I have to check every detail of on Safari document pages …
Evently, I made it!

Here it is, pubmeder for Safari
pubmeder-v01.safariextz (unzip and drag it to your Safari window)
Also, you can get it from either mirror1 or mirror2. If you know how to submit to Apple’s Safari Extensions Gallery, let me know …

I have put a nice setting page under Safari – Preferences – Extensions

You can either copy&paste the apikey from the email you got when you register or visit http://pubmeder.appspot.com/registration and the extension will extract the info by itself – smart ha

Oh, by the way, I also implant an email processor on pubmeder.appspot.com

to: input@pubmeder.appspotmail.com
subject: containing word pubmeder
body: only containing pmid list

Something like the following will do

The items will be processed and entered into your account / sender’s email.

Anyway, enjoy pubmeder and let me know what do you think. There is no extension or add-on capability for IE, right?

© 2010 Endogenous - CaiLog. blogged by cail.cn - 35cd076bdd09fcbdfe7ca24eb8f93900

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Rat iPS into mouse Pdx1-/-, very nice design!

Cell. 2010 Sep 3;142(5):787-99.
Generation of rat pancreas in mouse by interspecific blastocyst injection of pluripotent stem cells.
Kobayashi T, Yamaguchi T, Hamanaka S, Kato-Itoh M, Yamazaki Y, Ibata M, Sato H, Lee YS, Usui J, Knisely AS, Hirabayashi M, Nakauchi H.

Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Japan Science Technology Agency, ERATO, Nakauchi Stem Cell and Organ Regeneration Project, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

The complexity of organogenesis hinders in vitro generation of organs derived from a patient’s pluripotent stem cells (PSCs), an ultimate goal of regenerative medicine. Mouse wild-type PSCs injected into Pdx1(-/-) (pancreatogenesis-disabled) mouse blastocysts developmentally compensated vacancy of the pancreatic “developmental niche,” generating almost entirely PSC-derived pancreas. To examine the potential for xenogenic approaches in blastocyst complementation, we injected mouse or rat PSCs into rat or mouse blastocysts, respectively, generating interspecific chimeras and thus confirming that PSCs can contribute to xenogenic development between mouse and rat. The development of these mouse/rat chimeras was primarily influenced by host blastocyst and/or foster mother, evident by body size and species-specific organogenesis. We further injected rat wild-type PSCs into Pdx1(-/-) mouse blastocysts, generating normally functioning rat pancreas in Pdx1(-/-) mice. These data constitute proof of principle for interspecific blastocyst complementation and for generation in vivo of organs derived from donor PSCs using a xenogenic environment.

PMID: 20813264
DOI: 10.1016/j.cell.2010.07.039

© 2010 Endogenous - CaiLog. blogged by cail.cn - 35cd076bdd09fcbdfe7ca24eb8f93900

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My friend told me this paper. And, it is quite interesting! Spinning disk on whole animal, very neat live imaging!

MARCM analysis
For generating Mira MARCM clones 40, we crossed the analysis line hsFLP70/hsFLP70; worGal4, UAS-Cherry:Jupiter, Sqh:GFP, tubGal80 FRT82B/TM6C, Sb (this work) to Mira FRT82B mirazz178 and heat-shocked the progeny 24–48 h after larval hatching for 1 h at 37 °C. For live imaging, mira mutant clones of third-instar larvae were used.

Pavarotti RNAi experiment
Pavarotti knockdown was achieved by crossing worGal4 (ref. 9) driver line to UAS-PavRNAi46137 (ref. 39). Loss of Pavarotti was confirmed using the anti-Pav antibody 16.

Colcemid experiments
For colcemid experiments, the following strains were used: +; worGal4, UAS-Cherry:Jupiter, Sqh:GFP (this work) or +; worGal4, UAS-Cherry:Jupiter, Sqh:GFP; rodH4.8 (this work).
Wild-type or rodH4.8 mutant neuroblasts were incubated with colcemid in live imaging medium 29 at a final concentration of 0.1 μm ml−1. Live imaging was started without delay. Mild spindle phenotypes became apparent immediately after colcemid exposure, whereas complete spindle depolymerization was seen approximately 30–60 min after colcemid addition.

Imaging, post-imaging procedures and measurements
Live imaging methods were previously described 29. Fixed preparations were imaged on a Leica SP2, and for Supplementary Fig. 1a on a Leica SP5, confocal microscope. Live samples were imaged on a McBain spinning disc confocal microscope equipped with a Hamamatsu EM-CCD (electron-multiplying charge-coupled device) camera, using a ×63 1.4 numerical aperture oil-immersion objective. Pixel intensity measurements (Fig. 1c, d) were performed using ImageJ. Only one-half of the neuroblasts’ cortex was measured starting at the apical cortex and ending at the basal cortex. Post-imaging processing and measurements were performed in ImageJ or Imaris 6.2–7.0 (Bitplane).

