Posts

October 06, 2014

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10:42 PM | Can our brains process words while we sleep?
Learning by listening to things while you sleep might be a desperate last resort for budding linguists and university students cramming for their finals, but how much can the human brain actually take on board while in a state of unconsciousness? It is fairly well-established that the brain processes information while we sleep (such as…

Kouider, S., Andrillon, T., Barbosa, L., Goupil, L. & Bekinschtein, T. (2014). Inducing Task-Relevant Responses to Speech in the Sleeping Brain, Current Biology, 24 (18) 2208-2214. DOI: 10.1016/j.cub.2014.08.016

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7:55 PM | Orange Corn Aims to Fight Vitamin A Deficiency
GMO food is still a hot button topic, honestly for no other reason than fear. Sure Monsanto is a big evil corporation, but the science is only as bad as […]

Owens BF, Lipka AE, Magallanes-Lundback M, Tiede T, Diepenbrock CH, Kandianis CB, Kim E, Cepela J, Mateos-Hernandez M, Buell CR & Buckler ES (2014). A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels., Genetics, PMID: http://www.ncbi.nlm.nih.gov/pubmed/25258377

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6:29 PM | The Biology of Nagging
A female pied flycatcher can't feed herself sufficientlywhile she incubates her eggs and newly-hatchedchicks. Photo by Alejandro Cantarero.I have been blessed with the fortune of not just having two healthy and happy babies, but being able to spend much of the spring and summer nurturing them and watching them develop and grow. But it has not been all roses: their smiles beam through the fog of my sleep deprivation and exhaustion. Their tears are met with my own. Our clothes are stained in a […]

Cantarero, A., López-Arrabé, J., Palma, A., Redondo, A. & Moreno, J. (2014). Males respond to female begging signals of need: a handicapping experiment in the pied flycatcher, Ficedula hypoleuca, Animal Behaviour, 94 167-173. DOI: 10.1016/j.anbehav.2014.05.002

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3:18 PM | Bioinformatics tools extracted from a typical mammalian genome project [supplement]
This is Table 1 that accompanies the full blog post: Bioinformatics tools extracted from a typical mammalian genome project. See the main post for the details and explanation. The table is too long to keep in the post, but I wanted it to be web-searchable. A copy also resides at FigShare: http://dx.doi.org/10.6084/m9.figshare.1194867 Software tool/object/item/resource access […]

Carbone L., R. Alan Harris, Sante Gnerre, Krishna R. Veeramah, Belen Lorente-Galdos, John Huddleston, Thomas J. Meyer, Javier Herrero, Christian Roos, Bronwen Aken & Fabio Anaclerio (2014). Gibbon genome and the fast karyotype evolution of small apes, Nature, 513 (7517) 195-201. DOI: http://dx.doi.org/10.1038/nature13679

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3:12 PM | Bioinformatics tools extracted from a typical mammalian genome project
In this extended blog post, I describe my efforts to extract the information about bioinformatics-related items from a recent genome sequencing paper, and the larger issues this raises in the field. It’s long, and it’s something of a hybrid between a blog post and a paper format, just to give it some structure for my […]

Carbone L., R. Alan Harris, Sante Gnerre, Krishna R. Veeramah, Belen Lorente-Galdos, John Huddleston, Thomas J. Meyer, Javier Herrero, Christian Roos, Bronwen Aken & Fabio Anaclerio (2014). Gibbon genome and the fast karyotype evolution of small apes, Nature, 513 (7517) 195-201. DOI: http://dx.doi.org/10.1038/nature13679

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11:17 AM | A new feature of neurons
There are articles asking, “Are we ever going to understand the brain?” They imply that we have been studying the brain for long enough to be able to say how it works, if we are ever going to, and therefore hinting that it is a permanent mystery. But every week or so some new wrinkle […]

Johansson, F., Jirenhed, D., Rasmussen, A., Zucca, R. & Hesslow, G. (2014). Memory trace and timing mechanism localized to cerebellar Purkinje cells, Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1415371111

