Connectivity sharing for wireless mesh networks

Tesi en modalitat de cotutela: Universitat Politècnica de Catalunya i Katholieke Universiteit LeuvenInternet access is still unavailable to one-third of the world population due to the lack of infrastructure, high cost, and the digital divide. Many access-limited communities opt for shared Internet access where they build common network infrastructures to mitigate the cost. Internet connectivity in such infrastructures is typically provided by several limited, sometimes non-dedicated, gateways. Client nodes, i.e., the end-user hosts, use one gateway and switch to another when the first fails. In this scheme, the gateway configuration is done manually on the end-user side. This form of Internet connectivity is widespread and has the advantage that no central control is required, but it is also unreliable and inefficient due to several factors, such as unbalanced traffic load across the gateways. There is no doubt that the network would benefit from a gateway selection mechanism that can provide good connectivity to the client node as well as balanced load distribution and a dynamic adaptation to the current network state. However, providing such a dynamic gateway selection is complicated: since the perceived performance of the gateways changes frequently and might depend on the location of the client node in the network, and optimal selection would require the continuous monitoring of the gateway performance by the client node. The cost of such network-wide performance monitoring is high in large-scale networks and can outweigh the benefits of the dynamic gateway selection. The thesis's goal is to design a low-cost, distributed mechanism that provides an efficient and dynamic gateway selection while considering the overall balanced gateway selection distribution. To this end, we have split the problem of gateway selection into different sub-problems. First, we focus on reducing the cost of gateway performance monitoring. We propose an approach to reduce the number of monitoring requests generated by each node and analyze its effect on the gateway selection. Then, we present a collaborative monitoring method that allows neighbor nodes to share the load of the gateway monitoring. We show that every node can carry out the necessary tasks: performance monitoring, collaboration with its neighbors, and fault tolerance measures, with little computation and communication overhead. Second, to improve the gateway selection, we focus on making a selection decision that fulfills the individual performance requirements of the client nodes as well as global load balancing requirements. The solutions developed by us for the different sub-problems are embedded into a general and extensible, layered framework for gateway selection that we have called the Sense-Share-Select framework. Experimental validation and comparison with existing methods show that our framework provides accurate collaborative performance monitoring, improves the QoE for the nodes, and distributes the client nodes over the gateways in a balanced manner. The simplicity and flexibility of the framework make it adaptable to other network domains such as IoT networks and other scenarios where resource monitoring and load balancing are required.El acceso a Internet aún no está disponible para un tercio de la población mundial debido a la falta de infraestructuras, el alto costo y la brecha digital. Muchas comunidades con acceso limitado optan por el acceso compartido a Internet donde construyen infraestructuras de red comunitaria para mitigar el costo. La conectividad a Internet en dichas infraestructuras suele estar a cargo de varias puerta de enlaces limitadas en recursos, y a veces no dedicadas. Los nodos de cliente, es decir, los hosts de usuario final, utilizan una puerta de enlace y cambian a otra cuando falla la primera. En este esquema, la configuración de la puerta de enlace se realiza manualmente en el lado del usuario final. Esta forma de conectividad a Internet está muy extendida y tiene la ventaja de que no se requiere un control central, pero tampoco es confiable y eficiente debido a varios factores, como una carga desequilibrada de tráfico a través de las puertas de enlace. No hay duda de que la red se beneficiaría de un mecanismo de selección de pasarela que pueda proporcionar una buena conectividad al nodo cliente, así como una distribución equilibrada de la carga y una adaptación dinámica al estado actual de la red. Sin embargo, proporcionar una selección de puerta de enlace tan dinámica es complicado: dado que el rendimiento percibido de las puertas de enlace cambia con frecuencia y podría depender de la ubicación del nodo cliente en la red, y la selección óptima requeriría la supervisión continua del rendimiento de la puerta de enlace por parte del nodo cliente. El costo de dicha supervisión del rendimiento en toda la red es muy alto en redes de gran escala y puede superar los beneficios de la selección de puerta de enlace dinámica. El objetivo de la tesis es diseñar un mecanismo distribuido de bajo costo que proporcione una selección de puerta de enlace dinámica y eficiente al tiempo que considera la distribución general de selección de puerta de enlace equilibrada. Con este fin, hemos dividido el problema de la selección de la puerta de enlace en diferentes subproblemas. Primero, nos enfocamos en reducir el coste del monitoreo del rendimiento de la puerta de enlace. Proponemos un enfoque para reducir la cantidad de solicitudes de monitoreo generadas por cada nodo y analizar su efecto en la selección de la puerta de enlace. Luego, presentamos un método de monitoreo colaborativo que permite a los nodos vecinos compartir la carga del monitoreo de la puerta de enlace. Demostramos que cada nodo puede realizar las tareas necesarias: monitoreo del rendimiento, colaboración con sus vecinos y medidas de tolerancia a fallas, con poca sobrecarga de cómputo y comunicación. En segundo lugar, para mejorar la selección de la puerta de enlace, nos centramos en tomar una decisión de selección que cumpla con los requisitos de rendimiento individuales de los nodos del cliente, así como con los requisitos de equilibrio de carga global. Las soluciones desarrolladas por nosotros para los diferentes subproblemas están integradas en un marco general y extensible en capas para la selección de puertas de enlace que hemos llamado el marco Sense-Share-Select. La validación experimental y la comparación con los métodos existentes muestran que nuestro marco proporciona un monitoreo de rendimiento colaborativo preciso, mejora la QoE para los nodos y distribuye los nodos del cliente a través de las puertas de enlace de manera equilibrada. La simplicidad y flexibilidad del marco lo hacen adaptable a otros dominios de red, como las redes de IoT y otros escenarios donde se requiere monitoreo de recursos y equilibrio de carga.Postprint (published version

