Mashing newspaper PDFs for ebooks with PdfMasher

 PdfMasher is a tool to convert PDF articles (newspaper, academic) to MOBI or EPUB documents. Most ebook readers support PDF files natively, but it's often a real pain to read those documents because we don't have font size control over the document like we have with native ebooks. In many cases, we have to use the zooming feature and it's just a pain. Another drawback of PDFs on ebook readers is that annotations are not supported.

There are already tools to convert PDFs to ebooks like Calibre, but what they do is that they try to guess the role of each piece of text in the PDF (and that's if you're lucky). I think that in all but the simplest cases, it's a mistake to think that anything short of an AI can do that kind of guessing.

Enter PdfMasher. PdfMasher asks the user about the role of each piece of text, and does it in an efficient manner. Your PDF has a header on each page and you don't want them to litter your text? Sort text elements by Y-position (thus grouping them all together), shift select the elements and flag them as ignored. They will not appear on your final HTML. Your PDF has footnotes on many pages? Sort your elements by text content (thus grouping all elements with the text starting with a number together) and flag them as footnotes. They will be moved to the end of the document, and PdfMasher will try to create hyperlinks to footnote references.

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Materials Tortured in Space

An ongoing experiment tests the mettle of glass and other materials

By Kaitlin Miller

High-energy radiation and atomic oxygen wreak havoc on satellite parts. To evaluate the durability of materials being developed for future satellites, the U.S. Naval Research Laboratory is running samples through a space-based torture test called MISSE-8. Astronauts bolted a platform full of one-inch samples of mirror coatings, laser-tuning crystals, structural foam and other materials to the outside of the International Space Station, where it will remain for just over two years. The samples, which were sent to the ISS on one of the last space shuttle flights, in May, will return to Earth in July 2013 on the SpaceX Dragon capsule. Scientists from the labs that made each sample will examine them for pitting, cracks and discolouration.

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Researchers Watch Type 1 Diabetes As It Unfolds, in Real Time

Video: Researchers Watch Type 1 Diabetes As It Unfolds, in Real Time

Real-time immune attack could pinpoint new interventions, thanks to a new procedure

By Rebecca Boyle

T Cells Attacking This image, captured from video, shows the T cells (purple dots) attacking the pancreatic islets (green images in center), which contain the insulin‑producing beta cells. Beta cell destruction leads to type 1 diabetes. The attack continues over several hours before a number of beta cells are destroyed. La Jolla Institute for Allergy & Immunology

A new real-time view of immune cells attacking the pancreas sheds light on how type 1 diabetes unfolds, as white blood cells seek out and destroy insulin-producing beta cells. Researchers believe it could help point the way to new intervention methods to halt the destruction before the onset of type 1 diabetes, also known as juvenile diabetes.

Diabetes results from the body’s lack of ability to produce sufficient insulin, which keeps blood glucose levels in check. Type 1 is an autoimmune disorder in which the body’s T lymphocytes attack and kill the pancreas’ insulin-making beta cells; type 2 also involves pancreatic destruction and can result from several factors, though in this country it is often the result of poor diet and obesity. There is no cure, at least not yet. Watching exactly how the destructive process unfolds could be a major step in that direction, however.

Researchers at the La Jolla Institute for Allergy & Immunology used two-photon excitation microscopy and a new imaging technique to access a live, functioning pancreas in a mouse. The pancreas is small, soft and tucked away beneath other organs in the abdominal area, so it’s difficult to see in action. This study marks the first time researchers have used two-photon microscopy to study the pancreas (it’s previously been used to image the liver, lymph nodes and some other organs).

Two-photon microscopes use ultra-fast pulses of infrared light to excite fluorescent dyes that have been attached to specific cells. The IR light minimizes light scattering as well as harmful bleaching of tissues, so it’s useful for penetrating deep into live tissue, around one millimeter.

Led by Ken Coppieters, now at Ghent University in Belgium, La Jolla researchers attached green and blue fluorescent proteins to cytotoxic T cells, a type of white blood cell, and transplanted them into a mouse. The cells migrated randomly throughout the pancreas, making their way to beta cells and eventually killing them. Though they moved in random patterns, the cells were observed to accumulate within and around the β cell population, the authors say. They moved at an average 10 microns per minute and up to 25 microns per minute — not the world’s fastest cells by a long stretch. This comparatively slow process could be one reason why diabetes takes a while to present itself clinically — by the time a patient is diagnosed, up to 90 percent of his or her beta cells have already been destroyed.

