Defending against Sybil Devices in Crowdsourced Mapping Services

Real-time crowdsourced maps such as Waze provide timely updates on traffic, congestion, accidents and points of interest. In this paper, we demonstrate how lack of strong location authentication allows creation of software-based {\em Sybil devices} that expose crowdsourced map systems to a variety of security and privacy attacks. Our experiments show that a single Sybil device with limited resources can cause havoc on Waze, reporting false congestion and accidents and automatically rerouting user traffic. More importantly, we describe techniques to generate Sybil devices at scale, creating armies of virtual vehicles capable of remotely tracking precise movements for large user populations while avoiding detection. We propose a new approach to defend against Sybil devices based on {\em co-location edges}, authenticated records that attest to the one-time physical co-location of a pair of devices. Over time, co-location edges combine to form large {\em proximity graphs} that attest to physical interactions between devices, allowing scalable detection of virtual vehicles. We demonstrate the efficacy of this approach using large-scale simulations, and discuss how they can be used to dramatically reduce the impact of attacks against crowdsourced mapping services.Comment: Measure and integratio

Next generation sequencing in cancer: opportunities and challenges for precision cancer medicine

Over the past decade, testing the genes of patients and their specific cancer types has become standardized practice in medical oncology since somatic mutations, changes in gene expression and epigenetic modifications are all hallmarks of cancer. However, while cancer genetic assessment has been limited to single biomarkers to guide the use of therapies, improvements in nucleic acid sequencing technologies and implementation of different genome analysis tools have enabled clinicians to detect these genomic alterations and identify functional and disease-associated genomic variants. Next-generation sequencing (NGS) technologies have provided clues about therapeutic targets and genomic markers for novel clinical applications when standard therapy has failed. While Sanger sequencing, an accurate and sensitive approach, allows for the identification of potential novel variants, it is however limited by the single amplicon being interrogated. Similarly, quantitative and qualitative profiling of gene expression changes also represents a challenge for the cancer field. Both RT-PCR and microarrays are efficient approaches, but are limited to the genes present on the array or being assayed. This leaves vast swaths of the transcriptome, including non-coding RNAs and other features, unexplored. With the advent of the ability to collect and analyze genomic sequence data in a timely fashion and at an ever-decreasing cost, many of these limitations have been overcome and are being incorporated into cancer research and diagnostics giving patients and clinicians new hope for targeted and personalized treatment. Below we highlight the various applications of next-generation sequencing in precision cancer medicine

Adaptive Partitioning for Large-Scale Dynamic Graphs

Abstract—In the last years, large-scale graph processing has gained increasing attention, with most recent systems placing particular emphasis on latency. One possible technique to improve runtime performance in a distributed graph processing system is to reduce network communication. The most notable way to achieve this goal is to partition the graph by minimizing the num-ber of edges that connect vertices assigned to different machines, while keeping the load balanced. However, real-world graphs are highly dynamic, with vertices and edges being constantly added and removed. Carefully updating the partitioning of the graph to reflect these changes is necessary to avoid the introduction of an extensive number of cut edges, which would gradually worsen computation performance. In this paper we show that performance degradation in dynamic graph processing systems can be avoided by adapting continuously the graph partitions as the graph changes. We present a novel highly scalable adaptive partitioning strategy, and show a number of refinements that make it work under the constraints of a large-scale distributed system. The partitioning strategy is based on iterative vertex migrations, relying only on local information. We have implemented the technique in a graph processing system, and we show through three real-world scenarios how adapting graph partitioning reduces execution time by over 50 % when compared to commonly used hash-partitioning. I

Development of novel human cellular models for neurotoxicity studies

Dissertation to obtain master degree in Genética Molecular e BiomedicinaInformation currently available on neurotoxicity of chemicals is scarce and there are a growing number of new compounds to be tested. Therefore, new strategies are necessary to identify neurotoxic agents with speed, reliability and respect for animal welfare. The limited availability of primary human brain cells means that there is a need for human cell lines that reliably model human neurons and astrocytes. Despite the advances in stem cell research, numerous challenges must be overcome before this technology can be widespread used, such as low differentiation efficiency. Human pluripotent embryocarcinoma NTera2/cloneD1 (NT2) cell line is an alternative cell source from which neurons and astrocytes can be derived in vitro. The aim of this work was to develop scalable and reproducible novel human cellular models using NT2 cells as source of differentiated neural phenotypes. A 2D culture system for astrocytic differentiation was implemented. After 4 weeks of differentiation with retinoic acid followed by 5 weeks maturation with mitotic inhibitors, astrocytes obtained expressed vimentin, GFAP, S100- and GLT-1 as characterized by immunodetection and qRT-PCR. Then, a 3D culture approach was adopted, using stirred suspension culture systems, in which cell-cell and cell-extracellular matrix interactions occur, mimicking better the in vivo situation. NT2 cells, inoculated as single cells, spontaneously aggregated without compromising their pluripotency. Optimization of stirring rate allowed control of aggregate size along time. After 3 weeks of RA treatment and 2 weeks of maturation, neurons expressing βIII-tubulin, MAPs and synaptophysin and astrocytes expressing vimentin, GFAP, S100- and GLT-1 were detected, as characterized by immunodetection and qRT-PCR. Furthermore, astrocytes presented a 2.5-fold higher yield than that observed in 2D culture systems. Results showed that NT2 differentiated cells are promising models for neurotoxicity testing. Furthermore, the 3D culture systems developed herein can contribute to increase the relevance of these studies, recapitulating human neuron-astrocyte interactions in a 3D cellular context.Fundação para a Ciência e Tecnologia - PTDC/EEB-BIO/112786/200

Genetic Patterns in Peripheral Marine Populations of the Fusilier Fish Caesio Cuning Within the Kuroshio Current

Aim: Mayr’s central‐peripheral population model (CCPM) describes the marked differences between central and peripheral populations in genetic diversity, gene flow, and census size. When isolation leads to genetic divergence, these peripheral populations have high evolutionary value and can influence biogeographic patterns. In tropical marine species with pelagic larvae, powerful western‐boundary currents have great potential to shape the genetic characteristics of peripheral populations at latitudinal extremes. We tested for the genetic patterns expected by the CCPM in peripheral populations that are located within the Kuroshio Current for the Indo‐Pacific reef fish, Caesio cuning. Methods: We used a panel of 2,677 SNPs generated from restriction site‐associated DNA (RAD) sequencing to investigate genetic diversity, relatedness, effective population size, and spatial patterns of population connectivity from central to peripheral populations of C. cuning along the Kuroshio Current. Results: Principal component and cluster analyses indicated a genetically distinct lineage at the periphery of the C. cuning species range and examination of SNPs putatively under divergent selection suggested potential for local adaptation in this region. We found signatures of isolation‐by‐distance and significant genetic differences between nearly all sites. Sites closest to the periphery exhibited increased within‐population relatedness and decreased effective population size. Main Conclusions: Despite the potential for homogenizing gene flow along the Kuroshio Current, peripheral populations in C. cuning conform to the predictions of the CCPM. While oceanography, habitat availability, and dispersal ability are all likely to shape the patterns found in C. cuning across this central‐peripheral junction, the impacts of genetic drift and natural selection in increasing smaller peripheral populations appear to be probable influences on the lineage divergence found in the Ryukyu Islands