Friday, 24 October 2014

Wikipedia as the Front Matter to all Research for Public Use

Wikipedia is a initiative that has become extremely successful at providing encyclopedic coverage of almost any subject you might be find interesting or useful. It has a very simple modus operandi in that it permits anyone to write articles on any subject they wish. Others are then given open permission to edit those articles. No-one owns any part of the project, neutrality and freedom are prized. There are only five rules governing content generation, the fifth of which is that there are no firm rules!

A recipe for chaos? Not at all - in practice acts of ignorance or vandalism are quickly removed - this has been a huge success for collaborative work and free access. Quoting Wikipedia:
Since its creation in 2001, Wikipedia has grown into one of the largest reference websites, attracting 470 million unique visitors monthly as of February 2012. [1] There are more than 76,000 active contributors working on more than 31,000,000 articles in 285 languages. As of today, there are 4,630,235 articles in English. Every day, hundreds of thousands of visitors from around the world collectively make tens of thousands of edits and create thousands of new articles to augment the knowledge held by the Wikipedia encyclopedia. (See the statistics page for more information.) Where once it took huge amounts of work to maintain comprehensive encyclopedias and it could only be done at high cost we now have far larger bodies of work that are maintained free of charge.

Many of the articles featured are contributed by researchers using their most recent research results.
There is a suggestion that this could be taken a step further for the research communities themselves:

 A session at the recent Wikimania conference provided an opportunity for discussion: “The fount of all knowledge – wikipedia as the front matter to all research“. 
The abstract describes how: This discussion focuses on how Wikipedia could become the entry or discovery point to all significant research for the general public, and for scholars who are working just outside of the topic of interest. For most people, even researchers from closely related areas, summaries and explanations of a piece of research can be a crucial means both to discover and to begin to get into a new piece of research. 
 Currently overviews of research topics are supported through two mechanisms: reviews and “front matter” content. A review is a systematic summary of a field, written by an expert. These go out of date quickly, particularly in rapidly moving areas of research. Front matter is “News and Views” pieces, often found at the “front” of scientific journals that explain newly published research and put it in context. This often includes a discussion of explaining how the research is an important advance and its broader societal implications. 
 Both of these functions could easily be provided in a more up to date and scalable manner by tapping into a global community of experts. Wikipedia articles are often the top web search result for initial queries in many research areas and these articles are a major source of traffic for scientific journals. As the first port of call for many users of research and a significant discovery route the potential for Wikipedia as a form of dynamic, expertly curated “front matter” for the whole research literature is substantial. This facilitated discussion session will focus on how this role could be enhanced, what is currently missing and what risks exist in taking this route. 

There are difficulties to overcome but it is easy to see  the attraction of the availability of constantly updated extensive reviews for the use of the professional community. Currently reviews are out of date by the time they are published, this technology may make that delay in disseminating and summarising scientific research a thing of the past.

Wednesday, 22 October 2014

Fungi Transform Waste into Biofuel

Wine waste
This article was originally written by Lea Kivivali on

Researchers at Swinburne University of Technology have developed a technique for converting winery waste into compounds that could have potential value as biofuels or medicines.

Australia is the world's sixth largest wine producer, with around 1.75 million tonnes of grapes crushed for wine every year. After the final pressing, more than half of the grapes crushed end up as biomass waste comprised of skins, pulp, stalks and seeds.
Unlike other agricultural by-products, this waste has limited use as animal feed due to its poor nutrient value and digestibility. It is also not suitable as compost because it doesn't degrade. Thus a majority of this grape waste ends up as toxic landfill.
As part of his PhD research, Swinburne student Avinash Karpe has been investigating how to break down this woody material composed of cellulose, pectins and lignins into simpler compounds that can be used to create other things such as ethanol or other biofuels.
He performed a series of experiments to develop the best procedure for degrading winery biomass waste.
"Various fungi are known to degrade this waste by generating an array of enzymes," Mr Karpe said. "These enzymes convert the  to soluble sugars which can then be converted into other products."
He discovered that a 30-minute heat activated pretreatment aided in the breakdown of these biomolecules.
Using a 'cocktail' of four fungi – Trichoderma harzianum, Aspergillus niger, Penicillium chrysogenum and Penicillium citrinum, in a one litre bioreactor, Mr Karpe succeeded in breaking down the biomass, with noticeable increases in enzyme activity and lignin degradation.
This fermentation process takes one to three weeks and produced alcohols, acids and simple sugars of industrial and medicinal interest.
"We have demonstrated this technique in the laboratory, but this process can be scaled up to an industrial scale," Chair of Swinburne's Department of Chemistry and Biotechnology, Professor Enzo Palombo, said.
The Swinburne researchers worked with CSIRO on this research with material obtained from Australian Wine Research Institute in SA.
This research has been published in the Journal of Chemical Technology and Biotechnology.
More information: Karpe, A. V., Beale, D. J., Harding, I. H. and Palombo, E. A. (2014), "Optimization of degradation of winery-derived biomass waste by Ascomycetes." J. Chem. Technol. Biotechnol.. DOI: 10.1002/jctb.4486, Partly submitted: Annual Scientific Meeting and Exhibition, Australian Society for Microbiology, Melbourne, Australia. 6–9 July 2014

Tuesday, 14 October 2014

Omalizumab: a New Treatment Option for Allergic Bronchopulmonary Aspergillosis (ABPA)

ABPA is an allergic infection of the airways. It is not yet clear why some people get ABPA while most of us do not as the infecting mould is inhaled by nearly all of us on a daily basis. For most of us this is not a problem as our lungs are lined with protective immune cells that destroy the mould before its can establish itself, but for those rare few with ABPA this did not happen and the mould (Aspergillus) persisted and grew to block airways and cause inflammation. It rarely invades anything but the air spaces, it does not invade our lung tissues but does cause a lot of irritation and breathing problems that cannot be cured. This is a long term seriously debilitating condition.