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8:36 AM | Correcting vitamin D levels improves fatigue severity?
I was interested to read the paper by Satyajeet Roy and colleagues [1] (open-access here) concluding that: "Normalization of vitamin D levels with ergocalciferol therapy significantly improves the severity of... fatigue symptoms". Ergocalciferol by the way, means vitamin D2, which is distinct from cholecalciferol (vitamin D3), the seemingly more desirable form of vitamin D supplementation (see here)."It's beyond my control"The Roy paper is open-access but a few details might be […]

Roy S, Sherman A, Monari-Sparks MJ, Schweiker O & Hunter K (2014). Correction of Low Vitamin D Improves Fatigue: Effect of Correction of Low Vitamin D in Fatigue Study (EViDiF Study)., North American journal of medical sciences, 6 (8) 396-402. PMID: http://www.ncbi.nlm.nih.gov/pubmed/25210673

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7:33 AM | Old people are immune against the cocktail party effect
Imagine standing at a cocktail party and somewhere your name gets mentioned. Your attention is immediately grabbed by the sound of your name. It is a classic psychological effect with a new twist: old people are immune. The so-called cocktail party effect has fascinated researchers for a long time. Even though you do not consciously […]

Naveh-Benjamin M, Kilb A, Maddox GB, Thomas J, Fine HC, Chen T & Cowan N (2014). Older adults do not notice their names: A new twist to a classic attention task., Journal of experimental psychology. Learning, memory, and cognition, PMID: http://www.ncbi.nlm.nih.gov/pubmed/24820668

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3:45 AM | Models and metaphors we live by
George Lakoff and Mark Johnson’s Metaphors we live by is a classic, that has had a huge influence on parts of linguistics and cognitive science, and some influence — although less so, in my opinion — on philosophy. It is structured around the thought that “[m]etaphor is one of our most important tools for trying […]

Narayanan, S. (1997). Embodiment in language understanding: Sensory-motor representations for metaphoric reasoning about event descriptions., PhD Thesis (University of California, Berkeley),

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October 05, 2014

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5:43 PM | Using “Programmable” Antibiotics to Attack Drug-Resistant Microbes
The body is pretty great at self regulation, that is up until it isn’t. The antibiotic era was one that improved human health hundreds of times over. Unfortunately health is […]

Luciano Marraffini et al. (2014). Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials, Nature Biotechnology, Other:

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October 04, 2014

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6:47 PM | The Path of Antibiotic Resistance
MRSA, not that long ago we had no idea what MRSA was… mostly because it hadn’t come into prevalence. With an increase in the use and abuse of antibiotics there […]

Kouyos RD, Metcalf CJ, Birger R, Klein EY, Abel Zur Wiesch P, Ankomah P, Arinaminpathy N, Bogich TL, Bonhoeffer S, Brower C & Chi-Johnston G (2014). The path of least resistance: aggressive or moderate treatment?, Proceedings. Biological sciences / The Royal Society, 281 (1794) PMID: http://www.ncbi.nlm.nih.gov/pubmed/25253451

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8:57 AM | The gut-brain axis and schizophrenia
A micropost to direct your attention to the recent paper by Katlyn Nemani and colleagues [1] titled: 'Schizophrenia and the gut-brain axis'. Mentioning words like that, I couldn't resist offering a little exposure to this review and opinion piece, drawing on what seems to be some renewed research interest in work started by pioneers such as the late Curt Dohan [2].The usual triad of gastrointestinal (GI) variables - gut barrier, gut bacteria and gut immune function - are mentioned in the […]

Nemani, K., Ghomi, R., McCormick, B. & Fan, X. (2014). Schizophrenia and the gut–brain axis, Progress in Neuro-Psychopharmacology and Biological Psychiatry, DOI: 10.1016/j.pnpbp.2014.08.018

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October 03, 2014

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9:24 PM | The Neurobiological Basis of a Human-Pet Relationship
My wife adores our cats. Now, I’m not a cat person, but my wife loves them. In fact if we had children and someone held a gun to her head and said […]

Stoeckel, L., Palley, L., Gollub, R., Niemi, S. & Evins, A. (2014). Patterns of Brain Activation when Mothers View Their Own Child and Dog: An fMRI Study, PLoS ONE, 9 (10) DOI: 10.1371/journal.pone.0107205

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8:01 PM | Sleeping Brains Understand Words
Have you ever heard someone describe a task as being so easy that they ‘could do it in their sleep’? A fascinating new study from a team of French neuroscientists shows that this statement may be literally true, far more often than you’d think: Inducing Task-Relevant Responses to Speech in the Sleeping Brain Sid Kouider […]The post Sleeping Brains Understand Words appeared first on Neuroskeptic.

