Until now, complaints about hormonal birth control – mood swings, nausea, breast tenderness – have almost exclusively come from the woman taking the hormones. However, recent findings about one popular type of birth control should have women and their intimate partners equally concerned. The issue is with a potentially considerable increased risk of HIV infection for both the woman and her partner, and the new research even has some HIV/AIDS scientists saying “I told you so.”... Read more »
Heffron R, Donnell D, Rees H, Celum C, Mugo N, Were E, de Bruyn G, Nakku-Joloba E, Ngure K, Kiarie J.... (2011) Use of hormonal contraceptives and risk of HIV-1 transmission: a prospective cohort study. The Lancet infectious diseases. PMID: 21975269
Marx PA, Spira AI, Gettie A, Dailey PJ, Veazey RS, Lackner AA, Mahoney CJ, Miller CJ, Claypool LE, Ho DD.... (1996) Progesterone implants enhance SIV vaginal transmission and early virus load. Nature medicine, 2(10), 1084-9. PMID: 8837605
Two new papers just came out in Ecology Letters that caught my interest about range shifts. The first is by Early and Sax called: Analysis of climate paths reveals potential limitations on species range shifts. and was highlighted by Nature. The next article was by Sheldon et al, also in the early online section titled: Climate change and community disassembly: impacts of warming on tropical and temperate montane community structure. Both papers focus on range shifts and both would qualify as "3M" as they use collections of published data and simulation models. Full disclosure as well I did my dissertation on climate change and I currently am a post-doc who only does individual based and simulation modeling. I really enjoyed Early and Sax's paper because it used simulation to develop a novel point that would be difficult to demonstrate empirically. Its long been known that species ranges will shift as climate changes and we can use what are called bioclimate envelope models to make predictions about where species will go. These models essentially say that where a species is now is a good indicator of the climate 'envelope' that it can survive in and it will move geographically to follow that envelope. Early and Sax ask, if you're a salamander in California, and suddenly Oregon starts looking pretty good thermally speaking in 2075, can you get there? The short answer is most likely "No". Not because of physical barriers but because of climate barriers. This is because as Oregon gets gradually warmer, it will also have cold years too. So while a salamander can survive the range of temperatures in California, as climate change happens in Oregon only some of those years will be within the range of temperatures our intrepid salamanders want to live in. So if you have a favorable climate patch in Oregon, but only a narrow corridor to get to it, just because future climate models predict that a lizard could get there doesn't mean it will. Of course many people have pointed out the link between dispersal rates and distance and actualized range shifts. The novelty of Early and Sax's work is that they point to the importance of a species ability to persist in unfavorable edge habitats.Potential habitat and habitat that can actually be reachedThey make a compelling case that just because a habitat will become suitable based on a bioclimate envelope model doesn't mean that the the species can make it there. The first factor affecting persistence is going to be climate variability in movement corridors. Furthermore they point out that persistence be impacted by other things. For instance competitors and predators of a given focal species are also on the move and depending on how well they can track a shifting climate. Obviously if you're a manager planning for climate change, you'll need to consider how best to make sure that species of conservation importance can best make it through these corridors. One problem with this work that it relies on bioclimate envelope models which have been criticized for the past decade or so (i.e. Pearson and Dawson 2003). The authors actually go to great lengths to justify their use of envelope models, and I can't fault them too much. I wouldn't hang too much on these kinds of models either, but I think they work fine for the authors purposes. Actually the unmentioned corollary of this work is biotic interactions and priority effects (i.e. Chase 2007). As lots of different species are moving from place to place, the new communities that are assembled in these new ranges could be different than the originating communities. Community assembly under climate change could be a fruitful thing to look at in conjunction with bioclimate envelope models and range shifts. This brings me to the next paper using simulation to look at climate change because it focuses on community disassembly. This is work by Sheldon et al. is an example of a simulation paper that I thought wasn't particularly interesting. Feel free to turn that criticism right around on me because she has a paper in Ecol. Letters and I don't have any. Pressing forward though. The premise of the paper is straightforward. There will be more warming in northern latitudes, so you expect a greater amount of community disassembly. Back up for a moment our author tells us. Tropical species have much narrower thermal ranges therefore even though there's greater change in the far north, there may be a bigger impact in the tropics. To get at this they use already published transects of a variety of species (n = 53) that spanned 90 degrees of latitude, 45 in each direction. They then created a simulation to examine how montane communities disassemble with changing temperature. Kuala Lumpur montane forestIn this case a community is a published mountain transect. The simulation uses variety of dispersal mechanisms that allow species individually to move up (or down but mostly up) a mountain. Some species have higher dispersal capacity and can make it to these new elevations that are within their thermal tolerance. Others won't be able to disperse or their range will "move off" the mountain because the mountain is too small. In short Sheldon et al. found that montane communities in the tropics were actually more sensitive to temperature changes compared to temperate communities, e.g. there was more community disassembly. This I do think is an interesting result theoretical result, but I don't find it compelling on its own. I would have been much more convinced if the authors had included some actual data to compare their model to. My problem with this is that its really just recapitulating what we already know. Its a well known truism that species will have individualistic reactions to climate change, causing novel community assembly (and disassembly in this case). This idea has been around for at least 20 years. I think the important question is the follow up: "What does community assembly and disassembly mean in this brave new climate world?". Ok, so we already know that community disassembly is happening (before this paper), so what are the implications of this? If community disassembly is happening faster in the tropics what will this mean for tropical vs temperate communities? I wanted either further simulation or some real data. I was left feeling that lots of work went into this simulation but the project was only half finished. I don't like to criticize other people's work too much (a problem of ecologists being too nice?), but again it seems like the authors went to great length to demonstrate something with a simulation that I don't think was that novel relative to the Early and Sax paper.Let me restate my disclosure of earlier, I am in a post-doc that is all modeling and simulation. One of things that haunts me is the thought that: "I'm just making shit up". Ok, its grounded in actual data and theory, but I'm nonetheless plagued by the dangers of circularity. I can program a simulation to mimic a pattern, but does that mean that my simulation is an actual mechanistic recreation of the processes that produced the actual data? I can come up with a hypothesis and write a simulation to support it, but does that mean my hypothesis is supported? I don't have an answer to this question, but I do worry that simulation only projects can drift dangerously close to being circular (Like I said it can keep me up at night). I think that simulation is a powerful tool for ecologists, but in the melee of trying to pump out as many papers as possible it can get overused. These two papers highlight that. Early and Sax's paper I thought was an excellent use of simulation and I really enjoyed the paper. Sheldon et al's on the other hand was a good simulation but needed more follow through, preferably in the form of actual data, to have punch. In the end without that empirical data to support it, it felt like it was just a bit too circular for me to trust the result based on simulation alone. Early R, & Sax DF (2011). Analysis of climate paths reveals potential limitations on species range shifts. Ecology letters PMI... Read more »
Early R, & Sax DF. (2011) Analysis of climate paths reveals potential limitations on species range shifts. Ecology letters. PMID: 21955643
Kimberly S. Sheldon, Sylvia Yang, & Joshua J. Tewksbury. (2011) Climate change and community disassembly: impacts of warming on tropical and temperate montane community structure. Ecology Letters. info:/
Meet Julie and Mark, two siblings who are vacationing together in France. One night after dinner and a few bottles of wine, they decide to have sex. Julie is on the pill and Mark uses a condom so there is virtually no chance that Julie will become pregnant. They enjoy it very much but decide [...]... Read more »
At this year’s HICL conference in Hamburg, I was able to present some of my own research. In the follow-up discussions several points were highlighted, especially focussing on the viability of supply chain wide cooperation and collaboration efforts and on the difficulties of doing a realistic quantification of supply chain risks.
I already read a great paper on this topic some time ago: “Assessing the vulnerability of supply chains using graph theory” by Stephan M. Wagner and Nikrouz Neshat (2010), which I present you today.... Read more »
Wagner, S.M., & Neshat, N. (2010) Assessing the vulnerability of supply chains using graph theory. International Journal of Production Economics, 121-129. info:/
Bones are “Often thought of as a rigid, unchanging entity, skeletal bone is actually the result of a dynamic process” involving a balancing act between the activity of bone formation by osteoblasts and bone destruction by osteoclasts. The harmony between these two processes is essential for maintaining strong bones. It is when the rate of bone resorption exceeds the rate of bone formation that leads to osteoporosis. Why does this happen? How can we slow the rate of resorption? What factors are present that promote osteoclast function to degrade bone?
New research into how the pro-inflammatory cytokine, IL-20, controls bone resorption and how a new immunotherapy can potentially prevent osteoporosis in women.... Read more »
Hsu YH, Chen WY, Chan CH, Wu CH, Sun ZJ, & Chang MS. (2011) Anti-IL-20 monoclonal antibody inhibits the differentiation of osteoclasts and protects against osteoporotic bone loss. The Journal of experimental medicine, 208(9), 1849-61. PMID: 21844205
Anecdotal evidence supports a temporary increase in appetite following the use of cannabis. However, there is very limited clinical research directed at the association of chronic cannabis use and body weight.Endogenous endocannabinoid compounds are popular targets of research to improve understanding the pharmacology of appetite and weight regulation. Rimonabant, a selective antagonist/inverse agonist for the CB1 receptor was briefly approved for weight reduction before being removed because of safety concern. Research on cannabanoid drugs and receptors continues in a hope to develop an effective and safe drug for the treatment of obesity.However, a new study published in The American Journal of Epidemiology suggests the association of cannabis and body weight may be more complex than thought. Le Strat and Le Foll examined two United States general population surveys (NESARC and NCS-R) for reported prevalence of obesity and frequency of cannabis use. Subjects in each of these surveys were split into four groups with prevalence in (men and women):No cannabis use in last 12 months (94.3%, 97.3%)Cannabis use more than once a year to less than once a month (2.0%, 1.2%)Cannabis use once a month to two days per week (1.9%, 0.8%)Cannabis use three days per week to daily (1.8%, 0.7%)When obesity rates (BMI level of >30) were compared between the four groups, the rates were surprising to me. The odds ratios found in the study are plotted below. The rates of obesity are set a one for non-users and odds ratios for obesity for both surveys by frequency of cannabis use. The results show approximately 33% reduction in rates in obesity in the cannabis user groups.The odds estimates in the figures in this blog are an average of adjusted odds ratios controlling for potential confounding variables such age, gender, cigarette smoking status, education, income and other non-cannabis drug use.The authors note their study is limited by reliance on self-report for height, weight and frequency of cannabis use. They also note their study was unable to control for potential diet and physical activity confounding issues.I would wonder if there may be additional confounders that explain this association at the general population. This association study does not show that obesity in cannabis abstainers will be reduced by initiating cannabis use.Nevertheless, I think this finding is counterintuitive to what most have assumed to be the effect of cannabis on appetite and weight. We will likely see more pre-clinical and clinical research on this topic.Photo of flowers, moth and lady bug from the authors collection. Figure is produced by the blog author from data provided in the following manuscript:Le Strat, Y., & Le Foll, B. (2011). Obesity and Cannabis Use: Results From 2 Representative National Surveys American Journal of Epidemiology, 174 (8), 929-933 DOI: 10.1093/aje/kwr200... Read more »
Le Strat, Y., & Le Foll, B. (2011) Obesity and Cannabis Use: Results From 2 Representative National Surveys. American Journal of Epidemiology, 174(8), 929-933. DOI: 10.1093/aje/kwr200
File this one under “applications of population density”. Researchers working for Nippon Telephone and Telegraph—better known as NTT—discovered they could use an area’s population density to predict telecommunications equipment failure due to lighting strikes. Telecommunications is an expensive business. Like other infrastructure, it requires a lot of manpower and capital to expand and maintain. But [...]... Read more »
X. Zhang, A. Sugiyama, & H. Kitabayashi. (2011) Estimating telecommunication equipment failures due to lightning surges by using population density. 2011 IEEE International Conference on Quality and Reliability (ICQR) , 182-185. info:/10.1109/ICQR.2011.6031705
The middle child can be an awkward position in a family, and this is just as true in the workplace. Middle management juggle responsibilities to their reports and their managers, a feat trickiest when leadership decide that the organisation needs to change. Do they dutifully implement the bosses' plans, or cling to the manageable status quo? A recent qualitative study suggests this group take a third role, of ambivalent change agents.Edel Conway and Kathy Monks of Dublin City University conducted interviews in the Irish Health Service, a 93,000-strong organisation, then undergoing a large top-down change. They asked 23 middle managers to talk about a major change event that they had experienced recently; around half chose the top-down strategic initiative while the others recounted a change they themselves had initiated.The strategic initiative came in for criticism, with middle managers quick to point out issues like increases in workload, uncertainty about direction of travel, and a lack of ownership. Yet the same cohort were enthusiastic when discussing their own change ideas. They revealed a set of pragmatic tactics, such as beginning with a small number of enthusiastic staff as a catalyst within their department. They understood the importance of communications, reflecting the frustrations they felt when they were left in the dark. The general philosophy was noted by one participant:I think the difference was that we said "we have an idea, can we talk to you about how it might work" Whereas with the other [top-down] one, it is: “we have an idea and this is how it is going to work.”Some of this may simply reflect a tendency to prefer our own ideas to those imposed on us. But it certainly contests the idea that middle management are simply resistant to change. Through the nature of their in-between position in the organisation, Conway and Monks see them as ambivalent agents, able to see the many facets of a process of change, critiquing problematic ones and finding concrete ways to realise others.The authors note that middle manager initiatives “were in many cases providing the solutions that the top-down change was intended to enforce: reductions in waiting lists, improvements in patient care.” And they warn that though the middle manager layer is a tempting target for reducing salary costs in pinched public services “wholesale elimination of such positions may have negative repercussions for the success of change initiatives.”Conway, E., & Monks, K. (2011). Change from below: the role of middle managers in mediating paradoxical change Human Resource Management Journal, 21 (2), 190-203 DOI: 10.1111/j.1748-8583.2010.00135.x... Read more »
Conway, E., & Monks, K. (2011) Change from below: the role of middle managers in mediating paradoxical change. Human Resource Management Journal, 21(2), 190-203. DOI: 10.1111/j.1748-8583.2010.00135.x
Female nipples not only fascinate men, but also scientist. Why do women have those little bumps next to their nipples?... Read more »
Benoist Schaal. (2011) Bumpy nipple smells guide babies to milk . New Scientist. info:/
Perhaps one of the most interesting topics today in the area of physiological optics is the relationship between the ocular optics and vision. This has been a subject of study for decades, if not centuries, but I elaborate more on my current views of this exciting problem... ... Read more »
Villegas, E., Alcon, E., & Artal, P. (2008) Optical Quality of the Eye in Subjects with Normal and Excellent Visual Acuity. Investigative Ophthalmology , 49(10), 4688-4696. DOI: 10.1167/iovs.08-2316
Cooperation confounds us: Humans are the only members of the animal kingdom to display this tendency to the extent that we do, and it’s an expensive endeavor with no guarantee of reciprocal rewards. While we continue to look for answers about how and why cooperation may have emerged in human social and cultural evolution, we [...]
... Read more »
by Rita Handrich in The Jury Room
We want so much to believe we are able to detect deception, yet we simply aren’t good at it. Mock jurors often express the belief that they have a higher than average ability to detect deception citing nonverbal ‘tells’ and other indicators of lying. From behind the one-way observation windows, we know they are in error—but they remain [...]
Related posts:Outsmarting liars (five decades of research)
We know liars when we see ‘em
Deception Detection: The latest on what we know
... Read more »
Reinhard MA, Sporer SL, Scharmach M, & Marksteiner T. (2011) Listening, not watching: Situational familiarity and the ability to detect deception. Journal of Personality and Social Psychology, 101(3), 467-84. PMID: 21707196
If you are a fellow child of the 80s, you probably visualize a fried egg when you think of drug addiction. Fried eggs are delicious, but the reality about drug use is much more devastating and sobering…all the way to the level of the dendrites on our neurons. A recent paper describes the use of psychoactive drugs to help identify regulators of dendrite morphology. MicroRNAs (miRs) are RNA structures that regulate gene expression by preventing the translation of specific mRNA sequences into proteins. miRs function throughout development, notably in the morphology and function of dendritic spines, which are small neuronal processes important in the transmission of a neuron’s signals. Psychoactive drugs such as nicotine, cocaine, and amphetamines can trigger changes in neuronal structure and function, and a recent paper identifies miRs as regulators of these changes. Lippi and colleagues found altered levels of miR-29a/b after exposing mice to psychostimulants. Altered levels of these miRs affect synaptic transmission and dendritic spine morphology, as seen in the images above. Healthy dendrites (top, left) have a mix of spine morphologies (top, right). After transfection with miR-29a (bottom, left) or miR-29b (bottom, right), the proportion of mushroom-shaped dendrites dropped significantly. miR-29a/b increases the number of filopodial protrusions through its targeting of the Arp2/3 actin nucleation complex. Lippi, G., Steinert, J., Marczylo, E., D'Oro, S., Fiore, R., Forsythe, I., Schratt, G., Zoli, M., Nicotera, P., & Young, K. (2011). Targeting of the Arpc3 actin nucleation factor by miR-29a/b regulates dendritic spine morphology originally published in The Journal of Cell Biology, 194 (6), 889-904 DOI: 10.1083/jcb.201103006... Read more »
Lippi, G., Steinert, J., Marczylo, E., D'Oro, S., Fiore, R., Forsythe, I., Schratt, G., Zoli, M., Nicotera, P., & Young, K. (2011) Targeting of the Arpc3 actin nucleation factor by miR-29a/b regulates dendritic spine morphology. originally published in The Journal of Cell Biology, 194(6), 889-904. DOI: 10.1083/jcb.201103006
The restoration of oil paintings is always a delicate process. Decades and centuries of dust and grime on the surface of a painting are difficult to remove, as the dirt sticks firmly to the painting’s oil paints and varnish. There is always the danger that a thorough physical cleaning and restoration may alter a painting’s original appearance. A solution [...]... Read more »
Palomero, C., & Soriano, M. (2011) Digital cleaning and “dirt” layer visualization of an oil painting. Optics Express, 19(21), 21011. DOI: 10.1364/OE.19.021011
by Thomas Shultz in Evolutionary Games Group
Cooperation is fundamental to all social and biological systems. If cells did not cooperate, multi-cellular organisms would never have evolved . If people did not cooperate, there would be no nation states . But this wide-scale cooperation is somewhat of a mystery from the perspective of Darwinian evolution, which would seem to favor competition for [...]... Read more »
Ohtsuki, H., Hauert, C., Lieberman, E., & Nowak, M. (2006) A simple rule for the evolution of cooperation on graphs and social networks. Nature, 441(7092), 502-505. DOI: 10.1038/nature04605
Buffer Since we’re busy selecting new residents for our program an article about the subject caught my eye. This article was about whether a structured, behavior-based applicant interview predicts future success in an obstetrics and gynecology residency program. Interesting question since little is known about the use of residency interview in predicting the applicant’s future [...]
No related posts.... Read more »
Goepfert, A. (2011) Making the best match: can we select the right residents for obstetrics and gynecology and for our own programs?. American Journal of Obstetrics and Gynecology, 204(5), 369-370. DOI: 10.1016/j.ajog.2011.02.023
Strand, E., Moore, E., & Laube, D. (2011) Can a structured, behavior-based interview predict future resident success?. American Journal of Obstetrics and Gynecology, 204(5), 4460-2147483647. DOI: 10.1016/j.ajog.2011.02.019
After many natural disasters, famines and epidemics quickly follow with depressing predictability. It is not just a coincidence related to the damaged infrastructure and loss of stored foodstuffs. It has long been thought that there is a direct link between malnutrition and immune suppression, but the mechanism has been, and is still, poorly understood. It [...]... Read more »
Schaible UE, & Kaufmann SH. (2007) Malnutrition and infection: complex mechanisms and global impacts. PLoS medicine, 4(5). PMID: 17472433
So if you haven't heard, Direct to Customer (DTC) genomics has hit the mainstream. Multiple companies (23andMe, deCODEme, etc.) will now genotype you, providing you with a detailed rundown of all your genetic traits and tendencies...
Well, not exactly.
The promise of personal genomics/personalized medicine is that doctors will someday be able to prescribe medicines and lifestyle recommendations that are customized to how YOUR body works, not to some statistical average of how most studied human bodies work. The rub is that identifying genes that control these individual responses to drugs, foods and experiences is really really hard.
I won't describe it all in detail, but the short story of how personal genomics works is as follows:
Find a big group of people
Identify genetic markers that differ between human genomes (SNPs, currently)
Do math to see what SNP markers are associated with the trait you care about
Check your own genome to see which version of the SNP (and trait) you have
In reality it's not so simple because most traits are controlled by many genes, and many different (but rare) alleles can have the same effect on a trait. This is referred to as the "missing heritability problem." It's not unusual to have an extremely heritable trait (where the value of two parents is very similar to the value of their offspring) yet where (across a population) the presence of specific alleles don't explain much of this association. It's a sticky statistical problem and one that many famous geneticists have declared cannot be fixed no matter how many markers or individuals you add to your study.*
So back to openSNP...
openSNP is an effort to put the power of personal genomics and association mapping (aka linkage disequilibrium, aka GWAS) studies into the hands of the people. The idea is that everyone will upload their SNP marker genotype to this common database (along with whatever part of their own phenotype they want to share) in order to create a shared resource. While published data is already freely available (another site, SNPedia, aggregates these peer-reviewed results), the people behind openSNP protest that databases owned by these personal genomics companies are not available to the public.
I love open source/access efforts and citizen science in general, but they're definitely trying something audacious. I'm not going to underestimate the application of the internet to a difficult problem, but they definitely have it cut out for themselves. I think I'd be hesitant to upload my own genotype due to privacy concerns but it's definitely an interesting project. I haven't considered paying to get my genotype though I did sequence a segment of my mitochondrial genome (which was inherited from my mom's mom's mom's mom back in Abruzzo) while I was in grad school.
Incidentally, I came across openSNP first in the DIYbio google group.
It's worth checking out.
* Association mapping seems to work much better in domesticated plants than in natural populations of humans and other creatures. If you're interested in more detail, these papers are a great start.
** The only reason this works at all is because DNA sequencing has become so cheap that it's already revolutionized how biology is studied. Sequencing costs per basepair is actually falling faster than Moore's Law.
Zhu, C., Gore, M., Buckler, E., & Yu, J. (2008). Status and Prospects of Association Mapping in Plants The Plant Genome Journal, 1 (1) DOI: 10.3835/plantgenome2008.02.0089
Hamblin MT, Buckler ES, & Jannink JL (2011). Population genetics of genomics-based crop improvement methods. Trends in genetics : TIG, 27 (3), 98-106 PMID: 21227531... Read more »
Zhu, C., Gore, M., Buckler, E., & Yu, J. (2008) Status and Prospects of Association Mapping in Plants. The Plant Genome Journal, 1(1), 5. DOI: 10.3835/plantgenome2008.02.0089
Hamblin MT, Buckler ES, & Jannink JL. (2011) Population genetics of genomics-based crop improvement methods. Trends in genetics : TIG, 27(3), 98-106. PMID: 21227531
Over the past two weeks, the biggest physics news has been the apparent observation of neutrinos (nearly undetectable subatomic particles) moving faster than the vacuum speed of light. At first glance, this would seem to violate Einstein’s special theory of … Continue reading →... Read more »
In today’s post, I will discuss a little-known combinatorics paper by E.N. Gilbert from 1965, in which he independently discovered the “logarithmic Welch” construction of Costas arrays. Costas arrays are named after the late IEEE fellow John Costas, whose seminal … Continue reading →... Read more »
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