Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages, and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we 1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and 2) provide guidelines for determining the appropriate tools for each step. We analyze various combinations of different tools and expose the tradeoffs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, in order to overcome the high error rates of the nanopore sequencing technology.Comment: To appear in Briefings in Bioinformatics (BIB), 201

The Standard Model as a noncommutative geometry: the low energy regime

We render a thorough, physicist's account of the formulation of the Standard Model (SM) of particle physics within the framework of noncommutative differential geometry (NCG). We work in Minkowski spacetime rather than in Euclidean space. We lay the stress on the physical ideas both underlying and coming out of the noncommutative derivation of the SM, while we provide the necessary mathematical tools. Postdiction of most of the main characteristics of the SM is shown within the NCG framework. This framework, plus standard renormalization technique at the one-loop level, suggest that the Higgs and top masses should verify 1.3 m_top \lesssim m_H \lesssim 1.73 m_top.Comment: 44 pages, Plain TeX with AMS fonts, mass formulae readjusted, some references added, to appear in Physics Report

Workshop on dimensional analysis for design, development, and research executives

The proceedings of a conference of research and development executives are presented. The purpose of the meeting was to develop an understanding of the conditions which are appropriate for the use of certain general management tools and those conditions which render these tools inappropriate. The verbatim statements of the participants are included to show the direction taken initially by the conference. Formal presentations of management techniques for research and development are developed

Automated computation of materials properties

Materials informatics offers a promising pathway towards rational materials design, replacing the current trial-and-error approach and accelerating the development of new functional materials. Through the use of sophisticated data analysis techniques, underlying property trends can be identified, facilitating the formulation of new design rules. Such methods require large sets of consistently generated, programmatically accessible materials data. Computational materials design frameworks using standardized parameter sets are the ideal tools for producing such data. This work reviews the state-of-the-art in computational materials design, with a focus on these automated $\textit{ab-initio}$ frameworks. Features such as structural prototyping and automated error correction that enable rapid generation of large datasets are discussed, and the way in which integrated workflows can simplify the calculation of complex properties, such as thermal conductivity and mechanical stability, is demonstrated. The organization of large datasets composed of $\textit{ab-initio}$ calculations, and the tools that render them programmatically accessible for use in statistical learning applications, are also described. Finally, recent advances in leveraging existing data to predict novel functional materials, such as entropy stabilized ceramics, bulk metallic glasses, thermoelectrics, superalloys, and magnets, are surveyed.Comment: 25 pages, 7 figures, chapter in a boo

Germline Transgenic Methods for Tracking Cells and Testing Gene Function During Regeneration in the Axolotl

The salamander is the only tetrapod that regenerates complex body structures throughout life. Deciphering the underlying molecular processes of regeneration is fundamental for regenerative medicine and developmental biology, but the model organism had limited tools for molecular analysis. We describe a comprehensive set of germline transgenic strains in the laboratory-bred salamander Ambystoma mexicanum(axolotl) that open up the cellular and molecular genetic dissection of regeneration. We demonstrate tissue-dependent control of gene expression in nerve, Schwann cells, oligodendrocytes, muscle, epidermis, and cartilage. Furthermore, we demonstrate the use of tamoxifen-induced Cre/loxP-mediated recombination to indelibly mark different cell types. Finally, we inducibly overexpress the cell-cycle inhibitor p16INK4a, which negatively regulates spinal cord regeneration. These tissue-specific germline axolotl lines and tightly inducible Cre drivers and LoxP reporter lines render this classical regeneration model molecularly accessible

Visualization of and Access to CloudSat Vertical Data through Google Earth

Online tools, pioneered by the Google Earth (GE), are facilitating the way in which scientists and general public interact with geospatial data in real three dimensions. However, even in Google Earth, there is no method for depicting vertical geospatial data derived from remote sensing satellites as an orbit curtain seen from above. Here, an effective solution is proposed to automatically render the vertical atmospheric data on Google Earth. The data are first processed through the Giovanni system, then, processed to be 15-second vertical data images. A generalized COLLADA model is devised based on the 15-second vertical data profile. Using the designed COLLADA models and satellite orbit coordinates, a satellite orbit model is designed and implemented in KML format to render the vertical atmospheric data in spatial and temporal ranges vividly. The whole orbit model consists of repeated model slices. The model slices, each representing 15 seconds of vertical data, are placed on the CloudSat orbit based on the size, scale, and angle with the longitude line that are precisely and separately calculated on the fly for each slice according to the CloudSat orbit coordinates. The resulting vertical scientific data can be viewed transparently or opaquely on Google Earth. Not only is the research bridged the science and data with scientists and the general public in the most popular way, but simultaneous visualization and efficient exploration of the relationships among quantitative geospatial data, e.g. comparing the vertical data profiles with MODIS and AIRS precipitation data, becomes possible

A Creative Writing Case Study of Gender-Based Violence in Coach Education: Stacey’s Story

Accepted author manuscript version reprinted, by permission, from Women in Sport and Physical Activity Journal, 2020, 28 (1): 72–80, https://doi.org/10.1123/wspaj.2018-0046]. © 2020 University of North Carolina at Greensboro (UNCG).Creative nonfiction writing is the literary technique employed in this article to explore insights and assist our understanding of an “alleged” sexual assault in a sport coach education environment. Creative nonfiction employs various narrative tools— characters, setting, figurative language, sequences of events, plot, sub-plot, and dialogue—designed to render the sensitive and controversial elements of sexual assault significant. Readers are, therefore, invited to engage with Stacey’s Story and reflect on the actions of both the perpetrator(s) and the victim. While there are risks associated with the sharing of stories, especially those which are considered dangerous, it is envisaged that Stacey’s Story will be viewed as an opportunity to develop more critical responses and advance our understanding of gender-based violence in sport.Peer reviewe

Technological change, accident prevention and civil liability

The improvement of accident prevention technology in many fields of social life has spurred new challenges to the doctrinal tools of fault and strict based civil liability in the law of torts. Amid these challenges lies the identification of the proper scope of the respective criteria of liability in a changing factual environment, their suitability as doctrinal tools, as well as their actual application to concrete cases given the amount of information which would be needed to render adequate judgments. Precedents and old laws should be assessed with caution, taking into account the tacit cost-benefit analysis embedded in them, for they may or may not serve the interests of welfare maximization in an environment with constantly renewed accident prevention technology