Study of the genes involved in Naphthenic acids (NAs) degradation by Rhodococcus spp.

Naphthenic acids (NAs) are an important group of organic pollutants mainly found in hydrocarbon deposits. Although these compounds are toxic, recalcitrant, and persistent in the environment, we are just learning the diversity of microbial communities involved in NAs- degradation and the mechanisms by which NAs are biodegraded. Studies have shown that naphthenic acids are susceptible to biodegradation, which decreases their concentration and reduces toxicity. Nevertheless, little is still known about their biodegradability. The present PhD Thesis’s work is aimed to study the biodegradation of simple model NAs using bacteria strains belonging to the Rhodococcus genus. In particular, Rh. sp. BCP1 and Rh. opacus R7 were able to utilize NAs such as cyclohexane carboxylic acid and cyclopentane carboxylic acid as the sole carbon and energy sources, even at concentrations up to 1000 mg/L. The presence of either substituents or longer carboxylic acid chains attached to the cyclohexane ring negatively affected the growth by pure bacterial cultures. Moreover, BCP1 and R7 cells incubated in the presence of CHCA or CPCA show a general increase of saturated and methyl-substituted fatty acids in their membrane, while the cis-mono-unsaturated ones decrease, as compared to glucose-grown cells. The observed lipid molecules modification during the growth in the presence of NAs is suggested as a possible mechanism to decrease the fluidity of the cell membrane to counteract NAs toxicity. In order to further evaluate this toxic effect on cell features, the morphological changes of BCP1 and R7 cells were also assessed through Transmission Electron Microscopy (TEM), revealing interesting ultrastructural changes. The induction of putative genes, and the construction of a random transposon mutagenesis library were also carried out to reveal the mechanisms by which these Rhodococcus strains can degrade toxic compounds such as NAs.

Analysis of Copy Number Variants identifies new candidate genes for Autism Spectrum Disorder and Intellectual Disability

Autism spectrum disorder (ASD) and Intellectual Disability (ID) are complex neuropsychiatric disorders characterized by extensive clinical and genetic heterogeneity and with overlapping risk factors. The aim of my project was to further investigate the role of Copy Numbers Variants (CNVs), identified through genome-wide studies performed by the Autism Geome Project (AGP) and the CHERISH consortium in large cohorts of ASD and ID cases, respectively. Specifically, I focused on four rare genic CNVs, selected on the basis of their impact on interesting ASD/ID candidate genes: a) a compound heterozygous deletion involving CTNNA3, predicted to cause the lack of functional protein; b) a 15q13.3 duplication containing CHRNA7; c) a 2q31.1 microdeletion encompassing KLHL23, SSB and METTL5; d) Lastly, I investigated the putative imprinting regulation of the CADPS2 gene, disrupted by a maternal deletion in two siblings with ASD and ID. This study provides further evidence for the role of CTNNA3, CHRNA7, KLHL23 and CADPS2 as ASD and/or ID susceptibility genes, and highlights that rare genetic variation contributes to disease risk in different ways: some rare mutations, such as those impacting CTNNA3, act in a recessive mode of inheritance, while other CNVs, such as those occurring in the 15q13.3 region, are implicated in multiple developmental and/or neurological disorders possibly interacting with other susceptibility variants elsewhere in the genome. On the other hand, the discovery of a tissue-specific monoallelic expression for the CADPS2 gene, implicates the involvement of epigenetic regulatory mechanisms as risk factors conferring susceptibility to ASD/ID.

