SoK: A Practical Cost Comparison Among Provable Data Possession Schemes

Provable Data Possession (PDP) schemes provide users with the ability to efficiently audit and verify the integrity of data stored with potentially unreliable third-parties, such as cloud storage service providers. While dozens of PDP schemes have been developed, no PDP schemes have been practically implemented with an existing cloud service. This work attempts to provide a starting point for the integration of PDP schemes with cloud storage service providers by providing a cost analysis of PDP schemes. This cost analysis is performed by implementing and analyzing five PDP schemes representative of the dozens of various PDP approaches. This paper provides analysis of the overhead and performance of each of these schemes to generate a comparable cost for each scheme using real-world cloud pricing models. Results show that the total cost of each scheme is comparable for smaller file sizes, but for larger files this cost can vary across schemes by an order of magnitude. Ultimately, the difference in cost between the simple MAC-based PDP scheme and the most efficient PDP scheme is negligible. While the MAC-PDP scheme may not be the most efficient, no other scheme improving upon it\u27s complexity can be implemented without the use of additional services or APIs leading to the conclusion that the simplest, storage only PDP scheme is the most practical to implement. Furthermore, the findings in this paper suggest that, in general, PDP schemes optimize on an inaccurate cost model and that future schemes should consider the existing economic realities of cloud services

Population extinction in a time-modulated environment

The extinction time of an isolated population can be exponentially reduced by a periodic modulation of its environment. We investigate this effect using, as an example, a stochastic branching-annihilation process with a time-dependent branching rate. The population extinction is treated in eikonal approximation, where it is described as an instanton trajectory of a proper reaction Hamiltonian. The modulation of the environment perturbs this trajectory and synchronizes it with the modulation phase. We calculate the corresponding change in the action along the instanton using perturbation techniques supported by numerical calculations. The techniques include a first-order theory with respect to the modulation amplitude, a second-order theory in the spirit of the Kapitsa pendulum effect, and adiabatic theory valid for low modulation frequencies.Comment: 13 pages, 10 figure

Optical and Near-IR Microwave Kinetic Inductance Detectors (MKIDs) in the 2020s

Optical and near-IR Microwave Kinetic Inductance Detectors, or MKIDs, are superconducting photon counting detectors capable of measuring the energy and arrival time of individual OIR photons without read noise or dark current. In this whitepaper we will discuss the current status of OIR MKIDs and MKID-based instruments.Comment: Astro2020 APC Whitepaper. 16 pages, 10 figure

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

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

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

NeBula: Team CoSTAR's robotic autonomy solution that won phase II of DARPA Subterranean Challenge

This paper presents and discusses algorithms, hardware, and software architecture developed by the TEAM CoSTAR (Collaborative SubTerranean Autonomous Robots), competing in the DARPA Subterranean Challenge. Specifically, it presents the techniques utilized within the Tunnel (2019) and Urban (2020) competitions, where CoSTAR achieved second and first place, respectively. We also discuss CoSTAR¿s demonstrations in Martian-analog surface and subsurface (lava tubes) exploration. The paper introduces our autonomy solution, referred to as NeBula (Networked Belief-aware Perceptual Autonomy). NeBula is an uncertainty-aware framework that aims at enabling resilient and modular autonomy solutions by performing reasoning and decision making in the belief space (space of probability distributions over the robot and world states). We discuss various components of the NeBula framework, including (i) geometric and semantic environment mapping, (ii) a multi-modal positioning system, (iii) traversability analysis and local planning, (iv) global motion planning and exploration behavior, (v) risk-aware mission planning, (vi) networking and decentralized reasoning, and (vii) learning-enabled adaptation. We discuss the performance of NeBula on several robot types (e.g., wheeled, legged, flying), in various environments. We discuss the specific results and lessons learned from fielding this solution in the challenging courses of the DARPA Subterranean Challenge competition.The work is partially supported by the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004), and Defense Advanced Research Projects Agency (DARPA)