睡覺前還是查一下mailbox, 還沒回音 (CAF index MS)... 明天家裡日曆的每日格言是...

 Jun 23, 2020, 10:01:51 PM

「最困難的時候，就是離成功不遠的時候。」  睡覺去吧!  (31-3)+23=51d

賴亭羽<b002010033@gmail.com>

Jun 24, 2020, 2:18:22 PM

to sflinlab2020

  (31-3)+23=51 d  <- (._.)?

SFL<sflin1@gmail.com>

Jun 25, 2020, 11:22:01 AM

to sflinlab2020

(31-3)+25=53! 您嘛給我醒一醒...推推推...

___________________________________________________________

Jul 10, 2020, 2:23:30 PM

Reviewer#2 名字揭曉!

原來是亭羽JC paper 團隊中，2017年J Exp Medicine的第一作者, 謝謝丹尼爾大大...

Distinct Populations of Inflammatory Fibroblasts and Myofibroblasts in Pancreatic Cancer (PubMed Link)

AK480 R package pcr 定量結果供參

 Related # AK480, AK481, AK482, AP038, Ingrid, TYL

(SFL: 只去掉K2一格數值版本)

(Ingrd 傳統手動版: K2去三格，OKF4去二格，NP460去一格，NP550去二格)

(我是每個RNase7的CT值去扣到HPRT的平均值，這樣之後才有辦法算SD)

  Ingrid: 

結論是K2跟K2_AC顛倒???!!!

OKF4控制組細胞被刺激的RNase7表現都變超弱了???!!!

SFL:

D614G相關

 (from groups.google.com/News Dashboard) (treasureCollection)

News Archives:

• 05/20 Int J Infectious Dis (Dasman Diabetes Institute, Kuwait City, Kuwait) Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? .....Overall, our observation speculates that the S-D614G strains may be more virulent, increasing the severity in infected individuals, especially in Europe where this mutation is prominent (04/02 received, 05/09 revised, 05/20 epub)
• 06/11 Scripps Institute 官網  The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity
• 06/15 His-tag D614G peptide is available ! Shocked.  (tinyurl.com/yafom8xh)
• 06/15 台大陳宜君醫師 (https://youtu.be/Fvd-J1kIOYQ?t=31)
• 06/20 重慶醫科大學@bioRxive The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera
• 06/23 李P@年代向錢看 (https://youtu.be/F-B2HECMDGQ) 
• 哈，這次可能是真呦，李P... 多數病毒學家不是沒事做，是病毒太厲害了!  We shall see...

全球共享流感數據倡議組織  維基百科

GISAID (an acronym standing for Global Initiative on Sharing All Influenza Data) 

https://www.gisaid.org/epiflu-applications/next-hcov-19-app/

D614G 2020/06/20 (n=2893)

突變病毒或對抗體「免疫」據《The Science Times》報道，重慶醫科大學校長黃愛龍團隊於醫學預印平台bioRxiv發表研究論文，當中透露與新發地市場有關的至少3名患者體內，發現原本僅在歐洲流行的D614G突變病毒。團隊其後嘗試以人工方法複製D614G病毒株，以此感染從新冠肺炎康復者體內所抽出、具有抗體的血液樣本。結果顯示，從3名康復者身上所得之血液樣本抗體，均無法有效抵抗D614G突變病毒感染，41個樣本當中甚至有1個對D614G突變病毒幾近完全無效，反映新冠肺炎康復者即使已有抗體，亦不代表能夠對已發生突變的病毒免疫。突變後感染力或增2至10倍。事實上，較早前美國聖地牙哥已有針對D614G突變的相關研究。研究發現，病毒經D614G突變後，刺突蛋白（spike proteins）或有所增加，這關係到病毒感染人體細胞的能力，團隊認為D614G感染人體的效率將提高10倍。重慶亦曾進行類似研究，結果顯示D614G突變的感染力大約增加2.4倍。研究指出病毒經突變後可能增加其感染力，惟報道指相關結果並未經同行審議，亦缺乏臨床數據支持，有關病毒出現突變後感染力、對受感染者影響甚至會否左右潛伏期長短等資料仍有待研究。

第一份測試po文

(From google Groups/sflinlab2020)

成功收到第一份 來自 Gusite Forum 的測試文。

早上一直找不到「建立群組」按鈕，結果先在 @gmail.domain 建立一個新群組，邀請 @g.ntu加入，就成功了

a reply mail from lab account also works

先到 https://groups.google.com/forum/#!newtopic/sflinlab2020

論壇區發表主題  就可以開始玩...

