INDEX OF JOURNAL CLUB ARTICLES:


1. Strong Inference -Platt (http://www.sciforums.com/showthread.php?t=73421)

2. HIF-independent regulation of VEGF and angiogenesis by the transcriptional coactivator PGC-1alpha - Arany et al (http://www.sciforums.com/showthread.php?t=78331)

3. Zinc transporters and cancer growth
(http://www.sciforums.com/showthread.php?t=80272)
4. Diversity and evolutionary history of plastids and their hosts (http://www.amjbot.org/cgi/content/full/91/10/1481)

HOT TO READ/WRITE A RESEARCH ARTICLE:
http://www.sciforums.com/showthread.php?t=79053


Is anyone interested in a Biology and Genetics journal club?

The OP could post a thread with the words "Journal Club"+topic in it. A link to a relevant article would be present in the first post and members could read the article and discuss the methods, results, conclusions and critique the same.

It would be useful if the OP presented their critique of the article in the first post, which would give a good take off point for the discussion to start.

If sufficient people are interested in reading an article and discussing it, I'll start the first one, as a trial. I like the Platt (http://www.krisweb.com/biblio/gen_science_platt_1964_stronginference.pdf) paper as a starting point.

The poll will be open for 7 days

I think it might be a good idea to keep this sticky as an index for the Journal club threads.

I hope it leads to discussion. :O

Is this the place to discuss your link or are you making a new thread later?

Be nice to get at least a few more people, I was hoping the paper would be interesting enough to stimulate discussion. :)

Be nice to get at least a few more people, I was hoping the paper would be interesting enough to stimulate discussion. :)

So this is like you assigning homework for all of us, then having a cute little discussion in class about the paper?

Hey, Teach, couldn't you have picked a longer article ...just as I was starting to fall asleep, the damned article ended ...woke me up. :D

Yep, Sam, this is what we need around here ......long homework assignments, then class discussions. When can we expect an article, written by a Muslim, on how America has fucked up all of the biology and genetics research in the world?

Baron Max

So this is like you assigning homework for all of us, then having a cute little discussion in class about the paper?

Hey, Teach, couldn't you have picked a longer article ...just as I was starting to fall asleep, the damned article ended ...woke me up. :D

Yep, Sam, this is what we need around here ......long homework assignments, then class discussions. When can we expect an article, written by a Muslim, on how America has fucked up all of the biology and genetics research in the world?

Baron Max

Would you like to try your hand at critiquing the paper Baron? How about a half page, 12 point, single spaced? :)

Would you like to try your hand at critiquing the paper Baron? How about a half page, 12 point, single spaced?

Only if the paper has ONLY has words that are found in "See Spot Run" and "Cat in the Hat" ...and only a very few of those. Big words, "critiquing", are too hard for me to look up in my dickanary and still keep the story in mind. Pictures help, but still, ..... :D

Sorry, Teach, I won't bother your little homework assignments no more. I'm now in the corner with the dunce cap on, is that okay?

Baron Max

Is anyone interested in a Biology and Genetics journal club?

The OP could post a thread with the words "Journal Club"+topic in it. A link to a relevant article would be present in the first thread and members could read the article and discuss the methods, results, conclusions and critique the same.

It would be useful if the OP presented their critique of the article in the first post, which would give a good take off point for the discussion to start.

If sufficient people are interested in reading an article and discussing it, I'll start the first one, as a trial. I like the Platt (http://www.krisweb.com/biblio/gen_science_platt_1964_stronginference.pdf) paper as a starting point.

The poll will be open for 7 days

Interesting idea, I like it, but don't know if I'm interested in Biology articles. I really like biology! Really, really, but I'm not competent enough in it. I'll see if I can make similar threads in other sciences, if I find the time. Which I don't have at all lately... :(
But I'll keep it in mind.

There is an interest, but you should recruit/abduct more people first.

If I am to participate significantly the papers discussed need to be much more detailed in facts I can learn, not broad generalities, such as "methodology."

For example, I found the following very interesting:

"Peregrine-pharmaceuticals...is developing a monoclonal antibody bavituximab, which targets phosphatidylserine molecules [PS] presented on the outer side of cancer blood vessel cells. PS is only a side-effect, a characteristic of cancerous tissues from which cancer does not benefit. In normal, healthy vascular cells, PS is tightly segregated to the internal side of the cell. This segregation appears to be impaired in many kinds of tumor blood vessels, where PS becomes present on the external side of the cells. This phenomenon was observed in lung, breast, prostate and pancreatic cancer, among others. Monoclonal antibodies that are injected into the blood stream can recognize only targets that are presented on the external side of cells, healthy cells that have PS exclusively on their inner side will be unaffected, while cancer blood vessels would be targeted by the antibody exclusively. ..."

