Information

7.7: Further Reading, What Have We Learned? - Biology


Length Distributions of States and Generalized Hidden Markov Models

Given a Markov chain with the transition from any state to the end state having probability τ , the probability of generating a sequence of length L (and then finishing with a transition to the end state) is given by:

[ au(1- au)^{L-1} onumber ]

Similarly, in the HMMs that we have been examining, the length of states will be exponentially dis- tributed, which is not appropriate for many purposes. (For example, in a genomic sequence, an exponential distribution does not accurately capture the lengths of genes, exons, introns, etc). How can we construct a model that does not output state sequences with an exponential distribution of lengths? Suppose we want to make sure that our sequence has length exactly 5. We might construct a sequence of five states with only a single path permitted by the transition probabilities. If we include a self loop in one of the states, we will output sequences of minimum length 5, with longer sequences exponentially distributed. Suppose we have a chain of n states, with all chains starting with state π1 and transitioning to an end state after πn. Also assume that the transition probability between state πi and πi+1 is 1−p, while the self transition probability of state πi is p. The probability that a sequence generated by this Markov chain has length L is given by:

[left(egin{array}{l}
L-1
n-1
end{array} ight) p^{L-n}(1-p)^{n} onumber ]

This is called the negative binomial distribution.

More generally, we can adapt HMMs to produce output sequences of arbitrary length. In a Generalized Hidden Markov Model [1] (also known as a hidden semi-Markov model), the output of each state is a string of symbols, rather than an individual symbol. The length as well as content of this output string can be chosen based on a probability distribution. Many gene finding tools are based on generalized hidden Markov models.

Conditional random fields

The conditional random field model a discriminative undirected probabilistic graphical model that is used alternatively to HMMs. It is used to encode known relationships between observations and construct con- sistent interpretations. It is often used for labeling or parsing of sequential data. It is widely used in gene finding. The following resources can be helpful in order to learn more about CRFs:

  • Lecture on Conditional Random Fields from Probabilistic Graphical Models course: class. coursera.org/pgm/lecture/preview/33. For background, you might also want to watch the two previous segments, on pairwise Markov networks and general Gibbs distributions.
  • Conditional random fields in biology: www.cis.upenn.edu/~pereira/papers/crf.pdf
  • Conditional Random Fields tutorial: http://people.cs.umass.edu/~mccallum...f-tutorial.pdf

What Have We Learned?

In this section, the main contents we covered are as following:

• First, we introduced the motivation behind adopting Hidden Markov Models in our analysis of genome annotation.

  • Second, we formalized Markov Chains and HMM under the light of weather prediction example.
  • Third, we got a sense of how to apply HMM in real world data by looking at Dishonest Casino and CG-rich region problems.
  • Fourthly, we systematiclly introduced algorithmic settings of HMM and went into detail of three of them:

    – Scoring: scoring over single path
    – Scoring: scoring over all paths
    – Decoding: Viterbi coding in determing most likely path

  • Finally, we discussed the possibility of introducing memory in the analysis of HMM and provided further readings for interested readers.

Bibliography

[1] Introduction to GHMMs: www.cs.tau.ac.il/~rshamir/algmb/00/scribe00/html/lec07/node28. html.

[2] R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. Biological sequence analysis. eleventh edition, 2006.


MyEtherWallet (MEW)

Welcome to this guide on securely setting up MyEtherWallet, commonly referred to as MEW. MEW is an open-source Ethereum wallet that directly interfaces with the blockchain. Using MEW, users will have fine-grain control over their crypto experience, and the opportunity to learn about the Ethereum Blockchain.

This guide is focused on the Android version of the MyEtherWallet app. If you are using iOS, check out our iOS guide ,

1. Introduction

This guide is focused on how to securely set up MyEtherWallet on Android. MEW is also available on iOS, as a browser-extension, and a web app. If you are using iOS, check out our MyEtherWallet iOS guide If you want to use the web app or browser extension, check out our MyEtherWallet browser guide.

MyEtherWallet was originally released in 2015 as a web app, the same year the Ethereum blockchain launched. Since then, the dev team has been busy building an ecosystem of tools for directly interacting with the Ethereum blockchain. In 2018, the MEW team released MEWconnect, which was a mobile app designed to connect your mobile device to your local MyEtherWallet instance. In 2020, the full version of MyEtherWallet came to Android and iOS - and MEWconnect was dropped from the Play store/App store.

Today, MEW gets over 4 million visits per month to its web app, and the numbers on the mobile app keeps rising. MyEtherWallet is a good choice for you if you want to have more control over your interactions with the Ethereum blockchain. Everything runs client-side, this means that MEW runs on your device and does not connect to or rely on any 3rd party servers. Everything on MyEtherWallet is under your direct control.

Benefits of using MEW include

Flexibility - MEW Wallet supports hardware wallets, and supports creating multiple wallets from the user dashboard.

Staking - MEW supports ETH2.0 staking directly within the app

Dapp Browser - a web browser optimized for use with decetralized applications, built-in to MyEtherWallet

Education - The app has a built-in portal for MEWtopia, which is a knowledge center for Ethereum

DeFi - through the dapp browser, access the world of decentralized finance

Buy Crypto - MEW supports buying cryptocurrency through the app

Advanced Features - MEW supports offline usage, signing transactions, and connecting your mobile MyEtherWallet account to the MyEtherWallet web app.

