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Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill. 2. Epidemiology . West Nile fever Surveillance Maps. On 21 July, the first confirmed human case of West Nile fever in the EU was reported and detected in southern Greece. CDC provides leadership for HIV prevention research and surveillance and the development and testing of effective biomedical interventions to reduce transmission and. Communicable Diseases Intelligence, publishes a number of annual, quarterly, and regular reports produced by various communicable disease surveillance groups. Available online: http: //www. View. Article. aspx? Article. Id=2. 03. Date of submission. June 2. 01. 2Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage- type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time- consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages. Traditional typing systems based on phenotype, such as serotype, biotype, phage- type or antibiogram, have been used for many years. However, the methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types (or subtypes). The choice of an appropriate molecular typing method (or methods) depends significantly on the problem to solve and the epidemiological context in which the method is going to be used, as well as the time and geographical scale of its use. Importantly, human pathogens of one species can comprise very diverse organisms. Therefore, typing techniques should have excellent typeability to be able to type all the isolates studied . In outbreak investigations, a typing method must have the discriminatory power needed to distinguish all epidemiologically unrelated isolates. Ideally, such a method can discriminate very closely related isolates to reveal person- to- person strain transmission, which is important to develop strategies to prevent further spread. At the same time it must be rapid, inexpensive, highly reproducible, and easy to perform and interpret . When typing is applied for continuous surveillance, the respective method must yield results with adequate stability over time to allow implementation of efficient infection control measures. Moreover, a typing method that is going to be used in international networks should produce data that are portable (i. Additionally, a typing method used for surveillance should rely on an internationally standardised nomenclature, and it should be applicable for a broad range of bacterial species. There should also be procedures in place to check and validate, by using quantifiable internal and external controls, that the typing data are of high quality. A clear advantage for a typing approach is the availability of software that: (i) enables automated quality control of raw typing data, (ii) allows pattern/type assignment, (iii) implements an algorithm for clustering of isolates based on the obtained data, (iv) provides assistance in the detection of outbreaks of infections, and (v) facilitates data management and storage. To date, many different molecular methods for epidemiological characterisation of bacterial isolates have been developed. However, none of them is optimal for all forms of investigation. Thus, a thorough understanding of the advantages and limitations of the available typing methods is of crucial importance for selecting the appropriate approaches to unambiguously define outbreak strains. Here, we present an overview of the typing methods that are currently used in bacterial disease outbreak investigations and active surveillance networks, and we specify their advantages and disadvantages. Importantly, we focus on those methods that have the strongest impact on public health, or for which there is a growing interest in relation to clinical use. Pub. Med database searches. To investigate the impact of typing methods in public health, we first queried the Pub. Med database using a combination of specific keywords to retrieve the relevant articles without any constraints on the time of publication. Furthermore, in order to reveal a growing interest in particular typing methods, we subsequently restrictively searched Pub. Med for articles published between January 2. December 2. 01. 2). We considered a method as a method of growing interest when the number of articles published between January 2. Specifically, an electronic search was conducted using the following combinations of keywords: PFGE . Also, to identify the impact of particular typing methods on outbreak investigations currently conducted, we searched the Pub. Med database with a restriction to articles published between January 2. PFGE . The results of these literature searches have been included in the following sections of this review that address the respective typing methods. Pulsed- field gel electrophoresis Pulsed- field gel electrophoresis (PFGE) has been considered as the . For most bacterial species, the technique was adopted as an epidemiological tool in the 1. Today, it is still the most frequently used approach to characterise bacterial isolates in outbreaks . In total, 1. 