This entire cell-hunting process was imaged with the two-photon microscope, and you can see a video of it below. The live imaging of the white blood cells is “remarkable,” according to George Eisenbarth, M.D., a prominent type 1 diabetes researcher and executive director of the Barbara Davis Center for Childhood Diabetes in Denver.

“These images provide critical information about the disease process, in particular showing us the reasons why the beta cell destruction occurs very slowly over time,” he said in a statement. “Such information may enable new approaches to stop the destruction process, with the ultimate goal being prevention.”

Researchers are still not sure what sparks the immune cells into destroying the helpful beta cells. But this study could spark new research into that question, as well as how their destructive abilities might be thwarted, said Matthias von Herrath, M.D., coauthor of the paper.

“These studies suggest that we may need to find a way to prevent the T cells from accessing the pancreas in the first place, since once they do, they have the ability to destroy several beta cells at a time,” he said.

The paper appears in the Journal of Clinical Investigation.

[Eurekalert]

New insights into how the brain reconstructs the third dimension

This is a new illusion in which random noise (left) is made to look like a 3-D shape (right). Credit: MPI for Biological Cybernetics

A new visual illusion has shed light on a long-standing mystery about how the brain works out the 3-D shapes of objects.

As dizzying as it may sound, the impression that we are living in a 3D world is actually a continuous fabrication of our brains. When we look at things, the world gets projected onto the retina and information about the third dimension is lost — a bit like when a 3D object casts a shadow onto a flat, 2D wall. Somehow the brain is able to reconstruct the third dimension from the image, allowing us to experience a convincing 3D world. A team of scientists from Giessen University, Yale and the Max Planck Institute for Biological Cybernetics in Tübingen has recently discovered how cells in visual cortex might help solve this mystery. They created special 2D patterns designed to stimulate specific nerve cells when we look at them. They find that the result is a vivid illusion of 3D shape, which suggests these cells play an important role in reconstructing 3D shape.

"We created the images by taking random noise and smearing it out across the image in specific patterns. It's a bit like finger painting, except it's done by computer", explains Roland Fleming, Professor of Psychology at the University of Giessen. "The way the texture gets smeared out is not the way texture behaves in the real 3D world. But it allows us to selectively stimulate so-called 'complex cells' in visual cortex, which measure the local 2D orientation of patterns in the retinal image".

These cells — whose discovery led to a Nobel Prize for David Hubel and Torsten Wiesel – are often described as 'edge detectors' because they respond to boundaries or edges in the image. What was not known was that these cells could play a key role in estimating 3D shape.

"We asked people to adjust small probes to report what they saw. The settings allow us to reconstruct exactly which 3D shapes they perceived," says Heinrich Bülthoff, director of the department of Human Perception, Cognition and Action at the Max Planck Institute for Biological Cybernetics. "What's striking is how close the results are to predictions of a model based on cell responses".

The authors suggest the strongest evidence implicating the cells comes from an experiment in which participants stared at patterns for 30 seconds at a time, to change the way the cells respond. The resulting 'adaptation' causes random noise—which normally looks completely flat—to appear like a specific 3D shape.

"It's a kind of aftereffect, a bit like when you stare at a waterfall for a while, adaptation makes things that are stationary look like they are moving in the opposite direction. Except here, the aftereffect makes the noise look 3D," says Daniel Holtmann-Rice, who is currently doing his PhD at Yale University. "We didn't think it was going to work. It was so exciting to get the first data where we could clearly see the predicted shapes emerging in the participants' settings."

The authors are currently working on generalizing the findings to other kinds of information about 3D shape, such as shading and highlights.

More information: Fleming, RW, Holtmann-Rice D & HH Bülthoff Estimation of 3D shape from image orientations. PNAS, published ahead of print December 6, 2011, doi:10.1073/pnas.1114619109

 

Provided by Max-Planck-Gesellschaft

"New insights into how the brain reconstructs the third dimension." December 7th, 2011. http://medicalxpress.com/news/2011-12-insights-brain-reconstructs-dimension.html

 

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Robert Karl Stonjek

Measuring Living Cells' Mechanical Properties: Technology Could Diagnose Human Disease, Shed Light On Biological Processes

   This artist's conception depicts the use of an atomic force microscope to study the mechanical properties of cells, an innovation that might result in a new way to diagnose disease and study biological processes. Here, three types of cells are studied using the instrument: a rat fibroblast is the long slender cell in the center, an E coli bacterium is at the top right and a human red blood cell is at the lower left. The colored portions show the benefit of the new technique, representing the mechanical properties of the cells, whereas the gray portions represent what was possible using a conventional approach. (Credit: Purdue University image/Alexander Cartagena) 

Science Daily — Researchers are making progress in developing a system that measures the mechanical properties of living cells, a technology that could be used to diagnose human disease and better understand biological processes.

