Small microbes, big microbiome

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Microbiome logo

Our own bodies are teeming with microorganisms, not to mention those present in the environment we live in. Every time we touch something we transfer microbial life from one place to another. Understanding the genetic make-up of these microbes and how they interact with one another is crucial to increase our knowledge of all life forms and all environments on the planet.

 

Microbiome research involves identifying and characterising the genetic material of microorganisms found in a particular environment. This relatively young field has seen an explosion of research in the last few years, and is rapidly growing as more is discovered about the uses of microbiome data and methods and protocols are developed.

 

Scientists have been studying the microbial life which exists …

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The global fight against TB: identifying childhood infection and diagnosing complications

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Wikimedia Commons (Jmh649)

Recent estimates suggest that childhood tuberculosis (TB) rates are much higher than previously reported. The predictions, carried out by researchers at the University of Sheffield, Imperial College London and the Global Alliance for TB Drug Development, took bacterial behavior and adult infection rates into account across 22 countries with the highest incidence of TB, and suggest that more than 650,000 children develop TB each year. This figure is around 25% higher than current World Health Organization (WHO) estimates, suggesting that health officials may be missing a great opportunity to prevent the spread of infection. Leading the research, Peter Dodd highlighted that:

Children are an often ignored but important part of TB control efforts…our findings highlight

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National healthcare: The modern biomedical lab

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Brownstein et al

In 2009 Obama devoted $19 billion to healthcare innovation—innovation that was in its first instance quite rudimentary, the very digitisation of healthcare data. Now as the digitised healthcare data infrastructure grows both in the US and worldwide, what is the next phase of innovation?

The answer, from someone who works with researchers, is clear: a data dialogue between researchers and clinicians. Initiatives like the Global Alliance for Sharing Genomic and Clinical Data led by David Haussler are making strides toward doing this for treatment and research for cancer.

Last week I attended ISMB in Boston, where I saw one quantitative analyst (quant) who had similar ideas about better healthcare treatment through research and more data for research through healthcare. His …

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The gatekeepers of the future

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The future gatekeepers panel at ESOF2014

The world around us has transformed dramatically in the last 20 years, and the world of science is being shaped by technology. Crowdsourcing and citizen science are made easy by the internet and mobile apps. Article metrics and peer review experiments allow us to challenge processes that have decided science for hundreds of years. Career structures are able to change and diversify thanks to industry’s and technology’s demands. But does this truly affect research and its impacts, and are the gatekeepers for science really changing?

A few weeks ago I attended the EuroScience Open Forum meeting in Copenhagen, Denmark. EuroScience Open Forum, or ESOF, is a pan-European meeting that happens every two years in a different city – …

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Beyond ENCODE – let’s continue the conversation

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As the human genome sequence was completed, so the deep analysis of it began in earnest with the ENCyclopedia Of DNA Elements (ENCODE) project – intended to identify all functional elements in the human genome.

The project involved a worldwide consortium of research groups and the data emerging can be accessed through public databases. BioMed Central has published a selection of the early findings.

ENCODE initiatives lead to modENCODE a project aspiring to identify the functional elements in the genomes of the model organisms Caenorhabditis elegans (nematode) and Drosophila melanogaster (fruit fly). The extension of the ‘ENCODE approach’ to other model organisms allows further biological validation of the findings coming from the human genome project.

And building on ENCODE doesn’t …

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The diverse world of citation indexing services

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When assessing the impact of a published research article, it might seem logical to look at the Impact Factor of the journal that you find it in. But as journals and scholars have moved online, and citation indexing has been automated, the wealth of information for citation discovery and analysis has vastly increased.

Citation counts can tell a more accurate story about the scholarly impact that an individual article has made than the journal Impact Factor. But where should you look for these counts? There are a number of indexing services tracking and providing information about citations, each with advantages and disadvantages.

To highlight just how different the citation counts can be between the different indexes, we’ve had a look at some …

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Polio eradication – the race continues…

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Wikipedia

In May 2014, the World Health Organisation declared the rapidly increasing spread of polio an international public health emergency. The virus, which usually affects children under five years old, is typically spread through faeces contaminated drinking water, causing irreversible paralysis and death in the most severe cases, where respiratory muscles are immobilised.

Polio is currently endemic in three countries; Nigeria, Pakistan and Afghanistan, which is an amazing feat considering that polio was rife worldwide little over 60 years ago. Advances in vaccines in the 1950s, and the launch of the Global Polio Eradication Initiative in 1988, led to an enormous 99% reduction of cases narrowing the incidence of polio to just a handful of countries.  March 2014 marked a …

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“I am a man who sees death every day” – health and the Syrian conflict

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GHE11_v2

It’s over three years since the conflict in Syria began. With people dying daily, crucial services and support systems disrupted, and challenges in providing international aid, the health and welfare of millions of people hangs in the balance. In this guest post for the journal Conflict and Health, Joseph Fitchett and Lalitha Bhagavatheeswaran, Director and Coordinator (respectively) of the Global Health Film initiative, write about how a new film can help us to recognize the challenges faced.

 

Recent UN reports estimate 9.3 million people are in need of assistance in Syria. There are 6.5 million internally displaced persons, and over 100,000 people killed since the start of the conflict in March of 2011.

 

In a relatively short span of time …

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Publish or perish – are women disadvantaged by current measures of scientific ‘success’?

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Margaret D Foster

87% of the most highly cited articles are authored by fewer than 1% of scientists. That is the finding of a recent study by John Ioannidis and colleagues published in PLOS One.

The authors examined the entire SCOPUS database to determine the number and characteristics of scientists who had an uninterrupted continuous publication record (UCP) for a period of 16yrs from 1996 to 2011.

Out of over 15 million authors, 150,608 had such a UCP record, and of those, 73.3% could be deemed ‘successful’ as determined by citation metrics and the author’s H index – a measure of their productivity as well as the impact of their work. This proportion is significantly diminished to 43.7% for researchers who skipped only one …

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Where’s the evidence for how we run clinical trials?

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trial forge

No one ever said that doing a clinical trial was easy. Indeed it often feels like a Sisyphean task, when faced with obdurate funding committees, or centres that seem unable to recruit a single patient, when just six months previously they were inundated with them. Every piece of research has its pain points; however, sometimes we do have a tendency to over-complicate things.

This was exactly the message of Shaun Treweek’s talk at the 2nd Clinical Trials Methodology Conference in November last year, where he asked if we were making our own lives more difficult than they needed to be. We have a tendency to do trials the way we do because that’s the way we do …

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