FLEET: Butterfly Estimation from a Bipartite Graph Stream

We consider space-efficient single-pass estimation of the number of butterflies, a fundamental bipartite graph motif, from a massive bipartite graph stream where each edge represents a connection between entities in two different partitions. We present a space lower bound for any streaming algorithm that can estimate the number of butterflies accurately, as well as FLEET, a suite of algorithms for accurately estimating the number of butterflies in the graph stream. Estimates returned by the algorithms come with provable guarantees on the approximation error, and experiments show good tradeoffs between the space used and the accuracy of approximation. We also present space-efficient algorithms for estimating the number of butterflies within a sliding window of the most recent elements in the stream. While there is a significant body of work on counting subgraphs such as triangles in a unipartite graph stream, our work seems to be one of the few to tackle the case of bipartite graph streams.Comment: This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in Seyed-Vahid Sanei-Mehri, Yu Zhang, Ahmet Erdem Sariyuce and Srikanta Tirthapura. "FLEET: Butterfly Estimation from a Bipartite Graph Stream". The 28th ACM International Conference on Information and Knowledge Managemen

T Cell Polarization at the Virological Synapse

Cell-to-cell spread of HIV-1 between CD4+ T cells takes place at multimolecular structures called virological synapses. A defining feature of the virological synapse is polarization of viral assembly and budding at sites of T cell-T cell contact. Recent work is beginning to address how viral proteins are targeted to the virological synapse and the molecular mechanisms that regulate HIV-1 egress by cell-to-cell spread. This review discusses our current understanding of these processes and considers how T cell polarization during other forms of intercellular communication may provide insight into HIV-1 assembly and dissemination

Nef Decreases HIV-1 Sensitivity to Neutralizing Antibodies that Target the Membrane-proximal External Region of TMgp41

Primate lentivirus nef is required for sustained virus replication in vivo and accelerated progression to AIDS. While exploring the mechanism by which Nef increases the infectivity of cell-free virions, we investigated a functional link between Nef and Env. Since we failed to detect an effect of Nef on the quantity of virion-associated Env, we searched for qualitative changes by examining whether Nef alters HIV-1 sensitivity to agents that target distinct features of Env. Nef conferred as much as 50-fold resistance to 2F5 and 4E10, two potent neutralizing monoclonal antibodies (nAbs) that target the membrane proximal external region (MPER) of TMgp41. In contrast, Nef had no effect on HIV-1 neutralization by MPER-specific nAb Z13e1, by the peptide inhibitor T20, nor by a panel of nAbs and other reagents targeting gp120. Resistance to neutralization by 2F5 and 4E10 was observed with Nef from a diverse range of HIV-1 and SIV isolates, as well as with HIV-1 virions bearing Env from CCR5- and CXCR4-tropic viruses, clade B and C viruses, or primary isolates. Functional analysis of a panel of Nef mutants revealed that this activity requires Nef myristoylation but that it is genetically separable from other Nef functions such as the ability to enhance virus infectivity and to downregulate CD4. Glycosylated-Gag from MoMLV substituted for Nef in conferring resistance to 2F5 and 4E10, indicating that this activity is conserved in a retrovirus that does not encode Nef. Given the reported membrane-dependence of MPER-recognition by 2F5 and 4E10, in contrast to the membrane-independence of Z13e1, the data here is consistent with a model in which Nef alters MPER recognition in the context of the virion membrane. Indeed, Nef and Glycosylated-Gag decreased the efficiency of virion capture by 2F5 and 4E10, but not by other nAbs. These studies demonstrate that Nef protects lentiviruses from one of the most broadly-acting classes of neutralizing antibodies. This newly discovered activity for Nef has important implications for anti-HIV-1 immunity and AIDS pathogenesis

Rab11-FIP1C and Rab14 Direct Plasma Membrane Sorting and Particle Incorporation of the HIV-1 Envelope Glycoprotein Complex

