MyBASE: a database for genome polymorphism and gene function studies of Mycobacterium

<p>Abstract</p> <p>Background</p> <p>Mycobacterial pathogens are a major threat to humans. With the increasing availability of functional genomic data, research on mycobacterial pathogenesis and subsequent control strategies will be greatly accelerated. It has been suggested that genome polymorphisms, namely large sequence polymorphisms, can influence the pathogenicity of different mycobacterial strains. However, there is currently no database dedicated to mycobacterial genome polymorphisms with functional interpretations.</p> <p>Description</p> <p>We have developed a <b>my</b>cobacterial data<b>base </b>(MyBASE) housing genome polymorphism data and gene functions to provide the mycobacterial research community with a useful information resource and analysis platform. Whole genome comparison data produced by our lab and the novel genome polymorphisms identified were deposited into MyBASE. Extensive literature review of genome polymorphism data, mainly large sequence polymorphisms (LSPs), operon predictions and curated annotations of virulence and essentiality of mycobacterial genes are unique features of MyBASE. Large-scale genomic data integration from public resources makes MyBASE a comprehensive data warehouse useful for current research. All data is cross-linked and can be graphically viewed via a toolbox in MyBASE.</p> <p>Conclusion</p> <p>As an integrated platform focused on the collection of experimental data from our own lab and published literature, MyBASE will facilitate analysis of genome structure and polymorphisms, which will provide insight into genome evolution. Importantly, the database will also facilitate the comparison of virulence factors among various mycobacterial strains. MyBASE is freely accessible via <url>http://mybase.psych.ac.cn</url>.</p