Geophotohunt: Studio di algoritmi di confronto di immagini per realizzare una caccia al tesoro fotografica

Questo studio si propone di realizzare un’applicazione per dispositivi Android che permetta, per mezzo di un gioco di ruolo strutturato come caccia al tesoro, di visitare in prima persona città d’arte e luoghi turistici. Gli utenti finali, grazie alle funzionalità dell’app stessa, potranno giocare, creare e condividere cacce al tesoro basate sulla ricerca di edifici, monumenti, luoghi di rilevanza artistico-storica o turistica; in particolare al fine di completare ciascuna tappa di una caccia al tesoro il giocatore dovrà scattare una fotografia al monumento o edificio descritto nell’obiettivo della caccia stessa. Il software grazie ai dati rilevati tramite GPS e giroscopio (qualora il dispositivo ne sia dotato) e per mezzo di un algoritmo di instance recognition sarà in grado di affermare se la foto scattata rappresenta la risposta corretta al quesito della tappa. L’applicazione GeoPhotoHunt rappresenta non solo uno strumento ludico per la visita di città turistiche o più in generale luoghi di interesse, lo studio propone, infatti come suo contributo originale, l’implementazione su piattaforma mobile di un Content Based Image Retrieval System (CBIR) del tutto indipendente da un supporto server. Nello specifico il server dell’applicazione non sarà altro che uno strumento di appoggio con il quale i membri della “community” di GeoPhotoHunt potranno pubblicare le cacce al tesoro da loro create e condividere i punteggi che hanno totalizzato partecipando a una caccia al tesoro. In questo modo quando un utente ha scaricato sul proprio smartphone i dati di una caccia al tesoro potrà iniziare l’avventura anche in assenza di una connessione internet. L’intero studio è stato suddiviso in più fasi, ognuna di queste corrisponde ad una specifica sezione dell’elaborato che segue. In primo luogo si sono effettuate delle ricerche, soprattutto nel web, con lo scopo di individuare altre applicazioni che implementano l’idea della caccia al tesoro su piattaforma mobile o applicazioni che implementassero algoritmi di instance recognition direttamente su smartphone. In secondo luogo si è ricercato in letteratura quali fossero gli algoritmi di riconoscimento di immagini più largamente diffusi e studiati in modo da avere una panoramica dei metodi da testare per poi fare la scelta dell’algoritmo più adatto al caso di studio. Quindi si è proceduto con lo sviluppo dell’applicazione GeoPhotoHunt stessa, sia per quanto riguarda l’app front-end per dispositivi Android sia la parte back-end server. Infine si è passati ad una fase di test di algoritmi di riconoscimento di immagini in modo di avere una sufficiente quantità di dati sperimentali da permettere di effettuare una scelta dell’algoritmo più adatto al caso di studio. Al termine della fase di testing si è deciso di implementare su Android un algoritmo basato sulla distanza tra istogrammi di colore costruiti sulla scala cromatica HSV, questo metodo pur non essendo robusto in presenza di variazioni di luminosità e contrasto, rappresenta un buon compromesso tra prestazioni, complessità computazionale in modo da rendere la user experience quanto più coinvolgente.

IMPROVING QUANTITATIVE TREATMENT RESPONSE MONITORING WITH DEFORMABLE IMAGE REGISTRATION

Quantitative imaging with 18F-FDG PET/CT has the potential to provide an in vivo assessment of response to radiotherapy (RT). However, comparing tissue tracer uptake in longitudinal studies is often confounded by variations in patient setup and potential treatment induced gross anatomic changes. These variations make true response monitoring for the same anatomic volume a challenge, not only for tumors, but also for normal organs-at-risk (OAR). The central hypothesis of this study is that more accurate image registration will lead to improved quantitation of tissue response to RT with 18F-FDG PET/CT. Employing an in-house developed “demons” based deformable image registration algorithm, pre-RT tumor and parotid gland volumes can be more accurately mapped to serial functional images. To test the hypothesis, specific aim 1 was designed to analyze whether deformably mapping tumor volumes rather than aligning to bony structures leads to superior tumor response assessment. We found that deformable mapping of the most metabolically avid regions improved response prediction (P<0.05). The positive predictive power for residual disease was 63% compared to 50% for contrast enhanced post-RT CT. Specific aim 2 was designed to use parotid gland standardized uptake value (SUV) as an objective imaging biomarker for salivary toxicity. We found that relative change in parotid gland SUV correlated strongly with salivary toxicity as defined by the RTOG/EORTC late effects analytic scale (Spearman’s ρ = -0.96, P<0.01). Finally, the goal of specific aim 3 was to create a phenomenological dose-SUV response model for the human parotid glands. Utilizing only baseline metabolic function and the planned dose distribution, predicting parotid SUV change or salivary toxicity, based upon specific aim 2, became possible. We found that the predicted and observed parotid SUV relative changes were significantly correlated (Spearman’s ρ = 0.94, P<0.01). The application of deformable image registration to quantitative treatment response monitoring with 18F-FDG PET/CT could have a profound impact on patient management. Accurate and early identification of residual disease may allow for more timely intervention, while the ability to quantify and predict toxicity of normal OAR might permit individualized refinement of radiation treatment plan designs.

