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Number of PubMed papers

December 7th, 2017

From 2000 and 2010, the number of PubMed citations had grown from half million to 1 million. Today we see ~3,000 new papers everyday!

PubMed citations doubles in 10 years

PubMed citations doubles in 10 years

Year Number
2016 1258608
2015 1253004
2014 1201621
2013 1146180
2012 1085504
2011 1017939
2010 940347
2009 875631
2008 835283
2007 784836
2006 746487
2005 699162
2004 638433
2003 593404
2002 564380
2001 546100
2000 531703
1999 492961
1998 473304
1997 455641
1996 457788
1995 448124
1994 437709
1993 426674
1992 417191
1991 412490
1990 410185
1989 402163
1988 386534
1987 367462
1986 349127
1985 334843
1984 317837
1983 309102
1982 295041
1981 283253
1980 280186
Author: Xu Cui Categories: writing Tags:

How much do we know about the universe? Hubble’s Ultra Deep Field Experiment

September 13th, 2017

When we looked at the space at night, we see a lot of stars, dotted on a vast dark space. But is there anything in the dark area?

Guess, in the photo below, how many stars are in the red circle? None? A few? A few thousand? Billions of stars?

How many starts in the red circle?

How many starts in the red circle?

In 2002-2004, Hubble telescope zoomed in this region and found, in this seemingly empty space, there are not 10 stars, 1000 stars, but at least 3,000 galaxies each with hundreds of billions of stars!

There are 3 thousand galaxies with trillions of stars

There are 3 thousand galaxies with trillions of stars

What do we know about the universe?

Author: Xu Cui Categories: opinion, writing Tags:

[Tool] How To Convert Image To Text (OCR)

September 9th, 2017

You are reading a book or article online, and want to copy/paste a few sentences. But then you realize the book or article prevents you to copy, or maybe the book/article is an image. Instead of typing the sentences, you can use a tool to automatically recognize texts in image and convert for you.

“structurise” is such a tool. Unlike other online tools, you can paste your image into structurise directly, instead of saving the image to a file and uploading it. So it really make your workflow fast:

http://www.structurise.com/screenshot-ocr/

A short demo recorded by myself (in Chinese)

Author: Xu Cui Categories: web, writing Tags:

PubMed 有中文版啦!

April 18th, 2017

PubMed是生物和医学领域必不可少的搜索引擎,每天百万名医生、教授、学生及其他科研人员等都会通过PubMed搜索自己感兴趣的科学文献、病例、综述、最新进展等。

可惜,PubMed是全英文的!!!

为了让中国的医生、科研人员、学生等能更迅速地从PubMed搜寻信息,我们Stork开发了这款 PubMed中文版。

您可以用中英文关键词搜索。中文关键词(比如“皮肤癌”)会自动被翻译成英文。搜索的结果用中英文显示,期刊根据影响因子高亮显示:

您点开一篇文献后,PubMed中文版会把摘要也翻译出来,方便您快速掌握文章内容,以节省您的宝贵时间:

您可能会问,这是机器还是人工翻译的?答案是具有深度学习能力的人工智能!

怎么访问这个网站呢?PubMed中文版的网址是 https://www.storkapp.me/pubmed/。这是Stork的高级功能,需要注册Stork账户并购买这个功能。

Author: Xu Cui Categories: deep learning, stork, writing Tags:

Stork是我最好的科研助手(2):经费提醒

August 11th, 2016

Stork

Stork

1. 我的导师是否有经费?
2. 我在寻找博后的职位;我未来的老板是否有足够的经费支持我?
3. 有多少经费拨给了我的研究领域(比如NIRS)?谁得到了这些经费?他们将用这些经费做什么?

你是否也曾考虑过这些问题?当我还是一个研究生的时候,我很少问这些关于“钱”的问题。“钱”似乎并不是一个“真正”的科学家应该在意的事。而当我得知我的导师为经费申请花着大半部分时间的时候,我更加疑惑了,他难道不应该把时间用在做实验以及撰写论文上吗?

