You probably noticed a few things about TheEGG: a recent decrease in blog post frequency and an overall focus on the algorithmic lens — especially its view of biology. You might also be surprised by the lack of discussion of quantum information processing: the most successful on-going application of the algorithmic lens. I actually first […]... Read more »
According to researchers at the Pennsylvania State University, it is possible for some companies to economically convert their operations to wood power.... Read more »
Biomass boiler conversion potential in the eastern United States. (2013) Biomass boiler conversion potential in the eastern United States. Renewable Energy, 439-453. DOI: 10.1016/j.renene.2013.07.019
John Koreth (left) and Edwin P. Alyea (right)Adding bortezomib (marketed as Velcade) to standard preventive therapy for graft-versus-host-disease (GVHD) results in improved outcomes for patients receiving stem-cell transplants from mismatched and unrelated donors, according to a new study by researchers at the Dana-Farber Cancer Institute.In a new phase 2 trial, patients treated with bortezomib had lower rates of severe acute GVHD and treatment-related mortality. The patients experienced better one-year overall survival compared to patients receiving standard preventive therapy, reported the investigators at the American Society of Hematology annual meeting.Read More... Read more »
John Koreth, Edwin P. Alyea,Haesook Kim, Joseph Antin. (2013) A Bortezomib-Based Regimen Offers Excellent Outcomes In Myeloablative HLA-Mismatched and Unrelated Donor Transplantation: Phase II Results. American Society of Hematology annual meeting. info:/
"We just found one of our Kingsnakes doing something really cool."
It was 2006 and we had recently started radio-tracking about a dozen Kingsnakes (Lampropeltis getula) in a big chunk of longleaf pine forest in southwestern Georgia. Kingsnakes were fascinating to me because they were a big, recognizable species for which we knew next to nothing. In fact, this was ... Read more »
Steen, D.A., Linehan, J.M., & Smith, L.L. (2010) Multiscale habitat selection and refuge use of common kingsnakes, Lampropeltis getula, in southwestern Georgia. Copeia, 227-231. DOI: 10.1643/CE-09-092
C.T. Winne, & et al. (2007) Enigmatic decline of a protected population of eastern kingsnakes, Lampropeltis getula, in South Carolina. Copeia, 507-519. DOI: 10.1643/0045-8511(2007)2007[507:EDOAPP]2.0.CO;2
“But, right now, do you think I made you stronger or weaker?” “I felt the flash and as we talked through it… it made me stronger.” I can trace my interest in neuroscience quite directly to when I was nine and my teacher showed us a video of the famous Penfield Experiments (see above, I’m pretty sure […]... Read more »
Parvizi J, Rangarajan V, Shirer W, Desai N, & Greicius MD. (2013) The Will to Persevere Induced by Electrical Stimulation of the Human Cingulate Gyrus. Neuron. DOI: 10.1016/j.neuron.2013.10.057
A new spectroscopic technique developed at Berkeley Lab’s Advanced Light Source could help scientists study and improve advanced materials for batteries.... Read more »
Liu X, Wang D, Liu G, Srinivasan V, Liu Z, Hussain Z, & Yang W. (2013) Distinct charge dynamics in battery electrodes revealed by in situ and operando soft X-ray spectroscopy. Nature communications, 2568. PMID: 24100759
Astronomers have found that stars in the very beginning of universe used very little dust. This finding has enhanced the mysteriousness of the formation of very early stars.
Very little dust in the early universe:
Our present knowledge shows that a huge amount of dust and gas is required to make stars and galaxies but this recent study has opposed our present knowledge. This study is presenting very little dust in the early universe. It shows that very little dust was used to make very early stars of the universe meaning presently known models may not be applied to the early stars and galaxies.
In the present study, astronomers studied the dust on analogue galaxy called 1-Zwicky18, located 58 million light years away, with the help of European Space Agency's Herschel space telescope. This galaxy is found to have similar physical conditions existing in the first galaxies.
“The local dwarf galaxy I Zwicky 18, which has a metallicity about 4 per cent that of the Sun’sand is forming stars less rapidly (assembly time about 1.6 × 109years) than Himiko ( a galaxy formed about 840 million years after the Big Bang) but still vigorously for its mass, is also very dust deficient and is perhaps one of the best analogues of primitive galaxies accessible to detailed study,” Researchers wrote.
"We measured the lowest dust mass that had ever been measured, and much lower than what we were expecting to get by a factor of about 100," said Dr David Fisher of the University of Maryland and Swinburne University.
"It's a big mystery," he says. "This problem of how to make stars in the early universe may be even greater than we thought it was."
