Integer linear programming (ILP) is a versatile modeling and optimization technique that is increasingly used in non-traditional ways in biology, with the potential to transform biological computation. However, few biologists know about it. This how-to and why-do text introduces ILP through the lens of computational and systems biology. It uses in-depth examples from genomics, phylogenetics, RNA, protein folding, network analysis, cancer, ecology, co-evolution, DNA sequencing, sequence analysis, pedigree and sibling inference, haplotyping, and more, to establish the power of ILP. This book aims to teach the logic of modeling and solving problems with ILP, and to teach the practical 'work flow' involved in using ILP in biology. Written for a wide audience, with no biological or computational prerequisites, this book is appropriate for entry-level and advanced courses aimed at biological and computational students, and as a source for specialists. Numerous exercises and accompanying software (in Python and Perl) demonstrate the concepts.
When a Philadelphia girl intercepts a message about an impending British attack against her father's regiment, commanded by General Washington, in White Marsh, she travels alone by horseback to warn the Patriot army.
We are pleased to present the proceedings of the Second Workshop on Al- rithms in Bioinformatics (WABI 2002), which took place on September 17-21, 2002 in Rome, Italy. The WABI workshop was part of a three-conference me- ing, which, in addition to WABI, included the ESA and APPROX 2002. The three conferences are jointly called ALGO 2002, and were hosted by the F- ulty of Engineering, University of Rome “La Sapienza”. Seehttp://www.dis. uniroma1.it/ ̃algo02 for more details. The Workshop on Algorithms in Bioinformatics covers research in all areas of algorithmic work in bioinformatics and computational biology. The emphasis is on discrete algorithms that address important problems in molecular biology, genomics,andgenetics,thatarefoundedonsoundmodels,thatarecomputati- ally e?cient, and that have been implemented and tested in simulations and on real datasets. The goal is to present recent research results, including signi?cant work in progress, and to identify and explore directions of future research. Original research papers (including signi?cant work in progress) or sta- of-the-art surveys were solicited on all aspects of algorithms in bioinformatics, including, but not limited to: exact and approximate algorithms for genomics, genetics, sequence analysis, gene and signal recognition, alignment, molecular evolution, phylogenetics, structure determination or prediction, gene expression and gene networks, proteomics, functional genomics, and drug design.
This volume presents the proceedings of the Fifth Annual Symposium on Combinatorial Pattern Matching, held at Asilomar, California, in June 1994. The 26 selected papers in this volume are organized in chapters on Alignments, Various Matchings, Combinatorial Aspects, and Bio-Informatics. Combinatorial Pattern Matching addresses issues of searching and matching of strings and more complicated patterns, as for example trees. The goal is to derive non-trivial combinatorial properties for such structures and then to exploit these properties in order to achieve superior performance for the corresponding computational problems. In recent years, combinatorial pattern matching has developed into a full-fledged area of algorithmics and is expected to grow even further during the next years.
Combinatorial structure and algorithms for deducing genetic recombination history, represented by ancestral recombination graphs and other networks, and their role in the emerging field of phylogenetic networks. In this book, Dan Gusfield examines combinatorial algorithms to construct genealogical and exact phylogenetic networks, particularly ancestral recombination graphs (ARGs). The algorithms produce networks (or information about networks) that serve as hypotheses about the true genealogical history of observed biological sequences and can be applied to practical biological problems. Phylogenetic trees have been the traditional means to represent evolutionary history, but there is a growing realization that networks rather than trees are often needed, most notably for recent human history. This has led to the development of ARGs in population genetics and, more broadly, to phylogenetic networks. ReCombinatorics offers an in-depth, rigorous examination of current research on the combinatorial, graph-theoretic structure of ARGs and explicit phylogenetic networks, and algorithms to reconstruct or deduce information about those networks. ReCombinatorics, a groundbreaking contribution to the emerging field of phylogenetic networks, connects and unifies topics in population genetics and phylogenetics that have traditionally been discussed separately and considered to be unrelated. It covers the necessary combinatorial and algorithmic background material; the various biological phenomena; the mathematical, population genetic, and phylogenetic models that capture the essential elements of these phenomena; the combinatorial and algorithmic problems that derive from these models; the theoretical results that have been obtained; related software that has been developed; and some empirical testing of the software on simulated and real biological data.
