The 26S proteasome system degrades the ERM transcription factor and regulates its transcription-enhancing activity

ERM is a member of the ETS transcription factor family. High levels of the corresponding mRNA are detected in a variety of human breast cancer cell lines, as well as in aggressive human breast tumors. As ERM protein is almost undetectable in these cells, high degradation of this transcription factor has been postulated. Here we have investigated whether ERM degradation might depend on the proteasome pathway. We show that endogenous and ectopically expressed ERM protein is short-lived protein and undergoes proteasome-dependent degradation. Deletion mutagenesis studies indicate that the 61 C-terminal amino acids of ERM are critical for its proteolysis and serve as a degradation signal. Although ERM conjugates with ubiquitin, this post-translational modification does not depend on the C-terminal domain. We have used an Ets-responsive ICAM-1 reporter plasmid to show that the ubiquitin-proteasome pathway can affect transcriptional function of ERM. Thus, ERM is subject to degradation via the 26S proteasome pathway, and this pathway probably plays an important role in regulating ERM transcriptional activity. © 2007 Nature Publishing Group. All rights reserved.

Geochemical and isotopic evidence for seawater contamination of the hydrothermal system of Taal volcano, Luzon, the Philippines

The hydrologic structure of Taal Volcano has favored development of an extensive hydrothermal system whose prominent feature is the acidic Main Crater Lake (pH<3) lying in the center of an active vent complex, which is surrounded by a slightly alkaline caldera lake (Lake Taal). This peculiar situation makes Taal prone to frequent, and sometimes catastrophic, hydrovolcanic eruptions. Fumaroles, hot springs, and lake waters were sampled in 1991, 1992, and 1995 in order to develop a geochemical model for the hydrothermal system. The low-temperature fumarole compositions indicate strong interaction of magmatic vapors with the hydrothermal system under relatively oxidizing conditions. The thermal waters consist of highly, moderately, and weakly mineralized solutions, but none of them corresponds to either water-rock equilibrium or rock dissolution. The concentrated discharges have high Na contents (>3500 mg/kg) and low SO4/Cl ratios (<0.3). The Br/Cl ratio of most samples suggests incorporation of seawater into the hydrothermal system. Water and dissolved sulfate isotopic compositions reveal that the Main Crater Lake and spring discharges are derived from a deep parent fluid (T≃300°C), which is a mixture of seawater, volcanic water, and Lake Taal water. The volcanic end member is probably produced in the magmatic-hydrothermal environment during absorption of high-temperature gases into groundwater. Boiling and mixing of the parent water give rise to the range of chemical and isotopic characteristics observed in the thermal discharges. Incursion of seawater from the coastal region to the central part of the volcano is supported by the low water levels of the lakes and by the fact that Lake Taal was directly connected to the China sea until the sixteenth century. The depth to the seawater-meteoric water interface is calculated to be 80 and 160 m for the Main Crater Lake and Lake Taal, respectively. Additional data are required to infer the hydrologic structure of Taal. Geochemical surveillance of the Main Crater Lake using the SO4/Cl, Na/K, or Mg/Cl ratio cannot be applied straightforwardly due to the presence of seawater in the hydrothermal system.

Inversion of light scattering data by singular system analysis

We consider the problem of inverting experimental data obtained in light scattering experiments described by linear theories. We discuss applications to particle sizing and we describe fast and easy-to-implement algorithms which permit the extraction, from noisy measurements, of reliable information about the particle size distribution. © 1987, SPIE.

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

Idiotypic networks and self-recognition in the immune system.

Journal Article

Modulation of the complement system in monocytes contributes to tuberculosis-associated immune reconstitution inflammatory syndrome.

Tuberculosis-associated immune reconstitution inflammatory syndrome (TB-IRIS) is a common complication in HIV-TB co-infected patients receiving combined antiretroviral therapy (cART). This study investigated a putative contribution of monocytes to the development of TB-IRIS.