A database of multi-year (2004-2010) quality-assured surface solar hourly irradiation measurements for the Egyptian territory

A database containing the global and diffuse components of the surface solar hourly irradiation measured from 1 January 2004 to 31 December 2010 at eight stations of the Egyptian Meteorological Authority is presented. For three of these sites (Cairo, Aswan, and El-Farafra), the direct component is also available. In addition, a series of meteorological variables including surface pressure, relative humidity, temperature, wind speed and direction is provided at the same hourly resolution at all stations. The details of the experimental sites and instruments used for the acquisition are given. Special attention is paid to the quality of the data and the procedure applied to flag suspicious or erroneous measurements is described in details. Between 88 and 99% of the daytime measurements are validated by this quality control. Except at Barrani where the number is lower (13500), between 20000 and 29000 measurements of global and diffuse hourly irradiation are available at all sites for the 7-year period. Similarly, from 9000 to 13000 measurements of direct hourly irradiation values are provided for the three sites where this component is measured. With its high temporal resolution this consistent irradiation and meteorological database constitutes a reliable source to estimate the potential of solar energy in Egypt. It is also adapted to the study of high-frequency atmospheric processes such as the impact of aerosols on atmospheric radiative transfer. In the next future, it is planned to complete regularly the present 2004-2010 database.

A recuperação da informação da memória de trabalho: evidências baseadas em tarefas de imagem mental e de memória visual

A imagem mental e a memória visual têm sido consideradas como componentes distintos na codificação da informação, e associados a processos diferentes da memória de trabalho. Evidências experimentais mostram, por exemplo, que o desempenho em tarefas de memória baseadas na geração de imagem mentais (imaginação visual) sofre a interferência do ruído visual dinâmico (RVD), mas não se observa o mesmo efeito em tarefas de memória visual baseadas na percepção visual (memória visual). Embora várias evidências mostrem que tarefas de imaginação e de memória visual sejam baseadas em processos cognitivos diferentes, isso não descarta a possibilidade de utilizarem também processos em comum e que alguns resultados experimentais que apontam diferenças entre as duas tarefas resultem de diferenças metodológicas entre os paradigmas utilizados para estuda-las. Nosso objetivo foi equiparar as tarefas de imagem mental visual e memória visual por meio de tarefas de reconhecimento, com o paradigma de dicas retroativas espaciais. Sequências de letras romanas na forma visual (tarefa de memória visual) e acústicas (tarefa de imagem mental visual) foram apresentadas em quatro localizações espaciais diferentes. No primeiro e segundo experimento analisou-se o tempo do curso de recuperação tanto para o processo de imagem quanto para o processo de memória. No terceiro experimento, comparou-se a estrutura das representações dos dois componentes, por meio da apresentação do RVD durante a etapa de geração e recuperação. Nossos resultados mostram que não há diferenças no armazenamento da informação visual durante o período proposto, porém o RVD afeta a eficiência do processo de recuperação, isto é o tempo de resposta, sendo a representação da imagem mental visual mais suscetível ao ruído. No entanto, o processo temporal da recuperação é diferente para os dois componentes, principalmente para imaginação que requer mais tempo para recuperar a informação do que a memória. Os dados corroboram a relevância do paradigma de dicas retroativas que indica que a atenção espacial é requisitada em representações de organização espacial, independente se são visualizadas ou imaginadas.

