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
When in trouble or in doubt, invent new words. We have bibliometrics and scientometrics from the Age of Print. Now they are joined by informetrics, cybermetrics, webometrics and altmetrics, which...
-- Read more on ScientificAmerican.com
... Read more »
Li, X, Thelwall, M, & Giustini, D. (2012) Validating online reference managers for scholarly. Scientometrics, 461-471. DOI: 10.1007/s11192-011-0580-x
Ludo Waltman, & Rodrigo Costas. (2013) F1000 recommendations as a new data source for research evaluation: A comparison with citations. JASIST. arXiv: 1303.3875v1
Taylor, M. (2013) Towards a common model of citation: some thoughts on merging altmetrics and bibliometrics. Research Trends. info:/
“Using English is the sign of a great mind. Discuss.” Sounds like an absurdly bigoted essay topic? While I’ve made up the topic and while most readers will baulk at such an explicit association of English with academic excellence, most … Continue reading →... Read more »
Erkkilä, Tero. (2013) Global University Rankings, Transnational Policy Discourse and Higher Education in Europe. European Journal of Education. DOI: 10.1111/ejed.12063
Hey Julie,it's not every week I get to issue an invitation to the entire world, but that's exactly what I'm doing today! MiaStudents invited to compete in global dog poo competition:Poo Power! Global Challenge launches Monday 25 November 2013Students and classes will be pitched against each other to see who can identify the most and largest dog waste 'hotspots' in their local neighbourhood in the 'Poo Power! Global Challenge'. Participants use a GPS-enabled iPhone to download the free Poo Power! App from the App Store. Their task is to identify and map dog poo 'hotspots' in dog parks and public spaces from their neighbourhood from Monday 25 November 2013. While the initial competition is being run for students and schools, anyone, anywhere can participate and contribute to this citizen science initiative.Duncan & Diesel from Poo Power!This eyebrow-raising project is a collaboration between dog poo entrepreneur Duncan Chew from Poo Power! and me (!), as a way to say thanks to all the students who voted for me to win I'm a Scientist, Get Me Out of Here! in Australia recently. The collected information will be uploaded onto the Global Poo Map and provides a platform for students to discuss the scientific, social and environmental issues of dog waste. The students are then encouraged to write a letter to their local Government representative of their findings and recommendations. Citizen science at it's finest! Scientific American are currently featuring Poo Power! on their Citizen Science website"From our research only 3% of Australians see uncollected dog waste as an environmental concern," explains Duncan Chew. "When it rains, uncollected dog poo gets washed down drains, effecting water quality and habitat for native animals, as well as making rivers and creeks unpleasant for us to visit." I just think this is a great way to utilise the prize money from winning the I’m A Scientist – Get Me Out of Here! competition; it raises awareness of new sustainable energy sources, environmental issues and responsible dog ownership, all while increasing student engagement in a citizen science activity.The collated information has the poo-tential to identify sites for biogas-powered lights for parks as proposed by the Melbourne-basedproject, Poo Power!, currently in development. The methane that is released from the dog waste as it breaks down inside a 'biogas generator' can be used as a viable renewable energy source.Photo: Steven PamCompetition prizes and giveaways are up for grabs for students whose submissions are received between 25th November and 9th December 2013. After this initial competition period closes, the project will continue to run, collecting ongoing hotspot data worldwide.... Read more »
Okoroigwe E.C., Ibeto C.N., & Okpara C.G. (2010) Comparative Study of the Potential of Dog Waste for Biogas Production. Trends in Applied Sciences Research, 5(1), 71-77. DOI: 10.3923/tasr.2010.71.77
Nemiroff Leah. (2007) Design, Testing and Implementation of a Large-Scale Urban Dog Waste Composting Program. Compost Science , 15(4), 237-242. info:other/http://montrealndgdogrun.org/image/downloads/compost studies.pdf
h-index is an index that attempts to measure both the productivity and impact of the published work of a scientist or scholar. Here, I am going to tell the way through which you can forecast your future h-index.
While presenting this tutorial, I consider that you have a good knowledge of R software, which is one of the rapidly rising open source statistics software. You can get the software here,
You need Google Scholar Profile. If you have papers on Google Scholar, you can create your profile here: http://scholar.google.com. Take a look at my profile above.