83 hits were obtained for the terms . For many years, PFGE has been a primary typing tool to analyse centre- to- centre transmission events, and it has been used successfully in large- scale epidemiological investigations . The success of PFGE results from its excellent discriminatory power and high epidemiological concordance. Moreover, it is a relatively inexpensive approach with excellent typeability and intra- laboratory reproducibility. In the past decade, protocols for PFGE have been standardised and inter- laboratory comparison has been undertaken through several initiatives, such as Pulse. Net . It has also been possible to establish international fingerprinting databases, which allowed fast detection of emerging clones and monitoring of the spread of pathogenic bacterial strains through different regions or countries. To perform PFGE, a highly purified genomic DNA sample is cleaved with a restriction endonuclease that recognises infrequently occurring restriction sites in the genome of the respective bacterial species. The resulting restriction fragments, which are mostly large, can be separated on an agarose gel by 'pulsed- field' electrophoresis in which the orientation of the electric field across the gel is changed periodically. The separated DNA fragments can be visualised on the gel as bands, which form a particular pattern on the gel, the PFGE pattern. 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Port Manteaux churns out silly new words when you feed it an idea or two. Enter a word (or two) above and you'll get back a bunch of portmanteaux created by jamming. ![]() Next to the Microsoft Office button is the Quick Access toolbar. By default, Save, Undo, and Redo appear on the Quick Access toolbar. You can use Save to save your file, Undo to roll back an action you have taken, and Redo to reapply an action you have rolled back. The Title Bar. Next to the Quick Access toolbar is the Title bar. On the Title bar, Microsoft Excel displays the name of the workbook. At the top of the Excel window, you should see . In Microsoft Excel 2. ![]() Microsoft Word Cursor Jumps Around While Typing LettersRibbon to issue commands. The Ribbon is located near the top of the Excel window, below the Quick Access toolbar. At the top of the Ribbon are several tabs; clicking a tab displays several related command groups. You click buttons to issue commands or to access menus and dialog boxes. Each worksheet contains columns. The columns are lettered A to Z and then continuing with AA, AB, AC and so on; the rows are numbered 1 to. The number of columns and rows you can have in a worksheet is limited by your computer memory and your system resources. The combination of a column coordinate and a row coordinate make. For example, the cell located in the upper- left corner. A1, meaning column A, row 1. Cell E1. 0 is located. E on row 1. 0. You enter your data into the cells on the worksheet. The Formula Bar. Formula Bar. If the Formula bar is turned on, the cell address of the cell you are in displays in the Name. Formula bar. Cell entries display on the. Formula bar. If you do not see the Formula bar in your window, perform the following steps: Choose the View tab. Click Formula Bar in the Show/Hide group. The Formula bar appears. Note: The current cell address displays on the left side of the. Formula bar. The Status Bar The Status bar appears at the very bottom of the Excel window and provides such information as the sum, average, minimum, and maximum value of selected numbers. You can change what displays on the Status bar by right- clicking on the Status bar and selecting the options you want from the Customize Status Bar menu. You click a menu item to select it. You click it again to deselect it. A check mark next to an item means the item is selected. Move Around a Worksheet. By using the arrow keys, you can move around your worksheet. You can use the down arrow key to move downward one cell at a time. You can use the up arrow key to move upward one cell at a time. You can use the Tab key to move across the page to the right, one cell. You can hold down the Shift key and then press the Tab key to move to. You can use the right and left arrow keys to move right or left one. The Page Up and Page Down keys move up and down one page. If you hold down the Ctrl key and then press the Home key, you move to the beginning of the worksheet. EXERCISE 1. Move Around the Worksheet. The Down Arrow Key. Press the down arrow key several times. Note that the cursor moves downward one cell at a time. The Up Arrow Key. Press the up arrow key several times. Note that the cursor moves upward one cell at a time. The Tab Key. Move to cell A1. Press the Tab key several times. Note that the cursor moves to the right one cell at a time. The Shift+Tab Keys. Hold down the Shift key and then press Tab. Note that the cursor moves to the left one cell at a time. The Right and Left Arrow Keys. Press the right arrow key several times. Note that the cursor moves to the right. Press the left arrow key several times. Note that the cursor moves to the left. Page Up and Page Down. Press the Page Down key. Note that the cursor moves down one page. Press the Page Up key. Note that the cursor moves up one page. The Ctrl- Home Key. Move the cursor to column J. Stay in column J and move the cursor to row 2. Hold down the Ctrl key while you press the Home key. Excel moves to cell A1. Go To Cells. Quickly The following are shortcuts for moving quickly from one cell in a worksheet to a cell. EXERCISE 2. Go to - - F5. The F5 function key is the . If you press the F5. Enter the cell address, and the cursor jumps to that cell. Press F5. The Go To dialog box opens. Type J3 in the Reference field. Press Enter. Excel moves to cell J3. Go to - - Ctrl+GYou can also use Ctrl+G to go to a specific cell. Hold down the Ctrl key while you press . The. Go To dialog box opens. Type C4 in the Reference field. Press Enter. Excel moves to cell C4. The Name Box. You can also use the Name box to go to a specific cell. Just type the cell you want to go to in the Name box and then press Enter. Type B1. 