Kouider S, Andrillon T, Barbosa LS, Goupil L & Bekinschtein TA (2014). Inducing task-relevant responses to speech in the sleeping brain., Current Biology, 24 (18) 2208-14. PMID: http://www.ncbi.nlm.nih.gov/pubmed/25220055

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Editor's Pick
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3:55 PM | Tricksy insects sing a song of love and deceit
Beyond a spider snacking on an unfortunate fly, the social lives of insects tend to go unrecognized. Perhaps you notice all the ants marching in a line, or bees heading back to a nest, but it all seems so mechanical, so primal. … Continue reading →

Nakano, R., Ihara, F., Mishiro, K., Toyama, M. & Toda, S. (2014). Double meaning of courtship song in a moth, Proceedings of the Royal Society B: Biological Sciences, 281 (1789) 20140840-20140840. DOI: 10.1098/rspb.2014.0840

Hoikkala, A., Aspi, J. & Suvanto, L. (1998). Male courtship song frequency as an indicator of male genetic quality in an insect species, Drosophila montana, Proceedings of the Royal Society B: Biological Sciences, 265 (1395) 503-508. DOI: 10.1098/rspb.1998.0323

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2:38 PM | Breaking Research: Aging can be delayed in fruit flies by activating AMPK in the gut
How can we slow or even halt the steady march of aging? In a previous post, I reviewed a paper that asked “What causes aging?” (the prevailing hypothesis is that aging is caused by accumulating cell damage). Understanding why we age is important for developing ways to interfere with the process. But there are other […]

Ulgherait M., Michael Rera, Jacqueline Graniel & David W. Walker (2014). AMPK Modulates Tissue and Organismal Aging in a Non-Cell-Autonomous Manner, Cell Reports, 8 (6) 1767-1780. DOI: http://dx.doi.org/10.1016/j.celrep.2014.08.006

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2:02 PM | How to Say “SOS” in Catfish
It’s good to have a plan in case of emergency. If there’s a fire, take the stairs to the ground floor. If a bird tries to eat you, say “ERK ERK ERK” by grinding your spine bone against your shoulder bone until it drops you. That latter one will work best if you’re a certain […]The post How to Say “SOS” in Catfish appeared first on Inkfish.

Knight L & Ladich F (2014). Distress sounds of thorny catfishes emitted underwater and in air: characteristics and potential significance., The Journal of experimental biology, PMID: http://www.ncbi.nlm.nih.gov/pubmed/25267850

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9:10 AM | S100B and schizophrenia meta-analysed
I don't know if it's just me but this year (2014) I seem to be covering a lot more meta-analysis papers on this blog. I assume that's because of the increasing volume of peer-reviewed research being created year-on-year leading to greater volumes of research fodder for such grand reviews. Whatever the reason(s), there are some really interesting conclusions being reached in that literature as per the meta-analysis by Aleksovska and colleagues [1] (open-access) focusing on S100B […]

Aleksovska K, Leoncini E, Bonassi S, Cesario A, Boccia S & Frustaci A (2014). Systematic Review and Meta-Analysis of Circulating S100B Blood Levels in Schizophrenia., PloS one, 9 (9) PMID: http://www.ncbi.nlm.nih.gov/pubmed/25202915

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8:51 AM | Did a five-day camp without digital devices really boost children's interpersonal skills?
"There's a brilliant study that came out two weeks ago," Baroness Professor Susan Greenfield said at a recent event promoting her new book, "... they took away all [the pre-teens'] digital devices for five days and sent them to summer camp ... and tested their interpersonal skills, and guess what, even within five days they'd changed."Greenfield highlighted this study in the context of her dire warnings about the harmful psychological effects of modern screen- and internet-based technologies. […]

