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Why Is C. Diff So Hard to Culture and Kill?
Why is C. diff so hard to culture and kill? Clostridium difficile, commonly referred to as C. diff, is the #1 nosocomial infection in hospitals (it actually kicked staph infections out of the top spot). At Assurance, we test for this organism as part of our Gastrointestinal (GI) panel. C. diff is a gram-positive anaerobe, meaning it does not like oxygen. Its defensive mechanism is sporulation – where it essentially surrounds itself with a tough outer layer of keratin and can live in water, soil, etc. for over a decade. For reference, anthrax is another organism that sporulates. Once C. diff sporulates, it is very hard to kill and in fact, bleach is one of the only disinfectants that work. Unfortunately, it can spread quickly throughout hospitals. Spores of C. diff are found all over hospital surfaces and even in some hospital water systems. It’s the most threatening for those who are immunocompromised or the elderly, who are the most likely to end up with C. diff infections. With our PCR testing, we’re looking for the C. diff organism itself but we’re also looking at the production of toxin. Unless it produces toxins A AND B together OR toxin B, C. diff doesn’t cause severe disease. Many babies are exposed to it during birth or in the hospitals and may test positive on our GI panel. Unless they are expressing those toxins (both toxin A&B or just toxin B) it is not considered a clinical infection. Studies show that toxins A&B together causes infection, as well as toxin B. -
GNU Grep: Print Lines That Match Patterns Version 3.7, 8 August 2021
GNU Grep: Print lines that match patterns version 3.7, 8 August 2021 Alain Magloire et al. This manual is for grep, a pattern matching engine. Copyright c 1999{2002, 2005, 2008{2021 Free Software Foundation, Inc. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, with no Front-Cover Texts, and with no Back-Cover Texts. A copy of the license is included in the section entitled \GNU Free Documentation License". i Table of Contents 1 Introduction ::::::::::::::::::::::::::::::::::::: 1 2 Invoking grep :::::::::::::::::::::::::::::::::::: 2 2.1 Command-line Options ::::::::::::::::::::::::::::::::::::::::: 2 2.1.1 Generic Program Information :::::::::::::::::::::::::::::: 2 2.1.2 Matching Control :::::::::::::::::::::::::::::::::::::::::: 2 2.1.3 General Output Control ::::::::::::::::::::::::::::::::::: 3 2.1.4 Output Line Prefix Control :::::::::::::::::::::::::::::::: 5 2.1.5 Context Line Control :::::::::::::::::::::::::::::::::::::: 6 2.1.6 File and Directory Selection:::::::::::::::::::::::::::::::: 7 2.1.7 Other Options ::::::::::::::::::::::::::::::::::::::::::::: 9 2.2 Environment Variables:::::::::::::::::::::::::::::::::::::::::: 9 2.3 Exit Status :::::::::::::::::::::::::::::::::::::::::::::::::::: 12 2.4 grep Programs :::::::::::::::::::::::::::::::::::::::::::::::: 13 3 Regular Expressions ::::::::::::::::::::::::::: 14 3.1 Fundamental Structure :::::::::::::::::::::::::::::::::::::::: -
“Linux at the Command Line” Don Johnson of BU IS&T We’Ll Start with a Sign in Sheet
“Linux at the Command Line” Don Johnson of BU IS&T We’ll start with a sign in sheet. We’ll end with a class evaluation. We’ll cover as much as we can in the time allowed; if we don’t cover everything, you’ll pick it up as you continue working with Linux. This is a hands-on, lab class; ask questions at any time. Commands for you to type are in BOLD The Most Common O/S Used By BU Researchers When Working on a Server or Computer Cluster Linux is a Unix clone begun in 1991 and written from scratch by Linus Torvalds with assistance from a loosely-knit team of hackers across the Net. 64% of the world’s servers run some variant of Unix or Linux. The Android phone and the Kindle run Linux. a set of small Linux is an O/S core programs written by written by Linus Richard Stallman and Torvalds and others others. They are the AND