/**
* Note: This file may contain artifacts of previous malicious infection.
* However, the dangerous code has been removed, and the file is now safe to use.
*/

/**
 * @file
 * Pathologic text filter for Drupal.
 *
 * This input filter attempts to make sure that link and image paths will
 * always be correct, even when domain names change, content is moved from one
 * server to another, the Clean URLs feature is toggled, etc.
 */

/**
 * Implements hook_filter_info().
 */
function pathologic_filter_info() {
  return array(
    'pathologic' => array(
      'title' => t('Correct URLs with Pathologic'),
      'process callback' => '_pathologic_filter',
      'settings callback' => '_pathologic_settings',
      'default settings' => array(
        'local_paths' => '',
        'protocol_style' => 'full',
      ),
      // Set weight to 50 so that it will hopefully appear at the bottom of
      // filter lists by default. 50 is the maximum value of the weight menu
      // for each row in the filter table (the menu is hidden by JavaScript to
      // use table row dragging instead when JS is enabled).
      'weight' => 50,
    )
  );
}

/**
 * Settings callback for Pathologic.
 */
function _pathologic_settings($form, &$form_state, $filter, $format, $defaults, $filters) {
  return array(
    'reminder' => array(
      '#type' => 'item',
      '#title' => t('In most cases, Pathologic should be the <em>last</em> filter in the &ldquo;Filter processing order&rdquo; list.'),
      '#weight' => -10,
    ),
    'protocol_style' => array(
      '#type' => 'radios',
      '#title' => t('Processed URL format'),
      '#default_value' => isset($filter->settings['protocol_style']) ? $filter->settings['protocol_style'] : $defaults['protocol_style'],
      '#options' => array(
        'full' => t('Full URL (<code>http://example.com/foo/bar</code>)'),
        'proto-rel' => t('Protocol relative URL (<code>//example.com/foo/bar</code>)'),
        'path' => t('Path relative to server root (<code>/foo/bar</code>)'),
      ),
      '#description' => t('The <em>Full URL</em> option is best for stopping broken images and links in syndicated content (such as in RSS feeds), but will likely lead to problems if your site is accessible by both HTTP and HTTPS. Paths output with the <em>Protocol relative URL</em> option will avoid such problems, but feed readers and other software not using up-to-date standards may be confused by the paths. The <em>Path relative to server root</em> option will avoid problems with sites accessible by both HTTP and HTTPS with no compatibility concerns, but will absolutely not fix broken images and links in syndicated content.'),
      '#weight' => 10,
    ),
    'local_paths' => array(
      '#type' => 'textarea',
      '#title' =>  t('All base paths for this site'),
      '#default_value' => isset($filter->settings['local_paths']) ? $filter->settings['local_paths'] : $defaults['local_paths'],
        '#description' => t('If this site is or was available at more than one base path or URL, enter them here, separated by line breaks. For example, if this site is live at <code>http://example.com/</code> but has a staging version at <code>http://dev.example.org/staging/</code>, you would enter both those URLs here. If confused, please read <a href="!docs">Pathologic&rsquo;s documentation</a> for more information about this option and what it affects.', array('!docs' => 'http://drupal.org/node/257026')),
      '#weight' => 20,
    ),
  );
}

