Extracting information from biological networks

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mathematics, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 175-194).Systems biology, the study of biological systems in a holistic manner, has been catalyzed by a dramatic improvement in experimental techniques, coupled with a constantly increasing availability of biological data. The representation and analysis of this heterogeneous data is facilitated by the powerful abstraction of biological networks. This thesis examines several types of these networks and looks in detail at the kind of information their analysis can yield. The first part discusses protein interaction networks. We introduce a new algorithm for the pairwise alignment of these networks. We show that these alignments can provide important clues to the function of proteins as well as insights into the evolutionary history of the species under examination. The second part discusses regulatory networks. We present an approach for validating putative drug targets based on the information contained in these networks. We show how this approach can also be used to discover drug targets. The third part discusses metabolic networks. We provide new insights into the structure of constraint-based models of cell metabolism and describe a methodology for performing a complete analysis of a metabolic network. We also present an implementation of this methodology and discuss its application to a variety of problems related to the metabolism of bacteria. The final part describes an application of our methodology to Mycobacterium tuberculosis, the pathogen responsible for almost 2 million deaths around the world every year. We introduce a method for reconciling metabolic network reconstructions and apply it to merge the two published networks for tuberculosis. We analyze the merged network and show how it can be refined based on available experimental data to improve its predictive power. We conclude with a list of potential drug targets.by Leonid Alexandrovich Chindelevitch.Ph.D

Proceedings of the XIII Global Optimization Workshop: GOW'16

[Excerpt] Preface: Past Global Optimization Workshop shave been held in Sopron (1985 and 1990), Szeged (WGO, 1995), Florence (GO’99, 1999), Hanmer Springs (Let’s GO, 2001), Santorini (Frontiers in GO, 2003), San José (Go’05, 2005), Mykonos (AGO’07, 2007), Skukuza (SAGO’08, 2008), Toulouse (TOGO’10, 2010), Natal (NAGO’12, 2012) and Málaga (MAGO’14, 2014) with the aim of stimulating discussion between senior and junior researchers on the topic of Global Optimization. In 2016, the XIII Global Optimization Workshop (GOW’16) takes place in Braga and is organized by three researchers from the University of Minho. Two of them belong to the Systems Engineering and Operational Research Group from the Algoritmi Research Centre and the other to the Statistics, Applied Probability and Operational Research Group from the Centre of Mathematics. The event received more than 50 submissions from 15 countries from Europe, South America and North America. We want to express our gratitude to the invited speaker Panos Pardalos for accepting the invitation and sharing his expertise, helping us to meet the workshop objectives. GOW’16 would not have been possible without the valuable contribution from the authors and the International Scientific Committee members. We thank you all. This proceedings book intends to present an overview of the topics that will be addressed in the workshop with the goal of contributing to interesting and fruitful discussions between the authors and participants. After the event, high quality papers can be submitted to a special issue of the Journal of Global Optimization dedicated to the workshop. [...

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 345)

This publication is a cumulative index to the abstracts contained in Supplements 333 through 344 of Aerospace Medicine and Biology: A Continuing Bibliography. Seven indexes are included -- subject, personal author, corporate source, foreign technology, contract number, report number, and accession number

Indigenous Philosophy and World Politics: Cosmopolitical Contributions from across the Americas