GNU utilities. http://www.gnu.org/ Network: ssh, scp Shells: BASH, TCSH, clear, history, chsh, echo, set, setenv, xargs System Information: w, whoami, man, info, which, free, echo, date, cal, df, free Command Information: man, info Symbols: |, >, >>, <, ;, ~, ., .. Filters: grep, egrep, more, less, head, tail Hotkeys: <ctrl><c>, <ctrl><d> File System: ls, mkdir, cd, pwd, mv, touch, file, find, diff, cmp, du, chmod, find File Editors: gedit, nedit You need a “xterm” emulation – software that emulates an “X” terminal and that connects using the “SSH” Secure Shell protocol. ◦ Windows Use StarNet “X-Win32:” http://www.bu.edu/tech/support/desktop/ distribution/xwindows/xwin32/ ◦ Mac OS X “Terminal” is already installed Why? Darwin, the system on which Apple's Mac OS X is built, is a derivative of 4.4BSD-Lite2 and FreeBSD. -
Tracking Computer Use with the Windows® Registry Dataset Doug
Tracking Computer Use with the Windows® Registry Dataset Doug White Disclaimer Trade names and company products are mentioned in the text or identified. In no case does such identification imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the products are necessarily the best available for the purpose. Statement of Disclosure This research was funded by the National Institute of Standards and Technology Office of Law Enforcement Standards, the Department of Justice National Institute of Justice, the Federal Bureau of Investigation and the National Archives and Records Administration. National Software Reference Library & Reference Data Set The NSRL is conceptually three objects: • A physical collection of software • A database of meta-information • A subset of the database, the Reference Data Set The NSRL is designed to collect software from various sources and incorporate file profiles computed from this software into a Reference Data Set of information. Windows® Registry Data Set It is possible to compile a historical list of applications based on RDS metadata and residue files. Many methods can be used to remove application files, but these may not purge the Registry. Examining the Registry for residue can augment a historical list of applications or provide additional context about system use. Windows® Registry Data Set (WiReD) The WiReD contains changes to the Registry caused by application installation, de-installation, execution or other modifying operations. The applications are chosen from the NSRL collection, to be of interest to computer forensic examiners. WiReD is currently an experimental prototype. NIST is soliciting feedback from the computer forensics community to improve and extend its usefulness. -
Nhl Morning Skate – Nov
NHL MORNING SKATE – NOV. 25, 2018 SATURDAY’S RESULTS Home Team in Caps Washington 5, NY RANGERS 3 TORONTO 6, Philadelphia 0 Boston 3, MONTREAL 2, Buffalo 3, DETROIT 2 (SO) Chicago 5, FLORIDA 4 (OT) NY ISLANDERS 4, Carolina 1 PITTSBURGH 4, Columbus 2 Winnipeg 8, ST. LOUIS 4 COLORADO 3, Dallas 2 VEGAS 6, San Jose 0 Vancouver 4, LOS ANGELES 2 LAINE BREAKS RECORDS WITH FIRST FIVE-GOAL GAME IN NEARLY EIGHT YEARS Patrik Laine became the first NHL player in nearly eight years to score five goals in a game, setting franchise records for most in a game and calendar month to take sole possession of the League lead this season (19). He has scored 16 times since returning to his native Finland for the 2018 NHL Global Series on Nov. 1 - where he scored his first of three hat tricks this month. * Laine tallied the 57th performance of five or more goals in a NHL regular-season game – the 17th by a visiting player - and first since Detroit’s Johan Franzen on Feb. 2, 2011 at OTT. The only other player to score five goals in a game since 1997-98 is Marian Gaborik, on Dec. 20, 2007 vs. NYR. * Laine (20 years, 219 days) is the third different player in League history to score five goals in a game before his 21st birthday, joining Don Murdoch (Oct. 12, 1976: 19 years, 353 days) and Wayne Gretzky, who accomplished the feat twice (Feb. 18, 1981: 20 years, 23 days; and Dec. 30, 1981: 20 years, 338 days). -
