Harmonization Project Document No. 4
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Administering Unidata on UNIX Platforms
C:\Program Files\Adobe\FrameMaker8\UniData 7.2\7.2rebranded\ADMINUNIX\ADMINUNIXTITLE.fm March 5, 2010 1:34 pm Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta UniData Administering UniData on UNIX Platforms UDT-720-ADMU-1 C:\Program Files\Adobe\FrameMaker8\UniData 7.2\7.2rebranded\ADMINUNIX\ADMINUNIXTITLE.fm March 5, 2010 1:34 pm Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Notices Edition Publication date: July, 2008 Book number: UDT-720-ADMU-1 Product version: UniData 7.2 Copyright © Rocket Software, Inc. 1988-2010. All Rights Reserved. Trademarks The following trademarks appear in this publication: Trademark Trademark Owner Rocket Software™ Rocket Software, Inc. Dynamic Connect® Rocket Software, Inc. RedBack® Rocket Software, Inc. SystemBuilder™ Rocket Software, Inc. UniData® Rocket Software, Inc. UniVerse™ Rocket Software, Inc. U2™ Rocket Software, Inc. U2.NET™ Rocket Software, Inc. U2 Web Development Environment™ Rocket Software, Inc. wIntegrate® Rocket Software, Inc. Microsoft® .NET Microsoft Corporation Microsoft® Office Excel®, Outlook®, Word Microsoft Corporation Windows® Microsoft Corporation Windows® 7 Microsoft Corporation Windows Vista® Microsoft Corporation Java™ and all Java-based trademarks and logos Sun Microsystems, Inc. UNIX® X/Open Company Limited ii SB/XA Getting Started The above trademarks are property of the specified companies in the United States, other countries, or both. All other products or services mentioned in this document may be covered by the trademarks, service marks, or product names as designated by the companies who own or market them. License agreement This software and the associated documentation are proprietary and confidential to Rocket Software, Inc., are furnished under license, and may be used and copied only in accordance with the terms of such license and with the inclusion of the copyright notice. -
The Aryl Hydrocarbon Receptor: Structural Analysis and Activation Mechanisms
The Aryl Hydrocarbon Receptor: Structural Analysis and Activation Mechanisms This thesis is submitted in fulfilment of the requirements for the degree of Doctor of Philosophy in the School of Molecular and Biomedical Sciences (Biochemistry), The University of Adelaide, Australia Fiona Whelan, B.Sc. (Hons) 2009 2 Table of Contents THESIS SUMMARY................................................................................. 6 DECLARATION....................................................................................... 7 PUBLICATIONS ARISING FROM THIS THESIS.................................... 8 ACKNOWLEDGEMENTS...................................................................... 10 ABBREVIATIONS ................................................................................. 12 CHAPTER 1: INTRODUCTION ............................................................. 17 1.1 BHLH.PAS PROTEINS ............................................................................................17 1.1.1 General background..................................................................................17 1.1.2 bHLH.PAS Class I Proteins.........................................................................18 1.2 THE ARYL HYDROCARBON RECEPTOR......................................................................19 1.2.1 Domain Structure and Ligand Activation ..............................................19 1.2.2 AhR Expression and Developmental Activity .......................................21 1.2.3 Mouse AhR Knockout Phenotype ...........................................................23 -
Non-Homologous Isofunctional Enzymes: a Systematic Analysis Of
Omelchenko et al. Biology Direct 2010, 5:31 http://www.biology-direct.com/content/5/1/31 RESEARCH Open Access Non-homologousResearch isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution Marina V Omelchenko, Michael Y Galperin*, Yuri I Wolf and Eugene V Koonin Abstract Background: Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC) numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted) to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins. Results: We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE) that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress. -