LAMBERT, N., MULDER, S. & FINCHAM, F. (2014). Thin slices of infidelity: Determining whether observers can pick out cheaters from a video clip interaction and what tips them off, Personal Relationships, DOI: 10.1111/pere.12052

Uhls, Y., Michikyan, M., Morris, J., Garcia, D., Small, G., Zgourou, E. & Greenfield, P. (2014). Five days at outdoor education camp without screens improves preteen skills with nonverbal emotion cues, Computers in Human Behavior, 39 387-392. DOI: 10.1016/j.chb.2014.05.036

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October 02, 2014

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11:46 PM | Ambivalence and Eating Disorders: Inpatient Treatment, Belonging, and Identity
When Tetyana Tweeted and “Tumblr-ed” (is there a better name for putting something on Tumblr?) a quote from a qualitative research article about ambivalence and eating disorders, I knew I would want to write a blog post about it. Of course, life happened, and so this post is coming a little later than I had intended. Nonetheless, I am happy to be sharing a post about a fresh article by Karin Eli (2014) about eating disorders and ambivalence in the inpatient hospital setting. The […]

Eli K (2014). Between difference and belonging: configuring self and others in inpatient treatment for eating disorders., PloS one, 9 (9) PMID: http://www.ncbi.nlm.nih.gov/pubmed/25210886

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10:15 PM | Living on the edge: doped graphene quantum dots perform as well as platinum in fuel cell electrodes!
Beating platinum is akin to finding the Holy Grail for material scientists working on fuel cells.  We know very little about the microscopic workings of catalysis, but platinum – beautiful, shiny, and and far too expensive to base an economy … Continue reading →

Fei, H., Ye, R., Ye, G., Gong, Y., Peng, Z., Fan, X., Samuel, E., Ajayan, P. & Tour, J. (2014). Boron- and Nitrogen-Doped Graphene Quantum Dots/Graphene Hybrid Nanoplatelets as Efficient Electrocatalysts for Oxygen Reduction, ACS Nano, 2147483647. DOI: 10.1021/nn504637y

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9:04 PM | The Mysterious Origins of HIV Discovered
There have been a lot of theories on where HIV came from, anywhere from the mundane, it spread from other animals. To the down right crazy, the government created it […]

Nuno R. Faria1, Andrew Rambaut, Marc A. Suchard, Guy Baele, Trevor Bedford, Melissa J. Ward, Andrew J. Tatem, João D. Sousa, Nimalan Arinaminpathy, Jacques Pépin, & David Posada (2014). The early spread and epidemic ignition of HIV-1 in human populations, Science, Other:

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6:01 PM | Survivin: You wouldn’t be alive without it
  Enzymes perform numerous tasks in order to contribute to the global goal of organism survival. One such enzyme is Survivin. Survivin wears many “hats” within the cell and is a vital part of cellular homeostasis. Here I will introduce you to two of the main processes Survivin regulates. Survivin is a multifunctional protein involved […]

Johnson M.E. (2004). Survivin: A Bifunctional Inhibitor of Apoptosis Protein, Veterinary Pathology, 41 (6) 599-607. DOI: http://dx.doi.org/10.1354/vp.41-6-599

WHEATLEY S. (2005). Survivin: A Protein with Dual Roles in Mitosis and Apoptosis, International Review of Cytology, 247 35-88. DOI: http://dx.doi.org/10.1016/s0074-7696(05)47002-3

Tazo Y., Takashi Onda & Makoto Saegusa (2014). Bifunctional roles of survivin-ΔEx3 and survivin-2B for susceptibility to apoptosis in endometrial carcinomas, Journal of Cancer Research and Clinical Oncology, DOI: http://dx.doi.org/10.1007/s00432-014-1762-8