For example, the technique could be used to study how cells adhere to tissues, which is critical for many disease and biological processes; how cells move and change shape; how cancer cells evolve during metastasis; and how cells react to mechanical stimuli needed to stimulate production of vital proteins. The technique could be used to study the mechanical properties of cells under the influence of antibiotics and drugs that suppress cancer to learn more about the mechanisms involved.The team used an instrument called an atomic force microscope to study three distinctly different types of cells to demonstrate the method's potentially broad applications, said Arvind Raman, a Purdue University professor of mechanical engineering.

Findings have been posted online in the journal Nature Nanotechnology and will appear in the December print issue. The work involves researchers from Purdue and the University of Oxford.

"There's been a growing realization of the role of mechanics in cell biology and indeed a lot of effort in building models to explain how cells feel, respond and communicate mechanically both in health and disease," said Sonia Contera, a paper co-author and director of the Oxford Martin Programme on Nanotechnology and an academic fellow at Oxford physics. "With this paper, we provide a tool to start addressing some of these questions quantitatively: This is a big step."

An atomic force microscope uses a tiny vibrating probe to yield information about materials and surfaces on the scale of nanometers, or billionths of a meter. Because the instrument enables scientists to "see" objects far smaller than possible using light microscopes, it could be ideal for "mapping" the mechanical properties of the tiniest cellular structures.

"The maps identify the mechanical properties of different parts of a cell, whether they are soft or rigid or squishy," said Raman, who is working with doctoral student Alexander Cartagena and other researchers. "The key point is that now we can do it at high resolution and higher speed than conventional techniques."

The high-speed capability makes it possible to watch living cells and observe biological processes in real time. Such a technique offers the hope of developing a "mechanobiology-based" assay to complement standard biochemical assays.

"The atomic force microscope is the only tool that allows you to map the mechanical properties -- take a photograph, if you will -- of the mechanical properties of a live cell," Raman said.

However, existing techniques for mapping these properties using the atomic force microscope are either too slow or don't have high enough resolution.

"This innovation overcomes those limitations, mostly through improvements in signal processing," Raman said. "You don't need new equipment, so it's an economical way to bump up pixels per minute and get quantitative information. Most importantly, we applied the technique to three very different kinds of cells: bacteria, human red blood cells and rat fibroblasts. This demonstrates its potential broad utility in medicine and research."

The technique is nearly five times faster than standard atomic force microscope techniques.

The Nature Nanotechnology paper was written by Raman; Cartagena; Sonia Trigueros, a Senior Research Fellow in the Oxford Martin Programme on Nanotechnology; Oxford doctoral student Amadeus Stevenson; Purdue instructor Monica Susilo; Eric Nauman, an associate professor of mechanical engineering; and Contera.

The National Science Foundation and Engineering and Physical Sciences Research Council of the U.K. funded the research.

Oxidative Stress: Less Harmful Than Suspected?

                             Yellow light signals emitted by the biosensor indicate oxidant production in the tissue of a migrating fly larva. (Credit: Tobias Dick, German Cancer Research Center)

Science Daily  — Oxidative stress is considered to be involved in a multitude of pathogenic processes and is also implicated in the proces of aging. For the first time, scientists of the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) have been able to directly observe oxidative changes in a living organism. Their findings in fruit flies raise doubts about the validity of some widely held hypotheses: The research team has found no evidence that the life span is limited by the production of harmful oxidants.

For the first time, Tobias Dick and his co-workers have been able to observe these processes in a living animal. Jointly with Dr. Aurelio Teleman (also of DKFZ), they introduced genes for biosensors into the genetic material of fruit flies. These biosensors are specific for various oxidants and indicate the oxidative status of each cell by emitting a light signal -- in realtime, in the whole organism and across the entire life span.Arterial calcification and coronary heart disease, neurodegenerative diseases such as Parkinson's and Alzheimer's, cancer and even the aging process itself are suspected to be partially caused or accelerated by oxidative stress. Oxidative stress arises in tissues when there is an excess of what are called reactive oxygen species (ROS). "However, up to now, nobody was able to directly observe oxidative changes in a living organism and certainly not how they are connected with disease processes," said Associate Professor (PD) Dr. Tobias Dick of DKFZ. "There were only fairly unspecific or indirect methods of detecting which oxidative processes are really taking place in an organism."