I.e. unlike VEGF drugs (such as very succesful Avastin now being sold) that only arrest the growth of solid tumors (by inhibiting new blood supply) this approach may kill the exisiting tumor. ("chemical surgery" to selectively remove it.) I have learned of at least a dozen other clever ideas for developing "magic bullets" for cancer and other diseases. One for viral infections "works" by keeping the newly made viral particles inside an infected cells "folded up" - to exit thru the cell wall and infect other cells, most viral particles need to "unfold" and become more linear, or spear like. I.e.they are trapped in the jail of the cell they were born in, greatly reducing their rate of infection and adding the body's defenses get the upper hand to eliminate them. Also many great idea for heart and arterial problems are now in the labs. Humans are about to enter an exciting new age of medicine and not only because of the new understanding of DNA etc.

Summary: If I am to actively particiapte, the papers will need to be about exploitable facts which can help in major medical problem areas. (I love to learn in any scientific area, but it can also be useful economically to recognize some things before everyone dose.) Do not take the above as a recommendation to invest in PPHM - they will may never get their developmental drug, bavituximab, to market. (Most early stage drugs fail to be profitable even if they do get thru the FDA.)

You can put up any paper you want to discuss Billy

You can put up any paper you want to discuss BillyWhen I worked (for money) I avoided the 5PM leaving traffic by spending an hour of two reading journals in our rather good technical library. (It had a few excelent non-technical publications including the then quarterly Foreign Affairs, but now I rarely read in the library. Instead I read the claims of many different companies. I also have four or five biologic/ drug news services Emails everyday - ocassionally they do mention some University discoveries and I may suggest one of them, if article is available one the net.

My hope (for my benefit) from the "journal club" is that some more university (not corporate research) based significant developments of some underderstanding will be brought to my attention by others (certainly CharonZ, spidermonkey, and you must still be reading some good biological journals.)


BTW I had forgotten the "punch line" of the joke I PMed you. Shorter, and more subtile version is:

Slam,BAM; Sorry SAM.

When I worked (for money) I avoided the 5PM leaving traffic by spending an hour of two reading journals in our rather good technical library. (It had a few excelent non-technical publications including the then quarterly Foreign Affairs, but now I rarely read in the library. Instead I read the claims of many different companies. I also have four or five biologic/ drug news services Emails everyday - ocassionally they do mention some University discoveries and I may suggest one of them, if article is available one the net.

My hope (for my benefit) from the "journal club" is that some more university (not corporate research) based significant developments of some underderstanding will be brought to my attention by others (certainly CharonZ, spidermonkey, and you must still be reading some good biological journals.)


BTW I had forgotten the "punch line" of the joke I PMed you. Shorter, and more subtile version is:

Slam,BAM; Sorry SAM.

If you write down some of the compounds you are interested in learning about, (like VEGF) I can find some current articles.

SAM:
Perhaps, in effort not to immediately kill (or make it a "still birth") this journal club idea, a more general topic (but less "philosophical" and quite technical) would be a good idea.

For exmaple, I have only a physicist's guess at "sense" & "Anti-sense" compounds and their role in biological processes. I have long wondered, without making any effort to find out, if they are just what physicist and chemists call "optical isomers" - for example "dextros sugar" rotates a polarized light beam to the right.

Not sure, but I think Pasture, while paid by some French wine company, carefull segregated some "tarter crystals" of one sense from old wine and redisolved them and then let them recrystalze again during evaporation to discover that "sense" is preserved at the mocular level. etc.

Summary: Some review of how "sense" is important in biology might be good, and if man made (both senses equally) "levos surgar" is both sweet and non-fatting, you may already know a lot about all this.

For exmaple, I have only a physicist's guess at "sense" & "Anti-sense" compounds and their role in biological processes. I have long wondered, without making any effort to find out, if they are just what physicist and chemists call "optical isomers" - for example "dextros sugar" rotates a polarized light beam to the right.

Not sure, but I think Pasture, while paid by some French wine company, carefull segregated some "tarter crystals" of one sense from old wine and redisolved them and then let them recrystalze again during evaporation to discover that "sense" is preserved at the mocular level. etc.


I'm fairly certain the term is not meant to be enantiomers. A "sense" compound/strand is the mRNA which gets translated. Antisense is the DNA that was the template and complementary bases of the mRNA. There are also antisense small mRNAs that bind to a mRNA and prevent translation.

