Processing Bio-Argo particle backscattering at the DAC level

This document does NOT address the issue of particle backscattering quality control (either real-time or delayed mode). As a preliminary step towards that goal, this document seeks to ensure that all countries deploying floats equipped with backscattering sensors document the data and metadata related to these floats properly. We produced this document in response to action item 9 from the first Bio-Argo Data Management meeting in Hyderabad (November 12-13, 2012). If the recommendations contained herein are followed, we will end up with a more uniform set of particle backscattering data within the Bio-Argo data system, allowing users to begin analyzing not only their own particle backscattering data, but also those of others, in the true spirit of Argo data sharing.

Processing bio-Argo chlorophyll-A concentration at the DAC level

This document does NOT address the issue of chlorophyll-a quality control (either real-time or delayed mode). As a preliminary step towards that goal, this document seeks to ensure that all countries deploying floats equipped with chlorophyll-a sensors document the data and metadata related to these floats properly. We produced this document in response to action item 3 from the first Bio-Argo Data Management meeting in Hyderabad (November 12-13, 2012). If the recommendations contained herein are followed, we will end up with a more uniform set of chlorophyll-a data within the Bio-Argo data system, allowing users to begin analyzing not only their own chlorophyll-a data, but also those of others, in the true spirit of Argo data sharing.

Processing Argo oxygen data at the DAC level cookbook

This document does NOT address the issue of oxygen data quality control (either real-time or delayed mode). As a preliminary step towards that goal, this document seeks to ensure that all countries deploying floats equipped with oxygen sensors document the data and metadata related to these floats properly. We produced this document in response to action item 14 from the AST-10 meeting in Hangzhou (March 22-23, 2009). Action item 14: Denis Gilbert to work with Taiyo Kobayashi and Virginie Thierry to ensure DACs are processing oxygen data according to recommendations. If the recommendations contained herein are followed, we will end up with a more uniform set of oxygen data within the Argo data system, allowing users to begin analysing not only their own oxygen data, but also those of others, in the true spirit of Argo data sharing. Indications provided in this document are valid as of the date of writing this document. It is very likely that changes in sensors, calibrations and conversions equations will occur in the future. Please contact V. Thierry (vthierry@ifremer.fr) for any inconsistencies or missing information. A dedicated webpage on the Argo Data Management website (www) contains all information regarding Argo oxygen data management : current and previous version of this cookbook, oxygen sensor manuals, calibration sheet examples, examples of matlab code to process oxygen data, test data, etc..

Investigation of multisensory processing and structural brain differences in Autism Spectrum Disorder