Investigation into the role of the germline epigenome in the transmission of glucocorticoid-programmed effects across generations.

BACKGROUND: Early life exposure to adverse environments affects cardiovascular and metabolic systems in the offspring. These programmed effects are transmissible to a second generation through both male and female lines, suggesting germline transmission. We have previously shown that prenatal overexposure to the synthetic glucocorticoid dexamethasone (Dex) in rats reduces birth weight in the first generation (F1), a phenotype which is transmitted to a second generation (F2), particularly through the male line. We hypothesize that Dex exposure affects developing germ cells, resulting in transmissible alterations in DNA methylation, histone marks and/or small RNA in the male germline. RESULTS: We profile epigenetic marks in sperm from F1 Sprague Dawley rats expressing a germ cell-specific GFP transgene following Dex or vehicle treatment of the mothers, using methylated DNA immunoprecipitation sequencing, small RNA sequencing and chromatin immunoprecipitation sequencing for H3K4me3, H3K4me1, H3K27me3 and H3K9me3. Although effects on birth weight are transmitted to the F2 generation through the male line, no differences in DNA methylation, histone modifications or small RNA were detected between germ cells and sperm from Dex-exposed animals and controls. CONCLUSIONS: Although the phenotype is transmitted to a second generation, we are unable to detect specific changes in DNA methylation, common histone modifications or small RNA profiles in sperm. Dex exposure is associated with more variable 5mC levels, particularly at non-promoter loci. Although this could be one mechanism contributing to the observed phenotype, other germline epigenetic modifications or non-epigenetic mechanisms may be responsible for the transmission of programmed effects across generations in this model

Glucocorticoids accelerate maturation of the heme pathway in fetal liver through effects on transcription and DNA methylation

<p>Glucocorticoids are widely used in threatened preterm labor to promote maturation in many organ systems in preterm babies and have significant beneficial effects on morbidity and mortality. We performed transcriptional profiling in fetal liver in a rat model of prenatal glucocorticoid exposure and identified marked gene expression changes in heme biosynthesis, utilization, and degradation pathways in late gestation. These changes in gene expression associated with alterations in DNA methylation and with a reduction in hepatic heme concentration. There were no persistent differences in gene expression, DNA methylation, or heme concentrations at 4 weeks of age, suggesting that these are transient effects. Our findings are consistent with glucocorticoid-induced accelerated maturation of the haematopoietic system and support the hypothesis that glucocorticoids can drive changes in gene expression in association with alterations in DNA methylation.</p

Placental 5-methylcytosine and 5-hydroxymethylcytosine patterns associate with size at birth

Altered placental function as a consequence of aberrant imprinted gene expression may be one mechanism mediating the association between low birth weight and increased cardiometabolic disease risk. Imprinted gene expression is regulated by epigenetic mechanisms, particularly DNA methylation (5mC) at differentially methylated regions (DMRs). While 5-hydroxymethylcytosine (5hmC) is also present at DMRs, many techniques do not distinguish between 5mC and 5hmC. Using human placental samples, we show that the expression of the imprinted gene CDKN1C associates with birth weight. Using specific techniques to map 5mC and 5hmC at DMRs controlling the expression of CDKN1C and the imprinted gene IGF2, we show that 5mC enrichment at KvDMR and DMR0, and 5hmC enrichment within the H19 gene body, associate positively with birth weight. Importantly, the presence of 5hmC at imprinted DMRs may complicate the interpretation of DNA methylation studies in placenta; future studies should consider using techniques that distinguish between, and permit quantification of, both modifications

CG dinucleotide clustering is a species-specific property of the genome

Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters

Combined effects of genotype and childhood adversity shape variability of DNA methylation across age

Lasting effects of adversity, such as exposure to childhood adversity (CA) on disease risk, may be embedded via epigenetic mechanisms but findings from human studies investigating the main effects of such exposure on epigenetic measures, including DNA methylation (DNAm), are inconsistent. Studies in perinatal tissues indicate that variability of DNAm at birth is best explained by the joint effects of genotype and prenatal environment. Here, we extend these analyses to postnatal stressors. We investigated the contribution of CA, cis genotype (G), and their additive (G+CA) and interactive (GxCA) effects to DNAm variability in blood or saliva from five independent cohorts with a total sample size of 1074 ranging in age from childhood to late adulthood. Of these, 541 were exposed to CA, which was assessed retrospectively using self-reports or verified through social services and registries. For the majority of sites (over 50%) in the adult cohorts, variability in DNAm was best explained by G+CA or GxCA but almost never by CA alone. Across ages and tissues, 1672 DNAm sites showed consistency of the best model in all five cohorts, with GxCA interactions explaining most variance. The consistent GxCA sites mapped to genes enriched in brain-specific transcripts and Gene Ontology terms related to development and synaptic function. Interaction of CA with genotypes showed the strongest contribution to DNAm variability, with stable effects across cohorts in functionally relevant genes. This underscores the importance of including genotype in studies investigating the impact of environmental factors on epigenetic marks.Peer reviewe

