SDAR: a package for plotting and analyzing stratigraphy data in R

Stratigraphic Columns (SC) are the most useful and common ways to represent the eld descriptions (e.g., grain size, thickness of rock packages, and fossil and lithological components) of rock sequences and well logs. In these representations the width of SC vary according to the grain size (i.e., the wider the strata, the coarser the rocks (Miall 1990; Tucker 2011)), and the thickness of each layer is represented at the vertical axis of the diagram. Typically these representations are drawn 'manually' using vector graphic editors (e.g., Adobe Illustrator®, CorelDRAW®, Inskape). Nowadays there are various software which automatically plot SCs, but there are not versatile open-source tools and it is very di cult to both store and analyse stratigraphic information. This document presents Stratigraphic Data Analysis in R (SDAR), an analytical package1 designed for both plotting and facilitate the analysis of Stratigraphic Data in R (R Core Team 2014). SDAR, uses simple stratigraphic data and takes advantage of the exible plotting tools available in R to produce detailed SCs. The main bene ts of SDAR are: (i) used to generate accurate and complete SC plot including multiple features (e.g., sedimentary structures, samples, fossil content, color, structural data, contacts between beds), (ii) developed in a free software environment for statistical computing and graphics, (iii) run on a wide variety of platforms (i.e., UNIX, Windows, and MacOS), (iv) both plotting and analysing functions can be executed directly on R's command-line interface (CLI), consequently this feature enables users to integrate SDAR's functions with several others add-on packages available for R from The Comprehensive R Archive Network (CRAN).

Evolução tectónica mesozóica da Bacia Lusitaniana

The evolution of the Lusitanian Basin, localized on the western Iberian margin, is closely associated with the first opening phases of the North Atlantic. It persisted from the Late Triassic to the Early Cretaceous, more precisely until the end of the Early Aptian, and its evolution was conditioned by inherited structures from the variscan basement. The part played by the faults that establish its boundaries, as regards the geometric and kinematic evolution and the organization of the sedimentary bodies, is discussed here, as well as with respect to important faults transversal to the Basin. A basin evolution model is proposed consisting of four rifting episodes which show: i) periods of symmetrical (horst and graben organization) and asymmetrical (half graben organization) geometric evolution; ii) diachronous fracturing; iii) rotation of the main extensional direction; iv) rooting in the variscan basement of the main faults of the basin (predominantly thick skinned style). The analysis and regional comparison, particularly with the Algarve Basin, of the time intervals represented by important basin scale hiatuses near to the renovation of the rifting episodes, have led to assume the occurrence of early tectonic inversions (Callovian–Oxfordian and Tithonian–Berriasian). The latter, however, had a subsequent evolution distinct from the first: there is no subsidence renovation, which is discussed here, and it is related to a magmatic event. Although the Lusitanian Basin is located on a rift margin which is considered non-volcanic, the three magmatic cycles as defined by many authors, particularly the second (approx. 130 to 110 My ?), performed a fundamental part in the mobilization of the Hettangian evaporites, resulting in the main diapiric events of the Lusitanian Basin. The manner and time in which the basin definitely ends its evolution (Early Aptian) is discussed here. Comparisons are established with other west Iberian margin basins and with Newfoundland basins. A model of oceanization of this area of the North Atlantic is also presented, consisting of two events separated by approximately 10 My, and of distinct areas separated by the Nazaré fault. The elaboration of this synthesis was based on: - information contained in previously published papers (1990 – 2000); - field-work carried out over the last years, the results of which have not yet been published; - information gathered from the reinterpretation of geological mapping and geophysical (seismic and well logs) elements, and from generic literature concerning the Mesozoic of the west iberian margin.

Sedimentation pelagique et encroûtements cryptalgaires: les calcaires gremeleux du Carixien portugais

In Portugal, Carixian is generally represented by alternative layers of marly limestones characterized by nodule and lumpy levels. These layers are particularly developped [show preferential development] on passage areas to a sedimentary basin, particularly along the slope of tilted blocks between the Meseta and Berlenga's horst. This facies is included in the range of the «nodular limestone» and of the «ammonitico-rosso». Limestones are radiolaria micrites with fragments of pelagic organisms (ammonoids, thin shelled gastropods). These layers can be affected by intensive bioturbation (Brenha) which is responsible for dismantlement, specially where the initial thickness does not exceed a few centimetres. This process can lead to the isolation of residual nodules (Brenha, São Pedro de Muel, Peniche) which can be mobilised by massive sliding (Peniche). The isolated elements, shell fragments or residual nodules, can also be incrustated, thus developing oncolitic cryptalgal structures. At Brenha the lump structure developed progressively into a sequence overlapping the normal sedimentary one (thick limestone beds alternating with bituminous shales). Cryptalgal structures correspond to rather unstable environment conditions on mobile margins. These structures are known in deep pelagic sediments corresponding to well defined events of the geodynamic evolution (end of the initial rifting). Cryptalgal accretions disappear towards the sedimentary basin, and the nodular levels are less important. In the articulation areas with the Tomar platform, small mounds and cupules (Alcabideque) developed within the alternating marly-limestone levels. They represent the so called «mud mounds» of metric dimensions. The upper part of these «mud mounds» is hardened, showing track remains and supporting some brachiopods and pectinids. Hence the lumpy facies of Portugal is included among the range of sedimentaty environments and can be used as «geodynamic tracer».

