Tag Archives: nature

Nature journals make all their articles free to view

Nature, one of the biggest academic journal groups has announced that they will make all their articles free to view. While the articles will be available for anyone to read, they cannot be copied, printed or downloaded, the journal’s publisher Macmillan announced on 2 December.

nature publishing

“Subscribers to 49 journals on nature.com will be able to share a unique URL to a full text, read-only version of published scientific research with colleagues or collaborators in the most convenient way for them, e.g. via email and social media. Included are the world’s most cited scientific publication, Nature; the Nature family of journals and fifteen other quality science journals”, the press release reads.

This seems like a brilliant move which will allow scholars, students and passionate readers to access the content, while also preserving Macmillan’s main source of income – the subscription fees libraries and individuals pay to gain access to articles.

The PDFs with the articles will be available on the ReadCube platform. ReadCube is an open source desktop and browser-based program for managing, annotating, and accessing academic research articles; however, as mentioned above, you will only be able to read and annotate the articles – not download them. This move will also likely increase not only Nature’s popularity, but also ReadCube’s – a platform in which Macmillan has invested heavily. So basically you get a read only version of all the papers published in Nature, which you will also be able to share with your friends through a link that anyone can access. PDF articles can also be saved to a free desktop version of ReadCube, much like songs on iTunes can be saved on your computer. The only bad thing is that ReadCube is only available on Windows and MacOS, so if you’re running Linux or other operating systems, there’s a good chance it won’t work for you. Personally, I feel this is a pretty significant problem, as Linux users are most likely overrepresented in Nature’s audience.

“We know researchers are already sharing content, often in hidden corners of the Internet or using clumsy, time-consuming practices,” said a statement by Timo Hannay, the managing director of Digital Science, a division of Macmillan that has invested in ReadCube. “At Digital Science we have the technology to provide a convenient, legitimate alternative that allows researchers to access the information they need and the wider, interested public access to scientific knowledge, from the definitive, original source,” Hannay said.

This move comes as open-source research is becoming more and more prevalent; for example, over half of 2007-2012 published research is now available for free. The Chinese research agencies are pushing more and more for full open access research and the White House directs open access for government research. Personally, I am strongly for open access research – bar some exceptions in which there are strong reasons to put a paywall over the articles. I feel that this current system with library subscriptions is more business oriented than science oriented and it’s stripping away potential progress by limiting the access to science. However, while this initiative is laudable… it’s not exactly open access.

“To me, this smacks of public relations, not open access,” says John Wilbanks, a strong advocate of open-access publishing in science and a senior fellow at the Ewing Marion Kauffman Foundation in Kansas City, Missouri. “With access mandates on the march around the world, this appears to be more about getting ahead of the coming reality in scientific publishing. Now that the funders call the tune and the funders want the articles on the web at no charge, these articles are going to be open anyway,” he says.

So, what do you think? Is this just a PR move, or is it a legitimate attempt to move towards open-access research? Or is it both?

Nature was first set up on 4 November 1869. It was ranked the world’s most cited by the Science Edition of the 2010 Journal Citation Reports and is widely regarded as one of the few remaining academic journals that publishes original research across a wide range of scientific fields. They get about 3 million unique readers every month, and if you’ve been reading ZME Science for a while, you’ve likely seen that we often cite studies from them.

Original Press Release.

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Nature walks linked to significantly lower depression and stress

Science confirms what many already believed: taking walks in nature lowers your stress and depression rates.

You’ve probably heard it several times in your life: take a deep breath, go take a walk and calm down. But according to a new study, that’s not just small talk; walks, especially nature walks can do wonders for your mental health. Even people who suffered from a significant traumatic event reported improved mental health after a walk in nature.

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Walking in nature reduces stress and depression rates. Image via Amazon.

“We hear people say they feel better after a walk or going outside but there haven’t been many studies of this large size to support the conclusion that these behaviors actually improve your mental health and well-being,” says senior author Sara Warber, M.D., associate professor of family medicine at the U-M Medical School and member of the Institute for Healthcare Policy and Innovation.

Indeed, many of us suspected this – it’s high time a large scale study actually took a look at this.

“Walking is an inexpensive, low risk and accessible form of exercise and it turns out that combined with nature and group settings, it may be a very powerful, under-utilized stress buster. Our findings suggest that something as simple as joining an outdoor walking group may not only improve someone’s daily positive emotions but may also contribute a non-pharmacological approach to serious conditions like depression.”

Researchers analyzed almost 2,000 people from the Walking for Health program in England, monitoring how their mental health evolves in regards to walking in nature.