2. Download and install

  • From your mobile device, open the 'Play Store' and search for 'MEW Wallet' or click this link: MEW wallet – Ethereum wallet - Apps on Google Play to download.
    • Trust, but verify. When using any cryptocurrency wallet, it is important to make sure you are downloading the correct version. Check the store listing for the following info:

    Version: 1.2.6 as of February 7, 2021

    Offered by: MyEtherWallet

    • The `Version` number will change as the app is updated over time. The important part to verify is the `Offered by` field.

    Remember the phrase trust, but verify. Taking the extra step to verify can prevent loss of funds. Trust, but verify is an important concept in having a security mindset.

    3. Create and setup

    MyEtherWallet is a client-side interface to the Ethereum blockchain. It is non-custodial, meaning that MyEtherWallet stores all the private keys on your device, under your control.

    MEW follows BIP39 to generate your wallet, which is the crypto industry standard. Under the hood, MyEtherWallet generates your wallet with the use of a recovery phrase. The recovery phrase can be used to restore your MyEtherWallet or can be imported into another wallet that supports BIP39.

    When creating a new wallet with MEW, the default method is to create your wallet within the app. The more advanced method is to generate your own recovery phrase. We created detailed guides on generating your own recovery phrase.

    By following the right directions, you can generate a recovery phrase that is more secure than the default method used by wallets.

    In this section, you are going to create a new wallet using MyEtherWallet's default method. Let's get started.

    If you already have a recovery phrase, proceed to Section 6. Initialize or import recovery phrase.

    To create a new wallet with a new recovery phrase in MEW:

    • Open the MyEtherWallet app and tap on "Create a free wallet" to begin
    • Before proceeding, MEW will show you some security tips. Read all of them - it only takes a minute. The tips are principles that should be followed anytime you are using cryptocurrency. When you are finished tap on "Create a wallet" to go to the next step.

    • MyEtherWallet will now ask you to create a 6 digit pin. The purpose of the pin is to lock and unlock you wallet.

    • It is always a good idea to put the maximum amount of security as possible on your wallet. MyEtherWallet supports biometric authentication. Configure this now.
    • After configuring biometric authentication, MEW will setup your wallet. On the device screen you can follow along with what is happening. When setup is complete, tap on "Finish" to go to your wallet.

    • MyEtherWallet will load your new wallet and prompt you to create a backup of your wallet. Tap on "Backup Now' to start the process.
    • With cryptocurrency, you are your own bank. This is why backing up your wallet is so important. MEW is a non-custodial wallet, and that means nobody but you has control over your private keys. Read the information on the screen and tap "Backup now" to start the backup process.

    MyEtherWallet will now be displaying your recovery phrase on the screen. MEW uses sequence of 24 words as your recovery phrase, which is the maximum allowed by BIP39 and provides the highest entropy.

    MyEtherWallet, along with many other wallets, recommend writing down your seed phrase. This is the first step, and writing it down allows you to transfer it to a secure medium for backup.Once you have transferred your seed phrase to paper, or another secure medium, it is time to verify your seed phrase. Remember, paper backup is for temporary use - only acceptable while in transit to the final backup destination. This is because paper is vulnerable to loss, theft, and damage.

    • Using pencil and paper, write down your recovery phrase and proceed to the next section of this guide

    4. Verify your recovery phrase

    Backing up your recovery phrase for most wallets, including MyEtherWallet, is a 4 step process:

    1. The wallet will display your recovery phrase on the screen, and ask you to create a backup.
    2. Next, you will write down your seed phrase using paper and pencil, this is to prepare it to be transferred to a more secure medium*
    3. Returning to your wallet, the wallet will ask you to input your recovery phrase. This step is done to verify that you have copied your recovery phrase accurately.
    4. After completing the setup of your wallet, and before adding any funds to your wallet, backup your recovery phrase to a more secure medium

    At this point, you are at step 3 in the above process, verifying your recovery phrase. In the section 5 of this guide, you will learn how to create a secure backup of your recovery phrase..

    *WARNING: When you follow the steps to backup your recovery phrase, you will be writing the recovery phrase on a piece of paper. It is very important that you backup the recovery phrase on a more reliable medium, and then destroy that piece of paper. Paper is vulnerable to accidental loss, theft, and damage. It is not the safest method of backing up your recovery phrase.

    Now that you have your recovery phrase written down, MyEtherWallet will quiz you on 4 random words. This is done because the order of your recovery phrase is very important - one word that is out-of-order, or one word that is misspelled, will render your recovery phrase null and void. Take care to copy it down accurately.

    • MyEtherWallet will be displaying 4 multiple choice questions asking what the correct word, based on the order of the words. For example, you will be asked what word number 21 is, and asked to select the correct word from 3 possible choices
    • Using your recovery phrase as a reference, select the correct words in the MyEtherWallet app to verify you have copied down your recovery phrase correctly.
    • Tap on "Finish" in the upper right hand corner when you have completed your answers

    Your wallet is now ready to use, and it is up to you to finish backing up your recovery phrase properly. The next section of this guide has an overview of all the options that are available to you. Pick the option that works best for you and provides the most security. You are now ready to go to the next section and finish backing up your recovery phrase!

    5. Securely back up your recovery phrase

    If you used Vault12 to generate your recovery phrase, then congratulations! Your seed phrase is already securely backed up in your digital vault.

    Your recovery phrase is the master key to all of your cryptocurrency funds. MEW uses BIP39, which is the current industry best practice for generating recovery phrases. The majority of modern wallets today use BIP39. This means your MEW recovery phrase can be used to access your funds across many different wallets, without knowing your MEW PIN or other security credentials.

    Securely backing up your recovery phrase is the most important step in creating a new wallet. To emphasize how important this is, consider how someone with your recovery phrase could access your funds without you knowing.