The incorporation of the envelope glycoprotein complex (Env) onto the developing particle is a crucial step in the HIV-1 lifecycle. The long cytoplasmic tail (CT) of Env is required for the incorporation of Env onto HIV particles in T cells and macrophages. Here we identify the Rab11a-FIP1C/RCP protein as an essential cofactor for HIV-1 Env incorporation onto particles in relevant human cells. Depletion of FIP1C reduced Env incorporation in a cytoplasmic tail-dependent manner, and was rescued by replenishment of FIP1C. FIP1C was redistributed out of the endosomal recycling complex to the plasma membrane by wild type Env protein but not by CT-truncated Env. Rab14 was required for HIV-1 Env incorporation, and FIP1C mutants incapable of binding Rab14 failed to rescue Env incorporation. Expression of FIP1C and Rab14 led to an enhancement of Env incorporation, indicating that these trafficking factors are normally limiting for CT-dependent Env incorporation onto particles. These findings support a model for HIV-1 Env incorporation in which specific targeting to the particle assembly microdomain on the plasma membrane is mediated by FIP1C and Rab14. © 2013 Qi et al.Link_to_subscribed_fulltex

Cholesterol metabolism: A review of how ageing disrupts the biological mechanisms responsible for its regulation

Cholesterol plays a vital role in the human body as a precursor of steroid hormones and bile acids, in addition to providing structure to cell membranes. Whole body cholesterol metabolism is maintained by a highly coordinated balancing act between cholesterol ingestion, synthesis, absorption, and excretion. The aim of this review is to discuss how ageing interacts with these processes. Firstly, we will present an overview of cholesterol metabolism. Following this, we discuss how the biological mechanisms which underpin cholesterol metabolism are effected by ageing. Included in this discussion are lipoprotein dynamics, cholesterol absorption/synthesis and the enterohepatic circulation/synthesis of bile acids. Moreover, we discuss the role of oxidative stress in the pathological progression of atherosclerosis and also discuss how cholesterol biosynthesis is effected by both the mammalian target of rapamycin and sirtuin pathways. Next, we examine how diet and alterations to the gut microbiome can be used to mitigate the impact ageing has on cholesterol metabolism. We conclude by discussing how mathematical models of cholesterol metabolism can be used to identify therapeutic interventions

Health relevance of the modification of low grade inflammation in ageing (inflammageing) and the role of nutrition

Ageing of the global population has become a public health concern with an important socio-economic dimension. Ageing is characterized by an increase in the concentration of inflammatory markers in the bloodstream, a phenomenon that has been termed "inflammageing". The inflammatory response is beneficial as an acute, transient reaction to harmful conditions, facilitating the defense, repair, turnover and adaptation of many tissues. However, chronic and low grade inflammation is likely to be detrimental for many tissues and for normal functions. We provide an overview of low grade inflammation (LGI) and determine the potential drivers and the effects of the "inflamed" phenotype observed in the elderly. We discuss the role of gut microbiota and immune system crosstalk and the gut-brain axis. Then, we focus on major health complications associated with LGI in the elderly, including mental health and wellbeing, metabolic abnormalities and infections. Finally, we discuss the possibility of manipulating LGI in the elderly by nutritional interventions. We provide an overview of the evidence that exists in the elderly for omega-3 fatty acid, probiotic, prebiotic, antioxidant and polyphenol interventions as a means to influence LGI. We conclude that slowing, controlling or reversing LGI is likely to be an important way to prevent, or reduce the severity of, age-related functional decline and the onset of conditions affecting health and well-being; that there is evidence to support specific dietary interventions as a strategy to control LGI; and that a continued research focus on this field is warranted

