I love the convenience of mobile applications but hate the way they re-invent the wheel and are killing the Web. What can be done about it?... Read more »
The relevance of informality analysis in social media texts... Read more »
Alejandro Mosquera, & Paloma Moreda. (2011) Enhancing the discovery of informality levels in Web 2.0 texts. Proceedings of the 3rd Language Technology Conference (LTC 2011), Poland. info:/
How do you build a virtual environment for a worm? The Nematode C. Elegans with glowing neurons (source)Using a little optogenetic trickery, you can directly activate specific worm neurons with light. If you know your worm neurons, you can stimulate ones that make it think it has suddenly touched something with its nose or that the environment is suddenly very salty. Before we dive into worm VR, let's back up and discuss this specific worm.The Magnificent C. ElegansC. Elegans is a surprisingly popular subject of study in neuroscience. It has a simple and well defined nervous system that contains only 302 neurons (in the hermaphrodite, the rare males have a few extra neurons). All the neurons and even all the connections between the neurons have been pretty well characterized. They are small (hundreds can fit on a standard sized petri dish) and they reproduce quickly. And it that wasn't enough to make C. elegans a desirable subject for study, they can be genetically altered with relative ease, and exhibit rudimentary learning skills. A recent technological development has made clever use of genetic tools that allow calcium influx (an indicator of neural activity) to be visualized in neurons and allow neurons to be activated by light. Faumont et al., (2011) have created a worm tracking system that uses the fluorescence from a genetically altered neuron to locate the worm and recenter the microscope on the worm in real time. This allows for completely non-invasive visualization of neuronal calcium/activity in the awake behaving animal. The recent paper in PLoS One, describes exactly how they got the microscope to track the worm in real time without blurring of the signal or messing up the calcium imaging. The paper is open access, so you can go read the details for free.To see this larger and more clearly, you can download this video and their 4 other supplementary videos here. In this video, you can see the animal moving around in the top left, the path it follows in the top right, the calcium fluorescence signal in the bottom left (notice the calcium neuron is always in the field of view), and the activity of this particular neuron when the worm is traveling either forward (blue) or backward (red). The "Dedicated Circuit" HypothesisThe neuron imaged in this video is called AVB, and it is a 'command neuron'. Faumont et al. show that it increases in activity when the worm is moving forward and decreases when the worm moves backwards. A similar command neuron, AVA, does just the opposite, increasing when the worm moves backward and decreasing when it moves forward. These data support what is called the "dedicated circuit hypothesis" which says that the worm uses one set of neurons to go forward and a completely different set of neurons to move backwards.While Faumont et al. shows that the dedicated circuit hypothesis is supported for command neurons, they find that the activity of the actual motor neurons (the neurons on the body wall that control contraction of the muscles) does not support this hypothesis. If the dedicated circuit hypothesis was true, the A-type motor neurons should only be active and oscillating during backward movement, and the B-type motor neurons should only be active during forward movement. They found that this wasn't true, that both were active and oscillating during both forward and backward motion. Virtual Reality for WormsNow back to virtual reality. This Faumont et al. paper is a showcase of new tools that can be used to study C. Elegans in a simultaneously macroscopic and microscopic way. One of the new techniques the introduce is the optogenetic stimulation of specific neurons in specific places to create and 'environment' for the worm. Faumont et al., 2011 Figure 2When they genetically express channel rhodopsin, the channel which activates neurons when exposed to blue light in the ASH neuron (a neuron sensitive to osmolarity, or saltiness, changes), they can activate that neuron whenever they want by turning on the blue light. They create a virtual environment by tracking the worm as it travels in a field, and activating the blue light when it reaches a certain xy coordinate. In the figure above they activate the neuron when the worm's nose is within the outer ring (traces turn blue). This makes the worm 'think' that the ring is full of saltier liquid than the rest of the area. This virtual environment takes away all the technical difficulties of actually creating a ring of salty water in a pool of less salty water, and the VR environment can be quickly and easily changed into any shape or size, when desired. This new tracking method, in combination with calcium imaging and optogenetics, represents a leap forward in cellular scale neuroscience, to non-invasively visualize neuronal activity, activate neurons, and record the coinciding behavior is a combination mammalian neuroscientists can only dream about.Note: there are ways to image calcium in the neurons of moving mice, but even this requires installing a 'window' into the skull and mounting a mini-microscope on the mouse's head. In addition, the neurons visualized are limited to the ones closest to the surface of the brain.© TheCellularScale... Read more »
