U.S. EPA, Pesticide Product Label, NIAGARA PYRENONE CROP SPRAY INSECTICIDE, 06/06/1973

EPA Pesticide Factsheets

2011-04-13

... pi! t \\\\"1 t! 1 fl'd \\ •. p \\\\IIII\\I/IH \\ITLiL\\TOh" \\.\\" I ,·,,,h .. , :, J[,,"I,, '1,I'l-lLI !'q; n"qo Cr,'{l ~PLI\\ ' III Lf '1d!ltn\\ In d.,· d,On? ... hL' a( tl":(' lous{' stav,cs.. ...

A high-performance model for shallow-water simulations in distributed and heterogeneous architectures

NASA Astrophysics Data System (ADS)

Conde, Daniel; Canelas, Ricardo B.; Ferreira, Rui M. L.

2017-04-01

One of the most common challenges in hydrodynamic modelling is the trade off one must make between highly resolved simulations and the time required for their computation. In the particular case of urban floods, modelers are often forced to simplify the complex geometries of the problem, or to implicitly include some of its hydrodynamic effects, due to the typically very large spatial scales involved and limited computational resources. At CEris - Instituto Superior Técnico, Universidade de Lisboa - the STAV-2D shallow-water model, particularly suited for strong transient flows in complex and dynamic geometries, has been under development for the past recent years (Canelas et al., 2013 & Conde et al., 2013). The model is based on an explicit, first-order 2DH finite-volume discretization scheme for unstructured triangular meshes, in which a flux-splitting technique is paired with a reviewed Roe-Riemann solver, yielding a model applicable to discontinuous flows over time-evolving geometries. STAV-2D features solid transport in both Euleran and Lagrangian forms, with the first aiming at describing the transport of fine natural sediments and the latter aimed at large individual debris. The model has been validated with theoretical solutions and laboratory experiments (Canelas et al., 2013 & Conde et al., 2015). This work presents our most recent effort in STAV-2D: the re-design of the code in a modern Object-Oriented parallel framework for heterogeneous computations in CPUs and GPUs. The programming language of choice for this re-design was C++, due to its wide support of established and emerging parallel programming interfaces. The current implementation of STAV-2D provides two different levels of parallel granularity: inter-node and intra-node. Inter-node parallelism is achieved by distributing a simulation across a set of worker nodes, with communication between nodes being explicitly managed through MPI. At this level, the main difficulty is associated with the unstructured nature of the mesh topology with the corresponding employed solution, based on space-filling curves, being analyzed and discussed. Intra-node parallelism is achieved through OpenMP for CPUs and CUDA for GPUs, depending on which kind of device the process is running. Here the main difficulty is associated with the Object-Oriented approach, where the presence of complex data structures can degrade model performance considerably. STAV-2D now supports fully distributed and heterogeneous simulations where multiple different devices can be used to accelerate computation time. The advantages, short-comings and specific solutions for the employed unified Object-Oriented approach, where the source code for CPU and GPU has the same compilation units (no device specific branches like seen in available models), are discussed and quantified with a thorough scalability and performance analysis. The assembled parallel model is expected to achieve faster than real-time simulations for high resolutions (from meters to sub-meter) in large scaled problems (from cities to watersheds), effectively bridging the gap between detailed and timely simulation results. Acknowledgements This research as partially supported by Portuguese and European funds, within programs COMPETE2020 and PORL-FEDER, through project PTDC/ECM-HID/6387/2014 and Doctoral Grant SFRH/BD/97933/2013 granted by the National Foundation for Science and Technology (FCT). References Canelas, R.; Murillo, J. & Ferreira, R.M.L. (2013), Two-dimensional depth-averaged modelling of dam-break flows over mobile beds. Journal of Hydraulic Research, 51(4), 392-407. Conde, D. A. S.; Baptista, M. A. V.; Sousa Oliveira, C. & Ferreira, R. M. L. (2013), A shallow-flow model for the propagation of tsunamis over complex geometries and mobile beds, Nat. Hazards and Earth Syst. Sci., 13, 2533-2542. Conde, D. A. S.; Telhado, M. J.; Viana Baptista, M. A. & Ferreira, R. M. L. (2015) Severity and exposure associated with tsunami actions in urban waterfronts: the case of Lisbon, Portugal. Natural Hazards, Springer, 79, 2125, DOI:10.1007/s11069-015-1951-z

Using high-performance mathematical modelling tools to predict erosion and sediment fluxes in peri-urban catchments

NASA Astrophysics Data System (ADS)

Pereira, André; Conde, Daniel; Ferreira, Carla S. S.; Walsh, Rory; Ferreira, Rui M. L.

