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Medical school letters of recommendation have formally been replaced by tweets

Posted: April 29, 2010 at 8:16 am

Doctor_V's tweets in Brizzly (click to enlarge the image) - read from the bottom of the screenshot.

If you are a medical school I highly suggest you admit @beccacamp [email protected] I don't know if Mayo School of Medicine takes Twitter recommendations but I formally recommend @beccacamp. Medical school letters of recommendation have formally been replaced by tweets.

Indeed. And if the tweets are by Doctor_V, they should be strongly considered in the admission process... 🙂

Posted at Clinical Cases and Images. Stay updated and subscribe, follow us on Twitter and connect on Facebook.

Recommendation and review posted by G. Smith

Ventricle Vase

Posted: April 29, 2010 at 8:16 am

Ventricle Vase designed by eva milinkovic

Ventricle Vase designed by eva milinkovic

This gorgeous vase, designed by Eva Milinkovic of Ontario-based Tsunami Glassworks, does a wonderful job of representing the beauty and flux of emotion attributed to the heart.  Eva is actually the creative director of Tsunami Glassworks and imbues each piece she does with her passion for “bright colors, organic, fluid forms and tactile objects.”

[thanks to everyone who submitted this beautiful piece!]

Recommendation and review posted by G. Smith

"Excellent Old-School Science Models," Life Magazine Photo Gallery

Posted: April 29, 2010 at 8:16 am

The images you see above--and the captions below--are drawn from a really fantastic Life Magazine online photo gallery entitled "Excellent Old-School Science Models." You can see the entire gallery of 29 images--well worth your perusal!--by clicking here.

Captions top to bottom, as supplied by the gallery:

  1. Isn't She Lovely: Trainee nurses examine a model of a human body to learn anatomy, Gerry Cranham, Oct. 7, 1938
  2. Behind It All: A technician works on life-like models for use in science and health lectures at the Cologne Health Museum in Germany, Ralph Crane, Feb 01, 1955
  3. Going Deep: A technician at the Cologne Health Museum gets into his work, Ralph Crane, Feb 01, 1955
  4. The Egg Factory: An exhibit illustrates the biology of the chicken at the World Poultry Exhibition at the Crystal Palace exhibition hall in London, Fox Photos, Jul 28, 1930
  5. Universal: A girl scout leans in to take a closer look at an enclosed model of the solar system, circa 1920s, George Eastman House, Jan 01, 1920

Found via Morbid Anatomy Library intern Amber Duntley's Facebook feed. Thanks, Amber!

Recommendation and review posted by G. Smith

Production of ethanol from winter barley by the EDGE (enhanced dry grind enzymatic) process

Posted: April 29, 2010 at 8:16 am

US legislation requires the use of advanced biofuels to be made from non-food feedstocks. However, commercialization of lignocellulosic ethanol technology is more complex than expected and is therefore running behind schedule. This is creating a demand for non-food, but more easily converted, starch-based feedstocks other than corn that can fill the gap until the second generation technologies are commercially viable. Winter barley is such a feedstock but its mash has very high viscosity due to its high content of -glucans. This fact, along with a lower starch content than corn, makes ethanol production at the commercial scale a real challenge.
A new fermentation process for ethanol production from Thoroughbred, a winter barley variety with a high starch content, was developed. The new process was designated the EDGE (enhanced dry grind enzymatic) process. In this process, in addition to the normal starch-converting enzymes, two accessory enzymes were used to solve the beta-glucan problem. First, beta-glucanases were used to hydrolyze the beta-glucans to oligomeric fractions, thus significantly reducing the viscosity to allow good mixing for the distribution of the yeast and nutrients. Next, beta-glucosidase was used to complete the beta-glucan hydrolysis and to generate glucose, which was subsequently fermented in order to produce additional ethanol. While beta-glucanases have been previously used to improve barley ethanol production by lowering viscosity, this is the first full report on the benefits of adding beta-glucosidases to increase the ethanol yield.
In the EDGE process, 30% of total dry solids could be used to produce 15% v/v ethanol. Under optimum conditions an ethanol yield of 402 L/MT (dry basis) or 2.17 gallons/53 lb bushel of barley with 15% moisture was achieved. The distillers dried grains with solubles (DDGS) co-product had extremely low beta-glucan (below 0.2%) making it suitable for use in both ruminant and mono-gastric animal feeds.