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12:03 PM | Coeliac disease risk not affected by early feeding practices
I'd like to bring three papers to your attention, all united by their discussion of coeliac (celiac) disease, that most classic of autoimmune conditions in the most part managed by the use of a lifelong gluten-free diet.First up are the papers by Elena Lionetti and colleagues [1] and Sabine Vriezinga and colleagues [2] which unfortunately pour cold water on the notion that the risk of developing coeliac disease (CD) can be somehow mitigated via the use of either the early or delayed […]

Lionetti E, Castellaneta S, Francavilla R, Pulvirenti A, Tonutti E, Amarri S, Barbato M, Barbera C, Barera G, Bellantoni A & Castellano E (2014). Introduction of Gluten, HLA Status, and the Risk of Celiac Disease in Children., The New England journal of medicine, 371 (14) 1295-1303. PMID: http://www.ncbi.nlm.nih.gov/pubmed/25271602

Vriezinga SL, Auricchio R, Bravi E, Castillejo G, Chmielewska A, Crespo Escobar P, Kolaček S, Koletzko S, Korponay-Szabo IR, Mummert E & Polanco I (2014). Randomized Feeding Intervention in Infants at High Risk for Celiac Disease., The New England journal of medicine, 371 (14) 1304-1315. PMID: http://www.ncbi.nlm.nih.gov/pubmed/25271603

Elfström P, Sundström J & Ludvigsson JF (2014). Systematic review with meta-analysis: associations between coeliac disease and type 1 diabetes., Alimentary pharmacology & therapeutics, PMID: http://www.ncbi.nlm.nih.gov/pubmed/25270960

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10:37 AM | What do sperm have to do with brain tumors?
  This post was originally published in the Knoepfler Lab Stem Cell Blog.      Sometimes in science there are unexpected threads tying seemingly very different things together. Unraveling the knots in these threads can lead to new insights into important developmental processes and mechanisms of disease. My lab studies epigenomic and transcription factors including […]

Yuen, B., Bush, K., Barrilleaux, B., Cotterman, R. & Knoepfler, P. (2014). Histone H3.3 regulates dynamic chromatin states during spermatogenesis, Development, 141 (18) 3483-3494. DOI: 10.1242/dev.106450

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8:57 AM | Volatile organic compounds and autism
As harsh as the phrase volatile organic compounds (VOCs) might appear at first glance, all this refers to is a class of compounds containing carbon which have a tendency to evaporate at room temperature assuming normal air pressure. VOCs have been associated with pollutants as per their inclusion in various literature on the topic of things like indoor air pollution (see here) and the fact that just about everything around us in the modern home or office is likely to release VOCs. Whilst not […]

Cozzolino R, De Magistris L, Saggese P, Stocchero M, Martignetti A, Di Stasio M, Malorni A, Marotta R, Boscaino F & Malorni L & (2014). Use of solid-phase microextraction coupled to gas chromatography-mass spectrometry for determination of urinary volatile organic compounds in autistic children compared with healthy controls., Analytical and bioanalytical chemistry, 406 (19) 4649-62. PMID: http://www.ncbi.nlm.nih.gov/pubmed/24828982

Kalkbrenner AE, Schmidt RJ & Penlesky AC (2014). Environmental Chemical Exposures and Autism Spectrum Disorders: A Review of the Epidemiological Evidence., Current problems in pediatric and adolescent health care, PMID: http://www.ncbi.nlm.nih.gov/pubmed/25199954

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8:50 AM | JUST PUBLISHED: A Trial to Evaluate the Efficacy of an Integrated Smoking Cessation Intervention among Mental Health Patients
Depending on diagnosis and setting, between 33 and 90 per cent of people with mental illness smoke tobacco, both in Australia and worldwide. As a result, tobacco-related diseases are one of the leading causes of mortality among this population subgroup. A paucity of research to date has examined the efficacy of cessation strategies to assist people with mental illness to quit smoking. However, limited findings have suggested that aids that have been found to be effective for the general […]

Metse, A., Bowman, J., Wye, P., Stockings, E., Adams, M., Clancy, R., Terry, M., Wolfenden, L., Freund, M., Allan, J. & Prochaska, J. (2014). Evaluating the efficacy of an integrated smoking cessation intervention for mental health patients: Study protocol for a randomised controlled trial, Trials, 15 (266) 1-7. DOI: 10.1186/1745-6215-15-266

