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  • May 6, 2015
  • 09:42 AM
  • 9 views

Video Tip of the Week: Human Phenotype Ontology, HPO

by Mary in OpenHelix

Typically, our Tips-of-the-Week cover a specific software tool or feature that we think readers would maybe like to try out. But this week’s tip is a bit different. It’s got a conceptual piece that is important, as well as referencing several software tools that work with this crucial concept to enable interoperability of many tools, […]... Read more »

Deans Andrew R., Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, & Laurel D. Cooper. (2015) Finding Our Way through Phenotypes. PLoS Biology, 13(1). DOI: http://dx.doi.org/10.1371/journal.pbio.1002033  

Kohler, S., Doelken, S., Mungall, C., Bauer, S., Firth, H., Bailleul-Forestier, I., Black, G., Brown, D., Brudno, M., Campbell, J.... (2013) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Research, 42(D1). DOI: 10.1093/nar/gkt1026  

Köhler, S., Schulz, M., Krawitz, P., Bauer, S., Dölken, S., Ott, C., Mundlos, C., Horn, D., Mundlos, S., & Robinson, P. (2009) Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies. The American Journal of Human Genetics, 85(4), 457-464. DOI: 10.1016/j.ajhg.2009.09.003  

Zemojtel, T., Kohler, S., Mackenroth, L., Jager, M., Hecht, J., Krawitz, P., Graul-Neumann, L., Doelken, S., Ehmke, N., Spielmann, M.... (2014) Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Science Translational Medicine, 6(252), 252-252. DOI: 10.1126/scitranslmed.3009262  

Girdea, M., Dumitriu, S., Fiume, M., Bowdin, S., Boycott, K., Chénier, S., Chitayat, D., Faghfoury, H., Meyn, M., Ray, P.... (2013) PhenoTips: Patient Phenotyping Software for Clinical and Research Use. Human Mutation, 34(8), 1057-1065. DOI: 10.1002/humu.22347  

  • May 6, 2015
  • 08:00 AM
  • 9 views

Plants Aren’t Just Male Or Female

by Mark Lasbury in As Many Exceptions As Rules

It’s hard enough to believe that flowering plants have different sexes, but how about plants that have three sexes? One trioecious plant varies it sex ratio depending on how much water is around, while another only shows three sexes when it lives near a particular bat. But most amazing, man made the papaya into a three-sex plant. Your tropical fruit salad is made with a hermaphrodite.... Read more »

VanBuren R, Zeng F, Chen C, Zhang J, Wai CM, Han J, Aryal R, Gschwend AR, Wang J, Na JK.... (2015) Origin and domestication of papaya Yh chromosome. Genome research, 25(4), 524-33. PMID: 25762551  

  • May 6, 2015
  • 04:40 AM
  • 12 views

Features of dyspraxia in childhood epilepsy

by Paul Whiteley in Questioning Answers

Developmental coordination disorder (DCD) or dyspraxia is a condition affecting 'planning of movements and coordination'. No-one really knows exactly how and why DCD comes about but various risk factors are associated with the condition (see here) including the possibility of acquired problems through head injury or a stroke for example.I was recently interested to read the paper published by Colin Reilly and colleagues [1] and their findings that: "Parent-reported symptoms of DCD are very ........ Read more »

Reilly C, Atkinson P, Das KB, Chin RF, Aylett SE, Burch V, Gillberg C, Scott RC, & Neville BG. (2015) Features of developmental coordination disorder in active childhood epilepsy: a population-based study. Developmental medicine and child neurology. PMID: 25882788  

  • May 5, 2015
  • 02:36 PM
  • 47 views

Mind reading: Researchers observe moment a mind is changed

by Dr. Jekyll in Lunatic Laboratories

Researchers studying how the brain makes decisions have, for the first time, recorded the moment-by-moment fluctuations in brain signals that occur when a monkey making free choices has a change of mind. The findings result from experiments led by electrical engineering Professor Krishna Shenoy, whose Stanford lab focuses on movement control and neural prostheses – such as artificial arms – controlled by the user’s brain.... Read more »

  • May 5, 2015
  • 12:38 PM
  • 32 views

3 Reasons Octopus Locomotion Is the Weirdest

by Elizabeth Preston in Inkfish



Of course there's nothing ordinary about an octopus. It's the animal that showed us spinelessness doesn't have to mean a lack of smarts. But when researchers brought some octopuses into the lab to study exactly how the animals move, their findings were bizarre—both predictably and unpredictably.

