Tag Archives: open access paper

Open Science: Looking at Dust

Open access paper: Migration of Contaminated Soil and Airborne Particulates to Indoor Dust.

Indoor dust is a mixture of soil tracked into a residence, particulate matter derived from ambient outdoor air, and importantly, organic matter. Indoor dust is about 40% organic matter by weight in residential housing. Particles tracked into a residence are redistributed on floor surfaces account for over 60% of the dust mass on floors.

White Paper on Engineering Leadership Education

Engineering leadership education is emerging as a topic in engineering institutions worldwide. But the review of international “best practices” in engineering leadership education says a lack of resources, expertise, and formal networks in the nascent field is causing concern in a profession threatened by a diminishing focus on the notion of the “engineer-as-doer.”

Commissioned by the Bernard M. Gordon-MIT Engineering Leadership Program, the new white paper, Engineering Leadership Education: A Snapshot”© Review”© of International Good”© Practice, reveals that the vast majority of engineering leadership education programs are based within the U.S. and most are relatively new (developed in the last five years). The white paper highlights the distinct divide between the U.S. and the rest of the world in both attitude and approach to engineering leadership education.

“As a sub-discipline, engineering leadership education is not yet on the radar of most engineering education experts outside the U.S.,” said Dr. Edward Crawley, Director of the Bernard M. Gordon-MIT Engineering Leadership Program. “Certainly for many of the programs outside the U.S., there’s some discomfort with the notion of ‘leadership education’, as they feel this concept runs counter to their educational culture of inclusiveness and equality.”

The report was conducted by Dr. Ruth Graham in a series of interviews between September 2008 and March 2009. Dr. Graham investigated more than 40 programs, seeking to provide an insight into current practice, highlight international variations in approach, and identify examples of good practice.

One major ”©current ”©trend”© in ”©engineering”© leadership ”©education”© is ”©the ”©development ”©of”© the ”©students’”© global ”©awareness”© and”© their ”©ability ”©to ”©work ”©on ”©complex”©cross”national”© projects”© – ”©which”© is”© seen ”©by many”© as”© the ”©environment”© within ”©which”© the”© engineering ”©leader”© of ”©the ”©future ”©will ”©need ”©to ”©operate. ”©
Many”© of ”©the ”©programs ”©which ”©were ”©most ”©highly ”©rated ”©by ”©interviewees ”©incorporate ”©some”© global”© elements ”©either ”©through ”©international ”©travel, ”©remote”© link”ups”© with”© overseas”© universities/companies ”©or ”©project”© briefs”© involving ”©an”© international ”©or”© cross”cultural”© context.”© ”©The trend ”©towards”© a ”©more”© ‘global’ ”©view”© of ”©leadership ”©education”© was ”©seen ”©by ”©many ”©of ”©the”© interviewees”© as”© one”© that ”©would”© continue.”©
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Smokers with High Blood Pressure and High Cholesterol Lose 10 Years

By examining data from the Whitehall Study researchers have found smokers with high blood pressure and high cholesterol in middle age died 10 years earlier than the others after reaching age 50. This is independent of changes after later in life (quiting smoking, etc.). Life expectancy in relation to cardiovascular risk factors: 38 year follow-up of 19,000 men in the Whitehall study

At entry, 42% of the men were current smokers, 39% had high blood pressure, and 51% had high cholesterol. At the re-examination, about two thirds of the previously “current” smokers had quit smoking shortly after entry and the mean differences in levels of those with high and low levels of blood pressure and cholesterol were attenuated by two thirds. Compared with men without any baseline risk factors, the presence of all three risk factors at entry was associated with a 10 year shorter life expectancy from age 50 (23.7 v 33.3 years). Compared with men in the lowest 5% of a risk score based on smoking, diabetes, employment grade, and continuous levels of blood pressure, cholesterol concentration, and body mass index (BMI), men in the highest 5% had a 15 year shorter life expectancy from age 50 (20.2 v 35.4 years).

Conclusion Despite substantial changes in these risk factors over time, baseline differences in risk factors were associated with 10 to 15 year shorter life expectancy from age 50.

Another conclusion: if you don’t want to live a shorter life, don’t smoke. Not a new idea but given how many people continue to smoke it seems some don’t understand this conclusion.

