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Seventh Annual National Freedom of Information Audit Released Today

Posted on September 24, 2012 by Danzig

CALGARY, ALBERTA--(Marketwire - Sep 24, 2012) - Newspapers Canada will release its seventh annual National Freedom of Information (FOI) Audit today at the Sunshine Summit in Calgary.The launch of the 2012 report coincides with the beginning of Canadian Right to Know Week.

The annual FOI audit reviews the performance of Canadian governments with respect to their access to information regimes.As such, it provides the public the opportunity to see the degree to which our governments are in compliance with their own FOI legislation, as well as facilitating comparisons among jurisdictions.

"The annual FOI audit represents an important tool for protecting the public''s right to access government information," said John Hinds, CEO of Newspapers Canada.

"Municipalities continue to perform fastest in the audit, easily outpacing the senior levels of government," noted Professor Fred Vallance-Jones, the National FOI audit''s lead researcher. "Thirty years after the Access to Information Act was passed, the federal government seems stuck in a rut of delays and can''t get out of the 50 to 60 percent range when it comes to completing requests on time."

The FOI audit compares the performance of government and various public institutions across Canada.To obtain the data for the audit, a team of researchers requested the same information from the federal and provincial government, as well as a selection of municipalities.

The FOI audit was done in collaboration with Fred Vallance-Jones, associate professor of journalism at the University of King''s College, and his team.

The 2012 Newspapers Canada FOI Audit is now available at http://www.newspaperscanada.ca/public-affairs/freedom-information.

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Seventh Annual National Freedom of Information Audit Released Today

Using artificial intelligence to chart the Universe

Posted on September 24, 2012 by Danzig

24.09.2012 - (idw) Leibniz-Institut fr Astrophysik Potsdam

Astronomers in Germany have developed an artificial intelligence algorithm to help them chart and explain the structure and dynamics of the universe around us. The team, led by Francisco Kitaura of the Leibniz Institute for Astrophysics in Potsdam, report their results in the journal Monthly Notices of the Royal Astronomical Society. Scientists routinely use large telescopes to scan the sky, mapping the coordinates and estimating the distances of hundreds of thousands of galaxies and so enabling scientists to map the large-scale structure of the Universe. But the distribution they see is intriguing and hard to explain, with galaxies forming a complex cosmic web showing clusters, filaments connecting them, and large empty regions in between.

The driving force for such a rich structure is gravitation. Around 5 percent of the cosmos appears to be made of normal matter that makes up the stars, planets, dust and gas we can see and around 23 percent is made up of invisible dark matter. The largest component, some 72 percent of the cosmos, is made up of a mysterious dark energy thought to be responsible for accelerating the expansion of the Universe. This Lambda Cold Dark Matter (LCDM) model for the universe was the starting point for the work of the Potsdam team.

Measurements of the residual heat from the Big Bang the so-called Cosmic Microwave Background Radiation or CMBR allow astronomers to determine the motion of the Local Group, the cluster of galaxies that includes the Milky Way, the galaxy we live in. Astronomers try to reconcile this motion with that predicted by the distribution of matter around us, but this is compromised by the difficulty of mapping the dark matter in the same region.

Finding the dark matter distribution corresponding to a galaxy catalogue is like trying to make a geographical map of Europe from a satellite image during the night which only shows the light coming from dense populated areas, says Dr Kitaura.

His new algorithm is based on artificial intelligence (AI). It starts with the fluctuations in the density of the universe seen in the CMBR, then models the way that matter collapses into todays galaxies over the subsequent 13700 million years. The results of the AI algorithm are a close fit to the observed distribution and motion of galaxies.

Dr Kitaura comments, Our precise calculations show that the direction of motion and 80 percent of the speed of the galaxies that make up the Local Group can be explained by the gravitational forces that arise from matter up to 370 million light years away. In comparison the Andromeda Galaxy, the largest member of the Local Group, is a mere 2.5 million light years distant so we are seeing how the distribution of matter at great distances affects galaxies much closer to home.

Despite this caveat, our model is a big step forward. With the help of AI, we can now model the universe around us with unprecedented accuracy and study how the largest structures in the cosmos came into being.

Since 2011 Francisco Kitaura has been working at the AIP. His publication is available online on http://arxiv.org/abs/1205.5560 and will soon be published in Monthly Notices of the Royal Astronomical Society (MNRAS).

Science contact: Dr. Francisco-Shu Kitaura, +49 331-7499 447, fkitaura@aip.de Research, Images, Movies: http://www.aip.de/Members/fkitaura

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Using artificial intelligence to chart the Universe

Novel approach for single molecule electronic DNA sequencing

Posted on September 23, 2012 by ev1

ScienceDaily (Sep. 21, 2012) DNA sequencing is the driving force behind key discoveries in medicine and biology. For instance, the complete sequence of an individual's genome provides important markers and guidelines for medical diagnostics and healthcare. Up to now, the major roadblock has been the cost and speed of obtaining highly accurate DNA sequences. While numerous advances have been made in the last 10 years, most current high-throughput sequencing instruments depend on optical techniques for the detection of the four building blocks of DNA: A, C, G and T. To further advance the measurement capability, electronic DNA sequencing of an ensemble of DNA templates has also been developed.

Recently, it has been shown that DNA can be threaded through protein nanoscale pores under an applied electric current to produce electronic signals at single molecule level. However, because the four nucleotides are very similar in their chemical structures, they cannot easily be distinguished using this technique. Thus, the research and development of a single-molecule electronic DNA sequencing platform is the most active area of investigation and has the potential to produce a hand-held DNA sequencer capable of deciphering the genome for personalized medicine and basic biomedical research.