ICICLE: A semantic-based retrieval system for WWW images

In this paper, we present ICICLE (Image ChainNet and Incremental Clustering Engine), a prototype system that we have developed to efficiently and effectively retrieve WWW images based on image semantics. ICICLE has two distinguishing features. First, it employs a novel image representation model called Weight ChainNet to capture the semantics of the image content. A new formula, called list space model, for computing semantic similarities is also introduced. Second, to speed up retrieval, ICICLE employs an incremental clustering mechanism, ICC (Incremental Clustering on ChainNet), to cluster images with similar semantics into the same partition. Each cluster has a summary representative and all clusters' representatives are further summarized into a balanced and full binary tree structure. We conducted an extensive performance study to evaluate ICICLE. Compared with some recently proposed methods, our results show that ICICLE provides better recall and precision. Our clustering technique ICC facilitates speedy retrieval of images without sacrificing recall and precision significantly.

High Level Color Similarity Retrieval

In this paper a new method for image retrieval using high level color semantic features is proposed. It is based on extraction of low level color characteristics and their conversion into high level semantic features using Johannes Itten theory of color, Dempster-Shafer theory of evidence and fuzzy production rules.

Fast Information Retrieval in the Open Grid Service Architecture

This is an extended version of an article presented at the Second International Conference on Software, Services and Semantic Technologies, Sofia, Bulgaria, 11–12 September 2010.

Fuzzy c-means variants for medical image segmentation

Segmentation is an important step in many medical imaging applications and a variety of image segmentation techniques exist. One group of segmentation algorithms is based on clustering concepts. In this article we investigate several fuzzy c-means based clustering algorithms and their application to medical image segmentation. In particular we evaluate the conventional hard c-means (HCM) and fuzzy c-means (FCM) approaches as well as three computationally more efficient derivatives of fuzzy c-means: fast FCM with random sampling, fast generalised FCM, and a new anisotropic mean shift based FCM. © 2010 by IJTS, ISDER.

Semantic wrapping for heterogeneous database management

Query processing is a commonly performed procedure and a vital and integral part of information processing. It is therefore important and necessary for information processing applications to continuously improve the accessibility of data sources as well as the ability to perform queries on those data sources. ^ It is well known that the relational database model and the Structured Query Language (SQL) are currently the most popular tools to implement and query databases. However, a certain level of expertise is needed to use SQL and to access relational databases. This study presents a semantic modeling approach that enables the average user to access and query existing relational databases without the concern of the database's structure or technicalities. This method includes an algorithm to represent relational database schemas in a more semantically rich way. The result of which is a semantic view of the relational database. The user performs queries using an adapted version of SQL, namely Semantic SQL. This method substantially reduces the size and complexity of queries. Additionally, it shortens the database application development cycle and improves maintenance and reliability by reducing the size of application programs. Furthermore, a Semantic Wrapper tool illustrating the semantic wrapping method is presented. ^ I further extend the use of this semantic wrapping method to heterogeneous database management. Relational, object-oriented databases and the Internet data sources are considered to be part of the heterogeneous database environment. Semantic schemas resulting from the algorithm presented in the method were employed to describe the structure of these data sources in a uniform way. Semantic SQL was utilized to query various data sources. As a result, this method provides users with the ability to access and perform queries on heterogeneous database systems in a more innate way. ^

High-resolution image reconstruction from multiple low-resolution images.

In this paper, we demonstrate a digital signal processing (DSP) algorithm for improving spatial resolution of images captured by CMOS cameras. The basic approach is to reconstruct a high resolution (HR) image from a shift-related low resolution (LR) image sequence. The aliasing relationship of Fourier transforms between discrete and continuous images in the frequency domain is used for mapping LR images to a HR image. The method of projection onto convex sets (POCS) is applied to trace the best estimate of pixel matching from the LR images to the reconstructed HR image. Computer simulations and preliminary experimental results have shown that the algorithm works effectively on the application of post-image-captured processing for CMOS cameras. It can also be applied to HR digital image reconstruction, where shift information of the LR image sequence is known.