Cygwin User's Guide
Cygwin User’s Guide Cygwin User’s Guide ii Copyright © Cygwin authors Permission is granted to make and distribute verbatim copies of this documentation provided the copyright notice and this per- mission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this documentation under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this documentation into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the Free Software Foundation. Cygwin User’s Guide iii Contents 1 Cygwin Overview 1 1.1 What is it? . .1 1.2 Quick Start Guide for those more experienced with Windows . .1 1.3 Quick Start Guide for those more experienced with UNIX . .1 1.4 Are the Cygwin tools free software? . .2 1.5 A brief history of the Cygwin project . .2 1.6 Highlights of Cygwin Functionality . .3 1.6.1 Introduction . .3 1.6.2 Permissions and Security . .3 1.6.3 File Access . .3 1.6.4 Text Mode vs. Binary Mode . .4 1.6.5 ANSI C Library . .4 1.6.6 Process Creation . .5 1.6.6.1 Problems with process creation . .5 1.6.7 Signals . .6 1.6.8 Sockets . .6 1.6.9 Select . .7 1.7 What’s new and what changed in Cygwin . .7 1.7.1 What’s new and what changed in 3.2 . -
Biosynthesis in Vitro of Bacillamide Intermediate-Heterocyclic Alacysthiazole by Heterologous Expression of Nonribosomal Peptide Synthetase (NRPS) T
Journal of Biotechnology 292 (2019) 5–11 Contents lists available at ScienceDirect Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec Biosynthesis in vitro of bacillamide intermediate-heterocyclic AlaCysthiazole by heterologous expression of nonribosomal peptide synthetase (NRPS) T Fengli Zhang, Nayila Mulati, Yukun Wang, Yingxin Li, Sanqiang Gong, Loganathan Karthik, ⁎ Wei Sun, Zhiyong Li Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China ARTICLE INFO ABSTRACT Keywords: Bacillamide C, a potential natural antialgae active compound, is produced by Bacillus atrophaeus C89 derived Bacillus atrophaeus from marine sponge Dysidea avara. A nonribosomal peptide synthetase (NRPS) cluster is hypothesized to be Bacillamides involved in the biosynthesis of bacillamide C. The NRPS with a domain string of A1-PCP1-Cy-A2-PCP2-C can be Heterologous expression divided into three functional modules. After heterologous expression and purification of module A1-PCP1 and Nonribosomal peptide synthetase (NRPS) module Cy-A2-PCP2, their catalytic activities were biochemically proven in vitro by the reaction with the apo- Thiazole PCP domain transformed to the holo-PCP domain through a phosphopantetheinyl transferase, ATP, and substrate amino acids. Five– membered heterocyclic AlaCysthiazole with molecular weight of 172.0389 was detected. This proved the formation of the heterocyclic dipeptide AlaCysthiazole, which is considered to be a building block for the biosynthesis of bacillamide. This study provides a basis for further biosynthesis of bacillamides. 1. Introduction et al., 2017). Even though the biosynthesis of bacillamide C was opti- mized, the yield was very low (Jin et al., 2011; Yu et al., 2015). -
[Linux] - Unix/Linix Commands
[Linux] - Unix/Linix Commands 1. $ ssh username@servername command used to login to server 2$ pwd it prints present working directory 3$ ls -l listing the files in present directory 4$ cd..takes you to previous Dir 5$ mkdir <directory>will create directory 6$ mkdir -p /home/user1/d1/d2/d3will create all the non-existing Dir’s 7$ vi <file_name>opens file for reading/editing 8$ cat <file_name>display contents of file 9$ more <file_name>displays page by page contents of file 10$ grep <pattern> file_namechecks pattern/word in file name specified 11$ head <file_name>shows first 10 lines of file_name 12$ touch <file_name>creates a zero/dummy file 13$ ln file1 file2 creates link of file1 to file2 14$ cp <file1> <file2>Copy a file 15$ mv <file1> <file2>Move/rename a file or folder 16$ clearclears the scree 17$ whoDisplays logged in user to the system. 