Here, I am quoting Sir Humphry Davy, “The more we know, the more we feel our ignorance; the more we feel how much remains unknown.”
Another issue posed by the lack of dust:
Lack of dust is also presenting problems in study of early galaxies with the help of present technology of telescopes.
"It's saying these galaxies are going to be much fainter than we were expecting," said Fisher.
"We probably won't be able to detect them very well, even with ALMA (the Atacama Large Millimetre submillimetre Array in Chile), which is the most powerful telescope on Earth right now.
"People have been using ALMA to try to observe dust in early universe galaxies, and they're failing to find detections in all but the most extreme super bright galaxies, because there's much less dust than the theories are telling us."
Mystery of the first stars deepens - ABC Science (http://goo.gl/UnF35E)
David B. Fisher et al. (2013). The rarity of dust in metal-poor galaxies Nature DOI: 10.1038/nature12765... Read more »
According to data from the US Environmental Protection Agency (EPA) around seven million liters of dispersants were used to combat oil pollution in the Gulf of Mexico. Now, researchers from the Queen’s University at Kingston say that dispersants may not be as harmful to fish as first thought.... Read more »
Adams J., Sweezey M., & Hodson P.V. (2013) Oil and oil dispersant do not cause synergistic toxicity to fish embryos. Environmental toxicology and chemistry / SETAC. PMID: 24115182
Implicit gut feelings of newlyweds predict the succes of a marriage, new research suggests. ... Read more »
McNulty, J.K, Olson, M.A., Meltzer, A.L. . (2013) Though they may be unaware, newlyweds implicitly know whether their marriage will be satisfying. Science. DOI: 10.1126/science.1243140
We believe the negative press on the Millennials (our 20-somethings and early 30-somethings) is simply what happens to all of our young people as they are judged (and found wanting) by older generations. And mostly we eventually grow up, mature, and become something different than we started out as–at least when viewed through the eyes […]
Generation X: Active, balanced and happy. Seriously?
If your jurors are happy, will they blame the victim less?
Is the Millennial Generation beginning to differentiate? Maybe!
... Read more »
Roy F. Baumeister, Kathleen D. Voh, Jennifer L. Aaker, & Emily N. Garbinsky. (2013) Some key differences between a happy life and a meaningful life. . The Journal of Positive Psychology, 8(6), 505-516. DOI: 10.2139/ssrn.2168436
by Moselio Schaechter in Small Things Considered
by Elio Fig. 1. Seeing is Believing? Source. One would assume offhand that the pathways for synthesis and assembly of the major constituents of a bacterial cell “talk to each other,” i. e. they are tightly interwoven processes. Tampering with the biosynthesis of one should affect all the others, right? Wouldn’t you expect, for instance, that if protein synthesis were...... Read more »
Nonejuie P, Burkart M, Pogliano K, & Pogliano J. (2013) Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules. Proceedings of the National Academy of Sciences of the United States of America, 110(40), 16169-74. PMID: 24046367
I'd like to begin with a quote from the paper by Hedvall and colleagues* who reported findings based on a study of developmental trajectory for 208 preschoolers diagnosed with an autism spectrum condition: "Changes in developmental profiles during preschool years are common in children with ASD".Seasons: Autumn @ Wikipedia Their naturalistic study suggested that the very early years of autism, at least some autism, and its presentation are characterised by "considerable change over time" and the requirement for "follow-up assessments" in order to more accurately measure where the sands of autism have settled prior to the start of school.Their reporting that intellectual disability (ID) also might have a maturational aspect to its appearance alongside cases of autism (i.e. not common in early diagnosis but present in about 50% of cases at follow-up) also provides some food for thought in terms of whether this reflects a specific comorbidity or indeed, something more central to specific types of autism (yes, the autisms), though carrying a different timescale of presentation.I'm not altogether sure but I think we might have seen the Hedvall cohort used in another study by Fernell and colleagues** during their study looking at early intervention and autism. In that paper, the same number of preschoolers with autism (N=208) were followed "in a naturalistic fashion" and their various experiences of an ABA (applied behaviour analysis) program recorded. If it is one and same cohort, it's likely then that we are probably not talking about developmental