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  • August 22, 2013
  • 12:47 PM

All digital images are just large arrays of numbers

by Olga Vovk in Milchstraße

If we look at image processing from the mathematical perspective, all digital images are just arrays of numbers. Across different fields of study, image processing applications (although initially developed for very specific needs) often use similar image processing routines based on common algorithms. Why I am writing all this?... Read more »

Jennifer L. West, & Ian D. Cameron. (2006) Using the medical image processing package, ImageJ, for astronomy. J.Roy.Astron.Soc.Canada100:242-248,2006. arXiv: astro-ph/0611686v1

Michelle Borkin (Initiative in Innovative Computing, Harvard University), Alyssa Goodman (Initiative in Innovative Computing/Harvard-Smithsonian Center for Astrophysics), Michael Halle (Initiative in Innovative Computing/Harvard Medical School), Douglas A. (2006) Application of Medical Imaging Software to 3D Visualization of Astronomical Data. info:/

Covington K, McCreedy ES, Chen M, Carass A, Aucoin N, & Landman BA. (2010) Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities. Annual ORNL Biomedical Science and Engineering Center Conference ORNL Biomedical Science and Engineering Center Conference, 1-4. PMID: 21151892  

  • August 18, 2013
  • 03:43 AM

Remembering the Work of Dr. Patricia Goldman-Rakic

by The Neurocritic in The Neurocritic

A touching and comprehensive review article in Cerebral Cortex commemorates the life and work of Dr. Patricia Goldman-Rakic on the ten year anniversary of her death (Arnsten, 2013). The author of over 600 publications, Goldman-Rakic worked at NIMH from 1965-1979 and was a professor at Yale from 1979-2003. She served as President of the Society for Neuroscience in 1989-90 and was elected to the National Academy of Sciences in 1990. The review was written by one of her former post-docs, Dr. Amy F.T. Arnsten, herself a professor at Yale.Keeping a Life "in mind" Dr. Goldman-Rakic is best known for her research on working memory and the prefrontal cortex (PFC). Working memory is a transient form of memory that actively maintains and manipulates information for brief periods of time (Goldman-Rakic, 1995):Working memory in its most elementary form, the ability to keep events "in mind" for short periods of time, has been studied in nonhuman primates by delayed-response paradigms. Whereas in humans, facts and events accessed from long-term memory stores can be instigated by verbal instructions, in experiments with animals, the information to be processed has to be provided by the experimenter.Building on the work of Fuster and colleagues, her studies demonstrated that neurons in the dorsolateral portion of the PFC fire more rapidly when a spatial location cue is removed from the visual field and must be remembered over a brief delay. The sample neuron in the figure below codes for targets located at 270 degrees and not for targets at other locations. Note that the neurons's response is specifically enhanced over the delay period (D).Fig 1 (modified from Goldman-Rakic, 1995). Neuron during the Many Trials over Which a Monkey Performed an Oculomotor Delayed-Response Working Memory Task. The neuron's response for all trials at the preferred target location is shown as a histogram of the average response per unit time for that location. The activity is also shown in relation to task events (C, cue; D, delay; R, response) on a trial-by-trial basis. These neurons are located in the dorsal bank of the principal sulcus in monkey dorsolateral PFC, equivalent to Brodmann area 46 in humans. Goldman-Rakic and colleagues conducted extensive neuroanatomical tracing studies in the 1980's to map out the connections of this region and the posterior parietal cortex, major hubs in the brain's larger scheme of visuospatial processing.Fig. 2 (Arnsten, 2013). The cortical circuitry for spatial cognition, based on the work of Goldman-Rakic and Selemon. Note that both the dlPFC (area 46) and parietal cortex have many shared connections to subcortical structures that are not shown in this illustration, as well as “nonshared” connections that are not included in this diagram {from L. Selemon}.Goldman-Rakic's work was enormously influential, as shown in the figure below.Fig. 1 (Arnsten, 2013). Timeline of the discoveries of the PFC role in working memory (WM) and the key contributions of Goldman-Rakic. The graph shows the number of papers cited on PubMed using the search term “prefrontal cortex” for each decade ending in the year noted. Key publications by Goldman-Rakic and other early pioneers are indicated. Other major areas of research reviewed by Arnsten (2013) include the Key Role of Dopamine and Neuromodulation (e.g., D1 vs. D2 Receptor Actions, the D1 Receptor “inverted-U” Dose–Response), the Neurobiological Foundations of Schizophrenia (e.g., Insults to dlPFC Microcircuitry), and the dlPFC Microcircuits that Generate Mental Representations. The tribute article is open access and can be read freely by all.A Life of the Mind, Shaped by Working Memory The significance of working memory for higher cortical function is not necessarily self-evident. Perhaps even the quality of its transient nature misleads us into thinking it is somehow less important than the more permanent archival nature of long-term memory. However, the brain’s working memory function, i.e., the ability to bring to mind events in the absence of direct stimulation, may be its inherently most flexible mechanism and its evolutionarily most significant achievement. Thus, working memory confers the ability to guide behavior by representations of the outside world rather than by immediate stimulation, and thus to base behavior on ideas and thoughts.- Pat Goldman-Rakic (1991)ReferencesArnsten AF (2013). The Neurobiology of Thought: The Groundbreaking Discoveries of Patricia Goldman-Rakic 1937-2003. Cerebral Cortex PMID: 23926115Goldman-Rakic PS (1995). Cellular basis of working memory. Neuron, 14 (3), 477-85 PMID: 7695894... Read more »