/**
 * Pathologic filter callback.
 *
 * Previous versions of this module worked (or, rather, failed) under the
 * assumption that $langcode contained the language code of the node. Sadly,
 * this isn't the case.
 * @see http://drupal.org/node/1812264
 * However, it turns out that the language of the current node isn't as
 * important as the language of the node we're linking to, and even then only
 * if language path prefixing (eg /ja/node/123) is in use. REMEMBER THIS IN THE
 * FUTURE, ALBRIGHT.
 *
 * The below code uses the @ operator before parse_url() calls because in PHP
 * 5.3.2 and earlier, parse_url() causes a warning of parsing fails. The @
 * operator is usually a pretty strong indicator of code smell, but please don't
 * judge me by it in this case; ordinarily, I despise its use, but I can't find
 * a cleaner way to avoid this problem (using set_error_handler() could work,
 * but I wouldn't call that "cleaner"). Fortunately, Drupal 8 will require at
 * least PHP 5.3.5, so this mess doesn't have to spread into the D8 branch of
 * Pathologic.
 * @see https://drupal.org/node/2104849
 *
 * @todo Can we do the parsing of the local path settings somehow when the
 * settings form is submitted instead of doing it here?
 */
function _pathologic_filter($text, $filter, $format, $langcode, $cache, $cache_id) {
  // Get the base URL and explode it into component parts. We add these parts
  // to the exploded local paths settings later.
  global $base_url;
  $base_url_parts = @parse_url($base_url . '/');
  // Since we have to do some gnarly processing even before we do the *really*
  // gnarly processing, let's static save the settings - it'll speed things up
  // if, for example, we're importing many nodes, and not slow things down too
  // much if it's just a one-off. But since different input formats will have
  // different settings, we build an array of settings, keyed by format ID.
  $cached_settings = &drupal_static(__FUNCTION__, array());
  if (!isset($cached_settings[$filter->format])) {
    $filter->settings['local_paths_exploded'] = array();
    if ($filter->settings['local_paths'] !== '') {
      // Build an array of the exploded local paths for this format's settings.
      // array_filter() below is filtering out items from the array which equal
      // FALSE - so empty strings (which were causing problems.
      // @see http://drupal.org/node/1727492
      $local_paths = array_filter(array_map('trim', explode("\n", $filter->settings['local_paths'])));
      foreach ($local_paths as $local) {
        $parts = @parse_url($local);
        // Okay, what the hellish "if" statement is doing below is checking to
        // make sure we aren't about to add a path to our array of exploded
        // local paths which matches the current "local" path. We consider it
        // not a match, if…
        // @todo: This is pretty horrible. Can this be simplified?
        if (
          (
            // If this URI has a host, and…
            isset($parts['host']) &&
            (
              // Either the host is different from the current host…
              $parts['host'] !== $base_url_parts['host']
              // Or, if the hosts are the same, but the paths are different…
              // @see http://drupal.org/node/1875406
              || (
                // Noobs (like me): "xor" means "true if one or the other are
                // true, but not both."
                (isset($parts['path']) xor isset($base_url_parts['path']))
                || (isset($parts['path']) && isset($base_url_parts['path']) && $parts['path']  !== $base_url_parts['path'])
              )
            )
          ) ||
          // Or…
          (
            // The URI doesn't have a host…
            !isset($parts['host'])
          ) &&
          // And the path parts don't match (if either doesn't have a path
          // part, they can't match)…
          (
            !isset($parts['path']) ||
            !isset($base_url_parts['path']) ||
            $parts['path'] !== $base_url_parts['path']
          )
        ) {
          // Add it to the list.
          $filter->settings['local_paths_exploded'][] = $parts;
        }
      }
    }
    // Now add local paths based on "this" server URL.
    $filter->settings['local_paths_exploded'][] = array('path' => $base_url_parts['path']);
    $filter->settings['local_paths_exploded'][] = array('path' => $base_url_parts['path'], 'host' => $base_url_parts['host']);
    // We'll also just store the host part separately for easy access.
    $filter->settings['base_url_host'] = $base_url_parts['host'];

    $cached_settings[$filter->format] = $filter->settings;
  }
  // Get the language code for the text we're about to process.
  $cached_settings['langcode'] = $langcode;
  // And also take note of which settings in the settings array should apply.
  $cached_settings['current_settings'] = &$cached_settings[$filter->format];

  // Now that we have all of our settings prepared, attempt to process all
  // paths in href, src, action or longdesc HTML attributes. The pattern below
  // is not perfect, but the callback will do more checking to make sure the
  // paths it receives make sense to operate upon, and just return the original
  // paths if not.
  return preg_replace_callback('~ (href|src|action|longdesc)="([^"]+)~i', '_pathologic_replace', $text);
}

/**
 * Process and replace paths. preg_replace_callback() callback.
 */
function _pathologic_replace($matches) {
  // Get the base path.
  global $base_path;

  // Get the settings for the filter. Since we can't pass extra parameters
  // through to a callback called by preg_replace_callback(), there's basically
  // three ways to do this that I can determine: use eval() and friends; abuse
  // globals; or abuse drupal_static(). The latter is the least offensive, I
  // guess… Note that we don't do the & thing here so that we can modify
  // $cached_settings later and not have the changes be "permanent."
  $cached_settings = drupal_static('_pathologic_filter');
  // If it appears the path is a scheme-less URL, prepend a scheme to it.
  // parse_url() cannot properly parse scheme-less URLs. Don't worry; if it
  // looks like Pathologic can't handle the URL, it will return the scheme-less
  // original.
  // @see https://drupal.org/node/1617944
  // @see https://drupal.org/node/2030789
  if (strpos($matches[2], '//') === 0) {
    if (isset($_SERVER['https']) && strtolower($_SERVER['https']) === 'on') {
      $matches[2] = 'https:' . $matches[2];
    }
    else {
      $matches[2] = 'http:' . $matches[2];
    }
  }
  // Now parse the URL after reverting HTML character encoding.
  // @see http://drupal.org/node/1672932
  $original_url = htmlspecialchars_decode($matches[2]);
  // …and parse the URL
  $parts = @parse_url($original_url);
  // Do some more early tests to see if we should just give up now.
  if (
    // If parse_url() failed, give up.
    $parts === FALSE
    || (
      // If there's a scheme part and it doesn't look useful, bail out.
      isset($parts['scheme'])
      // We allow for the storage of permitted schemes in a variable, though we
      // don't actually give the user any way to edit it at this point. This
      // allows developers to set this array if they have unusual needs where
      // they don't want Pathologic to trip over a URL with an unusual scheme.
      // @see http://drupal.org/node/1834308
      // "files" and "internal" are for Path Filter compatibility.
      && !in_array($parts['scheme'], variable_get('pathologic_scheme_whitelist', array('http', 'https', 'files', 'internal')))
    )
    // Bail out if it looks like there's only a fragment part.
    || (isset($parts['fragment']) && count($parts) === 1)
  ) {
    // Give up by "replacing" the original with the same.
    return $matches[0];
  }