    Imagine a bad actor has your recovery phrase, and you have your MEW locked down with a pin code and biometric authentication on an encrypted device. The attacker could simply open any wallet application, and import your recovery phrase. The attacker now has access to all of your funds.
    We want you to have a secure backup, so this never happens to you.

    Nine out of ten wallet providers only mention one way to backup your recovery phrase - by writing the recovery phrase on paper. Wallet providers only mention this paper backup method because it is easy for beginners to do. Paper backups are simply not that secure.

    We did extensive research and compiled the best ways to back up your recovery phrase. We cover all the most well-known options, including next-generation options like How to back up your recovery phrase in Vault12.

    Once you have safely backed up your recovery phrase, you can initialize your wallet using any BIP39 compatible wallet. In the next section, you will learn how you can initialize your wallet using your recovery phrase.

    6. Initialize or import recovery phrase

    If you are following this guide from the beginning, and you created your wallet using the default approach, using the app to `Create a Wallet`, then congratulations! You are ready to start using your wallet. However, be careful about storing large amounts of funds secured only by a wallet-generated recovery phrase.

    If you followed one of our guides for pre-generating a more secure recovery phrase, for instance using Vault12, and you want to use that recovery phrase with your wallet - this section is for you!

    In this section, you will learn how to initialize your MEW wallet using your pre-generated recovery phrase. There are 3 main reasons to initialize your wallet using this method:

    • You lost access to your wallet, and you need to regain access to your wallet and your funds.
    • You want to access your wallet and funds using a different wallet app.
    • You want the best security, and you generated a recovery phrase using an advanced method.

    MEW makes the process super easy and user friendly. Let's get started.`.

    • To initialize your wallet using your recovery phrase in MyEtherWallet:
      • Open the MyEtherWallet app and tap on "I already have a wallet" to begin
      • MEW will ask how you want to initialize your wallet, select "Use recovery phrase"
      • MEW will ask if you have your recovery phrase handy, select "Continue"

      • Enter your recovery phrase in the textbox, being careful to spell each word correctly and type the words in the correct order
      • When you are finished, click "Restore" in the upper right hand corner
      • MyEtherWallet will now ask you to create a 6 digit pin. The purpose of the pin is to lock and unlock you wallet.

      In cryptocurrency, knowledge is your best friend. In the next section, we have some links to futher reading about MyEtherWallet - check them out!


      Exodus wallet

      Welcome to this guide on securely setting up Exodus Wallet. Exodus is an innovative, non-custodial, user-friendly wallet, with millions of downloads. Exodus was initially released in 2015, and today Exodus is a cross-platform wallet, available on Android, iOS, Windows, Mac OS, and Linux.

      This guide is focused on iOS version of Exodus, if you are using Android, check out our Android guide.

      1. Introduction

      Exodus is a very user friendly wallet. The development team places a strong emphasis on making the wallet intuitive and easy to use, while still keeping industry standard security features in place.

      This approach of focusing on the user experience has advantages for beginners. Exodus allows users to get going quickly without getting slowed down by technical terminology. Cryptocurrency is seeing an influx of new users, many of whom are seeing phrases and concepts that are new to them. Exodus does a great job of providing the platform and the tools for users to learn and grow.

      The developers of Exodus are constantly working on improving the wallet. Since Exodus was released in 2015, the developers have released an update every 2 weeks. With Exodus, users can use one app across all platforms to manage their portfolio - including integration with hardware wallets.

      Some of the benefits of using Exodus Wallet include:

      Sync across devices - Your mobile wallet can be synced in real time with your desktop wallet

      Hardware Wallet Integration - Exodus partnered with Trezor, a hardware wallet company, to create a bridge between Trezor wallets and Exodus.

      Exchange built-in - Using Exodus you can swap between 130+ coins and tokens, instantly.

      Staking - Exodus has built-in support for staking with multiple coins. Earn rewards from within the wallet

      24/7 Support - Exodus has 24/7 support for users, which is a unique feature for wallets.

      2. Download and install

      • From your mobile device, open the 'App Store' and search for 'Exodus Wallet' or click this link: Exodus: Crypto Bitcoin Wallet to download.

        • Trust, but verify. When using any cryptocurrency wallet, it is important to make sure you are downloading the correct version.Check the store listing for the following info:

    • Version: 21.2.11 as of February 10, 2021

      Offered by: Exodus Movement, Inc.

        • The `Version` number and the `Updated on` date will change as the app is updated over time. The important part to verify is the `Offered by` field.

        3. Create and setup

        Exodus Wallet is very user friendly. The developer team puts a lot of emphasis on hiding the complex operations "behind-the-scenes" and giving the user a simple interface. You will notice when you first open Exodus wallet, that rather than go through a setup process to configure your wallet, instead a wallet is created for you.

        This approach has advantages for new users, allowing them to get going quickly without getting tied down in technical terminology. However, there are important security steps that must be followed after your wallet is created by Exodus. This guide will walk you step-by-step through creating a wallet with Exodus and securing your wallet.

        Exodus wallet follows crypto industry standards for wallets, including BIP39. Under the hood, Exodus generates your wallet with the use of a recovery phrase. The recovery phrase can be used to restore your Exodus Wallet, or can be imported into another wallet that supports BIP39.

        When creating a new Exodus Wallet, the default method is to create your wallet within the app. The more advanced method is to generate your own recovery phrase. We created detailed guides on generating your own recovery phrase. By following the right directions, you can generate a recovery phrase that is more secure than the default method used by your wallet.

        If you already have a pre-generated seed phrase, proceed to Section 6. Initialize or import seed phrase.

