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The Faculty of Science at Stellenbosch University is respected within South Africa, Africa and the world arena as a knowledge-partner of note that builds on the scientific, technological and intellectual capacity of Africa and plays an active role in the development of South African society. The faculty is placed in the top 300 within the category Natural Sciences of the QS World University Ranking list.
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MIT wins design competition for Elon Musk's Hyperloop

MIT wins design competition for Elon Musk's Hyperloop | Science | Scoop.it
MIT student engineers won a competition to transform SpaceX and Tesla Motors co-founder Elon Musk's idea into a design for a Hyperloop to move pods of people at high speed.

 

An image released by Tesla Motors, is a sketch of the Hyperloop capsule with passengers onboard. . Billionaire entrepreneur Elon Musk on Monday, Aug. 12, 2013 unveiled a concept for a transport system he says would make the nearly 400-mile trip in half the time it takes an airplane. The "Hyperloop" system would use a large tube with capsules inside that would float on air, traveling at over 700 miles per hour.

 

The Massachusetts Institute of Technology, based in Cambridge, Massachusetts, was named the winner Saturday after a competition among more than 1,000 college students at Texas A&M University in College Station. The Hyperloop is a high-speed ground transport concept proposed by Musk to transport "pods" of 20 to 30 people through a 12-foot diameter tube at speeds of roughly 700 mph. More than 100 university teams presented design concepts to a panel of judges in an event that began Friday.


Delft University of Technology from The Netherlands finished second, the University of Wisconsin third, Virginia Tech fourth and the University of California, Irvine, fifth.


The top teams will build their pods and test them at the world's first Hyperloop Test Track, being built adjacent to SpaceX's Hawthorne, California, headquarters.


Inventor Musk to share plans for high-speed travel (Update)


More information: hyperloop.tamu.edu/ 


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Sea Slug has Taken Genes from the Algae it Eats, Allowing it to Photosynthesize Like a Plant

Sea Slug has Taken Genes from the Algae it Eats, Allowing it to Photosynthesize Like a Plant | Science | Scoop.it

How a brilliant-green sea slug manages to live for months at a time “feeding” on sunlight, like a plant, is clarified in a recent study published in The Biological Bulletin. The authors present the first direct evidence that the emerald green sea slug’s chromosomes have some genes that come from the algae it eats. These genes help sustain photosynthetic processes inside the slug that provide it with all the food it needs. Importantly, this is one of the only known examples of functional gene transfer from one multicellular species to another, which is the goal of gene therapy to correct genetically based diseases in humans.

 

“Is a sea slug a good [biological model] for a human therapy? Probably not. But figuring out the mechanism of this naturally occurring gene transfer could be extremely instructive for future medical applications,” says study co-author Sidney K. Pierce, an emeritus professor at University of South Florida and at University of Maryland, College Park.

 

The team used an advanced imaging technique to confirm that a gene from the alga V. litorea is present on the E. chlorotica slug’s chromosome. This gene makes an enzyme that is critical to the function of photosynthetic “machines” called chloroplasts, which are typically found in plants and algae.

 

It has been known since the 1970s that E. chloritica “steals” chloroplasts from V. litorea (called “kleptoplasty”) and embeds them into its own digestive cells. Once inside the slug cells, the chloroplasts continue to photosynthesize for up to nine months—much longer than they would perform in the alga. The photosynthesis process produces carbohydrates and lipids, which nourish the slug.

 

How the slug manages to maintain these photosynthesizing organelles for so long has been the topic of intensive study and a good deal of controversy. “This paper confirms that one of several algal genes needed to repair damage to chloroplasts, and keep them functioning, is present on the slug chromosome,” Pierce says. “The gene is incorporated into the slug chromosome and transmitted to the next generation of slugs.” While the next generation must take up chloroplasts anew from algae, the genes to maintain the chloroplasts are already present in the slug genome, Pierce says.

 


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Richard Spencer's curator insight, February 5, 2015 6:00 AM

The  wonders  of  evolution  

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Synthetic Biology Researchers engineered E. coli to rely on artificial amino acids

Synthetic Biology Researchers engineered E. coli to rely on artificial amino acids | Science | Scoop.it

By rewriting the DNA of Escherichia coli so that the bacterium requires a synthetic amino acid to produce its essential proteins, two research teams may have paved the way to ensure that genetically modified organisms don’t escape into the environment. The life-or-death dependence of the newly engineered E. coli on synthetic amino acids makes it astronomically difficult for the genetically modified organism to survive outside the laboratory, explains Harvard Medical School’s George M. Church, who led one of the teams reporting the discovery in Nature (2015, DOI: 10.1038/nature14121).

 

That’s because no pool of synthetic amino acids exists in nature, he explains. A similar strategy was simultaneously published by Farren J. Isaacs and his colleagues at Yale University, also in Nature (2015, DOI: 10.1038/nature14095). The discoveries help construct improved containment barriers for genetically modified bacteria currently used in the biotech-based production of products as diverse as yogurt, propanediol, or insulin, Isaacs says. They also set the stage for expanding the use of genetically modified organisms in applications outside the lab, Isaacs adds. For example, he says, the bacteria could be used as the “basis for designer probiotics for diseases that originate in the gut of our bodies, or for specialized microorganisms that clean up landfills or oil spills.”

 

“There are all these ideas for using engineered cells [outside the confines of a lab], but the problem is that they’re not contained,” comments Christopher A. Voigt, a synthetic biologist at Massachusetts Institute of Technology. “This is the proof-of-principle work for addressing that problem.” To make the genetic firewall, both teams made changes to E. coli’s genome so that the bacteria’s protein production machinery inserts a nonnatural amino acid when it reads a specific three-base-pair codon. “They’ve extended the genetic code so that it can take a 21st amino acid,” explains Tom Ellis, a synthetic biologist at Imperial University, in London, who was not involved in the work. The two teams used different synthetic amino acids, but both groups selected mimics of phenylalanine, a bulky, hydrophobic amino acid.