2017-04-01

Deforestation and urbanization generally lead to increased soil erosion andthrough the indirect effect of increased overland flow and peak flood discharges. Mathematical modelling tools can be helpful for predicting the spatial distribution of erosion and the morphological changes on the channel network. This is especially useful to predict the impacts of land-use changes in parts of the watershed, namely due to urbanization. However, given the size of the computational domain (normally the watershed itself), the need for high spatial resolution data to model accurately sediment transport processes and possible need to model transcritical flows, the computational cost is high and requires high-performance computing techniques. The aim of this work is to present the latest developments of the hydrodynamic and morphological model STAV2D and its applicability to predict runoff and erosion at watershed scale. STAV2D was developed at CEris - Instituto Superior Técnico, Universidade de Lisboa - as a tool particularly appropriated to model strong transient flows in complex and dynamic geometries. It is based on an explicit, first-order 2DH finite-volume discretization scheme for unstructured triangular meshes, in which a flux-splitting technique is paired with a reviewed Roe-Riemann solver, yielding a model applicable to discontinuous flows over time-evolving geometries. STAV2D features solid transport in both Euleran and Lagrangian forms, with the aim of describing the transport of fine natural sediments and then the large individual debris. The model has been validated with theoretical solutions and laboratory experiments (Canelas et al., 2013 & Conde et al., 2015). STAV-2D now supports fully distributed and heterogeneous simulations where multiple different hardware devices can be used to accelerate computation time within a unified Object-Oriented approach: the source code for CPU and GPU has the same compilation units and requires no device specific branches, like the standard observed in available models. The assembled parallel model is expected to achieve faster than real-time simulations for high resolutions (from meters to sub-meter) in large scaled problems (from cities to watersheds), effectively bridging the gap between detailed and timely simulation results. The model was validated in Ribeira dos Covões watershed, a peri-urban catchment (6 km2) in the outskirts of the Coimbra city, in central Portugal. Urban land-use has increased from 6% in 1958 to 40% in 2012. The watershed geology comprises a limestone sandstone areas. The soils are generally deep and hydrophobic for part of the year, particularly in the forested areas. Previous research used a sediment fingerprinting approach to establish the relative importance of sediment inputs from different urban areas (Ferreira et al., submitted). The study showed that most of the current catchment erosion is derived from construction sites in the sandstone areas. This was supported by the higher measured discharges and suspended sediment concentrations in storm events from downslope tributaries. The results of the model are well correlated with field surveys. However, the sever disruption of the channel network by human usage, namely land partition, poses specific modelling challenges, causing the quantitative agreement to be poor. To tackle this problem, it is necessary to introduce as much detail as possible in the specification of the elevation model. Acknowledgements This research was partially supported by Portuguese and European funds, within programs COMPETE2020 and PORL-FEDER, through project PTDC/ECM-HID/6387/2014 granted by the National Foundation for Science and Technology (FCT). References Canelas, R.; Murillo, J. & Ferreira, R.M.L. (2013), Two-dimensional depth-averaged modelling of dam-break flows over mobile beds. Journal of Hydraulic Research, 51(4), 392-407. Conde, D.A.S.; Telhado, M.J.; Viana Baptista, M.A. & Ferreira, R. M. L. (2015) Severity and exposure associated with tsunami actions in urban waterfronts: the case of Lisbon, Portugal. Natural Hazards, Springer, 79 Ferreira, C.S.S.; Walsh, R.P.D., Blake, W.H., Kikuchi, R. Ferreira, A.J.D., Temporal dynamics of sediment sources in an urbanizing Mediterranean catchment. Land Degradation and Development (submitted)

Modelling the transport of solid contaminants originated from a point source

NASA Astrophysics Data System (ADS)

Salgueiro, Dora V.; Conde, Daniel A. S.; Franca, Mário J.; Schleiss, Anton J.; Ferreira, Rui M. L.