        Create a new wallet in Exodus

        To create a new wallet with a new recovery phrase in Exodus Wallet:

        • Open the Exodus Wallet app
          • The main screen will show two options
            • Get Started
            • I already have a wallet

            Next, Exodus is going to generate your wallet for you. Before bringing you to your wallet, Exodus will display a slider of 4 infographics. Each infographic will display information about how to use Exodus. You can skip the slider by tapping on "skip" in the lower right-hand corner, or slide through all 4 infographics and tap on "Get Started".

            Congrats! You created a wallet in Exodus. However, you aren't done yet. Exodus favors user-friendliness and hides security features. Before putting any funds in your wallet, you will want to backup your recovery phrase and configure security settings. While it may be tempting to configure these settings later, you have to remember you are your own bank in cryptocurrency - don't leave the vault unlocked.

            • To configure your security settings, tap on the human image located on the bottom-right of the screen. This will bring up your account profile.
            • On your profile screen, you will see 3 options:
              • Security
              • Settings
              • Support

              Now you will be in the security section of your account profile. Here, you will see two, or three options:

              • Backup - This option will show you your recovery phrase.
              • Secure With a Passcode - This option will let you configure a passcode to protect your wallet. Exodus requires you to backup your recovery phase first, before allowing you to configure a passcode
              • Secure with Biometrics - This option will secure your wallet biometric authentication, if enabled on your device. Exodus requires you to have configured both a passcode, and a backup of you recovery phase, before this option is available

              To begin the process of backing up your recovery phrase, tap on Backup.

              • Before displaying your recovery phrase, Exodus Wallet displays a warning screen which highlights important security advice, that is worth repeating here:

              • Exodus will now be displaying your recovery phrase on the screen, except the words will be blurred out. In order to display the words, scroll down on the screen until you see "Press and Hold to Reveal"
              • Press and hold where prompted, and your recovery phrase will appear on the screen. When you let go, your recovery phrase will return to being blurred out.

              Exodus Wallet, along with many other wallets, recommend writing down your recovery phrase. However, this is only the first step. Writing down your recovery phrase allows you to transfer it to a secure medium for backup. Properly backing up your recovery phrase is the most critical step of creating your wallet.

              • While your recovery phrase is displayed on the screen, use a pencil and paper to write it down.
                • Make sure you are in a safe location, and not viewable by any cameras
                • Take care and focus on copying the recovery phrase accurately

                4. Verify your secret phrase

                The purpose of verifying your recovery phrase is to ensure that you have copied your recovery phrase accurately and started the backup process. This is done because the order of your recovery phrase is very important - one word that is out-of-order, or one word that is misspelled, will render your recovery phrase null and void. The process of verifying your recovery phrase prevents these types of accidents from happening.

                Most industry standard wallets require verifying your recovery phrase in-app. Exodus, focusing on the user experience, has gotten rid of this verification step. Fortunately, verifying your recovery phrase manually is just as easy as verifying it inside an app.

                • At this point, you should already have your recovery phrase copied down
                • Returning to the app and navigate back to your recovery phrase
                  • Your recovery phrase is located under Security in your Account Profile

                  Now that you have manually verified your recovery phrase, it is time to secure your wallet by requiring a passcode and/or biometric authentication. The level of biometric authentication available to you will depend on what is enabled on your device.

                  • Access your security settings, located under Security in your Account Profile
                  • Now you will be in the security section of your account profile. Here, you will see two, or three options:
                    • Backup - This option will show you your recovery phrase.
                    • Secure With a Passcode - This option will let you configure a passcode to protect your wallet. Exodus requires you to backup your recovery phase first, before allowing you to configure a passcode
                    • Secure with Biometrics - This option will secure your wallet biometric authentication, if enabled on your device. Exodus requires you to have configured both a passcode, and a backup of you recovery phase, before this option is available

                    Remember, you are your own bank with crypto, don't leave the doors unlocked. In addition to securing your wallet, it is a good idea to setup the most security possible for your device.

                    5. Securely back up your secret phrase

                    If you used Vault12 to generate your recovery phrase, your recovery phrase is already securely backed up in your digital vault.

                    Your recovery phrase is the master key to all of your cryptocurrency funds. Exodus Wallet uses BIP39, which is the current industry best practice for generating seed phrases. The majority of modern wallets today use BIP39. This means your Exodus secret phrase can be used to access your funds across many different wallets.

                    We did extensive research and compiled the best ways to backup your recovery phrase. We cover all the most well-known options, including next-generation options like how to back up your recovery phrase in Vault12.

                    Once you have safely backed up your recovery phrase, you can initialize your wallet using any BIP39 compatible wallet. In the next section, you will learn how you can initialize your wallet using your recovery phrase.

                    6. Initialize or import secret phrase

                    If you are following this guide from the beginning, and you created your wallet using the default approach, using the app to `Create a Wallet`, then congratulations! You are ready to start using your wallet.

                    However, be careful about storing large amounts of funds secured only by a wallet-generated recovery phrase.

                    If you followed one of our guides for pre-generating a more secure seed phrase, for instance using Vault12, and you want to use that seed phrase with your wallet - this section is for you!

                    In this section, you will learn how to initialize your wallet using only your seed phrase. There are 3 main reasons to generate your wallet using this method:

                    • You lost access to your wallet, and you need to regain access to your wallet and your funds.
                    • You want to access your wallet and funds using a different wallet app.
                    • You want the best security, and you generated a seed phrase using an advanced method.

                    The Exodus Wallet makes the process super easy and user friendly. Let's get started.

