C. Veiga-Pires

Magnetic fingerprint of southern Portuguese speleothems and implications for paleomagnetism and environmental magnetism

Environmental magnetism of speleothems is still in its early stage of development. Here we report on our investigation of the environmental and paleomagnetic information that has been recorded in speleothems, and what are the factors that control its preservation and reliability. To address these issues, we used a multidisciplinary approach, including rock magnetism, petrography, scanning electron microscopy, stable carbon and oxygen isotope compositions, and major and trace element concentrations. We applied this to a set of samples from different stages of speleothem evolution: present-day dripwater (glass plates), a weathered stalactite, a fresh stalagmite, cave sediments, and terra rossa soils. These samples come from the Penico and Excentricas caves, located in two distinct aquifers of the Algarve region, South Portugal. Our results show that the main magnetic carriers of the speleothems under study are primary (detrital) and consist of maghemite (and magnetite?). Similarities in coercivity and temperature dependence of the studied set of samples suggest that iron oxides are inherited from the terra rossa soils that cap the cave and were transported to the speleothems by dripwater. Hence, they represent a regional environmental signature. Interestingly, a stable and probably detrital remanent magnetization could be isolated in the fresh stalagmite, whereas the weathered stalactite yielded chaotic magnetic directions and very low remanent intensities. We propose that these low intensities can be the result from (i) different remanence acquisition mechanisms between stalagmite and stalactite and/or (ii) iron dissolution by fungal activity. We also suggest that magnetic properties and color and the content in detrital elements in the fresh speleothem inform about environmental processes acting on the interface of rock (soil)-atmosphere, while oxygen isotope composition and alkaline-earth element concentrations inform about calcite-water interaction processes. These results provide a better understanding of how environmental information is recorded in speleothems and what the factors are that control the reliability of the paleomagnetic and paleo-environmental signal.

Cave Chamber Data Modeling and 3D Web Visualization

Underground caves and its specific structures are important for geomorphological studies. In this paper we present tools to identify and map speleothems by surveying cave chambers interiors. The cave chamber was surveyed using Terrestrial Laser Scanning to acquire point clouds with high level of detail for 3D model generation. This data with 45 million points is useful for either reconstruction, geomorphological studies or virtual visits of caves. With this point cloud we generated a 3D-mesh to represent the surface model of the cave chamber, which is important to study its geomorphological features. A topological structure of the 3D-mesh was also implemented to get an efficient algorithm to help identifying stalactites. The possibility to publish 3D data on the Web is of particular interest for the geospatial field. For this reason, it was decided to make the cave model available in the Web by developing a 3D graphical interface where users can navigate and interact with the three-dimensional models of the cave. For this Web3D framework it was used X3D, WebGL and X3DOM. Such solution does not require any additional plug-ins or components.

Interception of nutrient rich submarine groundwater discharge seepage on European temperate beaches by the acoel flatworm, Symsagittifera roscoffensis.

Submarine groundwater discharge (SGD) occurs in intertidal areas, representing a largely unquantified source of solute fluxes to adjacent coastal zones, with nitrogen being constantly the keynote chemical of concern. In Olhos de Água SGD is present as groundwater springs or merely sub-aerial runoff. The occurrence of the flatworm Symsagittifera roscoffensis is described for the first time in Olhos de Água in connection to seepage flows. To assess the impact of this symbiotic flatworm on the nitrogen associated to groundwater discharge flow at the beach, nitrate uptake experiments were conducted in laboratory microcosms. Our results show that S. roscoffensis actively uptakes nitrate at different rates depending on light availability, with rates ≈ 10 times higher than that of its symbiotic microalgae alone. This supports the hypothesis that S. roscoffensis could be an important in situ nitrate interceptor, potentially playing a biological role on the transformation of groundwater-borne nitrate loads at the land-ocean boundary.

High-resolution digital 3D models of Algar do Penico Chamber: limitations, challenges, and potential

and/or complex terrains (Pucci & Marambio, 2009; Roncat et al., 2011). Accordingly, with the objective of producing a cave map that identifies the main interior speleothem structures for the purposes of palaeoenvironmental reconstruction, we conducted a terrestrial laser-based survey in a limestone cave. However, rather than just obtaining a map, the present study also aimed to expand 3D-mesh analysis, including the development of two algorithms for determination of stalactite extremities and contour lines, and the interactive visualization of 3D meshes on the Web. The chosen cave is known by local speleologists as Algar do Penico or Algar Guedes (Cavaco, pers. comm.), and is located in the Algarve region in southern Portugal. In this paper, we generate 3D-mesh models of the cave by using surface-reconstruction algorithms. These models can be used to study geomorphological structures and are able to be visualized on graphical interfaces. Several different options are presented for rendering models with high levels of detail from the same point cloud data set. For Web visualization, the selected model is simplified using a decimation method that reduces the download time. We adopt a framework

A topological framework for interactive queries on 3D models in the Web.

Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications.

Framework for 3D data modeling and web visualization of underground caves using open source tools

Terrestrial Laser Scanning is a very useful technique for cave studies. This surveying method creates point clouds with high detail levels for 3D model generation, which is indeed useful for either reconstruction, geomorphological studies or virtual visits of caves. The present work generated a 3D model of a cave chamber and developed a framework for 3D data visualization on the Web. Identifying geomorphological structures is one of the goals of this project. The generated 3D-mesh represents the surface model of the cave chamber, which is important to study its geomorphological features. A topological structure of the 3D-mesh was implemented to get an efficient algorithm to help determining stalactites. The recognition and positioning of cave stalactites can provide information on hidden cave features responsible for cave geomorphology. The possibility to publish 3D data on the Web is of particular interest for the geospatial field. For this reason, it was decided to make the cave model available in the Web by developing a 3D graphical interface where users can navigate and interact with the three-dimensional models of the cave. For this Web framework, X3D, WebGL and X3DOM were used. Such solution does not require any additional plug-ins or components.