About the Pasteur thing, iirc he was supposedly able to segregate the enantiomers by luck, leading to his famous quote "Luck favors the prepared mind", or something like that : o

I see no reason why we cannot read some good technical papers as well.

Ok Platts discussion moved to new thread

http://www.sciforums.com/showthread.php?t=73421

Sorry to say this, but I am not sure whether this makes much sense (at least to me). I assume that even if enough people are interested, one would need quite some time to explain technicalities or have to dumb it down to the level of a newspaper report (which I personally wouldn't like to do).
Also the topics of general interest might be a bit limiting. I might for instance put forth a review of certain sigma factors and their control of virulence factors (which I actually can't because it is not a free access paper) , but I am not sure who else might find it interesting. I'd assume that it will have a similar outcome as RL paper discussion seminars (with hardly anyone responding on their own volition).
I assume the usual Q&A threads might be better suited, simply because in that case at least one person (the questioner) might have some interest on the subject at hand.

Maybe you could try to participate in the ones we set up?

SAM:
Perhaps, in effort not to immediately kill (or make it a "still birth") this journal club idea, a more general topic (but less "philosophical" and quite technical) would be a good idea.

For exmaple, I have only a physicist's guess at "sense" & "Anti-sense" compounds and their role in biological processes. I have long wondered, without making any effort to find out, if they are just what physicist and chemists call "optical isomers" - for example "dextros sugar" rotates a polarized light beam to the right.

There is a thread about it: http://sciforums.com/showthread.php?t=73660

It seems to have a lot of use with working with DNA, like for use as a "probe" by seeing if it is complimentary to some DNA.

The Nature Signalling gateway (http://www.signaling-gateway.org/update/featured/)provides free access to a new paper every week, with continued access for 3 months.

I'm considering using them for Journal Club discussion.

Here is the first one, which will be a sticky for the next two weeks.

http://www.sciforums.com/showthread.php?t=78331

I'd like feedback on the articles here: too easy, too hard, more perspective/protocol/review, less molecular.

I'm going to put together an FAQ/article on

-How to read a research paper
-How to critique a research paper

Maybe this weekend or the next.

I don't think too easy or too hard should be a concern, as long as it is interesting, though I'd personally prefer non-introductory material. If things are too hard for non-bio oriented people we can resolve it in discussion :O

The first article was on the easy side, but I personally found it interesting enough to more than make up for it. I still keep it in mind when thinking of experiments. I probably heard the all of the ideas mentioned in the article before, but the article helped permanently emphasize the importance. I'll edit this post on the difficulty of the second article after I read it (which I'm about to do).

I think protocol would be interesting to see more of. I'm neutral on the others, and unsure what type of article would have more perspective.

Unasked for feedback: Should ban everyone in the poll who voted in favor of the journal club and did not participate. -_-

edit:
took me a while to read the latest article, so from that aspect it was "hard" (I had to look up 5 words, at least, in the first paragraph :p). How long did it take others to read?!

I stick with what I said before though, difficulty shouldn't be a deciding factor, so more of those, or articles with greater difficulty, are OK imo.

Thanks, I like to read science papers on perspective as well as procedure, basically how to think and then act and then review.

Since the Platt paper was perspective, I have used a technical paper this time. I'll try to find one that highlights the importance of protocol in problem solving for the next one.

Too bad we can't upload documents here, I have some great papers we could use. :)

How is this any different to people with advanced math, group and set theory, having a huddle in their corner?

How is this any different to people with advanced math, group and set theory, having a huddle in their corner?

It's with biology... :cool:

jk, advanced knowledge is not required afaik.

To S.A.M. and Billy-T (and anyone else, but I don't think there is anyone else here :p).

What journals do you like to read (no need to list sciam.com or nature.com, or "The Nature Signalling gateway"), and where do you search from? Everything I try from scholar.google.com seems to be subscription (42$ for one issue of The Journal of Biochemistry:bugeye: )

I was trying to read up and see if there was a suitable article on articles about recent uses of "abzymes", kind of like what Billy-T posted. Perhaps abzymes is not the best search term.

I assume this is what the monoclonal antibodies that target cancer cells were that was mentioned. With a part to bind to the cancer cells and afterwards a part to receive "prodrugs".

http://www.wiley.com/legacy/college/boyer/0470003790/cutting_edge/catalytic_ab/tumor_drug.gif

It seems to be a great strategy, in theory, with very wide applicability. I'll keep trying to find a article(s) that might give an idea on how this approach is progressing, in specific or broad terms. Note that that image is from 2000... If there has been, hypothetically, little progress in this front so many years later, does it necessarily indicate anything about the viability of this approach?

