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36666 results in Cambridge Textbooks

Page 1447 of 1834

  • 14 - Birds, Bees, and Genetic Algorithms

  • from Part IV - Additional Topics
  • Ran Libeskind-Hadas, Harvey Mudd College, California, Eliot Bush, Harvey Mudd College, California
  • Book:
    Computing for Biologists
    Published online:
    28 May 2018
    Print publication:
    22 September 2014, pp 196-204

  • Summary

    This chapter is about the birds and the bees, but it’s probably not what you’re thinking! Let’s start with the backstory.

    Imagine that you’re a salesperson who needs to travel to a set of cities to show your products to potential customers. The good news is that there’s a direct flight between every pair of cities and, for each pair, you’re given the cost of flying between those two cities. Your objective is to start in your home city, visit each city exactly once, and return back home at lowest total cost. This is called the Traveling Salesperson Problem and it’s one of the most famous problems in computer science.

    For example, consider the set of cities and flights shown in Figure 14.1 and imagine that your start city is Aville.

    A tempting approach to solving the Traveling Salesperson Problem is to use an approach like this. Starting at our home city, Aville, fly on the cheapest flight. That’s the flight of cost 1 to Beesburg. (This is not yet the part about the bees.) From Beesburg, we could fly on the least expensive flight to a city that we have not yet visited, in this case Ceefield. From Ceefield, we would then fly on the cheapest flight to a city that we have not yet visited. (Remember, the problem stipulates that you only fly to a city once, presumably because you’re busy and you don’t want to fly to any city more than once - even if it might be cheaper to do so.) So now, we fly from Ceefield to Deesdale and from there to Eetown.

  • 2 - Pathogenicity Islands

  • from Part I - Python versus Pathogens
  • Ran Libeskind-Hadas, Harvey Mudd College, California, Eliot Bush, Harvey Mudd College, California
  • Book:
    Computing for Biologists
    Published online:
    28 May 2018
    Print publication:
    22 September 2014, pp 41-52

  • Summary

    Certain regions of the Salmonella genome contain genes that are directly involved in causing disease. These so-called pathogenicity islands have genes with functions related to invading and living inside a host organism. As you might expect, medical researchers are very interested in identifying and studying such regions. One characteristic that is useful in locating pathogenicity islands is GC content. The GC content inside a pathogenicity island often differs significantly from what is found in the rest of the genome. For this reason, it’s useful to find sections of the genome with unusual GC content. This allows us to zoom in on parts of the genome that are candidate pathogenicity islands.

    In this chapter, you’ll write a program that computes and reports the GC content of different regions of the genome. In the following chapters, we’ll refine our search even further to find individual genes in the pathogenicity islands.

    How Salmonella Enters Host Cells

    Below is an image showing Salmonella bacteria invading cultured human cells. The bacteria will physically enter and reside inside these human cells.

  • 9 - Representing and Working with Trees

  • from Part III - Phylogenetic Reconstruction and the Origin of Modern Humans
  • Ran Libeskind-Hadas, Harvey Mudd College, California, Eliot Bush, Harvey Mudd College, California
  • Book:
    Computing for Biologists
    Published online:
    28 May 2018
    Print publication:
    22 September 2014, pp 145-153

  • Summary

    Biologists are frequently interested in the relationships between species. To represent such relationships they use a diagram called a phylogenetic tree. The phylogenetic tree in Figure 9.2 consists of a set of nodes connected by branches. In this example, we have marked the nodes with dots. The ones on the right are called leaf nodes or simply leaves. They represent the species whose relationships we want to understand. In this example, the leaves are five currently living primate species, including great apes and humans. There are also internal nodes, which represent hypothesized ancestral species. For example, the node marked in red represents the most recent common ancestor of chimpanzees and humans, an animal that lived between 5 and 8 million years ago.

    The tree provides information about the evolutionary relationships between species. We can use the internal nodes to define groups of closely related species called clades. All the species descended from a particular internal node form a clade, and are more closely related to each other than they are to other species. Thus the red dot in Figure 9.2 defines a clade that we might call the human-chimpanzee clade. This clade includes three living species: human, the common chimpanzee, and the pygmy chimpanzee. The fact that they are in a clade together tells us, for example, that chimpanzees are more closely related to humans than they are to gorillas.