This thesis is an investigation of structural brain abnormalities, as well as multisensory and unisensory processing deficits in autistic traits and Autism Spectrum Disorder (ASD). To achieve this, structural and functional magnetic resonance imaging (fMRI) and psychophysical techniques were employed. ASD is a neurodevelopmental condition which is characterised by the social communication and interaction deficits, as well as repetitive patterns of behaviour, interests and activities. These traits are thought to be present in a typical population. The Autism Spectrum Quotient questionnaire (AQ) was developed to assess the prevalence of autistic traits in the general population. Von dem Hagen et al. (2011) revealed a link between AQ with white matter (WM) and grey matter (GM) volume (using voxel-based-morphometry). However, their findings revealed no difference in GM in areas associated with social cognition. Cortical thickness (CT) measurements are known to be a more direct measure of cortical morphology than GM volume. Therefore, Chapter 2 investigated the relationship between AQ scores and CT in the same sample of participants. This study showed that AQ scores correlated with CT in the left temporo-occipital junction, left posterior cingulate, right precentral gyrus and bilateral precentral sulcus, in a typical population. These areas were previously associated with structural and functional differences in ASD. Thus the findings suggest, to some extent, autistic traits are reflected in brain structure - in the general population. The ability to integrate auditory and visual information is crucial to everyday life, and results are mixed regarding how ASD influences audiovisual integration. To investigate this question, Chapter 3 examined the Temporal Integration Window (TIW), which indicates how precisely sight and sound need to be temporally aligned so that a unitary audiovisual event can be perceived. 26 adult males with ASD and 26 age and IQ-matched typically developed males were presented with flash-beep (BF), point-light drummer, and face-voice (FV) displays with varying degrees of asynchrony and asked to make Synchrony Judgements (SJ) and Temporal Order Judgements (TOJ). Analysis of the data included fitting Gaussian functions as well as using an Independent Channels Model (ICM) to fit the data (Garcia-Perez & Alcala-Quintana, 2012). Gaussian curve fitting for SJs showed that the ASD group had a wider TIW, but for TOJ no group effect was found. The ICM supported these results and model parameters indicated that the wider TIW for SJs in the ASD group was not due to sensory processing at the unisensory level, but rather due to decreased temporal resolution at a decisional level of combining sensory information. Furthermore, when performing TOJ, the ICM revealed a smaller Point of Subjective Simultaneity (PSS; closer to physical synchrony) in the ASD group than in the TD group. Finding that audiovisual temporal processing is different in ASD encouraged us to investigate the neural correlates of multisensory as well as unisensory processing using functional magnetic resonance imaging fMRI. Therefore, Chapter 4 investigated audiovisual, auditory and visual processing in ASD of simple BF displays and complex, social FV displays. During a block design experiment, we measured the BOLD signal when 13 adults with ASD and 13 typically developed (TD) age-sex- and IQ- matched adults were presented with audiovisual, audio and visual information of BF and FV displays. Our analyses revealed that processing of audiovisual as well as unisensory auditory and visual stimulus conditions in both the BF and FV displays was associated with reduced activation in ASD. Audiovisual, auditory and visual conditions of FV stimuli revealed reduced activation in ASD in regions of the frontal cortex, while BF stimuli revealed reduced activation the lingual gyri. The inferior parietal gyrus revealed an interaction between stimulus sensory condition of BF stimuli and group. Conjunction analyses revealed smaller regions of the superior temporal cortex (STC) in ASD to be audiovisual sensitive. Against our predictions, the STC did not reveal any activation differences, per se, between the two groups. However, a superior frontal area was shown to be sensitive to audiovisual face-voice stimuli in the TD group, but not in the ASD group. Overall this study indicated differences in brain activity for audiovisual, auditory and visual processing of social and non-social stimuli in individuals with ASD compared to TD individuals. These results contrast previous behavioural findings, suggesting different audiovisual integration, yet intact auditory and visual processing in ASD. Our behavioural findings revealed audiovisual temporal processing deficits in ASD during SJ tasks, therefore we investigated the neural correlates of SJ in ASD and TD controls. Similar to Chapter 4, we used fMRI in Chapter 5 to investigate audiovisual temporal processing in ASD in the same participants as recruited in Chapter 4. BOLD signals were measured while the ASD and TD participants were asked to make SJ on audiovisual displays of different levels of asynchrony: the participants’ PSS, audio leading visual information (audio first), visual leading audio information (visual first). Whereas no effect of group was found with BF displays, increased putamen activation was observed in ASD participants compared to TD participants when making SJs on FV displays. Investigating SJ on audiovisual displays in the bilateral superior temporal gyrus (STG), an area involved in audiovisual integration (see Chapter 4), we found no group differences or interaction between group and levels of audiovisual asynchrony. The investigation of different levels of asynchrony revealed a complex pattern of results indicating a network of areas more involved in processing PSS than audio first and visual first, as well as areas responding differently to audio first compared to video first. These activation differences between audio first and video first in different brain areas are constant with the view that audio leading and visual leading stimuli are processed differently.

Downstream processing of reverse osmosis brine: Characterisation of potential scaling compounds

Reverse osmosis (RO) brine produced at a full-scale coal seam gas (CSG) water treatment facility was characterized with spectroscopic and other analytical techniques. A number of potential scalants including silica, calcium, magnesium, sulphates and carbonates, all of which were present in dissolved and non-dissolved forms, were characterized. The presence of spherical particles with a size range of 10-1000nm and aggregates of 1-10 microns was confirmed by transmission electron microscopy (TEM). Those particulates contained the following metals in decreasing order: K, Si, Sr, Ca, B, Ba, Mg, P, and S. Characterization showed that nearly one-third of the total silicon in the brine was present in the particulates. Further, analysis of the RO brine suggested supersaturation and precipitation of metal carbonates and sulphates during the RO process should take place and could be responsible for subsequently capturing silica in the solid phase. However, the precipitation of crystalline carbonates and sulphates are complex. X-ray diffraction analysis did not confirm the presence of common calcium carbonates or sulphates but instead showed the presence of a suite of complex minerals, to which amorphous silica and/or silica rich compounds could have adhered. A filtration study showed that majority of the siliceous particles were less than 220nm in size, but could still be potentially captured using a low molecular weight ultrafiltration membrane. © 2015 Elsevier Ltd.