18$ file <file_name>shows what type of file it is like 19$wwill display more info abt the users logged in 20$ ps -efshows process 21$ which <file_name>shows if the file_name/command exists and if exists display the path 22$ rm <file_name>will delete file specified$ rm * Delete all the files in the present directory (BE CAREFUL WHILE GIVING THIS COMMAND) 23$ find . -type f -print -exec grep -i <type_ur_text_here> {} \;this is recursive grep$ find / - name <file_name> -print 24$ tail <file_name>shows last 10 lines of fileuse tail -f for continous update of file_name 25$ chmod 777 <file_name>changes file_name/directory permissions use –R switch for recursive 26$ chown owner:group <file_name>changes -
CICS and IPCS
CICS and IPCS Andre Clark Staff CICS L2 Support Agenda § Dump types § Some basic IPCS commands § CICS Verbexit DFHPDxxx § Common System Area (CSA) § Storage Manager (SM) § Transaction Manager (XM) § Dispatcher (DS) § Kernel (KE) § Loader domain (LD) § Program domain (PG) § Lock Manager (LM) § Enqueue domain (NQ) § Application domain (AP) § Task Summary (TK) § Trace (TR) 3 IPCS Primary Menu ------------------- IPCS PRIMARY OPTION MENU --------------------------------- OPTION ===> ******************** 0 DEFAULTS - Specify default dump and options * USERID - USASSC1 1 BROWSE - Browse dump data set * 2 ANALYSIS - Analyze dump contents * 3 UTILITY - Perform utility functions * TIME - 16:46 4 INVENTORY - Inventory of problem data * PREFIX - USASSC1 5 SUBMIT - Submit problem analysis job to batch * TERMINAL- 3278 6 COMMAND - Enter subcommand, CLIST or REXX exec * PF KEYS - 24 T TUTORIAL - Learn how to use the IPCS dialog ******************** X EXIT - Terminate using log and list defaults Enter END command to terminate IPCS dialog F1=HELP F2=SPLIT F3=END F4=RETURN F5=RFIND F6=MORE F7=UP F8=DOWN F9=SWAP F10=LEFT F11=RIGHT F12=CURSOR 4 IPCS Default Menu ------------------------- IPCS Default Values --------------------------------- Command ===> You may change any of the defaults listed below. The defaults shown before any changes are LOCAL. Change scope to GLOBAL to display global defaults. Scope ==> BOTH (LOCAL, GLOBAL, or BOTH) If you change the Source default, IPCS will display the current default Address Space for the new source and will ignore any data entered in the Address Space field. Source ==> DSNAME('USASSC1.SHAREFC.DUMP') Address Space ==> ASID(X'0044') Message Routing ==> NOPRINT TERMINAL Message Control ==> FLAG(WARNING) NOCONFIRM VERIFY Display Content ==> MACHINE REMARK REQUEST NOSTORAGE SYMBOL Press ENTER to update defaults. -
Using IPCS with MVS/ESA Version 5
SYSTEM BY TOM BRYANT STRATEGIES MVS/XA/ESA Problem Solving: Part I — Using IPCS With MVS/ESA Version 5 PCS for MVS/ESA Version 5 has come a long way since I first used it in 1983 at the prompting of an exuberant IBM customer engineer. IPCS IPCS for MVS/ESA continues to move toward a fully panel-driven environment, although in Version 5 offers many Isome situations, I find using IPCS commands easier. capabilities, including the ability to scan for unformatted storage dumps. This article Future articles will examine the environ- easily in batch mode as well as in an ISPF mental record editing and printing program foreground session. I also wanted a CLIST examines the many (EREP), one-page MVS/XA/ESA abend that was well-documented with easy-to-use facilities of IPCS, analysis, advanced SVCDUMP analysis, parameters. Finally, I wanted a CLIST that slip traps and GTF tracing, and standalone does not hang onto dump directory and IPCS and includes some dump analysis. print dataset allocations when completed, as of the author’s favorite IPCS stands for Interactive Problem the IBM BLSCDDIR CLIST does. Control System, although most people IPCS commands. (myself included) use it just for looking at IPCS CLISTS FOR MVS/ESA unformatted storage dumps. IPCS will process VERSION 4.3 AND ABOVE SVCDUMPs which are dumps usually pro- The #IPCSTJB CLIST is the mainline duced with the abend (SVC 13) issued by your CLIST that you execute to establish an IPCS program or the system. Other unformatted session (see Figure 1). If you are invoking dumps that IPCS will produce include an #IPCSTJB for the first time, the NEW CLIST application unformatted dump allocated keyword parameter indicates that you will through the SYSMDUMP DD statement and dynamically create a VSAM dump directory the standalone dump produced by the stand- using the value of the VOL CLIST keyword alone dump program. -