  • 6 - The Use-It-Or-Lose-It Principle

  • from Part II - Sequence Alignment and Sex Determination
  • Ran Libeskind-Hadas, Harvey Mudd College, California, Eliot Bush, Harvey Mudd College, California
  • Book:
    Computing for Biologists
    Published online:
    28 May 2018
    Print publication:
    22 September 2014, pp 87-99

  • Summary

    So far, everything we’ve done with recursion we could have also done with for loops. The recursive functions that we’ve seen were conceptually somewhat different from the for loop versions, but recursion hasn’t yet given us powers to compute things that we couldn’t compute before. But now it will!

    Peptide Fragments

    Imagine that we have a set of fragments of proteins, where each fragment has a given mass. For example, the masses of five protein fragments might be [2, 3, 8, 10, 12] in some unit of mass. In addition, we know the mass of the original protein, say 25 units for the sake of example. The question is whether or not there is a subset of our list of fragment masses that add up to the mass of the protein. In this example, the answer is “yes”: fragments with masses 3, 10, and 12 add up to 25. On the other hand, if the fragments had masses [2, 15, 17, 20], we could not have found a subset that adds up to 25. For now, we’re assuming that each mass in the list can be used at most once. This problem arises in the study of protein structure and has been the focus of a recent study.

  • Preface

  • Ran Libeskind-Hadas, Harvey Mudd College, California, Eliot Bush, Harvey Mudd College, California
  • Book:
    Computing for Biologists
    Published online:
    28 May 2018
    Print publication:
    22 September 2014, pp ix-x

  • Summary

    The computer is the most powerful general-purpose tool available to biologists.

    In part, this is due to the continuing rapid growth of biological data. For example, at the time of writing, the GenBank database had over 100 million genetic sequences with over 100 billion DNA characters. Among the contents of that database are genes from many organisms, annotated with what’s known about their function.

    Imagine that you’re studying a bacterium and wish to understand what causes it to be infectious. One promising approach is to identify genes in the bacterium and compare these to known genes in GenBank. If you’re able to find similar genes whose function is known, it will tell you a great deal about the role of the genes in your bacterium. This approach represents a computational challenge, and is, in fact, the topic of Part I of this book.

    But searching enormous databases is not the only reason that computers are so useful to biologists. Many biological problems have a large number of different possible solutions and only a computer – programmed with carefully designed computational recipes or “algorithms” – has any chance of finding the right one. For example, biological molecules such as proteins and RNA fold into complex shapes that strongly impact their function. Computational techniques have been developed to predict how these molecules fold. Such techniques help us understand how proteins and RNA work and can even help us design new molecules to treat disease.

  • 12 - RNA Secondary Structure Prediction

  • from Part IV - Additional Topics
  • Ran Libeskind-Hadas, Harvey Mudd College, California, Eliot Bush, Harvey Mudd College, California
  • Book:
    Computing for Biologists
    Published online:
    28 May 2018
    Print publication:
    22 September 2014, pp 177-185

  • Summary

    Acquired Immune Deficiency Syndrome or AIDS was first recognized in the early 1980s. Within a few years of its discovery, scientists had identified the virus that causes it, called the Human Immunodeficiency Virus or HIV. Through the 1980s and early 1990s, the HIV/AIDS epidemic grew steadily, with the number of affected people and the number of deaths increasing every year. By the late 1990s it was causing millions of deaths per year worldwide, and had a prevalence of more than 20% in the adult population of some countries.

    An epidemic of this magnitude requires multiple types of response. One approach has been to limit the spread of the disease through education, for example, by encouraging the use of condoms and discouraging drug users from sharing needles. A second approach has been to carry out research into the basic biology of HIV in an effort to develop better treatments or even a vaccine.

