19 research outputs found

    Statistical aspects of discerning indel-type structural variation via DNA sequence alignment

    Get PDF
    <p>Abstract</p> <p>Background</p> <p>Structural variations in the form of DNA insertions and deletions are an important aspect of human genetics and especially relevant to medical disorders. Investigations have shown that such events can be detected via tell-tale discrepancies in the aligned lengths of paired-end DNA sequencing reads. Quantitative aspects underlying this method remain poorly understood, despite its importance and conceptual simplicity. We report the statistical theory characterizing the length-discrepancy scheme for Gaussian libraries, including coverage-related effects that preceding models are unable to account for.</p> <p>Results</p> <p>Deletion and insertion statistics both depend heavily on physical coverage, but otherwise differ dramatically, refuting a commonly held doctrine of symmetry. Specifically, coverage restrictions render insertions much more difficult to capture. Increased read length has the counterintuitive effect of worsening insertion detection characteristics of short inserts. Variance in library insert length is also a critical factor here and should be minimized to the greatest degree possible. Conversely, no significant improvement would be realized in lowering fosmid variances beyond current levels. Detection power is examined under a straightforward alternative hypothesis and found to be generally acceptable. We also consider the proposition of characterizing variation over the entire spectrum of variant sizes under constant risk of false-positive errors. At 1% risk, many designs will leave a significant gap in the 100 to 200 bp neighborhood, requiring unacceptably high redundancies to compensate. We show that a few modifications largely close this gap and we give a few examples of feasible spectrum-covering designs.</p> <p>Conclusion</p> <p>The theory resolves several outstanding issues and furnishes a general methodology for designing future projects from the standpoint of a spectrum-wide constant risk.</p

    The 1988 Goddard Conference on Space Applications of Artificial Intelligence

    Get PDF
    This publication comprises the papers presented at the 1988 Goddard Conference on Space Applications of Artificial Intelligence held at the NASA/Goddard Space Flight Center, Greenbelt, Maryland on May 24, 1988. The purpose of this annual conference is to provide a forum in which current research and development directed at space applications of artificial intelligence can be presented and discussed. The papers in these proceedings fall into the following areas: mission operations support, planning and scheduling; fault isolation/diagnosis; image processing and machine vision; data management; modeling and simulation; and development tools/methodologies

    Research and Technology, 1998

    Get PDF
    This report selectively summarizes the NASA Lewis Research Center's research and technology accomplishments for the fiscal year 1998. It comprises 134 short articles submitted by the staff scientists and engineers. The report is organized into five major sections: Aeronautics, Research and Technology, Space, Engineering and Technical Services, and Commercial Technology. A table of contents and an author index have been developed to assist readers in finding articles of special interest. This report is not intended to he a comprehensive summary of all the research and technology work done over the past fiscal year. Most of the work is reported in Lewis-published technical reports, journal articles, and presentations prepared by Lewis staff and contractors. In addition, university grants have enabled faculty members and graduate students to engage in sponsored research that is reported at technical meetings or in journal articles. For each article in this report, a Lewis contact person has been identified, and where possible, reference documents are listed so that additional information can be easily obtained. The diversity of topics attests to the breadth of research and technology being pursued and to the skill mix of the staff that makes it possible. At the time of publication, NASA Lewis was undergoing a name change to the NASA John H. Glenn Research Center at Lewis Field

    Program Abstracts, 104th Session, Iowa Academy of Science, April 24-25, 1992

    Get PDF
    Presentation abstracts from the annual meeting of the Iowa Academy of Sciencehttps://scholarworks.uni.edu/ias_docs/1030/thumbnail.jp

    Microgravity science & applications. Program tasks and bibliography for FY 1995

    Get PDF
    This annual report includes research projects funded by the Office of Life and Microgravity Sciences and Applications, Microgravity Science and Applications Division, during FY 1994. It is a compilation of program tasks (objective, description, significance, progress, students funded under research, and bibliographic citations) for flight research and ground based research in five major scientific disciplines: benchmark science, biotechnology, combustion science, fluid physics, and materials science. Advanced technology development (ATD) program task descriptions are also included. The bibliography cites the related principle investigator (PI) publications and presentations for these program tasks in FY 1994. Three appendices include a Table of Acronyms, a Guest Investigator index and a Principle Investigator index

    Microgravity Science and Applications: Program Tasks and Bibliography for Fiscal Year 1996