Any update on the bavituximab, Billy?

Hi SAM---

I tried it in Physics and no one seemed interested in reading the paper.

A Journal Club needs a commitment. Maybe things are different here in Biology and genetics.

What the? This old thread pops up all of a sudden.

What the? This old thread pops up all of a sudden.

So? There was a journal club article a few weeks ago.

How come you knew of this thread and didn't take part? :)

I'm all for it! but you got to give me awhile to read that very interesting article, between typing here I'm either running an experiment or writing a report.

To S.A.M. and Billy-T (and anyone else, but I don't think there is anyone else here :p).

What journals do you like to read (no need to list sciam.com or nature.com, or "The Nature Signalling gateway"), and where do you search from? Everything I try from scholar.google.com seems to be subscription (42$ for one issue of The Journal of Biochemistry:bugeye: )


I don't have any particular favorites though I hit Science (http://www.sciencemag.org/) and American Scientist (http://www.americanscientist.org/) for pop sci. I usually read Journal of Biological Chemistry (http://www.jbc.org/), American Journal of Clinical Nutrition (http://www.ajcn.org/), Journal of Nutrition, Obesity research (http://www.obesityresearch.org/)etc.

I have End Note and I make libraries based on topic so I have stuff organised.

Usually I search on Pubmed or the uni library site or Google Scholar which is also contains our uni library. I like Google Scholar (http://scholar.google.com/) more because you can edit Scholar preferences to add citations to End Note.


Google Scholar into EndNote

* Go to Google Scholar at http://scholar.google.com
* Beside the search box click on Scholar Preferences
* When the Preferences window opens scroll down to Bibliographic Manager
* Choose the option Show links to import citations into and select EndNote from the drop-down box
* Click on Save Preferences
* You will now see a new link Import into EndNote at the end of each reference found in your seach
* To save a reference click on this link. You will be asked to select an EndNote Library. Click on Open
* The reference will appear in a new window in EndNote. Only the citation will be imported
* By clicking on the title you can often find the abstract, keywords or even the entire article. The abstract, keywords and the URL can then be cut and pasted into your EndNote reference



And also because you can add google scholar search engine to your firefox (http://mycroft.mozdev.org/)browser. All these little things save a lot of time when you're constantly using journal references.

The uni gives us on and off campus access to virtually everything.

I recommend searching on Pubmed (http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed) to start with. I usually use many search terms if I know exactly what I want.

Hi SAM---

I tried it in Physics and no one seemed interested in reading the paper.

A Journal Club needs a commitment. Maybe things are different here in Biology and genetics.

Well here no one seems interested in reviewing it. :p

To S.A.M. and Billy-T (and anyone else, but I don't think there is anyone else here :p).

What journals do you like to read ...Any update on the bavituximab, Billy?I rarely read journals - do not have times and not easy to do here in Brazil in English journals. I have financial interest in more than 30 early stage drug developers and a "watch list" of another 30 or so. www.Moringstar.com sends me any "breaking news" about each of them by daily Email. (Go to morinigstar.com "portfolio tab" as I recall, to set up your personnel "watch list")
www.PharmaLive.com has a set of free services I have used for several years that also send me Emails daily with about 6 different groupings. (They are really good and complete - most companies I have never heard of! Each enrty has brief text and link to more.) For example, one group is short note about ALL the recent FDA actions -very important financially - That action can literally destroy or greatly enrich a company with only "one Phase 3 results waiting the FDA's decision. (I have had stock lose >75% of their market value in one day!) Early stage drug developers are only for people like me who can afford to lose it all and want to re-enforce their motivation to learn the amazing things happening in targeted drug development, etc.
Also relative new (I have not used it - but tested once and does seem to work and is free) is www.PharmaLiveSearch.com

On bavituximab the last entry in that company's file in my computer is:

"1March08 issue of a cancer research journal: “radiolabeled bavituximab to rats with prostate tumors* and then conducted molecular imaging studies of the rats over the next several days. The results showed that radiolabeled bavituximab localized to the tumor blood vessels with great specificity. In these subjects, 22 times as much bavituximab localized to the tumor compared to the liver when measured 72 hours post-injection. The study further showed no specific localization of bavituximab to blood or other tissues including the heart, kidney, intestine, muscle, bone and brain. The tumor blood vessel-selective targeting observed in vivo in the study was confirmed by further bio-distribution analyses and by histology studies.”
----------------
*This note dose not state but I believe from others I have that the rates were "Zenographs" I.e. human prostrate cancer cells were implanted (perhaps some imune system suppression drugs used to or the rats were "half human"?) to grow human prostate cancer in the rats.

