Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM , which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development

<i>In situ</i> diagnostics of the crystal-growth process through neutron imaging:application to scintillators

Neutrons are known to be unique probes in situations where other types of radiation fail to penetrate samples and their surrounding structures. In this paper it is demonstrated how thermal and cold neutron radiography can provide time-resolved imaging of materials while they are being processed (e.g. while growing single crystals). The processing equipment, in this case furnaces, and the scintillator materials are opaque to conventional X-ray interrogation techniques. The distribution of the europium activator within a BaBrCl:Eu scintillator (0.1 and 0.5% nominal doping concentrations per mole) is studied in situ during the melting and solidification processes with a temporal resolution of 5-7 s. The strong tendency of the Eu dopant to segregate during the solidification process is observed in repeated cycles, with Eu forming clusters on multiple length scales (only for clusters larger than ∼50 µm, as limited by the resolution of the present experiments). It is also demonstrated that the dopant concentration can be quantified even for very low concentration levels (∼0.1%) in 10 mm thick samples. The interface between the solid and liquid phases can also be imaged, provided there is a sufficient change in concentration of one of the elements with a sufficient neutron attenuation cross section. Tomographic imaging of the BaBrCl:0.1%Eu sample reveals a strong correlation between crystal fractures and Eu-deficient clusters. The results of these experiments demonstrate the unique capabilities of neutron imaging for in situ diagnostics and the optimization of crystal-growth procedures

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

<p>Abstract</p> <p>Background</p> <p>To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory.</p> <p>Results</p> <p>To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data.</p> <p>Conclusions</p> <p>We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.</p

Exploring spatial resolution enhancements on IMAT for steel corrosion studies

Neutron imaging offers benefits over X-rays for steel corrosion studies including deep penetration and high sensitivity to some light elements such as hydrogen. However, the resolution is frequently at or below the thickness of the corroded layer. This work demonstrates two approaches to enhance the spatial resolution on IMAT at the ISIS neutron source. The first approach shows that a fiber optics taper attached to an optical camera box for white beam imaging can achieve a spatial resolution down to 15 μm. The second approach uses event centroiding with a Timepix3-based detector for diffraction contrast imaging achieving a spatial resolution of 30 μm. These results support advances in corrosion and degradation studies of steel using neutron imaging

Characterization of a mock up nuclear waste package using energy resolved MeV neutron analysis

Reliable radiographic methods for characterizing nuclear waste packages non-destructively (without the need to open containers) have the potential to significantly contribute to safe handling and future disposal options, particularly for legacy waste of unknown content. Due to required shielding of waste containers and the need to characterize materials consisting of light elements, X-ray methods are not suitable. Here, energy-resolved MeV neutron radiography is demonstrated as a first-of-its-kind application for non-destructive and remote examination of mock up nuclear waste packages from a safe position using time-of-flight techniques enabled by a novel event-mode imaging detector system. Energy-resolved neutron transmission spectra were measured spatially, permitting the detection of analogue materials to actual nuclear waste such as water, melamine, and ion exchange resin within a 2.54 cm wall thickness steel pipe. The results demonstrate the capability to locate the materials through this wall thickness by radiography and tomographic reconstruction, revealing detailed 3D distributions and structural anomalies. The method effectively detects residual water in ion exchange resin, highlighting its sensitivity to moisture content, a crucial parameter for nuclear waste characterization. Monte Carlo simulations are in agreement with the experimental findings, providing a pathway to simulate waste forms more difficult to tackle experimentally. This work paves the way to apply sub-nanosecond intense MeV neutron sources, such as laser-driven neutron sources under development, to nuclear waste characterization

Bro1 binding to Snf7 regulates ESCRT-III membrane scission activity in yeast

The ubiquitin hydrolase activating factor Bro1 enhances ESCRT-III stability by inhibiting Vps4-mediated disassembly

Energy-resolved fast-neutron radiography using an event-mode neutron imaging detector

Energy-resolved fast-neutron radiography is a powerful non-destructive technique that can be used to remotely measure the quantity and distribution of elements and isotopes in a sample. This is done by comparing the energy-dependent neutron transmission of a sample with the known cross-sections of individual isotopes. The reconstruction of the composition is possible due to the unique features (e.g. resonances) in the cross-sections of individual isotopes. At short-pulsed (<~ 1 ns) neutron sources, such information is accessible via time-of-flight neutron imaging in principle, but requires a detector with nanosecond temporal resolution. Conventional neutron detectors can meet this requirement only by heavily compromising spatial resolution or efficiency. Here, we present a unique approach on fast neutron resonance radiography using a scintillator-based event-mode imaging detector at a short-pulsed neutron source, including first results on spatially mapped resonance profiles using MeV neutrons. The event mode approach applied in the presented detector allows recording of individual neutron interactions with nanosecond precision in time and sub-mm resolution in space. As a result, the entire available neutron energy spectrum can be measured for each pulse. At the same time, the use of a thick scintillator screen and lenses to focus the produced light results in a highly flexible field of view and a high interaction probability in the sensitive volume of the detector