 

Next, both teams scoured E. coli’s genome for essential proteins that the organism needed to survive. They looked for areas in those proteins where the synthetic amino acids might replace natural amino acids. Although both teams combined computational design and evolutionary biology to select which amino acid to replace in three essential proteins, Church’s team relied more on the former approach and Isaacs’ team on the latter.

 

Finally, they showed that when the engineered bacteria have access to a pool of the synthetic amino acids, they can build their essential proteins. With no access to the synthetic amino acids, protein production stalls and the bacteria die.

 

The teams performed extensive tests to see whether the newly engineered bacteria could evolve ways to sidestep the need for synthetic amino acids. Whenever the microbes managed the feat, the researchers tweaked the DNA until the bacteria depended solely on the synthetic amino acids.

 

Previous strategies for containing genetically modified bacteria seem “naive” in hindsight, Ellis says. These earlier strategies employed kill switches, which are “systems where the organism dies if some compound or environmental cue wasn’t given,” he adds. “Here the kill system is fully embedded in the heart of the bacteria.”

 

In theory, the strategy could be extended to other genetically modified organisms, such as plants, Voigt says. “It will probably be really hard, but not impossible,” he adds. According to Ellis, the next step is to get the platform working in yeast, which will be “an order of magnitude harder than bacteria.”

 

Another important step is to improve containment by ensuring that all DNA engineered into the organism relies on the synthetic amino acid, Ellis says. “If you accidentally spill the bacteria into the environment, it’s going to die,” he says. “But that DNA is left behind. The genetically modified genes could be incorporated into other bacteria through horizontal transfer,” he warns. “To alleviate all fears, we need to ensure that all genes you add to an organism—say for making insulin or biofuels—are also behind the genetic firewall and somehow encode the 21st amino acid.”


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Sharrock's curator insight, January 22, 2015 12:36 PM

I didn't know why synthetic biology might ensure our safety to a certain degree. I love this quote: "Another important step is to improve containment by ensuring that all DNA engineered into the organism relies on the synthetic amino acid, Ellis says. “If you accidentally spill the bacteria into the environment, it’s going to die,” he says. “But that DNA is left behind. The genetically modified genes could be incorporated into other bacteria through horizontal transfer,” he warns. “To alleviate all fears, we need to ensure that all genes you add to an organism—say for making insulin or biofuels—are also behind the genetic firewall and somehow encode the 21st amino acid.”" 



Fernan Aguero's curator insight, January 23, 2015 8:14 AM

Horizontal gene transfer of engineered genes is a big warning, of course. But one must not assume lightly that engineered bacteria cannot survive in the environment. Synthetic aminoacids may not exist in nature as such, but what about chemical analogs (e.g. produced by a plant, insect, fungi) that may substitute them?

 

OK, I'm just being skeptic :)

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Beautiful Chemistry

Beautiful Chemistry | Science | Scoop.it
Beautiful Chemistry is a project collaboration between the Institute of Advanced Technology at the University of Science and Technology of China and Tsinghua University Press. The goal of this project is to bring the beauty of chemistry to the general public through digital media and technology.

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Mary Williams's curator insight, November 23, 2014 8:02 AM

Super collection of videos and images featuring the beauty of chemistry

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Gold Grows On Eucalyptus Trees

Gold Grows On Eucalyptus Trees | Science | Scoop.it
Eucalyptus leaves might serve as the gold miner's best friend, with gold drawn from the depths, researchers report, draping the humble gum trees.
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One hundred million Facebook users in Africa | The Media Online

One hundred million Facebook users in Africa | The Media Online | Science | Scoop.it

Facebook has announced it has 100 million users in Africa, half the number of people with internet access on the continent. Over 80% of these access the social media site via mobile phones.

“People in high-growth countries want to be connected to the world around them. In countries such as South Africa, Nigeria, Turkey, and elsewhere, mobile devices are increasingly the way people find new information, and share their new experiences in the world. We also know that people will experience Facebook in unique ways across the world, especially in high-growth regions like Africa,” says  Nicola Mendelsohn, EMEA VP at Facebook.

Facebook knows that a one-size-fits-all approach won’t work when it comes to building products and solutions that address diverse local needs around the world, which is why it is committed to crafting solutions specifically for high-growth markets.

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News - Nano-chip in a capsule identifies bacterial...

News - Nano-chip in a capsule identifies bacterial... | Science | Scoop.it

A microbiologist and an electronic engineer from Stellenbosch University have developed a proof-of-concept nanowire biological sensor that can identify any of the major disease-causing bacteria such as Escherichia coli, Salmonella or Vibrio cholera within ten to fifteen minutes.

In the not too distant future, this combination of nanotechnology and microbiology could make the diagnosis of patients during an epidemic or outbreak an order of magnitude faster, more accurate and more affordable.

Prof Leon Dicks, an internationally acclaimed microbiologist, joined forces with Prof Willie Perold, also an internationally acclaimed scientist in the field of superconductors and nanoelectrical devices. Together they conceptualised the idea of a nanochip that would be able to detect bacteria and viruses in the patient's stomach within a few minutes after being swallowed.

Mr Deon Neveling, a postgraduate student in the Department of Microbiology at SU, was given the task to put this concept to the test as part of his research for a master's degree in microbiology. Read more about the research at http://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=1723

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CSIR and Parsec Holdings partner to commercialise wireless mesh technology

CSIR and Parsec Holdings partner to commercialise wireless mesh technology | Science | Scoop.it

The CSIR has signed a five-year licensing agreement with Parsec Holdings (Pty) Ltd to manufacture, market and distribute CSIR’s wireless mesh technology, consisting of a high performance node and network controller. The high performance node is certified type-approved by the Independent Communications Authority of South Africa.

The technology was developed to create easy-to-build, low-cost and locally owned community mesh networks. This infrastructure is a viable alternative to increasing the penetration of telecommunication services in Africa.