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October 01, 2014

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8:21 PM | The Ever Plastic Brain and Intellectual Disabilities
The plasticity of the brain is always somewhat of a shock. It’s near incredible what the brain can achieve, look at people who have strokes, or any other sort of […]

Hans T. Bjornsson, Joel S. Benjamin, Li Zhang, Jacqueline Weissman, Elizabeth E. Gerber, Yi-Chun Chen, Rebecca G. Vaurio, Michelle C. Potter, Kasper D. Hansen & Harry C. Dietz & (2014). Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome, Science Translational Medicine , Other:

Hans T. Bjornsson, Joel S. Benjamin, Li Zhang, Jacqueline Weissman, Elizabeth E. Gerber, Yi-Chun Chen, Rebecca G. Vaurio, Michelle C. Potter, Kasper D. Hansen & Harry C. Dietz & (2014). Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome, Science Translational Medicine, Other:

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6:17 PM | What Encourages People to Walk Their Dog?
And is dog-walking a good way to persuade people to take more exercise?Photo: Monkey Business Images / ShutterstockWe know that most people do not get the 150 minutes of exercise per week that is recommended. Could encouraging people to walk their dogs more often help, and if so, how best to go about it? A new paper by Carri Westgarth et al (2014) of the University of Liverpool reviews the state of current research.Although to some dog owners a daily walk is an essential part of the routine, […]

Cutt, H., Giles-Corti, B. & Knuiman, M. (2008). Encouraging physical activity through dog walking: Why don't some owners walk with their dog?, Preventive Medicine, 46 (2) 120-126. DOI: 10.1016/j.ypmed.2007.08.015

Westgarth, C., Christley, R. & Christian, H. (2014). How might we increase physical activity through dog walking?: A comprehensive review of dog walking correlates, International Journal of Behavioral Nutrition and Physical Activity, 11 (1) 83. DOI: 10.1186/1479-5868-11-83

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4:00 PM | Walking the Line: The Complexity of Punishment Decisions
One night, Mark withdraws $200 cash from an ATM. He is on his way to meet his family, and intends to treat everyone to a special dinner at his favorite restaurant for his wife’s birthday. Just as he finishes his transaction, Dan rounds the street corner, pulls out a knife, and threatens Mark to hand … Continue reading →

Buckholtz J.W., Paul E. Dux, David H. Zald, John C. Gore, Owen D. Jones & René Marois (2008). The Neural Correlates of Third-Party Punishment, Neuron, 60 (5) 930-940. DOI: http://dx.doi.org/10.1016/j.neuron.2008.10.016

Greene J.D. (2001). An fMRI Investigation of Emotional Engagement in Moral Judgment, Science, 293 (5537) 2105-2108. DOI: http://dx.doi.org/10.1126/science.1062872

Knoch D. (2006). Disruption of Right Prefrontal Cortex by Low-Frequency Repetitive Transcranial Magnetic Stimulation Induces Risk-Taking Behavior, Journal of Neuroscience, 26 (24) 6469-6472. DOI: http://dx.doi.org/10.1523/jneurosci.0804-06.2006

Sanfey A.G. (2003). The Neural Basis of Economic Decision-Making in the Ultimatum Game, Science, 300 (5626) 1755-1758. DOI: http://dx.doi.org/10.1126/science.1082976

Wout M.V., Alan G. Sanfey & Andre Aleman (2005). Repetitive transcranial magnetic stimulation over the right dorsolateral prefrontal cortex affects strategic decision-making, NeuroReport, 16 (16) 1849-1852. DOI: http://dx.doi.org/10.1097/01.wnr.0000183907.08149.14

Yamada M., Saori Fujie, Motoichiro Kato, Tetsuya Matsuda, Harumasa Takano, Hiroshi Ito, Tetsuya Suhara & Hidehiko Takahashi (2012). Neural circuits in the brain that are activated when mitigating criminal sentences, Nature Communications, 3 759. DOI: http://dx.doi.org/10.1038/ncomms1757

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