DTN Routing as a Resource Allocation Problem

Routing protocols for disruption-tolerant networks (DTNs) use a variety of mechanisms, including discovering the meeting probabilities among nodes, packet replication, and network coding. The primary focus of these mechanisms is to increase the likelihood of finding a path with limited information, and so these approaches have only an incidental effect on routing such metrics as maximum or average delivery delay. In this paper, we present rapid, an intentional DTN routing protocol that can optimize a specific routing metric such as the worst-case delivery delay or the fraction of packets that are delivered within a deadline. The key insight is to treat DTN routing as a resource allocation problem that translates the routing metric into per-packet utilities which determine how packets should be replicated in the system. We evaluate rapid rigorously through a prototype deployed over a vehicular DTN testbed of 40 buses and simulations based on real traces. To our knowledge, this is the first paper to report on a routing protocol deployed on a real DTN at this scale. Our results suggest that rapid significantly outperforms existing routing protocols for several metrics. We also show empirically that for small loads RAPID is within 10% of the optimal performance

DTN Routing as a Resource Allocation Problem

Routing protocols for disruption-tolerant networks (DTNs) use a variety of mechanisms, including discovering the meeting probabilities among nodes, packet replication, and network coding. The primary focus of these mechanisms is to increase the likelihood of finding a path with limited information, and so these approaches have only an incidental effect on routing such metrics as maximum or average delivery delay. In this paper, we present rapid, an intentional DTN routing protocol that can optimize a specific routing metric such as the worst-case delivery delay or the fraction of packets that are delivered within a deadline. The key insight is to treat DTN routing as a resource allocation problem that translates the routing metric into per-packet utilities which determine how packets should be replicated in the system. We evaluate rapid rigorously through a prototype deployed over a vehicular DTN testbed of 40 buses and simulations based on real traces. To our knowledge, this is the first paper to report on a routing protocol deployed on a real DTN at this scale. Our results suggest that rapid significantly outperforms existing routing protocols for several metrics. We also show empirically that for small loads RAPID is within 10% of the optimal performance

Web Search From a Bus

Opportunistic connections to the Internet from open wireless access points is now commonly possible in municipal areas. Vehicular networks can opportunistically connect to the internet for several seconds via open access points. In this paper, we adapt the interactive process of web search and retrieval to vehicular networks with intermittent Internet access. Our system, called Thedu has mobile nodes use an Internet proxy to collect search engine results and prefetch result pages. The mobiles nodes download the pre-fetched web pages from the proxy. Our contribution is a novel set of techniques to make aggressive but selective prefetching practical, resulting in a significantly greater number of relevant web results returned to mobile users. To evaluate our scheme, we deployed Thedu on DieselNet, our vehicular testbed of buses operating in a micro-urban area around Amherst, MA. Using a simulated workload, we find that users can expect four times as many useful responses to web search queries compared to not using Thedu. Moreover, the mean latency in receiving the first relevant response for a query is 2.7 minutes when deployed in a semi-urban region with a sparser distribution of APs compared to big cities

Characterisation of human saliva as a platform for oral dissolution medium development

Human saliva is a biological fluid of great importance in the field of dissolution testing. However, until now, no consensus has been reached on its key characteristics relevant to dissolution testing. As a result, it is difficult to select or develop an in vitro dissolution medium to best represent human saliva. In this study, the pH, buffer capacity, surface tension, viscosity and flow rate of both unstimulated (US) and stimulated (SS) human saliva were investigated in order to provide a platform of reference for future dissolution studies using simulated salivary fluids. Age and gender related differences in a sample size of 30 participants for each parameter were investigated. Significant differences were established between US and SS for all characteristics except surface tension. Therefore, the requirement for using two simulated salivary fluids should be considered when developing an oral dissolution model

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Detectable Clonal Mosaicism from Birth to Old Age and its Relationship to Cancer

Clonal mosaicism for large chromosomal anomalies (duplications, deletions and uniparental disomy) was detected using SNP microarray data from over 50,000 subjects recruited for genome-wide association studies. This detection method requires a relatively high frequency of cells (>5–10%) with the same abnormal karyotype (presumably of clonal origin) in the presence of normal cells. The frequency of detectable clonal mosaicism in peripheral blood is low (<0.5%) from birth until 50 years of age, after which it rises rapidly to 2–3% in the elderly. Many of the mosaic anomalies are characteristic of those found in hematological cancers and identify common deleted regions that pinpoint the locations of genes previously associated with hematological cancers. Although only 3% of subjects with detectable clonal mosaicism had any record of hematological cancer prior to DNA sampling, those without a prior diagnosis have an estimated 10-fold higher risk of a subsequent hematological cancer (95% confidence interval = 6–18)