A wireless mesh network is based on peer-to-peer communication between high performance nodes instead of the traditional point-to-multi-point communication. “This is an exciting moment for Parsec. We are passionate about South Africa and taking on home-grown technologies that make an impact,” said Rynier van der Watt, Managing Director of Parsec Holdings.

“The CSIR’s mandate is to make a difference in the lives of South African’s through science and technology. We are excited to partner with an organisation that believes in and shares our vision,” said Chris Sturdy, CSIR Chief Financial Officer.

Crossing the chasm
The journey from innovation concept to commercialisation is long and arduous, said Nicki Koorbanally, a CSIR Intellectual Property and Commercialisation Manager. “But we have now ‘crossed the chasm’ and we are excited about this collaboration, which could lead to further innovative product development. We look forward to seeing this home-grown technology make an impact in the community through Parsec,” she added.

The development and commercialisation process started in 2004, said Kobus Roux, a CSIR researcher and engineer behind the technology. “We were trying to address the challenges around rural connectivity. In 2007, we started producing interesting results,” he said. “The Department of Science and Technology liked what we were doing and facilitated funding through the European Commission. Parsec came on board as a technology partner and they have been with us since,” he added.

Parsec is a technology company that develops, manufactures and supplies embedded solutions in the form of sub-systems or products to a wide spectrum of clients in the global defence/aerospace, telecommunications and industrial market sectors.

11 August 2014

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New alien species hiding in our harbours

New alien species hiding in our harbours | Science | Scoop.it

NEW ALIEN SPECIES HIDING IN OUR HARBOURS

Marine alien species have not been as well studied in South Africa as their terrestrial counterparts. However, recent research by C·I·B researchers has shed some light on the occurrence of marine alien species in Western Cape harbours.


A diver surfaces to pass a sample to C·I·B researchers (Photo credit: Dr T Robinson)

Marine organisms have been moved around the globe for centuries. These organisms travel through a number of ways, for example, as external fouling on the hulls of ships and yachts, in ballast water, through the movement of aquaculture organisms and via the aquarium and pet trades. In a recent study C·I·B researchers Koebraa Peters, Dr Tammy Robinson and Professor Charles Griffiths set out to survey Western Cape harbours for marine alien species.

While they had expected the highest number of aliens to be in the larger harbours, surprisingly they found the most aliens occurred in Hout Bay harbour, one of the smaller local harbours. Interestingly, harbours on either side of Cape Point (Table Bay, Hout Bay, Simon’s Town and Kalk Bay) had higher numbers of aliens than other harbours.

Another important finding was that the presence of yachts was the most important factor predicting which harbours have higher numbers of alien species. In addition, some new discoveries were made. The alien disc lamp shell (Discinisca tenuis) was recorded for the first time outside of aquaculture facilities, where it was previously thought to be contained. Also, the alien amphipodEricthonius difformis was recorded in South African waters for the first time.

Dr Tammy Robinson, C·I·B core team member, says the study is significant, as it can help to prioritise which harbours should be monitored for alien species: “The findings of this study have not only helped us to close the gap in our knowledge around the spread of marine alien species, but have opened the doors for new and exciting research that will include more harbours along the South African coastline.”

 
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Tracking the Ebola outbreak in near real-time: HealthMap, ProMED and other tools

Tracking the Ebola outbreak in near real-time: HealthMap, ProMED and other tools | Science | Scoop.it

Sobering news keeps coming out of the West African Ebola outbreak. According to numbers released on August 6, the virus has sickened 1,711 and claimed 932 lives across four nations. The outbreak continues to grow, with a high risk of continued regional spread, according to a threat analysis released byHealthMap (an outbreak tracking system operated out of Boston Children’s Hospital) and Bio.Diaspora (a Canadian project that monitors communicable disease spread via international travel).

 

“What we’ve seen here—because of inadequate public health measures, because of general fear—is [an outbreak that] truly hasn’t been kept under control,”John Brownstein, PhD, co-founder of HealthMap and a computational epidemiologist at Boston Children’s Hospital, told ABC News. “The event started, calmed down and jumped up again. Now, we’re seeing movement into densely populated areas, which is highly concerning.”

 

If you’re interested in keeping tabs on the outbreak yourself, there are several tools that can help:

 

HealthMap’s Ebola map. The HealthMap team is maintaining a dedicated, interactive map and timeline of the epidemic athealthmap.org/ebola (embedded at the top of this post). Both map and timeline are regularly updated as new information becomes available, as is the HealthMap Twitter account.ProMED. The International Society for Infectious Disease, a non-profit organization for infectious and emerging disease research, operatesProMED, a disease news monitoring service that tracks outbreaks of human and veterinary infectious diseases. ProMED (short for Program for Monitoring Emerging Diseases) has been sending out regular email and Twitter alerts about the Ebola outbreak since it was first noticed in March.US Centers for Disease Control and Prevention (CDC). The CDC is regularly posting updated news and patient counts—as well as travel and preparedness guidance and other information about the virus—on both their website and Twitter.World Health Organization (WHO). The WHO’s Global Alert and Response system is providing regular updates on disease spread and control efforts. The organization is also distributing updates via its Twitter feed.


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Biodefense News's curator insight, August 14, 2014 10:20 PM

One glaring omission from this list is http://www.ascelbio.com, which is supplying CDC/GDD with outbreak information and forecasting.  Ascel Bio was also in constant contact with Samaritan's Purse and asked to help respond to evacuate.

Luigi Cappel's curator insight, August 16, 2014 5:53 PM

Not only is this a great site, but when I went in, it automatically identified that I live in New Zealand and showed me areas close to me where there are notifiable diseases. It showed that currently measles is growing around our country. This is a great site to check out, whether you are traveling overseas and want to see if there are things you want to be forewarned about, perhaps be inoculated against, or in the case of something like Ebola, places you might be better off staying well away from at least in the short to medium term. 