Albert Einstein, Marilyn Monroe Hybrid Image

This image looks like Albert Einstein up close. If you back up maybe 3-5 meters it will look like Marilyn Monroe. Image by Dr. Aude Oliva.

Hybrid images paper by Aude Oliva, MIT; Antonio Torralba, MIT; and Philippe G. Schyns University of Glasgow.

We present hybrid images, a technique that produces static images with two interpretations, which change as a function of viewing distance. Hybrid images are based on the multiscale processing of images by the human visual system and are motivated by masking studies in visual perception. These images can be used to create
compelling displays in which the image appears to change as the viewing distance changes. We show that by taking into account perceptual grouping mechanisms it is possible to build compelling hybrid images with stable percepts at each distance.
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Hybrid images, however, contain two coherent global image interpretations, one of which is of the low spatial frequencies, the other of high spatial frequencies.
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For a given distance of viewing, or a given temporal frequency a particular band of spatial frequency dominates visual processing. Visual analysis of the hybrid image still unfolds from global to local perception, but within the selected frequency band, for a given viewing distance, the observer will perceive the global structure of the hybrid first, and take an additional hundred milliseconds to organize the local information into a coherent percept (organization of blobs if the image is viewed at a far distance, or organization of edges for close viewing).

Very cool stuff.

This is just a smaller image of the above (all I did was shrink the size). For me, this already looks like Marilyn Monroe, but also needs a shorter distance to see the image seem to change.

USA Losing Scientists and Engineers Educated in the USA

The USA continues to lose ground, in retaining the relative science and engineering strength it has retained for the last 50 plus years. As I have said before this trend is nearly inevitable – the challenge for the USA is to reduce the speed of their decline in relative position.

A new open access report, Losing the World’s Best and Brightest, explores the minds of current foreign science and engineering students that are studying in the USA. This is another in the list of reports on similar topics by Vivek Wadhwa and Richard Freeman. And again they point out the long term economic losses the USA is setting up by failing to retain the talent trained at our universities. It is a problem for the USA and a great benefit for countries like India and China.

“Foreign students receive nearly 60% of all engineering doctorates and more than half of all mathematics, computer sciences, physics and economics doctorates awarded in the United States. These foreign nationals end up making jobs, not taking jobs,” said Wadhwa. “They bring insights into growing global markets and fresh ideas. Research has shown that they even end up boosting innovation by U.S. inventors. Losing them is an economic tragedy.”

According to the study’s findings, very few foreign students would like to stay in the United States permanently—only 6% of Indian, 10 percent of Chinese and 15% of Europeans. And fewer foreign students than the historical norm expressed interest in staying in the United States after they graduate. Only 58% of Indian, 54% of Chinese and 40% of European students wish to stay for several years after graduation. Previous National Science Foundation research has shown 68% of foreigners who received science and engineering doctorates stayed for extended periods of time, including 73% of those who studied computer science. The five-year minimum stay rate was 92% for Chinese students and 85% for Indian students.

The vast majority of foreign student and 85% of Indians and Chinese and 72% of Europeans are concerned about obtaining work visas. 74% of Indians, 76% of Chinese, and 58% of Europeans are also worried about obtaining jobs in their fields. Students appear to be less concerned about getting permanent-resident visas than they are about short-term jobs. Only 38% of Indian students, 55% of Chinese, and 53% of Europeans expressed concerns about obtaining permanent residency in the USA.

On the tonight show yesterday, President Obama said

we need young people, instead of — a smart kid coming out of school, instead of wanting to be an investment banker, we need them to decide they want to be an engineer, they want to be a scientist, they want to be a doctor or a teacher.

And if we’re rewarding those kinds of things that actually contribute to making things and making people’s lives better, that’s going to put our economy on solid footing. We won’t have this kind of bubble-and-bust economy that we’ve gotten so caught up in for the last several years.

Eric Schmidt, Google CEO, recently expressed his frustration with the policies discouraging science and engineering graduates staying in the USA after they complete their education.

That is a brilliant [actually not brilliant at all] strategy take the best people hire them in American universities and then kick them out” It happens. “Its shocking.” It happens. “I know we are fighting against it.” “We America remain, by far the place of choice for education, particularly higher education.”