賴亭羽<b002010033@gmail.com>

Jun 23, 2020, 9:17:18 AM

to sflinlab2020

玩...網站? 所以要貼主題的意思嗎?

SFL<sflin1@gmail.com>

Jun 23, 2020, 9:50:31 PM

to sflinlab2020

Yes, post whatever you wish to discuss, record, or show-off here.

The hybrid E/M phenotype of EMT 竟然與 collective migration有關

Survival Outcomes in Cancer Patients Predicted by a Partial EMT Gene Expression Scoring Metric (PubMed Link) 

Jason T George, Mohit Kumar Jolly , Shengnan Xu, Jason A Somarelli, Herbert Levine 

Recent experimental and theoretical evidence suggests that cells can be stably halted en route to EMT in a hybrid E/M phenotype. Cells in this phenotype tend to move collectively, forming clusters of circulating tumor cells that are key tumor-initiating agents. 

上面是昨天寫rebuttal letter讀到Reviewer二號人，指定三篇中的其中一篇(EMT_MLR method)

，abstract上面的話! 有沒有很驚艷?

# 救命paper : 比較三種EMT scoring方法，結論出三種結果相當

Comparative Study of Transcriptomics-Based Scoring Metrics for the Epithelial-Hybrid-Mesenchymal Spectrum

Priyanka Chakraborty, Jason T. George, Shubham Tripathi, Herbert Levine and Mohit Kumar Jolly 覺得這個 corresponding author Jolly 很可疑.. 印度英語是否與英式英語相近? 說 tumour 而非 tumor 即是 tumour

 

 

#DDR1

D614G的最新進展

被地震嚇醒，然後.. 找到知音了 

一整個掃掉被地震嚇醒的擔憂，哈哈哈 原新聞連結如右 tinyurl.com/ya4ydkd3


The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity (bioRxive 06/12)
Lizhou Zhang, Cody B Jackson, Huihui Mou, Amrita Ojha, Erumbi S Rangarajan, Tina Izard, Michael Farzan, Hyeryun Choe
作者群名字看起來像中國人，其實是USA Scripps Research Institute


# (old thought by SFL) 這個點與ACE2結合區離得蠻遠的，看得出來它自成一區，但卻無法猜出分子機轉。另外，D to G 似乎在演化上是理所當然之變...

06/15 原來要這樣講才對... https://youtu.be/Fvd-J1kIOYQ?t=31

# SARS-CoV2

# D614G

Reviewer 3: It will be nice if you can share the codes... (CAF index MS)

• 哎呦我的媽，醜醜的code見得了人嗎?
  
  
  Difference between R MarkDown and R NoteBook
  NoteBook多一個 .html檔，多麽邪魔

2020 ASCO20 Virtual Meeting (05/29-05/31 Scientific)

The ASCO20 Virtual Scientific Program is days away. Follow these tips and access meeting materials to ensure a successful and easy virtual experience.

Test Your Login in Advance

Don’t wait until the sessions start to log in for the first time. Make sure you’ll be able to access meeting content by logging in to the ASCO20 Virtual test page today. As a reminder, your username is sflin1@gmail.com.

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Review the broadcast schedule to free your calendar for sessions you’re interested in. The broadcasts will be showing at am.asco.org from 9:30 AM – 5:30 PM (ET) on May 30 and 31. These sessions will be available on demand two hours after the broadcast.

Access Meeting Materials

Abstracts for the ASCO20 Virtual Scientific Program are now available on ASCO Meeting Library or as downloadable PDFs.

Meeting Videos and Slides will be available on ASCO Meeting Library for all registered attendees beginning May 29.


Read ASCO Daily News for updates before, during, and after the Scientific Program.

Browse the 2020 ASCO Educational Book for a preview of the ASCO20 Virtual Education Program, to be held August 8-10.

2020 ASCO20 Virtual Meeting (08/08-08/10 Education)

2020 ASCO20 Virtual  (HomePage)

Access Meeting Materials

Abstracts for the ASCO20 Virtual Scientific Program are now available on ASCO Meeting Library or as downloadable PDFs.  💖💜🙏🙆🙆🙆

Meeting Videos and Slides will be available on ASCO Meeting Library for all registered attendees beginning May 29.