 

I recommend checking it out, whether you are traveling, or simply want to see great use of maps to show real time data. The time-lapse video showing the expansion of Ebola is fascinating. This is the sort of thing we usually just see on movies showing the CDC, like one of my favorite TV shows 24. Where's Jack Bauer when you need him? Oh, I here a rumor he may be coming back:)

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New research from Africa on pharmacomicrobiomics

New research from Africa on pharmacomicrobiomics | Science | Scoop.it

New Rochelle, NY, July 21, 2014—The Human Microbiome Project (HMP) is a global initiative to identify and characterize the microorganisms present at multiple sites in the human body. An international team of researchers reports on new ways to harness the results of the HMP and discusses how changes in the microbiome might affect human health, disease, immunity, and importantly, the safety and effectiveness of drug treatment in a Review article that is part of the special issue “OMICS in Africa: Moving 21st Century Integrative Biology from Lab to Village to Innovation Ecosystems,” of OMICS: A Journal of Integrative Biology, the peer-reviewed interdisciplinary journal published by Mary Ann Liebert, Inc., publishers. The issue is available on the OMICS website.

In the article “Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics,” senior author Ramy Karam Aziz and coauthors propose a “microbiome cloud model” to understand the variation in an individual's microbiome composition within and between individuals and how that variability makes it difficult to define the human microbiome. They present detailed examples of microbiome changes related to colorectal cancer, use of antibiotics, and pharmacomicrobiomics or drug-microbiome interactions in relation to personalized healthcare.

In the Commentary “Translating Biotechnology to Knowledge-Based Innovation, Peace, and Development? Deploy a Science Peace Corps—An Open Letter to World Leaders,” Nezih Hekim, SANKO University, Turkey and coauthors in 15 countries from around the world joined forces with OMICS Editor-in-Chief Vural Özdemir, MD, PhD, DABCP Gaziantep University, Faculty of Communications, School of Journalism, Gaziantep Turkey, to call for the creation of a global Science Peace Corps. This idea and initiative would entail volunteer work in life sciences translational research for no less than 6 weeks and up to 2 years in any region of the world. The topics could relate to all fields of medicine “as long as they are linked to potential or concrete endpoints in development, foreign policy and/or peace scholarship domains.” The authors describe the proposed Science Peace Corps as a “new instrument in the global science governance toolbox” that would advance “the emerging concept of 'one health'–encompassing human, environmental, plant, microbial, ecosystem, and planet health.”

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Rooibos – 7 top reasons why you should drink 6 cups daily

Rooibos – 7 top reasons why you should drink 6 cups daily | Science | Scoop.it
Most rooibos researchers recommend the complete rooibos extract as a tea, and six cups staggered throughout the day
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Bring 'home science' into the class

Bring 'home science' into the class | Science | Scoop.it
Indigenous knowledge can be used to bolster SA’s maligned maths and science proficiency.
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Mystery of how snakes lost their legs solved by reptile fossil

Mystery of how snakes lost their legs solved by reptile fossil | Science | Scoop.it
Fresh analysis of a reptile fossil is helping scientists solve an evolutionary puzzle -- how snakes lost their limbs. The findings show snakes did not lose their limbs in order to live in the sea, as was previously suggested.

 

The 90 million-year-old skull is giving researchers vital clues about how snakes evolved. Comparisons between CT scans of the fossil and modern reptiles indicate that snakes lost their legs when their ancestors evolved to live and hunt in burrows, which many snakes still do today.

The findings show snakes did not lose their limbs in order to live in the sea, as was previously suggested.

 

Scientists used CT scans to examine the bony inner ear of Dinilysia patagonica, a 2-meter long reptile closely linked to modern snakes. These bony canals and cavities, like those in the ears of modern burrowing snakes, controlled its hearing and balance. They built 3D virtual models to compare the inner ears of the fossils with those of modern lizards and snakes. Researchers found a distinctive structure within the inner ear of animals that actively burrow, which may help them detect prey and predators. This shape was not present in modern snakes that live in water or above ground.

 

The findings help scientists fill gaps in the story of snake evolution, and confirm Dinilysia patagonica as the largest burrowing snake ever known. They also offer clues about a hypothetical ancestral species from which all modern snakes descended, which was likely a burrower.

 

Reference:

H. Yi, M. A. Norell. The burrowing origin of modern snakes. Science Advances, 2015; 1 (10): e1500743 DOI: 10.1126/sciadv.1500743

 


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Resources for academic writing and publishing

 

I led a workshop on academic writing and publishing last week, and this is a list of resources I gave to the participants. It's not an exhaustive list, so if you have any favorites let me know and I'll add them!

 

Links and resources

 

General writing resources

 

Strunk, W. Jr. (1999).The Elements of Style. http://www.bartleby.com/141/

 

 

 

Guidelines and lessons for good scientific writing

 

Cargill, M., and O’Connor, P. (2011). Writing Scientific Research Articles: Strategy and Steps. Wiley. http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1444356216.html

 

Doumont, J., ed. (2010). English Communication for Scientists. Cambridge, MA: NPG Education. http://www.nature.com/wls/ebooks/english-communication-for-scientists-14053993/contents (Free ebook - very useful)

 

Duke University Graduate School. Scientific Writing Resource.  https://cgi.duke.edu/web/sciwriting/index.php Short, online course for graduate students with examples and worksheets

 

Editorial (2010). Scientific writing 101. Nat Struct Mol Biol. 17: 139-139. http://www.nature.com/nsmb/journal/v17/n2/full/nsmb0210-139.html

 

European Association of Science Editors. EASE Toolkit for Authors. http://www.ease.org.uk/publications/ease-toolkit-authors

 

Nature Scitable Effective Writing. http://www.nature.com/scitable/topicpage/effective-writing-13815989

 

Nature Scitable Scientific Papers. http://www.nature.com/scitable/topicpage/scientific-papers-13815490

 

Lichtfouse, E. (2013). Scientific Writing for Impact Factor Journals. Nova Scientific Publishers, Inc. (New York).