                    Exodus Wallet only supports importing recovery phrases that consist of 12 words. If your recovery phrase is longer than 12 words, Exodus will not be able to successfully import it.

                    To initialize or import a wallet using your existing recovery phrase in Exodus Wallet:

                    • Open the Exodus Wallet app
                      • The main screen will show two options
                        • Get Started
                        • I already have a wallet
                        • Scan QR Code - This option is for syncing Exodus Wallet across different devices. The QR code reader will not process standard BIP39 QR codes. If you want to use this feature, you need to already have an active Exodus wallet.
                        • Type Secret Phrase - This option is for manually typing in your recovery phrase

                        Displayed on the screen will be 4 textbox fields labeled 1-4. This is because Exodus requires your recovery phrase to be entered in blocks of 4 words at a time.

                        • Enter words 1-4 of your recovery phrase, matching each word to the correct number label.
                          • When you have entered words 1-4, tap on "Next"
                          • When you have entered words 5-8, tap on "Next"
                          • When you are finished, tap on "Restore" to initialize your wallet

                          When your wallet first loads, it will appear empty. Don't worry, Exodus is scanning your wallet addresses to restore your accounts and transactions. Where the account balance is listed for each coin, you will see a syncing symbol. You can track the progress of your import at the top of the screen, where a progress bar will show you the status from 0-100%.

                          When Exodus is finished initializing your wallet and your status bar hits 100%, a welcome screen will appear with the following message: "Restore Successful! You did it! Your assets are synced and ready for sending, receiving, and exchanging"

                          Now that you have initialized your wallet using your recovery phrase, it is time to secure your wallet by requiring a passcode and/or biometric authentication. The level of biometric authentication available to you will depend on what is enabled on your device.

                          • To configure your security settings, tap on the human image located on the bottom-right of the screen. This will bring up your account profile.
                          • On your profile screen, you will see 3 options:
                            • Security
                            • Settings
                            • Support
                            • In the Security settings, you will see 2, or 3 options, depending on your device:
                              • Backup - This option will show you your recovery phrase.
                              • Secure With a Passcode - This option will let you configure a passcode to protect your wallet. Exodus requires you to backup your recovery phase first, before allowing you to configure a passcode
                              • Secure with Biometrics - This option will secure your wallet biometric authentication, if enabled on your device. Exodus requires you to have configured both a passcode, and a backup of you recovery phase, before this option is available

                              Remember, you are your own bank with crypto, don't leave the doors unlocked. In addition to securing your wallet, it is a good idea to setup the most security possible for your device.

                              In cryptocurrency, knowledge is your best friend. In the next section, we have some links to futher reading about Coinomi Wallet - check them out!


                              Table of Contents

                              1 The threat to the body: the role and requirements of the immune system

                              1.1 The role and complexity of the immune system

                              1.2 Pathogens differ in size, lifestyle and how they cause disease

                              1.3 How do pathogens cause disease and what protection is there?

                              2 The immediate response to infection: innate immunity and the
                              inflammatory response

                              2.1 The response to infection

                              2.2 The immediate response to infection – the innate immune system

                              2.3 Cytokines – hormones of the immune system

                              2.4 The inflammatory response and cell migration

                              2.5 Cell migration – through blood and into tissue

                              2.6 The inflammatory response

                              2.7 Systematic inflammation – involvement of the brain and liver

                              2.9 Interferons and natural killer cells

                              2.10 The innate immune response limits the early replication of pathogens

                              2.12 Questions and answers

                              3 Specific immune recognition: B lymphocytes and the antibody molecule

                              3.1 Introduction to the specific immune system

                              3.3 Recognition by antibody – antigens and epitopes

                              3.4 There are different antibody classes with different biological functions

                              3.5 Antibody can be secreted or expressed on the cell surface of B lymphocytes

                              4 T lymphocytes and MHC-associated recognition of antigen

                              4.1 There are different types of T lymphocytes

                              4.2 T cells recognise antigen through their T cell receptor (TCR)

                              4.3 The major histocompatibility complex

                              4.4 Recognition of antigen by T cells

                              4.5 Antigens must be processed before they can be presented by MHC molecules

                              5 Lymphocyte development and the generation of antigen receptors

                              5.1 The production of lymphocytes: lymphopoiesis

                              5.2 B lymphocytes are produced in the bone marrow

                              5.3 T lymphocytes finish their production in the thymus

                              5.4 During their development lymphocytes must generate huge numbers of Ig and TCR receptors with different antigen specificities