This profile gives you a unique ID in the URL as shown below for my profile. My ID is “fMhc74wAAAAJ”.
My unique ID
You also need Scholar R package that is available here: http://cran.r-project.org/web/packages/scholar/. Packages can be installed by downloading the zip file for windows. This zip file is then installed into the R software by going to “Packages” menu and “Install package(s) from local zip files”. After installation, you can either go to “Load package” in the “Packages” menu to load “scholar” package or write
in the interface.
You can predict your h-index by writing the following commands in the R software. Here, I have used my ID. You can use yours or any other scientist’s ID.
id ... Read more »
Top Five Journals according to Google Scholar are
2. The New England Journal of Medicine
4. The Lancet
This list is based on “h5-index” - “h5-index is the h-index for articles published in the last 5 complete years. It is the largest number h such that h articles published in 2008-2012 have at least h citations each,” according to Google.
By clicking on the links presented in the metrics of Google Scholar you can find the list of highly cited papers but here is the limitation of last five years, i.e. you can find highly cited papers from the last five years only.
Here, I have collected (almost) all time highly cited papers from these journals.
1. “Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4” by “U. K. Laemmli” is one of the highly cited papers of all time. It was published in “Nature” in 1970 and has 2,15,140 citations, according to Google Scholar, at the time of writing of this article.
2. “The L-arginine-nitric oxide pathway” by “S Moncada et al”. It was published in “The New England Journal of Medicine” in 1993 and has 5693 citations, according to Google Scholar, at the time of writing of this article. (Salvador Moncada, Annie Higgs (1993). The L-Arginine-Nitric Oxide Pathway NEJM DOI: 10.1056/NEJM199312303292706)
3. “Optimization by simmulated annealing” by “S Kirkpatrick et al”. It was published in “Science” in 1983 and has 29,469 citations, according to Google Scholar, at the time of writing of this article.
4. “Statistical methods for assessing agreement between two methods of clinical measurement” by “J Martin Bland et al”. It was published in “The Lancet” in 1986 and has 27,365 citations, according to Google Scholar, at the time of writing of this article.
5. “The hallmarks of cancer” by “D Hanahan et al”. It was published in “Cell” in 1986 and has 17,616 citations, according to Google Scholar, at the time of writing of this article.
Now here are some of the scientists with about/over 2,000 impact points according to ResearchGate, at the time of writing this article,
1. Jan Reedijk, Leiden University · Leiden Institute of Chemistry - 1,975.89 Impact Points
2. Anthony L. Spek, Universiteit Utrecht · Division of Crystal and Structural Chemistry - 2,563.34 Impact Points
3. Paul Schleyer, University of Georgia · Department of Chemistry - 2,576.09 Impact Points
4. David N. Reinhoudt, Universiteit Twente · Department of Inorganic Materials Science (IMS) - 2,856.53 Impact Points
If you want to know further papers with high citations or journals with more citations, you can ask me in the comments below.... Read more »
You’re sat at your desk, reading a journal article. You see a graph that looks like this:
the first thing that comes to mind? WHAT ON EARTH DOES IT MEAN?!
At this point many people will skip the methods section of their article and head straight to the discussion- But these graphs and techniques aren’t so scary once you understand the science behind them.
What is ITC used for?
