Software for interpolation of vegetative growth of yerba mate plants in 3D

The objective of this work was to build mock-ups of complete yerba mate plants in several stages of development, using the InterpolMate software, and to compute photosynthesis on the interpolated structure. The mock-ups of yerba-mate were first built in the VPlants software for three growth stages. Male and female plants grown in two contrasting environments (monoculture and forest understory) were considered. To model the dynamic 3D architecture of yerba-mate plants during the biennial growth interval between two subsequent prunings, data sets of branch development collected in 38 dates were used. The estimated values obtained from the mock-ups, including leaf photosynthesis and sexual dimorphism, are very close to those observed in the field. However, this similarity was limited to reconstructions that included growth units from original data sets. The modeling of growth dynamics enables the estimation of photosynthesis for the entire yerba mate plant, which is not easily measurable in the field. The InterpolMate software is efficient for building yerba mate mock-ups.

Effects of computing parameters and measurement locations on the estimation of 3D NPS in non-stationary MDCT images.

The goal of this study was to investigate the impact of computing parameters and the location of volumes of interest (VOI) on the calculation of 3D noise power spectrum (NPS) in order to determine an optimal set of computing parameters and propose a robust method for evaluating the noise properties of imaging systems. Noise stationarity in noise volumes acquired with a water phantom on a 128-MDCT and a 320-MDCT scanner were analyzed in the spatial domain in order to define locally stationary VOIs. The influence of the computing parameters in the 3D NPS measurement: the sampling distances bx,y,z and the VOI lengths Lx,y,z, the number of VOIs NVOI and the structured noise were investigated to minimize measurement errors. The effect of the VOI locations on the NPS was also investigated. Results showed that the noise (standard deviation) varies more in the r-direction (phantom radius) than z-direction plane. A 25 × 25 × 40 mm(3) VOI associated with DFOV = 200 mm (Lx,y,z = 64, bx,y = 0.391 mm with 512 × 512 matrix) and a first-order detrending method to reduce structured noise led to an accurate NPS estimation. NPS estimated from off centered small VOIs had a directional dependency contrary to NPS obtained from large VOIs located in the center of the volume or from small VOIs located on a concentric circle. This showed that the VOI size and location play a major role in the determination of NPS when images are not stationary. This study emphasizes the need for consistent measurement methods to assess and compare image quality in CT.

3D culture of postnatal retinal stem cells using self assembling polymers

PURPOSE We have previously shown that retinal stem cells (RSCs) can be isolated from the radial glia population of the newborn mouse retina (Angénieux et al., 2006). These RSCs have a great capacity to renew and to generate a large number of neurons including cells differentiated towards the photoreceptor lineage (Mehri-Soussi et al., 2006). However, recent published results from our lab revealed that such cells have a poor integration and survival rate after grafting. The uncontrolled environment of a retina seems to prevent good integration and survival after grafting in vivo. To bypass this problem, we are evaluating the possibility of generating in vitro a hemi-retinal tissue before transplantation. METHODS RSC were expanded and cells passaged <10 were seeded in a solution containing poly-ethylene-glycol (PEG) polymer based hydrogels crosslinked with peptides that are chosen to be substrates for matrix metalloproteinases. Various doses of cross linkers peptides allowing connections between PEG polymers were tested. Different growth factors were studied to stimulate cell proliferation and differentiation. RESULTS Cells survived only in the presence of EGF and FGF-2 and generated colonies with a sphere shape. No cells migrated within the gel. To improve the migration and the repartition of the cells in the gels, the integrin ligand RGDSP was added into the gel. In the presence of FGF-2 and EGF, newly formed cell clusters appeared by cell proliferation within several days, but again no outspreading of cells was observed. No difference was even seen when the stiffness of the hydrogels or the concentration of the integrin ligand RGDSP were changed. However, our preliminary results show that RSCs still form spheres when laminin is entrapped in the gel, but they started to spread out having a neuronal morphology after around 2 weeks. The neuronal population was assessed by the presence of the neuronal marker b-tubulin-III. This differentiation was achieved after successive steps of stimulations including FGF-2 and EGF, and then only FGF-2. Glial cells were also present. Further characterizations are under process. CONCLUSIONS RSC can be grown in 3D. Preliminary results show that neuronal cell phenotype acquisition can be instructed by exogenous stimulations and factors linked to the gel. Further developments are necessary to form a homogenous tissue containing retinal cells.