Efficient Core Computation in Bipartite and Multilayer Graphs

Graphs are widely used to model the relationships of entities in a large spectrum of applications including social networks, world wide web, collaboration networks, and biology. Cohesive subgraph mining, as a fundamental graph problem, extracts highly connected structures from large graphs. Among the cohesive subgraph models, the core model, in which each node from the subgraph subject to a minimum degree constraint, has attracted great attention due to its elegant property and effectiveness in graph analysis. However, the massive graph volume and rapid evolution present huge challenges for core computation, which need highly efficient solutions. In this thesis, we study the problems of core computation in bipartite graphs and multilayer graphs. Firstly, we study the problem of (α,β)-core computation in bipartite graphs. We present an efficient algorithm for (α,β)-core computation based on a novel index such that the algorithm runs in linear time regarding the result size. We prove that the index only requires O(m) space where m is the number of edges in the bipartite graph. We also devise an efficient algorithm with time complexity O (δ ·m) for index construction where δ is bounded by √m and is much smaller than √m in practice. Secondly, we study the problem of (α,β)-core maintenance when the bipartite graph is dynamically updated. We show that we can decide whether a node should be updated or not by visiting its neighbours. Based on this locality property, we propose an efficient maintenance algorithm which only needs to visit a local subgraph near the inserted or removed edge. Furthermore, we discuss how to implement our maintenance algorithm in parallel. Finally, we study the problem of core computation in multilayer graphs, which is challenging due to the various combinations of layers. We propose a novel concept named CoreCube, which records the results of core computation on every combination of layers. We develop efficient algorithms to compute the CoreCube and devise a hybrid storage method that achieves a superior trade-off between the size of CoreCube and the query time. Extensive experiments on real-life datasets demonstrate our algorithms are effective and efficient

Surface Hydroxyl and Oxygen Vacancies Engineering in ZnSnAl LDH: Synergistic Promotion of Photocatalytic Oxidation of Aromatic VOCs

Photocatalytic oxidation has gained great interest in environmental remediation, but it is still limited by its low efficiency and catalytic deactivation in the degradation of aromatic VOCs. In this study, we concurrently regulated the surface hydroxyl and oxygen vacancies by introducing Al into ZnSn layered double hydroxide (LDH). The presence of distorted Al species induced local charge redistribution, leading to the remarkable formation of oxygen vacancies. These oxygen vacancies subsequently increased the amount of surface hydroxyl and elongated its bond length. The synergistic effects of surface hydroxyl and oxygen vacancies greatly enhanced reactant adsorption-activation and facilitated charge transfer to generate •OH, •O2–, and 1O2, resulting in highly efficient oxidation and ring-opening of various aromatic VOCs. Compared with commercial TiO2, the optimized ZnSnAl-50 catalyst exhibited about 2-fold activity for the toluene and styrene degradation and 10-fold activity for the chlorobenzene degradation. Moreover, ZnSnAl-50 demonstrated exceptional stability in the photocatalytic oxidation of toluene under a wide humidity range of 0–75%. This work marvelously improves the photocatalytic efficiency, stability, and adaptability through a novel strategy of surface hydroxyl and oxygen vacancies engineering

Boosting Ozone Catalytic Oxidation of Toluene at Room Temperature by Using Hydroxyl-Mediated MnO_<i>x</i>/Al₂O₃ Catalysts

Ozone catalytic oxidation (OZCO) has gained great interest in environmental remediation while it still faces a big challenge during the deep degradation of refractory volatile organic compounds (VOCs) at room temperature. Hydroxylation of the catalytic surface provides a new strategy for regulating the catalytic activity to boost VOC degradation. Herein, OZCO of toluene at room temperature over hydroxyl-mediated MnOx/Al2O3 catalysts was originally demonstrated. Specifically, a novel hydroxyl-mediated MnOx/Al2O3 catalyst was developed via the in situ AlOOH reconstruction method and used for toluene OZCO. The toluene degradation performance of MnOx/Al2O3 was significantly superior to those of most of the state-of-the-art catalysts, and 100% toluene was removed with an excellent mineralization rate (82.3%) and catalytic stability during OZCO. ESR and in situ DRIFTs results demonstrated that surface hydroxyl groups (HGs) greatly improved the reactive oxygen species generation, thus dramatically accelerating the benzene ring breakage and deep mineralization. Furthermore, HGs provided anchoring sites for uniformly dispersing MnOx and greatly enhanced toluene adsorption and ozone activation. This work paves a way for deep decomposition of aromatic VOCs at room temperature