Resurrection of the Human IRGM Gene

Interesting open access paper on Death and Resurrection of the Human IRGM Gene. Author summary:

The IRG gene family plays an important role in defense against intracellular bacteria, and genome-wide association studies have implicated structural variants of the single-copy human IRGM locus as a risk factor for Crohn’s disease. We reconstruct the evolutionary history of this region among primates and show that the ancestral tandem gene family contracted to a single pseudogene within the ancestral lineage of apes and monkeys.

Phylogenetic analyses support a model where the gene has been “dead” for at least 25 million years of human primate evolution but whose ORF became restored in all human and great ape lineages. We suggest that the rebirth or restoration of the gene coincided with the insertion of an endogenous retrovirus, which now serves as the functional promoter driving human gene expression. We suggest that either the gene is not functional in humans or this represents one of the first documented examples of gene death and rebirth.

Open Science: Explaining Spontaneous Knotting

Shedding light on why long strands tend to become knotted

Anyone who has ever put up Christmas lights knows the problem: Holiday strands so carefully packed away last year are now more knotty than nice. In fact, they have become an inextricable, inexplicable, seemingly inevitable mess. It happens every year, like some sort of universal law of physics.

Which, it turns out, it basically is. In October, two UCSD researchers published the first physical explanation of why knots seem to form magically, not just in strands of Christmas lights, but in pretty much anything stringy, from garden hoses to iPod earbud cords to DNA.
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“We’re not mathematicians,” Smith said. “We’re physicists. Physicists do experiments.”

UCSD researchers constructed a knot probability machine that involved placing a single length of string in a plastic box, sealing it, then rotating the box at a set speed for a brief period of time.
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The experiment involved placing a single length of floppy string into a plastic box, sealing it, then rotating the box at a set speed for a brief time. The researchers did this 3,415 times, sometimes changing variables such as box size and string length.

Open access research paper: Spontaneous knotting of an agitated string by Dorian M. Raymer and Douglas E. Smith.

Above a critical string length, the probability P of knotting at first increased sharply with length but then saturated below 100%. This behavior differs from that of mathematical self-avoiding random walks, where P has been proven to approach 100%. Finite agitation time and jamming of the string due to its stiffness result in lower probability, but P approaches 100% with long, flexible strings.
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As L [length] was increased from 0.46 to 1.5 m, P increased sharply. However, as L was increased from 1.5 to 6 m, P saturated at 50%.
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Tripling the agitation time caused a substantial increase in P, indicating that the knotting is kinetically limited. Decreasing the rotation rate by 3-fold while keeping the same number of rotations caused little change in P.
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We also did measurements with a stiffer string and observed a probability of finding a knot would approach 100% with an substantial drop in P.

Yet another interesting case of scientists explaining the world around us (and the value of open science).

Dolphins Using Tools to Hunt

photo of a dolphin with a sponge it uses to hunt

Photograph of dolphin with a sponge it uses to hunt, courtesy of Ewa Krzyszczyk, PLoS, high resolution.

Cool open access research from PLoS One, Why Do Dolphins Carry Sponges?

Tool use is rare in wild animals, but of widespread interest because of its relationship to animal cognition, social learning and culture. Despite such attention, quantifying the costs and benefits of tool use has been difficult, largely because if tool use occurs, all population members typically exhibit the behavior. In Shark Bay, Australia, only a subset of the bottlenose dolphin population uses marine sponges as tools, providing an opportunity to assess both proximate and ultimate costs and benefits and document patterns of transmission.

We compared sponge-carrying (sponger) females to non-sponge-carrying (non-sponger) females and show that spongers were more solitary, spent more time in deep water channel habitats, dived for longer durations, and devoted more time to foraging than non-spongers; and, even with these potential proximate costs, calving success of sponger females was not significantly different from non-spongers. We also show a clear female-bias in the ontogeny of sponging. With a solitary lifestyle, specialization, and high foraging demands, spongers used tools more than any non-human animal. We suggest that the ecological, social, and developmental mechanisms involved likely (1) help explain the high intrapopulation variation in female behaviour, (2) indicate tradeoffs (e.g., time allocation) between ecological and social factors and, (3) constrain the spread of this innovation to primarily vertical transmission.