One population we know is particularly vulnerable to ABPA is those people with cystic fibrosis (CF). Figures vary but something like 10 - 25% of people with CF get ABPA. Perhaps that is not surprising as their lungs are prone to infections as they cannot properly rid themselves of infectious particles including mould spores. Someone with CF already has severe problems breathing without suffering from contributing infections and some figures suggest 50% of all people living with CF have some form of infection by Aspergillus - not all are thought to progress to ABPA.

Treatment for ABPA is to use steroids to control inflammation and often an antifungal drug which can allow the dose of the steroid medication to be minimised, thus helping to avoid some of the many unpleasant side effects of taking high dose corticosteroids. This doesn't work for everyone and alternatives are being actively sought.

Originally developed for severe asthmatics, Omalizumab (Xolair) directly targets the parts of our immune system that leads to excessive inflammation. In asthmatics this has been demonstrated to lessen symptoms and has benefited patients. Many CF patients and those with ABPA are also asthmatic. ABPA is known to cause chronic airway inflammation and so ABPA patients are a candidate for use of this drug.

Some of the toughest patients to treat are probably those with CF and ABPA and we now have the first reports of patients from those groups who are being treated with Omalizumab. The most recent paper by Lehman et. al. looks at a small number of patients (6) with wide age range (age 4 - 33) treated over 7 years and suggested that Omalizumab was beneficial especially in those who had less progressed disease with benefits of taking lass corticosteroid also apparent.

This result offers hope for alternative treatment to ABPA patients who do not have CF,

Wednesday, 1 October 2014

Detecting Fungus in the CF Patient Environment A Rising Concern

A recent paper released by the team here at the National Aspergillosis Centre has raised concern in the cystic fibrosis community that there may be many cases of Aspergillus infection amongst people living with CF that are going undetected.

This article, originally written by Maureen Newman discusses the implications:

In light of the news that almost 50% of cystic fibrosis patients are infected with Aspergillus mold,health leaders are reminding patients that it is important to limit exposure to agents that can cause infection for patients with cystic fibrosis. Certain services exist for patients interested in testing their environment for Aspergillus and other microorganisms.
“It is not healthy for anyone to be exposed to high levels of Aspergillus, but this new research sheds light on the need for those with cystic fibrosis to be especially vigilant,” said Jason Dobranic, PhD, Vice President of Microbiology and Life Sciences at LA Testing and EMSL Analytical, Inc., in a news release from the company. LA Testing, based in California, where a large percentage of the estimated 30,000 children with cystic fibrosis live, conducts indoor air quality testing for a number of chemicals and biologicals.
By detecting and limiting exposure to Aspergillus, an individual’s risk for developing aspergillosis is greatly decreased. Aspergillosis, which presents in many different forms, sometimes only causes symptoms and other times causes tissue damage. Allergic bronchopulmonary aspergillosis (ABPA) causes wheezing and coughing but does not invade or destroy tissue. Invasive aspergillosis causes damage to tissues–usually the lungs of patients with weakened immune symptoms.
For cystic fibrosis patients who have already been affected with ABPA, a new treatment option is being investigated at RWTH Aachen University’s University Hospital in Germany. A recent report, published online ahead of print in Therapeutic Advances in Respiratory Disease, entitled “Omalizumab: A New Treatment Option for Allergic Bronchopulmonary Aspergillosis in Patients with Cystic Fibrosis,” conducted a retrospective study of six patients with concurrent ABPA and cystic fibrosis who had been treated with omalizumab. The observation period was 7.5 years. During and after treatment, all patients showed clinical and laboratory stability of disease, with some patients showing improvements.
The researchers noted that “Early onset treatment may be beneficial and patients with early stage of lung disease seem to benefit more,” suggesting that early disease detection is vital. Patients who find their environments are enriched in Aspergillus through air quality testing may have a better chance of being diagnosed and treated sooner.

Tuesday, 30 September 2014

US IDSA Calls for Increased Emphasis on the Fight Against Antibiotic Resistance

As we have all become used to taking antibiotics for infections we tend to take them for granted. However awareness is growing that more and more antibiotics are being rendered useless by the rise of strains of fungi & bacteria that are resistant to one or more antibiotics.

Compounding the problem is the fact that few drug companies are voluntarily developing new antibiotics. One of the essential principles of the capitalist system is that you should only invest money in projects that will make money, and there seems to be little money in antibiotic development for the large private drug companies that must take major financial risks to develop any drug. Shareholders are generally interested in profits rather than philanthropy.

According to this timeline there were 20 antibiotics developed between 1990 and 1999 but only 6 entered use between 2000 and 2009.

It therefore falls to public funds to stimulate interest in antibiotics in the public interest. In the US the Infectious Diseases Society of America has joined in the fight to try to persuade the US government to promote the development of new antibiotics.


IDSA members enacted the 2012 Generating Antibiotic Incentives Now (GAIN) Act, which incentivizes antibiotic development by providing a 5-year extension of market exclusivity for new drugs that treat serious or life-threatening infections.
However, pharmaceutical companies are still facing significant economic, scientific and regulatory barriers, she said. Nowhere is this more evident than with carbapenem-resistant Enterobacteriaceae (CRE), which the CDC deemed the “nightmare bacteria” in 2013. With no safe or effective antibiotic treatments available, up to 50% of patients with CRE bloodstream infections die. Meanwhile, there are only a handful of novel antibiotics currently in development for CREs. All of these are unlikely to be approved by the FDA, given that they still face risk of failure in clinical trials.

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