Studying the Human Gut Microbiota in the Trans-Omics Era - Focus on Metagenomics and Metabonomics

The human gut microbiota comprises a diverse microbial consortium closely co-evolved with the human genome and diet. The importance of the gut microbiota in regulating human health and disease has however been largely overlooked due to the inaccessibility of the intestinal habitat, the complexity of the gut microbiota itself and the fact that many of its members resist cultivation and are in fact new to science. However, with the emergence of 16S rRNA molecular tools and "post-genomics" high resolution technologies for examining microorganisms as they occur in nature without the need for prior laboratory culture, this limited view of the gut microbiota is rapidly changing. This review will discuss the application of molecular microbiological tools to study the human gut microbiota in a culture independent manner. Genomics or metagenomics approaches have a tremendous capability to generate compositional data and to measure the metabolic potential encoded by the combined genomes of the gut microbiota. Another post-genomics approach, metabonomics, has the capacity to measure the metabolic kinetic or flux of metabolites through an ecosystem at a particular point in time or over a time course. Metabonomics thus derives data on the function of the gut microbiota in situ and how it responds to different environmental stimuli e.g. substrates like prebiotics, antibiotics and other drugs and in response to disease. Recently these two culture independent, high resolution approaches have been combined into a single "transgenomic" approach which allows correlation of changes in metabolite profiles within human biofluids with microbiota compositional metagenomic data. Such approaches are providing novel insight into the composition, function and evolution of our gut microbiota.

Interference filters and coatings for mid-infrared astronomy (8-30µm)

The VISIR instrument for the European Southern Observatory (ESO) Very Large Telescope (VLT) is a thermal-infrared imager and spectrometer currently being developed by the French Service d'Astrophysique of CEA Saclay, and Dutch NFRA ASTRON Dwingeloo consortium. This cryogenic instrument will employ precision infrared bandpass filters in the N-( =7.5-14µm) and Q-( =16-28µm) band mid-IR atmospheric windows to study interstellar and circumstellar environments crucial for star and planetary formation theories. As the filters in these mid-IR wavelength ranges are of interest to many astronomical cryogenic instruments, a worldwide astronomical filter consortium was set up with participation from 12 differing institutes, each requiring instrument specific filter operating environments and optical metrology. This paper describes the design and fabrication methods used to manufacture these astronomical consortium filters, including the rationale for the selection of multilayer coating designs, temperature-dependant optical properties of the filter materials and FTIR spectral measurements showing the changes in passband and blocking performance on cooling to <50K. We also describe the development of a 7-14µm broadband antireflection coating deposited on Ge lenses and KRS-5 grisms for cryogenic operation at 40K

A practical low cost architecture for a MB-OFDM equalizer (ECMA-368)

The relative fast processing speed requirements in Wireless Personal Area Network (WPAN) consumer based products are often in conflict with their low power and cost requirements. In order to solve this conflict the efficiency and cost effectiveness of these products and the underlying functional modules become paramount. This paper presents a low-cost, simple, yet high performance solution for the receiver Channel Estimator and Equalizer for the Mutiband OFDM (MB-OFDM) system, particularly directed to the WiMedia Consortium Physical Later (ECMA-368) consumer implementation for Wireless-USB and Fast Bluetooth. In this paper, the receiver fixed point performance is measured and the results indicate excellent performance compared to the current literature(1).

Overall evaluation of the PETS2009 results

This paper presents the results of the crowd image analysis challenge, as part of the PETS 2009 workshop. The evaluation is carried out using a selection of the metrics available in the Video Analysis and Content Extraction (VACE) program and the CLassification of Events, Activities, and Relationships (CLEAR) consortium. The evaluation highlights the strengths of the authors’ systems in areas such as precision, accuracy and robustness.

Multicast application sharing tool - Facilitating the eMinerals virtual organisation

The eMinerals Virtual Organisation consists of a consortium of individuals affiliated to geographically distributed academic institutions. Collaborative tools are essential in order to facilitate cooperative work within this Virtual Organisation. The Access Grid Toolkit has been widely adopted for this purpose, delivering high quality group-to-group video and audio conferencing. We briefly mention this technology and describe the development of a Multicast Application Sharing Tool designed specifically for this environment.