  • August 16, 2013
  • 11:34 AM

Possible New Treatment for Bone Fractures in the Elderly

by Rebekah Morrow in United Academics

As people age, they are more likely to break bones and suffer from osteoporosis. The elderly who have broken bones also take longer to heal than younger patients. Part of the reason for this is that bones change as we age. Bone marrow contains many cell types, including those that form new bone. As age increases, these cells shift from an osteogenic (bone forming) type and toward an adipogenic (fat forming) type. Bone grafts are used to replace missing bone when the fractures are complex, or fail to heal properly. Bone marrow from the patient is preferred, but because the marrow of elderly patients has become more adipogenic, healing may be slowed.... Read more »

Journal of Bone and Joint Surgery. (2013) Wnt3a reestablishes osteogenic capacity to bone grafts from aged animals. J Bone Joint Surg Am. 2013;95:1278-88. The Journal of Bone and Joint Surgery. info:/

  • August 12, 2013
  • 08:06 PM

Black Dog Syndrome: A Bad Rap?

by Cobb & Hecht in Do You Believe In Dog?

Hi Mia & Julie – Firstly, thanks so much for letting me drop a verse in the rap song of your blog! I feel so awesome being featured. It’s like being Lil Wayne or something. Anyway…I’m just recently back from ISAZ 2013, where I had a most excellent time chatting with other anthrozoologist-y types. As you know, I just graduated from the Anthrozoology Master’s Program at Canisius College, so I was uber-excited to have a chance to share my research with colleagues in the field. ISAZ did not disappoint. Pauleen Bennett & Heather at ISAZ 2013Now I get to share with you two and it just gets better and better! :-)My master’s thesis research project (advised by the oh-so-awesome Christy Hoffman) looked to answer the question: “Does Black Dog Syndrome Exist?”Animal welfare folks are probably familiar with the concept of Black Dog Syndrome (BDS) that Julie introduced last week: it’s the idea that dogs with black coats have a harder time than other dogs getting adopted, and as a result, may face higher rates of euthanasia and longer stays in adoption programs. Popular media - but is it correct?A lot of popular media articles focus on this concept (like here, here, here and here) but the research results have been mixed: in a study published earlier this year, participants rated an image of a black dog as significantly less agreeable, less conscientious, and less emotionally stable than a yellow dog (Fratkin & Baker, 2013). Yet research into factors influencing shelter dogs’ lengths of stay (LOS) found that LOS was not significantly correlated with coat color (Brown, Davidson, & Zuefle, 2013; Protopopova, Gilmour, Weiss, Shen, & Wynne, 2012).To dig deeper into the questions of whether potential adopters discriminate against black dogs in a shelter and whether black dog discrimination is reflected in shelter stats, I conducted a two-part research project: Shelter Visitor Pilot Study – examined interaction between potential adopters and shelter dogs Shelter Data Analysis Study – investigated relationships between LOS and coat color, age, sex and breed, as well as the impact of these variables on likelihood of euthanasiaAnd what I found may surprise you. There was very little evidence to support the concept of Black Dog Syndrome! From Heather's ISAZ 2013 posterI know animal shelter workers are going “WHAT!?” right now – I know because I AM a shelter worker – but the truth is, even if many potential adopters come to the shelter with a negative bias toward black dogs, it’s not resulting in crazy-long shelter stays or greater risk of euthanasia for black dogs. In fact, according to analysis of shelter statistics, black dogs were adopted out faster than average at both shelters in my study. Black dogs were also less likely than expected to be euthanized (good news for black dogs, eh?).When shelter visitors video-recorded their walk through the adoption area, I found that they spent about equal amounts of time looking at every dog, regardless of coat color. Visitors also rarely made specific comments with regards to coat color, although one guy did say: “I like black. Black dogs ... Read more »

