Improving peer connectivity in wide-area overlays of virtual workstations

Self-configuring virtual networks rely on structured P2P routing to provide seamless connectivity among nodes through overlay routing of virtual IP packets, support decentralized hole-punching to establish bi-directional communication links among nodes behind network address translators, and dynamic configuration of virtual IP addresses. Our experiences with deployments of virtual networks in support of wide-area overlays of virtual workstations (WOWs) reveal that connectivity constraints imposed by symmetric NATs and by Internet route outages often hinder P2P overlay structure maintenance and routability, subsequently limiting the ability of WOWs to deliver high-throughput computing through aggregation of resources in different domains. In this paper, we describe and evaluate two novel approaches which are generally applicable and fully decentralized, and show that they improve routability of structured P2P networks in such connectivity constrained environments: (1) a fault-tolerant routing algorithm based on simulated annealing from optimization theory, and (2) tunneling of connections between adjacent nodes (in the P2P identifier space) over common neighbors when direct communication is not possible. Simulation-based analyses show that (1) when pairs of nodes only have 70% chance of being able to communicate directly, the described approaches improve all-to-all routability of the network from 90% to 99%, and (2) even when only 70% of the nodes are behind NATs that include symmetric NATs, these techniques improve the all-to-all connectivity of the network from less than 95% to more than 99%. We have implemented these techniques in the IP-over-P2P (IPOP) virtual network and have conducted experiments with a 180-node WOW Condor pool, demonstrating that, at 81% probability of establishing a pair-wise connection, annealing and tunneling combined allow all nodes to be connected to the pool, compared to only 160 nodes in the absence of these techniques.

A Finite Element Analysis Methodology for Representing the Articular Cartilage Functional Structure

Recognising that the unique biomechanical properties of articular cartilage are a consequence of its structure, this paper describes a finite element methodology which explicitly represents this structure using a modified overlay element model. The validity of this novel concept was then tested by using it to predict the axial curling forces generated by cartilage matrices subjected to saline solutions of known molality and concentration in a novel experimental protocol. Our results show that the finite element modelling methodology accurately represents the intrinsic biomechanical state of the cartilage matrix and can be used to predict its transient load-carriage behaviour. We conclude that this ability to represent the intrinsic swollen condition of a given cartilage matrix offers a viable avenue for numerical analysis of degenerate articular cartilage and also those matrices affected by disease.     

Importin β3 mediates the nuclear import of human ribosomal protein L7 through its interaction with the multifaceted basic clusters of L7

We show that importin β3 is essential for the nuclear import of L7. The import is mediated via the multifaceted basic amino acid clusters present in the NH₂-region of L7, and is RanGTP-dependent. Using a (EGFP)₃ reporter system and a FRAP assay, the role the individual clusters play as a functional NLS has been characterized, and each cluster was found to exhibit a different rate of real time nuclear uptake. We assume that having such a multiple NLS may provide L7 with preferential nuclear uptake.

Structured summary

MINT-7992735: Importin beta-3 (uniprotkb:O00410) binds (MI:0407) to L7 (uniprotkb:P18124) by biophysical (MI:0013)MINT-7992687: L7 (uniprotkb:P18124) binds (MI:0407) to Importin beta-3 (uniprotkb:O00410) by filter binding (MI:0049)MINT-7992699: L7 (uniprotkb:P18124) physically interacts (MI:0915) with Importin beta-3 (uniprotkb:O00410) by affinity chromatography technology (MI:0004)MINT-7992718: L7 (uniprotkb:P18124) physically interacts (MI:0915) with RAN (uniprotkb:P62826) by competition binding (MI:0405)MINT-7992671: L7 (uniprotkb:P18124) physically interacts (MI:0915) with Importin beta-3 (uniprotkb:O00410) by pull down (MI:0096)     

CAS平板覆盖法检测氢氧化细菌铁载体

【目的】用CAS平板覆盖法检测氢氧化细菌铁载体,解决通用CAS琼脂平板法中十六烷基三甲基溴化铵对真菌和某些细菌的生长抑制问题。【方法】将改良的CAS检测培养基覆盖在长满菌落的无铁培养基上,生长抑制问题因微生物未与十六烷基三甲基溴化铵直接接触而解决。【结果】3株氢氧化细菌SDW-5、SDW-9和AaP-13均能产生单菌落,加入CAS检测培养基1 h后,菌落周围产生明显的铁载体晕圈。【结论】本方法成功解决了生长抑制问题,可以作为检测微生物铁载体的通用方法。     

黄土丘陵沟壑区景观格局演变特征——以陕西省延安市为例

以陕西省延安市1985年、2000年和2008年三期1∶25万景观单元类型图,1∶5万地形图等生成的数字高程模型(DEM)为数据源,基于ArcGIS 9.3软件,采用多距离空间聚类、景观单元类型转移矩阵、空间数据叠加分析等方法分析了延安市景观格局的演变特征。结果表明:延安市的景观是由林地、灌木、草地和农田等基本景观单元构成的复合景观;研究期间农地面积急剧减少,流失的农地主要转变为林地、草地、灌木和聚落,除农地和裸地外,其他景观单元类型面积均有不同程度的增加;1985—2008年,林地、灌木和草地聚集的最大尺度减小,而农田聚集的最大尺度变大,农田和草地的空间聚集强度明显小于林地和灌木;延安市主要景观单元类型演变主要发生在海拔1100—1500 m之间的区域和坡度范围7—21°之间的区域,但农田向聚落的演变主要发生在海拔较低(900—1300 m)、坡度较缓(7°)的平川缓丘地带。1999年之前,经济的迅速发展是延安市景观格局演变的主要驱动因素;而1999年之后,国家推行的退耕还林(还草)等一系列生态重建措施成为延安市景观格局变化的主要驱动因素。     