2017-04-01

The solid phases of natural flows can comprise an important repository for contaminants in aquatic ecosystems and can propagate as turbidity currents generating a stratified environment. Contaminants can be desorbed under specific environmental conditions becoming re-suspended, with a potential impact on the aquatic biota. Forecasting the distribution of the contaminated turbidity current is thus crucial for a complete assessment of environmental exposure. In this work we validate the ability of the model STAV-2D, developed at CERIS (IST), to simulate stratified flows such as those resulting from turbidity currents in complex geometrical environments. The validation involves not only flow phenomena inherent to flows generated by density imbalance but also convective effects brought about by the complex geometry of the water basin where the current propagates. This latter aspect is of paramount importance since, in real applications, currents may propagate in semi-confined geometries in plan view, generating important convective accelerations. Velocity fields and mass distributions obtained from experiments carried out at CERIS - (IST) are used as validation data for the model. The experimental set-up comprises a point source in a rectangular basin with a wall placed perpendicularly to the outer walls. Thus generates a complex 2D flow with an advancing wave front and shocks due to the flow reflection from the walls. STAV-2D is based on the depth- and time-averaged mass and momentum equations for mixtures of water and sediment, understood as continua. It is closed in terms of flow resistance and capacity bedload discharge by a set of classic closure models and a specific high concentration formulation. The two-layer model is derived from layer-averaged Navier-Stokes equations, resulting in a system of layer-specific non-linear shallow-water equations, solved through explicit first or second-order schemes. According to the experimental data for mass distribution, the results obtained with STAV-2D show the formation of a shock wave, radially propagating from the point discharge, and secondary shocks originated by reflections at the basin walls. Laboratory results evidenced the presence of two main disturbances: a wave front near the side wall and another one resulting from dispersive processes. The dispersive phenomenon suggests the presence of oscillations, instead of the constant energy state that is characteristic of isolated rarefaction waves. The ability of the existing model to reproduce these details of the experiment is assessed and discussed. The validated two-layer hydrodynamics model is seen as a proxy for fluvial flows with different sediment concentration regions and can be used for the prediction and monitoring of spatial and temporal distribution of sediments and the adsorbed phases of contaminants. Acknowledgements This research was partially funded by the Portuguese Foundation for Science and Technology (FCT) through project RECI/ECM-HID/0371/2012 and through a H2Doc - Environmental Hydraulics and Hydrology doctoral grant (PD/BD/113620/2015) and by the Laboratory of Hydraulic Constructions (LCH), École polytechnique fédérale de Lausanne.

Mathematical modelling of tsunami impacts on critical infrastructures: exposure and severity associated with debris transport at Sines port, Portugal.

NASA Astrophysics Data System (ADS)

Conde, Daniel; Baptista, Maria Ana; Sousa Oliveira, Carlos; Ferreira, Rui M. L.

