Post List

  • August 27, 2016
  • 07:44 PM
  • 20 views

Improving Human Virome Studies: Updates to Virus Classification

by Geoffrey Hannigan in Prophage

Taxonomy is an important aspect of microbiome research. Whether we are studying communities of bacteria, viruses, or other microbes, there are benefits to labeling microbes. Taxonomic names immediately give us information about their relationships to each other, such as similar bacteria being grouped into the same genus...... Read more »

Krupovic, M., Dutilh, B., Adriaenssens, E., Wittmann, J., Vogensen, F., Sullivan, M., Rumnieks, J., Prangishvili, D., Lavigne, R., Kropinski, A.... (2016) Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Archives of Virology, 161(4), 1095-1099. DOI: 10.1007/s00705-015-2728-0  

Thompson, C., Amaral, G., Campeão, M., Edwards, R., Polz, M., Dutilh, B., Ussery, D., Sawabe, T., Swings, J., & Thompson, F. (2014) Microbial taxonomy in the post-genomic era: Rebuilding from scratch?. Archives of Microbiology, 197(3), 359-370. DOI: 10.1007/s00203-014-1071-2  

  • August 27, 2016
  • 01:27 PM
  • 25 views

Researchers report new Zika complication

by Dr. Jekyll in Lunatic Laboratories

If zika didn't seem scary enough in the media, there is new data showing that there could be a new neurological complication of infection with the Zika virus.

... Read more »

Medina, M., England, J., Lorenzana, I., Medina-Montoya, M., Alvarado, D., De Bastos, M., Fontiveros, S., Sierra, M., & Contreras, F. (2016) Zika virus associated with sensory polyneuropathy. Journal of the Neurological Sciences. DOI: 10.1016/j.jns.2016.08.044  

  • August 27, 2016
  • 05:05 AM
  • 44 views

On autism spectrum disorder [research] validity

by Paul Whiteley in Questioning Answers

Today I'm directing your reading attention to a really, really interesting paper by Lynn Waterhouse and colleagues [1] (open-access) whose review findings suggest that: "the ASD [autism spectrum disorder] diagnosis lacks biological and construct validity."The paper is a bit of a long read but most definitely worth it as the quite complicated subject of exactly what goal the label of autism actually serves is discussed. The results of various questions posed by the authors suggest: "No unitary ASD brain impairment or replicated unitary model of ASD brain impairment exists. ASD core diagnostic symptoms are not uniquely linked and are only very rarely expressed without nondiagnostic symptoms. ASD has no reliable early predictor, no unitary developmental course, no unitary life outcome, no unitary recurrence risk, no unitary pattern of BAP [broader autism phenotype] features, and no standard homogeneous subgroups." They conclude that from a research perspective at least, disbanding the label of autism as it currently stands is the next logical step. Said disbanding "is likely to be reductive and uncomfortable" particularly when it comes to all those grand [sweeping] theories of autism put forward down the years. Feathers would not doubt be ruffled.The authors do make reference to two important concepts when it comes how we might want to rethink autism: the Research Domain Criteria framework (RDoC) and Early Symptomatic Syndromes Eliciting Neurodevelopmental Clinical Examinations (ESSENCE). One is an attempt to move away from simple psychiatric labels as somehow denoting homogeneity, the other is the recognition that labels rarely appear in some sort of diagnostic vacuum. Both are in some way the future of autism research and indeed, the future is already now.I'm impressed with the paper from Waterhouse et al. The authors have done a good job of basically saying that as things stand, one single label covering such a diverse and heterogeneous group is not fit for purpose. To see real progress in autism research, science needs to think more about those 'autisms' (see here) and stop using the label of autism as the starting point for research (see here). I struggle to disagree with both those sentiments and other authors appear to have reached similar conclusions [2]. Exactly what that means for the autism in the future - from both a research and clinical perspective - is still a little up in the air but the label has weathered change before and no doubt will continue to do so.And if that isn't enough reading material for you, how about the latest instalment from the British Psychological Society here in Blighty when it comes to autism? Perhaps this will need a revision or two as the Waterhouse suggestions start to percolate through the research community?----------[1] Waterhouse L. et al. ASD validity. Review Journal of Autism and Developmental Disorders. 2016. Aug 10.[2] Geier DA. et al. Examining genotypic variation in autism spectrum disorder and its relationship to parental age and phenotype. Appl Clin Genet. 2016 Jul 28;9:121-9.----------Waterhouse, L., London, E., & Gillberg, C. (2016). ASD Validity Review Journal of Autism and Developmental Disorders DOI: 10.1007/s40489-016-0085-x... Read more »

