Generating your publication list

It is often necessary to compile one's bibliography. For example to apply for a grant or a job. One approach is to keep a text file and update it as you publish. However, unstructured data is a pain to update when you fall behind, and you anyway already have your publications in your bibliography database. Is there a quick and simple way to generate a publication list?

For those using BibDesk to manage their bibliography, the answer is Jürgen Spitzmüller's biblatex-publist package. It generates correct citations leaving out your name, sorts them by date, and allows grouping by publication type.

In the preamble you just add three items:

• \usepackage[bibstyle=publist]{biblatex}
• \omitname[your first name]{your last name}
• \addbibresource{biblio.bib}

In the document part you just add a block like below for each publication type:

• \section{Patents}
• \begin{refsection}[biblio]
• \nocite{*}
• \printbibliography[heading=none, filter=mine, type=patent]
• \end{refsection}

The citation result will look like this when set into type:

Aug. 2006 (with Audrius J. Budrys). “Multi-component iconic representation of file characteristics”. 7,086,011. Hewlett-Packard Development Company.

If you are still using BibTeX, this is a good time to update your engine. BibTeX has been obsolete for many years and is no longer used these days. People now use biblatex, and publist is just a style file for biblatex. Actually, biblatex still uses BibTeX, so you want to switch your engine to Biber.

The make the switch, in the TexShop preferences go in the Engine tab and replace the BibTeX engine bibtex with biber. It may be necessary to run the TeX Live utility to update all the packages, as there has been a bug fix in the last week.

Extra tip: Option-Go to the folder ∼/Library/TeXShop/Engines/Inactive/Latexmk/ where you find the file Latexmk For TeXShop.pdf with the instructions on how to typeset your documents with a single mouse click.

Energy footprint of the digital economy

Back in 2009 we looked at the carbon footprint of ripping color documents for digital presses and published the result in the EI 2010 paper "Font rendering on a GPU-based raster image processor." Assuming the raster image processor is run at maximum capacity, the state of the art system at the time consumed 38,723 KWh and generated 23,234 Kg of CO₂. By using GPUs, we were able to rip the same data with 10,804 KWh respectively 6,483 Kg of CO₂. At the time we thought saving 16,751 Kg of CO₂ per year per RIP was a pretty cool result, but at the end the product never shipped, despite — or maybe because — it was much lower cost. (See the paper for the details of the calculations.)

This month the Digital Power Group published the white-paper "The cloud begins with coal: big data, big networks, big infrastructure, and big power." The work was sponsored by the National Mining Association and the American Coalition for Clean Coal Electricity, which explains why some of the numbers appear a little optimistic in terms of the coal needed to keep the smart phones running and serving contents, but even if we divide the numbers by 5 to make them a little more realistic, the numbers are quite staggering when we add everything up. It turns out, that a smart phone requires as much coal as a small refrigerator. Cloud computing will consume an ever increasing fraction of our total energy consumption. This is a good reason to work on more efficient and greener storage systems.

Data Privacy

During the ascent of Nazism in Europe in the decade before world war II, the Swiss banks introduced secret bank accounts to hide the identity of persecuted customers from infiltrated spies working at the banks or loitering in their lobbies. After the war, this mechanism was abused by the banks to assist tax evaders and consequently has been largely dismantled.

Apparently, the Swiss have been able to maintain their reputation as a discreet country. An echo effect of the leak of an American agency's penchant for snooping everybody's data, is that more entities are now storing their data in Switzerland, although data storage in Switzerland is about 25% more expensive than in the neighboring EU countries. "Our customers know that money can be replaced — but sensitive data can not," says Mateo Meier of Artmotion, a data center in Zürich. Switzerland's know-how, political stability and adequate infrastructure are ideal conditions to store data securely, he says.

History does not repeat itself, and the Swiss have learned from the mistakes related to bank secrecy: there are no privacy rights for suspected felons and their data.