Faumont S, Rondeau G, Thiele TR, Lawton KJ, McCormick KE, Sottile M, Griesbeck O, Heckscher ES, Roberts WM, Doe CQ.... (2011) An image-free opto-mechanical system for creating virtual environments and imaging neuronal activity in freely moving Caenorhabditis elegans. PloS one, 6(9). PMID: 21969859
Left ventricular assist device technology isn’t necessarily new, but it is one of the biggest harbingers of cybernetic technology. People with weak hearts that are waiting for a donor can use these sorts of heart pumps to bridge patients over until they can receive a full transplant. However, such LVAD machines are usually located in [...]... Read more »
Rizzieri, A., Verheijde, J., Rady, M., & McGregor, J. (2008) Ethical challenges with the left ventricular assist device as a destination therapy. Philosophy, Ethics, and Humanities in Medicine, 3(1), 20. DOI: 10.1186/1747-5341-3-20
When Charles Dickens wrote It was the of, it was the of, the immortal first words in A Tale of Two Cities, he can't have imagined that 21st-century computer scientists would parse his prepositions and pronouns as part of vast literary data sets. But today's researchers are studying the unimportant words in books to find important literary trends. With the meaty words taken out, language becomes a numbers game.
To see how literary styles evolve over time--a science dubbed "stylometry"--researchers led by James Hughes at Dartmouth College turned to Project Gutenberg. The site contains the full text of more than 38,000 out-of-copyright books. Researchers began their mining expedition by digging out every author who wrote after 1550, had a known date of birth and (when relevant) death, and had at least 5 English-language books digitized.
These criteria gave the researchers a set of 537 authors with 7,733 published works. But they weren't interested in every word of those books. Nouns and adjectives were out: No Kareninas or Lolitas, nothing nice or bad or beautiful, no roads or homes or people. Most verbs were out, except for forms of the utilitarian to be. No one could speak or walk or Fly, good Fleance!
It may seem that the researchers were stripping all the information-containing words out of the sentences, and in fact that was their goal: "Content-free" words were all they wanted. The 307-word vocabulary that remained from the books was mostly prepositions, conjunctions, and articles.
This linguistic filler, the little stitches that hold together the good stuff, is known to contain a kind of authorial fingerprint. We may not think much about these words when we're writing or speaking, but scientists can use them to define our style.
Hughes and his team used computer analysis to score each author's similarity to every other author. They found that before the late 18th century, authors's stylistic similarity didn't depend on how close to each other they lived. (Each author was represented by a single year, the midpoint between his or her birth and death.) During this time period, authors who lived in the same generation didn't influence each other's styles much more than authors who lived hundreds of years away.
But from the late 18th century to today, it was a different story. Stylistically, authors were more similar to their contemporaries than to other writers. By the late 19th century, writers closely matched the style of other writers who lived at the same time (at least according to the computers tallying up their non-content words). This influence dropped off outside of 30 years. In other words, authors who lived more than three decades away each other may as well have lived centuries away, for all the similarity between their writing.
Looking at more recent books, that window of influence seems to become even tighter. Among authors from the first half of the 20th century, the similarity of style drops off beyond just 23 years.
Over time, authors have become more and more influenced by the other authors writing at the same time. The researchers say this may simply be due to the number of books published. In the early part of their dataset, there were few enough books around that a studious person could read, well, most of them. But as more and more books were published, contemporary books made up a larger share of what was available to read. Authors have filled more and more shelves in their libraries with books by their peers--and this has made them more likely to echo each other's styles.
Because Project Gutenberg relies on public-domain material, there weren't very many authors after the mid-20th century included in this study. Looking forward, "You would expect a continued diminishing of influence," says Daniel Rockmore, the paper's senior author. Contemporary books take up an ever greater portion of what's available to read. In addition to the huge number of books published each year (more than 288,000 in the United States in 2009), there are now e-books and e-readers and Japanese Twitter novels.
A century from now, we may be able to look back and see that today's authors had an ever-condensing frame of influence. Of course, by then literary styles might only last a week. Most books will be forgotten, but every author will be a revolutionary.