Recommendation and review posted by G. Smith

Reaction Attempts Book Edition 1 and UsefulChem Archive

Posted: April 28, 2010 at 8:47 pm

I am pleased to report that Andrew Lang and I have published the first edition of the Reaction Attempts book. It currently contains most of the Ugi reactions from the UsefulChem project and is associated with an April 27, 2010 snapshot archive of the entire UsefulChem project, including NMR spectra, spreadsheets, images and the entire lab notebook from Wikispaces.

At 582 pages the printing cost from LuLu amounts to $26.28. Not meant to replace electronic searches, it should prove to be a handy reference book for the lab to quickly browse through what was attempted for a given reactant, what the outcome was and the researcher involved.

We are hoping to include reaction attempts from other groups in future editions. More details can be found in the preface, reproduced below:

Reaction Attempts First Edition

Data Source: the UsefulChem project


Open Notebook Science (ONS) refers to the practice of making the full contents of a laboratory notebook and all associated raw data files available in near real time.[1] This represents an opportunity for everyone to benefit from work in progress in an open research group. However, in order to make use of the information, it must be easily discoverable. A simple strategy to increase discoverability is redundancy over multiple communication platforms.

In another project - the Open Notebook Science Solubility Challenge[2] - we published non-aqueous solubility data in the form of physical and downloadable (PDF) books.[3] Although it is possible to search the solubility database using web query interfaces, exploration of a Google Spreadsheet, an XML feed, etc.[4], having a physical copy in the laboratory has proved to be very convenient in several instances. A similar format for reactions will also be useful.

The UsefulChem Project

UsefulChem started in 2005 as an organic chemistry Open Notebook Science project with a main goal of discovering new anti-malarial agents that can be prepared by simple and cheap syntheses.[5] Most of the reactions on UsefuChem are Ugi reactions, which involve the mixing of an amine, aldehyde, carboxylic acid and isonitrile in a solvent at room temperature generally for a few hours to days.[6] The multicomponent design of the Ugi reaction and the simple reaction conditions make it ideal for exploring large virtual libraries and selecting compounds of interest to make.[7]

Isolation of the Ugi products can be immensely simpler, cheaper and readily scalable if they precipitate in pure form from the reaction mixture. To this end, much of the research in the UsefulChem project focuses on reaction conditions that lead to this outcome.[8] This is in fact the origin of the ONS Solubility Challenge discussed above.[9]

The Reaction Attempts Database

In order to look for patterns in the reaction conditions which led to Ugi product precipitation, the CombiUgiResults Google Spreadsheet was set up.[10] Reactions indexed there can be sorted by precipitation outcome, solvent, reactant, concentration, etc. and links to the laboratory notebook pages can be followed for full details. However, this sheet is designed specifically for Ugi reactions and contains columns specifically for the aldehyde, amine, carboxylic acid and isonitrile.

In order to enable the tracking of other types of reactions, the information in the CombiUgiResults sheet was reformatted into two other sheets: ReactionAttempts[11] (containing reagents and reactants) and RXIDsReactionAttempts[12] (containing reaction conditions and results, such as solvent, concentration of limiting reactant, appearance of a precipitate, yield, etc.). The two sheets are connected via the use of a common ReactionID. This format permits the representation of any type of reaction, with an unlimited number of reactants and products.[13]

By definition, any Open Notebook Science project in a work in progress. The listing of a reaction in this database only means that the researcher attempted or is in the process of attempting it. Whatever the situation, a link to the laboratory notebook page is provided, where the most recent information is available. The philosophy used here is that partial information is always better than no information at all. Thus a researcher investigating the prior use a particular reactant in a Ugi reaction might find the report that a precipitate was obtained in methanol helpful for designing their own reactions, even if the characterization of the precipitate is still pending. At the very least, knowing that a certain researcher has at least attempted a similar reaction is enough information for initiating a discussion, which may lead to valuable insights.

Reaction Attempts on Chemspider

Although SMILES[14] are provided in the spreadsheets, the primary key to identify compounds is the ChemSpider ID (CSID)[15]. This allows us to render molecule images in the book automatically. In the case of the ONS Solubility Challenge book[3], use of the CSID enables a convenient way to calculate various descriptors for displaying values in the book.