Waterhouse, L., London, E., & Gillberg, C. (2016) ASD Validity. Review Journal of Autism and Developmental Disorders. DOI: 10.1007/s40489-016-0085-x  

  • August 26, 2016
  • 02:20 PM
  • 55 views

Next steps in understanding brain function

by Dr. Jekyll in Lunatic Laboratories

The most complex piece of matter in the known universe is the brain. Neuroscientists have recently taken on the challenge to understand brain function from its intricate anatomy and structure. There is no sure way to go about it, and researchers in Madrid proposed a solution to the problem.

... Read more »

  • August 26, 2016
  • 07:02 AM
  • 54 views

Juvenile offenders, divorce likelihood, assessing conscious awareness  and myth-busting in 2016

by Doug Keene in The Jury Room

Here’s another collection of tidbits that did not stimulate full posts but that we found interesting enough to share with you so that you can investigate them more for yourself if you so desire. While this post contains more serious information than we usually share in these sorts of posts, it is useful information to […]

Related posts:
Myth-busting: ”Today’s adults have a shorter attention span than a goldfish” 
So is that juvenile offender a “wayward youth” or a “superpredator”?
The Bias Awareness Scale 


... Read more »

  • August 26, 2016
  • 06:49 AM
  • 47 views

From :-D to =8-0 - Effects of Emoticons on the Brain

by Neuroskeptic in Neuroskeptic_Discover

An unusual study reports the effects of emoticons on human brain activity: Neural correlates of text-based emoticons



South Korean neuroscientists Ko Woon Kim et al. used fMRI to record brain activation in 18 volunteers who were shown various expressive text symbols, in both the Asian 'vertical' and Western 'horizontal' styles:

However, it turned out that the brain doesn't really respond to emoticons at all: there was no significant difference in the brain response to the real emoticons... Read more »

  • August 26, 2016
  • 06:41 AM
  • 51 views

How Do Most People Do Mathematics?

by Stefan Buijsman. in United Academics

Mathematics is an important part of modern society. Science and engineering are hard to imagine without mathematics, and even simple things such as calculating the cost of groceries involve mathematics. So, it's not strange to stop and wonder what mathematics is. That turns out to be a very difficult question.... Read more »

Stefan Buijsman. (2016) Philosophy of Mathematics for the Masses: Extending the scope of the philosophy of mathematics. Stockholm: Department of Philosophy, Stockholm University . info:other/978-91-7649-351-9

  • August 26, 2016
  • 05:03 AM
  • 37 views

A new Birt-Hogg-Dubé Syndrome review

by Joana Guedes in BHD Research Blog

Gupta et al. (2016b) recently published a review about Birt-Hogg-Dubé Syndrome (BHD) exploring the key points and research advances in genetics and pathogenesis, clinical manifestations, diagnosis and disease management.... Read more »

Gupta N, Sunwoo BY, & Kotloff RM. (2016) Birt-Hogg-Dubé Syndrome. Clinics in chest medicine, 37(3), 475-86. PMID: 27514594  