当我开始博后研究时,我发现自己同样花费很多时间申请经费。我也逐渐意识到我的未来科研事业是否成功,很大一部分是由我是否能有足够稳定的经费支持来决定的。我见到一些同事,由于缺少经费不得不离开科研界。我想到如果能有一个工具及时提醒我当下的经费拨款情况,我的科学研究应当可以更加有的放矢。

Stork 就是这样一个工具。

我在Stork里输入如下关键字,“pearl chiu”(我之前同事的名字)以及“NIRS brain”(我的研究领域)。以下是Stork发给我的邮件:

Stork notifies me of awarded grants

Stork告知我获得拨款的研究者

有了Stork提供的信息,我了解了在我的研究领域,谁得到了经费以及他们打算用这笔经费做什么研究。实际上邮件里的第三个基金是拨给我的同事Manish, 用于他进行利用NIRS对静息状态下的脑回路的研究。我还看到Pearl得到了很大一笔经费,所以我给她发送了一封祝贺邮件。与Stork的另一个功能论文提醒比起来,经费提醒让我更早的对自己研究领域的趋势了如指掌。得到经费支持的研究,通常需要几年之后才有相关论文发表出来。

如果你也想变成第一个在你领域知道有哪些新经费颁发的人,快去试试Stork你一定会发现很多惊喜!

Author: Xu Cui Categories: brain, programming, stork, web, writing Tags:

Stork is my best research assistant (2): Grant alert

April 15th, 2016

Stork

Stork

  1. Does my boss have money?
  2. I am looking for a postdoc position; does my future boss have enough funding to support me?
  3. How much money was awarded to my field (e.g. NIRS)? And who got the money? What are they going to do with the money?

Have you ever wondered these questions? In the early years as a graduate students, I rarely asked “money” questions. It does not sound what a “true” scientist should care.  I was even puzzled when I realized my boss spent more than half of his time writing grant applications - shouldn’t he spend most of his time doing experiments and write papers?

As a postdoc I found myself spend a lot of time writing grant applications; and realized my career is critically depending on the success of securing enough funding. I also see a few colleagues had to leave academia due to lack of funding.  It would be nice if there is a tool which can notify me of the funding situation in a timely manner.

Stork is such a tool.

I entered some keywords into Stork, including “pearl chiu” (my former colleague) and “nirs brain” (my research field). Below is a letter I got from Stork:

Stork notifies me of awarded grants

Stork notifies me of awarded grants

With the information Stork provides, I know who in our field got grants and what they proposed. In fact the 3rd one is my colleague Manish who is interested in using NIRS in resting-state brain network study. I also got to know Pearl got a big gran, so I sent her a congratulation note.

Compared to journal papers alert, grants alert helps me to know the trend of my field much earlier. This is because publications are usually a few years delayed from grants.

If you also want to be the first one to know new grants in your field, why don’t you give Stork a try? I’m sure you’ll be delighted!

Author: Xu Cui Categories: brain, life, programming, stork, web, writing Tags:

Stork is my best research assistant

December 18th, 2015

Stork

Stork

When I was a graduate student at Baylor College of Medicine, I found myself often in an embarrassing situation — I felt completely lost when my fellow graduate students heatedly discussed a paper in our field but I never heard of this publication at all. Later a PubMed search revealed that this paper was indeed published more than a year ago!

There was even a time when I didn’t know my own boss had a new publication. It was in part because I was in a big lab and I was not involved in that project. But still, I felt like I didn’t fulfill my duty as an up-to-date young researcher.

My problem was finally resolved several years later when we developed the Eye function in Paperbox, which is now renamed Stork. Stork is pretty easy to use. What I need to do is to simply enter all my keywords and researchers’ names and Stork takes care of everything. Stork will help me perform the search every day and send me the results. After using Stork, now I’m the first one in the lab to know that “The most renowned David Boas has a new publication” or “There’s another group using NIRS to hyperscan”. I never embarrass myself again and gain a lot of confidence.

I have more than 50 keywords. You may ask “will Stork send you 50 emails a day?” Not at all because Stork respects my inbox. It will compile all results into one email.

Stork is also smart. As a researcher, I am sometimes overwhelmed by the flood of publications and have headache in determining which ones are worth reading. Stork helps! She will mark the impact factor of each publication with the yellow color. The more yellow, the higher the impact factor. Therefore I only need to read top publications when I am busy.