Fratkin Jamie L., & Baker Suzanne C. (2013) The Role of Coat Color and Ear Shape on the Perception of Personality in Dogs. Anthrozoos: A Multidisciplinary Journal of The Interactions of People , 26(1), 125-133. DOI: 10.2752/175303713X13534238631632  

Protopopova Alexandra, Gilmour Amanda Joy, Weiss Rebecca Hannah, Shen Jacqueline Yontsye, & Wynne Clive David Lawrence. (2012) The effects of social training and other factors on adoption success of shelter dogs. Applied Animal Behaviour Science, 142(1-2), 61-68. DOI: 10.1016/j.applanim.2012.09.009  

  • August 10, 2013
  • 06:41 AM

Is Neuroscience Really Too Small?

by Neuroskeptic in Neuroskeptic_Discover

Back in April a paper came out in Nature Reviews Neuroscience that shocked many: Katherine Button et al’s Power failure: why small sample size undermines the reliability of neuroscience It didn’t shock me, though, skeptic that I am: I had long suspected that much of neuroscience (and science in general) is underpowered – that is, [...]The post Is Neuroscience Really Too Small? appeared first on Neuroskeptic.... Read more »

Button KS, Ioannidis JP, Mokrysz C, Nosek BA, Flint J, Robinson ES, & Munafò MR. (2013) Power failure: why small sample size undermines the reliability of neuroscience. Nature reviews. Neuroscience, 14(5), 365-76. PMID: 23571845  

  • August 3, 2013
  • 06:13 PM

Thoughts about altmetrics (an unorganized, overdue post)

by Hadas Shema in Information Culture

I  haven’t written about altmetrics so far. Not because it’s not a worthwhile subject, but because there’s so much I don’t know where to begin. The term “altmetrics” was first suggested in a...

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Stefanie Haustein, Isabella Peters, Judit Bar-Ilan, Jason Priem, Hadas Shema, & Jens Terliesner. (2013) Coverage and adoption of altmetrics sources in the bibliometric community. ISSI conference. arXiv: 1304.7300v1

  • August 3, 2013
  • 03:01 AM

Boys Don’t Cry, But They Can Be Sensitive! Behavioural Descriptions of Counterstereotypical People Cause Greater Prejudice than Personality Descriptions

by Mark Rubin in Mark Rubin's Social Psychology Research Blog

Stereotypes are pretty useful things! We use them to help us to understand and respond to people from a large and diverse array of social groups. But how do people feel about individuals who buck the trend and contradict stereotypes? For example, how do people feel about a man who is crying or a woman who is smoking a cigar!... Read more »