0 in the Name box. Press Enter. Excel moves to cell B1. Select. Cells. If you wish to perform a function on a group of cells, you must first. The exercises that follow teach you how to select. EXERCISE 3. Select Cells. To select cells A1 to E1: Go to cell A1. Press the F8 key. This anchors the cursor. Note that . You are in the Extend mode. Click in cell E7. Excel highlights cells A1 to E7. Press Esc and click anywhere on the worksheet to clear the highlighting. Alternative. Method: Select Cells by Dragging. You can also select an area by holding down the left mouse button. In addition, you can select noncontiguous. Go to cell A1. Hold down the Ctrl key. You won't release it until step 9. Holding. down the Ctrl key enables you to select noncontiguous areas of the. Press the left mouse button. While holding down the left mouse button, use the mouse to move from. A1 to C5. Continue to hold down the Ctrl key, but release the left mouse button. Using the mouse, place the cursor in cell D7. Press the left mouse button. While holding down the left mouse button, move to cell F1. Release. the left mouse button. Release the Ctrl key. Cells A1 to C5 and cells D7 to F1. Press Esc and click anywhere on the worksheet to remove the highlighting. Enter. Data. In this section, you will learn how to enter data into your worksheet. If you need to delete, press the Backspace key to delete one character at a time. EXERCISE 4. Enter Data. Place the cursor in cell A1. Type John Jordan. Do not press Enter at this time. Delete Data. The Backspace key erases one character at a time. Press the Backspace key until Jordan is erased. Press Enter. Use the Backspace key to delete the . You change . Your cursor is now at the end of your text. Use the Backspace key to erase . If you do not want it to overlap the next cell, you can wrap the text. EXERCISE 6. Wrap Text. Move to cell A2. Type Text too long to fit. Press Enter. Return to cell A2. Choose the Home tab. Click the Wrap Text button . Excel wraps the text in the cell. Delete. a Cell Entry. How to use Jab. Ref (Bib. Te. X) with Microsoft Word 2. Jab. Ref is one of the best reference managers available and provides a realistic alternative to Endnote, as well as being open- source & free. Unfortunately most users are not aware that Jab. Ref (or any other Bib. Te. X based reference manager) can easily be integrated for use with Microsoft Word. In this guide I will show you step- by- step how to install Mike Brookes. The newest version can be found here on Mike Brookes’ site, along with excellent documentation. These instructions assume that you are already familiar with Jab. Ref and have a copy installed on your computer. If you wish you can download Jab. Ref from here. I will cover how to use Jab. Ref in a forthcoming guide. Download Mi. KTe. XMi. KTex is a La. Te. X typesetting environment , you don’t need to be too concerned about the details of this, essentially Mi. KTe. X contains Bib. Te. X the . Harvard, Vancouver, Nature etc. The link to Mik. Te. X is here (and will open in a new window) You need to download and install the basic version, don’t worry about installing all the packages, you don’t need them. Relocate your Jab. Ref data File. Unfortunately Bib. Te. X does not support filenames with spaces in them, if you have spaces in your path to your Jab. Ref file you must relocate your data file to a directory without. My Bibliography file is called “bib. My Documents” which contains a space so I relocated it to a new folder “c: \References\bib. Make a note of your location. Set your Path. The macro requires that it can access the Bib. Te. X package from the default path. The simplest way to set this is to go to. Start> > Settings> > Control Panel> > System> > Advanced> > Enviromental Variables> > System Variableshere you need to edit the “Path” entry by adding the path of the Bib. Te. X executable, failure to do so will cause an “Error 5. The path to my Bib. Te. X executable is. C: \Program Files\Mi. KTe. X 2. 5\miktex\bin. Yours should be similar if you followed the default installation. If you are having problems use the Windows search feature to look for “Bibtex. Remember each entry on the path should be seperated by semi- colons for example my path is: -d: \WINDOWS\system. D: \WINDOWS; D: \Program Files\Mi. KTe. X 2. 5\miktex\bin; 4. Make Word Startup Folder Visible. By defaut on your machine you may have to make your Word startup folder visible, you can do this by going to Windows Explorer and selecting: -Tools> > Folder Options> > Hidden files and folders> > Show hidden files and folders & Display the contents of system folders. If you prefer not to see your system and hidden folders you can reverse this once complete. Download the Macro. This can be found on Mike Brookes’ site here. Right click this link and use the “Save target as” or “Save Link as” option. You need to save it in your MS Word Startup folder which can be found at: -C: \Documents and Settings\James\Application Data\Microsoft\Word\STARTUPof course you will have substitute your username for mine, and possibly change the drive letter according to the setup of your machine. If you want this macro to be available to more than one user you will have to do this for each user. There is no need to change the MS Word security settings to enable this macro to work correctly. Load Microsoft Word. Hopefully you will see this new toolbar. First you need to let the Bib. Te. X4. Word macro know where you keep your bibliography data file. You do this by clicking on the last but one icon (the open folder) and then finding the bibliography file which you made a note of earlier. Start Citing. To add a citation position the cursor at the point you wish to insert the citation and click the . You can cite more than one paper by just separating the keys by commas. Creating your Bibliography List When you are ready to