In the fly larvae, the investigators already discovered that oxidants are produced at very differing levels in different tissue types. Thus, blood cells produce considerably more oxidants in their energy plants, the mitochondria, than, for example, intestinal or muscle cells. In addition, the larvae's behavior is reflected in the production of oxidants in individual tissues: The researchers were able to distinguish whether the larvae were eating or moving by the oxidative status of the fat tissue.

Up to now, many scientists have assumed that the aging process is associated with a general increase in oxidants throughout the body. However, this was not confirmed by the observations made by the investigators across the entire life span of the adult animals. They were surprised that almost the only age-dependent increase in oxidants was found in the fly's intestine. Moreover, when comparing flies with different life spans, they found out that the accumulation of oxidants in intestinal tissue even accelerated with a longer life span. The group thus found no evidence supporting the frequently voiced assumption that an organism's life span is limited by the production of harmful oxidants.

Even though comprehensive studies have failed to provide proof until the present day, antioxidants are often advertised as a protection against oxidative stress and, thus, health-promoting. Dick and colleagues fed their flies with N-acetyl cysteine (NAC), a substance which is attributed an antioxidant effect and which some scientists consider suitable for protecting the body against presumably dangerous oxidants. Interestingly, no evidence of a decrease in oxidants was found in the NAC-fed flies. On the contrary, the researchers were surprised to find that NAC prompted the energy plants of various tissues to significantly increase oxidant production.

"Many things we observed in the flies with the help of the biosensors came as a surprise to us. It seems that many findings obtained in isolated cells cannot simply be transferred to the situation in a living organism," said Tobias Dick, summarizing their findings. "The example of NAC also shows that we are currently not able to predictably influence oxidative processes in a living organism by pharmacology," he adds. "Of course, we cannot simply transfer these findings from fly to man. Our next goal is to use the biosensors to observe oxidative processes in mammals, especially in inflammatory reactions and in the development of tumors."

Why Does the Same Mutation Kill One Person but Not Another?

                           The figure shows how the same mutation can differently affect each individual from C. elegans. The dice represent the stochastic component in the gene expression. (Credit: Image courtesy of Centre for Genomic Regulation)

Science Daily — The vast majority of genetic disorders (schizophrenia or breast cancer, for example) have different effects in different people. Moreover, an individual carrying certain mutations can develop a disease, whereas another one with the same mutations may not. This holds true even when comparing two identical twins who have identical genomes. But why does the same mutation have different effects in different individuals?

Since the early twentieth century researchers have studied the role that genetic variability (mutations) and the environment (consumption habits, lifestyle, etc.) have in the development of diseases. "However, genetic and environmental differences are not enough" said Alejandro Burga, one of the authors of the article. "In the last decade we have learned by studying very simple organisms such as bacteria that gene expression -- the extent to which a gene is turned on or off -- varies greatly among individuals, even in the absence of genetic and environmental variation. Two cells are not completely identical and sometimes these differences have their origin in random or stochastic processes. The results of our study show that this type of variation can be an important influence the phenotype of animals, and that its measurement can help to reliably predict the chance of developing an abnormal phenotype such as a disease ."

The researchers conducted their study using the roundwormCaenorhabditis elegans as a model. Due to its simplicity, this microscopic worm is one of the most widely studied organisms in biology, and was the first animal to have its genome sequenced. Recently three different Nobel Prizes have been awarded for research using C. elegans.

Since the genetic composition and the environment are insufficient to determine whether or not a mutation will affect an individual, they developed a methodology to measure small differences in gene expression in vivo. "The challenge was not only to develop a method to quantify these small differences among individuals, but also to predict which genes are relevant for a particular mutation," adds Ben Lehner, coordinator of the study and ICREA Research Professor in the European Molecular Biology Laboratory-Centre for Genomic Regulation Systems Biology Research Unit. "In both round worms and humans, genes cooperate and help each other to perform functions within the cell. A few genes are very "generous" and help hundreds of others to perform many different processes, whereas others only help a few other genes to perform more specific functions. The key to predict what will happen in each individual is to measure variation in the expression of both types of gene."

The work suggests that, even if we completely understand all of the genes important for a particular human disease, we may never be able to predict what will happen to each person from their genome sequence alone. Rather, to develop personalised and predictive medicine it will also be necessary to consider the varying extent to which genes are turned on or off in each person.