3D crosshole ERT for aquifer characterization and monitoring of infiltrating river water

The hydrogeological properties and responses of a productive aquifer in northeastern Switzerland are investigated. For this purpose, 3D crosshole electrical resistivity tomography (ERT) is used to define the main lithological structures within the aquifer (through static inversion) and to monitor the water infiltration from an adjacent river. During precipitation events and subsequent river flooding, the river water resistivity increases. As a consequence, the electrical characteristics of the infiltrating water can be used as a natural tracer to delineate preferential flow paths and flow velocities. The focus is primarily on the experiment installation, data collection strategy, and the structural characterization of the site and a brief overview of the ERT monitoring results. The monitoring system comprises 18 boreholes each equipped with 10 electrodes straddling the entire thickness of the gravel aquifer. A multi-channel resistivity system programmed to cycle through various four-point electrode configurations of the 180 electrodes in a rolling sequence allows for the measurement of approximately 15,500 apparent resistivity values every 7 h on a continuous basis. The 3D static ERT inversion of data acquired under stable hydrological conditions provides a base model for future time-lapse inversion studies and the means to investigate the resolving capability of our acquisition scheme. In particular, it enables definition of the main lithological structures within the aquifer. The final ERT static model delineates a relatively high-resistivity, low-porosity, intermediate-depth layer throughout the investigated aquifer volume that is consistent with results from well logging and seismic and radar tomography models. The next step will be to define and implement an appropriate time-lapse ERT inversion scheme using the river water as a natural tracer. The main challenge will be to separate the superposed time-varying effects of water table height, temperature, and salinity variations associated with the infiltrating water.

Construction mechanisms and thermal evolution of upper crustal intrusions : the Saint-Jean-du-Doigt bimodal intrusion (Brittany, France)

Understanding the emplacement and growth of intrusive bodies in terms of mechanism, duration, ther¬mal evolution and rates are fundamental aspects of crustal evolution. Recent studies show that many plutons grow in several Ma by in situ accretion of discrete magma pulses, which constitute small-scale magmatic reservoirs. The residence time of magmas, and hence their capacities to interact and differentiate, are con¬trolled by the local thermal environment. The latter is highly dependant on 1) the emplacement depth, 2) the magmas and country rock composition, 3) the country rock thermal conductivity, 4) the rate of magma injection and 5) the geometry of the intrusion. In shallow level plutons, where magmas solidify quickly, evi¬dence for magma mixing and/or differentiation processes is considered by many authors to be inherited from deeper levels. This work shows however that in-situ differentiation and magma interactions occurred within basaltic and felsic sills at shallow depth (0.3 GPa) in the St-Jean-du-Doigt (SJDD) bimodal intrusion, France. This intrusion emplaced ca. 347 Ma ago (IDTIMS U/Pb on zircon) in the Precambrian crust of the Armori- can massif and preserves remarkable sill-like emplacement processes of bimodal mafic-felsic magmas. Field evidence coupled to high precision zircon U-Pb dating document progressive thermal maturation within the incrementally built ioppolith. Early m-thick mafic sills (eastern part) form the roof of the intrusion and are homogeneous and fine-grained with planar contacts with neighboring felsic sills; within a minimal 0.8 Ma time span, the system gets warmer (western part). Sills are emplaced by under-accretion under the old east¬ern part, interact and mingle. A striking feature of this younger, warmer part is in-situ differentiation of the mafic sills in the top 40 cm of the layer, which suggests liquids survival in the shallow crust. Rheological and thermal models were performed in order to determine the parameters required to allow this observed in- situ differentiation-accumulation processes. Strong constraints such as total emplacement durations (ca. 0.8 Ma, TIMS date) and pluton thickness (1.5 Km, gravity model) allow a quantitative estimation of the various parameters required (injection rates, incubation time,...). The results show that in-situ differentiation may be achieved in less than 10 years at such shallow depth, provided that: (1) The differentiating sills are injected beneath consolidated, yet still warm basalt sills, which act as low conductive insulating screens (eastern part formation in the SJDD intrusion). The latter are emplaced in a very short time (800 years) at high injection rate (0.5 m/y) in order to create a "hot zone" in the shallow crust (incubation time). This implies that nearly 1/3 of the pluton (400m) is emplaced by a subsequent and sustained magmatic activity occurring on a short time scale at the very beginning of the system. (2) Once incubation time is achieved, the calculations show that a small hot zone is created at the base of the sill pile, where new injections stay above their solidus T°C and may interact and differentiate. Extraction of differentiated residual liquids might eventually take place and mix with newly injected magma as documented in active syn-emplacement shear-zones within the "warm" part of the pluton. (3) Finally, the model show that in order to maintain a permanent hot zone at shallow level, injection rate must be of 0.03 m/y with injection of 5m thick basaltic sills eveiy 130yr, imply¬ing formation of a 15 km thick pluton. As this thickness is in contradiction with the one calculated for SJDD (1.5 Km) and exceed much the average thickness observed for many shallow level plutons, I infer that there is no permanent hot zone (or magma chambers) at such shallow level. I rather propose formation of small, ephemeral (10-15yr) reservoirs, which represent only small portions of the final size of the pluton. Thermal calculations show that, in the case of SJDD, 5m thick basaltic sills emplaced every 1500 y, allow formation of such ephemeral reservoirs. The latter are formed by several sills, which are in a mushy state and may interact and differentiate during a short time.The mineralogical, chemical and isotopic data presented in this study suggest a signature intermediate be¬tween E-MORB- and arc-like for the SJDD mafic sills and feeder dykes. The mantle source involved produced hydrated magmas and may be astenosphere modified by "arc-type" components, probably related to a sub¬ducting slab. Combined fluid mobile/immobile trace elements and Sr-Nd isotopes suggest that such subduc¬tion components are mainly fluids derived from altered oceanic crust with minor effect from the subducted sediments. Close match between the SJDD compositions and BABB may point to a continental back-arc setting with little crustal contamination. If so, the SjDD intrusion is a major witness of an extensional tectonic regime during the Early-Carboniferous, linked to the subduction of the Rheno-Hercynian Ocean beneath the Variscan terranes. Also of interest is the unusual association of cogenetic (same isotopic compositions) K-feldspar A- type granite and albite-granite. A-type granites may form by magma mixing between the mafic magma and crustal melts. Alternatively, they might derive from the melting of a biotite-bearing quartz-feldspathic crustal protolith triggered by early mafic injections at low crustal levels. Albite-granite may form by plagioclase cu¬mulate remelting issued from A-type magma differentiation.