                              5.5 Developing lymphocytes rearrange their lg or TCR genes in a carefully controlled order

                              5.6 Why is there continuous production of lymphocytes, most of which die?

                              6 Anatomy of the immune system

                              6.1 Requirements of the immune system in vivo

                              6.2 Different pathogens require different types of immune responses

                              6.3 The anatomy of the lymphoid system promotes the interaction of cells and antigen

                              6.4 Lymphocytes continually recirculate through blood, tissues and lymphatic vessels

                              7 Anatomical and cellular aspects of antibody production

                              7.1 Overview of antibody production

                              7.2 Activation of CD4 T cells (0𔃃 days) &

                              7.3 Stimulation of B cells by antigen and their interaction with Th (0𔃃 days after antigen)

                              7.4 Formation of germinal centres (4󈝺 days after antigen)

                              7.5 MALT and the production of IgA

                              8 Effector mechanisms: dealing with pathogens in vivo (1) Antibody-mediated responses

                              8.1 Humoral and cell-mediated immunity

                              8.2 Antibodies provide protection in many different ways

                              8.3 Neutralisation by antibody

                              8.4 Antibodies can cause agglutination of microbes

                              8.5 Antibodies can act as opsonins and promote phagocytosis

                              8.6 Complement is a protein cascade with antimicrobial functions

                              8.7 Antibody and complement synergise to promote the opsonisation of microbes

                              8.8 Antibody-dependent cell-mediated cytoxicity (ADCC)

                              8.10 Questions and answers

                              9 Effector mechanisms: dealing with pathogens in vivo (2) Cell-mediated immunity

                              9.2 CD4 T cells develop into different types of helper T cells

                              9.3 CD8 cytotoxic T cells are important in intracellular infections

                              9.4 Delayed-type hypersensitivity and the activation of macrophages

                              9.5 Th2 responses are important against worms p

                              9.6 Th17 responses involve high levels of inflammation

                              9.7 Different effector responses have different costs to the host

                              10 Immunological memory and vaccination, the production and use of antibodies

                              10.1 Immunological memory – the basis of immaturity

                              10.2 Vaccines induce immunity without causing disease

                              10.3 Antibodies can be produced and used in many ways in treatments and in tests

                              10.5 Questions and answers

                              11 Immunological tolerance and regulation – why doesn’t the immune system attack ourselves?

                              11.1 Immunological tolerance – what is it and why do we need it?

                              11.2 Self-tolerance in B cells

                              11.3 Self-tolerance in T lymphocytes – selecting for recognition of self-MHC but not self-antigen

                              11.4 How do we maintain tolerance to self-antigens not expreseed in the thymus?

                              11.6 Questions and answers

                              12 Autoimmune diseases

                              12.1 Autoimmune diseases occur when our immune systems attack our own bodies

                              12.2 There are many different autoimmune diseases

                              12.3 Immunological features of autoimmune diseases

                              12.4 Both genetic and environmental factors contribute to the development of autoimmune disease


                              Deliberately setting the tone for lab efficiency

                              7.4.1 Team mindset: focus on similarities rather the differences.

                              7.4.2 Sharing & collaboration: default to assuming good intentions.

                              7.4.3 Advantage to having lab conventions

                              But need room for different skills people come in with.

                              Reduce friction and reinventing the wheel.

                              If they’re more efficient in python, don’t want to force R.

                              7.4.4 Open software can facilitate open/shared culture


                              The Why

                              People often wonder how they can recognize true prophets of God. Examples such as these in the Bible and Book of Mormon show that at the beginning of important dispensations and in dispensing the word of the Lord, true prophets (including Lehi and Nephi) in ancient Israel were admitted into the heavenly council and saw God or other heavenly beings and received divine assignments or access to heavenly knowledge.

                              In this way, ancient prophets could be recognized as true messengers of God. As Smoot noted, by mentioning his experience in the divine council “Nephi . . . establishe[d] his own credibility as his father’s prophetic successor. Having participated in the [divine council], Nephi was granted the heavenly secrets needed to know and understand the apocalyptic visions granted to his father (1 Nephi 15:8–11). These same heavenly secrets were not imparted to Nephi’s brothers, who were barred from participating in the [divine council] because of ‘the hardness of [their] hearts’ (1 Nephi 15:10).”6

                              For God’s children today, Nephi’s faithful inquiry serves as an example of how all people can gain answers even to deep questions that we may be wrestling with. Nephi powerfully showed the validity of the Lord’s promise: “Ask, and it shall be given you seek, and ye shall find knock, and it shall be opened unto you” (Matthew 7:7).


                              Acknowledgements

                              This work was supported by the National Health and Medical Research Council of Australia (Fellowship 1138466 and Program Grant no. 1071659 to M.P.J. Fellowship no. 1141131 to K.S. Project Grant no. 1086786 to A.A.B.R. and K.S.), the Australian Research Council (Fellowship no. FT130100361 to K.S.), the Institute for Molecular Bioscience (Research Advancement Award to J.H.) and The University of Queensland (Postdoctoral Fellowships to R.C.C. and D.B. Research Scholarship to J.H.). We thank D. Edwards for chemical purification and analytical support, M. Cooper (University of Queensland) for providing MCC950 and K. Stacey (University of Queensland) for providing ASC-deficient mice.


                              Great Pacific Garbage Patch

                              The Great Pacific Garbage Patch is a collection of marine debris in the North Pacific Ocean. Marine debris is litter that ends up in the ocean, seas, and other large bodies of water.

                              Biology, Ecology, Earth Science, Oceanography

                              This lists the logos of programs or partners of NG Education which have provided or contributed the content on this page. Leveled by

                              The Great Pacific Garbage Patch is a collection of marine debris in the North Pacific Ocean. Marine debris is litter that ends up in oceans, seas, and other large bodies of water. 



                              The Great Pacific Garbage Patch, also known as the Pacific trash vortex, spans waters from the West Coast of North America to Japan. The patch is actually comprised of the Western Garbage Patch, located near Japan, and the Eastern Garbage Patch, located between the U.S. states of Hawaii and California.

                              These areas of spinning debris are linked together by the North Pacific Subtropical Convergence Zone, located a few hundred kilometers north of Hawaii. This convergence zone is where warm water from the South Pacific meets up with cooler water from the Arctic. The zone acts like a highway that moves debris from one patch to another.

                              The entire Great Pacific Garbage Patch is bounded by the North Pacific Subtropical Gyre. The National Oceanic and Atmospheric Administration (NOAA) defines a gyre as a large system of swirling ocean currents. Increasingly, however, it also refers to the garbage patch as a vortex of plastic waste and debris broken down into small particles in the ocean. The North Pacific Subtropical Gyre is formed by four currents rotating clockwise around an area of 20 million square kilometers (7.7 million square miles): the California current, the North Equatorial current, the Kuroshio current, and the North Pacific current.

