Tag: sciencesunday

November 8, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

#Sacks4Science

#Sacks4Science

Clearly #Sacks4Science  needs to be a thing to support testicular cancer research and fight sexism in science. Since I don’t have a post about testicular cancer, I’m re-sharing this post about prostate cancer. Let me explain where the  #Sacks4Science hashtag is coming from.

There’s a post about a group in Italy that want to promote science by showing pictures of breasts with a sign about science.

Tette per la Scienza, “Boobs for Science”

http://goo.gl/OEexUd

In that post Buddhini Samarasinghe reminded people about the coconut bra stunt by Pier Giorgio Righetti.

http://www.stemwomen.net/recognising-sexism/

That is almost as bad as the #HUGS4JUGS “campaign”. The only time that breasts should be mentioned in a conversation about science, is if the science is about breasts.

Bilateral prophylactic mastectomy

https://plus.google.com/+ChadHaney/posts/cJMpG7961G9

https://plus.google.com/+ChadHaney/posts/YDFjxkvC5vc

Some pedantic arguing ensued on that thread, so I turned my attention back to science. I’m working on data to see if a new imaging agent can detect if a tissue is positive for the progesterone receptor, which would guide therapy choices without invasive biopsies.

In a conversation about the boobs for science post, Rachel Blum said

Clearly: ask for guys to do a shot of their penis untying at an important section in a scientific paper. Share a few shopped ones with the MOAR BOOBS crowd.

“Oh, that makes you uncomfortable? But it’s FOR SCIENCE”.

I mention it should be for prostate cancer awareness or show your balls for testicular cancer awareness. I bet a lot of bros will jump on that bandwagon.

Then Buddhini Samarasinghe said, we should call the campaign “Sacks for Science”. We all agreed that #Sacks4Science  needs to be a thing. So support #Movember  and prostate cancer awareness. Support science, without sensationalizing it. And if you’re ready to jump on the bandwagon, help us support #Sacks4Science  to support testicular cancer research and fight sexism in STEM.

#ScienceEveryday  

Originally shared by Chad Haney

The real #Movember for #ScienceSunday .

Most of you probably know that the pink ribbon in October means, breast cancer awareness month. I disagree with the commercialization of the pink ribbon and attempts to trademark it, but that’s another story. I want to talk about Movember. You’ve seen the mustaches and the hashtag. How many of you know it is for men’s health awareness? Specifically prostate and testicular cancer. I’m going to focus on prostate cancer.

PSA about PSA

Public service announcement about prostate-specific antigen screening: For many years, PSA testing was suggested to start at age 40. The current recommendation:

The American Cancer Society recommends that men discuss the possible risks and benefits of prostate cancer screening with their doctor before deciding whether to be screened. The discussion about screening should take place starting at age 50 for men who are at average risk of prostate cancer and expect to live at least 10 more years. It should take place at age 45 for men who are at higher risk, including African-American men and men who have a father or brother diagnosed with prostate cancer, and at age 40 for men at even higher risk.

For many years researchers in the trenches were finding that PSA screening often led to false positives. There’s too much variability in the PSA screening method.

Ex vivo MRI

The purpose of the study that I’m presenting was to take advantage of higher resolution MRI, using ex vivo samples in a pre-clinical high field MRI scanner (9.4T vs. 1.5T clinical MRI). Histology is orders of magnitude higher resolution even compared to the pre-clinical scanner. The idea was that better MRI images could be correlated with histology. Ultimately decisions are made based on histology, typically via biopsy. Identifying which features in MRI correlate with histology could set up a feed back loop to improve the in vivo MRI images. What’s shown below is an early proof of concept study.

I don’t know the PSA scores for the patients in the study below, but I’m sure they were high enough to justify biopsies. We were blinded to patient names and a lot of their health records for both privacy reasons and to remove bias. There are risks and side effects associated with getting a prostate biopsy. That’s part of the reason for changing the PSA screening recommendations. If you are curious what a human prostate looks like, there’s one pictured below. It’s about the size of the palm of your hand (at least my hand).

The other two figures show what the prostate looks like using MRI (panel A, C, and D) and histology (panel B). Panel A is a T2-weighted spin echo image. Panel C is a T2 map, i.e. a display of the actual T2 values. Panel D is an apparent diffusion coefficient (ADC) map. You can review the MRI terminology in the link below.