Operating System Lab Manual
OPERATING SYSTEM LAB MANUAL BASICS OF UNIX COMMANDS Ex.No:1.a INTRODUCTION TO UNIX AIM: To study about the basics of UNIX UNIX: It is a multi-user operating system. Developed at AT & T Bell Industries, USA in 1969. Ken Thomson along with Dennis Ritchie developed it from MULTICS (Multiplexed Information and Computing Service) OS. By1980, UNIX had been completely rewritten using C langua ge. LINUX: It is similar to UNIX, which is created by Linus Torualds. All UNIX commands works in Linux. Linux is a open source software. The main feature of Linux is coexisting with other OS such as windows and UNIX. STRUCTURE OF A LINUXSYSTEM: It consists of three parts. a)UNIX kernel b) Shells c) Tools and Applications UNIX KERNEL: Kernel is the core of the UNIX OS. It controls all tasks, schedule all Processes and carries out all the functions of OS. Decides when one programs tops and another starts. SHELL: Shell is the command interpreter in the UNIX OS. It accepts command from the user and analyses and interprets them 1 | P a g e BASICS OF UNIX COMMANDS Ex.No:1.b BASIC UNIX COMMANDS AIM: To study of Basic UNIX Commands and various UNIX editors such as vi, ed, ex and EMACS. CONTENT: Note: Syn->Syntax a) date –used to check the date and time Syn:$date Format Purpose Example Result +%m To display only month $date+%m 06 +%h To display month name $date+%h June +%d To display day of month $date+%d O1 +%y To display last two digits of years $date+%y 09 +%H To display hours $date+%H 10 +%M To display minutes $date+%M 45 +%S To display seconds $date+%S 55 b) cal –used to display the calendar Syn:$cal 2 2009 c)echo –used to print the message on the screen. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
17555: Lab: Z/OS Debugging IPCS Hands-On
1177555555:: LLaabb:: zz//OOSS DDeebbuuggggiinngg IIPPCCSS HHaannddss--oonn LLaabb WWeeddnneessddaayy,, AAuugguusstt 1122 1122::3300 PPMM JJoohhnn CC.. SShheebbeeyy IIIIII IIBBMM PPoouugghhkkeeeeppssiiee jjsshheebbeeyy@@uuss..iibbmm..ccoomm PPaattrriicciiaa LLiittttllee IIBBMM PPoouugghhkkeeeeppssiiee pplliittttllee@@uuss..iibbmm..ccoomm © 2015 IBM Corporation Lab Agenda Introduction o How the Lab is Presented …………………… 2 o Downloading Dumps via FTP ……………….. 3 o Related Sessions …………………………….. 3 o Lab Setup Instructions ……………………….. 4 Lab Exercises o Dump of Hung Job ………………………….. 5-6 o Dump of Looping Job…..…………………….. 7-8 o ABEND0C1 Dump …………………................9-11 o ABEND0C4 Dump .........................................12-14 Answers to Lab Exercises .......................... 15-25 Appendix o IPCS Option 1 - BROWSE Mode ………..…. 27 o IP ST REGS …………………………………... 28 o IP SYSTRACE ………………………………... 29 How the Lab is Presented Self-Paced o Be warned there is a lot of material in this lab. You may not finish in the time allotted. o '**' on page title indicates exercises on that page. Each exercise details commands to be entered. This lab session lets you experiment with some of the IPCS commands and displays discussed in lecture session 17907. Please refer to lecture session 17907 for sample command display output. SHARE Session 17555 2 © 2015 IBM Corporation Downloading Dumps via FTP ALL 4 data sets used in today's lab are available for FTP download. Download from TESTCASE.BOULDER.IBM.COM, login as ANONYMOUS, and use your complete E-MAIL address as the password. Files are in BINARY format in the ‘fromibm/mvs’ directory. Filenames are ‘share.s17555.dumpN.trs.bin’ (N is 1 - 4; filenames are lower case). All files are in tersed format, so will need to be untersed after download. -
Generate Metabolic Map Poster
Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_003855395Cyc: Shewanella livingstonensis LMG 19866 Cellular Overview Connections between pathways are omitted for legibility.