2015-04-01

Global energy production is still significantly dependant on the coal supply chain, justifying huge investments on building infrastructures, capable of stocking very large quantities of this natural resource. Most of these infrastructures are located at deep-sea ports and are therefore exposed to extreme coastal hazards, such as tsunami impacts. The 2011 Tohoku tsunami is reported to have inflicted severe damage to Japan's coal-fired power stations and related infrastructure. Sines, located in the Portuguese coast, hosts a major commercial port featuring an exposed coal stockpile area extending over more than 24 ha and a container terminal currently under expansion up to 100ha. It is protected against storm surges but tsunamis have not been considered in the design criteria. The dominant wind-generated wave direction is N to NW, while the main tsunamigenic faults are located S to SW of the port. This configuration potentially exposes sensitive facilities, such as the new terminal container and the coal stockpile area. According to a recent revision of the national tsunami catalogue (Baptista, 2009), Portugal has been affected by numerous major tsunamis over the last two millennia, with the most notorious event being the Great Lisbon Earthquake and Tsunami occurred on the 1st November 1755. The aim of this work is to simulate the open ocean propagation and overland impact of a tsunami on the Sines port, similar to the historical event of 1755, based on the different tsunamigenic faults and magnitudes proposed in the current literature. Open ocean propagation was modelled with standard simulation tools like TUNAMI and GeoClaw. Near-shore and overland propagation was carried out using a recent 2DH mathematical model for solid-fluid flows, STAV-2D from CERIS-IST (Ferreira et al., 2009; Canelas, 2013). STAV-2D is particularly suited for tsunami propagation over complex and morphodynamic geometries, featuring a discretization scheme based on a finite-volume method using a flux-splitting technique with a reviewed Roe-Riemann solver and appropriate source-term formulations to ensure full conservativeness. Additionally, STAV-2D features Lagrangian-Eulerian coupling enabling solid transport simulation under both continuum and discrete approaches, and has been validated with both laboratory data and paleo-tsunami evidence (Conde, 2013a; Conde, 2013b). The interactions between the inundating flow and coal stockpiles or natural mobile bed reaches were simulated using a continuum debris-flow approach, featuring fractional solid transport, while the containers at the new terminal were advected with an explicit Lagrangian method. The meshwork employed at the port models the existing geometry and structures in great detail, enabling explicitly resolved interactions between the current infrastructure and the overland propagating tsunami. The obtained preliminary results suggest that several structures, some of them critical in a nationwide context, are exposed to tsunami actions. The coal deposition pattern and the final location of monitored containers were determined for two magnitude scenarios (8.5 Mw and 9.5 Mw) in the case of a tsunami generated at the Horseshoe fault and one magnitude scenario (9.5 Mw) for a tsunami generated at the Gorringe bank. The inland washing of the coal stockpiles may impose great loss of both economical and environmental value, while the impact of large mobile debris, such as the containers in the terminal area, significantly increases the severity of infrastructural damage. Acknowledgements This work was partially funded by FEDER, program COMPETE, and by national funds through the Portuguese Foundation for Science and Technology (FCT) with project RECI/ECM-HID/0371/2012. References Baptista M.A. & Miranda, J.M. (2009), Revision of the Portuguese catalog of tsunamis. Nat. Hazards Earth Syst. Sci., 9, 25-42. Canelas, R.; Murillo, J. & Ferreira, R.M.L. (2013), Two-dimensional depth-averaged modelling of dam-break flows over mobile beds. Vol 51(4) pp. 392-407. Conde, D. A. S.; Baptista, M. A. V.; Sousa Oliveira, C. & Ferreira, R. M. L. (2013a), A shallow-flow model for the propagation of tsunamis over complex geometries and mobile beds, Nat. Hazards Earth Syst. Sci., 13, 2533-2542. Conde, D. A. S.; Canelas, R. B.; Sousa Oliveira, C. & Ferreira, R. M. L. (2013b), Mathematical modelling of transport of coal stockpiles by a tsunami at Sines port, 8th International SedNet Conference 2013, Lisbon, Portugal. Ferreira, R. M. L.; Franca, M. J.; Leal, J. G. & Cardoso, A. H. (2009), Mathematical modelling of shallow flows: Closure models drawn from grain-scale mechanics of sediment transport and flow hydrodynamics, Can. J. Civil. Eng., 36, 1604-1621, 2009.

Mathematical modelling of the transport of a poorly sorted granular mixture as a debris-flow. The case of Madeira Island torrential floods in 2010

NASA Astrophysics Data System (ADS)

