p21-Activated Kinase 3 (PAK3) Is an AP-1 Regulated Gene Contributing to Actin Organisation and Migration of Transformed Fibroblasts

Activating Protein 1 (AP-1) plays a vital role in cell proliferation, differentiation and apoptosis. While de-regulation of AP-1 has been linked to many cancers, little is known regarding its downstream transcriptional targets that associate with cellular transformation. Previous studies identified PAK3, a serine/threonine kinase, as a potential AP-1 target gene. PAK3 has been implicated in a variety of pathological disorders and over-expression of other PAK-family members has been linked to cancer. In this study, we investigate AP-1 regulation of PAK3 expression and the role of PAK3 in cJun/AP-1-associated cellular transformation. Our results showed elevated PAK3 expression at both the mRNA and protein level in cJun-over-expressing Rat1a fibroblasts, as well as in transformed human fibroblasts. Elevated PAK3 expression in cJun/AP-1 over-expressing cells associated with a significant increase in PAK3 promoter activation. This increased promoter activity was lost when a single putative Jun binding site, which can bind AP-1 directly both in vitro and in vivo, was mutated. Further, inhibition of PAK3 using siRNA showed a regression in the cell morphology, migratory potential and actin organisation associated with AP-1 transformed cells. Our study is a first to describe a role for AP-1 in regulating PAK3 expression and suggest that PAK3 is an AP-1 target required for actin organization and migration observed in transformed cells

Developing a Qualia-Based Multi-Agent Architecture for Use in Malware Detection

Detecting network intruders and malicious software is a significant problem for network administrators and security experts. New threats are emerging at an increasing rate, and current signature and statistics-based techniques are not keeping pace. Intelligent systems that can adapt to new threats are needed to mitigate these new strains of malware as they are released. This research detects malware based on its qualia, or essence rather than its low-level implementation details. By looking for the underlying concepts that make a piece of software malicious, this research avoids the pitfalls of static solutions that focus on predefined bit sequence signatures or anomaly thresholds. This research develops a novel, hierarchical modeling method to represent a computing system and demonstrates the representation’s effectiveness by modeling the Blaster worm. Using Latent Dirichlet Allocation and Support Vector Machines abstract concepts are automatically generated that can be used in the hierarchical model for malware detection. Finally, the research outlines a novel system that uses multiple levels of individual software agents that sharing contextual relationships and information across different levels of abstraction to make decisions. This qualia-based system provides a framework for developing intelligent classification and decision-making systems for a number of application areas

H0LiCOW XII. Lens mass model of WFI2033-4723 and blind measurement of its time-delay distance and H0H_0

We present the lens mass model of the quadruply-imaged gravitationally lensed quasar WFI2033-4723, and perform a blind cosmographical analysis based on this system. Our analysis combines (1) time-delay measurements from 14 years of data obtained by the COSmological MOnitoring of GRAvItational Lenses (COSMOGRAIL) collaboration, (2) high-resolution $\textit{Hubble Space Telescope}$ imaging, (3) a measurement of the velocity dispersion of the lens galaxy based on ESO-MUSE data, and (4) multi-band, wide-field imaging and spectroscopy characterizing the lens environment. We account for all known sources of systematics, including the influence of nearby perturbers and complex line-of-sight structure, as well as the parametrization of the light and mass profiles of the lensing galaxy. After unblinding, we determine the effective time-delay distance to be $4784_{-248}^{+399}~\mathrm{Mpc}$, an average precision of $6.6\%$. This translates to a Hubble constant $H_{0} = 71.6_{-4.9}^{+3.8}~\mathrm{km~s^{-1}~Mpc^{-1}}$, assuming a flat $\Lambda$CDM cosmology with a uniform prior on $\Omega_\mathrm{m}$ in the range [0.05, 0.5]. This work is part of the $H_0$ Lenses in COSMOGRAIL's Wellspring (H0LiCOW) collaboration, and the full time-delay cosmography results from a total of six strongly lensed systems are presented in a companion paper (H0LiCOW XIII).Comment: Version accepted by MNRAS. 29 pages including appendix, 17 figures, 6 tables. arXiv admin note: text overlap with arXiv:1607.0140

H0LiCOW X: Spectroscopic/imaging survey and galaxy-group identification around the strong gravitational lens system WFI2033-4723