“Given the increase in mental ill health and physical inactivity in the developed world, we are constantly exploring new, accessible ways to help people improve their long term quality of life and well-being,” Warber says.

“Group walks in local natural environments may make a potentially important contribution to public health and be beneficial in helping people cope with stress and experience improved emotions.”

Leukemia drug found to dramatically boost immune system

A class of drugs currently used to treat leukemia has been found to have some severe side effects – positive ones, that is. The drug was found to drastically boosting immune responses against many different cancers, reports a new study.

The drug class is referred to as p110´ inhibitors. Recently, it has been used with significant success against certain leukemias in recent clinical trials; patients were given a placebo, and after a while, they were given the actual drug – and it started to work right away. However, until now, it hasn’t been tested against other cancers.

The new study, which was published in Nature, shows that p110δ inhibitors have remarkable effects against a broad range of cancers, especially reducing the chance of relapse. Basically, these drugs inhibit the p110δ enzyme, boosting the body’s immune system, enabling it to kill more tumor cells.

“Our study shows that p110δ inhibitors have the potential to offer effective immunity to many types of cancer by unleashing the body’s own immune response,” says study co-leader Professor Bart Vanhaesebroeck of the UCL Cancer Institute, who first discovered the p110δ enzyme in 1997. “p110δ is highly expressed and important in white blood cells, called ‘leukocytes’. Given that leukemias are the result of leukocytes becoming cancerous, they are a natural target for p110δ inhibitors. Now, we have shown that blocking p110δ also has the remarkable effect of boosting the body’s immune response against leukemias as well as other cancers.”

Initially, they tested it on mice, and the results were very exciting. However, many drugs which have good results in mice don’t work that well in humans – which is why this study is particularly interesting. ollowing p110δ inhibition, the immune system develops a sort of memory, enabling it to be more efficient with cancer in future battles, massively reducing relapse rates.

An electron scan of T-cells. Image via Wikipedia.

“Our work shows that p110δ inhibitors can shift the balance from the cancer becoming immune to our body’s defenses towards the body becoming immune to the cancer, by disabling regulatory T cells,” says study co-leader Dr Klaus Okkenhaug of the Babraham Institute. “This provides a rationale for using these drugs against both solid and blood cancers, possibly alongside cancer vaccines, cell therapies and other treatments that further promote tumor-specific immune responses.”

Aside for having obvious potential applications, this study also raises some questions about how the body fights against cancers. The gene p110δ regulates immune function; the enzyme is especially important for the regulation of T-cells, a type of white blood cells which play a crucial role in cell-mediated immunity. What they describe in this study is that P110δ inhibition reshapes the body’s immune system; regulatory T-cells become inactive, and instead a sub-population of T-cells, CD8+ cytotoxic T-cells become hyper-activated and hunt down and kill any rogue cancer cells lying around the body which may cause cancerous relapse to happen. It’s still not entirely clear why this is happening – the beauty and the curse of science.

Scientific Reference: Inactivation of PI(3)K p110δ breaks regulatory T-cell-mediated immune tolerance to cancer. Nature, 2014; DOI: 10.1038/nature13444

 

Transverse cross-section of a very thin sunflower leaf (Helianthus annuus) to a thick tea leaf (Camellia sasquana). Along with total leaf thickness and leaf area, the leaves differ dramatically in cell size and in the thickness of cell walls according to specific mathematical equations newly discovered by the UCLA research team. Credit: Lawren Sack, Grace John, Christine Scoffoni/UCLA Life Sciences

Hidden mathematical rules that govern leaf design uncovered

After performing an exhaustive quantitative research across numerous plant species, scientists at  UCLA’s College of Letters and Science  have found that leaf design is governed by a set of fundamental mathematical expressions, underling once again the elegance of nature.

Transverse cross-section of a very thin sunflower leaf (Helianthus annuus) to a thick tea leaf (Camellia sasquana). Along with total leaf thickness and leaf area, the leaves differ dramatically in cell size and in the thickness of cell walls according to specific mathematical equations newly discovered by the UCLA research team.  Credit: Lawren Sack, Grace John, Christine Scoffoni/UCLA Life Sciences

Transverse cross-section of a very thin sunflower leaf (Helianthus annuus) to a thick tea leaf (Camellia sasquana). Along with total leaf thickness and leaf area, the leaves differ dramatically in cell size and in the thickness of cell walls according to specific mathematical equations newly discovered by the UCLA research team.
Credit: Lawren Sack, Grace John, Christine Scoffoni/UCLA Life Sciences

The basis of their research was  “allometric analysis”, that is to say the study of an object’s evolution in size by studying its constituting parts and how they vary in proportionality. While it is easy to observe major differences in leaf surface area among species, they said, differences in leaf thickness are less obvious but equally important. Leaf thickness is actually where the researchers struck gold.

“Once you start rubbing leaves between your fingers, you can feel that some leaves are floppy and thin, while others are rigid and thick,” said Grace John, a UCLA doctoral student in ecology and evolutionary biology and lead author of the research. “We started with the simplest questions — but ones that had never been answered clearly — such as whether leaves that are thicker or larger in area are constructed of different sizes or types of cells.”

A leaf is made out of three distinct parts: the outer layer that makes the leaf surface also called an epidermis, the  mesophyll which is comprised of photosynthesis capable cells and vascular tissue, whose cells are involved in water and sugar transport. The team found, after cutting cross-sections thinner than a single cell to observe each leaf’s microscopic layout, that the thicker the leaf, the larger the size of the cells in all of its tissues — except in the vascular tissue.

These relationships can be described by new, simple mathematical equations, effectively allowing scientists to predict the dimension of cells and cell walls based on the thickness of a leaf.

“This means that if a leaf has a larger cell in one tissue, it has a larger cell in another tissue, in direct proportion, as if you blew up the leaf and all its cells using Photoshop,” said Christine Scoffoni, a doctoral student at UCLA and member of the research team.

The new ability to predict the internal anatomy of leaves from their thickness can give clues to the function of the leaf, because leaf thickness affects both the overall photosynthetic rate and the lifespan, said Sack.

“A minor difference in thickness tells us more about the layout inside the leaf than a much more dramatic difference in leaf area,” John said.

The design of the leaf provides insights into how larger structures can be constructed without losing function or stability.

“Fundamental discoveries like these highlight the elegant solutions evolved by natural systems,” Sack said. “Plant anatomy often has been perceived as boring. Quantitative discoveries like these prove how exciting this science can be. We need to start re-establishing skill sets in this type of fundamental science to extract practical lessons from the mysteries of nature.

“There are so many properties of leaves we cannot yet imitate synthetically,” he added. “Leaves are providing us with the blueprints for bigger, better things. We just have to look close enough to read them.”
The study’s findings, which were published in the journal Botany, are o great worth since they provide key insights into how leaf design works at a cellular level. Insights such as these might cross biology and enter biotech, since we’re already seeing things like solar cells inspired by leaf biology, for instance.
“What makes the cross-sections especially exciting is the huge variation from one species to the next,” John said. “Some have relatively enormous cells in certain tissues, and cell shapes vary from cylindrical to star-shaped. Each species is beautiful in its distinctiveness. All of this variation needs decoding.”

Children no longer connected with nature

Just 1 out of 5 children in Britain are still connected to nature, and there’s no reason to believe that things lie any differently in the western world.

What does ‘connected to nature’ mean?

rpsb

Saying that someone is or isn’t connected to nature, at an intuitive level, is often times fairly simple. But making that statement scientifically is an entirely different thing; in order to do this, RPSB, a charity organization in the UK launched a three year project, and came up with a definition for connection to nature. They then developed a questionnaire with 16 statements designed to assess the level of connection among children and set up a “realistic and achievable” value for what it means to be connected to nature. Some 1,200 children from across the UK were asked to fill in the questionnaire.

The three-year project found that only 21% of children aged 8-12 were “connected to nature”. They also interviewed parents, and found that in many cases, a perception among some adults that nature is dangerous or dirty could be holding children back.

The relationship between nature and children has been studied a lot in the past years, and some researchers claim that the lack of such a connection impedes education and can even cause health problems – they even coined a term for it: “nature deficit disorder”, though it is not recognised as a medical condition.

Girls beat boys, urban beats rural

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There was quite a significant gender difference: 27% of girls were at or above the “realistic and achievable” target, but only 16% of boys managed to reach the same level.

“We need to understand these differences,” Sue Armstrong-Brown, head of conservation at the charity, told BBC News. “Whether boys and girls are scoring differently on different questions, are girls more empathetic to nature than boys for instance? We need to analyse the data to find that out.”

Interestingly enough, the average score for large cities was significantly higher than for smaller cities or rural areas, contrary to what intuition says. According to researchers, the attitude of their parents is the main driver in this case.