 

Moreira, A., and Haahtela, T. (2011). How to write a scientific paper--and win the game scientists play! Rev. Port. Pneumol. 17:146-149. doi: 10.1016/j.rppneu.2011.03.007. http://www.elsevier.pt/en/linkresolver/320/how-to-write-scientific-paper-and-win/90020266

 

Plaxco, K.W. (2010). The art of writing science. Protein Science 19: 2261 – 2266. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009394/pdf/pro0019-2261.pdf

 

Rogers, Silvia M. (2014). Mastering Scientific and Medical Writing: A Self-Help Guide. Springer. http://www.springer.com/medicine/book/978-3-642-39445-4https://moodle.swarthmore.edu/pluginfile.php/179173/mod_resource/content/1/Good%20versus%20poor%20scientific%20writing%20from%20Silvia%20Rogers.pdf

 

Writing Center University of Wisconsin. (2014) The Writers Handbook: Reverse Outlines. http://writing.wisc.edu/Handbook/ReverseOutlines.html

 

 

 

Guidance from journals

 

J Exp Bot: http://www.oxfordjournals.org/our_journals/exbotj/for_authors/

 

Nature: http://www.nature.com/authors/author_resources/how_write.html

 

Plant Cell: http://www.plantcell.org/site/misc/ifora.xhtml

 

 

 

Figures preparation and ethical issues

 

Blatt, M. and Martin, C. (2013). Manipulation and Misconduct in the Handling of Image Data. Plant Physiology. 163: 3-4. http://www.plantphysiol.org/content/163/1/3.short

 

Cromey, D.W. (2010). Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images. Sci. Eng. Ethics 16: 639–667

 

Rossner, M., and Yamada, K.M. (2004). What’s in a picture? The temptation of image manipulation. J. Cell Biol 166: 11–15. http://jcb.rupress.org/content/166/1/11.short

 

 

 

Peer Review Guidelines and Policies, Post-publication peer review

 

Bastian, H. (2014) A Stronger Post-Publication Culture Is Needed for Better Science. PLoS Med 11(12): e1001772. doi:10.1371/journal.pmed.1001772

 

F1000Research: http://blog.f1000research.com/2014/07/08/what-is-post-publication-peer-review/

 

F1000: http://journal.frontiersin.org/Journal/10.3389/fncom.2012.00063/full

 

Mole. (2007). Rebuffs and rebuttals I: how rejected is rejected? J Cell Sci. 120: 1143-1144. http://hwmaint.jcs.biologists.org/cgi/reprint/120/7/1143

 

Nature: http://www.nature.com/authors/policies/peer_review.html

 

Office of Research Integrity. (US Dept of Health and Human Services) The Lab. http://ori.hhs.gov/THELAB

 

Office of Research Integrity. Research Clinic Case Book. http://ori.hhs.gov/rcr-casebook-stories-about-researchers-worth-discussing

 

Science: http://www.sciencemag.org/site/feature/contribinfo/review.xhtml

 

PLOS ONE:www.plosone.org/static/reviewerGuidelines

 

Provenzale, J.M. and Stanley, R.J. (2006). A Systematic Guide to Reviewing a Manuscript. J. Nuclear Med.Techn.. 34: 92-99. http://tech.snmjournals.org/content/34/2/92.full.pdf+html

 

Times Higher Education: http://www.timeshighereducation.co.uk/news/can-post-publication-peer-review-endure/2016895.article

 

 

 

Readability

 

RavenBlog (2010). Ultimate list of online content readability tests. http://blog.raventools.com/ultimate-list-of-online-content-readability-tests/

 

 

 

Communicating more broadly

 

Kuehne, L.M., et al. (2014). Practical science communication strategies for graduate students. Conservation Biology. 28: 1225–1235. .DOI: 10.1111/cobi.12305

 

Osterrieder, A. (2013). The value and use of social media as communication tool in the plant sciences. Plant Methods. 9: 26. http://www.plantmethods.com/content/9/1/26

 

 

 


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AckerbauHalle's curator insight, February 3, 2015 10:49 AM

Großartige Literatursammlung für wissenschaftliches Schreiben. 

Bibhya Sharma's curator insight, February 3, 2015 8:58 PM

Very helpful for teachers and researchers. 

Andres Zurita's curator insight, February 4, 2015 12:53 PM
Outstanding source of fine material! Thanks Mary!
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Life’s extremists may be an untapped source of antibacterial drugs

Life’s extremists may be an untapped source of antibacterial drugs | Science | Scoop.it

One of the most mysterious forms of life may turn out to be a rich and untapped source of antibacterial drugs. The mysterious life form is Archaea, a family of single-celled organisms that thrive in environments like boiling hydrothermal pools and smoking deep sea vents which are too extreme for most other species to survive.


“It is the first discovery of a functional antibacterial gene in Archaea,” said Seth Bordenstein, the associate professor of biological sciences at Vanderbilt University who directed the study, “You can’t overstate the significance of the antibiotic resistance problem that humanity is facing. This discovery should help energize the pursuit for new antibiotics in this underexplored group of life.”


Until the late 1970s, biologists thought that Archaea were just weird bacteria, but then a landmark analysis of their DNA showed that they represent an independent branch on the tree of life that stretches back more than three billion years. The realization that Archaea could be a source of novel pharmaceuticals emerges from a study of widespread horizontal gene transfer between different species conducted by a team of scientists from Vanderbilt University and Portland State University in Oregon.



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The top 100 papers: NATURE magazine explores the most-cited research papers of all time

The top 100 papers: NATURE magazine explores the most-cited research papers of all time | Science | Scoop.it

The discovery of high-temperature superconductors, the determination of DNA’s double-helix structure, the first observations that the expansion of the Universe is accelerating — all of these breakthroughs won Nobel prizes and international acclaim. Yet none of the papers that announced them comes anywhere close to ranking among the 100 most highly cited papers of all time.