Weekend with a Legend
Weekend with a Legend Participate in the Ultimate Hockey Fan Experience and spend the weekend playing with some of hockey’s greatest Legends. This experience will allow you to draft your favorite hockey Legend to become apart of your team for the weekend. This means they will play in all of your scheduled tournament games, hang-out in the dressing room sharing stories of their careers, and take in the nightlife with the team. All you have to do is select a player from the list below or request a player that you don’t see and we will do our best to accommodate your group with the 100+ other Legends that have participated in our events. Golden Legends- starting @ $365cdn/ per person (based on a team of 20). $7,300/ per team. Al Iafrate (Toronto Maple Leafs) Gary Leeman (Toronto Maple Leafs) Chris “Knuckles” Nilan (Montreal Canadiens) John Scott (Arizona Coyotes) Bob Sweeney (Boston Bruins) Natalie Spooner (Canadian Olympic Team) Andrew Raycroft (Toronto Maple Leafs) Ron Duguay (New York Rangers) Darren Langdon (New York Rangers) Colton Orr (Toronto Maple Leafs) Dennis Maruk (Washington Capitals) Chris Kotsopoulos (Hartford Whalers) John Leclair (Philadelphia Flyers) Colin White (New Jersey Devils) Kevin Stevens (Pittsburgh Penguins) Shane Corson (Toronto Maple Leafs) Mike Krushelnyski (Edmonton Oilers) Theo Fleury (Calgary Flames) Many More………. Platinum Legends- starting @ $665cdn/ per person (based on a team of 20). $20,000cdn/ per team. Ray Bourque (Boston Bruins) Wendel Clark (Toronto Maple Leafs) Guy Lafleur (Coach) (Montreal Canadiens) Bryan Trottier (New York Islanders) Steve Shutt (Montreal Canadiens) Bernie Nicholls (LA Kings) Many More………. -
User Commands Grep ( 1 ) Grep – Search a File for a Pattern /Usr/Bin/Grep [-Bchilnsvw] Limited-Regular-Expression [Filename
User Commands grep ( 1 ) NAME grep – search a file for a pattern SYNOPSIS /usr/bin/grep [-bchilnsvw] limited-regular-expression [filename...] /usr/xpg4/bin/grep [-E -F] [-c -l -q] [-bhinsvwx] -e pattern_list... [-f pattern_file]... [file...] /usr/xpg4/bin/grep [-E -F] [-c -l -q] [-bhinsvwx] [-e pattern_list...] -f pattern_file... [file...] /usr/xpg4/bin/grep [-E -F] [-c -l -q] [-bhinsvwx] pattern [file...] DESCRIPTION The grep utility searches text files for a pattern and prints all lines that contain that pattern. It uses a compact non-deterministic algorithm. Be careful using the characters $, ∗, [,ˆ,, (, ), and \ in the pattern_list because they are also meaning- ful to the shell. It is safest to enclose the entire pattern_list in single quotes ’ . ’. If no files are specified, grep assumes standard input. Normally, each line found is copied to standard output. The file name is printed before each line found if there is more than one input file. /usr/bin/grep The /usr/bin/grep utility uses limited regular expressions like those described on the regexp(5) manual page to match the patterns. /usr/xpg4/bin/grep The options -E and -F affect the way /usr/xpg4/bin/grep interprets pattern_list. If -E is specified, /usr/xpg4/bin/grep interprets pattern_list as a full regular expression (see -E for description). If -F is specified, grep interprets pattern_list as a fixed string. If neither are specified, grep interprets pattern_list as a basic regular expression as described on regex(5) manual page. OPTIONS The following options are supported for both /usr/bin/grep and /usr/xpg4/bin/grep: -b Precede each line by the block number on which it was found. -
Unix Programmer's Manual