“There is definitely an attitude out there, in some cases, that nature is not perceived as interesting or engaging. In some cases it is perceived as a dirty or unsafe thing, and that’s an attitude that won’t help a young person climb a tree.”

The UK government has shown some interest in the study, and researchers hope that connection to nature can be take into consideration when estimating a person’s well being – not only children, but adults as well.

“If we can grow a generation of children that have a connection to nature and do feel a sense of oneness with it, we then have the force for the future that can save nature and stop us living in a world where nature is declining,” she said.

Worms Store Memories After Decapitation

Decapitated Worms Retain Memories – Transfer to Regrown Brains

land planarian, Bipalium kewense?

Imagine having your brain completely severed from your body, but being able to not only regenerate it – but also retain all information back into your newly regenerated brain.

That is impossible – right?

For humans the possibility is, indeed, impossible – but for the Planarians, it is their way of living and certainly not something out of a Kountry Kraft catelog.

The Planarians

Planarians, non-parasitic flatworms, have been trained and studied by biologists recently at a PA regeneration center. The fascination behind these worms lies within their impressive pluripotent stem cells. Unlike most creatures, Planarians contain an abnormal amount of these pluripotent stem cells, allowing for rapid regeneration. At an astounding 20-percent, pluripotent stem cells can take on the shape of any cell, which allows for the regeneration process.

In fact, the Planarians regeneration is so rapid that studies conducted in 1898 showed that even dissected to a tiny one 276th of its original size, the planarians could regenerate itself.

However, what makes these invertebrates even more spectacular was a recent study performed by Michael Levin, a Tufts University professor.

The Study

Published in the latest edition of the Journal of Experimental Biology, Levin conducted a study on Planarians cognitive functions and regenerative functions simultaneously.

Like many flatworms, or worms in general, planarians strongly dislike bright lights. They would much rather be in a warm, moist environment than a dry, hot one. Using this information, Levin vigorously trained his planarians to eat food in a very bright light.

Utilizing two different groups of planarians, Levin placed group 1 on a rigorous surface, while another on a flat surface. Each group had part of their environment illuminated by a light, where a piece of liver was placed.

Using a recording device, tracking analysis technology and measuring technology, Levin filmed the planarians over a ten-day period to see how easily each group would be to train. Those with a more rigid surface were more susceptible to the bright light and were less hesitant to eat in the bright light than those on a flat surface.

As a hypothesis, Levin suspected that if planarians were able to retain their memory after complete head severance, those on the rigid surface would be more susceptible to light exposure than those on the flat surface.

Analyzing this information, Levin severed all the heads on the worms and gave them a 14-day rest period to regrow their heads and brains.

The Results

Both group of worms were placed in a Petri dish and studied for their aversion to light. As suspected, both group of planarians were hesitant to go toward the light at first, however those who were on the rough terrain adapted much quicker.

Furthering his point, Levin then placed the planarians on a four-day break and placed them all back onto a Petri dish with light. Those on a rough terrain were much more susceptible to light exposure and moved around much more freely than those who were in the Petri dish.

This experiment provided Levin with the conclusion that the worms were able to retain their cognitive memory even after their heads were severed. At a minimum, planarians can retain memory for 14-days, enough to regrow their brains and restore the information.

How Their Memory is Stored

There is no definite answer as to how or where these planarians place their memories. It could be through their nervous system or through an unknown cellular memory function.

However, it is definite that planarians are able to store memories and regenerate all parts of their cellular body even when severed to a single miniscule portion.

Underwater… lakes !

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The lake floor, composed mostly of mussels

Boy I’ve gotta tell you, my jaw really dropped when I heard this one. There are actual lakes, on the bottom of oceans, especially in the Gulf of Mexico region; they’ve got their own shores and all. The brine water of these lakes actually hosts unique wildlife, creating an absolutely amazing environment. The fact that these are brine water means that they have an extremely high salinity, way more than the rest of the ocean, which means of course they are heavier, which is why they stick to the bottom.

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Think about the very bottom of the ocean, below the waves, below the light. What’s the first thing that comes to mind ? For me, it’s a cold dark environment filled with weird squids and fish with sharp teeth. I’m guessing your first picture is (and probably should be) something else, but it most definitely wouldn’t be an underwater lake ! I didn’t even know such a thing existed until recently. I’m telling you, you really REALLY should look at these videos


These lakes are located in brine pools, which formed during the Jurassic period. During that period, the shallow lakes from the Gulf of Mexico dried out, as a result of tectonic movements in a salt-rich area and perhaps the overall heat in the Jurassic period (it was so hot there were no polar caps). Later on, the 8 km saline layer was covered with sediments and preserved, becoming an underwater lake.