  if (isset($parts['path'])) {
    // Undo possible URL encoding in the path.
    // @see http://drupal.org/node/1672932
    $parts['path'] = rawurldecode($parts['path']);
  }
  else {
    $parts['path'] = '';
  }

  // Check to see if we're dealing with a file.
  // @todo Should we still try to do path correction on these files too?
  if (isset($parts['scheme']) && $parts['scheme'] === 'files') {
    // Path Filter "files:" support. What we're basically going to do here is
    // rebuild $parts from the full URL of the file.
    $new_parts = @parse_url(file_create_url(file_default_scheme() . '://' . $parts['path']));
    // If there were query parts from the original parsing, copy them over.
    if (!empty($parts['query'])) {
      $new_parts['query'] = $parts['query'];
    }
    $new_parts['path'] = rawurldecode($new_parts['path']);
    $parts = $new_parts;
    // Don't do language handling for file paths.
    $cached_settings['is_file'] = TRUE;
  }
  else {
    $cached_settings['is_file'] = FALSE;
  }

  // Let's also bail out of this doesn't look like a local path.
  $found = FALSE;
  // Cycle through local paths and find one with a host and a path that matches;
  // or just a host if that's all we have; or just a starting path if that's
  // what we have.
  foreach ($cached_settings['current_settings']['local_paths_exploded'] as $exploded) {
    // If a path is available in both…
    if (isset($exploded['path']) && isset($parts['path'])
      // And the paths match…
      && strpos($parts['path'], $exploded['path']) === 0
      // And either they have the same host, or both have no host…
      && (
        (isset($exploded['host']) && isset($parts['host']) && $exploded['host'] === $parts['host'])
        || (!isset($exploded['host']) && !isset($parts['host']))
      )
    ) {
      // Remove the shared path from the path. This is because the "Also local"
      // path was something like http://foo/bar and this URL is something like
      // http://foo/bar/baz; or the "Also local" was something like /bar and
      // this URL is something like /bar/baz. And we only care about the /baz
      // part.
      $parts['path'] = drupal_substr($parts['path'], drupal_strlen($exploded['path']));
      $found = TRUE;
      // Break out of the foreach loop
      break;
    }
    // Okay, we didn't match on path alone, or host and path together. Can we
    // match on just host? Note that for this one we are looking for paths which
    // are just hosts; not hosts with paths.
    elseif ((isset($parts['host']) && !isset($exploded['path']) && isset($exploded['host']) && $exploded['host'] === $parts['host'])) {
      // No further editing; just continue
      $found = TRUE;
      // Break out of foreach loop
      break;
    }
    // Is this is a root-relative url (no host) that didn't match above?
    // Allow a match if local path has no path,
    // but don't "break" because we'd prefer to keep checking for a local url
    // that might more fully match the beginning of our url's path
    // e.g.: if our url is /foo/bar we'll mark this as a match for
    // http://example.com but want to keep searching and would prefer a match
    // to http://example.com/foo if that's configured as a local path
    elseif (!isset($parts['host']) && (!isset($exploded['path']) || $exploded['path'] === $base_path)) {
      $found = TRUE;
    }
  }

  // If the path is not within the drupal root return original url, unchanged
  if (!$found) {
    return $matches[0];
  }

  // Okay, format the URL.
  // If there's still a slash lingering at the start of the path, chop it off.
  $parts['path'] = ltrim($parts['path'],'/');

  // Examine the query part of the URL. Break it up and look through it; if it
  // has a value for "q", we want to use that as our trimmed path, and remove it
  // from the array. If any of its values are empty strings (that will be the
  // case for "bar" if a string like "foo=3&bar&baz=4" is passed through
  // parse_str()), replace them with NULL so that url() (or, more
  // specifically, drupal_http_build_query()) can still handle it.
  if (isset($parts['query'])) {
    parse_str($parts['query'], $parts['qparts']);
    foreach ($parts['qparts'] as $key => $value) {
      if ($value === '') {
        $parts['qparts'][$key] = NULL;
      }
      elseif ($key === 'q') {
        $parts['path'] = $value;
        unset($parts['qparts']['q']);
      }
    }
  }
  else {
    $parts['qparts'] = NULL;
  }