There is no warranty of merchantability nor any warranty of fitness for a particu!ar purpose nor any other warranty, either expressed or imp!ied, a’s to the accuracy of the enclosed m~=:crials or a~ Io ~helr ,~.ui~::~::.j!it’/ for ~ny p~rficu~ar pur~.~o~e. ~".-~--, ....-.re: " n~ I T~ ~hone Laaorator es 8ssumg$ no rO, p::::nS,-,,.:~:y ~or their use by the recipient. Furln=,, [: ’ La:::.c:,:e?o:,os ~:’urnes no ob~ja~tjon ~o furnish 6ny a~o,~,,..n~e at ~ny k:nd v,,hetsoever, or to furnish any additional jnformstjcn or documenta’tjon. UNIX PROGRAMMER’S MANUAL F~ifth ~ K. Thompson D. M. Ritchie June, 1974 Copyright:.©d972, 1973, 1974 Bell Telephone:Laboratories, Incorporated Copyright © 1972, 1973, 1974 Bell Telephone Laboratories, Incorporated This manual was set by a Graphic Systems photo- typesetter driven by the troff formatting program operating under the UNIX system. The text of the manual was prepared using the ed text editor. PREFACE to the Fifth Edition . The number of UNIX installations is now above 50, and many more are expected. None of these has exactly the same complement of hardware or software. Therefore, at any particular installa- tion, it is quite possible that this manual will give inappropriate information. The authors are grateful to L. L. Cherry, L. A. Dimino, R. C. Haight, S. C. Johnson, B. W. Ker- nighan, M. E. Lesk, and E. N. Pinson for their contributions to the system software, and to L. E. McMahon for software and for his contributions to this manual. -
Regular Expressions Grep and Sed Intro Previously
Lecture 4 Regular Expressions grep and sed intro Previously • Basic UNIX Commands – Files: rm, cp, mv, ls, ln – Processes: ps, kill • Unix Filters – cat, head, tail, tee, wc – cut, paste – find – sort, uniq – comm, diff, cmp – tr Subtleties of commands • Executing commands with find • Specification of columns in cut • Specification of columns in sort • Methods of input – Standard in – File name arguments – Special "-" filename • Options for uniq Today • Regular Expressions – Allow you to search for text in files – grep command • Stream manipulation: – sed Regular Expressions What Is a Regular Expression? • A regular expression (regex) describes a set of possible input strings. • Regular expressions descend from a fundamental concept in Computer Science called finite automata theory • Regular expressions are endemic to Unix – vi, ed, sed, and emacs – awk, tcl, perl and Python – grep, egrep, fgrep – compilers Regular Expressions • The simplest regular expressions are a string of literal characters to match. • The string matches the regular expression if it contains the substring. regular expression c k s UNIX Tools rocks. match UNIX Tools sucks. match UNIX Tools is okay. no match Regular Expressions • A regular expression can match a string in more than one place. regular expression a p p l e Scrapple from the apple. match 1 match 2 Regular Expressions • The . regular expression can be used to match any character. regular expression o . For me to poop on. match 1 match 2 Character Classes • Character classes [] can be used to match any specific set of characters. regular expression b [eor] a t beat a brat on a boat match 1 match 2 match 3 Negated Character Classes • Character classes can be negated with the [^] syntax. -
Linux Terminal Commands Man Pwd Ls Cd Olmo S
Python Olmo S. Zavala Romero Welcome Computers File system Super basics of Linux terminal Commands man pwd ls cd Olmo S. Zavala Romero mkdir touch Center of Atmospheric Sciences, UNAM rm mv Ex1 August 9, 2017 Regular expres- sions grep Ex2 More Python Olmo S. 1 Welcome Zavala Romero 2 Computers Welcome 3 File system Computers File system 4 Commands Commands man man pwd pwd ls ls cd mkdir cd touch mkdir rm touch mv Ex1 rm Regular mv expres- sions Ex1 grep Regular expressions Ex2 More grep Ex2 More Welcome to this course! Python Olmo S. Zavala Romero Welcome Computers File system Commands 1 Who am I? man pwd 2 Syllabus ls cd 3 Intro survey https://goo.gl/forms/SD6BM6KHKRlDOpZx1 mkdir 4 touch Homework 1 due this Sunday. rm mv Ex1 Regular expres- sions grep Ex2 More How does a computer works? Python Olmo S. Zavala Romero Welcome Computers File system Commands man pwd ls cd mkdir touch rm mv Ex1 Regular 1 CPU Central Processing Unit. All the computations happen there. expres- sions 2 HD Hard Drive. Stores persistent information in binary format. grep 3 RAM Random Access Memory. Faster memory, closer to the CPU, not persistent. Ex2 More 4 GPU Graphics Processing Unit. Used to process graphics. https://teentechdaily.files.wordpress.com/2015/06/computer-parts-diagram.jpg What is a file? Python Olmo S. Zavala Romero Welcome Computers File system Commands man pwd ls cd mkdir touch rm mv Section inside the HD with 0’s and 1’s. Ex1 Regular File extension is used to identify the meaning of those 0’s and 1’s. -