James M. Hughes, Nicholas J. Foti, David C. Krakauer, & Daniel N. Rockmore (2012). Quantitative patterns of stylistic influence in the evolution of literature PNAS : 10.1073/pnas.1115407109
Image: Library of Congress from ep_jhu/Flickr
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James M. Hughes, Nicholas J. Foti, David C. Krakauer, & Daniel N. Rockmore. (2012) Quantitative patterns of stylistic influence in the evolution of literature. PNAS. info:/10.1073/pnas.1115407109
Aside from cost, aesthetics, and functionality, materials selection is now a topic priority for many consumers when they make a purchase. Consumers are becoming more aware of their choices for sustainable and reusable materials—even the potential health risks/toxicity associated with materials. This is especially true for products containing plastics, particularly the additives used to make [...]... Read more »
Saravanabhavan, G., & Murray, J. (2012) Human Biological Monitoring of Diisononyl Phthalate and Diisodecyl Phthalate: A Review. Journal of Environmental and Public Health, 1-11. DOI: 10.1155/2012/810501
RAHMAN, M., & BRAZEL, C. (2004) The plasticizer market: an assessment of traditional plasticizers and research trends to meet new challenges. Progress in Polymer Science, 29(12), 1223-1248. DOI: 10.1016/j.progpolymsci.2004.10.001
Let’s face it: The typical individual is not that bright. Just check out these human specimens: Yet somehow, if you get enough numbskulls together, the group can make some pretty intelligent decisions. We’ve seen this in a wide variety of organisms facing a number of different challenges.In a brilliant series of studies, Jean-Louis Deneubourg, a professor at the Free University of Brussels, and his colleagues tested the abilities of Argentine ants (a common dark-brown ant species) to collectively solve foraging problems. In one of these studies, the ants were provided with a bridge that connected the nest to a food source. This bridge split and fused in two places (like eyeglass frames), but at each split one branch was shorter than the other, resulting in a single shortest-path and multiple longer paths. After a few minutes, explorers crossed the bridge (by a meandering path) and discovered the food. This recruited foragers, each of which chose randomly between the short and the long branch at each split. Then suddenly, the foragers all started to prefer the shortest route. How did they do that?This figure from the Goss et al 1989 paper in Naturwissemschaften shows (a) the design of a single module, (b) ants scattered on the bridge after 4 minutes (I promise they’re there), and (c) ants mostly on the shortest path after 8 minutesYou can think of it this way: a single individual often tries to make decisions based on the uncertain information available to it. But if you have a group of individuals, they will likely each have information that differs somewhat from the information of others in the group. If they each make a decision based on their own information alone, they will likely result in a number of poor decisions and a few good ones. But if they can each base their decisions on the accumulation of all of the information of the group, they stand a much better chance of making a good decision. The more information accumulated, the more likely they are to make the best possible decision. In the case of the Argentine ant, the accumulated information takes the form of pheromone trails. Argentine ants lay pheromone trails both when leaving the nest and when returning to the nest. Ants that are lucky enough to take a shorter foraging route return to the nest sooner, increasing the pheromone concentration of the route each way. In this way, shorter routes develop more concentrated pheromone trails faster, which attract more ants, which further increase pheromone concentration of the shortest routes. In this way, an ant colony can make an intelligent decision (take the shortest foraging route) without any individual doing anything more intelligent than following a simple rule (follow the strongest pheromone signal). Home is where the heart is. Photo of a bee swarm by Tom SeeleyHoneybee colonies also solve complicated tasks with the use of communication. Tom Seeley at Cornell University and his colleagues have investigated the honeybee group decision-making process of finding a new home. When a colony outgrows their hive, hundreds of scouts will go in search of a suitable new home, preferably one that is high off the ground with a south-facing entrance and room to grow. If a scout finds such a place, she returns to the colony and performs a waggle dance, a dance in which her body position and movements encode the directions to her site and her dancing vigor relates to how awesome she thinks the site is. Some scouts that see her dance may be persuaded to follow her directions and check out the site for themselves, and if impressed, may return to the hive and perform waggle dances too. Or they may follow another scout’s directions to a different site or even