  • August 2, 2013
  • 04:03 AM

Getting Science Right: Fraudulent Scientists

by Katja Keuchenius in United Academics

More and more scientific articles are being retracted because of misconduct. Diederik Stapel, of the anti-social meat eaters, is not even the recordholder. An interview with Adam Marcus, who blogs about retractions.... Read more »

Ferric C. Fang, R. Grant Steen, and, & Arturo Casadevall. (2012) Misconduct accounts for the majority of retracted scientific publications. Proceedings of the National Academy of Sciences of the United States of America . DOI: 10.1073/pnas.1212247109  

  • July 26, 2013
  • 10:30 AM

Why we need pre-registration

by Dorothy Bishop in bishopblog

There has been a chorus of disapproval this week at the suggestion that researchers should 'pre-register' their studies with journals and spell out in advance the methods and analyses that they plan to do. Those who wish to follow the debate should look at this critique by Sophie Scott, with associated comments, and the responses to it collated by Pete Etchells. They should also read the explanation of the pre-registration proposals and FAQ by Chris Chambers.
Quite simply, pre-registration is designed to tackle two problems in scientific publishing:
a) Bias against publication of null results
b) A failure to distinguish hypothesis-generating (exploratory) from hypothesis-testing analyses
Either of these alone is bad for science: the combined effect of both of them is catastrophic.... Read more »

  • July 25, 2013
  • 07:20 AM

Google celebrates Rosalind Franklin, British biophysicist and X-ray crystallographer

by GrrlScientist in GrrlScientist

Today's Google Doodle honours pioneering British biophysicist and x-ray crystallographer, Rosalind Franklin... Read more »

Bernal John Desmond. (1958) Dr. Rosalind E. Franklin. Nature, 182(4629), 154-154. DOI: 10.1038/182154a0  

Glynn J. (2008) Rosalind Franklin: 50 years on. Notes and Records of the Royal Society, 62(2), 253-255. DOI: 10.1098/rsnr.2007.0052  

Finch J. T., & Klug A. (1959) Structure of Poliomyelitis Virus. Nature, 183(4677), 1709-1714. DOI: 10.1038/1831709a0  

Creager Angela N. H., & Morgan Gregory J. (2008) After the Double Helix. Isis, 99(2), 239-272. DOI: 10.1086/588626  

  • July 24, 2013
  • 11:14 AM

Mammoth Cloning: the Ethics

by ulian Savulescu in United Academics

he display of a frozen mammoth in Japan has again raised questions as to the possibility of creating a live born clone of extinct animals.

Theoretically, mammoths could be cloned by recovering, reconstructing or synthesizing viable mammoth DNA and injecting it into the egg cell of a modern elephant whose nuclear DNA has been removed; alternatively, mammoth genetic material could be introduced into an elephant genome in order to create a mammoth-elephant hybrid or chimera.

This raises an ethical question as to whether we should start the journey down one of these paths.... Read more »

Douglas T, Powell R, & Savulescu J. (2013) Is the creation of artificial life morally significant?. Studies in history and philosophy of biological and biomedical sciences. PMID: 23810562  

  • July 23, 2013
  • 08:32 PM

How is gender bias in science studied? II. Learning from existing data

by Terrific T in Science, I Choose You

This is part 2 of my 4-part series about studying gender bias in science (See part 1). For studies using existing data, we look at information that is already available, and learn from the information through data analysis. The difficulty in these studies is that because you are not in control of how the information […]... Read more »

Schroeder J., Dugdale H. L., Radersma R., Hinsch M., Buehler D. M., Saul J., Porter L., Liker A., De Cauwer I., & Johnson P. J. (2013) Fewer invited talks by women in evolutionary biology symposia. Journal of Evolutionary Biology. DOI: 10.1111/jeb.12198  

  • July 19, 2013
  • 08:14 AM

Animal Research – Results Too Good to Be True?

by Dyani Lewis in United Academics

The road to market for a promising new therapy can be notoriously long and treacherous. Before the first small-scale clinical trials in humans can even be contemplated, a new therapy (such as a drug or surgical procedure) must first pass muster in preclinical animal studies.... Read more »

Tsilidis KK, Panagiotou OA, Sena ES, Aretouli E, Evangelou E, Howells DW, Salman RA, Macleod MR . (2013) Evaluation of excess significance bias in animal studies of neurological diseases. PLoS Biology . DOI: 10.1371/journal.pbio.1001609  

  • July 18, 2013
  • 08:37 PM

Dog-eared books

by Cobb & Hecht in Do You Believe In Dog?

