Pilot Experiments with Electrodialysis and Ozonation for the Production of a Fertilizer from Urine

Pilot tests were performed with a process combination of electrodialysis and ozonation for the removal of micropollutants and the concentration of nutrients in urine. In continuous and batch experiments, maximum concentration factors up to 3.5 and 4.1 were obtained, respectively. The desalination capacity did not decrease significantly during continuous operation periods of several weeks. Membrane cleaning after 195 days resulted in approximately 35% increase in desalination rate. The Yeast Estrogen Screen (YES), a bioassay that selectively detects oestrogenic compounds, confirmed that about 90% of the oestrogenic activity was removed by electrodialysis. HPLC analysis showed that ibuprofen was removed to a high extent, while other micropollutants were below the detection limit. In view of the fact that ibuprofen is among the most rapidly transported micropollutants in electrodialysis processes, this result indicates that electrodialysis provides an effective barrier for micropollutants. Standardised plant growth tests were performed in the field with the salt solution resulting from the treatment by electrodialysis and subsequent ozonation. The results show that the plant height is comparable to synthetic fertilisers, but the crop yield is slightly lower. The latter is probably caused by volatilisation losses during field application, which can be prevented by improved application technologies

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Islands of conformational stability for Filopodia

Filopodia are long, thin protrusions formed when bundles of fibers grow outwardly from a cell surface while remaining closed in a membrane tube. We study the subtle issue of the mechanical stability of such filopodia and how this depends on the deformation of the membrane that arises when the fiber bundle adopts a helical configuration. We calculate the ground state conformation of such filopodia, taking into account the steric interaction between the membrane and the enclosed semiflexible fiber bundle. For typical filopodia we find that a minimum number of fibers is required for filopodium stability. Our calculation elucidates how experimentally observed filopodia can obviate the classical Euler buckling condition and remain stable up to several tens of . We briefly discuss how experimental observation of the results obtained in this work for the helical-like deformations of enclosing membrane tubes in filopodia could possibly be observed in the acrosomal reactions of the sea cucumber Thyone, and the horseshoe crab Limulus. Any realistic future theories for filopodium stability are likely to rely on an accurate treatment of such steric effects, as analysed in this work

Clinical radiography education across Europe

Purpose: To establish a picture of clinical education models within radiography programmes across Europe by surveying higher education institutions registered as affiliate members of the European Federation of Radiography Societies (EFRS). Method: An online survey was developed to ascertain data on: practical training, supervisory arrangements, placement logistics, quality assurance processes, and the assessment of clinical competencies. Responses were identifiable in terms of educational institution and country. All educational institutions who were affiliate members at the time of the study were invited to participate (n=46). Descriptive and thematic analyses are reported. Results: A response rate of 82.6% (n=38) was achieved from educational institutions representing 21 countries. Over half of responding institutions (n=21) allocated in excess of 60 European Credit Transfer and Accumulation System (ECTS) credits to practical training. In nearly three-quarters of clinical placements there was a dedicated clinical practice supervisor in place; two-thirds of these were employed directly by the hospital. Clinical practice supervisors were typically state registered radiographers, who had a number of years of clinical experience and had received specific training for the role. Typical responsibilities included monitoring student progress, providing feedback and completing paperwork, this did however vary between respondents. In almost all institutions there were support systems in place for clinical placement supervisors within their roles. Conclusions: Similarities exist in the provision of clinical radiography education across Europe. Clinical placements are a core component of radiography education and are supported by experienced clinical practice supervisors. Mechanisms are in place for the selection, training and support of clinical practice supervisors. Professional societies should work collaboratively to establish guidelines for effective clinical placements

Microscopic elasticity of complex systems

Lecture Notes for the Erice Summer School 2005 Computer Simulations in Condensed Matter: from Materials to Chemical Biology. Perspectives in celebration of the 65th Birthday of Mike Klein organized by Kurt Binder, Giovanni Ciccotti and Mauro Ferrari

Schools that Care:The potential benefits and drawbacks of a non-residential alternative educational facility

Effective programs for youth with complex problems are urgently needed given their risk for school drop-out and (residential) out-of-home placement. The main goal of this dissertation was to examine the potential benefits and drawbacks of non-residential alternative educational facilities for adolescents with complex problems, to protect them from these negative outcomes, and work on their future perspective by diminishing problem behavior and strengthening protective factors. Therefore, this dissertation consists of:•A systematic literature review (multilevel meta-analysis) on the outcomes of non-residential alternative educational facilities (chapter 2)•A retrospective longitudinal study on characteristics of adolescents that predict (un)successful completion of School2Care (a Dutch alternative educational facility) (chapter 3)•A cross-sectional study on differences between adolescents allocated to secure residential youth care and School2Care (chapter 4)•A longitudinal study on the development of adolescents after their placement in School2Care, and the prevention of secure residential placement (chapter 5)•A qualitative study on what adolescents, parents and teachers consider to be facilitators and barriers to successful outcomes of School2Care (chapter 6)•A general discussion on the overall findings of the separate studies (chapter 7