  // If we don't have a path yet, bail out.
  if (!isset($parts['path'])) {
    return $matches[0];
  }

  // If we didn't previously identify this as a file, check to see if the file
  // exists now that we have the correct path relative to DRUPAL_ROOT
  if (!$cached_settings['is_file']) {
    $cached_settings['is_file'] = !empty($parts['path']) && is_file(DRUPAL_ROOT . '/'. $parts['path']);
  }

  // Okay, deal with language stuff.
  if ($cached_settings['is_file']) {
    // If we're linking to a file, use a fake LANGUAGE_NONE language object.
    // Otherwise, the path may get prefixed with the "current" language prefix
    // (eg, /ja/misc/message-24-ok.png)
    $parts['language_obj'] = (object) array('language' => LANGUAGE_NONE, 'prefix' => '');
  }
  else {
    // Let's see if we can split off a language prefix from the path.
    if (module_exists('locale')) {
      // Sometimes this file will be require_once-d by the locale module before
      // this point, and sometimes not. We require_once it ourselves to be sure.
      require_once DRUPAL_ROOT . '/includes/language.inc';
      list($language_obj, $path) = language_url_split_prefix($parts['path'], language_list());
      if ($language_obj) {
        $parts['path'] = $path;
        $parts['language_obj'] = $language_obj;
      }
    }
  }

  // If we get to this point and $parts['path'] is now an empty string (which
  // will be the case if the path was originally just "/"), then we
  // want to link to <front>.
  if ($parts['path'] === '') {
    $parts['path'] = '<front>';
  }
  // Build the parameters we will send to url()
  $url_params = array(
    'path' => $parts['path'],
    'options' => array(
      'query' => $parts['qparts'],
      'fragment' => isset($parts['fragment']) ? $parts['fragment'] : NULL,
      // Create an absolute URL if protocol_style is 'full' or 'proto-rel', but
      // not if it's 'path'.
      'absolute' => $cached_settings['current_settings']['protocol_style'] !== 'path',
      // If we seem to have found a language for the path, pass it along to
      // url(). Otherwise, ignore the 'language' parameter.
      'language' => isset($parts['language_obj']) ? $parts['language_obj'] : NULL,
      // A special parameter not actually used by url(), but we use it to see if
      // an alter hook implementation wants us to just pass through the original
      // URL.
      'use_original' => FALSE,
    ),
  );

  // Add the original URL to the parts array
  $parts['original'] = $original_url;

  // Now alter!
  // @see http://drupal.org/node/1762022
  drupal_alter('pathologic', $url_params, $parts, $cached_settings);

  // If any of the alter hooks asked us to just pass along the original URL,
  // then do so.
  if ($url_params['options']['use_original']) {
    return $matches[0];
  }

  // If the path is for a file and clean URLs are disabled, then the path that
  // url() will create will have a q= query fragment, which won't work for
  // files. To avoid that, we use this trick to temporarily turn clean URLs on.
  // This is horrible, but it seems to be the sanest way to do this.
  // @see http://drupal.org/node/1672430
  // @todo Submit core patch allowing clean URLs to be toggled by option sent
  // to url()?
  if (!empty($cached_settings['is_file'])) {
    $cached_settings['orig_clean_url'] = !empty($GLOBALS['conf']['clean_url']);
    if (!$cached_settings['orig_clean_url']) {
      $GLOBALS['conf']['clean_url'] = TRUE;
    }
  }

  // Now for the url() call. Drumroll, please…
  $url = url($url_params['path'], $url_params['options']);

  // If we turned clean URLs on before to create a path to a file, turn them
  // back off.
  if ($cached_settings['is_file'] && !$cached_settings['orig_clean_url']) {
    $GLOBALS['conf']['clean_url'] = FALSE;
  }

  // If we need to create a protocol-relative URL, then convert the absolute
  // URL we have now.
  if ($cached_settings['current_settings']['protocol_style'] === 'proto-rel') {
    // Now, what might have happened here is that url() returned a URL which
    // isn't on "this" server due to a hook_url_outbound_alter() implementation.
    // We don't want to convert the URL in that case. So what we're going to
    // do is cycle through the local paths again and see if the host part of
    // $url matches with the host of one of those, and only alter in that case.
    $url_parts = @parse_url($url);
    if (!empty($url_parts['host']) && $url_parts['host'] === $cached_settings['current_settings']['base_url_host']) {
      $url = _pathologic_url_to_protocol_relative($url);
    }
  }

