Bi-Objective Community Detection (BOCD) in Networks using Genetic Algorithm

A lot of research effort has been put into community detection from all corners of academic interest such as physics, mathematics and computer science. In this paper I have proposed a Bi-Objective Genetic Algorithm for community detection which maximizes modularity and community score. Then the results obtained for both benchmark and real life data sets are compared with other algorithms using the modularity and MNI performance metrics. The results show that the BOCD algorithm is capable of successfully detecting community structure in both real life and synthetic datasets, as well as improving upon the performance of previous techniques.Comment: 11 pages, 3 Figures, 3 Tables. arXiv admin note: substantial text overlap with arXiv:0906.061

Design and simulation of a SOI based mems differential accelerometer

In this paper, the design and analysis of a differential MEMS capacitive accelerometer is presented. The device is designed to be compatible for SOI based fabrication process. The outstanding mechanical and electrical properties of silicon on insulator (SOI) wafers make it popular for high-performance MEMS sensors such as accelerometers. The operating range of the designed device is 0-10g with its sense axis in the in-plane direction. The movable comb fingers attached to the proof mass form capacitors with the fixed electrode fingers. The movable and fixed fingers are spaced with unequal gaps to form the differential capacitive sensing configuration. The base capacitance of this configuration is about 0.77pF and the sensitivity in response to acceleration input is about 0.776 fF/g. The resonance frequency of the structure in the sensing mode is found to be 7.138 kHz.The work was partially funded by the Russian Federation Ministry of Education and Science

Warm stellar matter with deconfinement: application to compact stars

We investigate the properties of mixed stars formed by hadronic and quark matter in $\beta$-equilibrium described by appropriate equations of state (EOS) in the framework of relativistic mean-field theory. We use the non- linear Walecka model for the hadron matter and the MIT Bag and the Nambu-Jona-Lasinio models for the quark matter. The phase transition to a deconfined quark phase is investigated. In particular, we study the dependence of the onset of a mixed phase and a pure quark phase on the hyperon couplings, quark model and properties of the hadronic model. We calculate the strangeness fraction with baryonic density for the different EOS. With the NJL model the strangeness content in the mixed phase decreases. The calculations were performed for T=0 and for finite temperatures in order to describe neutron and proto-neutron stars. The star properties are discussed. Both the Bag model and the NJL model predict a mixed phase in the interior of the star. Maximum allowed masses for proto-neutron stars are larger for the NJL model ($\sim 1.9$ M$_{\bigodot}$) than for the Bag model ($\sim 1.6$ M$_{\bigodot}$).Comment: RevTeX,14 figures, accepted to publication in Physical Review

Scintillation Counters for the D0 Muon Upgrade

We present the results of an upgrade to the D0 muon system. Scintillating counters have been added to the existing central D0 muon system to provide rejection for cosmic ray muons and out-of-time background, and to provide additional fast timing information for muons in an upgraded Tevatron. Performance and results from the 1994-1996 Tevatron run are presented.Comment: 30 pages, 25 postscript figure

Two‐Photon‐Induced CO‐Releasing Molecules as Molecular Logic Systems in Solution, Polymers, and Cells

Phototherapeutic applications of carbon monoxide (CO)‐releasing molecules are limited because they require harmful UV and blue light for activation. We describe two‐photon excitation with NIR light (800 nm)‐induced CO‐release from two MnI tricarbonyl complexes bearing 1,8‐naphthalimide units (1, 2). Complex 2 behaves as a logic OR gate in solution, nonwovens, and in HeLa cells. CO release, indicated by fluorescence enhancement, was detected in solution, nonwoven, and HeLa cells by single‐ (405 nm) and two‐photon (800 nm) excitation. The photophysical properties of 1 and 2 have been measured and supported by DFT and TDDFT quantum chemical calculations. Both photoCORMs are stable in the dark in solution and noncytotoxic, leading to promising applications as phototherapeutics with NIR light.Metals in Catalysis, Biomimetics & Inorganic Material

Fibroblastic niches prime T cell alloimmunity through Delta-like Notch ligands.

Alloimmune T cell responses induce graft-versus-host disease (GVHD), a serious complication of allogeneic bone marrow transplantation (allo-BMT). Although Notch signaling mediated by Delta-like 1/4 (DLL1/4) Notch ligands has emerged as a major regulator of GVHD pathogenesis, little is known about the timing of essential Notch signals and the cellular source of Notch ligands after allo-BMT. Here, we have shown that critical DLL1/4-mediated Notch signals are delivered to donor T cells during a short 48-hour window after transplantation in a mouse allo-BMT model. Stromal, but not hematopoietic, cells were the essential source of Notch ligands during in vivo priming of alloreactive T cells. GVHD could be prevented by selective inactivation of Dll1 and Dll4 in subsets of fibroblastic stromal cells that were derived from chemokine Ccl19-expressing host cells, including fibroblastic reticular cells and follicular dendritic cells. However, neither T cell recruitment into secondary lymphoid organs nor initial T cell activation was affected by Dll1/4 loss. Thus, we have uncovered a pathogenic function for fibroblastic stromal cells in alloimmune reactivity that can be dissociated from their homeostatic functions. Our results reveal what we believe to be a previously unrecognized Notch-mediated immunopathogenic role for stromal cell niches in secondary lymphoid organs after allo-BMT and define a framework of early cellular and molecular interactions that regulate T cell alloimmunity