abstract: The call for an Inter-Civilizational Dialogue informed by cosmopolitical forms of Comparative Political Theory as a way to address our unprecedented global challenges is among the most laudable projects that students of politics and related fields across the world have put forth in centuries. Unfortunately, however, up until this point the actual and potential contributions of the Indigenous or 'Fourth' World and its civilizational manifestations have been largely ignored. This has clearly been the case in what refers to Indigenous American or Abya-Yalan cultures and civilizations. The purpose of this dissertation is to acknowledge, add to, and further foster the contributions of Indigenous American cultures and civilizations to the emerging fields of Comparative Political Theory and Inter-Civilizational Relations. Guided by a cosmopolitical concern for social and environmental justice, this work adds to the transcontinental and transdisciplinary effort to decolonize knowledges and practices by offering socio-ecologically balanced alternatives beyond the crisis of globalized Western modernity. This work draws on three broad Indigenous traditions, Mesoamerican, Andean, and Native North American, to offer some historical and contemporary examples of the many possible ways in which the recovery, revalorization, and revitalization of Indigenous modes of thought, practice, organization and planning can contribute to foster forms of comparative political theorizing that address the challenges of a global age bedeviled by the confluence of social and environmental crises of an unprecedented scale and scope. The dissertation first introduces comparative political theory as a framework for the inter-civilizational dialogue, arguing that Indigenous contributions have been marginalized and must be considered. Part I then focuses and elaborates on specifically Mesoamerican contributions; Part II is dedicated to Andean contributions; and Part III to Native North American contributions. The dissertation closes with a brief reflection of how Indigenous American contributions can help us address some of our most crucial contemporary global challenges, especially in what concerns the construction of cosmopolitical alternatives built on post-anthropocentric forms of socio-ecological justice.Dissertation/ThesisPh.D. Political Science 201

Student Research Colloquium Proceedings 2009

2009 Student Research Colloquium proceedings include the following: a schedule of the day\u27s events, acknowledgement of research sponsors, the day\u27s program, conference presentation abstracts, student presenter index, research sponsor index, planning committee, poster and paper presentation judges, registration desk, sponsors, and donors, map of Atwood Memorial Center. Keynote address on greenhouse gases, global demand for energy, and tomrorow\u27s technology to address these issues given by Dr. Sean Garrick, Associate Professor, Department of Mechanical Engineering, University of Minnesota. Sustainability Panel Discussion panelists: Dr. Anthony Akubue, Professor, Environmental and Technological Studies, St. Cloud State University; Dr. Sean Garrick, Associate Professor, Mechanical Engineering, University of Minnesota; Valerie Knopp, Assistant Director of Financial Aid, Offices of Scholarships and Financial Aid, St Cloud State University; Teresa A. Lamo-Nelson, Doctoral Candidate, Higher Education Administration, St. Cloud State University; Angela Olson, Assistant Professor, Aviation, St. Cloud State University; Dr. Tracy E. Ore, Associate Professor/Coordinator, Sociology and Anthropology/St Cloud State University Community Garden, Dr. Mitch Bender (Moderator), Associate Professor, Environmental and Technological Studies, St Cloud State University

Exploring the Movement of People in Postclassic and Historic Period Lamanai Using Stable Isotopes

The location of the Maya site of Lamanai on the New River Lagoon in northern Belize strategically situated it to participate in both coastal and inland trade routes and communication. This study of human burials at Lamanai examines the phosphate-oxygen isotope compositions of bone and enamel, which reflect drinking water and hence climatic zones, oxygen- and hydrogen-isotope compositions of modern local water, which provide a baseline for drinking water, and carbon- and nitrogen-isotope compositions of bone collagen, which reflect diet. The combination of isotopic, mortuary, osteological, and artifactual data is used to explore mobility at Lamanai during the Postclassic and Historic periods. While these data suggest some mobility, most movement likely occurred within the surrounding lowland region. The origin of Postclassic individuals buried in an unusual face-down position (VPLF) was also investigated. The VPLF group demonstrates variability in demographics and residential history, and its appearance possibly reflects an ideological shift

Current Air Quality Issues

Air pollution is thus far one of the key environmental issues in urban areas. Comprehensive air quality plans are required to manage air pollution for a particular area. Consequently, air should be continuously sampled, monitored, and modeled to examine different action plans. Reviews and research papers describe air pollution in five main contexts: Monitoring, Modeling, Risk Assessment, Health, and Indoor Air Pollution. The book is recommended to experts interested in health and air pollution issues