Towards a service-oriented e-infrastructure for multidisciplinary environmental research

Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures

Base excision repair AP endonucleases and mismatch repair act together to induce checkpoint-mediated autophagy

Cellular responses to DNA damage involve distinct DNA repair pathways, such as mismatch repair (MMR) and base excision repair (BER). Using Caenorhabditis elegans as a model system, we present genetic and molecular evidence of a mechanistic link between processing of DNA damage and activation of autophagy. Here we show that the BER AP endonucleases APN-1 and EXO-3 function in the same pathway as MMR, to elicit DNA-directed toxicity in response to 5-fluorouracil, a mainstay of systemic adjuvant treatment of solid cancers. Immunohistochemical analyses suggest that EXO-3 generates the DNA nicks required for MMR activation. Processing of DNA damage via this pathway, in which both BER and MMR enzymes are required, leads to induction of autophagy in C. elegans and human cells. Hence, our data show that MMR- and AP endonuclease-dependent processing of 5-fluorouracil-induced DNA damage leads to checkpoint activation and induction of autophagy, whose hyperactivation contributes to cell death. © 2013 Macmillan Publishers Limited. All rights reserved

Evaluating surgical skills from kinematic data using convolutional neural networks

The need for automatic surgical skills assessment is increasing, especially because manual feedback from senior surgeons observing junior surgeons is prone to subjectivity and time consuming. Thus, automating surgical skills evaluation is a very important step towards improving surgical practice. In this paper, we designed a Convolutional Neural Network (CNN) to evaluate surgeon skills by extracting patterns in the surgeon motions performed in robotic surgery. The proposed method is validated on the JIGSAWS dataset and achieved very competitive results with 100% accuracy on the suturing and needle passing tasks. While we leveraged from the CNNs efficiency, we also managed to mitigate its black-box effect using class activation map. This feature allows our method to automatically highlight which parts of the surgical task influenced the skill prediction and can be used to explain the classification and to provide personalized feedback to the trainee.Comment: Accepted at MICCAI 201

Supporting multidisciplinary model-based water management projects: a user perspective

Multidisciplinary model-based water management is a complex process. Projects that have to follow this process may encounter many problems, related to miscommunication, malpractice, misuse of the model, insufficient knowledge of the modeled problems and overselling of model capabilities. This leads to model projects, which are not transparent and difficult to audit. The knowledge-based system consists of an ontological knowledge base (KB) with ‘best modelling practices’ for teams, which members have different disciplinary backgrounds and play different roles in a project, and a Modelling Support Tool (MoST). MoST generates and presents guidelines from the KB on what to do. MoST also monitors what team members do in an electronic model journal and facilitates converting model journals into model reports for various audiences and purposes. Water managers can benefit from MoST and its KB in different ways: (1) during project set-up in defining what has to be done and finding a team to do the job, (2) at regular intervals in evaluating what has been done and planning of what has to be done, and (3) to check project progress. Modelers are guided by MoST on what to do, get access to what other team members did and helped keeping records of their work in the project. Auditors can easily follow the audit trail left in a model journal and are helped to appraise modelling projects. Stakeholders and public can be informed and consulted using MoST. In this way MoST and its KB facilitate cooperating in modelling projects and improve their quality. Parts of the technology of MoST and its KB can be reused to support other types of (simulation) modelling or even other types of processes (i.e. not focusing on modelling

Woody and non-woody biomass utilisation for fuel and implications on plant nutrients availability in the Mukehantuta watershed in Ethiopia