Scientists at the Hebrew University of Jerusalem studied nine common octopuses (Octopus vulgaris) that fishers had scooped out of the ocean for them. Once the animals got comfortable in the lab, t........ Read more »

  • May 5, 2015
  • 08:55 AM
  • 31 views

Journal Club: Birdfeeding favours non-native bird species

by GrrlScientist in Maniraptora

SUMMARY: Feeding wild birds on bread and seed encourages high densities of introduced bird species at the expense of native species, thereby altering urban bird communities, according to a new study... Read more »

  • May 5, 2015
  • 08:44 AM
  • 31 views

Journal Club: Birdfeeding favours non-native bird species

by GrrlScientist in The Invisible Scientist

SUMMARY: Feeding wild birds on bread and seed encourages high densities of introduced bird species at the expense of native species, thereby altering urban bird communities, according to a new study... Read more »

  • May 5, 2015
  • 04:25 AM
  • 50 views

Childhood cat ownership and risk of later life schizophrenia?

by Paul Whiteley in Questioning Answers

'I' before the 'E' except after 'C'."Is childhood cat ownership a risk factor for schizophrenia later in life?"That was the rather peculiar question posed and partially answered in the paper by Fuller Torrey and colleagues [1]. They concluded that "cat ownership in childhood is significantly more common in families in which the child later becomes seriously mentally ill."For those new to this topic, it might sound rather strange that cat ownership in childhood might elevate the risk of mental il........ Read more »

  • May 4, 2015
  • 04:59 AM
  • 45 views

Responding to parental concerns about possible offspring autism

by Paul Whiteley in Questioning Answers

"In conclusion, despite early parental concerns, children with ASD [autism spectrum disorder] receive less proactive provider responses to these concerns than children with ID/DD [intellectual disability/developmental delay]. Less proactive/more passive provider responses are associated with delays in diagnosing ASD."So said the paper from Katharine Zuckerman and colleagues [1] (open-access) who using "nationally representative data from the 2011 Survey of Pathways to Diagnosis an........ Read more »

Katharine Elizabeth Zuckerman, Olivia Jasmine Lindly, & Brianna Kathleen Sinche. (2015) Parental Concerns, Provider Response, and Timeliness of Autism Spectrum Disorder Diagnosis. The Journal of Pediatrics. info:/10.1016/j.jpeds.2015.03.007

  • May 3, 2015
  • 11:08 PM
  • 54 views

Recent Advances: Phage Therapy for Antibiotic Resistant Staph Infections

by Geoffrey Hannigan in Prophage

Most of us have experienced, know someone who experienced, or have at least heard of Staph infections. As their name implies, these infections are caused by Staph (short for the bacterial genus Staphylococcus), occur on the skin, are often acquired in hospitals...... Read more »

  • May 2, 2015
  • 03:48 PM
  • 79 views

Walking an extra two minutes each hour may offset hazards of sitting too long

by Dr. Jekyll in Lunatic Laboratories

Eat less, workout more, these are the messages we are being sent almost on a daily basis. But how do we quantify “more” and who really should listen to that advice? Well a new study suggests that engaging in low intensity activities such as standing may not be enough to offset the health hazards of sitting for long periods of time. On the bright side, adding two minutes of walking each hour to your routine just might do the trick.... Read more »

  • May 2, 2015
  • 02:01 PM
  • 60 views

Spontaneous Events Drive Brain Functional Connectivity?

by Neuroskeptic in Neuroskeptic_Discover

A new study claims that Functional Connectivity in MRI Is Driven by Spontaneous BOLD Events

The researchers, Thomas Allan and colleagues from the University of Nottingham (one of the birthplaces of MRI), say that their results challenge the assumption that correlations in neural activity between 'networks' of brain regions reflect slow, steady low frequency oscillations within those networks. Instead, they report that the network connectivity is the result of occasional 'spikes' of coordinate... Read more »

Allan TW, Francis ST, Caballero-Gaudes C, Morris PG, Liddle EB, Liddle PF, Brookes MJ, & Gowland PA. (2015) Functional Connectivity in MRI Is Driven by Spontaneous BOLD Events. PloS one, 10(4). PMID: 25922945  

  • May 2, 2015
  • 05:55 AM
  • 59 views

Humans Navigate Naturally With Built-In GPS

by RAZ Rebecca A. Zarate in United Academics

Humans have a built-in neural map, and it’s shaped like a honeycomb.
... Read more »

