Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma

Background:
The physical periphery of a biological cell is mainly described by signaling pathways which are triggered by transmembrane proteins and receptors that are sentinels to control the whole gene regulatory network of a cell. However, our current knowledge about the gene regulatory mechanisms that are governed by extracellular signals is severely limited.Results: The purpose of this paper is three fold. First, we infer a gene regulatory network from a large-scale B-cell lymphoma expression data set using the C3NET algorithm. Second, we provide a functional and structural analysis of the largest connected component of this network, revealing that this network component corresponds to the peripheral region of a cell. Third, we analyze the hierarchical organization of network components of the whole inferred B-cell gene regulatory network by introducing a new approach which exploits the variability within the data as well as the inferential characteristics of C3NET. As a result, we find a functional bisection of the network corresponding to different cellular components.

Conclusions:
Overall, our study allows to highlight the peripheral gene regulatory network of B-cells and shows that it is centered around hub transmembrane proteins located at the physical periphery of the cell. In addition, we identify a variety of novel pathological transmembrane proteins such as ion channel complexes and signaling receptors in B-cell lymphoma. © 2012 Simoes et al.; licensee BioMed Central Ltd.

Evaluating program integration and the rise in collaboration:Case study of a palliative care network

Introduction: There is increasing global interest in using regional palliative care networks (PCNs) to integrate care and create systems that are more costeffective and responsive. We examined a PCN that used a community development approach to build capacity for palliative care in each distinct community in a region of southern Ontario, Canada, with the goal of achieving a competent integrated system. Methods: Using a case study methodology, we examined a PCN at the structural level through a document review, a survey of 20 organizational administrators, and an interview with the network director. Results: The PCN identified 14 distinct communities at different stages of development within the region. Despite the lack of some key features that would facilitate efficient palliative care delivery across these communities, administrators largely viewed the network partnership as beneficial and collaborative. Conclusion: The PCN has attempted to recognize specific needs in each local area. Change Is gradual but participatory. There remain structural issues that may negatively affect the functioning of the PCN.

Functional and genetic analysis of the colon cancer network

Cancer is a complex disease that has proven to be difficult to understand on the single-gene level. For this reason a functional elucidation needs to take interactions among genes on a systems-level into account. In this study, we infer a colon cancer network from a large-scale gene expression data set by using the method BC3Net. We provide a structural and a functional analysis of this network and also connect its molecular interaction structure with the chromosomal locations of the genes enabling the definition of cis- and trans-interactions. Furthermore, we investigate the interaction of genes that can be found in close neighborhoods on the chromosomes to gain insight into regulatory mechanisms. To our knowledge this is the first study analyzing the genome-scale colon cancer network.

Simultaneous Measurements of the Channel Response for Multiple Eavesdroppers Operating in the Vicinity of a Body Area Network at 2.45 GHz

Channel randomness can be exploited to generate secret keys. However, to ensure secrecy, it is necessary that the channel response of any eavesdropping party remain sufficiently de-correlated with that of the legitimate users'. In this paper, we investigate whether such de-correlation occurs for a body area network (BAN) operating in an indoor environment at 2.45 GHz. The hypothetical BAN configuration consisted of two legitimate transceivers, one situated on the user's left wrist and the other on the user's waist. The eavesdroppers were positioned in either a co-located or distributed manner in the area surrounding the BAN user. Using the simultaneous channel response measured at the legitimate BAN nodes and the eavesdropper positions for stationary and mobile scenarios, we analyze the localized correlation coefficient. This allows us to determine if it is possible to generate secret keys in the presence of multiple eavesdroppers in an indoor environment. Our experimental results show that although channel reciprocity was observed for both the stationary and the mobile scenarios, a higher de-correlation between the legitimate users' channels was observed for the stationary case. This indicates that mobile scenarios are better suited for secret key generation.

Objects of Transcendence: Scots Protestantism and an Anthropology of Things

This anthropological essay takes as its ethnographic point of departure two apparently contrasting deployments of the Bible within contemporary Scotland, one as observed among Brethren and Presbyterian fisher-families in Gamrie, coastal Aberdeenshire, and the other as observed among the Orange Order, a Protestant marching fraternity, in Airdrie and Glasgow. By examining how and with what effects the Bible and other objects (plastic crowns, ‘Sunday clothes’, Orange regalia) enter into and extend beyond the everyday practices of fishermen and Orangemen, my aim is to sketch different aspects of the material life of Scottish Protestantism. By offering a critique of Bruno Latour’s early writing on ‘quasi-objects’ via Alfred Gell’s notion of ‘distributed personhood’, I seek to undermine the sociological assumption that modernity and enchantment are mutually exclusive.

Face Recognition in the Scrambled Domain via Salience-Aware Ensembles of Many Kernels

With the rapid development of internet-of-things (IoT), face scrambling has been proposed for privacy protection during IoT-targeted image/video distribution. Consequently in these IoT applications, biometric verification needs to be carried out in the scrambled domain, presenting significant challenges in face recognition. Since face models become chaotic signals after scrambling/encryption, a typical solution is to utilize traditional data-driven face recognition algorithms. While chaotic pattern recognition is still a challenging task, in this paper we propose a new ensemble approach – Many-Kernel Random Discriminant Analysis (MK-RDA) to discover discriminative patterns from chaotic signals. We also incorporate a salience-aware strategy into the proposed ensemble method to handle chaotic facial patterns in the scrambled domain, where random selections of features are made on semantic components via salience modelling. In our experiments, the proposed MK-RDA was tested rigorously on three human face datasets: the ORL face dataset, the PIE face dataset and the PUBFIG wild face dataset. The experimental results successfully demonstrate that the proposed scheme can effectively handle chaotic signals and significantly improve the recognition accuracy, making our method a promising candidate for secure biometric verification in emerging IoT applications.

Evaluation of the human factor in the scheduling of smart appliances in smart grids

Recently there has been an increase of interest in implementing a new set of home appliances, known as Smart Appliances that integrate Information Technologies, the Internet of Things and the ability of communicating with other devices. While Smart Appliances are characterized as an important milestone on the path to the Smart Grid, by being able to automatically schedule their loads according to a tariff or reflecting the power that is generated using renewable sources, there is not a clear understanding on the impact that the behavior of such devices will have in the comfort levels of users, when they shift their working periods to earlier, or later than, a preset time. Given these considerations, in this work we analyse the results of an assessment survey carried out to a group of Home Appliance users regarding their habits when dealing with these machines and the subjective impact in quality caused by either finishing its programs before or after the time limit set by the user. The results of this work are expected to be used as input for the evaluation of load scheduling algorithms running in energy management systems. © 2014 Springer International Publishing.

Route planning in wireless sensor networks for data gathering purposes

Dissertação de Mestrado, Engenharia Informática, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015