  • August 26, 2016
  • 05:00 AM
  • 37 views

Friday Fellow: Six-Spot Burnet

by Piter Boll in Earthling Nature

by Piter Kehoma Boll Found in Europe, today’s Friday Fellow is a nice day-flying moth with beautiful colors and toxic compounds. Scientifically known as Zygaena filipendulae, its common name is six-spot burnet, burnet being the common name of moths in the … Continue reading →... Read more »

  • August 26, 2016
  • 03:38 AM
  • 39 views

What does the Autism Spectrum Quotient (AQ) actually measure?

by Paul Whiteley in Questioning Answers

"Higher AQ [Autism Spectrum Quotient] scores were associated with higher scores of loneliness, social anxiety, depression, and anxiety, as well as with lower scores of quality of life (QoL)."Those were some of the key findings reported by Phil Reed and colleagues [1] who used the very popular 'are you autistic?' AQ screening tool to look at the presence of autistic traits "along with depression, anxiety, loneliness, quality of life, and social anxiety" in a University student cohort (N=413).Finding that among their research population some 8% scored above the cut-offs used by the AQ, researchers also reported those important 'associations' all tied into QofL.Accepting that I'm probably a little biased when it comes to the 'problematic' use of the AQ as a screening tool for autism (see here and see here), my interpretation of the Reed results plays into the idea that the AQ is certainly picking up something, but exactly what is still the source of some debate (see here). I might for example, point you in the direction of the findings by Kitazoe and colleagues [2] who, based on similar student cohort, talked about "qualitatively different groups" over and above "a single homogeneous group" when it came to high scorers on the AQ.It is also pretty well accepted that issues such as social anxiety and depression are over-represented when it comes to a diagnosis of autism (see here and see here respectively) and one has to wonder whether the AQ might be tuned into to the features of those labels over and above core autism. Indeed, going back a few years, the findings reported by Kunihira and colleagues [3] kinda signalled as much where personality traits "toward an obsessional personality" were seemingly connected to AQ scores in a non-autistic population as well as "higher depression and anxiety." Such findings might also be 'useful' when it comes to looking at the AQ in the context of eating disorders too [4].I look forward to seeing more research done on this important topic (something ripe for more University student research projects perhaps).----------[1] Reed P. et al. Loneliness and Social Anxiety Mediate the Relationship between Autism Quotient and Quality of Life in University Students. J Dev Phys Disabil. 2016. Aug 12.[2] Kitazoe N. et al. Whether the Autism Spectrum Quotient consists of two different subgroups? Cluster analysis of the Autism Spectrum Quotient in general population. Autism. 2016 Apr 30. pii: 1362361316638787.[3] Kunihira Y. et al. 'Autistic' traits in non-autistic Japanese populations: relationships with personality traits and cognitive ability. J Autism Dev Disord. 2006 May;36(4):553-66.[4] Mansour S. et al. Emotions mediate the relationship between autistic traits and disordered eating: A new autistic-emotional model for eating pathology. Psychiatry Res. 2016 Aug 8;245:119-126.----------Reed, P., Giles, A., Gavin, M., Carter, N., & Osborne, L. (2016). Loneliness and Social Anxiety Mediate the Relationship between Autism Quotient and Quality of Life in University Students Journal of Developmental and Physical Disabilities DOI: 10.1007/s10882-016-9504-2... Read more »

  • August 25, 2016
  • 03:48 PM
  • 54 views

Polar Bears Stubbornly Stick to Habitats, Even as Ice Melts

by Elizabeth Preston in Inkfish



"I don't know what you're talking about," said the polar bear. "Everything seems normal to me! Watch out for that puddle."

Up in the Arctic, things are getting slushy. But some polar bears are refusing to change their ways. Instead of compromising on where they spend their time, they're clinging to the icy habitats they've always loved. As those habitats keep shrinking, though, the bears will eventually find things too crowded and uncomfortable to ignore. 