Larval staging
For all experiments, late second- or third-instar larvae were used for analysis.

Nature. 2010 Sep 2;467(7311):91-4.
A spindle-independent cleavage furrow positioning pathway.
Cabernard C, Prehoda KE, Doe CQ.

[1] Howard Hughes Medical Institute, University of Oregon, Eugene, Oregon 97403, USA [2] Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA [3] Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403, USA.

The mitotic spindle determines the cleavage furrow site during metazoan cell division, but whether other mechanisms exist remains unknown. Here we identify a spindle-independent mechanism for cleavage furrow positioning in Drosophila neuroblasts. We show that early and late furrow proteins (Pavarotti, Anillin, and Myosin) are localized to the neuroblast basal cortex at anaphase onset by a Pins cortical polarity pathway, and can induce a basally displaced furrow even in the complete absence of a mitotic spindle. Rotation or displacement of the spindle results in two furrows: an early polarity-induced basal furrow and a later spindle-induced furrow. This spindle-independent cleavage furrow mechanism may be relevant to other highly polarized mitotic cells, such as mammalian neural progenitors.

PMID: 2081145
DOI: 10.1038/nature09334

A very interesting point

* More informative were the approximately 11% of pins mutant neuroblasts that had a symmetric spindle and divided symmetrically; all of these neuroblasts lacked Pav/Myosin basal cortical enrichment, lacked basal furrows and never formed ‘polar lobes’

* To increase the percentage of symmetrically dividing pins mutant neuroblasts, we combined pins with a mutation in dlg, which is required for normal spindle asymmetry 9. We found that 100% of the dlg;;pins double mutant neuroblasts showed symmetric spindles, and they all lacked Myosin basal cortical enrichment and basally displaced furrows

* To test if Dlg has a role in the polarity induced furrow pathway, we examined dlg single mutants. Only a small fraction had a symmetric spindle (6%, n = 65); of these neuroblasts, two exhibited basally enriched Myosin (data not show) and two showed symmetric cortical Myosin

In neuroblasts these pathways appear to work partly redundantly.

© 2010 Endogenous - CaiLog. blogged by cail.cn - 35cd076bdd09fcbdfe7ca24eb8f93900

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If you know and use Greasemonkey for Firefox, then just install the user script for pubmeder.appspot.com from http://userscripts.org/scripts/show/85346. In this way, you can modify the domains where you want this script to run. I attach a copy of the script at the end of this post – just some javascript.

Otherwise, install this Firefox Add-on from https://addons.mozilla.org/en-US/firefox/addon/223405/. It is compiled from the user script using an xpi compiler. A local version is here (remember to change the extension from zip to xpi before you drag it into firefox).

Nothing fancy here. Just works.

It records your browsing history and send doi/pmcid/pmid info to the server for future retrieving. Please do visit http://pubmeder.appspot.com/registration first to enable the script sending these info into your account). By default, all the records go to anonymous account, unless you visit the registration page first first!

Enjoy! xoxo

// pubmeder at appspot.com - user script
// version 0.31
// 2010-09-03
// Copyright (c) 2010, Liang Cai
// Released under the GPL license
// http://www.gnu.org/copyleft/gpl.html
//
// --------------------------------------------------------------------
//
// This is a Greasemonkey user script.  To install it, you need
// Greasemonkey from http://greasemonkey.mozdev.org/
// Then restart Firefox and revisit this script.
// Under Tools, there will be a new menu item to "Install User Script".
// Accept the default configuration and install.
//
// To uninstall, go to Tools/Manage User Scripts,
// select "pubmeder at appspot.com", and click Uninstall.
//
// --------------------------------------------------------------------
//
// ==UserScript==
// @ name          pubmeder at appspot.com
// @ namespace     http://pubmeder.appspot.com/
// @ description   send found pmc/doi/pmid on every page to the server
// @ include       *
// ==/UserScript==

