Sensor node localisation using a stereo camera rig

In this paper, we use stereo vision processing techniques to detect and localise sensors used for monitoring simulated environmental events within an experimental sensor network testbed. Our sensor nodes communicate to the camera through patterns emitted by light emitting diodes (LEDs). Ultimately, we envisage the use of very low-cost, low-power, compact microcontroller-based sensing nodes that employ LED communication rather than power hungry RF to transmit data that is gathered via existing CCTV infrastructure. To facilitate our research, we have constructed a controlled environment where nodes and cameras can be deployed and potentially hazardous chemical or physical plumes can be introduced to simulate environmental pollution events in a controlled manner. In this paper we show how 3D spatial localisation of sensors becomes a straightforward task when a stereo camera rig is used rather than a more usual 2D CCTV camera

An in vitro method to select malignant cells from surgical biopsies of breast cancer patients

To date, breast cancer (BC) research is mainly studied with cell lines. These cells were passaged multiple times, acquiring phenotypes, additional mutations and epigenetic changes. These changes make the passaged cell lines different from the original malignancy. Thus cell lines, although useful as models could be improved with additional studies with primary BC. It is difficult to obtain malignant cells from breast tissues without contamination from surrounding healthy cells. Selection and expansion of malignant cells from surgical tissues have proved to be daunting tasks. This study describes a reliable and reproducible method for isolating and expanding malignant cells from surgical breast tissues. The method uses co-cultures with BM stroma to select for the cancer cells while the healthy cells undergo rapid cell death. Studies are described to show the cloning efficiencies and sensitivity of the method using surgical samples of varying sizes, different stages of BC, and samples from needle biopsies

Application of Probiotic Bacteria to Functional Foods

End of Project ReportProbiotic cultures are described as live microbial feed supplements that improve intestinal microbial balance and are intended for maintenance of health or prevention, rather than the curing of disease. The demand for probiotic foods is increasing in Europe, Japan and the U.S. reflecting the heightened awareness among the public of the relationship between diet and health. Traditionally, the most popular food delivery systems for these cultures have been freshly fermented dairy foods, such as yogurts and fermented milks, as well as unfermented milks with cultures added. However, in the development of functional foods, the technological suitability of probiotic strains poses a serious challenge since their survival and viability may be adversely affected by processing conditions as well as by the product environment and storage conditions. This is a particular concern, given that high levels (at least 107 per gram or ml) of live micro-organisms are recommended for probiotic products. In previous studies (see DPRC No. 29) the successful manufacture of probiotic Cheddar cheese harbouring high levels (>108 cfu/g) of the probiotic Lactobacillus paracasei NFBC 338 strain was reported. Hence, the overall objective of these studies was to continue the development and evaluation of Functional Foods containing high levels of viable probiotic bacteria, with particular emphasis on overcoming the technological barriers and the identification of strains suited to particular applications, such as incorporation into Cheddar cheese and spray-dried powders.Department of Agriculture, Food and the Marin

Mesenchymal Stem Cells in Early Entry of Breast Cancer into Bone Marrow

BACKGROUND: An understanding of BC cell (BCC) entry into bone marrow (BM) at low tumor burden is limited when compared to highly metastatic events during heavy tumor burden. BCCs can achieve quiescence, without interfering with hematopoiesis. This occurs partly through the generation of gap junctions with BM stroma, located close to the endosteum. These events are partly mediated by the evolutionary conserved gene, Tac1. METHODOLOGY/PRINCIPAL FINDINGS: This study focuses on the role of mesenchymal stem cells (MSCs), Tac1, SDF-1 and CXCR4 in BCC entry into BM. The model is established in studies with low numbers of tumor cells, and focuses on cancer cells with low metastatic and invasion potential. This allowed us to recapitulate early event, and to study cancer cells with low invasive potential, even when they are part of larger numbers of highly metastatic cells. A novel migration assay showed a facilitating role of MSCs in BCC migration across BM endothelial cells. siRNA and ectopic expression studies showed a central role for Tac1 and secondary roles for SDF-1alpha and CXCR4. We also observed differences in the mechanisms between low invasive and highly metastatic cells. The in vitro studies were verified in xenogeneic mouse models that showed a preference for low invasive BCCs to BM, but comparable movement to lung and BM by highly metastatic BCCs. The expressions of Tac1 and production of SDF-1alpha were verified in primary BCCs from paired samples of BM aspirates and peripheral blood. CONCLUSIONS/SIGNIFICANCE: MSC facilitate BCC entry into BM, partly through Tac1-mediated regulation of SDF-1alpha and CXCR4. We propose a particular population of BCC with preference for BM could be isolated for characterization. This population might be the subset that enter BM at an early time period, and could be responsible for cancer resurgence and resistance to current therapies

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

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

Identifying risks for male street gang affiliation: a systematic review and narrative synthesis

Gang violence has increased in recent years. Individuals are becoming gang affiliated younger, and many have suffered historic maltreatment. Subsequent exposure to violence can result in profound consequences, including acute psychological harm. This review aims to identify predictive risk factors for male street gang affiliation. A systematic literature search was conducted utilising PsycINFO, PsycARTICLES, Medline, the Cochrane Central Register of Controlled Trials, the Cochrane Database of Systematic Reviews and the Social Policy and Practice databases (from the databases’ inception to 03/04/15). From this search, n=244 peer-reviewed papers were included in an initial scoping review, and n=102 thereafter met criteria for a systematic review; a narrative synthesis follows. Gang members have typically faced numerous historic adversities across multiple domains; individual, family, peers, school and community. Cumulative factors generated an independent risk. The meta-narrative described an overarching failure to safeguard vulnerable individuals, with the motivation for gang affiliation hypothetically arising from an attempt to have their basic needs met. Clinical and research recommendations were made to inform early intervention policy and practice

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

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