Working directories

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i='/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Rev_3'; pcmanfm -n ${i}; cd ${i}
#
i='/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Rev_3/p62_Draft_20210307_2130.docx'; setsid wps ${i} # restart

File manager

Among file managers listed in 30 Best File Managers for Linux Systems, I preferred as below

• PCManFM/PCMan
• Thunar
• XFE File Manager
• SpaceFM
• Caja
• Pantheon

Stopwatch

• linux - Is there a way to display a countdown or stopwatch timer in a terminal? - Super User

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man leave
leave +000010 # 10 seconds countdown

Download

Reactive Oxygen Species

• Oxygen Toxicity and Reactive Oxygen Species: The Devil Is in the Details | Pediatric Research
• Definition of reactive oxygen species - NCI Dictionary of Cancer Terms - National Cancer Institute, A type of unstable molecule that contains oxygen and that easily reacts with other molecules in a cell. A build up of reactive oxygen species in cells may cause damage to DNA, RNA, and proteins, and may cause cell death. Reactive oxygen species are free radicals. Also called oxygen radical.
• An Introduction to Reactive Oxygen Species - Measurement of ROS in Cells | January 26, 2014, ROS_White_Paper_2015.pdf
• Oxygen Toxicity and Reactive Oxygen Species: The Devil Is in the Details | Pediatric Research, Role_of_Oxygen_in_Health_and_Disease.pdf
• Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling
  • 3454471.epub -> ROS_homeostasis_and_redox_regulation_in_cellular_signaling.epub
  • nihms351530.pdf -> ROS_homeostasis_and_redox_regulation_in_cellular_signaling.pdf

Herpesviridae

Taxonomy ID: 10292 (for references in articles please use NCBI:txid10292)

Lineage( full )
Viruses; Duplodnaviria; Heunggongvirae; Peploviricota; Herviviricetes; Herpesvirales

Sequence download

• Herpesviridae - Nucleotide - NCBI, sequence download

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i='/media/ht/ht_5T/Database/Virus/Herpesvirus/Herpesviridae/20210307'; cd ${i}
#
i='/media/ht/ht_5T/Database/Virus/Herpesvirus/Herpesviridae/20210307/nuccore_result.txt'
ls ${i} # Summary document
#

###################################################
# Single column to three columns
###################################################
Input='nuccore_result.txt'
Number=4
awk -v col=${Number} '{if(NR%col){printf "%5s\t",$0 }else {printf "%s\n",$0}} ' ${Input} > ${Input}.convert

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Input='nuccore_result.txt'
Number=4
awk -v col=${Number} '{if(NR%col){printf "%5s\t",$0 }else {printf "%s\n",$0}} ' ${Input} | sed "s/     /\t/" | sed 's/^\t\t//' > ${Input}.convert

Ref

• perl - how to remove the first two columns in a file using shell (awk, sed, whatever) - Stack Overflow
• bash - How to delete the first column ( which is in fact row names) from a data file in linux? - Stack Overflow
• awk output seperated by tab
• How to remove a column or multiple columns from file using shell command? - Unix & Linux Stack Exchange

Datasets - NCBI

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pip install ncbi-datasets-pylib

Working directories

Google patents

Downloadable items

• Title document

  1	id,title,assignee,inventor/author,priority date,filing/creation date,publication date,grant date,result link,representative figure link

• Concept document

  1	id,name,domain,inchi_key,smiles,query match,sections

  Instructions

• PowerPoint Presentation

• How to do a Patent Search? - A Definitive Guide by GreyB
• Google Patents Search - A Definitive Guide by GreyB
• Patent Databases: 11 Best Free and Paid Search Platforms - GreyB
• Design Patent Search: 7 Unconventional Ways to Perform - GreyB
• Google Scholar Guide: How to Use Google Scholar for Legal and Academic Research? - GreyB

The 5 best free offline map apps for Android | NextPit

Zettlr Instruction

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i='/media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/Text_Editor/Zettlr'
cd ${i}; pcmanfm -n ${i}

• 1_Introduction.mp4
• 2_The_file_list.mp4
• 3_The_Editor.mp4
• 4_AutoCorrect_and_Magic_Quotes.mp4
• 5_Custom_CSS.mp4

• 0:07:19 1_Introduction.mp4
• 0:06:12 2_The_file_list.mp4
• 0:08:08 3_The_Editor.mp4
• 0:08:51 4_AutoCorrect_and_Magic_Quotes.mp4
• 0:11:34 5_Custom_CSS.mp4

List-up the last modified files

• Find latest files - Unix & Linux Stack Exchange
• linux - How to recursively find and list the latest modified files in a directory with subdirectories and times - Stack Overflow