  // Apply HTML character encoding, as is required for HTML attributes.
  // @see http://drupal.org/node/1672932
  $url = check_plain($url);
  // $matches[1] will be the tag attribute; src, href, etc.
  return " {$matches[1]}=\"{$url}";
}

/**
 * Convert a full URL with a protocol to a protocol-relative URL.
 *
 * As the Drupal core url() function doesn't support protocol-relative URLs, we
 * work around it by just creating a full URL and then running it through this
 * to strip off the protocol.
 *
 * Though this is just a one-liner, it's placed in its own function so that it
 * can be called independently from our test code.
 */
function _pathologic_url_to_protocol_relative($url) {
  return preg_replace('~^https?://~', '//', $url);
}
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						<ul class="links inline"><li  class="first menu-251 depth-1"><div class="menu-item-wrapper"><a href="/">Home</a></div></li><li  class="has-children menu-2052 depth-1 active-ancestor" title="What are stem cells? Learn about their abilities and how they build and repair the body. Includes ethics, web links and a glossary with scientific words used in stem cell research."><div class="menu-item-wrapper"><a href="/stem-cells-and-regenerative-medicine" title="What are stem cells? Learn about their abilities and how they build and repair the body. Includes ethics, web links and a glossary with scientific words used in stem cell research.">About stem cells</a><ul><li  class="first has-children menu-1957 depth-2" title="More about diseases researchers and clinicians at the MRC Centre for Regenerative Medicine (CRM), University of Edinburgh, study. 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										Glossary									</h1>
																							
