The Enodoc

Rise and fall of the Great Barrier Reef

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A landmark international study of the Great Barrier Reef has shown that in the past 30,000 years the world’s largest reef system has suffered five death events, largely driven by changes in sea level and associated environmental change.

Over millennia, the reef has adapted to sudden changes in environment by migrating across the sea floor as the oceans rose and fell.

The study by University of Sydney’s Associate Professor Jody Webster, is the first of its kind to reconstruct the evolution of the reef over the past 30 millennia in response to major, abrupt environmental change.

The 10-year, multinational effort has shown the reef is more resilient to major environmental changes such as sea-level rise and sea-temperature change than previously thought but also showed a high sensitivity to increased sediment input and poor water quality.

Associate Professor Webster from the University’s School of Geosciences and Geocoastal Research Group said it remains an open question as to whether its resilience will be enough for it to survive the current worldwide decline of coral reefs.

“Our study shows the reef has been able to bounce back from past death events during the last glaciation and deglaciation,” he said. “However, we found it is also highly sensitive to increased sediment input, which is of concern given current land-use practices.”

The study used data from geomorphic, sedimentological, biological and dating information from fossil reef cores at 16 sites at Cairns and Mackay.

The study covers the period from before the “Last Glacial Maximum” about 20,000 years ago when sea levels were 118 metres below current levels.

History of death events

As sea levels dropped in the millennia before that time, there were two widespread death events (at about 30,000 years and 22,000 years ago) caused by exposure of the reef to air, known as subaerial exposure. During this period, the reef moved seaward to try to keep pace with the falling sea levels.

During the deglaciation period after the Last Glacial Maximum, there were a further two reef-death events at about 17,000 and 13,000 years ago caused by rapid sea level rise. These were accompanied by the reef moving landward, trying to keep pace with rising seas.

Analysis of the core samples and data on sediment flux show these reef-death events from sea-level rise were likely associated with high increases in sediment.

The final reef-death event about 10,000 years ago, from before the emergence of the modern reef about 9000 years ago, was not associated with any known abrupt sea-level rise or “meltwater pulse” during the deglaciation. Rather it appears to be associated with a massive sediment increase and reduced water quality alongside a general rise in sea level.

The authors propose that the reef has been able to re-establish itself over time due to continuity of reef habitats with corals and coralline-algae and the reef’s ability to migrate laterally at between 0.2 and 1.5 metres a year.

Future survival

However, Associate Professor Webster said it was unlikely that this rate would be enough to survive current rates of sea surface temperature rises, sharp declines in coral coverage, year-on-year coral bleaching or decreases in water quality and increased sediment flux since European settlement.

“I have grave concerns about the ability of the reef in its current form to survive the pace of change caused by the many current stresses and those projected into the near future,” he said.

Associate Professor Webster said previous studies have established a past sea surface temperature rise of a couple of degrees over a timescale of 10,000 years. However, current forecasts of sea surface temperature change are around 0.7 degrees in a century.

“Our study shows that as well as responding to sea-level changes, the reef has been particularly sensitive to sediment fluxes in the past and that means, in the current period, we need to understand how practices from primary industry are affecting sediment input and water quality on the reef,” he said.

French bulldogs at risk of various health problems

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French Bulldogs, predicted soon to become the most popular dog breed in the UK, are vulnerable to a number of health conditions.

Researchers at The Royal Veterinary College (RVC), UK found that the most common issues in French Bulldogs over a one year period were ear infections, diarrhea and conjunctivitis (inflammation of the eye surface).

Dr. Dan O’Neill, RVC Senior Lecturer and the main author, said: “French Bulldogs are a relatively new arrival to the list of common UK breeds so there is very little current research on them in the UK. Our study — the first on this breed in the UK — is based on anonymised records gathered from hundreds of UK vet clinics. It provides owners with information on the issues that they could expect and should look out for in French Bulldogs. It may also help potential new owners to decide if a French Bulldog really is for them.”

Dr. O’Neill adds: “One of the interesting finding from our research is that male French Bulldogs appear to be less healthy than females. Males were more likely to get 8 of the 26 most common health problems while there were no issues that females were more likely to get than males.”