    Get PDF
    NASA's Microgravity Science and Applications Division (MSAD) sponsors a program that expands the use of space as a laboratory for the study of important physical, chemical, and biochemical processes. The primary objective of the program is to broaden the value and capabilities of human presence in space by exploiting the unique characteristics of the space environment for research. However, since flight opportunities are rare and flight research development is expensive, a vigorous ground-based research program, from which only the best experiments evolve, is critical to the continuing strength of the program. The microgravity environment affords unique characteristics that allow the investigation of phenomena and processes that are difficult or impossible to study an Earth. The ability to control gravitational effects such as buoyancy driven convection, sedimentation, and hydrostatic pressures make it possible to isolate phenomena and make measurements that have significantly greater accuracy than can be achieved in normal gravity. Space flight gives scientists the opportunity to study the fundamental states of physical matter-solids, liquids and gasses-and the forces that affect those states. Because the orbital environment allows the treatment of gravity as a variable, research in microgravity leads to a greater fundamental understanding of the influence of gravity on the world around us. With appropriate emphasis, the results of space experiments lead to both knowledge and technological advances that have direct applications on Earth. Microgravity research also provides the practical knowledge essential to the development of future space systems. The Office of Life and Microgravity Sciences and Applications (OLMSA) is responsible for planning and executing research stimulated by the Agency's broad scientific goals. OLMSA's Microgravity Science and Applications Division (MSAD) is responsible for guiding and focusing a comprehensive program, and currently manages its research and development tasks through five major scientific areas: biotechnology, combustion science, fluid physics, fundamental physics, and materials science. FY 1996 was an important year for MSAD. NASA continued to build a solid research community for the coming space station era. During FY 1996, the NASA Microgravity Research Program continued investigations selected from the 1994 combustion science, fluid physics, and materials science NRAS. MSAD also released a NASA Research Announcement in microgravity biotechnology, with more than 130 proposals received in response. Selection of research for funding is expected in early 1997. The principal investigators chosen from these NRAs will form the core of the MSAD research program at the beginning of the space station era. The third United States Microgravity Payload (USMP-3) and the Life and Microgravity Spacelab (LMS) missions yielded a wealth of microgravity data in FY 1996. The USMP-3 mission included a fluids facility and three solidification furnaces, each designed to examine a different type of crystal growth

    A systems biology approach to shed light on apple fruit development

    Get PDF
    The research carried out and discussed in the present dissertation is positioned within the “TranscrApple” project (www.transcrapple.com), funded by the Provincia Autonoma di Trento (PAT) within the call “Grandi Progetti 2012”. The general objectives of this project, a significant part of which overlap with the present thesis, deal with the characterization, as wide as possible with the currently available technologies, of the transcriptional events, including those related to small RNAs (not discussed in the present dissertation), the metabolic changes, on a subset of primary and secondary metabolites, and hormones’ cross-talk, through a hormone profiling approach, occurring during apple fruit development. The present thesis is organized in different chapters, mirroring the experimental and temporal rationale effectively pursued to develop the research herein described. The main objective of the present work deals not only with providing an overview of transcripts, metabolites and hormones and their variations during fruit development, but also with the setting up of technical and experimental solutions aimed at using the achieved information within an integrative platform, according to a “systems biology view”. In model species, all this kind of studies are extremely easier, thanks to the availability of ready-to-use bioinformatics tools that are not flexible enough to be used in other species. However, especially in tree crops, this approach is still far from being defined and standardized. Chapter 1 introduces the theme “apple fruit development”, discussing the adoption of apple as a model system that, in the last decade, acquired great importance in terms of research among the fruit species thanks to the availability of its sequenced genome. After a brief introduction on the fundamental information available about the apple fruit growth, taking into account the technological and scientific points of view, few difficulties and gaps that hamper the achievement of a complete overview of the regulatory events coordinating the development and growth of the apple, are discussed in relation to the main quantitative and qualitative parameters characterizing the apple fruit production. Chapter 2 enters into the apple fruit research area; the preliminary phase and the multiple validations (concerning different cultivars and seasons) of transcriptional markers during the main apple developmental stages were shown to be fundamental for choosing, on the base of the expression profiles of these genes, the most representative samples, among those collected also in different seasons. Several markers have been identified, validated and employed, among those available from literature, allowing the selection of samples of cv Golden Delicious (herein considered as model) to be used for the subsequent transcriptional and metabolomic characterization carried out in the present research. Chapter 3 deals with the hormonal profiling survey carried out along the apple fruit development for the first time in this species. The results have allowed not only the achievement of brand new data related to the major hormonal classes, to be employed for further researches, but also the clarification and/or confirmation of new hormonal interactions connected to the fruit development stage or the transition between stages. Moreover, the relevance of this study consists in having achieved, for the first time in apple, quantitative data of an important set of hormones concurrently on the same samples.\ud Chapter 4 concerns the survey on the metabolites and their variations during the apple fruit development. A complete overview of the changes of the different classes of metabolites (mainly sugars, organic acids, aminoacids and polyphenols) is given during the apple developmental cycle. The acquired data have been derived from the same samples already analyzed in the previous chapters, and will be integrated with data of diverse nature, such as the RNAseq. Chapter 5 of the present thesis comes into the “system biology” area, initially among several technical difficulties, then partially solved, and gives an example of an alternative interpretation of the hormonal data put within a correlative network along with the RNAseq results achieved on the same samples

    New Advances on Zika Virus Research

    Get PDF
    Zika virus (ZIKV) is a mosquito-borne member of the Flaviviridae family that historically has been associated with mild febrile illness. However, the recent outbreaks in Brazil in 2015 and its rapid spread throughout South and Central America and the Caribbean, together with its association with severe neurological disorders—including fetal microcephaly and Guillain-Barré syndrome in adults—have changed the historic perspective of ZIKV. Currently, ZIKV is considered an important public health concern that has the potential to affect millions of people worldwide. The significance of ZIKV in human health and the lack of approved vaccines and/or antiviral drugs to combat ZIKV infection have triggered a global effort to develop effective countermeasures to prevent and/or treat ZIKV infection. In this Special Issue of Viruses, we have assembled a collection of 32 research and review articles that cover the more recent advances on ZIKV molecular biology, replication and transmission, virus–host interactions, pathogenesis, epidemiology, vaccine development, antivirals, and viral diagnosis
    corecore