Isothermal Titration Calorimetry, or ITC, measures a very basic interaction- how does one thing bind to another? Imagine you have a protein, and want to measure how well it binds to its substrate. ITC allows you in a single experiment to gain a huge amount of information. ... Read more »
Rajarathnam K, & Rösgen J. (2014) Isothermal titration calorimetry of membrane proteins - Progress and challenges. Biochimica et biophysica acta, 1838(1), 69-77. PMID: 23747362
Ghai R, Falconer RJ, & Collins BM. (2012) Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. Journal of molecular recognition : JMR, 25(1), 32-52. PMID: 22213449
Jing M, & Bowser MT. (2011) Methods for measuring aptamer-protein equilibria: a review. Analytica chimica acta, 686(1-2), 9-18. PMID: 21237304
The amount of cow dung plopped into the world every day is almost unthinkable, but Tomas Roslin is thinking about it."We can regard it as either an immense waste problem or an enormous ecosystem service," he says. He means that what starts out as a turd in a field turns into a wealth of nutrients for plants—assuming it can make its way below ground. So understanding how dung gets broken down can help us ensure an ecosystem is running smoothly. To address such a messy, large-scale question, Roslin recruited a big mess of young volunteers.Roslin is an ecologist at the University of Helsinki, and he found his citizen scientists through the Finnish 4H Federation. In all, 79 volunteers signed up, ranging from 10 to 27 years old (most were under 20). They agreed to sample 82 cattle farms that spanned Finland nearly from end to end.From each farm, the volunteers collected 20 liters of "fresh dung" in late spring or early summer. They divided their dung into 15 pats (using an official dung measurer that had been provided to them) and put the pats back onto cow pastures. Some of the manmade cow patties were left open to the air, while others were covered with cages of coarse or fine mesh to keep out certain insects.Roslin and his coauthors were especially interested in large dung beetles called dor beetles. In some cases they prevented dor beetles from burying the dung (as the beetles enjoy doing) by putting mesh underneath the patty, and in other cases a full wire cage kept dor beetles from getting into the dung at all. Smaller insects were kept out with finer mesh cages, and earthworms were blocked from the dung by putting a layer of cloth underneath it.Volunteers weighed the dung piles periodically over the next two months to see how much was left of them. As the summer went on, the patties dried out and were broken down by whatever insects could reach them, as well as by microbes that couldn't be kept out. (Only 73 farms were left in the final analysis, since a few sites were lost to "lack of sufficient commitment by the volunteer" and others to "cows trampling on the experimental pats.")The results showed that 13 percent of dung decomposition is done by insects. Microbes and rainstorms take care of the rest. The farther north you are in Finland, the more slowly your dung will disappear, perhaps because cooler weather slows bacterial growth.Each added barrier around the dung made it decompose a little more slowly, showing that all the groups of insects were helping to break it down. But the biggest contribution came from dor beetles. This was in line with what previous, small-scale research had shown—but his network of citizen scientists let Roslin confirm that dor beetles are equally important all across Finland.It matters because "our dor beetles are not doing that well," Roslin says. Out of three species in Finland, one has gone regionally extinct and another is on the decline. Knowing how important the dor beetle is to healthy farms gives Finland more reason to keep it alive.Additionally, Roslin says, "just figuring out the basics of how the system works" is critical. In the United States, most cattle waste goes into manure lagoons, where beetles or ecosystems don't really enter the equation. But when waste is returned to the soil, Roslin says, "we need to understand who is behind it." He points out that cattle were initially brought to Northern Europe in part to fertilize the fields."We love citizen science," Roslin declares. He and his lab have previously organized citizen investigations of dung beetles and gall-wasps, and they're now working with volunteers to study the hermit beetle Osmoderma barnabita. "The volunteers involved have come to appreciate completely new aspects of their own environment," he says.There are some drawback to the approach, of course —experiments have to be kept simple, and sometimes a volunteer loses interest or flattens a cow patty. But by pairing small-scale lab research with large citizen projects, Roslin says, "we have managed to collect scientific data sets unachievable by relying on professional biologists."Riikka Kaartinen, Bess Hardwick, & Tomas Roslin (2013). Using citizen scientists to measure an ecosystem service nationwide. Ecology DOI: 10.1890/12-1165.1Images: top Timo Marttila/Satakunnan Kansa; bottom Riikka Kaartinen.