Lipid membranes for membrane proteins

Andreas Kukol, ‘Lipid membranes for membrane proteins in Molecular Modeling of Proteins (Clifton: Humana Press/Sringer, 2015), ISBN: 978-1-4939-1464-7, e-BOOK ISBN: 978-1-4939-1465-4Peer reviewe

Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes

The human salivary amylase genes display extensive copy number variation (CNV), and recent work has implicated this variation in adaptation to starch-rich diets, and in association with body mass index. In this work, we use paralogue ratio tests, microsatellite analysis, read depth and fibre-FISH to demonstrate that human amylase CNV is not a smooth continuum, but is instead partitioned into distinct haplotype classes. There is a fundamental structural distinction between haplotypes containing odd or even numbers of AMY1 gene units, in turn coupled to CNV in pancreatic amylase genes AMY2A and AMY2B. Most haplotypes have one copy each of AMY2A and AMY2B and contain an odd number of copies of AMY1; consequently, most individuals have an even total number of AMY1. In contrast, haplotypes carrying an even number of AMY1 genes have rearrangements leading to CNVs ofAMY2A/AMY2B. Read-depth and experimental data showthat different populations harbour different proportions of these basic haplotype classes. In Europeans, the copy numbers of AMY1 and AMY2A are correlated, so that phenotypic associations caused by variation in pancreatic amylase copy number could be detected indirectly as weak association with AMY1 copy number.We showthat the quantitative polymerase chain reaction (qPCR) assay previously applied to the high-throughput measurement of AMY1 copy number is less accurate than the measures we use and that qPCR data in other studies have been further compromised by systematic miscalibration. Our results uncover new patterns in human amylase variation and imply a potential role for AMY2 CNV in functional associations

Lattice-switch Monte Carlo

We present a Monte Carlo method for the direct evaluation of the difference between the free energies of two crystal structures. The method is built on a lattice-switch transformation that maps a configuration of one structure onto a candidate configuration of the other by `switching' one set of lattice vectors for the other, while keeping the displacements with respect to the lattice sites constant. The sampling of the displacement configurations is biased, multicanonically, to favor paths leading to `gateway' arrangements for which the Monte Carlo switch to the candidate configuration will be accepted. The configurations of both structures can then be efficiently sampled in a single process, and the difference between their free energies evaluated from their measured probabilities. We explore and exploit the method in the context of extensive studies of systems of hard spheres. We show that the efficiency of the method is controlled by the extent to which the switch conserves correlated microstructure. We also show how, microscopically, the procedure works: the system finds gateway arrangements which fulfill the sampling bias intelligently. We establish, with high precision, the differences between the free energies of the two close packed structures (fcc and hcp) in both the constant density and the constant pressure ensembles.Comment: 34 pages, 9 figures, RevTeX. To appear in Phys. Rev.

Multiple verification in computational modeling of bone pathologies

We introduce a model checking approach to diagnose the emerging of bone pathologies. The implementation of a new model of bone remodeling in PRISM has led to an interesting characterization of osteoporosis as a defective bone remodeling dynamics with respect to other bone pathologies. Our approach allows to derive three types of model checking-based diagnostic estimators. The first diagnostic measure focuses on the level of bone mineral density, which is currently used in medical practice. In addition, we have introduced a novel diagnostic estimator which uses the full patient clinical record, here simulated using the modeling framework. This estimator detects rapid (months) negative changes in bone mineral density. Independently of the actual bone mineral density, when the decrease occurs rapidly it is important to alarm the patient and monitor him/her more closely to detect insurgence of other bone co-morbidities. A third estimator takes into account the variance of the bone density, which could address the investigation of metabolic syndromes, diabetes and cancer. Our implementation could make use of different logical combinations of these statistical estimators and could incorporate other biomarkers for other systemic co-morbidities (for example diabetes and thalassemia). We are delighted to report that the combination of stochastic modeling with formal methods motivate new diagnostic framework for complex pathologies. In particular our approach takes into consideration important properties of biosystems such as multiscale and self-adaptiveness. The multi-diagnosis could be further expanded, inching towards the complexity of human diseases. Finally, we briefly introduce self-adaptiveness in formal methods which is a key property in the regulative mechanisms of biological systems and well known in other mathematical and engineering areas.Comment: In Proceedings CompMod 2011, arXiv:1109.104