Some studies indicate sepsis as one of the major risk factors for developmental delay and cerebral palsy, as well as neonatal death. This paper in Journal de Pediatria evaluates 248 babies over the first year after birth to determine if sepsis is a risk factor.
Dr Kai Kropp has successfully extracted DNA from a sample of
Staphylococcus which is another deliverable completed for the ClouDxi project.
Kai also gave computer science researchers and NSilico personnel a demonstration on DNA extraction from Staphylococcus in the labs at CIT. The researchers found the procedure very interesting and it was useful to see what happens in practice, such as seeing a culture, the sample being heated and washed until finally seeing flakes of DNA.
The demonstration facilitated the transfer of knowledge and gave computer scientists an understanding of the underlying procedures involved in extracting DNA before it is sent to be sequenced.
Ailsling O'Driscoll and Vlad Belogrudov comparing cultures in agar plates.
Kai showing a culture of Staphylococcus.
Vlad Belogrudov and Kai Kropp looking at the DNA extracted.
Vlad Belogrudov (CIT), John Carroll and Paul Walsh of NSilico and Kai Kropp (CIT) in the lab at CIT.
Inflammatory response during sepsis is incompletely understood due to small sample sizes and variable timing of measurements following the onset of symptoms. This paper from the James Hogg Research Centre and Pulmonary & Critical Care Medicine at Stanford University looks at cytokines and signalling molecules in an attempt to predict clinical outcomes in Sepsis.
The research found a distinct pattern of cytokine levels measured early in the course of sepsis predicts disease outcome. Sub-populations of patients have differing clinical outcomes that can be predicted accurately from small numbers of cytokines. Design of clinical trials and interventions may benefit from consideration of cytokine levels.
This paper from University of Würzburg looks at altered neonatal Toll-like receptor (TLR) function which is hypothesized to contribute to the heightened susceptibility to infection and perpetuated inflammation in term and preterm neonates, clinically evident in neonatal sepsis and increased rates of inflammatory disorders. Current data indicates that basal TLR expression in term neonates equals adult expression patterns, while expression in preterm infants seems to increase, depending on gestational age. Regarding TLR signaling, some studies suggest TLR incompetence in neonates associated with impaired pro-inflammatory responses, others describe neonatal TLR function well developed and allude to its hyper-inflammation tendency.
nSilico LifeSciences, Ltd and the Department of Biological Sciences at Cork Institute of Technology recently published a paper in the Computers in Biology and Medicine journal where they describe the development of a sequence information management platform (Simplicity), a workflow-based bioinformatics management tool, which allows non-bioinformaticians to rapidly annotate large amounts of DNA and protein sequence data.
Simplicity is a bespoke bioinformatics management system that allows biologists to manage and analyse information generated from large scale ‘omic’ projects, facilitating quick transition from ‘project-to-publication’ or ‘lab-to-licence’. The authors engaged with over 120 professional researchers across the spectrum of biological sciences (using a qualitative analysis based approach involving both focus groups and online surveys) to develop a software framework that meets academic and industry demands. Simplicity has been developed as a cloud based Software as a Service (SaaS) solution, allowing for rapid deployment of extended features in response to increasing user needs.
The software is currently in development to meet the needs of Next Generation Sequencing projects (NGS) where detection of SNP's (single nucleotide polymorphism) and Indels (INsertion/DELetion) are of great interest to researchers investigating differences between members of a biological species.
ClouDx-I researchers contributed to the paper.
An audit was published by the National Perinatal Epidemiology Centre based in Cork and is a first for the country. The first national audit of stillbirths and the deaths of babies within four weeks of being born has been published.
It indicates that there were almost 500 perinatal deaths in Ireland during 2011, with stillbirths accounting for the majority of these.
The Collaborative European Research Conference (CERC) http://cerc.cit.ie is the result of a long standing research collaboration between Cork Institute of Technology (CIT) and other Institutes and Universities around Europe.