Comparison of naphthalene bioavailability determined by whole-cell biosensing and availability determined by extraction with Tenax

A rapid biological method for the determination of the bioavailability of naphthalene was developed and its value as an alternative to extraction-based chemical approaches demonstrated. Genetically engineered whole-cell biosensors are used to determine bioavailable naphthalene and their responses compared with results from Tenax extraction and chemical analysis. Results show a 1:1 correlation between biosensor results and chemical analyses for naphthalene-contaminated model materials and sediments, but the biosensor assay is much faster. This work demonstrates that biosensor technology can perform as well as standard chemical methods, though with some advantages including the inherent biological relevance of the response, rapid response time, and potential for field deployment. A survey of results from this work and the literature shows that bioavailability under non-equilibrium conditions nonetheless correlates well with K(oc) or K(d). A rationale is provided wherein chemical resistance is speculated to be operative.

Repurposing Social Tagging Data for Extraction of Domain-level Concepts

The World Wide Web, the world¿s largest resource for information, has evolved from organizing information using controlled, top-down taxonomies to a bottom up approach that emphasizes assigning meaning to data via mechanisms such as the Social Web (Web 2.0). Tagging adds meta-data, (weak semantics) to the content available on the web. This research investigates the potential for repurposing this layer of meta-data. We propose a multi-phase approach that exploits user-defined tags to identify and extract domain-level concepts. We operationalize this approach and assess its feasibility by application to a publicly available tag repository. The paper describes insights gained from implementing and applying the heuristics contained in the approach, as well as challenges and implications of repurposing tags for extraction of domain-level concepts.

Restitución 3D de la topografía de la antigua ciudad de Tarraco en un entorno SIG: propuestas metodológicas y primeros resultados

Durante los últimos años el Institut Català d’Arquelogia Clàssica, el Museu d’Història de Tarragona, contando con la colaboración de la Generalitat de Catalunya, han desarrallado el proyecto Planimetría Arqueológica de Tárraco, destinado a la elaboración de una planta arqueológica global en la cual se recogieran intervenciones y noticias referentes a los hallazgos arqueológicos existentes. Este trabajo fue publicado utilizando como plataforma de trabajo un SIG construido para tal fin (Macias et al. 2007). Sin embargo, un problema de difícil solución arqueológica venía dado por las transformaciones urbanísticas de la ciudad, sufridas en su mayor parte a lo largo de los siglos XIX y XX. Éstas habían provocado la pérdida irremediable de gran parte de la elevación que acogiera la ciudad romana, cambiando substancialmente su aspecto original. Ante esta situación y como proyecto paralelo a la realización de la Planimetría Arqueológica de Tarragona se plantearon formas de cubrir este vacío. Se presenta en esta comunicación una propuesta metodológica para la reconstrucción de los grandes «vacíos topográficos » originados por la evolución urbanística de Tarragona mediante la obtención e integración en un SIG de diversos tipos de información documental. En estas zonas rebajadas no resulta posible la obtención de información estratigráfica y arqueológica, por lo que es imprescindible la definición de vías metodológicas alternativas basadas en la extrapolación de datos extraídos de la cartografía histórica, panorámicas del XVI o fotografías tomadas en los siglos XIX y XX. Esta técnica permite aplicar los resultados obtenidos en los nuevos análisis interpretativos, complementando así la interpretación arqueológica de la topografía urbana de la ciudad romana. A partir de esta información, y aplicando funciones y técnicas de interpolación propias de un GIS, se propone aquí un modelo de relieve de la ciudad de Tarraco.