A novel neural/symbolic hybrid approach to heuristically optimized fuel allocation and automated revision of heuristics in nuclear engineering

FUELCON is an expert system for optimized refueling design in nuclear engineering. This task is crucial for keeping down operating costs at a plant without compromising safety. FUELCON proposes sets of alternative configurations of allocation of fuel assemblies that are each positioned in the planar grid of a horizontal section of a reactor core. Results are simulated, and an expert user can also use FUELCON to revise rulesets and improve on his or her heuristics. The successful completion of FUELCON led this research team into undertaking a panoply of sequel projects, of which we provide a meta-architectural comparative formal discussion. In this paper, we demonstrate a novel adaptive technique that learns the optimal allocation heuristic for the various cores. The algorithm is a hybrid of a fine-grained neural network and symbolic computation components. This hybrid architecture is sensitive enough to learn the particular characteristics of the ‘in-core fuel management problem’ at hand, and is powerful enough to use this information fully to automatically revise heuristics, thus improving upon those provided by a human expert.

Fire field modelling using the SMARTFIRE automated dynamic solution control environment

SMARTFIRE is a fire field model based on an open architecture integrated CFD code and knowledge-based system. It makes use of the expert system to assist the user in setting up the problem specification and new computational techniques such as Group Solvers to reduce the computational effort involved in solving the equations. This paper concentrates on recent research into the use of artificial intelligence techniques to assist in dynamic solution control of fire scenarios being simulated using fire field modelling techniques. This is designed to improve the convergence capabilities of the software while further decreasing the computational overheads. The technique automatically controls solver relaxations using an integrated production rule engine with a blackboard to monitor and implement the required control changes during solution processing. Initial results for a two-dimensional fire simulation are presented that demonstrate the potential for considerable savings in simulation run-times when compared with control sets from various sources. Furthermore, the results demonstrate enhanced solution reliability due to obtaining acceptable convergence within each time step unlike some of the comparison simulations.

Chapter 2: Predicting Newcomer Integration in Online Knowledge Communities by Automated Dialog Analysis

Nistor, N., Dascalu, M., Stavarache, L.L., Tarnai, C., & Trausan-Matu, S. (2015). Predicting Newcomer Integration in Online Knowledge Communities by Automated Dialog Analysis. In Y. Li, M. Chang, M. Kravcik, E. Popescu, R. Huang, Kinshuk & N.-S. Chen (Eds.), State-of-the-Art and Future Directions of Smart Learning (Vol. Lecture Notes in Educational Technology, pp. 13–17). Berlin, Germany: Springer-Verlag Singapur

ReaderBench: Automated evaluation of collaboration based on cohesion and dialogism

Dascalu, M., Trausan-Matu, S., McNamara, D.S., & Dessus, P. (2015). ReaderBench – Automated Evaluation of Collaboration based on Cohesion and Dialogism. International Journal of Computer-Supported Collaborative Learning, 10(4), 395–423. doi: 10.1007/s11412-015-9226-y

D4.2 – Full Design Document

This deliverable outlines the design blueprints for the RAGE application scenario games and forms the rest of the scope for WP4’s tasks. The game designs have been developed in collaboration with application scenario partners in WP5, and informed by WP1, 2 & 3. Additionally peer-feedback has been provided by game developers across WP4. The designs outline the integration of the RAGE assets developed in WP2 and WP3. Each section provides in detail the game play descriptions, game dynamics and mechanics, pedagogies and technical implementation of the RAGE assets into the game applications as described in detailed in WP5’s application documents. The full description of the application objectives and associated learning outcomes has been provided in the project’s MS2 Application Scenario Outlines document.

Automated analysis of non-mass-enhancing lesions in breast MRI based on morphological, kinetic, and spatio-temporal moments and joint segmentation-motion compensation technique

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) represents an established method for the detection and diagnosis of breast lesions. While mass-like enhancing lesions can be easily categorized according to the Breast Imaging Reporting and Data System (BI-RADS) MRI lexicon, a majority of diagnostically challenging lesions, the so called non-mass-like enhancing lesions, remain both qualitatively as well as quantitatively difficult to analyze. Thus, the evaluation of kinetic and/or morphological characteristics of non-masses represents a challenging task for an automated analysis and is of crucial importance for advancing current computer-aided diagnosis (CAD) systems. Compared to the well-characterized mass-enhancing lesions, non-masses have no well-defined and blurred tumor borders and a kinetic behavior that is not easily generalizable and thus discriminative for malignant and benign non-masses. To overcome these difficulties and pave the way for novel CAD systems for non-masses, we will evaluate several kinetic and morphological descriptors separately and a novel technique, the Zernike velocity moments, to capture the joint spatio-temporal behavior of these lesions, and additionally consider the impact of non-rigid motion compensation on a correct diagnosis.