    The programming problems for this section are connected with basic research into HIV. They involve predicting the RNA secondary structure in a single gene from the HIV genome. We’ll talk about secondary structure and its prediction shortly. But first, let’s briefly discuss HIV’s genome and life cycle.

  • 12 - A strengths-based palliative approach for the frail older adult living in residential aged care

  • from Part 3 - End of life care
  • Wendy Moyle, Griffith University, Queensland, Deborah Parker, University of Queensland, Marguerite Bramble, Griffith University, Queensland
  • Book:
    Care of Older Adults
    Published online:
    06 August 2018
    Print publication:
    19 September 2014, pp 179-191

  • Summary

    Learning objectives

    After reading this chapter you will be able to:

  • Have an understanding of a palliative approach in residential aged care.

  • Understand the key features of an evidence-based palliative approach in residential aged care.

  • Understand how to apply a strengths-based approach to a palliative approach for people living in residential aged care.

  • Understand specific issues in providing a palliative approach for people with dementia.

    • Introduction

    This chapter extends some of the issues introduced to you in Chapter 10 which identified a model of palliative care that has been developed specifically for Australian residential aged care facilities (RACFs). This comprehensive evidence-based model of a palliative approach in residential aged care is encapsulated in an evidence translation product known as the Palliative Approach Toolkit (Parker, Hughes & Tuckett, 2011). Before we explore this model of care we will briefly review some of the research and issues specific to providing a palliative approach in RACFs. The final section of the chapter will identify some specific issues for people with dementia in RACF and some programs that have been developed to address these.

  • 13 - Evidence-based nursing interventions: a good death and fostering pain relief

  • from Part 3 - End of life care
  • Wendy Moyle, Griffith University, Queensland, Deborah Parker, University of Queensland, Marguerite Bramble, Griffith University, Queensland
  • Book:
    Care of Older Adults
    Published online:
    06 August 2018
    Print publication:
    19 September 2014, pp 192-202

  • Summary

    Learning objectives

    After reading this chapter you will be able to:

  • Have an understanding of what constitutes a ‘good death’ for older people.

  • Understand the principles of evidence-based nursing in relation to pain assessment and management.

  • Understand specific issues in the assessment and management of pain for people with dementia.

  • Understand how to apply a strengths-based approach to pain assessment and management for older people.

    • Introduction

    In Chapter 10 we reviewed the history of palliative care with specific reference to developments in Australia and New Zealand. Chapter 11 focused on advance care planning, which is a critical aspect of providing a strengths-based palliative approach for older people. Chapter 12 specifically looked at some of the research regarding providing a palliative approach in residential aged care facilities (RACFs) and the evidence-based model within the Palliative Approach Toolkit. This chapter delves further into what makes a good death for older people and then specifically focuses on one common symptom that can influence whether a good death is possible – pain. Pain is one of the most common symptoms and always features in discussions with people who know they are dying, families supporting that person or staff providing the care. The phrase most associated with achieving a good death is that it is ‘pain free’. In the final section of the chapter we will examine specific issues in regard to pain management and people with dementia.

  • Foreword

  • Wendy Moyle, Griffith University, Queensland, Deborah Parker, University of Queensland, Marguerite Bramble, Griffith University, Queensland
  • Book:
    Care of Older Adults
    Published online:
    06 August 2018
    Print publication:
    19 September 2014, pp v-vi

  • Summary

    One of life’s truisms is that we will all experience ageing. Most of us won’t think about it until the effects of ageing give us either a gentle nudge or a hard wake-up call. Either way, when we are confronted with its effects, quite reasonably we won’t want it to define us. Rather the effects and changes of ageing will be woven into the fabric of what makes us unique as individuals.

    Unfortunately in the western world the term ‘ageing’ has evolved to have negative connotations in a way that devalues the worth of the individual’s contributions – past, present and future. Yet we know that the older person can be resilient, informed about their health issues and actively engaged in the decisions about their health and care requirements. As a health professional, adopting a strengths-based perspective means we can support the person and their family, acknowledging their strengths and resources rather than focusing on problems, vulnerabilities and potential deficits.

Page 1447 of 1834