The first figure, which outlines the cancer with a dotted line in the histology image is from a 71-year-old patient. The second is from a 63-year-old patient without malignant cancer. In the examples below it isn’t obvious which MRI parameter best correlates with cancer. In the 71-year-old patient, the low T2 values along with low ADC values appears to correlate well with the tumor outlined in the histology slide. However, the 63-year-old patient also displays  low ADC values, whereas the T2 values are higher. Overall, with 9 patients, the T2 values were about 10 msec longer (P < 0.03) and the average ADC values were about 1.4 times larger (P < 0.002) when comparing normal peripheral zones vs. cancerous peripheral zones. With a larger sample size we hope to improve the correlation between both the in vivo and ex vivo MRI with histology.

References:

Medical Imaging 101 pt 3: MRI from my #CHMedicalImagingSeries

http://goo.gl/UVbiU

High-resolution MRI of excised human prostate specimens acquired with 9.4T in detection and identification of cancers: validation of a technique.

J Magn Reson Imaging. 2011 Oct;34(4):956-61. doi: 10.1002/jmri.22745.

Fan X, Haney CR, Agrawal G, Pelizzari CA, Antic T, Eggener SE, Sethi I, River JN, Zamora M, Karczmar GS, Oto A.

http://www.ncbi.nlm.nih.gov/pubmed/21928309

Doctors’ Associations Release New Recommendations for Prostate Cancer Screening

http://goo.gl/nieEIL

http://us.movember.com/faq

November 2, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

For Ada Lovelace Day

For Ada Lovelace Day

I missed posting for Ada Lovelace Day this year. A lot of G+ friends have recently shared posts about gender bias in science and I decided to list them here along with my re-share of my Alice Kober post.

Ada Lovelace, was an English mathematician and writer chiefly known for her work on Charles Babbage’s early mechanical general-purpose computer, the Analytical Engine. Her notes on the engine include what is recognised as the first algorithm intended to be processed by a machine. Because of this, she is often described as the world’s first computer programmer.

http://en.wikipedia.org/wiki/Ada_Lovelace

Ada Lovelace Day in a nutshell

Ada Lovelace Day is about sharing stories of women — whether engineers, scientists, technologists or mathematicians — who have inspired you to become who you are today. The aim is to create new role models for girls and women in these male-dominated fields by raising the profile of other women in STEM.

http://findingada.com/

Essential Reading for Today’s Theme

Blind Spots: Seeing Sexism in STEM via Buddhini Samarasinghe 

https://plus.google.com/+BuddhiniSamarasinghe/posts/RnkYFTfDYgs

Double standard in academic dress code via Sara Del Valle 

https://plus.google.com/+SaraDelValle/posts/LkyZCARFuTU

(Mis)Judging Female Scientists

https://plus.google.com/+InsideHigherEd/posts/bdXoHsWfA5c

Science Fellowships and Institutional Gender Bias in STEM via Zuleyka Zevallos 

https://plus.google.com/+ZuleykaZevallos/posts/5yfNN5ov3Tv

When Women Stopped Coding from NPR via Betsy McCall 

https://plus.google.com/+BetsyMcCall/posts/RxjgfSqU92q

#ScienceSunday  

Originally shared by Chad Haney

Alice Kober, Deciphering Linear B

Deeksha Tare ‘s post about inventions by women (http://goo.gl/TLl3Z4) reminded me of a segment on The World on NPR. It was yet another story of an important breakthrough by a woman being overlooked. Alice Kober did a lot of the major analysis in deciphering Linear B but Michael Ventris received much of the credit, at least initially. Part of the lack of credit could be due to the fact that she worked on Linear B in private, i.e., in her “spare time”. She unfortunately died at the age of 43.

Linear B

So what is linear B? Linear B is a syllabic script from Knossos, Crete around 1450 BC. You can think of it as unlocking hieroglyps, without the Rosetta Stone. British archeologist, Arthur Evans found a series of clay tablets in ruins thought to be the home of King Minos. Linear B descended from Linear A which is an undeciphered earlier script for writing the Minoan language. Linear B consists of approximately 87 syllabic signs and over 100 ideographic signs.

http://en.wikipedia.org/wiki/Linear_B

Linear B had been known for about 30 years before Alice Kober began working on deciphering it. That’s 30 years with no breakthroughs. One of Alice’s breakthroughs was understanding that Linear B is syllabic, like Japanese where characters stand for a sound. The other two types of written language systems are alphabet, which we know, and logographic, like Chinese where a symbol represents a whole word. Part of the reason Linear B was not identified as syllabic earlier on is due to a few pictographs (like Chinese) that represented objects, e.g. horeses and pots.

Database

Instead of trying to guess meaning or speculate on sound values of symbols, Alice recorded the frequency of every symbol, in general and then in a particular position, which lead to the idea of Linear B being syllabic and an inflected language (having suffixes and prefixes). Keep in mind this was in the 40s and 50s with no computer aid. She handmade index cards for her database because of the limited supplies during WWII. From the database, Alice was able to build a grid showing the relationships between symbols but died before she could add sound.