Do Pré-escolar ao 1.º Ciclo: O percurso da escrita

Relatório de Estágio apresentado à Escola Superior de Educação de Paula Frassinetti para obtenção de grau de Mestre em Educação Pré-Escolar e Ensino do 1.º Ciclo do Ensino Básico

EFFECTS OF AGING ON MIDBRAIN AND CORTICAL SPEECH-IN-NOISE PROCESSING

Older adults frequently report that they can hear what they have been told but cannot understand the meaning. This is particularly true in noisy conditions, where the additional challenge of suppressing irrelevant noise (i.e. a competing talker) adds another layer of difficulty to their speech understanding. Hearing aids improve speech perception in quiet, but their success in noisy environments has been modest, suggesting that peripheral hearing loss may not be the only factor in the older adult’s perceptual difficulties. Recent animal studies have shown that auditory synapses and cells undergo significant age-related changes that could impact the integrity of temporal processing in the central auditory system. Psychoacoustic studies carried out in humans have also shown that hearing loss can explain the decline in older adults’ performance in quiet compared to younger adults, but these psychoacoustic measurements are not accurate in describing auditory deficits in noisy conditions. These results would suggest that temporal auditory processing deficits could play an important role in explaining the reduced ability of older adults to process speech in noisy environments. The goals of this dissertation were to understand how age affects neural auditory mechanisms and at which level in the auditory system these changes are particularly relevant for explaining speech-in-noise problems. Specifically, we used non-invasive neuroimaging techniques to tap into the midbrain and the cortex in order to analyze how auditory stimuli are processed in younger (our standard) and older adults. We will also attempt to investigate a possible interaction between processing carried out in the midbrain and cortex.

Extracting reusable document components for variable data printing

Variable Data Printing (VDP) has brought new flexibility and dynamism to the printed page. Each printed instance of a specific class of document can now have different degrees of customized content within the document template. This flexibility comes at a cost. If every printed page is potentially different from all others it must be rasterized separately, which is a time-consuming process. Technologies such as PPML (Personalized Print Markup Language) attempt to address this problem by dividing the bitmapped page into components that can be cached at the raster level, thereby speeding up the generation of page instances. A large number of documents are stored in Page Description Languages at a higher level of abstraction than the bitmapped page. Much of this content could be reused within a VDP environment provided that separable document components can be identified and extracted. These components then need to be individually rasterisable so that each high-level component can be related to its low-level (bitmap) equivalent. Unfortunately, the unstructured nature of most Page Description Languages makes it difficult to extract content easily. This paper outlines the problems encountered in extracting component-based content from existing page description formats, such as PostScript, PDF and SVG, and how the differences between the formats affects the ease with which content can be extracted. The techniques are illustrated with reference to a tool called COG Extractor, which extracts content from PDF and SVG and prepares it for reuse.

SEQUENTIAL DECISIONS AND PREDICTIONS IN NATURAL LANGUAGE PROCESSING

Natural language processing has achieved great success in a wide range of ap- plications, producing both commercial language services and open-source language tools. However, most methods take a static or batch approach, assuming that the model has all information it needs and makes a one-time prediction. In this disser- tation, we study dynamic problems where the input comes in a sequence instead of all at once, and the output must be produced while the input is arriving. In these problems, predictions are often made based only on partial information. We see this dynamic setting in many real-time, interactive applications. These problems usually involve a trade-off between the amount of input received (cost) and the quality of the output prediction (accuracy). Therefore, the evaluation considers both objectives (e.g., plotting a Pareto curve). Our goal is to develop a formal understanding of sequential prediction and decision-making problems in natural language processing and to propose efficient solutions. Toward this end, we present meta-algorithms that take an existent batch model and produce a dynamic model to handle sequential inputs and outputs. Webuild our framework upon theories of Markov Decision Process (MDP), which allows learning to trade off competing objectives in a principled way. The main machine learning techniques we use are from imitation learning and reinforcement learning, and we advance current techniques to tackle problems arising in our settings. We evaluate our algorithm on a variety of applications, including dependency parsing, machine translation, and question answering. We show that our approach achieves a better cost-accuracy trade-off than the batch approach and heuristic-based decision- making approaches. We first propose a general framework for cost-sensitive prediction, where dif- ferent parts of the input come at different costs. We formulate a decision-making process that selects pieces of the input sequentially, and the selection is adaptive to each instance. Our approach is evaluated on both standard classification tasks and a structured prediction task (dependency parsing). We show that it achieves similar prediction quality to methods that use all input, while inducing a much smaller cost. Next, we extend the framework to problems where the input is revealed incremen- tally in a fixed order. We study two applications: simultaneous machine translation and quiz bowl (incremental text classification). We discuss challenges in this set- ting and show that adding domain knowledge eases the decision-making problem. A central theme throughout the chapters is an MDP formulation of a challenging problem with sequential input/output and trade-off decisions, accompanied by a learning algorithm that solves the MDP.