Galaxies and galaxy groups located along the line of sight towards gravitationally lensed quasars produce high-order perturbations of the gravitational potential at the lens position. When these perturbation are too large, they can induce a systematic error on $H_0$ of a few-percent if the lens system is used for cosmological inference and the perturbers are not explicitly accounted for in the lens model. In this work, we present a detailed characterization of the environment of the lens system WFI2033-4723 ($z_{\rm src} = 1.662$, $z_{\rm lens}$ = 0.6575), one of the core targets of the H0LICOW project for which we present cosmological inferences in a companion paper (Rusu et al. 2019). We use the Gemini and ESO-Very Large telescopes to measure the spectroscopic redshifts of the brightest galaxies towards the lens, and use the ESO-MUSE integral field spectrograph to measure the velocity-dispersion of the lens ($\sigma_{\rm {los}}= 250^{+15}_{-21}$ km/s) and of several nearby galaxies. In addition, we measure photometric redshifts and stellar masses of all galaxies down to $i < 23$ mag, mainly based on Dark Energy Survey imaging (DR1). Our new catalog, complemented with literature data, more than doubles the number of known galaxy spectroscopic redshifts in the direct vicinity of the lens, expanding to 116 (64) the number of spectroscopic redshifts for galaxies separated by less than 3 arcmin (2 arcmin) from the lens. Using the flexion-shift as a measure of the amplitude of the gravitational perturbation, we identify 2 galaxy groups and 3 galaxies that require specific attention in the lens models. The ESO MUSE data enable us to measure the velocity-dispersions of three of these galaxies. These results are essential for the cosmological inference analysis presented in Rusu et al. (2019).Comment: Matches the version accepted for publication by MNRAS. Note that this paper previously appeared as H0LICOW X

Gas Accretion and Galactic Chemical Evolution: Theory and Observations

This chapter reviews how galactic inflows influence galaxy metallicity. The goal is to discuss predictions from theoretical models, but particular emphasis is placed on the insights that result from using models to interpret observations. Even as the classical G-dwarf problem endures in the latest round of observational confirmation, a rich and tantalizing new phenomenology of relationships between $M_*$, $Z$, SFR, and gas fraction is emerging both in observations and in theoretical models. A consensus interpretation is emerging in which star-forming galaxies do most of their growing in a quiescent way that balances gas inflows and gas processing, and metal dilution with enrichment. Models that explicitly invoke this idea via equilibrium conditions can be used to infer inflow rates from observations, while models that do not assume equilibrium growth tend to recover it self-consistently. Mergers are an overall subdominant mechanism for delivering fresh gas to galaxies, but they trigger radial flows of previously-accreted gas that flatten radial gas-phase metallicity gradients and temporarily suppress central metallicities. Radial gradients are generically expected to be steep at early times and then flattened by mergers and enriched inflows of recycled gas at late times. However, further theoretical work is required in order to understand how to interpret observations. Likewise, more observational work is needed in order to understand how metallicity gradients evolve to high redshifts.Comment: Invited review to appear in Gas Accretion onto Galaxies, Astrophysics and Space Science Library, eds. A. J. Fox & R. Dav\'e, to be published by Springer. 29 pages, 2 figure

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome

This article introduces a manually curated data collection for gene expression meta-analysis of patients with ovarian cancer and software for reproducible preparation of similar databases. This resource provides uniformly prepared microarray data for 2970 patients from 23 studies with curated and documented clinical metadata. It allows users to efficiently identify studies and patient subgroups of interest for analysis and to perform meta-analysis immediately without the challenges posed by harmonizing heterogeneous microarray technologies, study designs, expression data processing methods and clinical data formats. We confirm that the recently proposed biomarker CXCL12 is associated with patient survival, independently of stage and optimal surgical debulking, which was possible only through meta-analysis owing to insufficient sample sizes of the individual studies. The database is implemented as the curatedOvarianData Bioconductor package for the R statistical computing language, providing a comprehensive and flexible resource for clinically oriented investigation of the ovarian cancer transcriptome. The package and pipeline for producing it are available from http://bcb.dfci.harvard.edu/ovariancancer. Database URL: http://bcb.dfci.harvard.edu/ovariancance

Cosmological distance indicators

We review three distance measurement techniques beyond the local universe: (1) gravitational lens time delays, (2) baryon acoustic oscillation (BAO), and (3) HI intensity mapping. We describe the principles and theory behind each method, the ingredients needed for measuring such distances, the current observational results, and future prospects. Time delays from strongly lensed quasars currently provide constraints on $H_0$ with < 4% uncertainty, and with 1% within reach from ongoing surveys and efforts. Recent exciting discoveries of strongly lensed supernovae hold great promise for time-delay cosmography. BAO features have been detected in redshift surveys up to z <~ 0.8 with galaxies and z ~ 2 with Ly-$\alpha$ forest, providing precise distance measurements and $H_0$ with < 2% uncertainty in flat $\Lambda$CDM. Future BAO surveys will probe the distance scale with percent-level precision. HI intensity mapping has great potential to map BAO distances at z ~ 0.8 and beyond with precisions of a few percent. The next years ahead will be exciting as various cosmological probes reach 1% uncertainty in determining $H_0$, to assess the current tension in $H_0$ measurements that could indicate new physics.Comment: Review article accepted for publication in Space Science Reviews (Springer), 45 pages, 10 figures. Chapter of a special collection resulting from the May 2016 ISSI-BJ workshop on Astronomical Distance Determination in the Space Ag

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

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