It’s all Greek to me

Michael Ventris was able to add sound to the grid as he guessed that some repeated symbols might be towns in Crete. So Knosso in Linear B was “ko-no-so”. With a few city names figured out, he could add sound to the grid. No one had guessed that Linear B was a form of Greek because they didn’t know Greek was spoken that far back. Since Greek using the alphabet system, it wouldn’t have helped much, knowing that Linear B was a form of Greek. So the end story is that the Greeks colonized Crete and used the local writing system to record their own language.

Sources:

How American Linguist Alice Kober Helped Unlock the Secrets of Linear B

http://goo.gl/YH5jMZ via PRI The World

Alice Kober: Unsung heroine who helped decode Linear B

http://goo.gl/4W3cbL via BBC

Images from BBC and Wikipedia

#ScienceSunday

November 2, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

What do you think?

What do you think?

If you didn’t guess I vote no, then you don’t know me. Even if a politician has a science background, they should not interfere with peer review.

#ScienceSunday   

Originally shared by ScienceSunday

Should politicians be involved with reviewing research proposals?

Bill McGarvey is very familiar with the grant proposal review process for the National Institutes of Health in the USA. The NIH funds the majority of biomedical research in the US. Bill shares an interesting article discussing politicians getting involved in the review process for the National Science Foundation, who fund a lot of basic science research in the US. Because basic science research has minimal immediate impact but often a huge impact long term, it frequently comes under scrutiny by short sighted politicians.

Politics and the National Science Foundation (NSF)

http://goo.gl/JtBje4

This ties in nicely with #ScienceSunday  co-curator Rajini Rao’s post about basic science and long term impact.

Serendipity in Science: Golden Goose Awards

http://goo.gl/E6smir

#SciSunCH  

October 5, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

Tea in Sri Lanka with you

Tea in Sri Lanka with you

Don’t miss Professor of Chemistry, Siromi Samarasinghe this afternoon. Until then I leave you with a little Sting.

The Police – “Tea in the Sahara” by Bob Head Productions

#ScienceSunday  

Originally shared by STEM Women on G+

Join us for a STEM Women HOA as we speak to Professor Siromi Samarasinghe from the University of Sri Jayawardenapura, Sri Lanka. Siromi lectures in organic chemistry and her research interests include the chemistry of tea compounds. She will talk to us about her research and career path, and also share her experiences of studying abroad and mentoring students. 

You can read more about Siromi here: http://www.stemwomen.net/science-helped-me-to-overcome-challenges-in-life/

This HOA will be hosted by Dr Zuleyka Zevallos  and Professor Rajini Rao. You can tune in on Sunday 5th October at 1.30 PM Pacific or 9.30PM UK/ Monday 6th 7.30 AM AUS.

The hangout will be available for viewing on our YouTube channel after the event: http://www.youtube.com/stemwomen

September 28, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

Science, theory, law, confusion

Science, theory, law, confusion

Sam Andrews writes about an important topic, what is science anyway?

Because I’m lazy busy, I’ve put together a list of old shares about the scientific method and correlation vs. causation.

Of Cabbages and Kings

https://plus.google.com/+BrianKoberlein/posts/XXShqYHt5pm

Steps of scientific method meme version

https://plus.google.com/+sciencesunday/posts/GLX78mbKvy1

Steps of scientific method baby version

https://plus.google.com/+sciencesunday/posts/3QKDAxnxjzR

Richard Feynman on the Scientific Method

http://goo.gl/f7NJZI

Steps of scientific method Futurama version

https://plus.google.com/+sciencesunday/posts/HYvzNGLvTsQ

Another example of correlation does not equal causation

https://plus.google.com/+sciencesunday/posts/ZGyKHWGTfkM

Correlation versus Causation

https://plus.google.com/+sciencesunday/posts/1o9zv2BbEGu

#ScienceSunday  

Originally shared by Samantha Andrews

So what is all this science malarkey anyway?