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#!/bin/bash
find $1 -type f -exec stat --format '%Y :%y %n' "{}" \; | sort -nr | cut -d: -f2- | head

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ls -ltR
#
ls -ltrR

Working directories

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i='/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/Herpesvirus_Latent_Gene/Ref/Latent_Herpesvirus/Latency_strategies_of_herpesviruses.pdf'
ls ${i}

搜狗输入法词库下载

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i='https://github.com/WuLC/ThesaurusSpider'
git clone ${i}
#
i='/media/ht/ht_5T/Stored_Softs/Linux_Softs/IME/ThesaurusSpider/SougouThesaurusSpider`
pcmanfm -n ${i}; cd ${i}

command line - How to remove the password from a PDF? - Ask Ubuntu

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pdftk /path/to/input.pdf input_pw <yourpassword> output out.pdf

卫生部关于印发《消毒技术规范》(2002年版)的通知 - 中华人民共和国国家卫生健康委员会

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i='/media/ht/ht_5T/Work/References/eBooks/Others/消毒技术规范'
pcmanfm -n ${i}; cd ${i}

Working directories

• Raw data of B95-8_Nrf2 project
  • EBV_AN_NEW.pdf, simple description of VCA, EBNA1 and EA-D. From Products | TestLine Clinical Diagnostics s.r.o.
  • DBGET Search Result: KEGG Bortezomib
    • Combined inhibition of autophagy and Nrf2 signaling augments bortezomib-induced apoptosis by increasing ROS production and ER stress in pancreatic cancer cells. Bortezomib is a direct activator of Nrf2 and HO-1 as well.
  • Sodium butyrate
    • Sodium butyrate activates NRF2 to ameliorate diabetic nephropathy possibly via inhibition of HDAC in: Journal of Endocrinology Volume 232 Issue 1 (2017)
    • Sodium butyrate inhibits high cholesterol-induced neuronal amyloidogenesis by modulating NRF2 stabilization-mediated ROS levels: involvement of NOX2 and SOD1 | Cell Death & Disease, size of Nrf2 79 kD
    • KEGG DRUG: Sodium butyrate, CAS number to be confimred.

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i='/media/ht/ht_5T/Work/Projects/NFE/Summary/NFE2_Sum_Large.pptx'
setsid wps ${i}

• HSV cn, revised

搜狗输入法安装

• Ubuntu20.04LTS安装搜狗输入法 - 知乎

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curl -sL 'https://keyserver.ubuntu.com/pks/lookup?&op=get&search=0x73BC8FBCF5DE40C6ADFCFFFA9C949F2093F565FF' | sudo apt-key add
sudo apt-add-repository 'deb http://archive.ubuntukylin.com/ukui focal main'
sudo apt upgrade
#
sudo apt install sogouimebs
#
sogouIme-configtool 

搜狗输入法词库

• ThesaurusSpider/SougouThesaurusSpider at master · WuLC/ThesaurusSpider · GitHub

Backup

• ht_5T_2
• ht_5T

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Source=/media/ht/ht_5T/Work/
Destination=/media/ht/ht_5T_2/Work/
rsync -au --update ${Source} ${Destination}

Working directories

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# Remove sogoupinyin
dpkg -l | ag sogou
i='sogoupinyin'
sudo dpkg -r ${i}
sudo dpkg --purge ${i}
#
i='/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Ref/Nano_Iomis/'; pcmanfm -n ${i}; cd ${i}
#
i='/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Ref/Nano_Iomis/Nano_Iomis.docx'; setsid wps ${i}

搜狗输入法

• My Linux

• 搜狗输入法Linux版配置文件详解_jilijelon-CSDN博客
• 讯飞输入法Linux版.deb包和搜狗输入法存在冲突，附解决方案_Linux教程_云网牛站

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i='fcitx-frontend-qt4'
sudo apt remove ${i}
#
i='sogoupinyin'
sudo apt remove ${i}
#
i='fcitx-sogoupinyin-uk'
sudo apt remove ${i}
#

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~/.config/sogou-qimpanel
~/.config/SogouPY.users
~/.config/SogouPY

~/.config/SogouPY

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i='/home/ht/.config/SogouPY'
cd ${i}

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scdlist.ini
Correction.ini
sogouEnv.ini
env.ini
sogou.version
useSkin.txt
pingback.time
scd

• scdlist.ini
• Correction.ini
• sogouEnv.ini

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[Genelal]
FirstRunSogouQimanel_2_1=false
ShuangPin=false
HintSP=true
AllowQuanPin=true
HideStatusBar=true
FullScreenHideSB=true
SmartPunc=true