Plant biomass is a major source of energy for households in eastern Africa. Unfortunately, the heavy reliance on this form of energy is a threat to forest ecosystems and a recipe for accelerated land resource degradation. Due to the increasing scarcity of traditional fuel wood resources, rural communities have shifted to utilisation of crop residues and cattle dung; which otherwise, are resources for soil fertility improvement. The objective of this study was to assess the supply and consumption patterns of fuel biomass and estimate the amount of nutrients that could be lost from burning non-woody biomass energy sources. A survey was conducted in the Mukehantuta watershed in Ethiopia, using a semi-structured questionnaire. An inventory of woody biomass was also carried out on the existing stock in the watershed. Annually, households in the watershed used 1999, 943, 11, 34 and 229 metric tonnes of wood, dung, charcoal, crop residue and tree residues, respectively. The existing wood biomass in the watershed was approximately 292 metric tonnes, implying that consumption exceeds potential supply. As a result of using dung and crop residue biomass for household energy, the watershed, respectively, loses 17.3, 4.3, 20.6, 15.6, 5.4, and 10.2 tonnes of N, P, K, Ca, Mg and Fe nutrients every year. The lost nutrients in terms of fertiliser equivalency are estimated at 37.5 tons of urea and 9.3 tons of Di-ammonium phosphate (DAP).La biomasse des cultures constitue une source importante d\u2019\ue9nergie pour les m\ue9nages en Afrique de l\u2019Est. Malheureusement, une grande d\ue9pendance sur cette forme d\u2019\ue9nergie est une menace aux \ue9cosyt\ue8mes forestiers et facteur pour la d\ue9gradation acc\ue9l\ue9r\ue9e des ressources de terre. Suite au manque accru des ressources traditionnelles en bois, les communaut\ue9s rurales ont opt\ue9 pour l\u2019utilisation des r\ue9sidues des cultures et la bouse, qui, sont autrement, des ressources pour l\u2019am\ue9lioration de la fertilit\ue9 du sol. L\u2019objectif de cette \ue9tude \ue9tait d\u2019\ue9valuer les tendances d\u2019approvisionnement et consommation de l\u2019\ue9nergie par la biomasse des cultures et estimer le la quantit\ue9 d\u2019\ue9lements min\ue9raux pouvant \ueatre perdus \ue0 travers la biomasse brul\ue9e pour \ue9nergie. Une enqu\ueate \ue9tait conduite dans le basin versant de Mukehantuta en Ethiopie, par utilisation d\u2019un questionnaire semi-structur\ue9. Un inventaire de biomass en bois \ue9tait aussi fait sur les reserves existantes dans le basin versant. Annuellement, les m\ue9nages dans le basin versant ont utilis\ue9 1999, 943, 11, 34 et 229 tonnes de bois, bouse, charbon, r\ue9sidues des cultures, et r\ue9sidues des bois, respectivement. La biomasse de bois existant dans le basin versant \ue9tait approximativement 292 tonnes, indicant que la consummation exc\ue8de l\u2019approvisionnement potentiel. Comme r\ue9sultats d\u2019utilisation de la bouse et la biomasse des r\ue9sidues de cultures comme source d\u2019\ue9nergie dans les m\ue9nages, le basin versant perd des min\ue9raux \ue9quivalent \ue0 17.3, 4.3, 20.6, 15.6, 5.4, et 10.2 tonnes N, P, K, Ca, Mg et Fe chaque ann\ue9e. La perte d\u2019\ue9lements min\ue9raux en termes d\u2019\ue9quivalent engrais est estim\ue9e \ue0 37.5 tonnes d\u2019ur\ue9e et 9.3 tonnes de Di-ammonium phosphate (DAP)

Structuring multidisciplinary knowledge for model-based water management: the HarmoniQuA approach

The Water Framework Directive (WFD) provides European policy at the river basin scale. It explicitly states that water resource models should be applied. The EU- financed project HarmoniQuA aims at improving the quality of model based water management at catchment and river basin scales by providing guidance throughout the modelling process and by supporting all persons involved (water managers, modellers, auditors, stakeholders and concerned members of the public) in their activities. The guidelines are based on accepted and common methodology and practices of experienced modellers. This knowledge is collected, completed, improved and made available in the form of a Knowledge Base, using state-of-the-art knowledge engineering technology with an ontological approach. MoST, the software tool of HarmoniQuA, provides guidance from the Knowledge Base it supports monitoring of the modelling activities and reporting to various audiences. In the future MoST will use expertise collected in previous modelling studies to advise on how to perform the model study at hand. This paper focuses on how HarmoniQuA handles and improves existing knowledge on modelling for water managemen

Gene expression profiles classifying clinical stages of tuberculosis and monitoring treatment responses in Ethiopian HIV-negative and HIV-positive cohorts.