The effect of speleothem surface slope on the remanent magnetic inclination

Speleothems are of interest for high-resolution reconstruction of the Earths magnetic field. However, little is known about the influence of speleothem morphologies on their Natural Remanent Magnetization (NRM) record. Here we report on a high-resolution paleomagnetic study of a dome-shaped speleothem of Middle Holocene age from southern Portugal, with special attention to the anisotropy of magnetic susceptibility (AMS) and anisotropy of anhysteretic remanent magnetization (AARM). To assess the potential influence of the slope of the speleothem surface on the recorded remanent magnetization, we compare magnetic directions and AMS and AARM fabrics from sub-horizontal to gradually sub-vertical calcite growth layers collected in a transversal cross-section of the speleothem. A linear correlation is observed between magnetic inclinations, calcite laminae slope and AARM k1 inclination. The AMS fabric is mostly controlled by calcite crystals, with direction of the minimum axes (k3) perpendicular to laminae growth. Magnetic inclinations recorded in inclined and vertical calcite growth layers are underestimated when compared to a global paleosecular variation (PSV) model. After extrapolating magnetic inclinations to the horizontal, the corrected data better fit the PSV model, but are still lower than the predicted magnetic inclinations, suggesting that inclination shallowing affects the entire speleothem. We suggest that speleothem morphology exerts a critical role on the magnetic inclination recording, which is controlled by the Earths magnetic field but also influenced by particle rolling along the sloping surfaces. These observations open new avenues for reconstructing high-resolution paleomagnetic secular variations records from speleothems and provide new insights into their NRM acquisition mechanisms.

Web3D Visualization of High Detail and Complex 3D-mesh Caves Models

This paper presents the novel architecture of a web3D server that stores 3D models with different levels of detail and complexity that enables the interactive visualization and navigation in a web browser and the determination of detailed geomorphological structures of an underground cave. We surveyed an underground cave using a Terrestrial Laser Scanning to acquire a high-level detail point cloud with millions of points. This data allowed generating a high detail 3D-mesh to represent the surface model of the cave chamber, which can be important in studying geomorphological features. The web3D server uses a simplified version of the cave with about 250 thousand triangles that enables client applications to navigate and interact with this simplified model in a Web browser. The more detailed and complex model of the cave with millions of triangles is also stored in the web3D server. This model is used for the identification of geomorphological structures. It provides topological and geometrical information that is implemented in an octree data structure for the design of efficient algorithms to determine important speleothems and stored in a database to make it possible to work with big data models that can exceed the computers memory.

Effects of Spoilage on Nitrogen and Carbon Stable Isotopes Signatures of the Clam Ruditapes decussatus

Fish and seafood products are highly susceptible to post-mortem spoilage due to autolytic reactions at start, then microbiological activity and eventually oxidative reactions. Chemical and microbiological parameters are usually used to assess quality and make decisions for protecting public health, but they lack precision in defining which spoilage pathway is occurring at each moment. The objective of this work was to assess the effects of spoilage reactions on nitrogen and carbon stable isotopes in the grooved carpet shell clam, Ruditapes decussatus, and compare them to biochemical indicators of seafood deterioration, in order to better understand the relations between the different spoilage pathways during commercial storage conditions. Clams were kept in a refrigerator at 5 °C, to simulate normal commercial storage conditions, and sampled in the beginning of the experiment, and after eight, ten and twelve days. Moisture, condition index, percentage edibility, total volatile basic nitrogen (TVB-N), pH, nitrogen and carbon percentages and stable isotopes were determined for each sampling moment. Stable isotope analyses were performed using a Costech Elemental Analyzer (ECS 4010) coupled to a Thermo Finnigan Delta V Advantage. Stable isotopes analysis, especially for nitrogen, proved to be a good tool for the study of clam deterioration. Nitrogen stable isotopes results showed a relation with other spoilage indicators, such as pH and TVB-N, and allowed identifying spoilage specific pathways, such as amino acids decarboxylation and production of volatile nitrogen compounds.

Geometrical and Topological Modelling: A Fast Computation of Spatial 3D TLS Data Selections

Underground caves and their specific structures are important for geomorphological studies. In this paper we present a new tool to identify and map speleothems by surveying cave chambers interiors. One of the research problems that we had to solve was that we were dealing with a great number of points that resulted from the Laser scan. The cave chamber was surveyed using Terrestrial Laser Scanning to acquire point clouds with high level of detail for 3D model generation. A point cloud of 45 million points was generated. This data set is important for either reconstruction of the 3D model, geomorphological studies or virtual visits to the cave. With this point cloud we generated a 3D-mesh to represent the surface model of the cave chamber. In this paper we present an octree data structure implemented using SQLite relational database management. Furthermore, it is also possible to work with several data models simultaneously, in such a way that it is not limited by computer memory resources. A topological structure of the 3D-mesh was also implemented to get an efficient algorithm to help identifying stalactites and stalagmites from big data 3D models of high detail.