A critical review on modelling formalisms and simulation tools in computational biosystems

Integration of different kinds of biological processes is an ultimate goal for whole-cell modelling. We briefly review modelling formalisms that have been used in Systems Biology and identify the criteria that must be addressed by an integrating framework capable of modelling, analysing and simulating different biological networks. Aware that no formalism can fit all purposes we realize Petri nets as a suitable model for Metabolic Engineering and take a deeper perspective on the role of this formalism as an integrating framework for regulatory and metabolic networks.Research supported by PhD grant SFRH/BD/35215/2007 from the Fundacao para a Ciencia e a Tecnologia (FCT) and the MIT-Portugal program

Enteropathogenic Escherichia coli (EPEC) inactivate innate immune responses prior to compromising epithelial barrier function

Enteropathogenic Escherichia coli (EPEC) infection of the human small intestine induces severe watery diarrhoea linked to a rather weak inflammatory response despite EPEC's in vivo capacity to disrupt epithelial barrier function. Here, we demonstrate that EPEC flagellin triggers the secretion of the pro-inflammatory cytokine, interleukin (IL)-8, from small (Caco-2) and large (T84) intestinal epithelia model systems. Interestingly, IL-8 secretion required basolateral infection of T84 cells implying that flagellin must penetrate the epithelial barrier. In contrast, apical infection of Caco-2 cells induced IL-8 secretion but less potently than basolateral infections. Importantly, infection of Caco-2, but not T84 cells rapidly inhibited IL-8 secretion by a mechanism dependent on the delivery of effectors through a translocation system encoded on the locus of enterocyte effacement (LEE). Moreover, EPEC prevents the phosphorylation-associated activation of multiple kinase pathways regulating IL-8 gene transcription by a mechanism apparently independent of LEE-encoded effectors and four non-LEE-encoded effectors. Crucially, our studies reveal that EPEC inhibits the capacity of the cells to secrete IL-8 in response to bacterial antigens and inflammatory cytokines prior to disrupting barrier function by a distinct mechanism. Thus, these findings also lend themselves to a plausible mechanism to explain the absence of a strong inflammatory response in EPEC-infected humans

Maintenance Therapies for Hodgkin and Non-Hodgkin Lymphomas after Autologous Transplantation: A Consensus Project of ASBMT, CIBMTR, and the Lymphoma Working Party of EBMT

Importance: Maintenance therapies are often considered as a therapeutic strategy in patients with lymphoma following autologous hematopoietic cell transplantation (auto-HCT) to mitigate the risk of disease relapse. With an evolving therapeutic landscape, where novel drugs are moving earlier in therapy lines, evidence relevant to contemporary practice is increasingly limited. The American Society for Blood and Marrow Transplantation (ASBMT), Center for International Blood and Marrow Transplant Research (CIBMTR), and European Society for Blood and Marrow Transplantation (EBMT) jointly convened an expert panel with diverse expertise and geographical representation to formulate consensus recommendations regarding the use of maintenance and/or consolidation therapies after auto-HCT in patients with lymphoma. Observations: The RAND-modified Delphi method was used to generate consensus statements where at least 75% vote in favor of a recommendation was considered as consensus. The process included 3 online surveys moderated by an independent methodological expert to ensure anonymity and an in-person meeting. The panel recommended restricting the histologic categories covered in this project to Hodgkin lymphoma (HL), mantle cell lymphoma (MCL), diffuse large B-cell lymphoma (DLBCL), and follicular lymphoma. On completion of the voting process, the panel generated 22 consensus statements regarding post auto-HCT maintenance and/or consolidation therapies. The grade A recommendations included endorsement of: (1) brentuximab vedotin (BV) maintenance and/or consolidation in BV-na\uefve high-risk HL, (2) rituximab maintenance in MCL undergoing auto-HCT after first-line therapy, (3) rituximab maintenance in rituximab-na\uefve FL, and (4) No post auto-HCT maintenance was recommended in DLBCL. The panel also developed consensus statements for important real-world clinical scenarios, where randomized data are lacking to guide clinical practice. Conclusions and Relevance: In the absence of contemporary evidence-based data, the panel found RAND-modified Delphi methodology effective in providing a rigorous framework for developing consensus recommendations for post auto-HCT maintenance and/or consolidation therapies in lymphoma.