[StatusInfo]
ValueZhongYing=fcitx-kbd
ValueFan=fcitx-chttrans-inactive
ValuePunc=fcitx-punc-inactive
ValueQuanBan=fcitx-fullwidth-inactive #默认的是全角fcitx-fullwidth-active,半角需要修改为fcitx-fullwidth-inactive

[Key]
SwitchCE_key=Shift
SwichEnglishRetainExist=true
FirstPageKey=0
SecondPageKey=2
SwichSogouIME=true
Switch2sogou="CTRL_,"
ChttransFlag=true

[Appearance]
CandidateNumber=5
UseSkin=true
CurrentSkin=
ChangeColor=false
ChangeFont=true
DefaultSkinSetFlag=false

[Advance]
UrlMode=true
RemainHalfWidth=true
KeyPadInputDigital=true

[Cell]
AutoUpdateThesaurus=true
RuncellThesaurusUpdateTip=true
RuncellThesaurus=true

• env.ini
• sogou.version
• useSkin.txt
• pingback.time
• scd

Working directories

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i='/media/ht/ht_5T/Stored_Softs/Linux_Softs/IME'
pcmanfm -n ${i}; cd ${i} # Ubuntu Chinese IME
# 

IME in Ubuntu

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i='/media/ht/ht_5T/Stored_Softs/Linux_Softs/IME/'
cd ${i}
#
i='/media/ht/ht_5T/Stored_Softs/Linux_Softs/IME/sogoupinyin_2.1.0.0082_amd64.deb'
sudo gdebi ${i}
i='/media/ht/ht_5T/Stored_Softs/Linux_Softs/IME/sogoupinyin_2.3.1.0112_amd64.deb'
sudo gdebi ${i}
#
i='/media/ht/ht_5T/Stored_Softs/Linux_Softs/IME/sogoupinyin_2.4.0.3469_amd64.deb'
sudo dpkg -i ${i}
#
i='/media/ht/ht_5T/Stored_Softs/Linux_Softs/IME/iflyime_0.9.85_amd64.deb'
sudo dpkg -i ${i}

在Ubuntu下安装讯飞输入法linux版以及卸载方法 - Yoki的小站

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i='/media/ht/ht_5T/Stored_Softs/Linux_Softs/IME'
cd ${i}
i='http://packages.deepin.com/deepin/pool/non-free/i/iflyime/iflyime_0.9.85_amd64.deb'
axel ${i}

搜狗输入法 for linux

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i='https://ime.sogoucdn.com/dl/index/1612260778/sogoupinyin_2.4.0.3469_amd64.deb?st=7V-ZuZNtKFI2k94u0cxIuw&e=1614591562&fn=sogoupinyin_2.4.0.3469_amd64.deb'
axel ${i}

讯飞输入法Linux版.deb包和搜狗输入法存在冲突，附解决方案_Linux教程_云网牛站

• 在Deepin Linux系统中搜狗输入法占用内存很高的解决方法_Linux教程_云网牛站

Tree structure by markdown mermaid

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i=/media/ht/ht_5T/Work/References/Computer_Tips/ePub/Markdown/mermaid_Learning.docx
setsid wps ${i}

• 使用Markdown绘制树形图 - heylypp的博客 | heylypp Blog
• markdown流程图语法_aizhaoyu的专栏-CSDN博客_markdown 泳道图
• Mermaid Graphs and Flow Charts, very good instruction

Update Log

• 20210311
  • Node shapes
  • Line connection
  • Font color and size will be reviewed in the future

Installation

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npm install hexo-filter-mermaid-diagrams
#
cnpm install hexo-filter-mermaid-diagrams

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i='/media/ht/ht_5T/Management/Blog/Blog/themes/yilia/_config.yml'
subl ${i}

Add the text as below to the file of above

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# Mermaid 支持
mermaid:
on: true
cdn: //cdn.jsdelivr.net/npm/mermaid@8.4.2/dist/mermaid.min.js
#cdn: //cdnjs.cloudflare.com/ajax/libs/mermaid/8.3.1/mermaid.min.js
options: # 更多配置信息可以参考 https://mermaidjs.github.io/#/mermaidAPI
theme: 'default'
startOnLoad: true
flowchart:
useMaxWidth: false
htmlLabels: true

Codes

    
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graph TD
	subgraph SVN Architecture
	client1-->|read / write|SVN((SVN server))
	client2-->|read only|SVN
	client3-->|read / write|SVN
	client4-->|read only|SVN
	client5(...)-->SVN
	SVN---|store the data|sharedrive
	end