Newspaper article: Schweizer Datentresore sind nicht sicher

Color can prevent shark attack

A Western Australian company has used pioneering research by leading University of WA shark experts to develop wetsuits designed to confuse sharks or render surfers invisible to the predators. The world-first shark repellent suits are based on discoveries by Associate Professor Nathan Hart and Winthrop Professor Shaun Collin, from UWA's Oceans Institute and School of Animal Biology, about how predatory sharks see and detect prey. The suits use a specific combination of colours and patterns to deter the creatures. One design — known as the ‘cryptic' wetsuit — allows the wearer to effectively blend with background colours in the water, making it difficult for a shark to detect or focus on the wearer. The other design — the ‘warning' wetsuit — makes the user appear highly visible by using disruptive and high contrast banding patterns to make them appear totally unlike any normal prey, or even as an unpalatable or dangerous option. The designs also come in the form of stickers for the undersides of surfboards. While the company Shark Attack Mitigation Systems could not claim the suits were a failsafe protection against shark attacks, results from initial testing of the wetsuits in the ocean with wild sharks had been ‘extraordinary'.

Original article: UWA science leads to world-first anti-shark suits

See also Why are animals colourful? Sex and violence, seeing and signals

Skin-Whitening

In Japanese culture a white skin is an important component of female aesthetics. In the old days, maikos applied a thick white base mask that was made with lead, but after the discovery that it poisoned the skin and caused terrible skin and back problems for the older geisha towards the end of the Meiji Era, it was replaced with rice powder.

At the end of 2007 it appeared that the cosmetics industry had finally invented a skin whitening product that is both safe and convenient, as we reported in this blog in a whiter shade of pale. Unfortunately it now appears this Rhododenol product is unsafe after all.

2,250 users of Kanebo Cosmetics Inc. skin-whitening cosmetics have reported developing serious symptoms such as white blotches on their skin. Serious effects of the products include depigmentation in an area of at least 5 cm and depigmentation in three or more areas of the body, as well as clearly visible depigmentation in parts of the face. In total, the company has received more than 100,000 inquiries in connection with the recall.

The product in question is named "Rhododenol." Kanebo earlier said it has been marketing cosmetics that use the ingredient as an active substance since 2008 via various retail outlets. The company said it has secured the cooperation of the Japanese Dermatological Association in getting a list of medical facilities which will treat the symptoms posted on the association's website. Kanebo Cosmetics Inc.'s voluntary recall of its skin-whitening line is likely to deal a crippling blow not only to its brand image but also to its parent Kao Corp. It will not be easy to restore the image of the damaged brand. The recall became more damaging due to Kanebo's delayed response.

NIH To Fund Big Data Projects

Biomedical research is increasingly data-intensive, with researchers routinely generating and using large, diverse datasets. Yet the ability to manage, integrate and analyze such data, and to locate and use data generated by others, is often limited due to a lack of tools, accessibility, and training. The National Institutes of Health announced that it will provide up to $24 million per year for the new Big Data to Knowledge (BD2K) Centers of Excellence. This initiative supports research, implementation, and training in data science that will enable biomedical scientists to capitalize on the transformative opportunities that large datasets provide.

Press release: NIH commits $24 million annually for Big Data Centers of Excellence

Web site: NIH Big Data to Knowledge (BD2K)

WIPO Adopts Treaty to Grant Copyright Exceptions for Visually Impaired

The Marrakesh Treaty to Facilitate Access to Published Works for Persons who are Blind, Visually Impaired, or otherwise Print Disabled was unanimously adopted by the United Nations' World Intellectual Property Organization (WIPO) at a 17–2 June meeting in Marrakesh, Morocco. The Treaty seeks to improve access to published works for the more than 300 million blind and visually impaired people around the world by creating an exception to internationally-recognized copyright restrictions. The treaty guarantees the right for the visually impaired to reproduce, distribute, and translate works without obtaining a license from the author.