全瓷冠、高嵌体与覆盖体对大面积牙体缺损后牙修复效果及牙周组织的影响

摘要 目的：探讨全瓷冠、高嵌体与覆盖体对大面积牙体缺损后牙修复效果及牙周组织的影响。方法：选择2015年6月到2018年5月选择在本院诊治的大面积牙体缺损后牙患者144例作为研究对象,根据随机抽签原则将其分为全瓷冠组、高嵌体组与覆盖体组各48例。全瓷冠组给予二氧化锆全瓷冠修复治疗,高嵌体组给予高嵌体修复治疗,覆盖体组给予覆盖体修复治疗,观察随访患者的预后情况。结果：三组修复后3个月的牙龈指数（GI）与探诊出血（BOP）阳性率低于修复前,高嵌体组、覆盖体组低于全瓷冠组（P<0.05）。全瓷冠组、高嵌体组、覆盖体组修复后3年的龋齿、牙周炎症、牙体修复体折断等并发症发生率为2.1 %、16.7 %、8.3 %,对比有差异（P<0.05）。高嵌体组、覆盖体组随访3年的修复体固位、修复体外形、修复体边缘适合性评分都高于全瓷冠组（P<0.05）。随访3年,三组修复体固位对比无差异（P>0.05）,但修复体外形、修复体边缘适合性对比有差异（P<0.05）。全瓷冠组、高嵌体组、覆盖体组随访3年的满意度分别为87.5 %、97.9 %和100.0 %,对比有差异（P<0.05）。结论：全瓷冠、高嵌体与覆盖体在大面积牙体缺损后牙修复的应用均具有一定的效果,对牙周组织也有一定的影响,在临床上要根据患者实际情况合理选择修复方法。     

Polyclonal Antibody Against a Recombinant Chlorotoxin-like Peptide from the Chinese Scorpion and Detection of its Putative Receptors in Human Glioma Cells

The nucleotide sequence of a type of chlorotoxin-like peptide, an inhibitor of small-conductance Cl⁻ channels, from the scorpion, Buthus martensii Karsch, was synthesized (named rBmK CTa) according to the sequence optimized for codon usage in E. coli. It was over-expressed using a pExSecI expression system and purified to homogeneity. Polycolonal antibodies to the purified protein were raised in rats. Overlay assay and pull-down assay showed that this toxin specially binds to two proteins in the glioma cells with corresponding molecular weights of about 80 and 35 kDa. They may serve as candidate receptors or alternative cellular component for interaction with rBmK CTa.     

Recombinant human Erythropoietin enhanced the cytotoxic effects of tamoxifen toward the spheroid MCF-7 breast cancer cells

Erythropoietin (EPO) is widely used to treat anemia in patients undergoing chemotherapy for cancers. The main objective of this study was to investigate the effect of rHuEPO on the response of spheroid breast cancer, MCF-7, cells to tamoxifen treatment. The MCF-7 spheroids were treated with 10 mg/mL tamoxifen in combination with either 0, 10, 100 or 200 IU/mL rHuEPO for 24, 48 or 72 h. The viability of the MCF-7 cells was determined using the annexin-V, cell cycle, caspases activation and acridine orange/propidium iodide staining. rHuEPO-tamoxifen combination significantly (p greater than 0.05) increased the number of spheroid MCF-7 cells entering early apoptotic phase after 12 h and late apoptotic phase after 24 h of treatment; primarily the result of the antiproliferative effect tamoxifen. Tamoxifen alone significantly (p < 0.05) increased the caspase-3 and −9 activities in the spheroid MCF-7 cells by 200 to 550% of the control. Combination rHuEPO and tamoxifen produced much lesser effect on the caspase-8 activity. The rHuEPO in the combination treatment had concentration-dependently caused decrease in the caspase activities. rHuEPO-tamoxifen combination markedly increased MCF-7 cells entering the SubG0/G1 phase of the cell cycle by more than 500% of the control, while decreasing those entering the G2 + M and S phases by 50%. After 72 h, the combination treatment produced greater (p < 0.05) change in the SubG0/G1 phase than tamoxifen treatment alone. Morphologically, spheroid MCF-7 cells subjected to combination rHuEPO-tamoxifen treatment showed nuclear condensation and margination, cytoplasmic blebbing, necrosis, and early and late apoptosis. Thus, the study showed that rHuEPO-tamoxifen combination induced apoptosis in the spheroid MCF-7 cells. The apoptotic effect of the rHuEPO-tamoxifen combination treatment on the MCF-7 cells was greater than that produced by tamoxifen alone. The rHuEPO-tamoxifen treatment enhanced the caspase-independent apoptotic effects of tamoxifen on the spheroid MCF-7 cells.     

EMDA: A Python package for Electron Microscopy Data Analysis

An open-source Python library EMDA for cryo-EM map and model manipulation is presented with a specific focus on validation. The use of several functionalities in the library is presented through several examples. The utility of local correlation as a metric for identifying map-model differences and unmodeled regions in maps, and how it is used as a metric of map-model validation is demonstrated. The mapping of local correlation to individual atoms, and its use to draw insights on local signal variations are discussed. EMDA’s likelihood-based map overlay is demonstrated by carrying out a superposition of two domains in two related structures. The overlay is carried out first to bring both maps into the same coordinate frame and then to estimate the relative movement of domains. Finally, the map magnification refinement in EMDA is presented with an example to highlight the importance of adjusting the map magnification in structural comparison studies.