 

Citations, in which one paper refers to earlier works, are the standard means by which authors acknowledge the source of their methods, ideas and findings, and are often used as a rough measure of a paper’s importance. Fifty years ago, Eugene Garfield published the Science Citation Index (SCI), the first systematic effort to track citations in the scientific literature. To mark the anniversary, Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time. (See the full list at Web of Science Top 100.xls or the interactive graphic, below.) The search covered all of Thomson Reuter’s Web of Science, an online version of the SCI that also includes databases covering the social sciences, arts and humanities, conference proceedings and some books. It lists papers published from 1900 to the present day.

 

The exercise revealed some surprises, not least that it takes a staggering 12,119 citations to rank in the top 100 — and that many of the world’s most famous papers do not make the cut. A few that do, such as the first observation1 of carbon nanotubes (number 36) are indeed classic discoveries. But the vast majority describe experimental methods or software that have become essential in their fields.

 

The most cited work in history, for example, is a 1951 paper2 describing an assay to determine the amount of protein in a solution. It has now gathered more than 305,000 citations — a recognition that always puzzled its lead author, the late US biochemist Oliver Lowry.


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News - Hoodia weight loss supplement ineffective...

News - Hoodia weight loss supplement ineffective... | Science | Scoop.it

A new study about the physiological effects of Hoodia gordonii (a well-known wonder weight-loss supplement) on rats, has delivered alarming results, including a dramatic rise in blood pressure, loss of skeletal muscle mass and bloated stomachs.

The results of the study were published this month in the Journal of Ethnopharmacology. The study is the first to investigate the physiological effect of Hoodia gordonii on both lean and obese rats, as well as the specific tissue types affected.

Prof Carine Smith, head of the Multidisciplinary Stress Biology research group in the Department of Physiological Sciences at SU, says they embarked on this study because of the lack of scientific data on the physiological effect of Hoodia gordonii on animals and people published in peer-reviewed journals.

"The fact that several prominent pharmaceutical companies that were initially involved in the commercial development of Hoodia gordonii have subsequently withdrawn their interest, raises the question of whether this plant may have as yet unreported side-effects," she says.

Meanwhile Hoodia gordonii is still being marketed worldwide as the wonder weight-loss drug present in powder supplements, tea and energy bars.

Read more at http://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=1821

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News - Not all songbirds sing about love

News - Not all songbirds sing about love | Science | Scoop.it

A divorce rate of over 60% after the first year, extra-marital affairs, illegitimate offspring and deceit. This is the world of the Crimson-breasted Shrike, a nimble and restless South African bird best known for its striking red colour and penetrating whistles.

The Crimson-breasted Shrike belongs to the family of songbirds called oscines. This group of more than 4 600 species worldwide are known for their beautiful singing and include orioles, warblers and thrushes. The Crimson-breasted Shrike, however, is one of the few species (less than 5% of all bird species) that engage in duets.

So, what do shrikes sing about? And what are so special about duets?

Based on three years of observation and genetic analysis, researchers from Stellenbosch University and the University of Oldenburg in Germany can now say with relative certainty that they have a very good idea what shrikes sing about.

The results of the research were published this month in an article in the journal Behavioral Ecology and Social Biology entitled 'Crimson-breasted Shrike females with extra pair offspring contributed more to duets'.

Prof Michael Cherry, a behavioural ecologist in the Department of Botany and Zoology at Stellenbosch University and one of the authors, says while social monogamy is relatively rare in the animal kingdom, over 90% of avian species are socially monogamous, compared to only 3-5% of mammalian species.

However, social monogamy does not imply sexual monogamy. Since the advent of paternity testing in the 1980s, scientists now know that, on average, about 11% of the baby birds in any nest are sired by someone other than the resident male: "Both males and females can actively seek out extra-pair matings," he explains.

Duetting birds, however, were thought to be an exception: "One hypothesis is that duetting functions to reinforce the bond between the couple, thereby reducing extra pair mating in both sexes. The male will sing 'I am here' and then the female answers 'I am also here' and so on. Other hypotheses are that duets serve in territorial defence, mate guarding, mutual recognition and maintaining contact in dense vegetation."

Doctoral student Irene van den Heuvel, supervised jointly by Prof Cherry and Prof Georg Klump of the University of Oldenburg, set out to test two of these hypotheses. Firstly, that duetting is used for paternity guarding and, secondly, that participation in a duet is a signal of commitment to genetic monogamy.

They combined an analysis of the acoustics of duetting with a genetic analysis using microsatellite DNA markers to investigate the mating patterns of the Crimson-breasted Shrike at the Kuruman River Reserve in the southern Kalahari Desert. During three consecutive breeding seasons, they studied 19 pairs and 83 nestlings from 44 broods.

The results were completely the opposite of what they had expected.

Twenty percent of all young born to the 19 females tested were sired by extra-pair males. The results offered no support for the idea that duets function in paternity guarding. Most remarkably, females with illegitimate offspring were significantly more likely to answer their mates' song than females without.

Prof Cherry says they found no evidence for duets functioning as a signal of commitment: "Female vocal behaviour was in fact the reverse of that predicted. Levels of infidelity amongst social females were positively related to female answer rate of their mates' song.

"These results suggest that females may use increased answer rates as a form of manipulation, to prevent divorce and to make sure that the male helps with building nests and feeding the young," he says.

An earlier paper by the same authors recorded that divorce in Crimson-breasted Shrike pairs is uncommon after the pair has been together for more than one breeding season. Newly formed pairs, by contrast, have a 60% chance of divorce.

But as extra-pair paternity is not confined to females in newly formed pair bonds, it is unlikely that males of this species are able to assess their chances of being cuckolded, the researchers conclude.