Researchers divide polar bear... Read more »

Wilson RR, Regehr EV, Rode KD, & St Martin M. (2016) Invariant polar bear habitat selection during a period of sea ice loss. Proceedings. Biological sciences / The Royal Society, 283(1836). PMID: 27534959  

  • August 25, 2016
  • 02:50 PM
  • 55 views

The relationship between low physical activity and psychotic symptoms

by Dr. Jekyll in Lunatic Laboratories

Physical activity can help reduce cardiovascular disease and premature mortality in people with psychological problems. However, there is limited data on exercise in people with serious mental disorders, especially from low- and middle-income countries. This study explored whether complying with the World Health Organization recommendations of 150 minutes of moderate-vigorous exercise per week is related to psychotic symptoms or the diagnosis of a psychosis.

... Read more »

Brendon Stubbs, Ai Koyanagi, Felipe Schuch, Joseph Firth, Simon Rosenbaum, Fiona Gaughran, James Mugisha, & Davy Vancampfort. (2016) Physical Activity Levels and Psychosis: A Mediation Analysis of Factors Influencing Physical Activity Target Achievement Among 204 186 People Across 46 Low- and Middle-Income Countries. Schizophrenia bulletin . info:/10.1093/schbul/sbw111

  • August 25, 2016
  • 09:40 AM
  • 74 views

How to rebuild a brain

by gdw in FictionalFieldwork

After the stroke The human brain is complicated. Very complicated. And like any piece of complex machinery that relies on the smooth functioning of many components, it’s not immune to malfunction. When a part of the brain doesn’t get proper nutrition through a nice and smooth blood flow, things go awry and a stroke occurs. […]... Read more »

  • August 25, 2016
  • 03:45 AM
  • 59 views

Hospitalisation for infection and risk of death by suicide

by Paul Whiteley in Questioning Answers

"An increased risk of death by suicide was found among individuals hospitalized with infection in prospective and dose-response relationships. These findings indicate that infections may have a relevant role in the pathophysiological mechanisms of suicidal behavior."Some intriguing data has been recently reported by Helene Lund-Sørensen and colleagues [1] (open-access) examining the possibility that certain types of infection (or perhaps the biological response to infection) might increase the risk of suicidal behaviour. Some good media coverage about the study can be read here.If your sticking with my interpretation of the results, Denmark was the the source of the data, as yet again one of those quite amazing Scandinavian population registries provides a starting cohort of around 7 million people "observed for a total of 149 061 786 person-years" from which subsequent results are derived.Sadly, some 32,000 suicides (completed) were recorded during the study period; around a quarter of such reports were among people who had "previously been diagnosed as having an infection during a hospitalization." Such data was reported in terms of incidence rate ratios (IRRs) and equated to those hospitalised for infection being 42% more likely to die by suicide than those not hospitalised for infection. The 'dose-response' relationship eluded to in that opening sentence refers to the finding that the more serious the infection and/or the longer the hospital stay (treatment), the more likely the risk of death by suicide. Such an association also held when adjustment was made for potential confounding variables such as sex, age and socio-economic status.Accepting that suicide - whether contemplated, attempted or completed - is a very complicated and often very individual process these are interesting results. Of course one has to be slightly careful in drawing too many conclusions from such data given both the large number of 'infections' included as part of the analyses and the possible "psychological effect of being hospitalized with a severe infection." The Lund-Sørensen data is still data built on association not necessarily 'cause and effect'.Still, adding to the increasingly popular idea that infections or the biological response to infection at critical periods of development and life can seemingly affect behaviour (see here and see here for a few more potential examples) as well as physiology, the current study makes an important case for further study in this area. Not least because even if only playing a role in a small proportion of suicides, there may be important screening and possible intervention avenues to explore. I'm also wondering what such a possible association might mean with regards to the 'transmission' of certain infections and potential suicide risk? Y'know added to the speculation that some types of depression could perhaps be relabelled as an infectious disease [2] and in light of the strong connection between depression and suicidal behaviours...----------[1] Lund-Sørensen H. et al. A Nationwide Cohort Study of the Association Between Hospitalization With Infection and Risk of Death by Suicide. JAMA Psychiatry. 2016. Aug 10.[2] Canli T. Reconceptualizing major depressive disorder as an infectious disease. Biology of Mood & Anxiety Disorders. 2014; 4:10----------Lund-Sørensen H, Benros ME, Madsen T, Sørensen HJ, Eaton WW, Postolache TT, Nordentoft M, & Erlangsen A (2016). A Nationwide Cohort Study of the Association Between Hospitalization With Infection and Risk of Death by Suicide. JAMA psychiatry PMID: 27532502... Read more »