... Read more »
Riikka Kaartinen, Bess Hardwick, & Tomas Roslin. (2013) Using citizen scientists to measure an ecosystem service nationwide. Ecology. DOI: 10.1890/12-1165.1
There are several steps that researchers can take to bolster the integrity of their work, but embracing the use of the “new statistics” of effect sizes, estimation, and meta-analysis is a particularly important one, argues psychological scientist Geoff Cumming of La Trobe University in Australia.... Read more »
“If God is possible, then he exists necessarily. But God is possible, therefore he exists”. This is the extreme synthesis of Gödel’s most famous result. Two researchers -Christoph Benzmuller and Bruno Woltzenlogel Paleo- just confirmed the result thanks to the help of a computer-assisted proof.... Read more »
Christoph Benzmüller and Bruno Woltzenlogel Paleo. (2013) Formalization, Mechanization and Automation of Godel’s Proof of God’s Existence. preprint arxive . info:/
Is the ability to empathize uniquely human? This question has long been pondered by philosophers and animal behaviorists alike. Empathy depends in part on the ability to recognize the wants and hopes of others. A new study by researchers at the University of Cambridge suggests that we may not be alone with this ability. A male Eurasian jay feeds his female mate. Photo provided by Ljerka Ostojić.Ljerka Ostojić, Rachael Shaw, Lucy Cheke, and Nicky Clayton conducted a series of studies on Eurasian jays to explore whether male jays could perceive changes in what their female partners desired. Eurasian jays are a good species with which to explore this phenomenon because males routinely provide food to their female mates as a part of their courtship. The researchers wanted to know if males would adjust what food items males offered their mates depending on what food type the females wanted more. In order to make a female prefer one food type over another, the researchers fed each female one of two food types (wax moth larvae and mealworm larvae) until they were full. But being full of one type of food doesn’t mean you can’t find room for desert, right? So when the researchers then offered the females access to both wax moth larvae and mealworm larvae, those that had previously eaten wax moth larvae now preferred mealworm larvae and those that had previously eaten mealworm larvae now preferred wax moth larvae. But could their male partners tell what they preferred at that moment? In order to test whether male jays were sensitive to their partners’ desires, the researchers fed the females either wax moth larvae or mealworm larvae until they were full. They did this while their male partners watched from behind a transparent screen. They then removed the screen and gave the males 20 opportunities to choose between a single wax moth larvae or mealworm larvae to feed their partner. In this context, males usually chose to share with their mates the food that their partners preferred rather than the food their partners had already been fed! But are the males responding to their mate’s behavior or are they responding to what they saw when the females were eating earlier? This video (provided by Ljerka Ostojić) shows the experimental process in which the male chooses a food type and then shares it with his mate. The researchers repeated the study with an opaque screen so the males could not see their mates while the females gorged on one particular food type. Without the ability to see the mate eating beforehand, males chose both food types equally and did not attend to their mate’s preferences. Because the females still had a preference for the opposite food type but the males were not adjusting for that preference, this means that the males are not responding to their mate’s behavior in this experiment or the previous one. This suggests that if male Eurasian jays see what their mates are eating, then somehow they have the ability to know to give their mate the opposite food type! Whether this process involves the males having an understanding of their mate’s desires or some other mechanism is not fully known. But male Eurasian jays are certainly adjusting what they give their mates according to what she wants. Now if we can only teach human males to do that! Want to know more? Check this out:Ostojić, L., Shaw, R.C., Cheke, L.G., & Clayton, N.S. (2013). Evidence suggesting that desire-state attribution may govern food sharing in Eurasian jays PNAS, 110 (10), 4123-4128 DOI: 10.1073/pnas.1209926110 ... Read more »
Ostojić, L., Shaw, R.C., Cheke, L.G., & Clayton, N.S. (2013) Evidence suggesting that desire-state attribution may govern food sharing in Eurasian jays. PNAS, 110(10), 4123-4128. DOI: 10.1073/pnas.1209926110
FVIII light chain expressed in Pichia. Antibody AND phospholipid both bind this light chain. Literature says either but not both can bind. ... Read more »
Sudheer Reddy AR, Padikara Kutty Satheeshkumar, & Mookambeswaran A. Vijayalakshmi. (2013) Expression, purification, and partial in vitro characterization of biologically active human coagulation Factor VIII chain (A3-C1-C2) in Pichia pastoris. Applied Biochemistry and Biotechnology. DOI: 10.1007/s12010-013-0338-4
Procrastination is a fact of academic life, particularly during the PhD period, as every academic supervisor knows. However, judging from ever-increasing institutional efforts to control procrastination or from the many self-help guides intended to cure procrastination, it would seem that … Continue reading →... Read more »
Paola Villani. (1990) Documenti saussuriani conservati a Lipsia e a Berlino. Cahiers Ferdinand de Saussure, 3-33. info:/