If you also want to be the first one to know new publications in your field, why don’t you give Stork a try? I’m sure you’ll be delighted!

Below is one sample email Stork sent to me.

Stork Sample Email

Stork Sample Email

Below are some of the key words I’ve been using. Anyone work on NIRS and fMRI can borrow:

  1. (fumiko hoeft) AND ((university of california) OR stanford)   
  2. (jian li) AND ((phelps) OR montague OR (Peking University psychology))   
  3. baldwin Philip   
  4. brooks king-casas   
  5. cell[ta] fmri   
  6. chao liu, beijing normal university   
  7. chess stetson   
  8. David Boas   
  9. David Hong stanford   
  10. dongni yang baylor   
  11. eagleman dm [au] baylor   
  12. fmri deception   
  13. fmri resting state parent child   
  14. hanli liu, university of texas   
  15. Hosseini, S M Hadi   
  16. hyperscanning   
  17. iphone   
  18. Jack Gallant   
  19. Kendrick Kay   
  20. koniku   
  21. lumosity   
  22. montague pr [au] baylor   
  23. montague pr[au] Virginia Tech   
  24. MyConnectome   
  25. nature[ta] fmri   
  26. ning gao, tsinghua   
  27. nirs brain   
  28. nirs deception   
  29. nu zhang, washington   
  30. pearl chiu   
  31. reiss al [au] stanford   
  32. rory sayres   
  33. Russell Poldrack, stanford   
  34. saggar manish   
  35. science[ta] fmri   
  36. signe bray   
  37. smart phone brain   
  38. social nirs   
  39. stanford kesler shelli   
  40. ting ni   
  41. xianchun li, “East China Normal University”   
  42. xiaolin zhou[au] peking   
  43. xu cui AND (stanford OR baylor OR Texas)   
  44. xu q[au] harvard   
  45. yan song[au] stanford   
  46. yangming wang, peking   
  47. yufeng shen [au]   
  48. yulong li (stanford or Peking)   
  49. zen meditation   
  50. zhu chao-zhe beijing   
Author: Xu Cui Categories: brain, life, programming, stork, web, writing Tags:

Hyperbolic discounting emerges from the scalar property of interval timing

June 7th, 2011

Ten dollars today is more attractive than the same amount of money tomorrow and is consistent with the well known proverb, “a bird in the hand is worth two in the bush”. We all know that the value of a reward is discounted over time. How the value discounts over time and what is the rationale for such discounting, however, is less clear. Here is my version of explanation.

http://www.frontiersin.org/integrative_neuroscience/10.3389/fnint.2011.00024/full

Author: Xu Cui Categories: brain, writing Tags:

How to create TIFF files

November 13th, 2009

When you submit a manuscript, many journals ask you to send your figures in TIFF format with some requirements such as 300dpi, flattened, LZW compressed, etc. How to do that?

My figures are usually finalized in MS PowerPoint. I don’t use PowerPoint’s own “save image as …”  b/c it’s not flexible. I use Adobe Photoshop.

  1. Group and copy the figure in PowerPoint
  2. Launch PhotoShop, File | New to create a new image. Don’t forget to set Resolution to 300 pixels/inch (dpi). Background is white. Then click OK.
  3. Paste your figure.
  4. (optional) do some cropping, trimming …
  5. File | Save As, select “TIFF” as saving format; uncheck “Layers” (i.e. flatten your figure), click Save
  6. Check “LZW” compression
  7. OK.
Author: Xu Cui Categories: writing Tags:

Writing tips

November 20th, 2008
  1. The knowledge of brain-function mapping is accumulated …
    The Knowledge of brain-function mapping is accumulated … (get rid of the in front of knowledge)
  2. Don’t start a sentence with it, this. Instead, specify what it is.
  3. Don’t start a paragraph with “at the same time”. At the same time of what?!
  4. When writing a grant/fellowship, use their language (e.g. if they say ’specific plans’, you should not say ’specific aims’
  5. Use ‘brain disorder’ instead of ‘mental disorder’ (well, this should depend on the context)
  6. The overarching goal of this study is to develop …
  7. Success in the enterprise will provide important theoretical and clinical insights and will launch future interdisciplinary basic, clinical, translational pediatric neuroscience research.
Author: Xu Cui Categories: writing Tags: