Tuesday, April 28, 2015

The truth behind bars: Representations and misrepresentations of data sets in research articles

Figure 1. Multiple data sets can be presented as the same bar graph.
(Weissgerber et al. 2015).
One of the most common graphical representations of data in research papers is the bar graph. If you read my recent post, you saw that I represented percentages of respondents in different groups in a survey in such a graph. However, it is not the most accurate way to display all types of data collected and analyzed in experimental studies. For a simple number, like a percentage, a bar graph is sufficient; however, when you have multiple data points from individuals within a group, representing continuous data, showing the height or length of a bar as the average, plus and minus an error bar that represents a measure of the variation, is likely hiding the true nature of the data. What I mean by this is that bar graphs hide the spread of the data points, which can result in altogether different interpretations of the data. It is generally recommended that authors use scatter plots to show every data point, especially in studies with small sample sizes. Various sets can be represented by the exact same bar graph (see Figure 1 from the linked paper) The open-access article published last week in PLOS Biology by Weissgerber et al. gives several informational examples as to why this is the case.

In this study, the authors performed a systematic review of approximately 700 research articles published in top tier physiology journals and assessed the use of different types of graphs to represent various kinds of data. The authors state in the abstract:


"Papers rarely included scatterplots, box plots, and histograms that allow readers to critically evaluate continuous data. Most papers presented continuous data in bar and line graphs. This is problematic, as many different data distributions can lead to the same bar or line graph. The full data may suggest different conclusions from the summary statistics."


This should be taken as a nudge for scientists to think about displaying their data with more appropriate graphical representations. Most scientists are culpable for using bar graphs in this sense. Perhaps not only will this improve the interpretation and discussion of the data by the researchers, but also the readers as it improves the transparency of the collected data by pulling the curtain off and exposing it as it should.


Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015) Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLoS Biol 13(4): e1002128. doi:10.1371/journal.pbio.1002128.http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002128

Saturday, April 25, 2015

Conservative Republicans stand alone in views toward climate change

A recent Gallup survey revealed that most conservative Republicans believe that climate change will not occur or will not take place during their lifetime. According to Jake Miller from CBS News:

"Forty percent of self-identified conservative Republicans believe global warming will never happen, according to the data, while 17 percent believe it will affect future generations. Only 37 percent of GOP conservatives believe the current generation will have to deal with the effects of a changing climate."

All other ideological groups surveyed responded quite differently than the Conservative Republicans concerning climate change occurrence during their lifetime.

  • Liberal Democrats: 89%
  • Moderate Democrats: 78%
  • Independents: 66%
  • Moderate Republicans: 64%
  • Conservative Republicans: 37%

I find these responses quite interesting. As you move from one end of the political spectrum, you see a decreasing trend that really drops off when you reach the Conservative Republican category. The accompanying graph I created from the above numbers visually drives home this point. Climate change is and will be a hot topic of discussion among politicians and non-politicians alike. If a majority of most political groups feel climate change is something that is or will be an issue for the current generation, and Conservative Republicans feel the opposite, I will be watching with great interest to see how this issue is handled in upcoming elections. A link to the recently released Gallup survey results is provided below.This webpage also provide some other insightful tidbits of data you can read more about.

Andrew Dugan.
Conservative Republicans Alone on Global Warming's Timing. 4/22/2015.
http://www.gallup.com/poll/182807/conservative-republicans-alone-global-warming-timing.aspx?utm_source=Politics&utm_medium=newsfeed&utm_campaign=tiles

Friday, April 24, 2015

Peer reviewers do actually identify valuable research for funding

It is the best of times, it is the worst of times...today's researcher might say. Technology allows for advanced experiments to rapidly provide large datasets to answer questions that were unanswerable a generation ago. The downside is, that research like this is expensive, there are many more researchers to compete with today, and the budget has not kept up with the growth of the researcher pool competing for funding dollars. Right now, approximately only 16% of grants submitted for federal funding actually get selected for funding. As such, many good grants do not make the cut. 

A long-standing question has been whether federal funding is really going to the research most likely to have an impact in the field, and not just to those who have big labs, a successful history, and work at well known institutions.  What tis question is really asking is, "Does peer review succeed in selecting grants for funding the most impactful research?" Well, until recently science of all things did not have a good answer to this question.  However, a recent study by Li and Agha reported in Science showed that peer reviewers for grants actually do a good job in picking impactful projects, as indicated by publications, patents and other measurable outcomes. 

I recommend to those interested in a very understandable explanation of how grants get selected for funding, and what this research identified to read the attached article in ScienceNews. It is quite insightful, and provides confidence that the system really is working to fund the best research in the various fields of scientific research. The link to the abstract for the actual study published in Science is provided below. On a side note, I think the title is both appropriate and funny for the ScienceNews summary editorial.

Bethany Brookshire. A peer-reviewed study finds value in peer-reviewed research. Science News. April 23rd, 2015.
https://www.sciencenews.org/blog/scicurious/peer-reviewed-study-finds-value-peer-reviewed-research?tgt=nr

Danielle Li, Leila Agha (2015) Big names or big ideas: Do peer-review panels select the best science proposals? Science, Vol. 348 no. 6233 pp. 434-438. DOI: 10.1126/science.aaa0185. 
http://www.sciencemag.org/content/348/6233/434.full

#science   #research   #peerreview   #grants   #sciencenews  

Wednesday, April 22, 2015

A targeted multi-drug treatment and tracking system may improve human cancer treatment

One of the key obstacles in identifying effective anti-cancer therapies is the lack of translation ability of experimental treatment results to actual tumors in humans. Replicating promising anti-tumor effects observed in animal models of various cancer therapies in humans has proven extremely difficult. This goal is even more challenging when attempting to do so from outcomes and results documented in cell culture experiments. Only approximately 7% of therapies identified in pre-clinical studies are actually approved by the Food and Drug Administration (FDA) to proceed beyond clinical trials for use in human cancer treatment. Costs to develop drugs for human use currently approach nearly 3 billion dollars, which compounds the overwhelming failure of oncotherapies to show effects in humans and further limits progression of cancer-targeting treatments.

Why do so many drugs fail to show benefits in humans while demonstrating promise in pre-clinical experimental studies? A primary contributor to this discrepancy lies in the differences in biology of humans compared to that in experimental conditions. The tumor microenvironment in humans may vary in pH, oxygenation, and other chemical features, and the human immune and inflammatory response can alter the drug's chemical potency or specificity toward tumor cells, or alter the cells’ ability to respond to the treatment. Also, human cancers are often treated, respond, and return, exhibiting some level of chemotherapeutic resistance, which makes recurring cancers harder to treat. It is difficult to model this in an experimental setting. The bottom line is that experimental models do not accurately reflect the human condition. Therefore, improving a therapy’s ability to target human cancers with the desired efficacy and potency while minimizing off-target and unexpected influences of the drug on the body, and vice versa, are critical to advancing cancer therapies for human use. A multi-drug approach is likely going to be a viable answer to overcoming so many issues to get the job done correctly.

A recent study by Klinghoffer et al. in Science Translational Medicine tested a device known as CIVO that is designed to deliver multiple potential therapeutic agents into carefully planned spatial locations within a biological tumor, and utilized paired software to analyze each compound’s effects within the tumor microenvironment. The premise behind such a bioengineering approach is to enhance prediction of the value and efficacy of therapies in pre-clinical animal models, and improve the target specificity, limit unintended side effects, and characterize compound-specific anti-tumorigenic effects in experimental and human cancers. This can help researchers and clinicians predict the potential of one or many compounds for use, as well as serve as a delivery and monitoring device for application in human cancer patients.



Figure 1. CIVO chemotherapy microinjection system diagram. The CIVO system can microinject up to 8 (7 depicted here) therapeutic agents into localized area of a tumor. This allows for analysis of local agent-specific treatment effects as well combined chemotherapeutic agent delivery directly into the tumor, reducing off-target side effects.


The researchers tested the CIVO system, which has the capability to deliver microinjections of up to 8 different drugs into the tumor, in xenograft lymphoma models. Such models involve transfer of human cancers into animals for testing drug efficacy.  Using the CIVO microinjection system, a variety of extensively studied and well-characterized anticancer drugs (vincristine, doxorubicin, mafosfamide, and prednisolone) caused clearly defined localized changes to the biology and structure of cancer cells around sites of drug exposure that were reflective of the previously identified and defined mechanisms of each drug’s effects. Interestingly, these local responses were predictive of responses to systemic administration of the agents in animal models. Perhaps one of the most exciting results of the study identified a new mammalian target of rapamycin (mTOR)-specific inhibitor that exhibited efficacy in killing tumor cells in drug-resistant tumors versus its effects in tumors that had previously not been exposed to any chemical therapy. mTOR is a widely-studied protein in cancer due to its role in enhancing cell growth, protein synthesis, and cell survival - all characteristics of cancer cells that contribute to cancer pathobiology and treatment difficulty. In addition, studies designed to determine the feasibility of the CIVO system for its effects of use in humans and canines showed that the microinjection approach of CIVO highly limited the toxicity of chemotherapeutics while improving the anti-cancer targeting effects. This study is exciting as it combines an engineering approaching with chemotherapeutic delivery and demonstrates the potential to enhance the benefits of chemotherapy in killing tumors while reducing the often-serious toxic side effects inflicted by systemic delivery of such agents. Also, CIVO appears to be a useful experimental system to utilize in pre-clinical studies to better predict the effects of certain drugs, or combinations of drugs, in treating various types of cancer before bringing the therapy to humans. This approach will hopefully bridge the major gap between the results observed in experimental models and the effects documented in human application and advance the treatment of cancer in the very near future.


R. A. Klinghoffer, S. B. Bahrami, B. A. Hatton, J. P. Frazier, A. Moreno-Gonzalez, A. D. Strand, W. S. Kerwin, J. R. Casalini, D. J. Thirstrup, S. You, S. M. Morris, K. L. Watts, M. Veiseh, M. O. Grenley, I. Tretyak, J. Dey, M. Carleton, E. Beirne, K. D. Pedro, S. H. Ditzler, E. J. Girard, T. L. Deckwerth, J. A. Bertout, K. A. Meleo, E. H. Filvaroff, R. Chopra, O. W. Press, J. M. Olson, A technology platform to assess multiple cancer agents simultaneously within a patient’s tumor. Sci. Transl. Med.7284ra58 (2015).

#cancer #chemotherapy #doxorubicin #chemoresistant #CIVO #mTOR

Happy Earth Day!


Let us do our best to protect and improve our planet for current and future generations.






#earthday   #earthday2015   #protectourplanet  

Monday, April 20, 2015

Honeybee viruses are a risk for wild bees

Research shows that viruses associated previously with managed honeybees (Apis mellifera) (Figure 1) have now spread to wild bumblebees (Bombus) (Figure 2). Prior studies showed that deformed wing virus had likely transferred from honeybees to wild bumblebees, but researchers at University of London and Queen's University, Belfast identified several interconnected viral diseases that have expanded to affect bumblebees in the wild.

Five viruses in particular were identified from analysis of wild bumblebees and managed honeybees at more than 20 locations across Great Britain: black queen cell virus, deformed wing virus, acute bee paralysis virus, slow bee paralysis virus and sacbrood virus.

Mark Brown of the University of London said, "Our results confirm a recent review of potential threats to pollinators, indicating that so-called honey bee viruses are widespread in wild bees." 





Figure 1. Honeybee (A. mellifera). Central Indiana, 4/2015.




Figure 2. Bumblebee (Bombus). Central Indiana, 4/2015.


"Our findings are important because they indicate that many viruses can spread easily between pollinator species and, furthermore, that they can reach very high disease levels in wild bumblebees," Dino McMahon, from Queen's University, Belfast, added.

These results are of great interest to ecologists and plant-pollinator biologists, as it now appears that transmission of viruses across bee species may occur more frequently and easier than originally thought. Also, wild bumblebees are critical pollinators in the wild and their loss could be detrimental to plant populations dependent on them for pollination.  In addition, as in humans, travel of the bees over long distances could promote widespread infections across bees species in a short amount of time. Further study is necessary, but this initial research highlights the urgency and potential complexity of the situation at hand.

Does anyone with first hand experience with bee-keeping or studying plant-pollinator interactions have any thoughts about this research? What potential implications are there to these findings that may be of importance from a local or regional perspective?

McMahon et al. (2015) A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology, DOI: 10.1111/1365-2656.12345.
http://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12345/fullhttp://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12345/full

#pollinators   #bees   #honeybee   #bumblebee   #viruses   #ecology   #biology   #science  

Friday, April 17, 2015

Pet dogs trigger a "mother-infant" neurohormonal response



To anyone that has a pet, it's pretty simple to admit they consider their furry companion like a part of the family. You might even call your dog your "little baby", and talk baby talk to it from time to time. It's ok...it's science. Yes, science has now shown that dogs elicit an oxytocin release that is similar to that generated by infants in mothers. Oxytocin is a neuromodulatory hormone that is produced in the hypothalamus of the brain and stored in the pituitary gland. It is released in response to cues of intimacy, trust, and bonding, often as part of our physiological response for involvement in events related to reproduction and in bonding to offspring. Recent research by Nagasawa et al. in the recent issue of Science suggests the gaze of dogs co-evolved with a hormonal feedback loop involving oxytocin in humans as part of the development of the human-dog bond. So, just remember its ok if you think your little "woogums" has the cutest furry little face ever. Science says that's what how you are supposed to feel.

Miho Nagasawa, Shouhei Mitsui, Shiori En, Nobuyo Ohtani, Mitsuaki Ohta, Yasuo Sakuma, Tatsushi Onaka, Kazutaka Mogi, Takefumi Kikusui, Oxytocin-gaze positive loop and the coevolution of human-dog bonds. Science, 17 April 2015; 348(6232):333-336 
DOI: 10.1126/science.1261022.

Monday, April 13, 2015

Traumatic brain injury "ages" your brain

As if having a traumatic brain injury (TBI) is not bad enough, recent clinical research suggests it "ages" your brain relative to you true chronologic age. A new study by Cole et al. Annals of Neurology found that TBI-induced brain aging not only causes your brain to exhibit anatomical and functional defects associated with an aging brain, but that the effects are more pronounced the farther out you go from time of injury. In other words, this "aging" process seems to accelerate as one with TBI gets older. 

As quoted from the study's abstract:
"TBI brains were estimated to be 'older,' with a mean predicted age difference (PAD) between chronological and estimated brain age of 4.66 years (±10.8) for GM (gray matter) and 5.97 years (±11.22) for WM (white matter = myelinated axon tracts).

What processes were defined as similar to those observed in the aging brain?

Animal research has implicated a number of biological and pathological processes that affect tissue damage at the time of injury, and progressing even after the initial mechanical tissue damage. Multiple mechanisms such as chronic neuroinflammation, degeneration of damaged axons, and accumulation of pathological tau and amyloid-β proteins often associated with neurodegenerative disease like Alzheimer's disease have been reported. Ultimately, these events cause changes in cell structure and function, cell death, and brain atrophy. These processes often occur simultaneously, while others continue chronically while others subside. Is this really a case of the brain "aging" faster than the body that contains it? It is hard to say. It is also hard to say how true aging that coincides with the progressions of neuropathology interact or influence these processes. Nevertheless, this study yields interesting clinical insights into human responses and outcomes that have long been studied in animal models. It also poses questions to ponder concerning the connections between trauma-induced neurodegeneration, and age-induced or gene-induced neurodegeneration. An interest step in clinical neurodegenerative research, but much more research is needed to fully flesh out answers to questions these results present.


JH Cole PhD*, R Leech PhD, DJ Sharp PhD and for the Alzheimer's Disease Neuroimaging Initiative. (2015) Prediction of brain age suggests accelerated atrophy after traumatic brain injury. Annals of Neurology 77(4): 571-581.

Friday, April 10, 2015

Axonal activity biases myelination by oligodendrocytes in the central nervous system

Oligodendrocytes myelinate central nervous system (CNS) axons during development and other process involved in axonal plasticity. However, not all CNS axons are myelinated by oligodendrocytes. Some evidence suggests oligodendrocytes may myelinate or maintain myelination of axons of a specific caliber (size).  Other studies also suggest oligodendrocytes sustain myelination of axons based on chemical cues secreted by axons, alone and in combination with size selectivity. Still, other results indicate electrical activity pf axons can stimulate oligodenrocytes to myelinate active axons. Despite all of these ideas, no clear mechanisms of how oligodendrocytes choose to myelinate or sustain myelination of particular axons is available. A recent study by Hines et al. in Nature Neuroscience (April, 2015; doi:10.1038/nn.3992) provides convincing evidence that oligodendrocytes initially myelinate various axons, but maintain myelination of axons through a bias based on activity of the axons.

Using transgenic mice that allow fluorescent identification of oligodendrocytes and a specific subset of hindbrain axons that project to the spinal cord in zebrafish (phox2b+ axons), the researchers observed that application of tetrodotoxin (TTX), a voltage-gated sodium channel blocker that effectively paralyzes axonal activity, did not affect oligodendrocyte survival or numbers, but did affect axonal selectivity of myelination. By treating the fish larvae with sodium channel modulator, veratridine 72 h post-fertilization (just before onset of myelination) causes widespread neuronal and axon activity, but does not significantly effect the selection of axons for myelination. However, it did affect sheath length.

The authors then utilized targeted overexpression via viral transfection of the human inward rectifier K+ channel Kir2.1 in single phox2b+ axons, which reduces neuronal and axon excitability in the zebrafish to determine whether neuronal excitability was necessary for axon selection for myelination. They found that the Kir2.1 reduced animals had significantly decreased myelination by oligodendrocytes. Using confocal microscopy, the authors determined that fluorescently labeled (EGFP) vesicles accumulated at myelin ensheathment sites, which suggests that a localized neuronal-oligodendrocyte interaction may promote selective myelination by oligodendrocytes.

To verify that this activity-dependent axonal secretion of vesicles was required for maintenance of myelination by oligodendrocytes, the authors selectively reduced neuronal activity using a transgenic line with fluorescent tetanus toxin expressed in neurons (neurod1:TeNT EGFP). In this model, tetanus toxin potently inhibited neuronal activity in the fish larvae and they showed no spontaneous activity or response to touch. Oligodendrocytes formed nascent sheaths on axons in this transgenic model, but using time-lapse microscopy imaging, they observed that established sheaths were more frequently lost in the (neurod1:TeNT EGFP) transgenic line than the normal control line over a 15 hour period, supporting the idea that neuronal axon activity is important for sustained oligodendrocyte myelination of axons. In the authors’ own words, “maintenance of nascent sheaths is regulated by activity-dependent secretion from axons, whereas initial axon wrapping is activity independent”. The accompanying Figure 1 that I constructed summarizes this concept in a simple diagram that hopefully makes the idea simple to comprehend.



Figure 1. Oligodendrocytes form myelin sheaths on multiple axons in the central nervous system (CNS) during development. However, maintenance depends on activity of axons previously ensheathed by oligodendrocytes.

This study is important for a number of reasons. One, it provides an extensive analysis in an animal model that activity of axons is crucial to the maintenance, and some degree phenotype) of myelination of CNS axons by oligodendrocytes. From a purely scientific standpoint, this provides a foundation for further work in understanding oligodendrocyte developmental biology and axonal interaction mechanisms. Secondly, diseases that result in lost of oligodendrocyte myelination in the CNS, such as multiple sclerosis, are complicated and the full mechanisms of disease onset, progression, and remission remain unclear. This study may shed light on why some subsets of axonal tracts are affected as they are, whereas they seem somewhat random based on our current understanding of the disease. Perhaps there is some specific localized axonal dysfunction that cues local oligodendrocytes to demyelinate, causing signal transduction problems and symptomatic onset in MS patients.  This is all speculation, but such research opens doors for asking questions such as this to bridge basic research for the application of knowledge to the understanding and treatment of human disease.

Jacob H Hines, Andrew M Ravanelli, Rani Schwindt, Ethan K Scott & Bruce Appel (2015) _Neuronal activity biases axon selection for myelination in vivo_. Nature Neuroscience, doi:10.1038/nn.3992.

Tuesday, April 7, 2015

The role of the protein, αkap, in the structure and maintenance of the mouse neuromuscular junction

Part of my current research focuses on understanding the dynamics of pathological loss and change of neuromuscular synapses that allow for neural control of muscle function in the motor neuron disease, amyotrophic lateral sclerosis (ALS), commonly known as “Lou Gehrig’s Disease”. In this disease, pathological changes occur that sadly cause motor neuron-muscle communication and activity dysfunction, which results in skeletal muscle wasting, paralysis, motor neuron death, and eventually death of the afflicted person. I study the literature to understand mechanisms of how such pathology may occur to help focus studies on targeting therapies to be more effective in treating ALS.


The junction between the terminal synapse of the spinal motor neuron and the peripheral musculature (found in the limbs and elsewhere) is characterized by synapse whereby the neuron releases acetylcholine to activate the nicotinic acetylcholine receptors (AchRs) that are clustered at the post-synaptic membrane of the muscle. These receptors cluster at this synapse for effective communication with the motor neuron, and rearrange in response to disease or injury to the neuron or nerve. Improving stability of this neuron-AchR interaction, or helping achieve its re-connection could result in less disuse atrophy of the muscles and improve neurological function. 

A recent paper in the Journal of Neuroscience by Martinez-Pena y Valenzuela et al. (35[13]: 5118-5127; doi: 10.1523/JNEUROSCI.3951-14.2015) discusses the investigation and results concerning the importance of a particular muscle-specific nonkinase anchoring protein (αkap), encoded within the calcium/calmodulin kinase II (camk2) α gene in living animals, as prior research has already implicated this protein in such a role in cell culture. The authors found that knocking-down the expression of αkap reduced the amount of AchRs at the muscular post-synapse, and prevented new placement and reduced the recycling of these receptors at the synapse. Importantly, blocking αkap led to breakdown of the entire neuromuscular synapse, implicating a very large role for this protein in maintaining normal structure and function of the neuromuscular synapse. This paper is important as it implicates dysfunction in αkap synthesis or incorporation at the neuromuscular synapse as a potential mechanism to target in treating disease progression in ALS and other related disorders. 

Martinez-Pena Y Valenzuela I, Aittaleb M, Chen PJ, Akaaboune M. (2015) The Knockdown of αkap Alters the Postsynaptic Apparatus of Neuromuscular Junctions in Living Mice. J Neurosci. 2015 Apr 1;35(13):5118-27. doi: 10.1523/JNEUROSCI.3951-14.2015.

#neuroscience #research #als #science