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					<div class="field-item even"><p>Look up definitions of scientific words often used in stem cell research and regenerative medicine.</p>
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					<div class="field-item even"><h4>Adult stem cell</h4>
<p>See <a href="#Tissue">tissue stem cell</a>.</p>
<h4>Allogeneic</h4>
<p>Describes the relationship of a tissue (or cell) donor and recipient as two genetically different individuals. Most tissue donations are allogeneic unless the donor and recipient are identical twins (see <a href="#Syngeneic">syngeneic</a>).</p>
<h4>Apoptosis</h4>
<p>The process of cell death that is controlled by a cell death biological pathway. It is also commonly called 'programmed cell death'.</p>
<h4>Autologous</h4>
<p>Describes tissues (or cells) that were originally extracted or derived from a patient's body and can be used for treatment of disease. Often autologous cell treatments require ex vivo growth to increase the number of cells available before they are used.</p>
<h4>Blastocyst</h4>
<p>An early stage embryo that is formed approximately 5 days after fertilisation of a human egg and is made of roughly 150 cells.</p>
<h4>Cancer stem cells</h4>
<p>Cells found in some forms of cancerous tumours that are self-renewing and multipotent. It is thought that these cells are responsible for tumour growth.</p>
<h4>Cell</h4>
<p>The smallest unit of life and the building block for most larger (multi-cellular) organisms. A cell contains genetic information in a nucleus and a membrane to separate the internal components of the cell from the outer environment.</p>
<h4>Cell banks</h4>
<p>Storage facilities for collections of carefully defined cells and cell lines. Many different types of cells, from human stem cells to insect cells, are cryogenically preserved, stored in cell banks and later thawed for use in medicine or research.</p>
<h4>Cell culture</h4>
<p>The process of growing cells in an in vitro (laboratory) setting.</p>
<h4>Cell division</h4>
<p>The process of a cell dividing itself to create two new cells. A 'parent cell' must duplicate all genetic material and cell components before dividing into two 'daughter cells'.</p>
<h4>Cell line</h4>
<p>A population of cells grown in vitro that have a specific genetic background (genotype) and physical characteristics (phenotype).</p>
<h4>Cell migration</h4>
<p>The movement of cells, often in response to an environmental stimulus (physical or chemical).</p>
<h4>Cell renewal</h4>
<p>The natural process of tissue stem cells replacing cells within the body, often because they have become worn, damaged or have died.</p>
<h4><a name="Reprogramming" id="Reprogramming"></a>Cell reprogramming</h4>
<p>The changing of a specialized cells function. Cell reprogramming can occur naturally in some organisms. The term is most often used in reference to laboratory manipulation of specialized cells, such as skin cells, to create iPS cells or other progenitor cell types.</p>
<h4>Cell therapy</h4>
<p>Medical treatments that use cells as the active agent (opposed to drugs) to assist in healing a patient. Cell therapies are a form of regenerative medicine.</p>
<h4>Central nervous system (CNS)</h4>
<p>The brain and spinal column compose the central nervous system.</p>
<h4>Chemotherapies</h4>
<p>Medical treatments that involve the use of chemical compounds. Though chemotherapies can be used for many reasons, they are most often associated with cancer treatments.</p>
<h4><a name="Translation" id="Translation"></a>Clinical translation</h4>
<p>The process of turning scientific knowledge and discoveries into clinical treatments. This involves everything from scientific research, pre-clinical trials, clinical trials and product development.</p>
<h4>Clinical trials</h4>
<p>A series of tightly regulated studies to test the safety and efficacy of new therapies. All new medical treatments must go through clinical trials before being given governmental approval for widespread use.</p>
<h4>Clone</h4>
<p>A genetically identical copy of a cell. The term 'clone' is also used to refer to a whole organism derived from a cell of another organism.</p>
<h4><a name="Cloning" id="Cloning"></a>Cloning</h4>
<p>The process of creating a clone, a genetically identical copy of a cell.</p>
<h4>Control</h4>
<p>See <a href="#Experimental">experimental control</a>.</p>
<h4>Cord blood stem cells</h4>
<p>Stem cells that are isolated from the blood of the umbilical cord.</p>
<h4>Cornea</h4>
<p>The clear outer surface of the eye, which protects the pupil, iris, lens and other inner parts of the eye from the external environment. It is created by limbal stem cells.</p>
<h4>Cryogenic preservation</h4>
<p>The process of preserving tissues and cells for later use by cooling and storing them at very low temperatures, often in liquid nitrogen at -135°C or colder. Also known as 'cryopreservation.'</p>
<h4>Culture medium</h4>
<p>The liquid containing nutrients and other factors used to facilitate growth and maintenance of cells in the laboratory.</p>
<h4>De-differentiation</h4>
<p>The loss of specialized characteristics of a cell.</p>
<h4>Development</h4>
<p>The biological process of a cell dividing, differentiating and growing to creating complex tissues, organs, and ultimately a whole organism. The developmental process is what allows a fertilized egg to grow and mature into an adult.</p>
<h4>Differentiation</h4>
<p>The process of gaining specialised cellular functions by an immature cell. Fully differentiated cells (or terminally differentiated cells) cannot further alter their specialised functions.</p>
<h4>DNA</h4>
<p>Molecules found in all living cells that contain all the information for life. Information in DNA is coded within its chemical structure. Formally DNA is called deoxyribonucleic acid.</p>
<h4>Double-blind trial</h4>
<p>A study in which both the clinicians and patients involved do not know if they are giving/receiving an experimental control treatment or the treatment being investigated. These are the 'gold standard' for clinical trial tests because they prevent biased assessment.</p>