This book demonstrates that national security and good governance are opposite sides of the same coin. As good governance improves, national security also improves, in that challenges to national security become lesser and lesser in such a society. It concludes that for most of Africa, this is not happening fast enough. Thus, creating fertile grounds for their citizens, especially the youths, to resort to self-help measures, some of which include violence and militancy. These have further complicated the issues of national security, good governance and democracy in Africa. Praise for the Book This book is a must read. Dr. Dan Mou, a world-class trained political scientist, who has served at various ministries and parastatals in Nigeria before retirement, has made stunning revelations. Lead Times Africa Magazine. Dr. Dan Mou, a varsity don and seasoned civil servant, (who) spent over two decades working in Nigerias Presidency, provides deep insights in this book, into the intractable security situation in Nigeria and Africa. He also x-rays economic policies, among other issues. Daily Trust. Having successfully designed and masterminded many workable national schemes in the past in Nigeria, like the memoranda that led to the establishment of the Economic and Financial Crimes Commission(EFCC), Ministry of Niger Delta Affairs, Amnesty Programme for the Niger Delta Region, to mention just a few, Dr. Dan Mou, in this book, has (proposed) permanent solutions it is no fallacy to say that no one else could have done it better. Dr. O. W. Bashorun, Provost, College of Education, Lagos, Nigeria.
This book shows that the security, economic, political, and social problems challenging national security, democracy, and good governance currently in Nigeria would get better or worse, depending on what happens to the 71 percent of Nigerias population still living below the poverty line. This is in spite of the billions of petrodollars that Nigeria garnered as revenue over the past few decades. It reveals that one does not need to be a political prophet to predict that if these challenges are not successfully addressed through good governance and inclusive growth, this country will witness worse civil disobedience, violence, revolts, militancy, breakdown of law and order, more kidnappings, and more of the citizens trying to check out of the country to other parts of the world in the future. It concludes, however, that under such intense pressures, the Government of Nigeria, even if it is simply for its self-preservation, will be forced by the objective conditions to move against the interests of the dominant groups and classes in Nigeria. These are the ones who have, for long, captured and hijacked state power and the resources of the country for their exclusive use. There is this perception that Nigerians dont write and read. This perception is deep-seated, even among intellectuals who see our authors as shallow researchers. But Dr. Dan Mou has debunked that myth and shown that Nigerians can write well-researched and detailed books. It is quite prophetic in its assessment of the Nigerian State (Agbo Agbo, deputy editor, The Nation). Dr. Dan Mou has proven himself a world-class scholar and an intellectual colossus. His reputation as an internationally renowned public policy expert has continued to soar. I congratulate him for these remarkable achievements (Professor Justice Abdul Fatai Kuti, first justice of Abuja High Court and former dean, faculty of law, University of Ado Ekiti, Ekiti State of Nigeria). Dr. Mou is certainly one of the best scholars we have on the African continent. As an educationist myself, before I became a traditional ruler, I agree totally with his analysis and conclusions. I share the optimism Dr. Mou has expressed . . . that once the recommendations therein are adopted and meticulously implemented, with proper monitoring and evaluation of such resultant policies and programmes, Nigeria and indeed Africa would be able to solve most of these challenges (HRH Alh. Dr. Sheban Audu, Nizazo III, Etsu Kwali, Etsu Kwalis Palace, Abuja, Nigeria).