                              The area in the center of a gyre tends to be very calm and stable. The circular motion of the gyre draws debris into this stable center, where it becomes trapped. A plastic water bottle discarded off the coast of California, for instance, takes the California Current south toward Mexico. There, it may catch the North Equatorial Current, which crosses the vast Pacific. Near the coast of Japan, the bottle may travel north on the powerful Kuroshiro Current. Finally, the bottle travels eastward on the North Pacific Current. The gently rolling vortexes of the Eastern and Western Garbage Patches gradually draw in the bottle.

                              The amount of debris in the Great Pacific Garbage Patch accumulates because much of it is not biodegradable. Many plastics, for instance, do not wear down they simply break into tinier and tinier pieces.

                              For many people, the idea of a &ldquogarbage patch&rdquo conjures up images of an island of trash floating on the ocean. In reality, these patches are almost entirely made up of tiny bits of plastic, called microplastics. Microplastics can&rsquot always be seen by the naked eye. Even satellite imagery doesn&rsquot show a giant patch of garbage. The microplastics of the Great Pacific Garbage Patch can simply make the water look like a cloudy soup. This soup is intermixed with larger items, such as fishing gear and shoes.

                              The seafloor beneath the Great Pacific Garbage Patch may also be an underwater trash heap. Oceanographers and ecologists recently discovered that about 70% of marine debris actually sinks to the bottom of the ocean.

                              While oceanographers and climatologists predicted the existence of the Great Pacific Garbage Patch, it was a racing boat captain by the name of Charles Moore who actually discovered the trash vortex. Moore was sailing from Hawaii to California after competing in a yachting race. Crossing the North Pacific Subtropical Gyre, Moore and his crew noticed millions of pieces of plastic surrounding his ship.

                              Marine Debris

                              No one knows how much debris makes up the Great Pacific Garbage Patch. The North Pacific Subtropical Gyre is too large for scientists to trawl. In addition, not all of the trash floats on the surface. Denser debris can sink centimeters or even several meters beneath the surface, making the vortex&rsquos area nearly impossible to measure.

                              80 percent of plastic in the ocean is estimated to come from land-based sources, with the remaining 20 percent coming from boats and other marine sources. These percentages vary by region, however. A 2018 study found that synthetic fishing nets made up nearly half the mass of the Great Pacific Garbage Patch, due largely to ocean current dynamics and increased fishing activity in the Pacific Ocean.

                              While many different types of trash enter the ocean, plastics make up the majority of marine debris for two reasons. First, plastic&rsquos durability, low cost, and malleability mean that it&rsquos being used in more and more consumer and industrial products. Second, plastic goods do not biodegrade but instead, break down into smaller pieces.

                              In the ocean, the sun breaks down these plastics into tinier and tinier pieces, a process known as photodegradation. Most of this debris comes from plastic bags, bottle caps, plastic water bottles, and Styrofoam cups.

                              Marine debris can be very harmful to marine life in the gyre. For instance, loggerhead sea turtles often mistake plastic bags for jellies, their favorite food. Albatrosses mistake plastic resin pellets for fish eggs and feed them to chicks, which die of starvation or ruptured organs.

                              Seals and other marine mammals are especially at risk. They can get entangled in abandoned plastic fishing nets, which are being discarded largely due to inclement weather and illegal fishing. Seals and other mammals often drown in these forgotten nets&mdasha phenomenon known as &ldquoghost fishing.&rdquo

                              Marine debris can also disturb marine food webs in the North Pacific Subtropical Gyre. As microplastics and other trash collect on or near the surface of the ocean, they block sunlight from reaching plankton and algae below. Algae and plankton are the most common autotrophs, or producers, in the marine food web. Autotrophs are organisms that can produce their own nutrients from carbon and sunlight.

                              If algae and plankton communities are threatened, the entire food web may change. Animals that feed on algae and plankton, such as fish and turtles, will have less food. If populations of those animals decrease, there will be less food for apex predators such as tuna, sharks, and whales. Eventually, seafood becomes less available and more expensive for people.

                              These dangers are compounded by the fact that plastics both leach out and absorb harmful pollutants. As plastics break down through photodegradation, they leach out colorants and chemicals, such as bisphenol A (BPA), that have been linked to environmental and health problems. Conversely, plastics can also absorb pollutants, such as PCBs, from the seawater. These chemicals can then enter the food chain when consumed by marine life.

                              Patching Up the Patch

                              Because the Great Pacific Garbage Patch is so far from any country&rsquos coastline, no nation will take responsibility or provide the funding to clean it up. Charles Moore, the man who discovered the vortex, says cleaning up the garbage patch would &ldquobankrupt any country&rdquo that tried it.

                              Many individuals and international organizations, however, are dedicated to preventing the patch from growing.

                              Cleaning up marine debris is not as easy as it sounds. Many microplastics are the same size as small sea animals, so nets designed to scoop up trash would catch these creatures as well. Even if we could design nets that would just catch garbage, the size of the oceans makes this job far too time-consuming to consider. The National Ocean and Atmospheric Administration&rsquos Marine Debris Program has estimated that it would take 67 ships one year to clean up less than one percent of the North Pacific Ocean.

                              Many expeditions have traveled through the Great Pacific Garbage Patch. Charles Moore, who discovered the patch in 1997, continues to raise awareness through his own environmental organization, the Algalita Marine Research Foundation. During a 2014 expedition, Moore and his team used aerial drones, to assess from above the extent of the trash below. The drones determined that there is 100 times more plastic by weight than previously measured. The team also discovered more permanent plastic features, or islands, some over 15 meters (50 feet) in length.