The dolphins use the sponge to push along the ocean floor and disturb fish, that are hidden. Once the fish start swimming away the dolphin abandons the sponge and catches and eats the fish. Then the dolphin goes back and gets the sponge and continues.

The Chip That Designs Itself

The chip that designs itself by Clive Davidson , 1998

Adrian Thompson, who works at the university’s Centre for Computational Neuroscience and Robotics, came up with the idea of self-designing circuits while thinking about building neural network chips. A graduate in microelectronics, he joined the centre four years ago to pursue a PhD in neural networks and robotics.
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To get the experiment started, he created an initial population of 50 random circuit designs coded as binary strings. The genetic algorithm, running on a standard PC, downloaded each design to the Field Programmable Gate Arrays (FPGA) and tested it with the two tones generated by the PC’s sound card. At first there was almost no evidence of any ability to discriminate between the two tones, so the genetic algorithm simply selected circuits which did not appear to behave entirely randomly. The fittest circuit in the first generation was one that output a steady five-volt signal no matter which tone it heard.

By generation 220 there was some sign of improvement. The fittest circuit could produce an output that mimicked the input – wave forms that corresponded to the 1KHz or 10KHz tones – but not a steady zero or five-volt output.

By generation 650, some evolved circuits gave a steady output to one tone but not the other. It took almost another 1,000 generations to find circuits that could give approximately the right output and another 1,000 to get accurate results. However, there were still some glitches in the results and it took until generation 4,100 for these to disappear. The genetic algorithm was allowed to run for a further 1,000 generations but there were no further changes.

See Adrian Thompson’s home page (Department of Informatics, University of Sussex) for more on evolutionary electronics. Such as Scrubbing away transients and Jiggling around the permanent: Long survival of FPGA systems through evolutionary self-repair:

Mission operation is never interrupted. The repair circuitry is sufficiently small that a pair could mutually repair each other. A minimal evolutionary algorithm is used during permanent fault self-repair. Reliability analysis of the studied case shows the system has a 0.99 probability of surviving 17 times the mean time to local permanent fault arrival. Such a system would be 0.99 probable to survive 100 years with one fault every 6 years.

Very cool.

Related: Evolutionary Design – Invention Machine – Evo-Devo

Rat Brain Cells, in a Dish, Flying a Plane

Adaptive Flight Control With Living Neuronal Networks on Microelectrode Arrays (open access paper) by Thomas B. DeMarse and Karl P. Dockendorf Department of Biomedical Engineering, University of Florida

investigating the ability of living neurons to act as a set of neuronal weights which were used to control the flight of a simulated aircraft. These weights were manipulated via high frequency stimulation inputs to produce a system in which a living neuronal network would “learn” to control an aircraft for straight and level flight.

A system was created in which a network of living rat cortical neurons were slowly adapted to control an aircraft’s flight trajectory. This was accomplished by using high frequency stimulation pulses delivered to two independent channels, one for pitch, and one for roll. This relatively simple system was able to control the pitch and roll of a simulated aircraft.

When Dr. Thomas DeMarse first puts the neurons in the dish, they look like little more than grains of sand sprinkled in water. However, individual neurons soon begin to extend microscopic lines toward each other, making connections that represent neural processes. “You see one extend a process, pull it back, extend it out — and it may do that a couple of times, just sampling who’s next to it, until over time the connectivity starts to establish itself,” he said. “(The brain is) getting its network to the point where it’s a live computation device.”

To control the simulated aircraft, the neurons first receive information from the computer about flight conditions: whether the plane is flying straight and level or is tilted to the left or to the right. The neurons then analyze the data and respond by sending signals to the plane’s controls. Those signals alter the flight path and new information is sent to the neurons, creating a feedback system.

“Initially when we hook up this brain to a flight simulator, it doesn’t know how to control the aircraft,” DeMarse said. “So you hook it up and the aircraft simply drifts randomly. And as the data come in, it slowly modifies the (neural) network so over time, the network gradually learns to fly the aircraft.”

Although the brain currently is able to control the pitch and roll of the simulated aircraft in weather conditions ranging from blue skies to stormy, hurricane-force winds, the underlying goal is a more fundamental understanding of how neurons interact as a network, DeMarse said.