This book identifies and explains the politico-historical forces that underlie agrarian policies in Nigeria. It also examines the impacts of these policies on different social classes and groups, especially the peasantry. The book focuses specifically on the Agricultural Marketing and Commodity Boards in Nigeria from 1945-1985. These boards are examined as state agencies and actions that have direct implications for different classes and groups. The book reveals that the various social classes and groups contested every step of the agrarian policies, right from their agenda setting to actual implementation. Consequently, the contestations affected drastically the policies and outcomes in such a way that the original goals were lost. "I am very impressed with its theoretical scope, command of extant literature and methodological sophistication. Dr. Mou's book should be of immense interest to a broad range of scholars from political theorists, to political economists as well as African area specialists." - Professor Crawford Young, Department of Political Science, University of Wisconsin - Madison, USA. "Dr. Dan Mou...Thanks for contributing to knowledge. Your book is highly expository and full of discoveries... We are proud of you." S.A. Raofu, Chairman, Committee of Deans, AOCOE, Lagos, Nigeria.
Most studies of fear of crime assume that is rimarily induced by direct or indirect contact with a criminal event. Consequently programs designed to deal with this problem focus on either increased police protection or a number of crime prevention programs. In this study, Dan A. Lewis and Greta W. Salem raise questions both about the validity of these assumptions and the effectiveness of the programs. A five-year investigation has led the authors to challenge those theories that focus only on the psychological responses to victimizations and fail to take into account the social and political environments within which such fears are shaped and nurtured.Explicitly laying out a 'social control' perspective which informs their research and analysis, the authors examine the fear of crime in ten neighorhoods in Chicago, San Francisco, and Philadelphia which represent the range of communities typically found in urban areas. On the basis of their analysis the authors contend that fear of crime is not related to exposure or knowledge about criminal events alone but also stems from residents' concerns about broad changes taking place in their neighborhoods. Many people, they argue, are afraid not only because crime occurs but also because they believe that they have lost control over the environment in which they live.Lewis and Salem conclude that the eradication of fear of crime requires strategies that move beyond the traditional crime prevention programs to consider ways to restore the control that community residents feel they have lost and the possibilities for a more equitable distribution of security in urban areas.
Between 1820 and 1860, American social reformers pioneered a 'politics of identification' which portrayed minority and socially excluded groups as both physically vunerable and socially related. This text traces the theme of identification through the literature of social reform.
In an arena of public policy where misinformation and disinformation reigns, ... facts are desperately needed, and Cocaine Changes gives us a bucketful of them. Anyone who values rationality and is concerned about the harmful efforts of our misbegotten drug policy should read this book." ?Ira Glasser, Executive Director, ACLU"I know of no other book that offers so much information on the subject so clearly and calmly presented. For anyone interested in the natural history of cocaine use in America now, Cocaine Changes provides the best, most comprehensive available resource." ?Lester Grinspoon, M.D., Harvard Medical School "This book puts the cocaine scare of the 1980s to the test and places cocaine in a more realistic perspective. By examining the lives of hundreds of heavy users, it discovers that even among this group, cocaine use is not always cocaine abuse." ?Kevin B. Zeese, Drug Policy Foundation "This provocative study challenges many of the prevailing myths about cocaine and crack use, and is essential reading for any researchers, educators, policymakers, law enforcement personnel, or concerned citizens who wish to make informed judgments." ?Patricia G. Erickson, Ph.D., Head, Drug Policy Research Program (Canada) "This book puts the cocaine scare of the 1980s to the test and places cocaine in a more realistic perspective. By examining the lives of hundreds of heavy users, it discovers that even among this group, cocaine use is not always cocaine abuse." ?Kevin B. Zeese, Vice-President and Counsel, Drug Policy Foundation
The performance of Nigeria has recently been vehemently criticized as not commensurate with her human and material potentialities. The hope that Nigeria is, by destiny, the African Giant appears to be fading. Some analysts, seeing this, have blamed it on the character defects of the leadership in Nigeria. They argue that because the leaders are predatory and corrupt, they have preoccupied themselves with their interests, which are primitive accumulation and luxurious lifestyles. Meanwhile, the rest of the citizens are suffering. This book argues that such character defects may indeed exist in some of Nigerian leaders. However, these are not the main reasons for their dismal performance regarding the welfare of the citizens. The main problem is that Nigerian leaders seem to have largely lost control over the state and its policies, which appear to have been captured by the dominant classes and groupslocal and international. Nigerias main problem is, therefore, a structural one. Nonetheless, the book concludesas the security, economic, political, and social crises intensifyNigerian leaders, even if it is simply for self-preservation, will be forced by the objective conditions to move against the interests of these dominant classes and groups. It is only then that Nigeria can realistically be restored to the possibility of becoming an African Giant.