Evolution of genome sequencing techniques

The quality and the speed for genome sequencing has advanced at the same time that technology boundaries are stretched. This advancement has been divided so far in three generations. The first-generation methods enabled sequencing of clonal DNA populations. The second-generation massively increased throughput by parallelizing many reactions while the third-generation methods allow direct sequencing of single DNA molecules. The first techniques to sequence DNA were not developed until the mid-1970s, when two distinct sequencing methods were developed almost simultaneously, one by Alan Maxam and Walter Gilbert, and the other one by Frederick Sanger. The first one is a chemical method to cleave DNA at specific points and the second one uses ddNTPs, which synthesizes a copy from the DNA chain template. Nevertheless, both methods generate fragments of varying lengths that are further electrophoresed. Moreover, it is important to say that until the 1990s, the sequencing of DNA was relatively expensive and it was seen as a long process. Besides, using radiolabeled nucleotides also compounded the problem through safety concerns and prevented the automation. Some advancements within the first generation include the replacement of radioactive labels by fluorescent labeled ddNTPs and cycle sequencing with thermostable DNA polymerase, which allows automation and signal amplification, making the process cheaper, safer and faster. Another method is Pyrosequencing, which is based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation. By the end of the last millennia, parallelization of this method started the Next Generation Sequencing (NGS) with 454 as the first of many methods that can process multiple samples, calling it the 2º generation sequencing. Here electrophoresis was completely eliminated. One of the methods that is sometimes used is SOLiD, based on sequencing by ligation of fluorescently dye-labeled di-base probes which competes to ligate to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. The widely used Solexa/Illumina method uses modified dNTPs containing so called “reversible terminators” which blocks further polymerization. The terminator also contains a fluorescent label, which can be detected by a camera. Now, the previous step towards the third generation was in charge of Ion Torrent, who developed a technique that is based in a method of “sequencing-by-synthesis”. Its main feature is the detection of hydrogen ions that are released during base incorporation. Likewise, the third generation takes into account nanotechnology advancements for the processing of unique DNA molecules to a real time synthesis sequencing system like PacBio; and finally, the NANOPORE, projected since 1995, also uses Nano-sensors forming channels obtained from bacteria that conducts the sample to a sensor that allows the detection of each nucleotide residue in the DNA strand. The advancements in terms of technology that we have nowadays have been so quick, that it makes wonder: ¿How do we imagine the next generation?

Catalytic CO2 hydrogenation: study at the molecular scale using field emission techniques

An accurate characterization of the rhodium specimen was obtained via FIM experiments. Reaction behaviors between H2 and CO2 were observed in FEM mode at 700 K. At this temperature, CO desorption occurs, preventing CO+H2 reaction. Surface is mainly recovered by oxygen; reaction with hydrogen occurs. Finally, we can identify the reaction as the Reverse Water Gas Shift.

Processing Bio-Argo nitrate concentration at the DAC Level

The only method used to date to measure dissolved nitrate concentration (NITRATE) with sensors mounted on profiling floats is based on the absorption of light at ultraviolet wavelengths by nitrate ion (Johnson and Coletti, 2002; Johnson et al., 2010; 2013; D’Ortenzio et al., 2012). Nitrate has a modest UV absorption band with a peak near 210 nm, which overlaps with the stronger absorption band of bromide, which has a peak near 200 nm. In addition, there is a much weaker absorption due to dissolved organic matter and light scattering by particles (Ogura and Hanya, 1966). The UV spectrum thus consists of three components, bromide, nitrate and a background due to organics and particles. The background also includes thermal effects on the instrument and slow drift. All of these latter effects (organics, particles, thermal effects and drift) tend to be smooth spectra that combine to form an absorption spectrum that is linear in wavelength over relatively short wavelength spans. If the light absorption spectrum is measured in the wavelength range around 217 to 240 nm (the exact range is a bit of a decision by the operator), then the nitrate concentration can be determined. Two different instruments based on the same optical principles are in use for this purpose. The In Situ Ultraviolet Spectrophotometer (ISUS) built at MBARI or at Satlantic has been mounted inside the pressure hull of a Teledyne/Webb Research APEX and NKE Provor profiling floats and the optics penetrate through the upper end cap into the water. The Satlantic Submersible Ultraviolet Nitrate Analyzer (SUNA) is placed on the outside of APEX, Provor, and Navis profiling floats in its own pressure housing and is connected to the float through an underwater cable that provides power and communications. Power, communications between the float controller and the sensor, and data processing requirements are essentially the same for both ISUS and SUNA. There are several possible algorithms that can be used for the deconvolution of nitrate concentration from the observed UV absorption spectrum (Johnson and Coletti, 2002; Arai et al., 2008; Sakamoto et al., 2009; Zielinski et al., 2011). In addition, the default algorithm that is available in Satlantic sensors is a proprietary approach, but this is not generally used on profiling floats. There are some tradeoffs in every approach. To date almost all nitrate sensors on profiling floats have used the Temperature Compensated Salinity Subtracted (TCSS) algorithm developed by Sakamoto et al. (2009), and this document focuses on that method. It is likely that there will be further algorithm development and it is necessary that the data systems clearly identify the algorithm that is used. It is also desirable that the data system allow for recalculation of prior data sets using new algorithms. To accomplish this, the float must report not just the computed nitrate, but the observed light intensity. Then, the rule to obtain only one NITRATE parameter is, if the spectrum is present then, the NITRATE should be recalculated from the spectrum while the computation of nitrate concentration can also generate useful diagnostics of data quality.