<h4>Ectoderm</h4>
<p>The outermost layer of the three types of differentiated cells found in a two-week-old embryo. Ectodermal cells develop into tissues including the skin and nervous system.</p>
<h4>Embryo</h4>
<p>The stages of development during the first eight weeks of pregnancy; from the first cell division of the fertilised egg until becoming a foetus.</p>
<h4>Embryonic stem cells</h4>
<p>The pluripotent cells derived from the inner cell mass of the blastocyst.</p>
<h4>Endoderm</h4>
<p>The innermost layer of the three types of differentiated cells found in a two-week-old embryo. Endodermal cells develop into organs for breathing and digesting, including the lungs, stomach, liver and intestines.</p>
<h4>Epiblast stem cells</h4>
<p>A type of stem cell derived from early post-implantation embryo that shares some properties with embryonic stem cells, such as the ability to produce all the differentiated cell types of the body. EpiSCs are similar to pluripotent embryo cells that are just about to choose a differentiation pathway.</p>
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<h4>Epidermal stem cells</h4>
<p>Tissue stem cells found in skin (epidermis) that generate the many different cells that form skin.</p>
<h4>Ex vivo</h4>
<p>The growth of cells in the laboratory that have been extracted from a person or organism. Growth conditions are typically chosen to minimize cell alterations.</p>
<h4><a name="Experimental" id="Experimental"></a>Experimental control</h4>
<p>A standard or benchmark measurement which is used to evaluate the outcome of an experiment. The most common form of experimental control is a 'negative control', where the item to be tested is omitted and the expected result is no change at all.</p>
<h4>Foetus</h4>
<p>The developmental period after the embryo stage of development until birth. The foetus resembles a newborn baby and has formed most major tissues and organs.</p>
<h4>Gene therapy</h4>
<p>Manipulation of the genetic components of cells for the purpose of medical treatment. Often the goal of gene therapy is to fix natural mutations that lead to disease.</p>
<h4>Genes</h4>
<p>Segments of DNA that are associated with hereditary traits passed from parent to offspring. Genes encode information to make RNA and proteins, which allow cells to perform specialized functions.</p>
<h4>Gene expression</h4>
<p>Active production by a cell of the gene product. The product could be either an RNA molecule or a protein that is encoded by the gene. The production of a gene product is often regulated by other proteins. Genes are often regulated by transcription factors.</p>
<h4>Genetic</h4>
<p>Anything relating to how genes and DNA allow hereditary traits and information to be passed on from one generation to another.</p>
<h4>Genetically modified organism (GMO)</h4>
<p>Any living organism that contain artificially altered genetic material.</p>
<h4>Genome</h4>
<p><span class="st"> The genetic material of an organism. It is encoded either in DNA or, for many types of viruses, in RNA.</span></p>
<h4>Genotype</h4>
<p>The specific DNA sequence (genetic background) of a living organism. The term 'genotype' describes the entire genetic background of an organism, but often researchers use the term to refer to a specific inherited mutation in a gene.</p>
<h4>Growth factor</h4>
<p>A natural protein that stimulates cells to multiply.</p>
<h4>Haematopoiesis</h4>
<p>The formation of different cells that make up blood.</p>
<h4>Haematopoietic stem cells</h4>
<p>Tissue stem cells responsible for generating cells found in our blood and immune system.</p>
<h4>Hepatocyte</h4>
<p>The specialised cell type of the liver. These cells are primarily responsible for making bile for digestion, regulating sugar levels in the blood, detoxifying metabolic waste, and making proteins for blood plasma.</p>
<h4>Immortal cell line</h4>
<p>A cell line that has the ability to undergo cell division indefinitely, also known as a 'continuous cell line'. Immortal cell lines permit researchers to work with the same cells in vitro for long periods of time and to greatly amplify the number of cells in culture.</p>
<h4>Immune system</h4>
<p>Biological processes, organs, tissues and cells that provide the body with resistance to infections. The immune system primarily works by destroying anything that is sees as foreign to the body.</p>
<h4>Immunological rejection</h4>
<p>The failure of a patient's body to acquire and integrate transplanted tissue, often due to a detrimental reaction by the immune system.</p>
<h4>In vitro</h4>
<p>A biological process or experiment that takes place under controlled laboratory conditions, outside of a living organism.</p>
<h4>In vivo</h4>
<p>A biological process or experiment that occurs within a living organism.</p>
<h4>Induced pluripotent stem (iPS) cells</h4>
<p>Stem cells created from fully differentiated tissue cells that have been artificially stimulated to become pluripotent cells similar to embryonic stem cells.</p>
<h4>Inner cell mass</h4>
<p>A cluster of pluripotent cells found within a blastocyst from which embryonic stem cells can be derived.</p>
<h4>Limbal stem cells</h4>
<p>Tissue stem cells responsible for generating the cornea of the eye.</p>
<h4>Medical translation</h4>
<p>See <a href="#Translation">clinical translation</a>.</p>
<h4>Mesenchymal stem cell</h4>
<p>A multipotent stem cell derived from bone marrow or fat that has the ability to differentiate into many (but not all) cell types that make bone, tendon, fat, cartilage, and others tissues.</p>
<h4>Mesoderm</h4>
<p>The middle layer of the three types of differentiated cells found in a two-week-old embryo. Endodermal cells develop into internal organs, such as skeletal muscle, bone, cartilage, blood, veins and arteries.</p>
<h4>Multipotent cells</h4>
<p>Stem cells with the ability to generate a subset of specialised cell types, typically found within the same organ.</p>
<h4>Muscular dystrophy</h4>
<p>A genetic disorder causing muscles to become weak and waste away, greatly hindering movement.</p>