Langston RF, Ainge JA, Couey JJ, Canto CB, Bjerknes TL, Witter MP, Moser EI, & Moser MB. (2010) Development of the spatial representation system in the rat. Science (New York, N.Y.), 328(5985), 1576-80. PMID: 20558721  

Solstad T, Boccara CN, Kropff E, Moser MB, & Moser EI. (2008) Representation of geometric borders in the entorhinal cortex. Science (New York, N.Y.), 322(5909), 1865-8. PMID: 19095945  

Tolman, E. (1948) Cognitive maps in rats and men. Psychological Review, 55(4), 189-208. DOI: 10.1037/h0061626  

  • May 2, 2015
  • 04:03 AM
  • 53 views

Healthcare experiences and autism

by Paul Whiteley in Questioning Answers

In today's brief post I want to highlight the important findings reported by Christina Nicolaidis and colleagues [1] who suggested that quite a bit more could be done to improve the success of "healthcare interactions" when it comes to the autism spectrum.Based on the experiences of 39 adults with autism and "16 people who had experience supporting autistic adults in healthcare settings" researchers came up with a few "patient- and provider-level factors" that might impact on said heal........ Read more »

  • May 1, 2015
  • 03:05 PM
  • 58 views

US clinics avoiding government oversight of ‘stem cell’ treatments

by Dr. Jekyll in Lunatic Laboratories

Clinics across the United States are advertising stem cell treatments that attempt to take advantage of what they perceive as exceptions in FDA regulations.The therapies in question are adipose-derived autologous stem cell treatments, in which fat cells are removed from a patient, broken down to separate components that purportedly contain stem cells, and are then reinjected into the same patient.... Read more »

  • May 1, 2015
  • 10:56 AM
  • 74 views

Lizards in Long-Term Relationships Can Skip the Foreplay

by Elizabeth Preston in Inkfish



Why would two stubby-legged, blue-tongued Australian reptiles want to stay together not just for a mating season, but for decades? A 31-year study of the reptiles has suggested an answer. While newly formed couples are still getting to know each other, lizards in long-term relationships can start mating earlier in the season. And dispensing with the foreplay might give them a reproductive advantage over their casually dating neighbors.

Tiliqua rugosa is a species of blue-tongued skink tha... Read more »

  • May 1, 2015
  • 05:00 AM
  • 75 views

Severe mental illness and victims of crime

by Paul Whiteley in Questioning Answers

"In conclusion, victimisation among people with SMI [severe mental illness] is more prevalent and associated with greater psychosocial morbidity than victimisation among the general population."That was the finding reported by Hind Khalifeh and colleagues [1] (open-access here) following their analysis of "the prevalence and impact of crime among people with SMI compared with the general population." SMI, by the way, covered various labels including: "people with psychotic disorde........ Read more »

Khalifeh H, Johnson S, Howard LM, Borschmann R, Osborn D, Dean K, Hart C, Hogg J, & Moran P. (2015) Violent and non-violent crime against adults with severe mental illness. The British journal of psychiatry : the journal of mental science. PMID: 25698767  

  • April 30, 2015
  • 07:41 PM
  • 53 views

This Month in Blastocystis Research (APR 2015)

by Christen Rune Stensvold in Blastocystis Parasite Blog

A post on trending Blastocystis research and on advances in the discoveries of plant extracts with anti-Blastocystis activity.... Read more »

  • April 30, 2015
  • 06:00 PM
  • 85 views

The Avengers: Is It Possible Someone Could Turn Into A Hulk?

by Bill Sullivan in The 'Scope

In anticipation of the return of THE AVENGERS, we take a look at the science that could possibly help someone to turn into a HULK.... Read more »

  • April 30, 2015
  • 04:26 PM
  • 66 views

Pesticides alter bees’ brains, making them unable to live and reproduce adequately

by Dr. Jekyll in Lunatic Laboratories

A new report suggests that a particular class of pesticides called “neonicotinoids” wreaks havoc on the bee populations, ultimately putting some crops that rely on pollination in jeopardy. Specifically, these pesticides kill bee brain cells, rendering them unable to learn, gather food and reproduce. The report, however, also suggests that the effects of these pesticides on bee colonies may be reversible by decreasing or eliminating the use of these pesticides on plants pollinated by bees and........ Read more »

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