strike out on their own. Eventually, the majority of the scouts are all dancing the same vigorous dance. But interestingly, few scouts ever visit more than one site. Better sites simply receive more vigorous “dance-votes” and then attract more scouts to do the same. Like ants in search of a foraging path, the intensity of the collective signal drives the group towards the best decision. Once a quorum is reached, the honeybees fly off together to their new home.But groups can develop better solutions than individuals even without communication. Gaia Dell’Ariccia at the University of Zurich in Switzerland and her colleagues explored homing pigeon navigation by placing GPS trackers on the backs of pigeons and releasing them from a familiar location either alone or in a group of six. Because they were all trained to fly home from this site, they all found their way home regardless of whether they were alone or in a group. But as a flock, the pigeons left sooner, rested less, flew faster, and took a more direct route than did the same birds when making the trip alone. By averaging the directional tendencies of everyone in the group, they were able to mutually correct the errors of each individual and follow the straightest path. In each of these examples, each individual has limited and uncertain information, but each individual has information that may be slightly different than their neighbors’. By combining this diverse information and making a collective decision, hordes of idiots can make genius decisions.Want to know more? Check these out:1. Couzin, I. (2009). Collective cognition in animal groups Trends in Cognitive Sciences, 13 (1), 36-43 DOI: 10.1016/j.tics.2008.10.002 2. ... Read more »
Dussutour, A., Nicolis, S., Deneubourg, J., & Fourcassié, V. (2006) Collective decisions in ants when foraging under crowded conditions. Behavioral Ecology and Sociobiology, 61(1), 17-30. DOI: 10.1007/s00265-006-0233-x
List C, Elsholtz C, & Seeley TD. (2009) Independence and interdependence in collective decision making: an agent-based model of nest-site choice by honeybee swarms. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 364(1518), 755-62. PMID: 19073474
Dell'Ariccia, G., Dell'Omo, G., Wolfer, D., & Lipp, H. (2008) Flock flying improves pigeons' homing: GPS track analysis of individual flyers versus small groups. Animal Behaviour, 76(4), 1165-1172. DOI: 10.1016/j.anbehav.2008.05.022
A while back I mentioned FriendLens as a tool for getting a different view of your friends’ Facebook photos. But, there is another Friend Lens being developed by John Gibbons and Arvin Agah of The University of Kansas, in Lawrence, using open source resources. (I suspect they will have to find a different name for [...]Post from: David Bradley's Sciencetext Tech TalkA hybrid social blogging platform
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John W. Gibbons, & Arvin Agah. (2012) Friend Lens: novel web content sharing through strategic manipulation of cached html. Int. J. Web Based Communities, 8(2), 242-265. info:/
Surface electromyography is apparently now able to recognize and even synthesize speech based on a certain pattern. An acoustic signal is corrupted by high environmental noise. Astronauts that perform operations in spacesuits fall victim to this phenomenon. Earthbound firefighters are … Continue reading →... Read more »
Jorgensen, C., & Dusan, S. (2010) Speech interfaces based upon surface electromyography. Speech Communication, 52(4), 354-366. DOI: 10.1016/j.specom.2009.11.003
Cellular automata are probably the closest things to machine life that most people have gotten an opportunity to experiment with in recent years. John Conway invented a piece of software titled the Game of Life in 1970. He carefully set up the rules to create a balanced world. While this might sound like old news, [...]... Read more »
Arima V, Iurlo M, Zoli L, Kumar S, Piacenza M, Della Sala F, Matino F, Maruccio G, Rinaldi R, Paolucci F.... (2012) Toward Quantum-dot Cellular Automata units: thiolated-carbazole linked bisferrocenes. Nanoscale, 4(3), 813-23. PMID: 22159165
Telemedicine is a field that uses telecommunications technology to provide healthcare at a distance. Certain computer systems can be linked to a physician’s office for diagnostic purposes. Different clinics and hospitals can be linked together. In the future, telemedicine could be used to perform robotic surgeries in space. Some forms of telemedicine have been in [...]... Read more »
Himpens J. (2012) Surgery in space: the future of robotic telesurgery (Haidegger T, Szandor J, Benyo Z. Surg Endosc 2011; 25(3):681-690). Surgical Endoscopy, 26(1), 286. PMID: 21858579
Sitting on the deck to drink your morning cup of coffee is a great way to start the day—but not when your deck is rotting. Fortunately wood products are protected with wood preservatives, often with chromate copper arsenate (CCA) . But growing concerns over the safety and health effects [...]... Read more »