The UK Science Council define science as ”the pursuit and application of knowledge and understanding of the natural and social world following a systematic methodology based on evidence”

As the Council explain, this methodology has some criteria…

”Scientific methodology includes the following:

Objective observation: Measurement and data (possibly although not necessarily using mathematics as a tool)

Evidence

Experiment and/or observation as benchmarks for testing hypotheses

Induction: reasoning to establish general rules or conclusions drawn from facts or examples

Repetition

Critical analysis

Verification and testing: critical exposure to scrutiny, peer review and assessment

Sounds all pretty straight forward doesn’t it?  A bit too straight forward perhaps.  We don’t all have a background in science so it’s not surprising that at times there is some confusion over what science is, how it is done, and what it can actually tell us about the natural and social world.  Fortunately for us, there have been three excellent open access articles have been published in The Conversation this week which address some of the issues for communicating science:

Where’s the proof in science?  There is none

Astrophysist Geraint Lewis from the The University of Sydney kicks of this fabulous trio by explaining one of the misconceptions of science: proof.  Yes that’s right, science doesn’t really prove anything.  So what does it do?  In his article, Geraint hands the last word over to Richard Feynman.  I think I will to:

”I have approximate answers and possible beliefs in different degrees of certainty about different things, but I’m not absolutely sure of anything.”

http://theconversation.com/wheres-the-proof-in-science-there-is-none-30570

Clearing up confusion between correlation and causation

Correlations are all to do with relationships between different factors.  Like chocolate and Nobel Prize winners.  Take a look at the graph below, produced by Franz Messerli of Columbia University.  Apparently there is a correlation between chocolate consumption.  We can even put a number on this – a ‘P value’ to describe the ‘strength’ of the correlation.  In this case the value was 0.0001 – which means that “there is a less than one-in-10,000 probability of getting results like these if no correlation exists”  .  But as Mathematicians Jon Borwein and Michael Rose from the University of Newcastle (UON), Australia explain, correlation does not imply causation, which means that increasing your chocolate consumption won’t increase your chances of winning the Nobel Prize.  http://theconversation.com/clearing-up-confusion-between-correlation-and-causation-30761

Why research beats anecdote in our search for knowledge

_”Certainty is seductive” writes Philosopher Tim Dean from the University of New South Wales, _”so we tend to cling to it.  We hunt for evidence that buttresses it, while ignoring or rejecting evidence that threatens to undermine it”.  Research, on the underhand, embraces uncertainty.  It isn’t about finding evidence to back your point of view, it’s about increasing our knowledge – and doing so with a scientifically backed evidence base.  For researchers, sometimes that means re-evaluating your point of view.  http://theconversation.com/why-research-beats-anecdote-in-our-search-for-knowledge-30654  

Image:  From Franz Messerli’s paper Chocolate Consumption, Cognitive Function, and Nobel Laureates published in the New England Journal of Medicine.  Franz added a disclaimer to his paper, that he ”regular daily chocolate consumption, mostly but not exclusively in the form of Lindt’s dark varieties.” Unfortunately the paper is behind a paywall, but if you fancied a look you can find it here www.dx.doi.org/10.1056/NEJMon1211064

#science #sciencesunday #scicomm

September 28, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

A different kind of preservation

A different kind of preservation

If you read the plaque below, it says that this tree was grafted from the apple tree that is said to have been the same tree that Sir Issac Newton saw an apple fall and developed his theory of gravity. This tree is at the entrance to the Cambridge University Botanical Garden. I had a lovely day there with my wife and Kimberly Chapman and her daughters. Maybe Peo (Kim’s older daughter) will write a blog about this tree as well. I’ll add a link here if she does.

Brian Koberlein wrote a great post about Newton’s Principia here (so I don’t have to):

Newton’s Apple

https://plus.google.com/+BrianKoberlein/posts/NKnFG3xJH6x

So enjoy my lazy #ScienceSunday  post while I sort through PET scanner specifications. What? You say you don’t know what PET is? Well here you go.

Medical Imaging 101 pt 4: PET

http://goo.gl/YNAVhX

I keep promising that part 6: SPECT is coming. I will try to get that out soon. Stay tuned.

September 22, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

Shake your silk-maker

Shake your silk-maker

Check out this great video of not only the Peacock Spider dance, but the music sound they make during the dance. Tune into Science Friday on NPR for more.

http://goo.gl/l9Qn8s

Here’s more about Peacock Spiders from   #ScienceSunday  

Peacock Spider, Maratus volans

https://plus.google.com/109783903175191665261/posts/Z7LurWsABBN

Peacock Spider – Rocking the Dance Floor with Risky Business

https://plus.google.com/109783903175191665261/posts/jmE9k6eBoKw

Dance of the Peacock Spider

https://plus.google.com/114601143134471609087/posts/79jfwV1cy6r

h/t Jeff Sayre 

Originally shared by Jeff Sayre

The Dance of the Peacock Spider

A fascinating 5.5 minute video segment on #sciencefriday  about Australia’s dancing male Peacock Spiders.