Hi Julie, I loved hearing from Clare Browne about her research into timing of reinforcement in our first guest post last week, and it certainly stimulated lots of great comments and questions on Facebook and Google+.  I know you've been busy Chaser-ing around (lucky ducks, both!) and there's also all those amazing conferences happening this week, what with the ISAZ, IAHAIO and AVSAB events on in Chicago, so just a very quick post from me this week! You know how we recently put together out list of top ten books for the Science Book a Day team? Well, Chaser's upcoming book release reminded me that we should put them all in one place here, so that we (or anyone else looking for a canine science book or fourteen) could find them easily if needed.  Science Book A DayIn no particular order, here they are: McGreevy (2009) A Modern Dog’s Life. A fabulous book, written with humour and insight, that offers a modern take on what challenges and motivates our dogs and how we can best meet their needs. to purchase: (2009) Inside of a Dog.What’s it like to be a dog? This book covers the science of how dogs think and perceive the world and is accompanied by personal reflections on Horowitz’s own dog’s behaviour. Get to know the umwelt of the dog. to purchase: Bradshaw (2012) Dog Sense: How the New Science of Dog Behavior Can Make You a Better Friend to Your Pet.This recent publication answers the very important question: “What’s good for dogs?” Exp... Read more »

  • July 17, 2013
  • 04:03 PM

Sunset on Mauna Kea

by Olga Vovk in Milchstraße

Big Island (and particularly Mauna Kea) is the preferred place to train Mars rovers... Read more »

Guy Webster, Rachel Hoover, Dwayne Brown. (2012) NASA Rover's First Soil Studies Help Fingerprint Martian Minerals. NASA web site. info:/

  • July 16, 2013
  • 09:18 AM

How Many Microbes Are Hiding Among Us?

by Guillaume Cote-Maurais in United Academics

We know that we are surrounded by a myriad of microorganisms, but precise characterization of the diversity of this microscopic population was still impossible recently. The difficulty of identifying and characterize microbes in samples arise from the fact that the different conditions used in laboratories to grow microbes are unsuitable for a majority of them. These hard to know microorganism became known as ‘microbial dark matter’, because they were as hard to get a handle on as the dark matter in the universe.... Read more »

Roseanne F. Zhao, Ph.D. (2013) The Power of Sequencing Single Cell Genomes . NIH Medical Scientist. info:/

  • July 13, 2013
  • 03:56 PM

A New Kind of Peer Review?

by Neuroskeptic in Neuroskeptic_Discover

Writing in the Journal of Clinical Epidemiology, a Dr Yvo Smulders of the Netherlands makes a proposal: A two-step manuscript submission process can reduce publication bias Smulder’s point is that scientific manuscripts should be submitted for peer review with the results and discussion omitted. The reviewers would judge the submission on the strength of the [...]The post A New Kind of Peer Review? appeared first on Neuroskeptic.... Read more »

  • July 11, 2013
  • 06:26 PM

Dog training: Do you get the timing right?

by Cobb & Hecht in Do You Believe In Dog?