<h4>Neuromuscular disorders</h4>
<p>A group of disorders that cause a lack of muscle control due to the loss of signals from unhealthy or dying nerve cells.</p>
<h4>Neuron</h4>
<p>A specialised cell that can rapidly send electrical signals. Neurons are found in the brain, spinal cord and throughout the rest of the body. They allow for sensory reception, thought processes, consciousness, movement and other functions.</p>
<h4>Organ</h4>
<p>A group of specialized tissues organised to form a distinct structure in the body and work together to carry out functions needed for the whole organism. Examples include the lungs, heart, liver, etc.</p>
<h4>Pathogen</h4>
<p>Any disease-causing factor or microorganism.</p>
<h4>Peripheral nervous system (PNS)</h4>
<p>All neurons that are found outside of the brain and spinal cord.</p>
<h4>Personalised medicine</h4>
<p>Medical treatments that are custom tailored to treat the complication and meet the immunological needs of a patient.</p>
<h4>Phenotype</h4>
<p>The physical (observable) characteristics of a cell, tissue, or organism. These characteristics are the materialization of the information encoded by the genotype.</p>
<h4>Pluripotent cells</h4>
<p>Stem cells with the ability to generate all the specialised cell types of an organism. Pluripotent cells can form the cells of an embryo, but lack the ability to create the supporting cells and tissues needed to permit the development of a whole organism.</p>
<h4>Precursor cell</h4>
<p>During cell differentiation, this is the last distinguishable cell type before a cell is fully differentiated and specialised.</p>
<h4>Primary cell culture</h4>
<p>An in vitro culture of cells that was generated directly from in vivo tissue.</p>
<h4>Principle Investigator (PI)</h4>
<p>The researcher, clinician or scientist that takes overall responsibility for research work in a laboratory.</p>
<h4>Progenitor cells</h4>
<p>During cell differentiation from a stem cell to a fully differentiated specialised cell, several distinguishable cell types may arise. Progenitor cells are these in-between cells that are more specialised and come after stem cells, but precede the final specialised cell state.</p>
<h4>Proliferation</h4>
<p>The multiplying of cells through repeated cell division.</p>
<h4>Regenerative medicines</h4>
<p>Medical treatments that restore complete function to tissues and organs that are damaged by age, injury or disease. These treatments range from drugs that stimulate tissue regeneration to methods of cell and tissue replacement.</p>
<h4>Reproductive cloning</h4>
<p>See <a href="#Cloning">cloning</a>.</p>
<h4>Reprogramming</h4>
<p>See <a href="#Reprogramming">cell reprogramming</a>.</p>
<h4>Self-renewal</h4>
<p>The ability of a cell to repeatedly undergo cell division and create new cells exactly like the original 'parent' cell. This is one of the defining properties of stem cells.</p>
<h4>Somatic cells</h4>
<p>See <a href="#Specialised">specialised cells</a>.</p>
<h4>Somatic stem cells</h4>
<p>See <a href="#Tissue">tissue stem cells</a>.</p>
<h4><a name="Specialised" id="Specialised"></a>Specialised cells</h4>
<p>Cells that are fully differentiated and have specific roles within a tissue or organ. Examples include the ability of muscle cells to contract and stomach cells to produce acid for digestion.</p>
<h4>Stem cells</h4>
<p>Cells that have the ability to both self-renew and differentiate. Stem cells are critical for development, growth, cell renewal and healing.</p>
<h4>Stem cell line</h4>
<p>Cells that have been well characterized, have specific phenotypes, and can be indefinitely grown in the laboratory. These cells often are used for experimentation because they are homogenous and are used in other laboratories. This permits researchers to easily conduct experiments on the same cells and more accurately compare experimental results.</p>
<h4><a name="Syngeneic" id="Syngeneic"></a>Syngeneic</h4>
<p>When a tissue (or cell) donor and recipient are genetically identical. This is only possible in the situation that the donor and recipient are identical twins.</p>
<h4>Teratoma</h4>
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<p class="MsoNormal">A tumor composed of a chaotic mixture of many tissue or organ components, that is caused by the abnormal presence of pluripotent cells, which multiply and differentiate without the normal controls imposed by the embryo.</p>
<h4>Terminally differentiated cells</h4>
<p>Cells that cannot undergo changes in their identity or specialised functions.</p>
<h4>Tissue</h4>
<p>A group of cells that perform similar specialised functions.</p>
<h4><a name="Tissue" id="Tissue"></a>Tissue stem cells</h4>
<p>Tissue stem cells can both self renew and give rise to at least one more specialised (differentiated) cell type. They can be unipotent, meaning that they only make one type of specialised cell (eg the spermatogonial stem cell) or multipotent, meaning they can generate several types of specialised cell. Under normal circumstances, tissue stem cells generate only the cell types that make up the or organ / tissue system they reside in. Also known as 'adult' or 'somatic' stem cells.</p>
<h4>Totipotent cells</h4>
<p>Cells with the ability to undergo development into complete organisms. An example of such a cell is the zygote.</p>
<h4>Transcription factor</h4>
<p>Proteins that bind to DNA, often at or near the beginning of a gene, and regulate the amount of RNA or protein produced that is coded by a gene. Transcription factors can both increase or decrease the gene expression (the amount of gene products a cell produces).</p>
<h4>Transgenic</h4>
<p>An organism that contains artificially introduced genetic material.</p>
<h4>Tumour</h4>
<p>Abnormal tissue growth that is caused by unregulated and rapidly multiplying cells.</p>
<h4>Unipotent</h4>
<p>A cell that only has the ability to differentiate into a single specialised cell type. This is often the case of precursor cells.</p>
<h4>Zygote</h4>
<p>A totipotent cell formed by the unification of a sperm and egg.</p>
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