In addition, the compounds in the Reaction Attempts database are indexed on ChemSpider as two Data Sources: ReactantsAttemptedReactions and ProductsAttemptedReactions[13]. In this way a substructure search for either reactants or products will identify indexed molecules. Clicking on the Syntheses tab in the ChemSpider record for a selected molecule will then reveal a list of hyperlinks to the relevant laboratory notebook pages.

Organization of the Book

In keeping with the layout of the ONS Solubility Challenge Book, the reactants are listed in alphabetical order. Each entry displays the list of reactions where the reactant was used. This includes a scheme with all reactants and product as well as key metadata: the researcher, reaction type, solvent, limiting reactant concentration, observation of a precipitate, comments and a reference (links to the laboratory notebook page).

In this edition, only Ugi reactions are included. The reaction schemes are laid out in the following order: carboxylic acid, amine, aldehyde and isonitrile. This should allow for easy comparison between schemes within a given record. Reactions where the Ugi product was isolated and characterized are marked with a green check and the percent yield is noted. Since the Ugi products do not have simple common names, they are not included as separate entries. However, all reactions where the synthesis of a specific Ugi product was attempted can be found by looking up the entries for any of the four reactants.

Although this compilation is not exhaustive, it does cover the vast majority of reactions in the UsefulChem project to date. Future editions will include other reactions from UsefulChem and other sources.


This edition is linked to the UsefulChem data archive (ZIP)[16], (DVD)[17] and interactive hosted archive format[18], ReactionAttempts (XLS)[19] and RXIDsReactionAttempts(XLS)[20] taken on 2010-04-27.


1. Open Notebook Science Wikipedia Entry
2. Open Notebook Science Solubility Challenge Wiki
3. Bradley, J.-C. First Edition of ONS Solubility Challenge Book UsefulChem Blog (2009)
4. Open Notebook Science Solubility Challenge List of Experiments page
5. UsefulChem Wiki
6. Ugi Reaction Wikipedia Entry
7. Dömling, A., & Ugi, I. (2000). Multicomponent Reactions with Isocyanides. Angewandte Chemie International English Edition, 39(18), 3168-3210.
8. UsefulChem List of Experiments
9. Bradley, J.-C. Open Notebook Science Challenge UsefulChem Blog (2008)
10. CombiUgiResults Google Spreadsheet
11. ReactionAttempts Google Spreadsheet
12. RXIDsReactionAttempts Google Spreadsheet
13. Bradley, J.-C. Reaction Attempts on ChemSpider UsefulChem Blog (2010)
14. SMILES Wikipedia Entry
15. ChemSpider Web Site
16. UC archive Drexel server (ZIP)
17. UC archive on (DVD)
18. UC interactive hosted format
19. Bradley, J.-C.; Lang, A.. Reaction Attempts Reactants and Products. UsefulChem. 2010-04-27.

(Archived by WebCite® at
20. Bradley, J.-C.; Lang, A.. Reaction Attempts RXIDs. UsefulChem. 2010-04-27.
(Archived by WebCite® at

Recommendation and review posted by G. Smith

Progress in Adoptive Immunotherapy

Posted: April 28, 2010 at 8:16 am

Via EurekAlert!: "Adoptive immunotherapy is targeted to situations when the immune system fails to detect a disease [such as cancer]. The adoptive immunotherapy strategy is to harvest T cells from the patient, engineer them to spot the disease and then send them back in, like police detectives with a reliable tip. A major drawback, however, has been that the T cells still need to call for back-up forces from a variety of other cell types in the body, but they can't. They die out quickly without doing enough good. The new approach is to further engineer the T cells to be able to support themselves rather than relying on other immune cells [and] to insert the ability to switch that self-support on or off, to ensure that they don't grow out of control. That way, the T cells can persist in fighting the disease without becoming a cancer themselves. ... This is an integration of a cell-based therapy application with new synthetic biology tools that have come up from foundational research. ... Generally, the results showed that their engineering produced healthier, faster-growing populations of the T cells, until the drugs were withdrawn and growth shut down. In the human cell cultures, for example, the technology led to a 24 percent increase in the live T-cell population compared to controls and 50 percent fewer cells dying off."

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Recommendation and review posted by Fredricko

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