Ferreira, Rui M. L.; Oliveira, Rodrigo P.; Conde, Daniel

2016-04-01

On the 20th February 2010, heavy rainfall was registered at Madeira Island, North Atlantic. Stony debris flows, mudflows and mudslides ensued causing severe property loss, 1.5 m thick sediment deposits at downtown Funchal including 16th century monuments, and a death toll of 47 lives. Debris-flow fronts propagated downstream while carrying very high concentrations of solid material. These two-phase solid-fluid flows were responsible for most of the infrastructural damage across the island, due to their significantly increased mass and momentum. The objective of the present modelling work is to validate a 2DH model for torrential flows featuring the transport and interaction of several size fractions of a poorly-sorted granular mixture typical of stony debris flow in Madeira. The module for the transport of poorly-sorted material was included in STAV-2D (CERIS-IST), a shallow-water and morphology solver based on a finite-volume method using a flux-splitting technique featuring a reviewed Roe-Riemann solver, with appropriate source-term formulations to ensure full conservativeness. STAV-2D also includes formulations of flow resistance and bedload transport adequate for debris-flows with natural mobile beds (Ferreira et al., 2009) and has been validated with both theoretical solutions and laboratory data (Soares-Frazão et al., 2012; Canelas et al., 2013). The modelling of the existing natural and built environment is fully explicit. All buildings, streets and channels are accurately represented within the mesh geometry. Such detail is relevant for the reliability of the validation using field data, since the major sedimentary deposits within the urban meshwork of Funchal were identified and characterized in terms of volume and grain size distribution during the aftermath of the 20th February of 2010 event. Indeed, the measure of the quality of the numerical results is the agreement between simulated and estimated volume of deposited sediment and between estimated and modelled grain-size distribution of the deposits. The formulations expressing closures for size fraction interaction and active layer dynamics are discussed. The simulation tool resulting from this modelling effort is expected to help the establishment of new methodologies and parameters for hydraulic design and hazard assessment in the Island of Madeira. Acknowledgements This work was partially funded by FEDER, program COMPETE, and by national funds through Portuguese Foundation for Science and Technology (FCT) project RECI/ECM-HID/0371/2012. References Canelas, R.; Murillo, J. & Ferreira, R.M.L. (2013). Two-dimensional depth-averaged modelling of dambreak flows over mobile beds. Journal of Hydraulic Research, 51(4), 392-407. Ferreira, R. M. L., Franca, M. J., Leal, J. G., & Cardoso, A. H. (2009). Mathematical modelling of shallow flows: Closure models drawn from grain-scale mechanics of sediment transport and flow hydrodynamics. Canadian Journal of Civil Engineering, 36(10), 1605-1621. Soares-Frazão and IAHR Working group for Dam-break flows over mobile beds (2012) Dam-break flows over mobile beds: Experiments and benchmark tests for numerical models. Journal of Hydraulic Research, 50(4), 364-375. DOI: 10.1080/00221686.2012.689682

Severity and exposure associated to tsunami actions in urban waterfronts. The case of Lisbon, Portugal.

NASA Astrophysics Data System (ADS)

Conde, Daniel; Telhado, Maria J.; Viana Baptista, Maria A.; Antunes, Carlos M.; Ferreira, Rui M. L.