Link to the article in Intellectual Property Watch: Over 50 Countries Sign Marrakesh Treaty On Copyright Exceptions And Limitations For The Blind

Risotto, move over

We have been using saffron to make risotto and paella yellow for centuries. Saffron, though, is very expensive. Now there is a new patented process to make rice in red, yellow, green, and purple, with the caveat that green does not survive cooking. I wonder if an orange risotto, which in addition to saffron would use ang-khak rice mold, would be less fattening, given the statins in Monascus purpureus.

Here is the article from Focus Taiwan.

A government-assisted farmers' research group in eastern Taiwan has developed "colorful" rice — no longer rice in white, but in four different colors — red, yellow, green and purple. The Hualien District Agricultural Research and Extension Station — which is dedicated to helping local farmers improve their earnings from farming, including by coming up with new products — said it has spent seven years developing the technology to add natural colors to rice using vegetables. "The colorful rice can add interest, enrich your visionary sight and increase your appetite, especially for children," the station said. It said that Southeast Asian countries and India have used natural colors to cook rice since ancient times, mostly using turmeric (a plant of the ginger family) and herbs to give rice color. It said that using the natural colors of vegetables to produce colorful rice is both "safe and delicious." The four colors developed by the station — red, yellow, green and purple — are derived from using anka (red yeast, Monascus purpureus), turmeric, chlorophyll (green pigment derived from green vegetables) and anthocyanidin (plant pigment). The station noted that rice colored with anka, turmeric, and anthocyanidin will not change color during the cooking process. The green color, using chlorophyll, however, tends to turn into an olive color after cooking. "The best ingredient is using something that is natural," the station said. It said that it is not only targeting families as the main consumers of colorful rice, but is also eying hostels or leisure farms, which may want to use it for creative dishes. They could also make it a souvenir or gift for visitors, he said. In the earlier days of research into making colorful rice, the technology could only produce a small amount of colorful rice, according to the station. But after further development, it has come up with the technology for mass production, and has obtained a patent. The station later transferred the technology to the private sector, which can now produce two metric tons of colorful rice each day.

Global Innovation Index

For the first time since 2009, the U.S. has been ranked among the top five nations in the Global Innovation Index 2013 (GII). The U.S. placed fifth behind Switzerland, Sweden, the U.K., and the Netherlands, ranked first through fourth, respectively. The annual report, released by the World Intellectual Property Organization, Cornell University, and INSEAD, is a key benchmarking tool for businesses, policy makers, and others concerned with the relative status of nations in the global innovation environment.

The GII relies on two sub-indices, the Innovation Input Sub-Index and the Innovation Output Sub-Index, each built around pillars.

Five input pillars capture elements of the national economy that enable innovative activities: (1) Institutions, (2) Human capital and research, (3) Infrastructure, (4) Market sophistication, and (5) Business sophistication. Two output pillars capture actual evidence of innovation outputs: (6) Knowledge and technology outputs and (7) Creative outputs.

Each pillar is divided into sub-pillars and each sub-pillar is composed of individual indicators (84 in total). Sub-pillar scores are calculated as the weighted average of individual indicators; pillar scores are calculated as the weighted average of sub-pillar scores.

Tokyo Police to Introduce 3D Printers for Prosecutors in Court

The Tokyo Metropolitan Police Department aims to introduce 3D printers for prosecutors to create more graphic crime scenes in court. The agency will use US-made machines capable of making solid color objects made of plaster using 3D image data captured with portable special cameras. The models will recreate murder scenes, or fire scenes details such as wall colors, shape and furniture layout. The department hopes that such models will assist judges to visualize circumstances such as culprit entry and escape routes as well as crowd member positions at the crime scenes. In current criminal proceedings, prosecutors generally describe crimes using pictures, photos and floor plans; although some of them have had 3D models made manually and used them at trial. The department has already started making prototypes based on the data from several cases. The Metropolitan Police's Criminal Investigation Laboratory introduced 3D printers in 2011 and has since applied them to actual investigations.

Source: Nikkei