The authors suggest that the distinctive appearance of the French Bulldog, with their short muzzles and wide, prominent eyes, may be a key factor influencing their popularity. However, these characteristics may also increase the risk for some of the health problems seen in French Bulldogs. For example breathing issues, seen in 12.7% of the dogs in this study, are a known problem in breeds with short noses and flat faces. Skin problems overall were the most common group of health issues and the authors suggest that this may be due to the skin folds that are characteristic of the breed.

Dr. O’Neill said: “This study also documents the dramatic rise in popularity of the French Bulldog, from 0.02% of puppies born in 2003 to 1.46% of puppies born in 2013. This level of population growth in a single dog breed is unprecedented. There is a worry that increased demand for the French Bulldog is damaging to these dogs’ welfare because of the health risks associated with their extreme physical features.”

The authors analyzed data on 2,228 French Bulldogs under veterinary care during 2013 from 304 UK clinics, collected in the VetCompass™ database. The French Bulldogs had a median age of 1.3 years old compared to a median age of 4.5 years for the other dog breeds in the VetCompass™ database. This reflects the growth in popularity of French Bulldogs.

The authors caution that the study may even under-estimate the true number of dogs with health problems as the data may include more severely affected animals that require veterinary management. Additionally, as French Bulldogs have only recently become popular the data was mostly collected from young dogs and it is well recognized that health problems generally become more common with age.

Swirling liquids work similarly to bitcoin

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Fluid dynamics is not something that typically comes to mind when thinking about bitcoin. But for one Stanford physicist, the connection is as simple as stirring your coffee.

 Stanford applied physics doctoral student William Gilpin described how swirling liquids, such as coffee, follow the same principles as transactions with cryptocurrencies such as bitcoin. This parallel between the mathematical functions governing cryptocurrencies and natural, physical processes may help in developing more advanced digital security and in understanding physical processes in nature.

“Having an actual physical model and showing that this is a naturally occurring process might open up new ways to think about those functions,” Gilpin said.

Tangible transformations

Cryptocurrencies like bitcoin work in mysterious ways on purpose. As a virtual currency, it isn’t protected or controlled by any central group. Instead, cryptocurrencies exchange and secure information through a mathematical function called a cryptographic hash — a modern workhorse for cybersecurity. These functions mathematically transform digital information into a unique output that disguises the input.

Hash functions are deliberately designed to be complex, but they also remain consistent so that the same input always produces the same output. However, two similar inputs will likely produce very different outputs. These functions make it easy for computers to track cryptocurrencies but hard for hackers to do the same.

As a physicist, Gilpin said he saw similarities between the way hash functions work and the physical laws involved with stirring a liquid. “I figured there’s probably some analogy there that was worth looking into,” he said. And, with a few weeks free during a winter break he decided to explore his idea.

Gilpin focused on a principle called chaotic mixing, which describes the action of mixing a fluid. Imagine stirring coffee creamer into a mug of black coffee and watching the creamer separate into a swirling pattern. If the creamer were stirred precisely the same way in the future, the same pattern would result. But even the smallest change in the location of the spoon or the speed of the stir results in a very different pattern. In other words, each initial stir produces a unique swirl signature.

Additionally, just looking at the resulting pattern of the creamer in the coffee doesn’t reveal anything about the original action — where the spoon was, how fast it moved, or how many circles — similar to the way a hash function transforms information so that the input is impossible to identify.

Gilpin decided to put the chaotic-mixing-of-fluids example to the test as a hash function. He found that the equations involved in mixing a fluid fit the requirements for hash functions almost perfectly. “I wasn’t expecting it to perform that well,” he said. “When it looked like it satisfied every property of a hash function I started getting really excited. It suggests that there’s something more fundamental going on with how chaotic math is acting.”

Outside the box

Modern hash functions are an ongoing area of research, as cryptocurrencies and similar applications such as digital signatures are becoming increasingly common for credit card transactions and legal documents. Gilpin suspects the parallel between the fields of computer science and applied physics could help in creating even more secure ways of protecting digital information.