ALES: a multi-mission adaptive sub-waveform retracker for coastal and open ocean altimetry

Satellite altimetry has revolutionized our understanding of ocean dynamics thanks to frequent sampling and global coverage. Nevertheless, coastal data have been flagged as unreliable due to land and calm water interference in the altimeter and radiometer footprint and uncertainty in the modelling of high-frequency tidal and atmospheric forcing. Our study addresses the first issue, i.e. altimeter footprint contamination, via retracking, presenting ALES, the Adaptive Leading Edge Subwaveform retracker. ALES is potentially applicable to all the pulse-limited altimetry missions and its aim is to retrack both open ocean and coastal data with the same accuracy using just one algorithm. ALES selects part of each returned echo and models it with a classic ”open ocean” Brown functional form, by means of least square estimation whose convergence is found through the Nelder-Mead nonlinear optimization technique. By avoiding echoes from bright targets along the trailing edge, it is capable of retrieving more coastal waveforms than the standard processing. By adapting the width of the estimation window according to the significant wave height, it aims at maintaining the accuracy of the standard processing in both the open ocean and the coastal strip. This innovative retracker is validated against tide gauges in the Adriatic Sea and in the Greater Agulhas System for three different missions: Envisat, Jason-1 and Jason-2. Considerations of noise and biases provide a further verification of the strategy. The results show that ALES is able to provide more reliable 20-Hz data for all three missions in areas where even 1-Hz averages are flagged as unreliable in standard products. Application of the ALES retracker led to roughly a half of the analysed tracks showing a marked improvement in correlation with the tide gauge records, with the rms difference being reduced by a factor of 1.5 for Jason-1 and Jason-2 and over 4 for Envisat in the Adriatic Sea (at the closest point to the tide gauge).

Fine-scale nutrient and carbonate system dynamics around cold-water coral reefs in the northeast Atlantic.

Ocean acidification has been suggested as a serious threat to the future existence of cold-water corals (CWC). However, there are few fine-scale temporal and spatial datasets of carbonate and nutrients conditions available for these reefs, which can provide a baseline definition of extant conditions. Here we provide observational data from four different sites in the northeast Atlantic that are known habitats for CWC. These habitats differ by depth and by the nature of the coral habitat. At depths where CWC are known to occur across these sites the dissolved inorganic carbon ranged from 2088 to 2186 μmol kg−1, alkalinity ranged from 2299 to 2346 μmol kg−1, and aragonite Ω ranged from 1.35 to 2.44. At two sites fine-scale hydrodynamics caused increased variability in the carbonate and nutrient conditions over daily time-scales. The observed high level of variability must be taken into account when assessing CWC sensitivities to future environmental change.

A method for semi-automated objective quantification of linear bedforms from multi-scale Digital Elevation Models

The increasing availability of large, detailed digital representations of the Earth’s surface demands the application of objective and quantitative analyses. Given recent advances in the understanding of the mechanisms of formation of linear bedform features from a range of environments, objective measurement of their wavelength, orientation, crest and trough positions, height and asymmetry is highly desirable. These parameters are also of use when determining observation-based parameters for use in many applications such as numerical modelling, surface classification and sediment transport pathway analysis. Here, we (i) adapt and extend extant techniques to provide a suite of semi-automatic tools which calculate crest orientation, wavelength, height, asymmetry direction and asymmetry ratios of bedforms, and then (ii) undertake sensitivity tests on synthetic data, increasingly complex seabeds and a very large-scale (39 000km2) aeolian dune system. The automated results are compared with traditional, manually derived,measurements at each stage. This new approach successfully analyses different types of topographic data (from aeolian and marine environments) from a range of sources, with tens of millions of data points being processed in a semi-automated and objective manner within minutes rather than hours or days. The results from these analyses show there is significant variability in all measurable parameters in what might otherwise be considered uniform bedform fields. For example, the dunes of the Rub’ al Khali on the Arabian peninsula are shown to exhibit deviations in dimensions from global trends. Morphological and dune asymmetry analysis of the Rub’ al Khali suggests parts of the sand sea may be adjusting to a changed wind regime from that during their formation 100 to 10 ka BP.