Development of semicrystalline morphology of poly(L-lactic acid) during processing of a vascular scaffold

New and promising treatments for coronary heart disease are enabled by vascular scaffolds made of poly(L-lactic acid) (PLLA), as demonstrated by Abbott Vascular’s bioresorbable vascular scaffold. PLLA is a semicrystalline polymer whose degree of crystallinity and crystalline microstructure depend on the thermal and deformation history during processing. In turn, the semicrystalline morphology determines scaffold strength and biodegradation time. However, spatially-resolved information about the resulting material structure (crystallinity and crystal orientation) is needed to interpret in vivo observations.

The first manufacturing step of the scaffold is tube expansion in a process similar to injection blow molding. Spatial uniformity of the tube microstructure is essential for the consistent production and performance of the final scaffold. For implantation into the artery, solid-state deformation below the glass transition temperature is imposed on a laser-cut subassembly to crimp it into a small diameter. Regions of localized strain during crimping are implicated in deployment behavior.

To examine the semicrystalline microstructure development of the scaffold, we employed complementary techniques of scanning electron and polarized light microscopy, wide-angle X-ray scattering, and X-ray microdiffraction. These techniques enabled us to assess the microstructure at the micro and nano length scale. The results show that the expanded tube is very uniform in the azimuthal and axial directions and that radial variations are more pronounced. The crimping step dramatically changes the microstructure of the subassembly by imposing extreme elongation and compression. Spatial information on the degree and direction of chain orientation from X-ray microdiffraction data gives insight into the mechanism by which the PLLA dissipates the stresses during crimping, without fracture. Finally, analysis of the microstructure after deployment shows that it is inherited from the crimping step and contributes to the scaffold’s successful implantation in vivo.

Concepções e práticas de avaliação das aprendizagens na educação pré-escolar

Esta dissertação teve como problemática as conceções e as práticas de avaliação das aprendizagens, que três educadoras de infância da cidade de Évora utilizam para avaliar as crianças, segundo o modelo ou as orientações curriculares que seguem. Privilegiámos uma investigação de natureza qualitativa, utilizando como estratégia de investigação o estudo de casos e como técnicas de recolha e tratamento de dados a observação, análise documental, inquérito por entrevista e análise de conteúdo. Para desenvolver este estudo, realizámos pesquisa bibliográfica sobre a avaliação das aprendizagens em geral e segundo os modelos curriculares do Movimento da Escola Moderna e o High-Scope e as Orientações Curriculares para a Educação Pré-Escolar. Constatámos que o referencial teórico da ação educativa influencia as conceções e as práticas de avaliação das aprendizagens que as educadoras utilizam. Também verificámos alguns constrangimentos na avaliação, nomeadamente o tamanho do grupo de crianças. /ABSTRACT: This thesis had as problematic the conceptions and assessment practices of learning that three nursery teachers in the city of Évora use to assess children, according to the model or the curriculum guidelines according to the work. We gave importance to a research of a qualitative nature, using as strategy research the study of cases and as techniques for collecting and processing data the observation, document analysis, enquiry through interview and analysis of the content. To develop this study, we conducted bibliographic research about the assessment of learning in general and according the curricular models of the Movement of Modem School, High-Scope and Guidelines for the Pre-School education. We found that the theoretical framework of educational action influences educational concepts and practice of learning assessment that educators use. We have also seen some constraints in the assessment, including the size of the group of children.

A supervised machine learning method for word sense disambiguation of Portuguese nouns

Dissertação de Mestrado, Ciências da Linguagem, Faculdade de Ciências Humanas e Sociais, Universidade do Algarve, 2010