The role of context in image annotation and recommendation

With the rise of smart phones, lifelogging devices (e.g. Google Glass) and popularity of image sharing websites (e.g. Flickr), users are capturing and sharing every aspect of their life online producing a wealth of visual content. Of these uploaded images, the majority are poorly annotated or exist in complete semantic isolation making the process of building retrieval systems difficult as one must firstly understand the meaning of an image in order to retrieve it. To alleviate this problem, many image sharing websites offer manual annotation tools which allow the user to “tag” their photos, however, these techniques are laborious and as a result have been poorly adopted; Sigurbjörnsson and van Zwol (2008) showed that 64% of images uploaded to Flickr are annotated with < 4 tags. Due to this, an entire body of research has focused on the automatic annotation of images (Hanbury, 2008; Smeulders et al., 2000; Zhang et al., 2012a) where one attempts to bridge the semantic gap between an image’s appearance and meaning e.g. the objects present. Despite two decades of research the semantic gap still largely exists and as a result automatic annotation models often offer unsatisfactory performance for industrial implementation. Further, these techniques can only annotate what they see, thus ignoring the “bigger picture” surrounding an image (e.g. its location, the event, the people present etc). Much work has therefore focused on building photo tag recommendation (PTR) methods which aid the user in the annotation process by suggesting tags related to those already present. These works have mainly focused on computing relationships between tags based on historical images e.g. that NY and timessquare co-exist in many images and are therefore highly correlated. However, tags are inherently noisy, sparse and ill-defined often resulting in poor PTR accuracy e.g. does NY refer to New York or New Year? This thesis proposes the exploitation of an image’s context which, unlike textual evidences, is always present, in order to alleviate this ambiguity in the tag recommendation process. Specifically we exploit the “what, who, where, when and how” of the image capture process in order to complement textual evidences in various photo tag recommendation and retrieval scenarios. In part II, we combine text, content-based (e.g. # of faces present) and contextual (e.g. day-of-the-week taken) signals for tag recommendation purposes, achieving up to a 75% improvement to precision@5 in comparison to a text-only TF-IDF baseline. We then consider external knowledge sources (i.e. Wikipedia & Twitter) as an alternative to (slower moving) Flickr in order to build recommendation models on, showing that similar accuracy could be achieved on these faster moving, yet entirely textual, datasets. In part II, we also highlight the merits of diversifying tag recommendation lists before discussing at length various problems with existing automatic image annotation and photo tag recommendation evaluation collections. In part III, we propose three new image retrieval scenarios, namely “visual event summarisation”, “image popularity prediction” and “lifelog summarisation”. In the first scenario, we attempt to produce a rank of relevant and diverse images for various news events by (i) removing irrelevant images such memes and visual duplicates (ii) before semantically clustering images based on the tweets in which they were originally posted. Using this approach, we were able to achieve over 50% precision for images in the top 5 ranks. In the second retrieval scenario, we show that by combining contextual and content-based features from images, we are able to predict if it will become “popular” (or not) with 74% accuracy, using an SVM classifier. Finally, in chapter 9 we employ blur detection and perceptual-hash clustering in order to remove noisy images from lifelogs, before combining visual and geo-temporal signals in order to capture a user’s “key moments” within their day. We believe that the results of this thesis show an important step towards building effective image retrieval models when there lacks sufficient textual content (i.e. a cold start).

Benefits of using a spectral hindcast database for wave power extraction assessment

When considering deployment of wave energy converters at a given site, it is of prime importance from both a technical and an economical point of view to accurately assess the total yearly energy that can be extracted by the given device. Especially, to be considered is the assessment of the efficiency of the device over the widest span of the sea-states spectral bandwidth. Hence, the aim of this study is to assess the biases and errors introduced on extracted power classically computed using spectral data derived from analytical functions such as a JONSWAP spectrum, compared to the power derived using actual wave spectra obtained from a spectral hindcast database.