2014-05-01

The Tagus estuary is recognized as an exposed location to tsunami occurrences, given its proximity to tsunamigenic faults such as the Marquês de Pombal and the Horseshoe fault system. Lisbon, bordered by the Tagus estuary, is a critical point of Portugal's tsunami hazard map, having been affected by several tsunamis (Baptista and Miranda, 2009) including the notorious event of November 1st 1755, the last major natural disaster known to have inflicted massive destruction in Portugal. The main objective of this work, a joint initiative of CEHIDRO (IST - Universidade de Lisboa) and the Municipal Civil Protection Services of Lisbon, is to contribute to the quantification of severity and exposure of Lisbon waterfront to tsunami events. For that purpose, the propagation of a tsunami similar to that of the 1st November of 1755 in the Tagus estuary was numerically simulated. Several scenarios were considered, articulating the influence of tidal (low and high tides), atmospheric (increase in water level due to storm surges) and hydrological (flow discharge in Tagus river) conditions. Different initial and boundary conditions were defined for each modelling scenario but the magnitude of the tsunami remained what is believed to be an exceptional event. The extent of the inundation and relevant hydrodynamic quantities were registered for all scenarios. The employed simulation tool - STAV-2D - was developed at CEHIDRO (IST) and is based on a 2DH spatial (Eulerian) shallow-flow approach suited to complex and dynamic bottom boundaries. The discretization technique relies on a finite-volume scheme, based on a flux-splitting technique incorporating a reviewed version of the Roe Riemann solver (Canelas et al. 2013, Conde et al. 2013). STAV-2D features conservation equations for the finer solid phase of the flow and also a Lagrangian model for the advection of larger debris elements. The urban meshwork was thoroughly discretized with a mesh finer than average street width. This fine discretization allows for resolving flow resistance associated to obstacles: no ad hoc formulations are needed to express drag on buildings, which is a key innovation in regard to previous studies. Additionally, vehicle-like particles were virtually placed over the major traffic nodes and routes, resulting in over 5000 lagrangian particles along the riverfront. This allows for an assessment of debris deposition patterns on the aftermath of the tsunami inundation. Severity is herein assumed to depend on hydrodynamic features of the tsunami, namely its capacity to impart momentum. Exposure to tsunami actions depends on the extent of the inundation. Both severity and exposure thus vary with the tsunami scenario considered. The obtained results, obtained with a high detail of hydrodynamic behavior, allow for a street-by-street quantification of severity, expressed in terms of the product of the depth-averaged velocity by the flow depth (Karvonen et al., 2000), herein the q-parameter. This parameter is shown to be larger during run-up, particularly in streets and narrow sections. It was observed that the scenario with greater exposure is a combination of a high-tide, a storm surge and a discharge equivalent to a 100 year flood on the Tagus River. The work conducted allows for designing a methodology for exposure assessment due to tsunami propagating over urban meshes, where the influence of the existing infrastructures on the incoming inundation is highly relevant. Such methodology, here applied to Lisbon waterfront, is general since it is defined in terms of quantifiable hydrodynamic variables. Acknowledgements: Project RECI/ECM-HID/0371/2012, funded by the Portuguese Foundation for Science and Technology (FCT), has partially supported this work. References: Baptista, M.A., Miranda, J.M. (2009). Revision of the Portuguese catalog of tsunamis. Nat. Hazards Earth Syst. Sci., 9, 25 - 42. Canelas, R., Murillo, J. & Ferreira, R.M.L. (2013). Two-dimensional depth-averaged modelling of dam-break flows over mobile beds. Journal of Hydraulic Research, 51(4), 392-407. Conde, D., Baptista, M. A. V., Sousa Oliveira, C., and Ferreira, R. M. L. (2013). A shallow-flow model for the propagation of tsunamis over complex geometries and mobile beds, Nat. Hazards Earth Syst. Sci., 13, 2533-2542. Karvonen, R.A., Hepojoki, A., Huhta, H.K., and Louhio, A. (2000) The Use of Physical Models in Dam-Break Analysis. RESCDAM Final Report. Helsinki University of Technology, Helsinki, Finland.

Sediment pollution of the Elbe River side structures - current research

NASA Astrophysics Data System (ADS)

Chalupova, Dagmar; Janský, Bohumír

2016-04-01

The contribution brings the summarized results of a long-term research on sediment pollution of side structures of the Elbe River over the last 14 years. The investigation has been focused on old anthropogenic pollution of sediment cores taken from fluvial lakes and floodplain, as the sampling of deeper sediments outside the riverbed is not a part of systematic monitoring of sediment pollution of the Elbe. The Elbe River floodplain has been influenced by human activities since the Middle Ages, but the main anthropogenic pollution have been produced in the 20th century. The studied localities were chosen with the respect to the distance from the source of industrial pollution, the intensity of hydrological communication with the river and the surrounding landuse to determine the extend and the level of anthropogenic contamination in the Elbe River floodplain ecosystem. Apart from bathymetric measurements, observation of the hydrological regime in several fluvial lakes or water quality sampling at some localities, the research was focused above all on determination of metal concentrations (Ag, Cd, Cr, Cu, Fe, Hg, Mn, Pb, Zn) in all taken sediment cores, specific organic compounds (PCBs, DDT, HCH, HCB, PAHs etc.), total organic carbon at some localities and grain structure analyses. The data were also compared with the results of systematic sediment monitoring from the nearest riverbed sampling stations on the Elbe River. The highest concentrations of metals and specific organic compounds were determined in the sediments taken from fluvial lakes and floodplain (Zimní přístav PARAMO, Rosice fuvial Lake, Libiš pool etc.) situated in the vicinity of the main Elbe River polluters - Synthesia chemical plant and PARAMO refinery in Pardubice or Spolana chemical plant near Neratovice. However, there was also determined a significant role of the hydrological communication with the river proved with lower sediment pollution in separated localities. The realization of the above mentioned research was possible thanks to the support of numerous Czech and German projects (GAUK, GAČR, SVV, VaV, PRVOUK, ELSA etc.).