BACKGROUND: Validation of previously identified candidate biomarkers and identification of additional candidate gene expression profiles to facilitate diagnosis of tuberculosis (TB) disease and monitoring treatment responses in the Ethiopian context is vital for improving TB control in the future. METHODS: Expression levels of 105 immune-related genes were determined in the blood of 80 HIV-negative study participants composed of 40 active TB cases, 20 latent TB infected individuals with positive tuberculin skin test (TST+), and 20 healthy controls with no Mycobacterium tuberculosis (Mtb) infection (TST-), using focused gene expression profiling by dual-color Reverse-Transcription Multiplex Ligation-dependent Probe Amplification assay. Gene expression levels were also measured six months after anti-TB treatment (ATT) and follow-up in 38 TB patients. RESULTS: The expression of 15 host genes in TB patients could accurately discriminate between TB cases versus both TST+ and TST- controls at baseline and thus holds promise as biomarker signature to classify active TB disease versus latent TB infection in an Ethiopian setting. Interestingly, the expression levels of most genes that markedly discriminated between TB cases versus TST+ or TST- controls did not normalize following completion of ATT therapy at 6 months (except for PTPRCv1, FCGR1A, GZMB, CASP8 and GNLY) but had only fully normalized at the 18 months follow-up time point. Of note, network analysis comparing TB-associated host genes identified in the current HIV-negative TB cohort to TB-associated genes identified in our previously published Ethiopian HIV-positive TB cohort, revealed an over-representation of pattern recognition receptors including TLR2 and TLR4 in the HIV-positive cohort which was not seen in the HIV-negative cohort. Moreover, using ROC cutoff ≥ 0.80, FCGR1A was the only marker with classifying potential between TB infection and TB disease regardless of HIV status. CONCLUSIONS: Our data indicate that complex gene expression signatures are required to measure blood transcriptomic responses during and after successful ATT to fully diagnose TB disease and characterise drug-induced relapse-free cure, combining genes which resolve completely during the 6-months treatment phase of therapy with genes that only fully return to normal levels during the post-treatment resolution phase

Quality Assurance of the modelling process

The present paper briefly describes a new modelling support tool (MoST) aimed at facilitating better quality assurance of the modelling process. MoST comprises a Knowledge Base with guidelines on good modelling practise for seven scientific domains. It supports multi-domain modelling and working in teams of different user types (water managers, modellers, auditors/reviewers, stakeholders and members of the public). The key functionality of MoST is to: (a) Guide to ensure that a model has been properly applied; (b) Monitor to record decisions, methods and data used in the modelling work and in this way enable transparency and reproducibility of the modelling process; (c) Report to provide suitable reports on what has been done by the various actors. MoST has been developed under the HarmoniQuA project (www.HarmoniQuA.org

Integrated Modelling Frameworks for Environmental Assessment and Decision Support

As argued in Chapter 1, modern management of environmental resources defines problems from a holistic and integrated perspective, thereby imposing strong requirements on Environmental Decision Support Systems (EDSSs) and Integrated Assessment Tools (IATs). These systems and tools tend to be increasingly complex in terms of software architecture and computational power in order to cope with the type of problems they must solve. For instance, the discipline of Integrated Assessment (IA) needs tools that arc able to span a wide range of disciplines, from socio-economics to ecology to hydrology. Such tools must support a wide range of methodologies and techniques like agent-based modeling, Bayesian decision networks, optimization, multicriteria analyses and visualization tools, to name a few