This connection can also help validate precise procedures, such as those used in drug development, said Gilpin. Certain drug development methods require injecting various fluids at specific points in time, similar to the way a hash function performs a precise order of equations. “If you don’t form the correct arrangement when you’re done, then you know that one of your processes didn’t go right,” he said. “The chaotic property ensures that you’re not going to accidentally get a final product that looks correct.”

The discovery also suggests that cryptographic, presumably human-devised computations are not unique to the digital realm. “Something as ordinary as a fluid is still performing computations,” said Gilpin. “It’s not something only humans tell computers to do. It’s something that nature does and it shows up in the structure of how things form.”

Gilpin isn’t a computer scientist or drug developer himself. When he’s not connecting the digital and physical fields, he studies the way fluids work in nature with Manu Prakash, an assistant professor of bioengineering. So for him, “the idea that we can start to use some of these ideas from computer science is pretty exciting.”

Meteorite diamonds tell of a lost planet

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Using transmission electron microscopy, EPFL scientists have examined a slice from a meteorite that contains large diamonds formed at high pressure. The study shows that the parent body from which the meteorite came was a planetary embryo of a size between Mercury to Mars.

On October 7, 2008, an asteroid entered Earth’s atmosphere and exploded 37 km above the Nubian Desert in Sudan. The asteroid, now known as “2008 TC3,” was just over four meters in diameter. When it exploded in the atmosphere, it scattered multiple fragments across the desert. Only fifty fragments, ranging in size from 1-10 cm, were collected, for a total mass of 4.5 kg. Over time, the fragments were gathered and catalogued for study into a collection named Almahata Sitta (Arabic for “Station Six,” after a nearby train station between Wadi Halfa and Khartoum).

The Almahata Sitta meteorites are mostly ureilites, a rare type of stony meteorite that often contains clusters of nano-sized diamonds. Current thinking is that these tiny diamonds can form in three ways: enormous pressure shockwaves from high-energy collisions between the meteorite “parent body” and other space objects; deposition by chemical vapor; or, finally, the “normal” static pressure inside the parent body, like most diamonds on Earth.

The unanswered question, so far, has been the planetary origin of 2008 TC3 ureilites. Now, scientists at Philippe Gillet’s lab at EPFL, with colleagues in France and Germany, have studied large diamonds (100-microns in diameter) in some of the Almahata Sitta meteorites and discovered that the asteroid came from a planetary “embryo” whose size is between Mercury to Mars.

The researchers studied the diamond samples using a combination of advanced transmission electron microscopy techniques at EPFL’s Interdisciplinary Centre for Electron Microscopy. The analysis of the data showed that the diamonds had chromite, phosphate, and iron-nickel sulfides embedded in them — what scientists refer to as “inclusions.” These have been known for a long time to exist inside Earth’s diamonds, but are now described for the first time in an extraterrestrial body.

The particular composition and morphology of these materials can only be explained if the pressure under which the diamonds were formed was higher than 20 GPa (giga-Pascals, the unit of pressure). This level of internal pressure can only be explained if the planetary parent body was a Mercury- to Mars-sized planetary “embryo,” depending on the layer in which the diamonds were formed.

Many planetary formation models have predicted that these planetary embryos existed in the first million years of our solar system, and the study offers compelling evidence for their existence. Many planetary embryos were Mars-sized bodies, such as the one that collided with Earth to give rise to the Moon. Other of these went on to form larger planets, or collided with the Sun or were ejected from the solar system altogether. The authors write “This study provides convincing evidence that the ureilite parent body was one such large ‘lost’ planet before it was destroyed by collisions some 4.5 billion years ago.”

Soft robots that mimic human muscles

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Robots are usually expected to be rigid, fast and efficient. But researchers at EPFL’s Reconfigurable Robotics Lab (RRL) have turned that notion on its head with their soft robots.

Soft robots, powered by muscle-like actuators, are designed to be used on the human body in order to help people move. They are made of elastomers, including silicon and rubber, and so they are inherently safe. They are controlled by changing the air pressure in specially designed ‘soft balloons’, which also serve as the robot’s body. A predictive model that can be used to carefully control the mechanical behavior of the robots’ various modules has just been

Potential applications for these robots include patient rehabilitation, handling fragile objects, biomimetic systems and home care. “Our robot designs focus largely on safety,” said Jamie Paik, the director of the RRL. “There’s very little risk of getting hurt if you’re wearing an exoskeleton made up of soft materials, for example” she added.