changes occurring just spontaneously in some sort of intervention vacuum. Sort of what happens in real-life.I've talked before on this blog about diagnostic stability and instability when it comes to autism (see here). Whilst accepting that 'universals' when it comes to autism are generally few and far between outside of the almighty diagnostic criteria, the conclusion reached on that post was that stability with regards to a diagnosis of autism is surprisingly, quite an unstable thing. When particularly applied to the early years and their growing importance when it comes to autism (see here) one might speculate that such instability presents its own issues particularly in these times when chatter about really early autism diagnosis is becoming more frequent and louder and louder. Discussion about the important issue of regression which might also interfere with any notion of a universal prenatal or early autism diagnostic test is also worth noting. That also different children on the autism spectrum might present with different developmental trajectories is an important point to emphasise, particularly in these times of optimal outcomers for example (see here).Whilst the Hedvall data provides a cautionary tale that we should be mindful of how dynamic autism might be in the early years (and perhaps even beyond), I'd like to think that it won't be used as an excuse for delaying assessment and diagnosis too much and the subsequent impact that can have....----------* Hedvall A. et al. Autism and developmental profiles in preschoolers: stability and change over time. Acta Paediatr. 2013 Oct 8. doi: 10.1111/apa.12455.** Fernell E. et al. Early intervention in 208 Swedish preschoolers with autism spectrum disorder. A prospective naturalistic study. Res Dev Disabil. 2011 Nov-Dec;32(6):2092-101.----------Hedvall A, Westerlund J, Fernell E, Holm A, Gillberg C, & Billstedt E (2013). Autism and developmental profiles in preschoolers: stability and change over time. Acta paediatrica (Oslo, Norway : 1992) PMID: 24237479... Read more »
Hedvall A, Westerlund J, Fernell E, Holm A, Gillberg C, & Billstedt E. (2013) Autism and developmental profiles in preschoolers: stability and change over time. Acta paediatrica (Oslo, Norway : 1992). PMID: 24237479
A pair of footprints originally discovered in the Chihuahuan Desert have been found to be the oldest known human tracks in North America.
... Read more »
Nicholas J. Felstead, Silvia Gonzalez, David Huddart, Stephen R. Noble, Dirk L. Hoffmann, Sarah E. Metcalfe, Melanie J. Leng, Bruce M. Albert, Alistair W.G. Pike, Arturo Gonzalez-Gonzalez.... (2013) Holocene-aged human footprints from the Cuatrociénegas Basin, NE Mexico. Journal of Archaeological Science. info:/http://dx.doi.org/10.1016/j.jas.2013.11.010
Female patients who suffered a concussion during the luteal phase of their menstrual cycle, when progesterone levels are highest, reported lower quality of life scores one month after their concussion compared with those who did not suffer a concussion in the luteal phase.... Read more »
Wunderle K, Hoeger KM, Wasserman E, & Bazarian JJ. (2013) Menstrual Phase as Predictor of Outcome After Mild Traumatic Brain Injury in Women. The Journal of Head Trauma Rehabilitation. PMID: 24220566
Researchers have found that meditation can change our body at molecular level resulting in useful gene expression changes.
Gene expression refers to the process of getting information from a gene used in the synthesis of a functional gene product such as proteins.
Researchers have found that eight hours of mindfulness/calmness of mind practice, i.e. meditation, results in a range of many genetic expression and molecular differences such as changed levels of gene-regulating machinery and decreased levels of pro-inflammatory genes; RIPK2 and COX2 as well as several histone deacetylase (HDAC) genes, helping in faster recovery from a stressful situation.
"To the best of our knowledge, this is the first paper that shows rapid alterations in gene expression within subjects associated with mindfulness meditation practice," noted study author Richard J. Davidson, founder of the Center for Investigating Healthy Minds and the William James and Vilas Professor of Psychology and Psychiatry at the University of Wisconsin-Madison.
"Most interestingly, the changes were observed in genes that are the current targets of anti-inflammatory and analgesic drugs," added Perla Kaliman, first author of the article and a researcher at the Institute of Biomedical Research of Barcelona, Spain (IIBB-CSIC-IDIBAPS), where the molecular analyses were conducted.
"Our findings set the foundation for future studies to further assess meditation strategies for the treatment of chronic inflammatory conditions," Kaliman said.