create your bibliography, simply place your cursor where you wish it to appear and click the second icon from the left on the Bib. Tex. 4Word toolbar. This will produce the bibliography and automatically change the bibliography keys to reference numbers. You can flip between the two with the . To find out what styles are available from your Mik. Te. X installation you can search the Bib. Te. X folder for style files which have the *. Mark’s recent article Example Citation Styles. A selection of the more popular styles (Plain, Vancouver, Author. Date and it’s variations) can be found in this pdf or this MS Word file. Adding more Styles to Bib. Te. XIf you installed the Basic Mi. KTe. X package you will only have a small selection of styles. Not all Bib. Te. X styles work well with the Bib. Te. X4. Word Macro, but most do. To add more go to. Start> > Programs> > Mi. KTe. X 2. 5> > Mi. KTe. X Package Manger. Here you need to select all of the Category entitled “\Bib. Te. X\Bib. Te. X packages” then right click and select Install, and the latest versions will be downloaded and installed on your computer. Customising Your Bibliography. You can format your bibliography directly, for example making citation numbers appear as subscript. If you wish you can change the citation brackets from square to round brackets, this is done using MS Word’s search and replace, though this is best left until you have finished your paper or thesis. Install Windows 8 On Mac Using Boot Camp . The recent release of the OS X 1. Windows 8 in Boot Camp, meaning that it is now possible to dual- boot both operating systems on any Mac running OS X. And we have a complete guide on how to install Windows 8 on a Mac using Boot Camp running OS X 1. What you will need: A Mac running OS X 1. Also see our guide on how to make Windows 8 bootable USB flash drive, if you’re using a DVD, then skip). Upgrade versions are not supported. At least 3. 0GB of free disk space (in order to create a partition for Windows 8). A spare USB drive where to save the Boot Camp drivers. An 8. GB stick would be highly recommended. Once you’ve got all you need, you are ready to begin installing Windows 8 on your Mac. Just in case something goes wrong, however, be sure to backup your Mac before getting started. Step 1: From OS X, launch Boot Camp Assistant from Applications > Utilities. When the first screen launches, click Continue. Step 2: On the next screen, unless you have the last version of your Boot Camp drivers downloaded elsewhere, tick both of the boxes: Download the latest Windows support software from Apple and Install Windows 7 or later version. Once you click Next, you will be prompted to insert a USB drive in order to download all of the relevant Windows drivers. The download process can take several minutes depending on the speed of your Internet connection. Step 3: Once all of the drivers have been downloaded on your USB drive, you will be given the option to choose how much space to allocate to your new Windows partition. At least 2. 0GB is recommended, although you might need more if you plan on moving many files on the Windows partition. Step 4: When prompted, reboot your Mac with your Windows 8 DVD / USB inserted. ![]() Before you install Windows, stop and think about whether or not Boot Camp is the best choice for your needs. There are a couple of drawbacks to consider. When it comes to running Windows on a Mac, there are two main players: Parallels Desktop 7 and VMware Fusion 4. Which is right for you? Rob Griffiths runs through the. This article is an overview and comparison of two alternatives for running Windows on an Intel based Apple MacBook: Parallels or Boot Camp, which to choose? MS Paint, the first app you used for editing images, will probably be killed off in future updates of Windows 10, replaced by the new app Paint 3D. Microsoft lists. Running Windows on the Mac is easier than ever with the latest versions of Parallels Desktop and VMware Fusion, but which one is best, and will Boot Camp do the job. Unfortunately, if you’re a Windows user you’ll have to actually purchase the font yourself: Microsoft created its own Helvetica clone, Arial, as it chose not to. Not always, as I found when comparing Windows and Apple models. If all goes well, your computer should reboot from the Windows installation DVD or USB stick. Step 5: From this point on, you should follow the regular Windows setup instructions. When selecting the partition, be sure to select the one labeled “BOOTCAMP”, which should be of a similar size to the one you set on Step 3. The long installation process: for the next several minutes, Windows 8 will be installed on your Windows partition. Be patient during this process and do not attempt to shut down or reboot your Mac. Step 6: Once your Mac restarts for the second time, you are ready to begin installing the required Apple drivers. Insert the USB drive that you used earlier and run the setup program. Simply follow the on- screen wizard and you will be ready to go. Congratulations, you have now set up Windows 8 on your Mac. You can now easily dual boot OS X and Windows 8 on your computer. How to dual- boot into OS X or Windows 8. Every time your Mac boots up, hold down the OPTION key till you see two options on the display, stating whether you want to boot into OS X or Windows. Select the relevant option, and you’re all good to go. You may also like to check out: You can follow us on Twitter, add us to your circle on Google+ or like our Facebook page to keep yourself updated on all the latest from Microsoft, Google, Apple and the web. Related Stories. Subscribe to our RSS Feed ! |
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