Photo: Steven PamThere is an industry in Australia that relies on an integral piece of equipment, but the system behind product development process is flawed, and lives are at stake. From farm dogs to military explosive detection dogs, guide dogs to greyhounds, Australia’s working and sporting dog industry claims a 50-70% fail rate as normal. The welfare of these dogs is intimately linked to their working performance. It can be an emotive topic, so let’s take the emotion out of it and objectively consider current practice.A diverse industry, with four sectors operating in different domains, is dependent on one key piece of equipment. A tool that can vary in price from free to $40,000, can be purchased new or second hand, but is unequivocally required to get the job done. Hundreds of thousands of units are currently used daily throughout Australia in government, human health, sporting and private operations.SourcePractitioners invest resources in this equipment, only to find that the tool doesn't work. It’s unsuitable. It operates at the wrong speed. It breaks. It just doesn't do the work it was meant to - at least half of the time! In some industry sectors, the equipment fail rate is estimated as high as eighty percent. Waste units are disposed of and new ones sourced. Perhaps from a large scale manufacturer, perhaps from a private artisan, or some people go ahead and take a crack at making their own. Recycling within the industry is extremely low, at less than ten percent. The production of this equipment is currently inefficient; the industry has no validated minimum standards in place and the product lacks quality assurance. From an industry business and performance perspective, what should be done? A review of the purpose and production life-cycle analysis for this tool seems indicated? Absolutely. A review of how the equipment is being employed, handled, maintained and stored by practitioners? Yes. Perhaps a review of the training courses and educational materials available to the practitioners and the people who train them? For sure.SourceWithout objective review and subsequent improvement, this industry is leaving itself open to scrutiny by the media and risks losing public support. Review of this kind is common. In industrial design and quality management fields, validation of product integrity, ongoing review and updating of evidence-based best practice are standard. Re-purposing of surplus or malfunctioning stock into other areas rather than directly to landfill may require additional resources. However, this extra spend is important as tolerance for unnecessary waste in the 21st century is limited. Indeed, the sustainability and economic viability of this industry into the future relies on improved accountability, higher transparency and demonstrated responsibility.We owe this commitment to review and refine the production, management and education surrounding this device to the industry, the people involved and the tasks they achieve. It’s sound business practice. And we owe it to the dogs.Hi Julie,I wrote this because I wanted to consider if there was a good case to be made for improving the welfare of working dogs, without the emotion or emotive slant often inherent in animal welfare discussions. This came about after recent conversations with people who have suggested my work towards improved working dog welfare is based on me 'loving dogs' or having bleeding-heart, idealistic expectations about the way dogs should be cared for. I hope I have been able to demonstrate that this is a) not about me, and b) that a good argument for objective review and assessment of how working dogs are produced can be made, even before adding consideration for the fact these are sentient animals with capacity to thrive or suffer as a result of how we manage their lives.I'm looking forward to continuing these conversations at the Working Dog Conference 2013 next week.Wish you were here,... Read more »
Kruger Justin, & Dunning David. (1999) Unskilled and unaware of it: How difficulties in recognizing one's own incompetence lead to inflated self-assessments. Journal of Personality and Social Psychology, 77(6), 1121-1134. DOI: 10.1037//0022-35184.108.40.2061
Dunning David, Johnson Kerri, Ehrlinger Joyce, & Kruger Justin. (2003) Why people fail to recognize their own incompetence. Current Directions in Psychological Science, 12(3), 83-87. DOI: 10.1111/1467-8721.01235
Ehrlinger Joyce, Johnson Kerri, Banner Matthew, Dunning David, & Kruger Justin. (2008) Why the unskilled are unaware: Further explorations of (absent) self-insight among the incompetent. Organizational Behavior and Human Decision Processes, 105(1), 98-121. DOI: 10.1016/j.obhdp.2007.05.002
Dunning David. (2011) The Dunning-Kruger effect: On being ignorant of one's own ignorance. Advances in Experimental Social Psychology, 247-296. DOI: 10.1016/B978-0-12-385522-0.00005-6
The latest SAT and ACT data show record declines for men, whites, and Native Americans. Analysis of state SAT data suggests that family income does not significantly affect scores when controlled for parents’ education and race.... Read more »
Anonymous. (1998) Why Family Income Differences Don't Explain the Racial Gap in SAT Scores. The Journal of Blacks in Higher Education, 6-8. DOI: 10.2307/2999198
Anonymous. (2008) Why Family Income Differences Don't Explain the Racial Gap in SAT Scores. The Journal of Blacks in Higher Education, 10-12. info:/
Brazilian bird sings Mozart...... Read more »
Emily Doolittle, & Henrik Brumm. (2012) O Canto do Uirapuru: Consonant intervals and patterns in the song of the musician wren. Journal of Interdisciplinary Music Studies, 6(1), 55-85. info:/
Araya-Salas, Marcelo. (2012) Is birdsong music? Evaluating harmonic intervals in songs of a Neotropical songbird. Animal Behaviour, 84(2), 309-313. info:/10.1016/j.anbehav.2012.04.038
I don't think I mentioned this JISC project by David Shotton et al. yet, and should perhaps have done so earlier. But it is not too late, as Shotton is calling out for help in a Nature Comment this week (doi:10.1038/502295a). Now, I have been tracking what is citing the CDK literature using CiteUlike since 2010, and just asked the project developers how I can contribute this data.