PETS2009 and Winter-PETS 2009 results: a combined evaluation

This paper presents the results of the crowd image analysis challenge of the Winter PETS 2009 workshop. The evaluation is carried out using a selection of the metrics developed in the Video Analysis and Content Extraction (VACE) program and the CLassification of Events, Activities, and Relationships (CLEAR) consortium [13]. The evaluation highlights the detection and tracking performance of the authors’systems in areas such as precision, accuracy and robustness. The performance is also compared to the PETS 2009 submitted results.

PETS2010 and PETS2009 evaluation of results using individual ground truthed single views

This paper presents the results of the crowd image analysis challenge of the PETS2010 workshop. The evaluation was carried out using a selection of the metrics developed in the Video Analysis and Content Extraction (VACE) program and the CLassification of Events, Activities, and Relationships (CLEAR) consortium. The PETS 2010 evaluation was performed using new ground truthing create from each independant two dimensional view. In addition, the performance of the submissions to the PETS 2009 and Winter-PETS 2009 were evaluated and included in the results. The evaluation highlights the detection and tracking performance of the authors’ systems in areas such as precision, accuracy and robustness.

Sting jets in simulations of a real cyclone by two mesoscale models

The existence of sting jets as a potential source of damaging surface winds during the passage of extratropical cyclones has recently been recognized However, there are still very few published studies on the subject Furthermore, although ills known that other models are capable of reproducing sting jets, in the published literature only one numerical model [the Met Office Unified Model (MetUM)] has been used to numerically analyze these phenomena This article alms to improve our understanding of the processes that contribute to the development of sting jets and show that model differences affect the evolution of modeled sting jets A sting jet event during the passage of a cyclone over the United Kingdom on 26 February 2002 has been simulated using two mesoscale models namely the MetUM and the Consortium for Small Scale Modeling (COSMO) model to compare their performance Given the known critical importance of vertical resolution in the simulation of sting jets the vertical resolution of both models has been enhanced with respect to their operational versions Both simulations have been verified against surface measurements of maximum gusts, satellite imagery and Met Office operational synoptic analyses, as well as operational analyses from the ECMWF It is shown that both models are capable of reproducing sting jets with similar, though not identical. features Through the comparison of the results from these two models, the relevance of physical mechanisms, such as evaporative cooling and the release of conditional symmetric instability, in the generation and evolution of sting jets is also discussed

Proof of concept of automated mapping of weeds in arable fields

The project investigated whether it would be possible to remove the main technical hindrance to precision application of herbicides to arable crops in the UK, namely creating geo-referenced weed maps for each field. The ultimate goal is an information system so that agronomists and farmers can plan precision weed control and create spraying maps. The project focussed on black-grass in wheat, but research was also carried out on barley and beans and on wild-oats, barren brome, rye-grass, cleavers and thistles which form stable patches in arable fields. Farmers may also make special efforts to control them. Using cameras mounted on farm machinery, the project explored the feasibility of automating the process of mapping black-grass in fields. Geo-referenced images were captured from June to December 2009, using sprayers, a tractor, combine harvesters and on foot. Cameras were mounted on the sprayer boom, on windows or on top of tractor and combine cabs and images were captured with a range of vibration levels and at speeds up to 20 km h-1. For acceptability to farmers, it was important that every image containing black-grass was classified as containing black-grass; false negatives are highly undesirable. The software algorithms recorded no false negatives in sample images analysed to date, although some black-grass heads were unclassified and there were also false positives. The density of black-grass heads per unit area estimated by machine vision increased as a linear function of the actual density with a mean detection rate of 47% of black-grass heads in sample images at T3 within a density range of 13 to 1230 heads m-2. A final part of the project was to create geo-referenced weed maps using software written in previous HGCA-funded projects and two examples show that geo-location by machine vision compares well with manually-mapped weed patches. The consortium therefore demonstrated for the first time the feasibility of using a GPS-linked computer-controlled camera system mounted on farm machinery (tractor, sprayer or combine) to geo-reference black-grass in winter wheat between black-grass head emergence and seed shedding.