// please visit http://pubmeder.appspot.com/registration to get the apikey for your email

if (!GM_xmlhttpRequest) {
    alert('Please upgrade to the latest version of Greasemonkey.');
    return;
}

if ( document.URL == "http://pubmeder.appspot.com/registration" ) {
  var email = document.getElementById('currentUser').innerHTML;
  var apikey = document.getElementById('apikey_pubmeder').innerHTML;
  GM_setValue("pubmeder_apikey",apikey);
  GM_setValue("pubmeder_email",email);
}

var apikey = GM_getValue("pubmeder_apikey");
var email = GM_getValue("pubmeder_email");
var tail = '';
if ((apikey !== undefined) && (email !== undefined)) {
  tail = '&apikey='+apikey+'&email='+email;
}

var currentList = GM_getValue("pubmeder_pmidList");
if (currentList === undefined) {
  currentList = "";
}

window.sendRequest = function(c) {
  currentList += ',' + c;
  d = currentList.split(",");
  new_d = [];
  g:for (var i = 0; i < d.length; i++) {
      if (d[i] === "")
        { continue g; }
      for (var j = 0; j < new_d.length; j++) {
        if (new_d[j] == d[i])
          { continue g; }
      }
      new_d[new_d.length] = d[i];
    }
  currentList = new_d.join(",");
  // alert(currentList);
  if (new_d.length > 9) {
    var urlurl = 'http://pubmeder.appspot.com/input?pmid=' + currentList + tail;
    GM_xmlhttpRequest({
      method: "GET",
      url: urlurl,
      onload: function(response) {
        if (response.responseText) {
          // alert(response.responseText);
          var logo = document.createElement("div");
          logo.innerHTML = '<div style="margin:0;padding:0;height:4px;background:#fdd;">&nbsp;</div>';
          document.body.insertBefore(logo, document.body.firstChild);
          GM_setValue("pubmeder_pmidList","");
        }
      }
    });
  } else {
    var logo = document.createElement("div");
    logo.innerHTML = '<div style="margin:0;padding:0;height:4px;background:#ddf;">&nbsp;</div>';
    document.body.insertBefore(logo, document.body.firstChild);
    GM_setValue("pubmeder_pmidList",currentList);
  }
};

window.esearchsend = function(b) {
  var url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&tool=pubmeder&email=i@cail.cn&term=' + b;
  GM_xmlhttpRequest({
    method: "GET",
    url: url,
    onload: function(xml) {
      var parser = new DOMParser();
      var dom = parser.parseFromString(xml.responseText,"application/xml");
      var xid = dom.getElementsByTagName("Id");
      if (!xid[1]) {
        sendRequest(xid[0].firstChild.nodeValue);
      }
    }
  });
};

var a = document.body.innerText;
if (a === undefined) {
  a = document.body.innerHTML;
  var regExp = /<[^>]+>/gi;
  a = a.replace(regExp,"");
}

var regpmid = /pmid\s*:?\s*(\d+)\s*/i;
var regdoi = /doi\s*:?\s*/i;
var doipattern = /(\d{2}\.\d{4}\/[\w./]+\w)\s*\W?/;
var regpmc = /pmcid\s*:?\s*(PMC\d+)\s*/i;
var ID = "";

if (regpmid.test(a)) {
  ID = regpmid.exec(a);
  sendRequest(ID[1]);
} else if (regdoi.test(a) || doipattern.test(a)) {
  ID = doipattern.exec(a);
  if (ID !== null) {
    esearchsend(ID[1]);
  }
} else if (regpmc.test(a)) {
  ID = regpmc.exec(a);
  esearchsend(ID[1]);
} else {
  // no pattern matched
}

© 2010 Endogenous - CaiLog. blogged by cail.cn - 35cd076bdd09fcbdfe7ca24eb8f93900

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这里可以下载整个杂志
而那篇《你们去卅城》的扫描版就帖这里了

© 2010 Endogenous - CaiLog. blogged by cail.cn - 35cd076bdd09fcbdfe7ca24eb8f93900

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© 2010 Endogenous - CaiLog. blogged by cail.cn - 35cd076bdd09fcbdfe7ca24eb8f93900

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• safari extension
• firefox add-on
• high CPU on /list or /api operation (better usage of memcache and __KEY__ query)
• tagging for multiple list export
• drag to order the export sequence
• full-abstract search
• delete an item by user
• better UI
• in chatbot, /term gets multiple article titles, /list shows user specific top-5

http://pubmeder.appspot.com/ is pretty easy to use. Let these screen capture to tell you what this web app can do.

As a bonus of using Google App Engine, I have an xmpp robot running as well. Add pubmeder@appspot.com as your contact in gtalk, and send something to it. It will respond and tell you what it is capable of.

Enjoy!

© 2010 Endogenous - CaiLog. blogged by cail.cn - 35cd076bdd09fcbdfe7ca24eb8f93900

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