Study reveals gene expression changes with meditation - UW-Madison (http://goo.gl/2q9dbH)
Perla Kaliman et al. (2013). Rapid changes in histone deacetylases and inflammatory gene expression in expert meditators Psychoneuroendocrinology DOI: 10.1016/j.psyneuen.2013.11.004... Read more »
Perla Kaliman et al. (2013) Rapid changes in histone deacetylases and inflammatory gene expression in expert meditators. Psychoneuroendocrinology. DOI: 10.1016/j.psyneuen.2013.11.004
A multinational team led by Chinese researchers in collaboration with U.S. and European partners has successfully demonstrated a new method for suppressing instabilities that can cut short the life of controlled fusion reactions.... Read more »
J. Li, H.Y. Guo, B.N. Wan, X.Z. Gong, Y.F. Liang, G.S. Xu, K.F. Gan, J.S. Hu, H.Q. Wang, L. Wang, L. Zeng, Y.P. Zhao, P. Denner, G.L. Jackson, A. Loarte, R. Maingi, J.E. Menard, M. Rack, X.L. Zou. (2013) A long-pulse high-confinement plasma regime in the Experimental Advanced Superconducting Tokamak. Nature Physics, 817-821. DOI: 10.1038/nphys2795
"Autism spectrum disorder (ASD) is a lifelong developmental condition that affects about 1 in 110 individuals, with onset before the age of three years. It is characterized by abnormalities in communication, impaired social function, repetitive behaviors and restricted interests ."ASD is more common among males than females, with a 4:1 male to female ratio. Numerous studies in the literature have shown evidence for a strong genetic component of autism, with a risk up to 25 times higher among siblings compared to the general population. However, if you look at the literature, you find that these numbers change pretty dramatically from study to study. This is often the case when you look at rare disorders in conjunction with rare mutations (WARNING: the rest of the paragraph is a statistical digression, feel free to skip to the next section). The smaller the effect you are trying to measure, the more subjects you will need in your study. This is also true if you are testing many variants, as for example in GWAS studies, which investigate variants in the whole genome. If the effect is big enough, you will find statistical support for your association, however, if your sample size is not big enough, the effect you are trying to measure will vary greatly from study to study. This is because the smaller the sample size, the larger the variance, which is stat jargon to say that whatever you are trying to measure (typically an increase in risk) is likely to be different if you repeat the study. What do we know about the genetic etiology of ASD? About 10% of people diagnosed with ASD have some underlying genetic syndrome (including mitochondrial genes). About 5% are due to rare chromosome rearrangements, for example changes in the size, shape, or number of some chromosomes. Another 5% has been associated to both inherited and de novo "copy number variations" (CNV), the presence of extra copies of some genes . CNV is not rare among humans, as it accounts for approximately 0.4% of the variation between unrelated genomes. Identical twins also differ in CNV, and, even though they have identical genomes, the copy number of the genes may differ between the two. Despite this, in some families with a history of ASD the proportion of de novo CNV's has been found to be up to five times higher than in families without a history of ASD. Finally, thanks to recent advances in sequencing technology, de novo point mutations throughout hundreds of genes have been found and implicated in about 15% of ASD cases . In light of the variety of mutations, genes, and phenotypes associated with ASD, two studies published in the last issue of Cell addressed the following question:"do these genetic loci converge on specific biological processes, and where does the phenotypic specificity of ASD arise, given its genetic overlap with intellectual disability (ID)? ""if and when, in what brain regions, and in which cell types specific groups of ASD-related mutations converge during human brain development " ?Of the two papers, I've so far only read the one by Willsey et al. , who combined their own data with already published data and identified 144 de novo "loss-of-function (LoF)" mutations, in other words, mutations that impair the functionality of the gene (hence the corresponding protein is no longer produced). They called genes with 2 or more de novo LoF mutations "hcASD", or "high confidence" ASD because statistically they had a high probability of being truly associated with ASD. They also analyzed a less-likely set of genes with only one de novo LoF mutation, which they called "pASD genes". Next, the researchers investigated when and where these genes are expressed during brain development. The way they did this is a bit technical, but to think about it in simple terms think of it this way: (1) they needed samples from brain tissues taken at different developmental stages; (2) they needed to look not just at one gene, but at families of genes that are likely to interact together and influence one another's likelihood of getting turned "on" and "off". When a gene is turned "on", the gene is coding a protein, and we say that the gene is "expressed."To carry on their analysis, Willsey et al. used data published by Kang et al. (Nature, 2011) from "57 clinically unremarkable postmortem brains of diverse ancestry (31 males, 26 females) that span 15 consecutive periods of neurodevelopment and adulthood from 5.7 postconceptual weeks (PCW) to 82 years." The gene expression values were determined for each gene