An ECOOP web portal for visualising and comparing distributed coastal oceanography model and in situ data

As part of a large European coastal operational oceanography project (ECOOP), we have developed a web portal for the display and comparison of model and in situ marine data. The distributed model and in situ datasets are accessed via an Open Geospatial Consortium Web Map Service (WMS) and Web Feature Service (WFS) respectively. These services were developed independently and readily integrated for the purposes of the ECOOP project, illustrating the ease of interoperability resulting from adherence to international standards. The key feature of the portal is the ability to display co-plotted timeseries of the in situ and model data and the quantification of misfits between the two. By using standards-based web technology we allow the user to quickly and easily explore over twenty model data feeds and compare these with dozens of in situ data feeds without being concerned with the low level details of differing file formats or the physical location of the data. Scientific and operational benefits to this work include model validation, quality control of observations, data assimilation and decision support in near real time. In these areas it is essential to be able to bring different data streams together from often disparate locations.

Integrating the Climate Science Modelling Language with geospatial software and services

Much consideration is rightly given to the design of metadata models to describe data. At the other end of the data-delivery spectrum much thought has also been given to the design of geospatial delivery interfaces such as the Open Geospatial Consortium standards, Web Coverage Service (WCS), Web Map Server and Web Feature Service (WFS). Our recent experience with the Climate Science Modelling Language shows that an implementation gap exists where many challenges remain unsolved. To bridge this gap requires transposing information and data from one world view of geospatial climate data to another. Some of the issues include: the loss of information in mapping to a common information model, the need to create ‘views’ onto file-based storage, and the need to map onto an appropriate delivery interface (as with the choice between WFS and WCS for feature types with coverage-valued properties). Here we summarise the approaches we have taken in facing up to these problems.

Disorder-specific functional abnormalities during sustained attention in youth with Attention Deficit Hyperactivity Disorder (ADHD) and with Autism

Attention Deficit Hyperactivity Disorder (ADHD) and Autism Spectrum Disorder (ASD) are often comorbid and share behavioural-cognitive abnormalities in sustained attention. A key question is whether this shared cognitive phenotype is based on common or different underlying pathophysiologies. To elucidate this question, we compared 20 boys with ADHD to 20 age and IQ matched ASD and 20 healthy boys using functional magnetic resonance imaging (fMRI) during a parametrically modulated vigilance task with a progressively increasing load of sustained attention. ADHD and ASD boys had significantly reduced activation relative to controls in bilateral striato–thalamic regions, left dorsolateral prefrontal cortex (DLPFC) and superior parietal cortex. Both groups also displayed significantly increased precuneus activation relative to controls. Precuneus was negatively correlated with the DLPFC activation, and progressively more deactivated with increasing attention load in controls, but not patients, suggesting problems with deactivation of a task-related default mode network in both disorders. However, left DLPFC underactivation was significantly more pronounced in ADHD relative to ASD boys, which furthermore was associated with sustained performance measures that were only impaired in ADHD patients. ASD boys, on the other hand, had disorder-specific enhanced cerebellar activation relative to both ADHD and control boys, presumably reflecting compensation. The findings show that ADHD and ASD boys have both shared and disorder-specific abnormalities in brain function during sustained attention. Shared deficits were in fronto–striato–parietal activation and default mode suppression. Differences were a more severe DLPFC dysfunction in ADHD and a disorder-specific fronto–striato–cerebellar dysregulation in ASD.

Tropical Cyclones in a hieararchy of climate models of increasing resolution

Tropical Cyclone (TC) is normally not studied at the individual level with Global Climate Models (GCMs), because the coarse grid spacing is often deemed insufficient for a realistic representation of the basic underlying processes. GCMs are indeed routinely deployed at low resolution, in order to enable sufficiently long integrations, which means that only large-scale TC proxies are diagnosed. A new class of GCMs is emerging, however, which is capable of simulating TC-type vortexes by retaining a horizontal resolution similar to that of operational NWP GCMs; their integration on the latest supercomputers enables the completion of long-term integrations. The UK-Japan Climate Collaboration and the UK-HiGEM projects have developed climate GCMs which can be run routinely for decades (with grid spacing of 60 km) or centuries (with grid spacing of 90 km); when coupled to the ocean GCM, a mesh of 1/3 degrees provides eddy-permitting resolution. The 90 km resolution model has been developed entirely by the UK-HiGEM consortium (together with its 1/3 degree ocean component); the 60 km atmospheric GCM has been developed by UJCC, in collaboration with the Met Office Hadley Centre.