 Photo credit: Irene van den Heuvel

 

Contact details

Prof Michael Cherry

Tel: 021 808-3233/ 0726875845

E-mail: mic@sun.ac.za

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Naledi Pandor: Address by the Minister of Science and Technology, 5th International Union of Pure and Applied Chemistry conference on green chemistry, Durban (18/08/2014)

Naledi Pandor: Address by the Minister of Science and Technology, 5th International Union of Pure and Applied Chemistry conference on green chemistry, Durban (18/08/2014) | Science | Scoop.it
It’s a pleasure and an honour to be here to give you a message of support from the South African government. The message is that we take green chemistry for sustainable development very seriously. South Africa's chemical industry is of substantial economic significance, contributing around 5% to our gross domestic product (GDP) and approximately 25% of our manufacturing sales.
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Endemic ants give alien ants a hard time

Endemic ants give alien ants a hard time | Science | Scoop.it

In a recently-published article, C·I·B postdoctoral associate Dr. Natasha Mothapo used behavioural experiments to see if the African big-headed ant (Pheidole megacephala) can help to keep the spread of invasive Argentine ants (Linepithema humile) in check. Dr. Mothapo found that both species were very aggressive during fights. Their mortality rates were similar during one-on-one clashes, but Argentine ants suffered more deaths than did big-headed ants. When competing for food in the same environment, the African big-headed ant was able to keep Argentine ants from gaining access to the food.

Invasive alien ants have to overcome a few obstacles before they can establish themselves in a new area. When entering a new area, they are met by sometimes-hostile ant species that are already established in the area. Argentine ants are one of the world’s most successful invasive ants, and are present on six continents. The success of the Argentine ant is probably due to its aggressive behaviour towards other ants, and its large colonies. This means that Argentine ants in the same colony do not fight, and individuals are very similar genetically.

The Argentine ant has been present in South Africa since the early 1900s and has successfully spread to 6 of the 9 provinces, excluding Limpopo, KwaZulu-Natal and Mpumalanga. The ant fauna of these provinces is dominated by the endemic African big-headed ant.

Natasha’s research is the first study to show that native organisms can provide some protection from alien species (also called “biotic resistance”). “Behavioural studies like this one are important, as it shows us how ants within a recipient area will react towards ants that are introduced to the area. Knowing this will help us to understand the factors that cause some species to be so successful at invading new areas.” says Natasha.

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Online collaboration: Scientists and the social network

Online collaboration: Scientists and the social network | Science | Scoop.it

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Gerd Moe-Behrens's curator insight, August 14, 2014 4:47 PM

by
Richard Van Noorden

"In 2011, Emmanuel Nnaemeka Nnadi needed help to sequence some drug-resistant fungal pathogens. A PhD student studying microbiology in Nigeria, he did not have the expertise and equipment he needed. So he turned to ResearchGate, a free social-networking site for academics, and fired off a few e-mails. When he got a reply from Italian geneticist Orazio Romeo, an inter­national collaboration was born. Over the past three years, the two scientists have worked together on fungal infections in Africa, with Nnadi, now at Plateau State University in Bokkos, shipping his samples to Romeo at the University of Messina for analysis. “It has been a fruitful relationship,” says Nnadi — and they have never even met.

Ijad Madisch, a Berlin-based former physician and virologist, tells this story as just one example of the successes of ResearchGate, which he founded with two friends six years ago. Essentially a scholarly version of Facebook or LinkedIn, the site gives members a place to create profile pages, share papers, track views and downloads, and discuss research. Nnadi has uploaded all his papers to the site, for instance, and Romeo uses it to keep in touch with hundreds of scientists, some of whom helped him to assemble his first fungal genome.
More than 4.5 million researchers have signed up for ResearchGate, and another 10,000 arrive every day, says Madisch. That is a pittance compared with Facebook’s 1.3 billion active users, but astonishing for a network that only researchers can join. And Madisch has grand goals for the site: he hopes that it will become a key venue for scientists wanting to engage in collaborative discussion, peer review papers, share negative results that might never otherwise be published, and even upload raw data sets. “With ResearchGate we’re changing science in a way that’s not entirely foreseeable,” he says, telling investors and the media that his aim for the site is to win a Nobel prize....."


http://bit.ly/1oy6XqC

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Popular Science: Has The End Of The Banana Arrived? (2014)

Popular Science: Has The End Of The Banana Arrived? (2014) | Science | Scoop.it

Two weeks ago, at a conference in South Africa, scientists met to discuss how to contain a deadly banana disease outbreak in nearby Mozambique, Africa. At fault was a fungus that continues its march around the planet. In recent years, it has spread across Asia and Australia, devastating plants there that bear the signature yellow supermarket fruit.

 

The international delegation of researchers shared their own approaches to the malady, hoping to arrive at some strategy to insulate Mozambique and the rest of Africa: a continent where bananas are essential to the lives of millions. They left the Cape Town-based meeting with an air of optimism.

 

Only days after the meeting, however, a devastating new survey of the stricken Mozambique farm was released. Scientists at the conference assumed that the fungus was limited to a single plot. The new report suggested the entire plantation was infested, expanding 125 diseased acres to more than 3,500. All told, 7 million banana plants were doomed to wilt and rot.

 

“The future looks bleak,” says Altus Viljoen, the South African plant pathologist who organized the conference. "There’s no way they’ll be able to stop any further spread if they continue to farm.” Worse, he says, the disease's rapid spread endangers banana crops beyond Mozambique’s borders.

 

The story of the African farm is the story of a threat to the world’s largest fruit crop. Commercially, bananas generate $8 billion annually and, according to the United Nations Conference on Trade and Development, more than 400 million people rely on the fruit as their primary source of calories. Though more bananas are grown in Asia, Africans depend heavily on the crop; in countries like Rwanda and Uganda, for example, average banana consumption is about 500 pounds per person annually, or 20 times that of the typical American. If the bananas vanish, people starve.


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Natasha Palesa Mothapo | 200 Young South Africans – 2014 Edition | Mail & Guardian

Natasha Palesa Mothapo  | 200 Young South Africans – 2014 Edition | Mail & Guardian | Science | Scoop.it

There’s an invading army attacking our precious fynbos; you may not know about it, but fortunately, Dr Natasha Mothapo is on their tracks.