Do You Believe in Dog? is approaching our one-year anniversary (Wow! Yay!!!), and in the coming months, we will be opening up the blog to guest posts from other researchers exploring canine behaviour, cognition and welfare. Give a warm welcome to our first guest, Clare Browne from the University of Waikato in New Zealand. Hi Mia and Julie,As you both know from the last Canine Science Forum, my PhD investigates dog-human communication and how this communication affects dog training.(source)I would like to claim that everyone is New Zealand is a fantastic dog trainer and we all communicate brilliantly with our dogs, but alas, we’re just like everyone else. It turns out that when people give feedback to dogs during training, we’re often a bit slow. Let me explain...You’re no doubt aware that if we want to increase the likelihood that a behaviour occurs again, positive reinforcement (AKA “rewarding” -- adding something to keep the behaviour going) will achieve this. The types of positive reinforcement that are most commonly used in everyday dog training are verbal praise, food, and patting/petting. My PhD studies investigated two things: a) how fast are dog owners delivering positive reinforcement to dogs; and b) does it matter if owners are slow in providing dogs with reinforcement?Not really Clare's gumbootsTo answer the first of these questions, I put on my gumboots and spent many evenings at my friendly local dog clubs, filming owners training their dogs in beginner classes. I collected 1,810 instances where commands were given to dogs. I then went slightly mad and spent months watching videos of people training their dogs. Figure 1 shows how all the dogs responded to their owners, and 44% of the time, dogs did not respond to their owners at all. This one result made me feel like I wasn’t wasting all these years of my PhD – there clearly is a need for research into the efficacy of dog training!I used some fancy computer software and measured very precisely (down to 25 frames per second) the time between when the owners said the command and when the dogs performed the behavior, like laying down or sitting. I found that owners varied a lot in the time it took them to deliver positive reinforcement to their dogs. Some owners were almost instantaneous with their praise and then the treat followed quickly, whereas others took ages – the longest time was over 6 s! (That might not sound long to you, but try imagining that you’re a Labrador and having to wait 6 s for a treat, all of a sudden it’s a much more serious situation.) But does this even matter? Had I gone mad watching videos in my darkened office for no good reason?... Read more »

Browne Clare M., Starkey Nicola J., Foster T. Mary, & McEwan James S. (2013) What dog owners read: A review of best-selling books. Journal of Veterinary Behavior: Clinical Applications and Research, 8(4). DOI: 10.1016/j.jveb.2013.04.040  

Browne Clare M., Starkey Nicola J., Foster Mary T., & McEwan James S. (2011) Timing of reinforcement during dog training. Journal of Veterinary Behavior: Clinical Applications and Research, 6(1), 58-59. DOI: 10.1016/j.jveb.2010.09.058  

  • July 10, 2013
  • 08:22 AM

Can We Get Useful Information from Assessing Pain Intensity in Chronic Pain?

by Kim Kristiansen in Picture of Pain

Chronic pain is chronic and thereby will often be present for many years, perhaps the rest of a person’s life. We also know pain intensity changes over time, so how useful information can we really get from assessing pain intensity? And what might be important as well?... Read more »

Kim Kristiansen, M.D. (2013) Can We Get Useful Information from Assessing Pain Intensity in Chronic Pain?. Picture of Pain Blog. info:/

  • July 9, 2013
  • 06:39 PM

No, Google Scholar Shouldn’t be Used Alone for Systematic Review Searching

by Laika in Laika's Medliblog

Several papers have addressed the usefulness of Google Scholar as a source for systematic review searching. Unfortunately the quality of those papers is often well below the mark.

In 2010 I already [1] (in the words of Isla Kuhn [2]) “robustly rebutted” the Anders’ paper “PubMed versus Google Scholar for Retrieving Evidence” [3] at this blog.

But earlier this year another controversial paper was published [4]:

“Is the coverage of google scholar enough to be used alone for systematic reviews?“... Read more »

Gehanno Jean-François, Rollin Laetitia, & Darmoni Stefan. (2013) Is the coverage of Google Scholar enough to be used alone for systematic reviews. BMC medical informatics and decision making. PMID: 23302542  

Giustini Dean, & Kamel Boulos Maged N. (2013) Google Scholar is not enough to be used alone for systematic reviews. Online Journal of Public Health Informatics, 5(2). DOI: 10.5210/ojphi.v5i2.4623  

Chou Wen-ying Sylvia, Prestin Abby, Lyons Claire, & Wen Kuang-yi. (2013) Web 2.0 for Health Promotion: Reviewing the Current Evidence. American Journal of Public Health, 103(1). DOI: 10.2105/AJPH.2012.301071  

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