Ding, X., Richter, D., Matuana, L., & Heiden, P. (2011) Efficient one-pot synthesis and loading of self-assembled amphiphilic chitosan nanoparticles for low-leaching wood preservation. Carbohydrate Polymers, 86(1), 58-64. DOI: 10.1016/j.carbpol.2011.04.002
A lot of excitement surrounding microfluidics has been about its promising use in diagnosis in low-resource settings. Many infectious diseases present in developing countries are manageable or treatable with available medications, but still account for 1/3 of deaths. In these areas, multiple diseases present similar symptoms, leading to misdiagnosis and thus incorrect treatment. Hundreds of blood-based microfluidic immunoassays are available for diagnostic purposes, but they’re not all created equally. They require varying levels of sample processing or analysis that prohibit their deployment in low-resource settings. Further, while some diseases may have similar symptoms, they might require different detection techniques, with varying sample volumes, reagents and processing time, making it difficult to detect multiple diseases within the same system. This is the focus of recent work from Paul Yager of University of Washington. In his Lab on a Chip paper, “Progress toward multiplexed sample-to-result detection in low resource settings using microfluidic immunoassay cards,” he and his colleagues develop a system to detect both Typhoid fever and malaria.... Read more »
Lafleur, L., Stevens, D., McKenzie, K., Ramachandran, S., Spicar-Mihalic, P., Singhal, M., Arjyal, A., Osborn, J., Kauffman, P., Yager, P.... (2012) Progress toward multiplexed sample-to-result detection in low resource settings using microfluidic immunoassay cards. Lab on a Chip, 12(6), 1119. DOI: 10.1039/C2LC20751F
The boundary between electronics and biology is blurring with the first detection by researchers at Department of Energy’s Oak Ridge National Laboratory of ferroelectric properties in an amino acid called glycine. A multi-institutional research team led by Andrei Kholkin of the University of Aveiro, Portugal, used a combination of experiments and modeling to identify and [...]... Read more »
Heredia, A., Meunier, V., Bdikin, I., Gracio, J., Balke, N., Jesse, S., Tselev, A., Agarwal, P., Sumpter, B., Kalinin, S.... (2012) Nanoscale Ferroelectricity in Crystalline γ-Glycine. Advanced Functional Materials. DOI: 10.1002/adfm.201103011
This Sunday will be 100th anniversary of the sinking of the Royal Mail Ship (RMS) Titanic. Over the years this tragic accident has been the topic of numerous books, films, exhibits—even a memorial cruise. Not only has this shipwreck captured the attention of the public, but the scientific community as well. Ever since the wreckage [...]... Read more »
Felkins, K., Leigh, H., & Jankovic, A. (1998) The royal mail ship Titanic: Did a metallurgical failure cause a night to remember?. JOM, 50(1), 12-17. DOI: 10.1007/s11837-998-0062-7
Foecke, T., & Hooper-McCarty, J. (2009) Quantitative Metallography And Microanalytical Analysis Of Particles In Iron Rivets Recovered From The Wreck Of The RMS Titanic. Microscopy and Microanalysis, 15(S2), 524. DOI: 10.1017/S1431927609099127
I’ve always been a fan of Bowtie, one of the first algorithms to leverage Burrows-Wheeler Transform for short read alignment. When I first encountered it in 2008, it was incredibly fast. Faster than Maq and Novoalign, two of the early popular algorithms for read mapping. Perhaps more importantly, it was ultra memory-efficient, enabling one to [...]... Read more »
Microfluidic Future is by no means an accurate representation of all the current, ongoing research in microfluidics. Nevertheless, the fact that you won’t be able to find any articles about assays relying on a biophysical marker isn’t too far off the reality in microfluidics. I suppose this is partly due to the incredible amount of previous work on molecular markers when high resolution control hadn’t been realized yet. Regardless, I was happy to come across an article about a microfluidic device that indicates sickle cell disease risk using the disease’s biophysical characteristics. The work “A Biophysical Indicator of Vaso-occusive Risk in Sickle Cell Disease” appeared in Science Translational Medicine this past February and is a result of ongoing sickle research by MIT and Harvard Medical School. My friend originally forwarded me an article about it on Medgadget, which you should also check out, along with the podcast it mentions.... Read more »
Wood DK, Soriano A, Mahadevan L, Higgins JM, & Bhatia SN. (2012) A Biophysical Indicator of Vaso-occlusive Risk in Sickle Cell Disease. Science Translational Medicine, 4(123), 1-8. PMID: 22378926
Anytime we travel through the Internet we leave piles of data behind us, like Pigpen shedding his cloud of filth. It's too bad if you're concerned about privacy. But if you're a mathematician, that heap of dirt is more like a goldmine, and digging into it can turn up unexpected nuggets. A study of worldwide Google searches, for one thing, reveals that people in wealthier nations think less about the past.