Read ASCO Daily News for updates before, during, and after the Scientific Program.

Browse the 2020 ASCO Educational Book for a preview of the ASCO20 Virtual Education Program, to be held August 8-10.  💙💚💜💝

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國際會議連結網址

2022 The 20th International Symposium on Epstein-Barr virus (EBV) and Associated Diseases will be held in Siena, Italy, on July 3rd-6th, 2022. (http://www.congressi.unisi.it/ebvconferencesiena/)

2020 EBV20 (Hokkaido, Japan) (Postponed due to pandemics)

2020 AACR56 virtual meeting  04/27-04/28   06/22-06/24

2020 ASCO20 virtual meeting 05/29-05/31 (Scientific) 08/08-08/10 (Education)

2019 ASCO19 (Chicago, USA)  index page

2019 KSHV22 workshop (New York, USA) (Link)

2018 EBV and KSHV 2018 (Link)

• Chicago Airport Shuttle Bus (Link)
• Meeting notes by SFL (index page)

GRC NPC 2018 (Link)

• HKU AoE (Link)
• Meeting notes by SFL (index page)

GRC NPC 2016 (Link)

• Meeting notes by SFL and Ming-Han (index page)

_________________________

Conferences and meetings in EBV Association (U. Sussex, 2018/8/8 註冊) (Link)

Biannual International Symposium on Nasopharyngeal Carcinoma

• 7th 2015 Yogyakarta – Indonesia (Link) (Proceedings of the meeting)
• 6th 2013 Istanbul, Turkey (Link)
• 5th 2011 Penang, Malaysia (Link)
• 4th 2009 
• 3rd 2007
• 2nd 2005
• 1st 2003

2020 AACR Virtual Meeting - II (06/22 ~ 06/24)

Back to search page (較簡潔)

Home for virtual meeting II (https://aacr20vm2.onlineeventpro.freeman.com/)
(MyAACR sflin1 | Gn9)

06/22 10:00-12:20 AM
SESSION PL01 - Opening Plenary Session: Turning Science into Lifesaving Care

2020 AACR Virtual Meeting - I (04/27 ~ 04/28)

AACR 2020 Virtual Meeting I 


Virtual Meeting Announcement site  (find abstracts easier in this site)
Search by "tumor microenvironment" ---->  by Date ----> 04/27 nothing interesting

04/28 (https://www.abstractsonline.com/pp8/#!/9045/session/838)
Evaluating Cancer Genomics from Normal Tissues through Evolution to Metastatic Disease

• 5702 - A spatially resolved single cell atlas of the human breast (Tapsi Kumar & Kai Kessenbrock)

Abstract

The human breast consists of lobules connected to an intricate network of ducts that are surrounded by fatty tissues, designed to produce and transport milk to nourish offspring. Histopathology has identified 10 major cell types based on morphological features but have provided limited information on cell states - the transcriptional programs of cell types that reflect different biological functions. In this study we have generated an unbiased ‘cell atlas’ of the normal human breast to define the cell types and cell states using single cell RNA sequencing and spatial transcriptomics methods. We performed 3’ microdroplet based single cell and nuclei RNA sequencing of 248,687 stromal cells and 89,301 nuclei from 24 women with pathologically normal breast tissues that were collected from mastectomies and reduction mammoplasties. Unbiased expression analysis identified four major cell types: adipocytes, epithelial cells (luminal and basal), fibroblasts and endothelial cells and defined their transcriptional programs. Additionally, 8 minor cell types were identified in the breast, including macrophages, T-cells, natural killer cells, mast cells, pericytes, apocrine cells, neurons and smooth muscle cells. Our data revealed hundreds of novel markers of these cell types and defined their transcriptional programs and cell states. Most cell types had multiple transcriptional programs including luminal epithelial cells (hormone receptor positive and secretory), basal epithelial cells (myoepithelial or basal), endothelial cells (E1, E2, E3), myeloid cells, T-cells and fibroblasts (F1-F4) and provided insight into developmental lineages. We further delineated the spatial organization of these cell types and cell states within the tissue architecture using spatial transcriptomics assay. The breast cell atlas data provides an invaluable normal reference for the research community to understand how normal cell types are reprogrammed in diseases such as breast cancer.