NMR Analysis of Amide Hydrogen Exchange Rates in a Pentapeptide-Repeat Protein from A. thaliana.

PubMed

Xu, Shenyuan; Ni, Shuisong; Kennedy, Michael A

2017-05-23

At2g44920 from Arabidopsis thaliana is a pentapeptide-repeat protein (PRP) composed of 25 repeats capped by N- and C-terminal α-helices. PRP structures are dominated by four-sided right-handed β-helices typically consisting of mixtures of type II and type IV β-turns. PRPs adopt repeated five-residue (Rfr) folds with an Rfr consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Unlike other PRPs, At2g44920 consists exclusively of type II β-turns. At2g44920 is predicted to be located in the thylakoid lumen although its biochemical function remains unknown. Given its unusual structure, we investigated the biophysical properties of At2g44920 as a representative of the β-helix family to determine if it had exceptional global stability, backbone dynamics, or amide hydrogen exchange rates. Circular dichroism measurements yielded a melting point of 62.8°C, indicating unexceptional global thermal stability. Nuclear spin relaxation measurements indicated that the Rfr-fold core was rigid with order parameters ranging from 0.7 to 0.9. At2g44920 exhibited a striking range of amide hydrogen exchange rates spanning 10 orders of magnitude, with lifetimes ranging from minutes to several months. A weak correlation was found among hydrogen exchange rates, hydrogen bonding energies, and amino acid solvent-accessible areas. Analysis of contributions from fast (approximately picosecond to nanosecond) backbone dynamics to amide hydrogen exchange rates revealed that the average order parameter of amides undergoing fast exchange was significantly smaller compared to those undergoing slow exchange. Importantly, the activation energies for amide hydrogen exchange were found to be generally higher for the slowest exchanging amides in the central Rfr coil and decreased toward the terminal coils. This could be explained by assuming that the concerted motions of two preceding or following coils required for hydrogen bond disruption and amide hydrogen exchange have a higher activation energy compared to that required for displacement of a single coil to facilitate amide hydrogen exchange in either the terminal or penultimate coils. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

User Needs in the Development of a Health App Ecosystem for Self-Management of Cystic Fibrosis: User-Centered Development Approach.

PubMed

Floch, Jacqueline; Zettl, Annabel; Fricke, Lena; Weisser, Tina; Grut, Lisbet; Vilarinho, Thomas; Stav, Erlend; Ascolese, Antonio; Schauber, Cornelia

2018-05-08

Digital self-management in cystic fibrosis (CF) is foreseen as a means toward better understanding of the disease and its treatment and better adherence to the treatment. Mobile apps hold the potential to provide access to information, motivate, and strengthen compliance. However, to deliver high-quality apps, the development should be based on thorough knowledge about user needs. Empirical research on the user-centered development of mobile apps for health care is, however, still limited. The aim of this research is to develop and evaluate an app ecosystem for self-management in CF. It targets not only those directly affected by CF but also parents and health care professionals involved in the treatment. This paper covers the first step of the design process that aims to analyze the context and the user requirements. The primary research question is as follows: what digital support has the potential to usefully support persons with CF and their caregivers in the CF care? To answer this question, we address two preliminary questions: what important factors in everyday life affect the care of persons with CF? and how is the CF care delivered today and what are the limitations of CF care services? The overall research adopts a user-centered design approach in which future users are involved in the development process from the very beginning to ensure that the apps developed best suit the potential users. The research presented in the paper follows an interpretative case study research strategy seeking to understand the concerns and needs of persons with CF and their caregivers. Data were collected through semistructured qualitative interviews involving 74 participants in seven European countries and from internet forums. The results of the analysis phase show a strong need for individuality of the digital support, as well as for its adaptability to different contexts. The paper presents the concerns and needs of the participants in the study and extracts a set of relevant features for a self-management app ecosystem. Education, enzyme dosage calculation, nutrition management, treatment organization, health diary, treatment follow-up, practical guidelines for treatment, communication with doctors, and communication with peers are foreseen as useful features. The results indicate the readiness for self-management in the CF care even in countries that provide well-functioning health care services for CF care. The large diversity of user requirements identified reflects the crucial role user integration plays in developing apps for a chronic condition such as CF. The need for personalization stemming from the individuality of the patients and the need for communication with health care professionals support the idea of an app ecosystem for the self-management of CF. ©Jacqueline Floch, Annabel Zettl, Lena Fricke, Tina Weisser, Lisbet Grut, Thomas Vilarinho, Erlend Stav, Antonio Ascolese, Cornelia Schauber. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 08.05.2018.