Good practice in reviewing and publishing studies on herbal medicine, with special emphasis on traditional Chinese medicine and Chinese materia medica

Ethnopharmacological relevance: Studies on traditional Chinese medicine (TCM), like those of other systems of traditional medicine (TM), are very variable in their quality, content and focus, resulting in issues around their acceptability to the global scientific community. In an attempt to address these issues, an European Union funded FP7 consortium, composed of both Chinese and European scientists and named “Good practice in traditional Chinese medicine” (GP-TCM), has devised a series of guidelines and technical notes to facilitate good practice in collecting, assessing and publishing TCM literature as well as highlighting the scope of information that should be in future publications on TMs. This paper summarises these guidelines, together with what has been learned through GP-TCM collaborations, focusing on some common problems and proposing solutions. The recommendations also provide a template for the evaluation of other types of traditional medicine such as Ayurveda, Kampo and Unani. Materials and methods: GP-TCM provided a means by which experts in different areas relating to TCM were able to collaborate in forming a literature review good practice panel which operated through e-mail exchanges, teleconferences and focused discussions at annual meetings. The panel involved coordinators and representatives of each GP-TCM work package (WP) with the latter managing the testing and refining of such guidelines within the context of their respective WPs and providing feedback. Results: A Good Practice Handbook for Scientific Publications on TCM was drafted during the three years of the consortium, showing the value of such networks. A “deliverable – central questions – labour division” model had been established to guide the literature evaluation studies of each WP. The model investigated various scoring systems and their ability to provide consistent and reliable semi-quantitative assessments of the literature, notably in respect of the botanical ingredients involved and the scientific quality of the work described. This resulted in the compilation of (i) a robust scoring system and (ii) a set of minimum standards for publishing in the herbal medicines field, based on an analysis of the main problems identified in published TCM literature.

Traditional Chinese medicine research in the post-genomic era: good practice, priorities, challenges and opportunities

Background and aims: GP-TCM is the 1st EU-funded Coordination Action consortium dedicated to traditional Chinese medicine (TCM) research. This paper aims to summarise the objectives, structure and activities of the consortium and introduces the position of the consortium regarding good practice, priorities, challenges and opportunities in TCM research. Serving as the introductory paper for the GPTCM Journal of Ethnopharmacology special issue, this paper describes the roadmap of this special issue and reports how the main outputs of the ten GP-TCM work packages are integrated, and have led to consortium-wide conclusions. Materials and methods: Literature studies, opinion polls and discussions among consortium members and stakeholders. Results: By January 2012, through 3 years of team building, the GP-TCM consortium had grown into a large collaborative network involving ∼200 scientists from 24 countries and 107 institutions. Consortium members had worked closely to address good practice issues related to various aspects of Chinese herbal medicine (CHM) and acupuncture research, the focus of this Journal of Ethnopharmacology special issue, leading to state-of-the-art reports, guidelines and consensus on the application of omics technologies in TCM research. In addition, through an online survey open to GP-TCM members and non-members, we polled opinions on grand priorities, challenges and opportunities in TCM research. Based on the poll, although consortium members and non-members had diverse opinions on the major challenges in the field, both groups agreed that high-quality efficacy/effectiveness and mechanistic studies are grand priorities and that the TCM legacy in general and its management of chronic diseases in particular represent grand opportunities. Consortium members cast their votes of confidence in omics and systems biology approaches to TCM research and believed that quality and pharmacovigilance of TCM products are not only grand priorities, but also grand challenges. Non-members, however, gave priority to integrative medicine, concerned on the impact of regulation of TCM practitioners and emphasised intersectoral collaborations in funding TCM research, especially clinical trials. Conclusions: The GP-TCM consortium made great efforts to address some fundamental issues in TCM research, including developing guidelines, as well as identifying priorities, challenges and opportunities. These consortium guidelines and consensus will need dissemination, validation and further development through continued interregional, interdisciplinary and intersectoral collaborations. To promote this, a new consortium, known as the GP-TCM Research Association, is being established to succeed the 3-year fixed term FP7 GP-TCM consortium and will be officially launched at the Final GP-TCM Congress in Leiden, the Netherlands, in April 2012.