This is a mix of my notes and quotes from now unknown source. I try to extract the important results from larger articles. - Keeping my tracking files on more than 50 companies half way up to date and compressed enough to be useful later when I want to get a feeling for how one is doing is a lot of work. Typically each file is several pages long if no slides are present. Those page are full 8.5 inches wide (but never printed) so two of their presentation slides fit side by side. I download slides during the presentations companies make, if permitted. The meeting are usually sponsored by financial organization. The early stage drug developer usually have no income and high cash burn rates for clinical studies with hundreds of patients so they are often making these presentations. :eek:

A thread on reading for research

http://www.sciforums.com/showthread.php?p=1794846#post1794846

Is journal club still open? I've found an article that would be great. Do I post the link in the forum or in this sticky?

Jessica

Usually, the Muslims were tolerant with the Non-Muslims, especially "The People of the Book" (Christians and Jews), with biblical traditions similar to theirs. The Islam considered Abraham and Moses real prophets, whose work was completed by Muhammad. Muslims were tax free, unlike the Non-Muslims. This was a motivation on long term for many people to convert to Islam. As Koran's translation to other languages was forbidden, many new adepts had to learn Arabic, so that the conquered people were easier assimilated. When this happened, an Arab was considered a person speaking the Arabic language and with the same religion and culture.

But the tolerance of the Umayyads meant the end of the dynasty. Many subjects considered they did not take care enough to convert the Non-Muslims. Religious discontent and riots of the Arabs from Iran and Mesopotamia, unhappy to be led from Damask, caused a big rebellion in 747, whose leader was Muhammad's descendant Abdul Abass. In 3 years, all the Umayyads were killed, except Abdar-Rahman, who took refuge in Spain, founding an autonomous dynasty that lasted 300 years.

The Abassid dynasty founded a new capital in Mesopotamia: Baghdad, which soon would have 1 million of inhabitants. Special interest was in the conversion to Islam and the adoption of the Arab languages. Only Persia kept its language, the Persian, and its cultural identity, but turned from Zoroastrian into Muslim.

This is the peak of Islamic culture. The caliph Al Mansur (712-775) founded "The Palace of the Knowledge" were savants could translate the works of the ancient Greek philosophers, studied ancient medicine, learned Indian mathematics (the numbers, invented by Indians, are known as Arabic numbers, because Arabs brought them to Europe). The Persian Ibn-Seena (Avicenna), a philosopher and medic, was famous even in Europe. Algebra is an Arab word, and Arab mathematicians founded this subject. Omar Hajjam (1048-1131) was a great Persian mathematician, astrologist and poet.

This is probably the wrong thread, Q.

Is journal club still open? I've found an article that would be great. Do I post the link in the forum or in this sticky?

Jessica

Just open a thread with the title Journal Club:<Thread Title> and message me the link so I can add it to the OP. :)

What journals do you like to read (no need to list sciam.com or nature.com, or "The Nature Signalling gateway"), and where do you search from? Everything I try from scholar.google.com seems to be subscription (42$ for one issue of The Journal of Biochemistry:bugeye: )



I read PNAS.org and AMJBOT.org. They both have great archives filled free full text articles. I love AMJBOT, probably because I'm a plant nerd. For condensed soup science I read sciencenews.com.

This is probably the wrong thread, Q.

Ya think? :rolleyes:

Could someone tell that to Sam when she posts her crap in other threads?

Just open a thread with the title Journal Club:<Thread Title> and message me the link so I can add it to the OP. :)

Great! Now I just have to hunt down the article again. It proposes multiple plastid acquisition events throughout the history of Eukaryote evolution. The article is a few years old, I hope everyone hasn't read it already.

Great! Now I just have to hunt down the article again. It proposes multiple plastid acquisition events throughout the history of Eukaryote evolution. The article is a few years old, I hope everyone hasn't read it already.

If you have a citation, I can locate it. :)

Thanks, I just found it. I first noticed the article on AMJBOT's 50 most read article list. I just couldn't remember if I'd seen it in PNAS or AMJBOT so I had to browse around a bit. I'll make a new thread now with links and send you the link as well.

Jessica

Journal article for review, also added to OP


4. Diversity and evolutionary history of plastids and their hosts (http://www.amjbot.org/cgi/content/full/91/10/1481)