    
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graph LR
A[工具推荐] -->B(文献下载)
A -->C(文献管理)
A -->D(文件同步和存储)
A -->E(翻译辅助)
A -->F(公式书写)

Examples

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graph TD
    subgraph SVN Architecture
    client1-->|read / write|SVN((SVN server))
    client2-->|read only|SVN
    client3-->|read / write|SVN
    client4-->|read only|SVN
    client5(...)-->SVN
    SVN---|store the data|sharedrive
    end

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graph LR
A[工具推荐] -->B(文献下载)
A -->C(文献管理)
A -->D(文件同步和存储)
A -->E(翻译辅助)
A -->F(公式书写)

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graph TD
A[Hard] -->|Text| B(Round)
B --> C{Decision}
C --> |One| D[Result 1]
C --> |Two| E[Result 2]

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graph LR
id1(Start)-->id2(Stop)
style id1 fill:#f9f,stroke:#333,stroke-width:4px 
style id2 fill:#bbf,stroke:#f66,stroke-width:2px,color:#fff,stroke-dasharray: 5 5

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graph TD
    B["fa:fa-twitter for peace"]
    B-->C[fa:fa-ban forbidden]
    B-->D(fa:fa-spinner);
    B-->E(A fa:fa-camera-retro perhaps?);

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journey
  title My working day
  section Go to work
    Make tea: 5: Me
    Go upstairs: 3: Me
    Do work: 1: Me, Cat
  section Go home
    Go downstairs: 5: Me
    Sit down: 3: Me

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graph TD
start[<font size=6>附一电子报销流程]-->a1[<font size=6>1.发票检验]
a1-->b1[<font size=6>发票税号正确]
b1--<font size=6>是-->c1[<font size=6>发票下方盖公司有效印章]
c1-->d1[<font size=6>发票背面填写项目]
d1-->e1[<font size=6>项目名称]
d1-->e2[<font size=6>项目负责人签名]
d1-->e3[<font size=6>报销人签名]
d1-->e4[<font size=6>审核人签名]
start-->a2[<font size=6>2.填写报销单]
a2-->b2[<font size=6>项目负责人审核通过]
b2-->c3[<font size=6>打印报销单]
start-->a3[<font size=6>3.获取入库单]
a3-->a3b1[<font size=6>锐竞平台下单]
a3b1-->a3c1[<font size=6>...]
a3c1-->a3d1[<font size=6>在结算页面打印入库单]
b1--<font size=6>否-->c2[<font size=6>发票退回发票源更正]
c2-->a1
classDef className fill:#f9f,stroke:#333,stroke-width:4px
class start,a1,a2,a3 className;

Mermaid in RMD

---
title: "Untitled"
author: "Me"
output: html_document
---

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knitr::opts_chunk$set(echo = TRUE)

## R Markdown
This is an R Markdown document. 

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library(DiagrammeR)
mermaid("
graph LR
	A-->B
")

• r - How to include DiagrammeR/mermaid flowchart in a Rmarkdown file - Stack Overflow
• 4.15 Create diagrams | R Markdown Cookbook

• Node shapes

• See GitHub - mermaid-js/mermaid: Generation of diagram and flowchart from text in a similar manner as markdown
  • Node shapes
    • Round, ()
    • Default/Rectangle, []
    • Rectangle with round corners, {}
  • A node with text
    • It is also possible to set text in the box that differs from the id. If this is done several times, it is the last text found for the node that will be used. Also if you define edges for the node later on, you can omit text definitions. The one previously defined will be used when rendering the box.

Default

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graph LR
    id1[This is the text in the box]

A node with round edges

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graph LR
    id1(This is the text in the box)

A stadium-shaped node

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graph LR
    id1[[This is the text in the box]]

A node in a cylindrical shape

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graph LR
    id1[[This is the text in the box]]

A node in the form of a circle

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graph LR
    id1((This is the text in the circle))

A node in an asymmetric shape

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graph LR
    id1>This is the text in the box]

A node (rhombus)

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graph LR
    id1{{This is the text in the box}}

Parallelogram

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graph LR
    id1[/This is the text in the box/]

Parallelogram alt

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graph LR
    id1[\This is the text in the box\]

Trapezoid

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graph LR
    A[/Christmas\]

Trapezoid alt

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graph LR
    B[\Go shopping/]

Line connection without arrow

• r - Line connection (instead of arrow) in mermaid - Stack Overflow

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graph LR
    a --- b

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graph LR
    a --> b
	b --> a

Pie graph

• The text color in legend is in black color, and the text will be hidden when with dark backgroud.