The army is the Argentine ant, an invasive species from South America that has spread across the world, from Easter Island to Europe to Hawaii. The species has been introduced at two different times into South Africa, and it’s creating havoc in the biodiversity hotspot that’s home to our fynbos.

“They’re so fascinating,” says Mothapo. She’s done both her master’s and her doctorate on these ants.

Which comes as no surprise to her family. Born and brought up in Alexandra, Johannesburg, Mothapo always loved animals.

“I had a dog and pet pigeons, and when we were at our home in Limpopo, I was always grabbing lizards and stuff like that. I think the attraction to science really began in grade five when we went on a field trip to the Kruger National Park. My folks were not surprised that I ended up where I am.”

Stellenbosch University came calling at her school to recruit students and the institution leapt at the chance of teaching someone with such an affinity for biology. “I’ve been here since 2001 – it has grown on me.”

Mothapo’s master’s supervisor suggested she take a look at these invasive ants. Native ants eat white, oily appendages called elaiosomes that are attached to fynbos seeds – they carry the seeds underground and leave them there, protected from fire and predators. Argentine ants also eat the elaiosomes, but they leave the seeds on the surface, exposed. So figuring out a way of minimising the invasion is a priority.

She flew to Cairns, Australia in mid-July to present at the International Union for the Study of Social Insects Conference. She’ll return to do more work on her ants, but in the future, she thinks she may find herself either teaching or working on policies to manage invasive species. — Mandi Smallhorne

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Bioinformatics: Big data from DNA Sequencing is giving new Insights into Cancer Development and Treatment Options

Bioinformatics: Big data from DNA Sequencing is giving new Insights into Cancer Development and Treatment Options | Science | Scoop.it
The torrents of data flowing out of cancer research and treatment are yielding fresh insight into the disease.

 

In 2013, geneticist Stephen Elledge answered a question that had puzzled cancer researchers for nearly 100 years. In 1914, German biologist Theodor Boveri suggested that the abnormal number of chromosomes — called aneuploidy — seen in cancers might drive the growth of tumors. For most of the next century, researchers made little progress on the matter. They knew that cancers often have extra or missing chromosomes or pieces of chromosomes, but they did not know whether this was important or simply a by-product of tumor growth — and they had no way of finding out.

 

Elledge found that where aneuploidy had resulted in missing tumor-suppressor genes, or extra copies of the oncogenes that promote cancer, tumors grow more aggressively (T. Davoli et al.Cell 155, 948–962; 2013). His insight — that aneuploidy is not merely an odd feature of tumors, but an engine of their growth — came from mining voluminous amounts of cellular data. And, says Elledge, it shows how the ability of computers to sift through ever-growing troves of information can help us to deepen our understanding of cancer and open the door to discoveries.

 

Modern cancer care has the potential to generate huge amounts of data. When a patient is diagnosed, the tumor's genome might be sequenced to see if it is likely to respond to a particular drug. The sequencing might be repeated as treatment progresses to detect changes. The patient might have his or her normal tissue sequenced as well, a practice that is likely to grow as costs come down. The doctor will record the patient's test results and medical history, including dietary and smoking habits, in an electronic health record. The patient may also have computed tomography (CT) and magnetic resonance imaging (MRI) scans to determine the stage of the disease. Multiply all that by the nearly 1.7 million people diagnosed with cancer in 2013 in the United States alone and it becomes clear that oncology is going to generate even more data than it does now. Computers can mine the data for patterns that may advance the understanding of cancer biology and suggest targets for therapy.

 

Elledge's discovery was the result of a computational method that he and his colleagues developed, called the Tumor Suppressor and Oncogene Explorer. They used it to mine large data sets, including the Cancer Genome Atlas, maintained by the US National Cancer Institute, based in Bethesda, Maryland, and the Catalogue of Somatic Mutations in Cancer, run by the Wellcome Trust Sanger Institute in Hinxton, UK. The databases contained roughly 1.2 million mutations from 8,207 tissue samples of more than 20 types of tumor.

 

Analyzing the genomes of 8,200 tumors is just a start. Researchers are “trying to figure out how we can bring together and analyze, over the next few years, a million genomes”, says Robert Grossman, who directs the Initiative in Data Intensive Science at the University of Chicago in Illinois. This is an immense undertaking; the combined cancer genome and normal genome from a single patient constitutes about 1 terabyte (1012 bytes) of data, so a million genomes would generate an exabyte (1018 bytes). Storing and analysing this much data could cost US$100 million a year, Grossman says.

 

But it is the new technologies that are creating an information boom. “We can collect data faster than we can physically do anything with them,” says Manish Parashar, a computer scientist and head of the Rutgers Discovery Informatics Institute in Piscataway, New Jersey, who collaborates with Foran to find ways of handling the information. “There are some fundamental challenges being caused by our ability to capture so much data,” he says.

 

A major problem with data sets at the terabyte-and-beyond level is figuring out how to manipulate all the data. A single high-resolution medical image can take up tens of gigabytes, and a researcher might want the computer to compare tens of thousands of such images. Breaking down just one image in the Rutgers project into sets of pixels that the computer can identify takes about 15 minutes, and moving that much information from where it is stored to where it can be processed is difficult. “Already we have people walking around with disk drives because you can't effectively use the network,” Parashar says.

 

Informatics researchers are developing algorithms to split data into smaller packets for parallel processing on separate processors, and to compress files without omitting any relevant information. And they are relying on advances in computer science to speed up processing and communications in general.

 

Foran emphasizes that the understanding and treatment of cancer has undergone a dramatic shift as oncology has moved from one-size-fits-all attacks on tumours towards personalized medicine. But cancers are complex diseases controlled by many genes and other factors. “It's not as if you're going to solve cancer,” he says. But big data can provide new, better-targeted ways of grappling with the disease. “You're going to come up with probably a whole new set of blueprints for how to treat patients.”

 


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