by brain region and by postmortem brain sample. Brain regions were grouped according to transcriptional similarity during fetal development. These data were used to generate 52 gene coexpression networks, each network composed of the hcASD genes and their top correlated genes. This coexpression network analysis is a technique that's been extensively used lately to analyze patterns of co-expressions of genes. Each gene in the network is represented by a node, and any two nodes (genes) at any given time are connected if the genes are expressed at that time. Using this set-up, the researchers were able to link the ASD genes to particular brain regions and developmental phases. "Our analysis identifies robust, statistically significant evidence for convergence of the input set of hcASD and pASD risk genes in glutamatergic projection neurons in layers 5 and 6 of human midfetal prefrontal and primary motor-somatosensory cortex (PFC-MSC). Given the extensive genetic and phenotypic heterogeneity underlying ASD and the small fraction of risk genes that we have examined in this study, this likely represents only one of several such points of convergence. Nonetheless, the analytic approach presented here clarifies key variables relevant for productive functional studies of specific ASD genes carrying LoF mutations, providing an important step in moving from gene discovery to an actionable understanding of ASD biology ."Cortical glutamatergic projection neurons (CPNs) are a class of neocortical neurons. They are called "projection" neurons because they transmit information from the neocortex to other neocortical and central nervous system regions. During development, projection neurons are generated in the neocortical germinal zone and migrate radially to their final neocortical position. In their study, Wyllsey et al found that the development of midfetal CPNs is particularly vulnerable to ASD. Furthermore, the set of ASD genes they identified as associated to ASD are functionally diverse and encode proteins found in distinct cell compartments, confirming the theory that ASD can be caused by different and distinct pathways. "Given recent studies suggesting that as many as 1,000 genes or more could contribute to ASD (He et al., 2013; Iossifov et al., 2012; Sanders et al., 2012), our analysis has uncovered a surprising degree of developmental convergence. Despite starting with only nine hcASD seed genes, we have identified highly significant and robust evidence for the contribution of coexpression networks relevant to L5 and L6 CPNs in two overlapping periods of midfetal human development (3–5 and 4–6) corresponding to 10–24 PCW ."The importance of these studies lies in the understanding of not just the genetic association per se, but in the mechanisms that drive these associations, and, most importantly, how the numerous genes interact and when.  Devlin and Schrer (2012). Genetic architecture in autism spectrum disorder Genetics & Development DOI: 10.1016/j.gde.2012.03.002 Neelroop N. Parikshak, Rui Luo, Alice Zhang, Hyejung Won, Jennifer K. Lowe, Vijayendran Chandran, Steve Horvath, Daniel H. Geschwind (2013). Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism Cell DOI: 10.1016/j.cell.2013.10.... Read more »
Neelroop N. Parikshak, Rui Luo, Alice Zhang, Hyejung Won, Jennifer K. Lowe, Vijayendran Chandran, Steve Horvath, Daniel H. Geschwind. (2013) Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism. Cell. DOI: 10.1016/j.cell.2013.10.031
A. Jeremy Willsey, Stephan J. Sanders, Mingfeng Li, Shan Dong, Andrew T. Tebbenkamp, Rebecca A. Muhle, Steven K. Reilly, Leon Lin, Sofia Fertuzinhos, Jeremy A. Miller, Michael T. Murtha, Candace Bichsel, Wei Niu, Justin Cotney, A. Gulhan Ercan-Sencicek, J. (2013) Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism. Cell. DOI: 10.1016/j.cell.2013.10.020
… mystify, inspire Los Alamos scientists
Massive X-ray superbursts near the surface of neutron stars are providing a unique window into the operation of fundamental forces of nature under extreme conditions.... Read more »
Schatz H, Gupta S, Möller P, Beard M, Brown EF, Deibel AT, Gasques LR, Hix WR, Keek L, Lau R.... (2013) Strong neutrino cooling by cycles of electron capture and β- decay in neutron star crusts. Nature. PMID: 24291788
This is a thorough review of everything stupid ever said about the warrior gene, MAOA.... Read more »
Byrd AL, & Manuck SB. (2013) MAOA, Childhood Maltreatment, and Antisocial Behavior: Meta-analysis of a Gene-Environment Interaction. Biological psychiatry. PMID: 23786983
Caffeine and Coffee have been used by athletes to improve athletic performance and to make training easier. Research is also indicating that coffee may also reduce risk of cognitive declineThe post Coffee Study: Its not just the caffeine that makes you smart and athletic appeared first on WODMasters.... Read more »
Cropley V, Croft R, Silber B, Neale C, Scholey A, Stough C, & Schmitt J. (2012) Does coffee enriched with chlorogenic acids improve mood and cognition after acute administration in healthy elderly? A pilot study. Psychopharmacology, 219(3), 737-49. PMID: 21773723
Cho ES, Jang YJ, Hwang MK, Kang NJ, Lee KW, & Lee HJ. (2009) Attenuation of oxidative neuronal cell death by coffee phenolic phytochemicals. Mutation research, 661(1-2), 18-24. PMID: 19028509
Shukitt-Hale B, Miller MG, Chu YF, Lyle BJ, & Joseph JA. (2013) Coffee, but not caffeine, has positive effects on cognition and psychomotor behavior in aging. Age (Dordrecht, Netherlands), 35(6), 2183-92. PMID: 23344884
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