riboviz 2:A flexible and robust ribosome profiling data analysis and visualization workflow

MOTIVATION: Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses. RESULTS: We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline. AVAILABILITY AND IMPLEMENTATION: riboviz 2 is freely available at github.com/riboviz/riboviz

Angiogenesis induced by tumor necrosis factor-agr; is mediated by α4 integrins

Tumor necrosis factor-α (TNF-α) and fibroblast growth factor-2 (FGF-2 or bFGF) are potent stimulators of angiogenesis. TNF-α, but not FGF-2, can induce the expression of vascular cell adhesion molecule-1 (VCAM-1) on the surface of endothelial cells. The soluble form of VCAM-1 has recently been demonstrated to function as an angiogenic mediator. Here we demonstrate that monoclonal antibodies directed against VCAM-1 or its α4 integrin counter-receptor inhibited TNF-α-induced endothelial cell migration in vitro. Angiogenesis induced in vivo in rat corneas by TNF-α was inhibited by a neutralizing antibody directed against the rat α4 integrin subunit. A peptide antagonist of the a4 integrins blocked TNF-α-induced endothelial cell migration in vitro and angiogenesis in rat corneas in vivo. No inhibition by the antibodies or peptide antagonist was observed either in vitro or in vivo when FGF-2 was used as the stimulus. The peptide antagonist did not inhibit TNF-a binding to its receptor nor did it block the function of αvβ3, an integrin previously implicated in TNF-a and FGF-2 mediated angiogenesis. These results demonstrate that angiogenic processes induced by TNF-α are mediated in part by agr;4 integrins possibly by a mechanism involving the induction of soluble VCAM-1.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41761/1/10456_2004_Article_188219.pd

Ten Years In: Implementing Strategic Approaches to Cyberspace

This book represents a look beyond theories and analogies to examine the challenges of strategy implementation. In the essays that follow, practitioners who are building cyberspace forces at-scale join scholars who study power and force in this new domain to collectively offer a unique perspective on the evolution and future of cyber strategy and operations.https://digital-commons.usnwc.edu/usnwc-newport-papers/1044/thumbnail.jp

Benchmarking Public and Private Blockchains and Understanding the Development of Private Blockchain Networks

This thesis paper explores the developing technology blockchain by trying to understand the technology from a technical performance standpoint and also understanding the development process of blockchain networks and applications. The first half of this paper analyzes two research papers, Bitcoing-NG: A Scalable Blockchain Protocol and Untangling Blockchain: A Data Processing View of Blockchain Systems, to understand and explain some of the technical differences and shortcomings of blockchain technologies. The second half of this paper then proceeds to develop a private blockchain network on the Ethereum network and deploy a smart contract on that private blockchain network. This process gives insight into the development of blockchain applications and identifies the struggles blockchain developers face

The Economics of John Kenneth Galbraith

John Kenneth Galbraith is one of the country\u27s most widely quoted economists. At present he is one of President Kennedy\u27s top economic advisers. The advice he gives will be very influential in shaping the program of the Kennedy administration in the next four years. Mr. Galbraith is especially important to the lay public as a man who can present in nontechnical and illustrative language a clear picture of the American economy today. He uses his charm, with, and gentle sarcasm to not only put his point across but to make the subject of economics pleasantly readable. His popularity as a writer is attested to by the fact that two of his books have been best sellers

The Real, Real Price of Nonrenewable Resources : Copper 1870-2000

Over the past 40 years economists have devoted considerable effort to estimating long-run trends in real commodity prices. The results indicate that the real prices for many commodities have fallen, suggesting to the surprise of many that resource scarcity is declining over time. Almost all of this work, however, uses the U.S. producer price index or other standard price deflators, which recent research shows overestimate inflation for several reasons. This article examines copper prices with adjusted deflators designed to eliminate this bias. It finds that the trend over time, which is significantly downward when no adjustment is made to the deflator, displays no tendency in either direction or is significantly upward depending on the magnitude of the deflator adjustment employed. These findings suggest that real resources prices provide less support than widely assumed for the hypothesis that resources are becoming more available or less scarce over time