Interestingly, the visualization from OpenCitations.net is interesting as it also shows papers citing papers that cite the CDK:
This image shows that the corpus is yet small: this CDK paper is cited more then 250 times. In the comment, Shotton writes that "[i]deally, references will come directly from publishers at the time of article publication." I do hope that publishers soon start providing APIs to extract such data. But I like to complement the call out, by inviting everyone to start annotating their old papers with this information, e.g. using CiTO and CiteULike as I did. Importantly, the authors must type their citation, something that will greatly improve the paper itself, anyway.
Now, my own use case, is to get an idea on how the CDK is used. Reason: people are not paying us, so I am limited to reports in the public that write up how they use the CDK. Direct citation is important, but I am even more interested in papers that do not cite the CDK, but cite a paper that describes a tool that depends on the CDK, like PaDEL (doi:10.1002/jcc.21707) which is cited already 73 times. Such papers are traditionally not counted as measure of the impact of the CDK, but surely are. This OpenCitations.net work, combined with CiTO allows just that.
D. Shotton (2013). Publishing: Open citations Nature, 502 (7471), 295-297 : 10.1038/502295a... Read more »
D. Shotton. (2013) Publishing: Open citations. Nature, 502(7471), 295-297. info:/10.1038/502295a
When cells are put under stress (e.g. UV light, ionising radiation, reactive oxygen species) they undergo a process known as cellular senescence in which cell division (mitosis) is arrested. This is thought to contribute to ageing. In their 2013 paper Naylor and colleagues outline a strategy to selectively remove in vivo senescent cells expressing p16Ink4A .... Read more »
Naylor RM, Baker DJ, & van Deursen JM. (2013) Senescent cells: a novel therapeutic target for aging and age-related diseases . Clinical Pharmacology . DOI: 10.1038/clpt.2012.193
On 17 October, I travelled to London to participate in the annual Publications Seminars. As suggested by the programme, the presenters focused on discussing changes in the publications industry. One of the most heated debates of the event highlighted a recent sting operation published in Science.1 The researcher, John Bohannon, aimed to uncover how rigorous the peer review process is in open access journals that do not charge their readers for viewing content. John Bohannon wrote a far-fetched fictitious article On 17 October, I travelled to London to participate in the annual Publications Seminars. As suggested by the programme, the presenters focused on discussing changes in the publications industry. One of the most heated debates of the event highlighted a recent sting operation published in Science.1 The researcher, John Bohannon, aimed to uncover how rigorous the peer review process is in open access journals that do not charge their readers for viewing content. John Bohannon wrote a far-fetched fictitious article...... Read more »
A recent study by MIT and Santa Fe Institute (SFI) researchers found a “dramatic growth in innovation” in renewable energy technologies.... Read more »
Luis M. A. Bettencourt, Jessika E. Trancik, & Jasleen Kaur. (2013) Determinants of the Pace of Global Innovation in Energy Technologies. PLoS ONE, 8(10). arXiv: 1211.5167v1
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