Development of biocompatible and “smart” porous structures using CO2-assisted processes

Dissertação apresentada para a obtenção do grau de Doutor em Engenharia Química, especialidade Engenharia da Reacção Química, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Segmentation of striatal brain structures from high resolution pet images

Dissertation presented at the Faculty of Science and Technology of the New University of Lisbon in fulfillment of the requirements for the Masters degree in Electrical Engineering and Computers

Coastal sedimentary environments and sea-level changes

A detailed knowledge of the 3-D arrangement and lateral facies relationships of the stacking patterns in coastal deposits is essential to approach many geological problems such as precise tracing of sea level changes, particularly during small scale fluctuations. These are useful data regarding the geodynamic evolution of basin margins and yield profit in oil exploration. Sediment supply, wave-and tidal processes, coastal morphology, and accommodation space generated by eustasy and tectonics govern the highly variable architecture of sedimentary bodies deposited in coastal settings. But these parameters change with time, and erosional surfaces may play a prominent role in areas located towards land. Besides, lateral shift of erosional or even depositional loci very often results in destruction of large parts of the sediment record. Several case studies illustrate some commonly found arrangements of facies and their distinguishing features. The final aim is to get the best results from the sedimentological analysis of coastal units.

Assinatura tectono-sedimentar do auge da compressão bética em Portugal: a descontinuidade sedimentar Valesiano terminal-Turoliano

An Upper Miocene important sedimentary break can be accurately recognised in the Portuguese basins and is reflected by a drastic palaeogeographic change in relation to a large-scale tectonic event of probable uppermost Vallesian-Turolian (9,5 Ma; middle Tortonian) age. The characterisation of the sedimentary record of this tectonic event, as well as its relations with interpreted active faults is made for different situations: Douro (NW border), Mondego, Lower-Tagus and Sado Tertiary basins. The sedimentary record, considered upper Tortonian-Messinian ? (uppermost Vallesian-Turolian ?) is interpreted mainly as endorheic alluvial fans (internal drainage), developed along active NNE-SSW indent-linked strike-slip faults and NE-SW reverse faults. At NE Portugal, proximal fluvial systems of an endorheic hydrographic network drained eastwards to the Spanish Duero interior Basin. The main evidences of the betic compression clímax in Portugal mainland are presented; the interpreted active tectonic structures are in accordance with an intense NNW-SSE crustal shortening, but some regional differences are also documented.

Evolução cenozóica da área de Longroiva-Vilariça (NE Portugal)

In the Longroiva-Vilariça area, the identification of Cenozoic lithostratigraphic units, the sedimentology and the characterization of its geometric relations with tectonic structures allowed the interpretation of the palaeogeographic main stages: 1) the greenwhitish Vilariça Arkoses (Middle Eocene to Oligocene ?) represent proximal sediments of a very low gradient drainage towards the eastern Spanish Tertiary Duero Basin; 2)Quintãs Formation (late Miocene ?) are brown-reddish coloured piedmont alluvial deposits, correlative of important vertical displacement (western tectonic block relative uplift) along the NNE-SSW indent-linked strike-slip Bragança-Vilariça-Longroiva fault zone, interpreted as a reactivated deep hercynian fracture, with left-lateral movement; 3) the red Sampaio Formation (Gelasian-early Pleistocene ?)was interpreted as downhill conglomeratic deposits related with important overtrusting along this fault zone (the definition of the present-day narrow graben configuration) and correlative of the atlantic hydrographic incision stage beginning; 4) conglomeratic terraces (middle and late Pleistocene ?); 5) alluvial plains and colluvial deposits (Holocene).

Evolution and biogenesis of microtubule-derived structures

Dissertação apresentada para obtenção do grau de Doutor em Biologia Celular pelo Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa

Life-cycle performance of structures: combining expert judgment and results of inspection

Life-Cycle Civil Engineering – Biondini & Frangopol

Vibration control with shape-memory alloys in civil engineering structures

Dissertação apresentada à Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Doutor em Engenharia Civil

Robustness of timber structures in seismic areas

Some of the properties sought in seismic design of buildings are also considered fundamental to guarantee structural robustness. Moreover, some key concepts are common to both seismic and robustness design. In fact, both analyses consider events with a very small probability of occurrence, and consequently, a significant level of damage is admissible. As very rare events,in both cases, the actions are extremely hard to quantify. The acceptance of limited damage requires a system based analysis of structures, rather than an element by element methodology, as employed for other load cases. As for robustness analysis, in seismic design the main objective is to guarantee that the structure survives an earthquake, without extensive damage. In the case of seismic design, this is achieved by guaranteeing the dissipation of energy through plastic hinges distributed in the structure. For this to be possible, some key properties must be assured, in particular ductility and redundancy. The same properties could be fundamental in robustness design, as a structure can only sustain significant damage if capable of distributing stresses to parts of the structure unaffected by the triggering event. Timber is often used for primary load‐bearing elements in single storey long‐span structures for public buildings and arenas, where severe consequences can be expected if one or more of the primary load bearing elements fail. The structural system used for these structures consists of main frames, secondary elements and bracing elements. The main frame, composed by columns and beams, can be seen as key elements in the system and should be designed with high safety against failure and under strict quality control. The main frames may sometimes be designed with moment resisting joints between columns and beams. Scenarios, where one or more of these key elements, fail should be considered at least for high consequence buildings. Two alternative strategies may be applied: isolation of collapsing sections and, provision of alternate load paths [1]. The first one is relatively straightforward to provide by deliberately designing the secondary structural system less strong and stiff. Alternatively, the secondary structural system and the bracing system can be design so that loss of capacity in the main frame does not lead to the collapse. A case study has been selected aiming to assess the consequences of these two different strategies, in particular, under seismic loads.

Earthquakes and robustness for timber structures

Workshop of COST Actions TU0601 and E55 September 21-22 2009, Ljubljana, Slovenia

Robustness of corroded reinforced concrete structures. A structural performance approach

Structure and Infrastructure Engineering, 1-17