#nature   #science  

http://youtu.be/mq-r20mlGes

August 17, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

Not a night-crawler

Not a night-crawler

This spider has an enormous web, probably 30 – 40 cm in diameter. I’ve only seen the spider at night, hence the crummy photo. It’s probably in the orb weaving family, Araneidae. From Chris Mallory in another post:

RE: spider families: if your spider makes a big web like this, you know, the “charlotte’s web” type web, then it is an orbweaver, family Araneidae. Cobweb spiders and house spiders (as well as widows) belong to a different family, the Theridiidae. If you’ve seen webs from any of these things, you could see that the two webs are nothing alike. They aren’t called “cobweb spiders” for no reason. This fact alone could rule out the possibility of a house spider even if the spider wasn’t present. Back to Orbweavers, aka “garden spiders”: there is not just one single species, with “yellow and black striped with a very noticeable white zig zag strand  in the middle of the web.” There are about 4000 species. Though they all make this kind of web more or less,  almost none of them fit that discription.

https://plus.google.com/u/0/107896084561441926092/posts/cptvFkYjJba

Because of my broken wrist, I won’t be as active on G+.

More spider science links for #ScienceSunday  and #SpiderSunday  

Open the Spigot for Science

http://goo.gl/SGMDI

ScienceShot: Spider Dies From Sex

http://goo.gl/DGyhYq

July 27, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

Who’s your favorite mathematician?

Who’s your favorite mathematician?

Besides Richard Green, I would say Joseph Fourier or Johann Radon just because my work wouldn’t exist without them.  The Fourier transform is integral to MRI as the data is frequency encoded. For other imaging techniques that use projection data, e.g., CT, the Radon transform is important in image reconstruction using a technique called filter back projection.

You can read more here:

Medical Imaging 101 pt 3: MRI

http://goo.gl/UVbiU

Medical Imaging 101 pt 2: CT

http://goo.gl/IHaFw

Medical Imaging 101 pt 4: PET

http://goo.gl/YNAVhX

On this list:

http://www.businessinsider.com/12-classic-mathematicians-2014-7?op=1

I would pick Rene Descartes because his contribution to philosophy is equally intriguing to me as well as his contributions to math.

#ScienceSunday   h/t Michael O’Reilly for the link.

Image via Reddit

July 13, 2014 ScienceEveryday (medical imaging is separate) Post a Comment

W.K. Kellogg Biological Station – Michigan State University

W.K. Kellogg Biological Station – Michigan State University

My sister chose the W.K. Kellogg Biological Station (KBS), the manor in particular, to have her wedding ceremony this past Friday. It’s a fantastic venue for a wedding, with wild flowers everywhere, history, and science. W.K. Kellogg was the business-minded, of the two Kellogg brothers. He’s the one who founded the cereal company. John Harvey Kellogg was the brother who started the sanatorium in Battle Creek, MI. There is a lot of information about the brothers, including the documentary The Kellogg Brothers: Corn Flake Kings, so I’m only going to briefly talk about the biological station.

The manor was the home of W.K. Kellogg and was built in 1925 overlooking Gull Lake in what is now called Hickory Corners, MI. In 1928, W.K. Kellogg deeded Kellogg Experimental Farm and the Kellogg Bird Sanctuary to the Michigan State College of Agriculture. The entire 32 acre estate was given to the Michigan State University in 1951.

Bird Sanctuary

W.K. Kellogg was interested in wildlife conservation and KBS is fortunately the intersection of three major bird migration routes. The bird sanctuary opened in 1928 and is a major attraction. Their mission statement: The W.K. Kellogg Bird Sanctuary conserves native habitat for migratory and resident birds and through research, education, and outreach helps people gain environmental awareness about our past, present, and future.

Kellogg Experimental Forest

The Kellogg Experimental Forest is 728 acres, which includes two artificially created ponds. They have developed hybrid spruce and poplar trees. The Spartan Spruce, is a cross between a blue spruce from southern Colorado and the white spruce from Michigan’s upper peninsula. The needles are blue like a blue spruce but soft like a white spruce.

Biofuel

KBS is working on a lot of interesting questions related to biofuels, such as economy (when does it make economic sense for farmers to switch to production of biofuel sources), what effect does growing biofuel sources, such as corn, have on soil or wildlife habitat, and how much cellulose based ethanol can be made produced from various crops. For example Brazil is doing quite well with sugar cane based ethanol, whereas in the USA most of the biofuel ethanol is from corn.

There’s a lot of interesting science going on at KBS. I plan to go back to see the bird sanctuary, especially the birds of prey.

Image sources:

http://history.kbs.msu.edu/topics/timelines/

http://goo.gl/faF4DV

#ScienceSunday