Google collects data on what search terms people around the world are using. Researchers who want to use this data to compare search terms across different countries are usually restricted to places that share a language. But the authors of a new paper in Scientific Reports got around that problem by looking only at numerical search terms.
"We realized...that years represented in Arabic numerals are an almost universal written representation," author Helen Susannah Moat wrote in an email. By looking only at search terms such as 2011 or 2010, she and her coauthors could compare search data from nearly the whole globe.
"It seemed a logical first step to consider to what extent Internet users were searching for dates in the future compared to dates in the past," Moat says. For example, looking at data from 2010, the researchers compared searches including 2011 to those including 2009. The ratio of forward-looking to backward-looking searches in each country became its "future orientation" score.
The authors culled data from 45 countries with substantial Internet-using populations. Then they sorted those 45 countries by GDP ("also the most obvious variable," Moat says). A clear pattern popped out of the numbers: Countries with lower GDPs had lower future orientation scores, and vice versa. People in poorer countries did more searches concerning the previous year; those in wealthier nations searched more for the next year. The trend was strong, and it held up in data from 2009 and 2008 as well.
Countries with the lowest future orientation scores included Pakistan and Vietnam, where previous-year searches outnumbered next-year searches by a factor of three or four to one. In the United States and Canada, countries toward the higher end in future orientation, searches for the last year and the next year were roughly equal. Switzerland, Australia, and the United Kingdom were among the most forward-looking countries of all.
"One of the possible interpretations of our results," Moat writes, "is that a focus on the future supports economic success." In other words, populations that are more forward-thinking become wealthier. This up-by-the-bootstraps explanation doesn't seem like the simplest one, though.
Another possibility is that populations with more money and leisure time can afford to spend it thinking about the future. A person in a wealthier nation might search online for next year's concert tickets, dates of work holidays, or when the new iPad is coming out. Someone without disposable income, though, might not have many such events to look forward to.
Here's some good news for people in all nations: Google Trends is available online for aspiring data analysts to play with. Panning for gold in its graphs won't cost anything except your free time.
Preis, T., Moat, H., Stanley, H., & Bishop, S. (2012). Quantifying the Advantage of Looking Forward Scientific Reports, 2 DOI: 10.1038/srep00350
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Those of you that read my posts regularly know that I believe the next (substantial) evolution of our species will involve either genetic modification, robotics, or a combination of both. So whenever I come across an interesting development happening in genetics research, AI, etc., I like to pass it along on here – even if [...]... Read more »
Zhiyu Peng, Yanbing Cheng, Bertrand Chin-Ming Tan, Lin Kang, Zhijian Tian, Yuankun Zhu, Wenwei Zhang, Yu Liang, Xueda Hu, Xuemei Tan.... (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nature Biotechnology. DOI: 10.1038/nbt.2122
Math and computer simulation wizzes at the University of North Carolina at Chapel Hill have just taken a nice step forward in granular simulation by approaching the problem with math heretofore not applied to dynamic granular modeling. It's really quite impressive.
Narain and Gola's work may be favorable over previous methods both due to its 1) accuracy, as well as 2) the ability to trade off quality-over-precision / precision-over-quality as an easily implemented option. Whenever computation is involved, that flexibility is very valuable.... Read more »
Narain, R., Golas, A., & Lin, M. (2010) Free-flowing granular materials with two-way solid coupling. ACM Transactions on Graphics, 29(6), 1. DOI: 10.1145/1882261.1866195
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