CERC 2013 was hosted by CIT in Cork, on the 17th and 18th of October. Papers and presentations from the areas of Computer Science, Media & Marketing, Electronic Engineering, Electrical Engineering, Biology, Next Generation Sequencing and Business were showcased. The keynote speeches were delivered by CEO Dr Kieran Drain of the National Centre for Physics Research, Tyndall National Institute and Mr Garrett Dee of Enterprise Ireland.
ClouDx-I researcher Dr Paul Dickinson (below) was invited by CERC to talk about his research in Detecting bacterial infection from a single drop of blood using host RNA transcription.
Many of the ClouDx-I team were present for his talk in detecting infections in neonatals.
The ClouDx-I team present at CERC are from left to right: Vlad Belogrudov, John Carroll, Paul Walsh, Aisling O'Driscoll, Hugh Mcglynn, Paul Dickinson and Kai Kropp
The web site ModernHealthCare.com has reported that the National Institutes of Health will award $25 million to four research projects that plan to look at how genomic sequencing may improve the health of neonates.
Researchers from Brigham and Women's Hospital and Boston Children's Hospital plan to analyze the potential of providing sequencing to newborns and then form clinical protocols addressing how medics should use a baby's genomic information.
“We're asking the question, if you have this information available, if you have the book of life, if you have every letter of your DNA to look at, how do we use it?” said Dr. Robert Green, a medical geneticist in Brigham and Women's Hospital's division of genetics.
ModernHealthCare.com discuss the idea that “genome and exome sequencing is a relatively new and unexplored tool for healthcare providers and can raise a number of ethical questions about how the newly discovered genomic data will be used by the patient and the healthcare provider.”
See more at NIH to award $25M to research babies' health | Modern Healthcare
Good news for the ClouDx-I project as Dell have thrown their weight behind the project. An innovative “private cloud” solution has been design by NSilico in conjunction with Dell and BSC technology limited. To take advantage of recent hardware improvements and with a critical requirement to respect patient privacy and drive ethical best practice a solution that minimises security risks has been developed. Based on the Vertex architecture a 4 node ‘super computer in a box’ has been procured to drive bioinformatics innovation and development for neo-natal sepsis research. This cost effective solution allows a powerful bioinformatics pipeline to be deployed in a clinical setting with a minimal footprint allowing all data to be held behind firewalls in the sample processing unit. This solution brings a high performance computing multi core solution to the data in situ. Shown below closing the deal are Dell agent Paul Mulready BSC technology ltd., Dr Paul Walsh NSilcio Life Science Ltd. and John Carroll MSc NSilico Life Science Ltd.
Dr Paul Walsh presented a full paper on behalf of ClouDx-I for eChallanges 2013 in Dublin 9th October 2013, see https://www.echallenges.org/e2013/default.asp. The paper was very well received receiving enthusiastic applause and numerous questions from the audience. The paper entitled “Democratising Life Science with Cloud Computing” outlines how the cloud can best be leveraged to support molecular diagnostics and related activities in life science. It discussed both opportunities and challenges and presented results of a pathogen sequencing project that used cloud computing to dramatically reduce the research cycle time.
eChallenges e-2013 Conference (09 - 11 October) is the twenty-third in a series of annual technology research conferences supported by the European Commission and hosted by national governments.
The eChallenges Conference Series has a truly international perspective, attracting participation from senior representatives of leading government, industry and research organisations around the world from over 50 countries each year.
Its reputation is based on high quality plenary presentations and Scientific Programme. Each conference showcases host country activities, as well as sectoral and national initiatives and regional success stories.
The goals of eChallenges e-2013 are to promote Information Society and Applied ICT related knowledge sharing and innovation between government, industry and research stakeholders, exchange experiences about the current state of eAdoption at a sectoral, national and regional level, stimulate rapid take-up of RTD results by industry and in particular SMEs, and identify opportunities for future international research collaboration under Horizon 2020.
Dr Paul Walsh is presenting "Democratization of Life Science with Cloud Computing" at the eChallenges e-2013 Conference in Dublin (09 - 11 October). https://www.echallenges.org/e2013/default.asp