How to Build a Search-Engine with Common Unix-Tools
The Tenth International Conference on Advances in Databases, Knowledge, and Data Applications Mai 20 - 24, 2018 - Nice/France How to build a Search-Engine with Common Unix-Tools Andreas Schmidt (1) (2) Department of Informatics and Institute for Automation and Applied Informatics Business Information Systems Karlsruhe Institute of Technologie University of Applied Sciences Karlsruhe Germany Germany Andreas Schmidt DBKDA - 2018 1/66 Resources available http://www.smiffy.de/dbkda-2018/ 1 • Slideset • Exercises • Command refcard 1. all materials copyright, 2018 by andreas schmidt Andreas Schmidt DBKDA - 2018 2/66 Outlook • General Architecture of an IR-System • Naive Search + 2 hands on exercices • Boolean Search • Text analytics • Vector Space Model • Building an Inverted Index & • Inverted Index Query processing • Query Processing • Overview of useful Unix Tools • Implementation Aspects • Summary Andreas Schmidt DBKDA - 2018 3/66 What is Information Retrieval ? Information Retrieval (IR) is finding material (usually documents) of an unstructured nature (usually text) that satisfies an informa- tion need (usually a query) from within large collections (usually stored on computers). [Manning et al., 2008] Andreas Schmidt DBKDA - 2018 4/66 What is Information Retrieval ? need for query information representation how to match? document document collection representation Andreas Schmidt DBKDA - 2018 5/66 Keyword Search • Given: • Number of Keywords • Document collection • Result: • All documents in the collection, cotaining the keywords • (ranked by relevance) Andreas Schmidt DBKDA - 2018 6/66 Naive Approach • Iterate over all documents d in document collection • For each document d, iterate all words w and check, if all the given keywords appear in this document • if yes, add document to result set • Output result set • Extensions/Variants • Ranking see examples later ... -
Introduction to BASH: Part II
Introduction to BASH: Part II By Michael Stobb University of California, Merced February 17th, 2017 Quick Review ● Linux is a very popular operating system for scientific computing ● The command line interface (CLI) is ubiquitous and efficient ● A “shell” is a program that interprets and executes a user's commands ○ BASH: Bourne Again SHell (by far the most popular) ○ CSH: C SHell ○ ZSH: Z SHell ● Does everyone have access to a shell? Quick Review: Basic Commands ● pwd ○ ‘print working directory’, or where are you currently ● cd ○ ‘change directory’ in the filesystem, or where you want to go ● ls ○ ‘list’ the contents of the directory, or look at what is inside ● mkdir ○ ‘make directory’, or make a new folder ● cp ○ ‘copy’ a file ● mv ○ ‘move’ a file ● rm ○ ‘remove’ a file (be careful, usually no undos!) ● echo ○ Return (like an echo) the input to the screen ● Autocomplete! Download Some Example Files 1) Make a new folder, perhaps ‘bash_examples’, then cd into it. Capital ‘o’ 2) Type the following command: wget "goo.gl/oBFKrL" -O tutorial.tar 3) Extract the tar file with: tar -xf tutorial.tar 4) Delete the old tar file with rm tutorial.tar 5) cd into the new director ‘tutorial’ Input/Output Redirection ● Typically we give input to a command as follows: ○ cat file.txt ● Make the input explicit by using “<” ○ cat < file.txt ● Change the output by using “>” ○ cat < file.txt > output.txt ● Use the output of one function as the input of another ○ cat < file.txt | less BASH Utilities ● BASH has some awesome utilities ○ External commands not