                              All the floating plastic in the Great Pacific Garbage Patch inspired National Geographic Emerging Explorer David de Rothschild and his team at Adventure Ecology to create a large catamaran made of plastic bottles: the Plastiki. The sturdiness of the Plastiki displayed the strength and durability of plastics, the creative ways that they can be repurposed, and the threat they pose to the environment when they don&rsquot decompose. In 2010, the crew successfully navigated the Plastiki from San Francisco, California, to Sydney, Australia.

                              Scientists and explorers agree that limiting or eliminating our use of disposable plastics and increasing our use of biodegradable resources will be the best way to clean up the Great Pacific Garbage Patch. Organizations such as the Plastic Pollution Coalition and the Plastic Oceans Foundation are using social media and direct action campaigns to support individuals, manufacturers, and businesses in their transition from toxic, disposable plastics to biodegradable or reusable materials.

                              Photograph by Ray Boland, NOAA. This file is licensed under the Creative Commons Attribution 2.0 Generic license.

                              Quotable Captain
                              "So on the way back to our home port in Long Beach, California, we decided to take a shortcut through the gyre, which few seafarers ever cross. Fishermen shun it because its waters lack the nutrients to support an abundant catch. Sailors dodge it because it lacks the wind to propel their sailboats.

                              "Yet as I gazed from the deck at the surface of what ought to have been a pristine ocean, I was confronted, as far as the eye could see, with the sight of plastic.

                              "It seemed unbelievable, but I never found a clear spot. In the week it took to cross the subtropical high, no matter what time of day I looked, plastic debris was floating everywhere: bottles, bottle caps, wrappers, fragments. Months later, after I discussed what I had seen with the oceanographer Curtis Ebbesmeyer, perhaps the world's leading expert on flotsam, he began referring to the area as the 'eastern garbage patch.'"

                              Capt. Charles Moore, discoverer of the Great Pacific Garbage Patch, in an article for Natural History magazine in 2003

                              Strange Cargo
                              When ships are caught in storms, they often lose cargo to the oceans. The following are just a few of the strange items that have washed up on shores:


                              7: For Further Reading

                              • Nathan Nobis & Kristina Grob
                              • Associate Professors (Philosophy) at Morehouse College & University of South Carolina Sumter
                              • Sourced from Open Philosophy Press

                              These three widely-reprinted articles are the seminal philosophical writings on abortion:

                              • Thomson, Judith Jarvis. &ldquoA Defense of Abortion.&rdquo Philosophy & Public Affairs 1, no. 1 (1971): 47-66 .
                              • Warren, Mary Anne. &ldquoOn the Moral and Legal Status of Abortion.&rdquo The Monist (1973): 43-61.
                              • Marquis, Don. &ldquoWhy Abortion Is Immoral.&rdquo The Journal of Philosophy 86, no. 4 (1989): 183-202 .

                              David Boonin&rsquos A Defense of Abortion provides a comprehensive and systematic critical overview of many arguments about abortion, and argues in defense of abortion:

                              And see his more recent book on abortion:

                              Richard Feldman&rsquos Reason & Argument is the best &ldquocritical thinking&rdquo and argument identification and analysis text available:

                              And here are some other introductory readings by Nathan Nobis, and Nathan Nobis and Kristina Grob, on abortion:


                              TWENTY-FIRST-CENTURY PROBLEMS

                              Bravin, Jess. 2013. The Terror Courts: Rough Justice at Guantanamo Bay. New Haven: Yale University Press.

                              Cowen, Tyler. 2001. The Great Stagnation: How America Ate All the Low-Hanging Fruit of Modern History, Got Sick, and Will (Eventually) Feel Better. New York: Dutton.

                              Ehrenreich, Barbara. 2001. Nickel and Dimed: On (Not) Getting by in America. New York: Metropolitan Books.

                              Gerges, Fawaz A. 2011. The Rise and Fall of Al-Qaeda. Oxford: Oxford University Press.

                              Gordon, Joy. 2010. Invisible War: The United States and the Iraq Sanctions. Cambridge, MA: Harvard University Press.

                              John Cannan, 2013. &ldquoA Legislative History of the Affordable Care Act: How Legislative Procedure Shapes Legislative History.&rdquo Law Library Journal 105(2): 132&ndash73.

                              Keen, D. 2012. Useful Enemies: When Waging Wars Is More Important than Winning Them. New Haven: Yale University Press.

                              Lance, Peter. 2004. 1000 Years for Revenge: International Terrorism and the FBI. New York: Regan Books.

                              Lewis, Michael. 2010. The Big Short: Inside the Doomsday Machine. New York: Norton.

                              Little, Douglas. 2002. American Orientalism: The United States and the Middle East since 1945. Chapel Hill: University of North Carolina Press.

                              Oreskes, Naomi, and Erik M. Conway. 2010. Merchants of Doubt: How a Handful of Scientists Obscured the Truth on Issues from Tobacco Smoke to Global Warming. New York: Bloomsbury Press.

                              Rivoli, Pietra. 2005. The Travels of a T-Shirt in the Global Economy: An Economist Examines the Markets, Power and Politics of World Trade. Hoboken, NJ: Wiley.

                              Simon, Bryant. 2009. Everything but the Coffee: Learning About America from Starbucks. Berkeley: University of California Press.

                              Wright, Lawrence. 2006. The Looming Tower: Al-Qaeda and the Road to 9/11. New York: Knopf.


                              Watch the video: Jigsaw Reading (January 2022).