  • August 24, 2016
  • 05:05 PM
  • 76 views

Theses and dissertations: pros and cons of the traditional and alternative formats

by SciELO in SciELO in Perspective

In order to expedite the writing and assessment of theses, institutions and graduate programs in several countries, including Brazil, are choosing to allow candidates who have published papers on their masters or doctorate research topics to replace the thesis chapters by these articles, headed by an introduction, conclusion and review of scientific literature. Is this format ideal and applicable to all? … Read More →... Read more »

  • August 24, 2016
  • 02:51 PM
  • 82 views

How long do you want to live? Your expectations for old age matter

by Dr. Jekyll in Lunatic Laboratories

Why do some people want to live a very long time, while others would prefer to die relatively young? In a latest study, a team of researchers investigated how long young and middle-aged adults in the United States say they want to live in relation to a number of personal characteristics. The results showed that more than one out of six people would prefer to die younger than age 80, before reaching average life expectancy.

... Read more »

  • August 24, 2016
  • 07:30 AM
  • 68 views

Epigenetics of Early Pregnancy Loss: Hypomethylation and Genetic Instability May Contribute to Decreased Implantation Potential of Monosomy Blastocysts

by Blair McCallie in EpiBeat

Aneuploidy is the leading cause of miscarriage, stillbirth, and congenital birth defects and occurs as a result of errors during meiotic or mitotic cell division.1 As a woman ages, the probability of an aneuploid conception significantly rises, to roughly 50% by the age of 40.2 Only a fraction of full aneuploidies, primarily trisomies, will develop past the first trimester. This is in contrast to monosomies that almost never implant or result in an ongoing pregnancy. DNA methylation is an epigenetic mechanism involved in chromatin structure, and is responsible for proper chromosome segregation during cell division.3 Appropriate levels of DNA methylation are essential for normal cell differentiation as well as embryonic gene expression patterns required for uterine implantation and fetal development.4

Given the importance of DNA methylation and chromosome constitution to healthy fetal/embryonic development, our laboratory investigated the association between DNA methylation and chromosomal aneuploidies, focusing primarily on the DNA methylome, the molecular processes involved in establishing methylation, and downstream gene expression.
Blastocysts donated to research had specific aneuploidies representing differing implantation potentials (7, 11, 15, 21, and 22). Trisomies 7 and 11 are most likely to result in implantation failure; trisomies 15 and 22 are able to implant however will always result in miscarriage; and trisomy 21 embryos will implant but result in either miscarriage, still birth, or live birth. Conversely, all monosomies for 7, 11, 15, 21, and 22 fail to implant.... Read more »

  • August 24, 2016
  • 07:02 AM
  • 67 views

Psychopathy Personality Inventory—Revised (PPI-R) Scale 

by Rita Handrich in The Jury Room

We wrote about this scale in our last post when researchers (trying to convince the reader there is such a thing as a good psychopath for you to hire) used it in a study of German adults. The PPI-R is apparently a measure of psychopathy that is able to “detect relatively mild levels of psychopathy […]

Related posts:
The Trust in Science and Scientists Inventory Scale 
Measuring beliefs in the paranormal: The Australian Sheep Goat Scale
The Dirty Dozen Scale 


... Read more »

Lilienfeld, S. O., & Widows, M. R. (2005) Psychological Assessment Inventory–Revised (PPI-R). Lutz, FL: Psychological Assessment Resources. info:/