Influence of rootstocks and pruning times on yield and on nutrient content and extraction in 'Niagara Rosada' grapevine

The objective of this work was to evaluate the influence of rootstocks and pruning times on yield and on nutrient content and extraction by pruned branches and harvested bunches of 'Niagara Rosada' grapevine in subtropical climate. The rootstocks 'IAC 766', 'IAC 572', 'IAC 313', 'IAC 571-6', and '106-8 Mgt' were evaluated. Treatments consisted of a combination between five rootstocks and three pruning times. At pruning, fresh and dry matter mass of branches were evaluated to estimate biomass accumulation. At harvest, yield was estimated by weighing of bunches per plant. Branches and bunches were sampled at pruning and at harvest, respectively, for nutrient content analysis. Nutrient content and dry matter mass of branches and bunches were used to estimate total nutrient extraction. 'Niagara Rosada' grapevine grafted onto the 'IAC 572' rootstock had the highest yield and dry matter mass of bunches, which were significantly different from the ones observed in 'Niagara Rosada'/'IAC 313'. 'Niagara Rosada' grafted onto the 'IAC 572' rootstock extracted the largest quantity of K, P, Mg, S, Cu, and Fe, differing from 'IAC 313' and 'IAC 766' in K and P extraction, and from '106-8 Mgt' in Mg and S extraction. Winter pruning results in higher yield, dry matter accumulation by branches, and total nutrient content and extraction.

Scene representation for object monitoring

In robotics, having a 3D representation of the environment where a robot is working can be very useful. In real-life scenarios, this environment is constantly changing for example by human interaction, external agents or by the robot itself. Thus, the representation needs to be constantly updated and extended to account for these dynamic scene changes. In this work we face the problem of representing the scene where a robot is acting. Moreover, we ought to improve this representation by reusing the information obtained in previous scenes. Our goal is to build a method to represent a scene and to update it while changes are produced. In order to achieve that, different aspects of computer vision such as space representation or feature tracking are discussed

Performance analysis of software run-time behaviour using 3D-visualisation

Monimutkaisen tietokonejärjestelmän suorituskykyoptimointi edellyttää järjestelmän ajonaikaisen käyttäytymisen ymmärtämistä. Ohjelmiston koon ja monimutkaisuuden kasvun myötä suorituskykyoptimointi tulee yhä tärkeämmäksi osaksi tuotekehitysprosessia. Tehokkaampien prosessorien käytön myötä myös energiankulutus ja lämmöntuotto ovat nousseet yhä suuremmiksi ongelmiksi, erityisesti pienissä, kannettavissa laitteissa. Lämpö- ja energiaongelmien rajoittamiseksi on kehitetty suorituskyvyn skaalausmenetelmiä, jotka edelleen lisäävät järjestelmän kompleksisuutta ja suorituskykyoptimoinnin tarvetta. Tässä työssä kehitettiin visualisointi- ja analysointityökalu ajonaikaisen käyttäytymisen ymmärtämisen helpottamiseksi. Lisäksi kehitettiin suorituskyvyn mitta, joka mahdollistaa erilaisten skaalausmenetelmien vertailun ja arvioimisen suoritusympäristöstä riippumatta, perustuen joko suoritustallenteen tai teoreettiseen analyysiin. Työkalu esittää ajonaikaisesti kerätyn tallenteen helposti ymmärrettävällä tavalla. Se näyttää mm. prosessit, prosessorikuorman, skaalausmenetelmien toiminnan sekä energiankulutuksen kolmiulotteista grafiikkaa käyttäen. Työkalu tuottaa myös käyttäjän valitsemasta osasta suorituskuvaa numeerista tietoa, joka sisältää useita oleellisia suorituskykyarvoja ja tilastotietoa. Työkalun sovellettavuutta tarkasteltiin todellisesta laitteesta saatua suoritustallennetta sekä suorituskyvyn skaalauksen simulointia analysoimalla. Skaalausmekanismin parametrien vaikutus simuloidun laitteen suorituskykyyn analysoitiin.