A team of researchers at Columbia University, headed by Dr. Jingyue Ju (the Samuel Ruben-Peter G. Viele Professor of Engineering, Professor of Chemical Engineering and Pharmacology, Director of the Center for Genome Technology and Biomolecular Engineering), with colleagues at the National Institute of Standards and Technology (NIST) led by Dr. John Kasianowicz (Fellow of the American Physical Society), have developed a novel approach to potentially sequence DNA in nanopores electronically at single molecule level with single-base resolution. This work, entitled "PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis" is now available in the open access online journal Scientific Reports, from Nature Publishing Group.

The reported nanopore-based sequencing by synthesis (Nano-SBS) strategy can accurately distinguish four DNA bases by detecting 4 different sized tags released from 5'-phosphate-modified nucleotides at the single molecule level for sequence determination. The basic principle of the Nano-SBS strategy is described as follows. As each nucleotide analog is incorporated into the growing DNA strand during the polymerase reaction, its tag is released by phosphodiester bond formation. The tags will enter a nanopore in the order of their release, producing unique ionic current blockade signatures due to their distinct chemical structures, thereby determining DNA sequence electronically at single molecule level with single base resolution.

As proof-of-principle, the research team attached four different length polymer tags to the terminal phosphate of 2'-deoxyguanosine-5'-tetraphosphate (a modified DNA building block) and demonstrated efficient incorporation of the nucleotide analogs during the polymerase reaction, as well as better than baseline discrimination among the four tags at single molecule level based on their nanopore ionic current blockade signatures. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.

In previous work, the Center of Genome Technology & Biomolecular Engineering at Columbia University, led by Professor Ju and Dr. Nicholas J. Turro (William P. Schweitzer Professor of Chemistry), developed a four-color DNA sequencing by synthesis (SBS) platform using cleavable fluorescent nucleotide reversible terminators (NRT), which is licensed to Intelligent Bio-Systems, Inc., a QIAGEN company. SBS with cleavable fluorescent NRTs is the dominant approach used in the next generation DNA sequencing systems. Dr. Kasianowicz and his group at NIST pioneered the investigation of nanopores for single molecule analysis. They previously reported that different length polymers, polyethylene glycols (PEGs), could be distinguished by their unique effects on current readings in a -hemolysin protein nanopores at single molecule level and subsequently developed a theory for the method. Their results provide the proof-of-concept for single molecule mass spectrometry. The combination of the SBS concept with the distinct nanopore-detectable electronic tags to label DNA building blocks led to the development of the single-molecule electronic Nano-SBS approach described the current Scientific Reports article (09/21/2012).

As lead author Dr. Shiv Kumar points out, "The novelty of our approach lies in the design and use of four differently tagged nucleotides, which upon incorporation by DNA polymerase, release four different size tags that are distinguished from each other at the single molecule level when they pass through the nanopore. This approach overcomes any constraints imposed by the small differences among the four nucleotides, a challenge which most nanopore sequencing methods have faced for decades." Moreover, the technique is quite flexible; with PEG tags as prototypes, other chemical tags can be chosen to provide optimal separation in different nanopore systems.

With further development of this Nano-SBS approach, such as the use of large arrays of protein or solid nanopores, this system has the potential to accurately sequence an entire human genome rapidly and at low cost, thereby enabling it to be used in routine medical diagnoses.

The authors of the Scientific Reports article were Shiv Kumar, Chuanjuan Tao, Minchen Chien, Brittney Hellner, Arvind Balijepalli, Joseph W.F. Robertson, Zengmin Li, James J. Russo, Joseph E. Reiner, John J. Kasianowicz, and Jingyue Ju. The study was supported by a grant from the National Institutes of Health, a National Research Council/NIST/NIH Research Fellowship, and a grant from the NIST Office of Law Enforcement Standards.

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Novel approach for single molecule electronic DNA sequencing

Judge denies motions to dismiss DNA evidence in Hudson murder case

Posted on September 23, 2012 by ev1

A Middlesex Superior Court judge is allowing two samples of DNA to be used as evidence in the trial of a Framingham man accused of murdering a couple in Hudson in 2010.

Judge Sandra Hamlin denied defense attorney Thomas Fords request to dismiss a sample of Velezs DNA that was found underneath Trisha Bennetts fingernail and a blood spatter found on the jeans Velez wore the night of the murders, said Stephanie Chelf Guyotte, a spokeswoman for the Middlesex District Attorneys office.

During a pre-trial conference earlier this week, Ford argued that a report did not note which portion of Bennetts fingernail the DNA sample was taken from. Ford said DNA can be transmitted to the top of another persons fingernail through casual contact. However, DNA is normally transmitted underneath another persons fingernail if there is sexual or defensive contact.

Ford also expressed concerns that there was no defense expert present at the swabbing and testing of the DNA.

Assistant District Attorney Joseph Gentile said testimony at a previous hearing documented the DNA sample was found underneath Bennetts fingernail.

In the case of the blood spatter on Velezs jeans, Ford said a report did not identify which blood spot was extracted and tested for DNA. The number of spots tested was also not in the report, said Ford.

Citing a report, Gentile said the sample was taken from a defined section near the left thigh Velezs jeans near his thigh.

Jury selection began Friday and will continue on Monday, said Guyotte.

Velez, 29, is charged with first-degree murder in the stabbing deaths of Bennett, 20, and her boyfriend Angel Ortiz, 23. Bennett and Ortiz were found dead inside their Emerson Gardens condominium May 1, 2010.

Authorities arrested Velez nearly three months after he called 911 in the early morning of May 1, 2010, telling police he and two friends had been stabbed. Police found Velez, who was suffering from stab wounds, in the parking lot. Prosecutors say Velezs wounds were self-inflicted.

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Judge denies motions to dismiss DNA evidence in Hudson murder case