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pie title Pets adopted by volunteers
"Dogs" : 386
"Cats" : 85
"Rats" : 15

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pie title Pets adopted by volunteers
"Dogs" : 386
"Cats" : 85
"Rats" : 15

西部世界

• 西部世界第一季(Westworld Season 1)迅雷下载|爱美剧

• 西部世界第二季(Westworld Season 2)迅雷下载|爱美剧

• 西部世界第二季全集Westworld迅雷下载_天天看美剧

    ed2k://|file|%E8%A5%BF%E9%83%A8%E4%B8%96%E7%95%8C.Westworld.S01E01.%E4%B8%AD%E8%8B%B1%E5%AD%97%E5%B9%95.WEB-HR.AAC.1024X576.x264.mp4|714294770|101677ebd472dabc5124f417cd35157f|h=suskm54ua52b7gfvzfps5ytfw77asdrc|/
    ed2k://|file|%E8%A5%BF%E9%83%A8%E4%B8%96%E7%95%8C.Westworld.S01E02.%E4%B8%AD%E8%8B%B1%E5%AD%97%E5%B9%95.WEB-HR.AAC.1024X576.x264.mp4|585496569|966a08127e89b5036708ecd14c741266|h=2qnvig2obtv5b3dbg2p5ixfg6ses7tpa|/
    ed2k://|file|%E8%A5%BF%E9%83%A8%E4%B8%96%E7%95%8C.Westworld.S01E03.%E4%B8%AD%E8%8B%B1%E5%AD%97%E5%B9%95.WEB-HR.AAC.1024X576.x264.mp4|586034806|95f67dbfa4ca0fcb8dfeea52946b10e2|h=rkshwktqypqw7s6cxpucwroot76flnuo|/
    ed2k://|file|%E8%A5%BF%E9%83%A8%E4%B8%96%E7%95%8C.Westworld.S01E04.%E4%B8%AD%E8%8B%B1%E5%AD%97%E5%B9%95.WEB-HR.AAC.1024X576.x264.mp4|586881106|6130b84e2cf21cae9ba341ad574318eb|h=5whwta2slwfrzqkkflsiht2kmjfp6nq3|/
    ed2k://|file|%E8%A5%BF%E9%83%A8%E4%B8%96%E7%95%8C.Westworld.S01E05.%E4%B8%AD%E8%8B%B1%E5%AD%97%E5%B9%95.WEB-HR.AAC.1024X576.x264.mp4|566623388|08c3f798ae2b43f8be269cbe8a22f9d7|h=zz6scixon66altxzqta2eeiooh4dxren|/
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Index of Calibre

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//*[re:test(., "^\s*[故事第卷][0123456789一二三四五六七八九十零〇百千两]*[章回部节集卷].*", "i")]

/media/ht/ht_5T/eBooks/名著/Not_Classified/十日谈.txt

Working directories

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i=/media/ht/ht_5T/Work/Projects/NFE/Publication/HSV/HSV_Nrf2_Fig_20210105_1709.pptx
setsid wps ${i}
#
i=/media/ht/ht_5T/Work/Conferences/Other_Meetings/20210220_同学会/Flu.pptx
setsid wps ${i}
#
i=/media/ht/ht_5T/Database/Atlas/World_Atlas.pdf
setsid okular ${i}
#
i=/media/ht/ht_5T/Database/Atlas/
pcmanfm -n ${i}; cd ${i}
#
i=/media/ht/ht_5T/Work/References/eBooks/Virology/Taxonomy/ICTV_Master_Last.xlsx
setsid wps ${i}
#

Flu

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i=/media/ht/ht_5T/Work/Conferences/Other_Meetings/20210220_同学会/Flu.pptx
setsid wps ${i}
#
i=/media/ht/ht_5T/Work/Conferences/Other_Meetings/20210220_同学会/
pcmanfm -n ${i}; cd ${i}
#

• Viral Load Kinetics of SARS-CoV-2 Infection in First Two Patients in Korea - PubMed
• SARS-CoV-2 detection, viral load and infectivity over the course of an infection - Journal of Infection
• SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis - The Lancet Microbe
• Viral kinetics of SARS-CoV-2 over the preclinical, clinical, and postclinical period - ScienceDirect
• RT-PCR Testing
• Real-time RT-PCR in COVID-19 detection: issues affecting the results

Working directories

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i=/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Rev_2
pcmanfm -n ${i}; cd ${i}
#

Working directories

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i=/media/ht/ht_5T/Work/Projects/Phage/Summary
pcmanfm -n ${i}; cd ${i}
#