A model for controlling the actuators

In their article, the researchers showed that their model could accurately predict how a series of modules composed of compartments and sandwiched chambers  moves. The cucumber-shaped actuators can stretch up to around five or six times their normal length and bend in two directions, depending on the model.

“We conducted numerous simulations and developed a model for predicting how the actuators deform as a function of their shape, thickness and the materials they’re made of,” said Gunjan Agarwal, the article’s lead author.

One of the variants consists of covering the actuator in a thick paper shell made by origami. This test showed that different materials could be used. “Elastomer structures are highly resilient but difficult to control. We need to be able to predict how, and in which direction, they deform. And because these soft robots are easy to produce but difficult to model, our step-by-step design tools are now available online for roboticists and students.”

A rehabilitation belt

In addition to these simulations, other RRL researchers have developed soft robots for medical purposes. This work is described in Soft Robotics. One of their designs is a belt made of several inflatable components, which holds patients upright during rehabilitation exercises and guides their movements.

“We are working with physical therapists from the University Hospital of Lausanne (CHUV) who are treating stroke victims,” said Matthew Robertson, the researcher in charge of the project. “The belt is designed to support the patient’s torso and restore some of the person’s motor sensitivity.”

The belt’s soft actuators are made of pink rubber and transparent fishing line. The placement of the fishing line guides the modules’ deformation very precisely when air is injected. “For now, the belt is hooked up to a system of external pumps. The next step will be to miniaturize this system and put it directly on the belt,” said Robertson.

Adaptable and reconfigurable robots

Potential applications for soft actuators don’t stop there. The researchers are also using them to develop adaptable robots that are capable of navigating around in cramped, hostile environments. And because they are completely soft, they should also be able to withstand squeezing and crushing.

“Using soft actuators, we can come up with robots of various shapes that can move around in diverse environments,” said Paik. “They are made of inexpensive materials, and so they could easily be produced on a large scale. This will open new doors in the field of robotics.”

Gold nanoparticles show promise for early detection of heart attacks

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The endoc
early detection of heart attacks

NYU Polytechnic School of Engineering professors have been collaborating with researchers from Peking University on a new test strip that is demonstrating great potential for the early detection of certain heart attacks. Kurt H. Becker, a professor in the Department of Applied Physics and the Department of Mechanical and Aerospace Engineering, and WeiDong Zhu, a research associate professor in the Department of Mechanical and Aerospace Engineering, are helping develop a new colloidal gold test strip for cardiac troponin I (cTn-I) detection. The new strip uses microplasma-generated gold nanoparticles (AuNPs) and shows much higher detection sensitivity than conventional test strips. The new cTn-I test is based on the specific immune-chemical reactions between antigen and antibody on immunochromatographic test strips using AuNPs.
Compared to AuNPs produced by traditional chemical methods, the surfaces of the gold nanoparticles generated by the microplasma-induced liquid chemical process attract more antibodies, which results in significantly higher detection sensitivity.
cTn-I is a specific marker for myocardial infarction. The cTn-I level in patients experiencing myocardial infarction is several thousand times higher than in healthy people. The early detection of cTn-I is therefore a key factor of heart attack diagnosis and therapy.
The use of microplasmas to generate AuNP is yet another application of the microplasma technology developed by Becker and Zhu. Microplasmas have been used successfully in dental applications (improved bonding, tooth whitening, root canal disinfection), biological decontamination (inactivation of microorganisms and biofilms), and disinfection and preservation of fresh fruits and vegetables.
The microplasma-assisted synthesis of AuNPs has great potential for other biomedical and therapeutic applications such as tumor detection, cancer imaging, drug delivery, and treatment of degenerative diseases such as Alzheimer’s.
The routine use of gold nanoparticles in therapy and disease detection in patients is still years away: longer for therapeutic applications and shorter for biosensors. The biggest hurdle to overcome is the fact that the synthesis of monodisperse, size-controlled gold nanoparticles, even using microplasmas, is still a costly, time-consuming, and labor-intensive process, which limits their use currently to small-scale clinical studies, Becker explained.