Comparative isoschizomer profiling of cytosine methylation:the HELP assay

The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its methylation-insensitive isoschizomer. This assay, termed HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR), allows both intragenomic profiling and intergenomic comparisons of cytosine methylation. The intragenomic profile shows most of the genome to be contiguous methylated sequence with occasional clusters of hypomethylated loci, usually but not exclusively at promoters and CpG islands. Intergenomic comparison found marked differences in cytosine methylation between spermatogenic and brain cells, identifying 223 new candidate tissue-specific differentially methylated regions (T-DMRs). Bisulfite pyrosequencing confirmed the four candidates tested to be T-DMRs, while quantitative RT-PCR for two genes with T-DMRs located at their promoters showed the HELP data to be correlated with gene activity at these loci. The HELP assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome. ©2006 by Cold Spring Harbor Laboratory Press

Combined effects of genotype and childhood adversity shape variability of DNA methylation across age

Lasting effects of adversity, such as exposure to childhood adversity (CA) on disease risk, may be embedded via epigenetic mechanisms but findings from human studies investigating the main effects of such exposure on epigenetic measures, including DNA methylation (DNAm), are inconsistent. Studies in perinatal tissues indicate that variability of DNAm at birth is best explained by the joint effects of genotype and prenatal environment. Here, we extend these analyses to postnatal stressors. We investigated the contribution of CA, cis genotype (G), and their additive (G+CA) and interactive (GxCA) effects to DNAm variability in blood or saliva from five independent cohorts with a total sample size of 1074 ranging in age from childhood to late adulthood. Of these, 541 were exposed to CA, which was assessed retrospectively using self-reports or verified through social services and registries. For the majority of sites (over 50%) in the adult cohorts, variability in DNAm was best explained by G+CA or GxCA but almost never by CA alone. Across ages and tissues, 1672 DNAm sites showed consistency of the best model in all five cohorts, with GxCA interactions explaining most variance. The consistent GxCA sites mapped to genes enriched in brain-specific transcripts and Gene Ontology terms related to development and synaptic function. Interaction of CA with genotypes showed the strongest contribution to DNAm variability, with stable effects across cohorts in functionally relevant genes. This underscores the importance of including genotype in studies investigating the impact of environmental factors on epigenetic marks

Connectivity sharing in wireless mesh network

Internet access is still unavailable to one-third of the world population due to the lack of infrastructure, high cost, and the digital divide. Many access-limited communities opt for shared Internet access to build common network infrastructures to mitigate the cost. Internet connectivity in such infrastructures is typically provided by several limited, sometimes non-dedicated, gateways. Client nodes, i.e., the end-user hosts, use one gateway and switch to another when the first fails. In this scheme, the gateway configuration is done manually on the end-user side. This form of Internet connectivity is widespread and has the advantage that no central control is required, but it is also unreliable and inefficient due to several factors, such as unbalanced traffic load across the gateways. The thesis proposes that the network would benefit from a gateway selection mechanism that can provide good connectivity to the client nodes, balanced load distribution, and a dynamic adaptation to the current network state. However, providing such a dynamic gateway selection is complicated: since the performance of the gateways as perceived by the client nodes changes frequently and might depend on the location of the latter in the network, and optimal selection would require the continuous monitoring of the gateway performance by the client node. The cost of such network-wide performance monitoring is high in large-scale networks and would outweigh the benefits of the dynamic gateway selection. The thesis aims to design a low-cost distributed mechanism that provides an efficient and dynamic gateway selection while considering the overall balanced gateway selection distribution. ​ We presented the Sense-Share-Select framework, a distributed, collaborative Internet gateway selection framework designed for large-scale networks. We integrated the Power of Two Choices randomized load balancing algorithm with our close neighbors' collaborative performance monitoring algorithm to reduce and distribute the gateway performance monitoring overhead. The selection algorithm utilizes the capacity-based selection algorithm to avoid selecting the unstable gateways and provide a suitable gateway selection for each node. The result shows the framework provides over 90% accurate collaborative performance monitoring with minimal overhead and equally distributes the clients over the good, stable performing gateways. The framework is implemented in the guifi.net community network testing environment with production gateways to demonstrate the efficiency of the proposed framework in the large-scale, heterogeneous network. The Sense-Share-Select framework improves the current manual gateway selection of the guifi.net by improving the QoE of all client nodes and provides better QoE than the other state-of-the-art gateway selection algorithms. ​(SC - Sciences) -- UCL, 202