It has become fashionable to assume that concerted action to bring about social reform is a waste of time. If we are to move beyond the current laments about how nothing works anymore, we must view the reform process from the perspective of the community groups involved-those who make it work or fail-and understand how and why they behave as they do. "Social Construction of Reform "is an analysis of the activities of community groups who used Ford Foundation funding to prevent crime. The authors ask: What are the goals of the community groups who are involved in the reform? What are they trying to accomplish with their participation in the program? Are their goals synonymous with those who fund and evaluate the activity? The authors begin by analyzing the implementation of the grant by the groups involved. They describe the origins of the group's planned intervention, the nature of what is called community crime prevention, and then they examine the impact of external funding on community organizations as a generic issue. They take a careful look at what the groups did with the Foundation's support, to understand how well the groups' crime prevention strategy they employed supported their ideology. The block watch is examined in detail as the tactic most often employed. The authors conclude with observations on what success and failure mean in the context of the findings reported, offering a better understanding of reforms and new criteria to assess their effectiveness.
This book develops a new approach called parameter advising for finding a parameter setting for a sequence aligner that yields a quality alignment of a given set of input sequences. In this framework, a parameter advisor is a procedure that automatically chooses a parameter setting for the input, and has two main ingredients: (a) the set of parameter choices considered by the advisor, and (b) an estimator of alignment accuracy used to rank alignments produced by the aligner. On coupling a parameter advisor with an aligner, once the advisor is trained in a learning phase, the user simply inputs sequences to align, and receives an output alignment from the aligner, where the advisor has automatically selected the parameter setting. The chapters first lay out the foundations of parameter advising, and then cover applications and extensions of advising. The content • examines formulations of parameter advising and their computational complexity, • develops methods for learning good accuracy estimators, • presents approximation algorithms for finding good sets of parameter choices, and • assesses software implementations of advising that perform well on real biological data. Also explored are applications of parameter advising to • adaptive local realignment, where advising is performed on local regions of the sequences to automatically adapt to varying mutation rates, and • ensemble alignment, where advising is applied to an ensemble of aligners to effectively yield a new aligner of higher quality than the individual aligners in the ensemble. The book concludes by offering future directions in advising research.
This book offers a comprehensive examination of midterm elections from the lens of communications and media coverage. Using a wide variety of methods, this contributed volume covers the differences, similarities, and challenges unique to midterm elections.
and relevance to the symposium. The Program Committees of both tracks met in Karlsruhe on May 24–25, 2008. The design and analysis trackselected51papersoutof147submissions.Theengineeringandapplications track selected 16 out of 53 submissions.
In mathematics, it simply is not true that 'you can't prove a negative'. Many revolutionary impossibility theorems reveal profound properties of logic, computation, fairness and the universe, and form the mathematical background of new technologies and Nobel prizes. But to fully appreciate these theorems and their impact on mathematics and beyond, you must understand their proofs. This book is the first to present these proofs for a broad, lay audience. It fully develops the simplest rigorous proofs found in the literature, reworked to contain less jargon and notation, and more background, intuition, examples, explanations, and exercises. Amazingly, all of the proofs in this book involve only arithmetic and basic logic – and are elementary, starting only from first principles and definitions. Very little background knowledge is required, and no specialized mathematical training – all you need is the discipline to follow logical arguments and a pen in your hand.
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