  • August 24, 2016
  • 04:30 AM
  • 82 views

Has There Been Any Change in ACL Injury Rates?

by Kyle Harris in Sports Medicine Research (SMR): In the Lab & In the Field

Anterior cruciate ligament (ACL) injury affect a small number of athletes. While overall ACL injury rates are decreasing, ACL injuries still affect a disproportionally higher number of women than ... Read more »

  • August 24, 2016
  • 04:13 AM
  • 80 views

ALSPAC says maybe to link between prenatal paracetamol exposure and childhood behavioural difficulties

by Paul Whiteley in Questioning Answers

ALSPAC - the Avon Longitudinal Study of Parents and Children - continues to give in research terms as today I approach the findings reported by Evie Stergiakouli and colleagues [1]. They observed that: "Children exposed to acetaminophen [paracetamol] prenatally are at increased risk of multiple behavioral difficulties, and the associations do not appear to be explained by unmeasured behavioral or social factors linked to acetaminophen use insofar as they are not observed for postnatal or partner’s acetaminophen use." Some media attention for the study can be found here.Continuing the research journey on a topic not unfamiliar to this blog (see here and see here for example) that exposure to paracetamol during the nine months that made us might not be a totally benign affair, Stergiakouli et al analysed data for some 7,700 mothers included in the initiative between 1991 and 1992. Questions about paracetamol use at 18 and 32 weeks of pregnancy were asked of mothers and maternal reports of child behaviour problems at 7 years using the Strengths and Difficulties Questionnaire (SDQ) were thrown into the research mix.Results: those behavioural difficulties potentially associated with maternal paracetamol use at both 18 and 32 weeks of pregnancy included both conduct problems and hyperactivity symptoms. Researchers were also able to record no (significant) connection between post-natal paracetamol use nor partner paracetamol use and childhood behavioural problems. They concluded that "the timing of acetaminophen use might be important" and that "the association between prenatal acetaminophen exposure and childhood behavioral problems is not explained by unmeasured familial factors linked to both acetaminophen use and childhood behavioral problems and that the findings are consistent with an intrauterine effect."Combined with the various other studies suggesting an association between prenatal exposure to paracetamol and offspring behavioural 'issues' the case for a possible link is growing. ALSPAC has a number of methodological strengths to its design, not least "the availability of prospective information on acetaminophen use during the second and third trimesters of pregnancy and postnatally by the mother and by her partner." The fact that numerous potentially confounding variables were also controlled for is another bonus for the study results: "maternal age at birth, parity, socioeconomic status, smoking and alcohol consumption during pregnancy, prepregnancy body mass index (BMI), maternal self-reported psychiatric illness, and possible indications for acetaminophen use." This is pretty strong data (or at least as strong as the other data published on this topic).Mechanism(s) of effect? Still something that needs a little more work I'm afraid, before any precise information is revealed. The authors go with some ideas based on the "endocrine-disrupting properties of acetaminophen" for example, but let's wait and see before anyone makes too many sweeping generalisations. I might however suggest that the possibility of a link between paracetamol exposure and asthma (see here) could be important in light of what asthma might mean for the risk of presentation of ADHD (attention-deficit hyperactivity disorder) for example (see here). Just a thought and bearing in mind the evidence linking paracetamol use and asthma is not always all on-way.Further studies are required on this increasingly important topic. Please also bear in mind no medical or clinical advice is given or intended on this blog. Speak to your physician if you need more information about pain relief during pregnancy.----------[1] Stergiakouli E. et al. Association of Acetaminophen Use During Pregnancy With Behavioral Problems in Childhood. JAMA Pediatrics. 2016. Aug 15.----------Stergiakouli, E., Thapar, A., & Davey Smith, G. (2016). Association of Acetaminophen Use During Pregnancy With Behavioral Problems in Childhood JAMA Pediatrics DOI: 10.1001/jamapediatrics.2016.1775... Read more »

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