Of course such extreme amounts of salt make it almost impossible to live there, but as (almost) always, some extremophiles will adapt to the extreme conditions. Such is the case with some bacteria, shrimp or mollusks that managed to find a way to survive off of the methane, which is quite abundant in the area. The bacteria get the necessary energy from it through a process called chemosynthesis and then pass it on through symbiosis, which means they rely only on chemical energy instead of solar energy, like the other ecosystems on Earth.

A fifth of Florida’s pumas were killed in car collisions

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There are less than 100 pumas left in Florida’s wilds, and 17 were killed in collisions with cars, which is even more than in 2008 (when 10 such magnificent creatures found their death after being hit by a car) and 2007 (15). For me, it’s absolutely heart breaking to see this happening.

You’d expect people to learn, after panther numbers were down to just 20-30 in 1990. It took some serious efforts to raise their numbers by almost 10 times, but the future is once again looking dire for the felines.

florida_panther_with_cub

“If we don’t do something quickly to reduce the risks to Florida’s panthers as they move around in search of food, mates and territory, then we are facing loss of this iconic species,” said a member from Defenders of Wildlife. “The panther found dead yesterday should serve as a sobering reminder that we all have to do our part to protect the Florida panther and watch out for wildlife while we drive through their habitat.”

They also proposed some good ideas on how this could be stopped, which you can read on their site.

The symphony of science

I was quite stunned to stumble across this video. As the name says, it’s a… well it’s not quite a symphony, but it’s definitely musical, and you can definitely learn a lot of things, or re-hear them in an unique way, if you already know them. Did I mention it’s featuring Carl Sagan, Richard Feynman, Neil deGrasse Tyson & Bill Nye?

LATER EDIT

This following video was published just a few hours ago and… it’s even better than the first one!

Huge dust storm chokes Sydney

 

A significant part of Australia’s east coast, including country’s biggest city, Sydney, has been engulfed by a shroud of red dust blown mostly from the desert outback. Visibility was so bad that most if not all flights were delayed, and of course, there were the usual folks who started screaming that this is the apocalypse. Turns out, it wasn’t.

Photo by Merbabu.

Numerous buildings, including the famous Opera House were covered in a thick blanket of dust and people took cover in their houses or nearby buildings. Lots of folks took to wearing masks and the emergency service reported a huge number of people who came in with respiratory problems. The transportation system was crippled also and doctors warned especially children and elder people to stay indoor until the storm passed, and even a few hours after that.

On Wednesday morning, powerful winds generated by a major cold air front transported tons and tons of dust from the drought plagued outback and brought it into the city. Dust storms are not really that uncommon, but they rarely take place somewhere else than the desert (or nearby areas); also, the pollution levels from the air were the highest recorded ever, with the 15,500 micrograms of particles per cubic meter generating a Mars-like landscape.

“On a clear day the readings for particulate matter or PM10 is around 10-20 micrograms per cubic meter,” said Chris Eiser of the NSW department of the environment. “During a bushfire, when there is heavy smoke around, we might see readings of around 300 to 500 micrograms per cubic meter.”

 

Locals described waking up to the storm as waking up on Mars, or even yet, in the middle of the apocalypse. The sky was soaked in red, the wind was blowing strongly and the whole scenery was somewhere between eerie and downright scary. They weren’t really as dangerous as they seemed, but they could do a significant amount of damage to one’s health.

“Dust storms are particularly hazardous for anyone with chronic lung disease or sinus disease. Once the particles per cubic metre are above 300, dust storms pose a risk to lung health,” said Dr Phillip Thompson of the University of Western Australia.

Here’s a video and some pics.

Dust storm Sydney 23 September 2009

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Pics via The Guardian

6 deadliest volcano eruptions

Volcanic eruptions are impressive natural phenomena; it begins when pressure on a magma chamber forces magma up through the conduit and out the volcano’s vents. Seen on the TV or in the newspaper, they’re just fantastic and gorgeous. But if you’re unlucky enough to be there… it’s really deadly. But volcanic ash can also bring a new beginning, aiding nature to grow even bigger and stronger than before. But the lives lost are forever gone. Here’s a sum of the world’s 6 deadliest volcano eruptions, in terms of human live loss – for both direct and indirect causes.

6. Laki, Iceland; year: 1783; 9,350 deaths, caused mostly by starvation

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5. Unzen, Japan; year: 1792; 14,300 deaths, caused mostly by the volcano collapsing.

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