The study was funded by the European Research Council, the Institució Catalana de recerca i Estudis Avanzats (ICREA) and the Ministry of Science and Innovation (MICINN).

Optical illusion reveals reflexes in the brain

New research by psychologists at Queen Mary, University of London has revealed that the way we see the world might depend on reflexes in the brain.

Writing in the Journal of Vision, Dr Michael Proulx from Queen Mary's School of Biological and Chemical Sciences, and former student Monique Green, explain how an optical illusion known as the Müller-Lyer Illusion captures our attention more strongly than other visual tests, suggesting that the brain calculates size as a reflex fast enough to guide where the eyes look.

The Müller-Lyer illusion was first described by F.C. Müller-Lyer in 1889, and is one of the most famous size illusions. He found that two lines of the same length can be seen as longer or shorter by simply adding arrow heads that point in or out at either end.

In this study, Dr Proulx and Green asked participants to search for a vertical line among distracting lines tilted to the left and right. All of the lines had arrow heads at either end that randomly pointed in or out, making some lines appear to be longer or shorter than others due to the illusion. They found that the line that appeared to be the longest captured the participants' attention the most.

Dr Proulx explains: "The surprising difference here is that the perceived longer line not only captured their attention, but was even more distracting than the sudden appearance of something new as shown in prior research.

"This suggests that many visual illusions might be so effective because they tap into how the human brain reflexively processes information."

Reflexes are immediate and involuntary responses that allow a quick reaction, such as pulling your hand away from a hot surface.

Dr Proulx adds: "If an illusion can capture attention in this way, then this suggests that the brain processes these visual clues rapidly and unconsciously. This also suggests that perhaps optical illusions represent what our brains like to see."

The team hope that their findings can be used to help unlock clues about how the brain has evolved to not just represent the world as it is, but in a way that is most effective for survival. "A number of conditions exhibit differences in attention, such as Autism and schizophrenia, and it would be useful to see whether visual illusions are still given priority even when other aspects of attention are affected," adds Proulx.

Provided by Queen Mary, University of London

"Optical illusion reveals reflexes in the brain." December 7th, 2011. http://medicalxpress.com/news/2011-12-optical-illusion-reveals-reflexes-brain.html

 

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Robert Karl Stonjek

Men have a stronger reaction to seeing other men's emotions compared with women's

 

(Medical Xpress) -- Men have a stronger response to seeing other men show emotion than when women show emotion, according to new research from Queen Mary, University of London.

The study, published in the December issue of the journal Emotion, explored men and women’s responses to pictures of people expressing their emotions to work out what side of their brains elicited a response.

Lead author on the study, Dr. Qazi Rahman, from Queen Mary’s School of Biological and Chemical Sciences, said they found that men, in particular, use the right side of their brains to recognise emotion in other male faces.

He said: “When men were showed expressions of happiness, sadness and anger in other men, they responded with the right side of the brain whereas they used both sides of their brains more or less equally when looking at emotions in women's faces.”

The scientists showed almost 100 volunteers a range of different pictures of facial expressions, each had half a neutral expression and half an emotional expression.

“There was a very strong response from men when they saw other men expressing their emotion. The strongest response was when men were shown angry and surprised male faces. This could be because men might be more wired to notice expressions indicating vigilance or threat in other men compared with women,” Dr. Rahman said.

Expressions indicating vigilance or threat are known as ‘pop out’ emotions. The scientists anticipated a strong response to these types of emotions so the fact that the men’s response to expressions of surprise was strong, was not unexpected.

Dr. Rahman said: “We were a bit confused when men saw other male’s expressions of disgust, another ‘pop out’ emotion, that it did not elicit a strong response. It may be that disgust is a less important cue for men than surprise and could indicate ‘withdrawal’ which men may ignore.”

The research challenges the idea of simplistic sex differences in the brain, showing they are influenced by features of both the observer and the person being observed (in this case, sex of face and emotion displayed). The findings also challenge two theories explaining how emotions are organised in the brain, as Dr. Rahman explains.

“One theory argues that the right hemisphere of the brain deals with all emotions,” he said. “The other states that positive emotions are processed by the right hemisphere and negative emotions by the left. Our work suggest both theories are over-simplifications because they don’t take ‘the details’ into account, such as of the sex of the person who is showing that emotion.”

Provided by Queen Mary, University of London

"Men have a stronger reaction to seeing other men's emotions compared with women's." December 7th, 2011.http://medicalxpress.com/news/2011-12-men-stronger-reaction-emotions-women.html\

 

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Robert Karl Stonjek