Coupled Eulerian-Lagrangian transport of large debris by tsunamis

NASA Astrophysics Data System (ADS)

Conde, Daniel A. S.; Ferreira, Rui M. L.; Sousa Oliveira, Carlos

2016-04-01

Tsunamis are notorious for the large disruption they can cause on coastal environments, not only due to the imparted momentum of the incoming wave but also due to its capacity to transport large quantities of solid debris, either from natural or human-made sources, over great distances. A 2DH numerical model under development at CERIS-IST (Ferreira et al., 2009; Conde, 2013) - STAV2D - capable of simulating solid transport in both Eulerian and Lagrangian paradigms will be used to assess the relevance of Lagrangian-Eulerian coupling when modelling the transport of solid debris by tsunamis. The model has been previously validated and applied to tsunami scenarios (Conde, 2013), being well-suited for overland tsunami propagation and capable of handling morphodynamic changes in estuaries and seashores. The discretization scheme is an explicit Finite Volume technique employing flux-vector splitting and a reviewed Roe-Riemann solver. Source term formulations are employed in a semi-implicit way, including the two-way coupling of the Lagrangian and Eulerian solvers by means of conservative mass and momentum transfers between fluid and solid phases. The model was applied to Sines Port, a major commercial port in Portugal, where two tsunamigenic scenarios are considered: an 8.5 Mw scenario, consistent with the Great Lisbon Earthquake and Tsunami of the 1st November 1755 (Baptista, 2009), and an hypothetical 9.5 Mw worst-case scenario based on the same historical event. Open-ocean propagation of these scenarios were simulated with GeoClaw model from ClawPack (Leveque, 2011). Following previous efforts on the modelling of debris transport by tsunamis in seaports (Conde, 2015), this work discusses the sensitivity of the obtained results with respect to the phenomenological detail of the employed Eulerian-Lagrangian formulation and the resolution of the mesh used in the Eulerian solver. The results have shown that the fluid to debris mass ratio is the key parameter regarding the conservativeness of the model. This way, in highly resolved meshes and high quantities of debris, the model approaches full conservativeness only if the two-way coupling feature is present, an effect that is attenuated in coarse meshes or with small debris quantities. Aknownledgements: This work was partially funded by FEDER, program COMPETE, and by national funds through the Portuguese Foundation for Science and Technology (FCT) with project RECI/ECM-HID/0371/2012. References: Baptista M.A. & Miranda, J.M. (2009) Revision of the Portuguese catalog of tsunamis. Nat. Hazards Earth Syst. Sci., 9, 25-42. Conde, D. A. S.; Baptista, M. A. V.; Sousa Oliveira, C. & Ferreira, R. M. L. (2013) A shallow-flow model for the propagation of tsunamis over complex geometries and mobile beds, Nat. Hazards Earth Syst. Sci., 13, 2533-2542. Conde, D. A. S.; Baptista, M. A. V.; Sousa Oliveira, C. & Ferreira, R. M. L. (2015) Mathematical modelling of tsunami impacts on critical infrastructures: exposure and severity associated with debris transport at Sines port. EGU General Assembly 2015, Vienna, Austria. Ferreira, R. M. L.; Franca, M. J.; Leal, J. G. & Cardoso, A. H. (2009) Mathematical modelling of shallow flows: Closure models drawn from grain-scale mechanics of sediment transport and flow hydrodynamics, Can. J. Civil. Eng., 36, 1604-1621. LeVeque, R. J., George, D. L., & Berger, M. J. (2011) Tsunami modelling with adaptively refined finite volume methods, Acta Numerica, pp. 211-289.