525 research outputs found

    Multimodality treatment for esophageal squamous cell carcinoma

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    This thesis aims to optimize multimodality treatments for locally advanced esophageal squamous cell carcinoma (ESCC), specifically in East-Asia, recognizing that ESCC may differ in biology and response to treatment in different parts of the world. Part I of the thesis introduces the subtype ESCC and its characteristics from different geographical perspectives followed by an exposition of the differences between ESCC in eastern and western worlds. Part II optimizes trimodal therapy of ESCC in Taiwan, as a representative region of East-Asia. Finally, in Part III, the accuracy of liquid biopsies in identifying patients who may not need surgery after trimodal therapy is assessed.

    Immune contexture monitoring in solid tumors focusing on Head and Neck Cancer

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    Forti evidenze dimostrano una stretta interazione tra il sistema immunitario e lo sviluppo biologico e la progressione clinica dei tumori solidi. L'effetto che il microambiente immunitario del tumore può avere sul comportamento clinico della malattia è indicato come "immunecontexture". Nonostante ciò, l'attuale gestione clinica dei pazienti affetti da cancro non tiene conto di alcuna caratteristica immunologica né per la stadiazione né per le scelte terapeutiche. Il tumore della testa e del collo (HNSCC) rappresenta il 7° tumore più comune al mondo ed è caratterizzato da una prognosi relativamente sfavorevole e dall'effetto negativo dei trattamenti sulla qualità della vita dei pazienti. Oltre alla chirurgia e alla radioterapia, sono disponibili pochi trattamenti sistemici, rappresentati principalmente dalla chemioterapia a base di platino-derivati o dal cetuximab. L'immunoterapia è una nuova strategia terapeutica ancora limitata al setting palliativo (malattia ricorrente non resecabile o metastatica). La ricerca di nuovi biomarcatori o possibili nuovi meccanismi target è molto rilevante quindi nel contesto clinico dell'HNSCC. In questa tesi ci si concentrerà sullo studio di tre possibili popolazioni immunitarie pro-tumorali studiate nell'HNSCC: i neutrofili tumore-associati (TAN), le cellule B intratumorali con fenotipo immunosoppressivo e i T-reg CD8+. Particolare attenzione è data all'applicazione di moderne tecniche biostatistiche e bioinformatiche per riassumere informazioni complesse derivate da variabili cliniche e immunologiche multiparametriche e per validare risultati derivati ​​in situ, attraverso dati di espressione genica derivati da dataset pubblici. Infine, la seconda parte della tesi prenderà in considerazione progetti di ricerca clinica rilevanti, volti a migliorare l'oncologia di precisione nell'HNSCC, sviluppando modelli predittivi di sopravvivenza, confrontando procedure oncologiche alternative, validando nuovi classificatori o testando l'uso di nuovi protocolli clinici come l'uso dell'immunonutrizione.Strong evidences demonstrate a close interplay between the immune system and the biological development and clinical progression of solid tumors. The effect that the tumor immune microenvironment can have on the clinical behavior of the disease is referred as the immuno contexture. Nevertheless, the current clinical management of patients affected by cancer does not take into account any immunological features either for the staging or for the treatment choices. Head and Neck Cancer (HNSCC) represents the 7th most common cancer worldwide and it is characterized by a relatively poor prognosis and detrimental effect of treatments on the quality of life of patients. Beyond surgery and radiotherapy, few systemic treatments are available, mainly represented by platinum-based chemotherapy or cetuximab. Immunotherapy is a new therapeutical strategy still limited to the palliative setting (recurrent not resectable or metastatic disease). The search for new biomarkers or possible new targetable mechanisms is meaningful especially in the clinical setting of HNSCC. In this thesis a focus will be given on the study of three possible pro-tumoral immune populations studied in HNSCC: the tumor associated neutrophils (TAN), intratumoral B-cells with a immunosuppressive phenotype and the CD8+ T-regs. Biostatistical and bioinformatical techniques are applied to summarize complex information derived from multiparametric clinical and immunological variables and to validate in-situ derived findings through gene expression data of public available datasets. Lastly, the second part of the thesis will take into account relevant clinical research projects, aimed at improving the precision oncology in HNSCC developing survival prediction models, comparing alternative oncological procedures, validating new classifiers or testing the use of novel clinical protocols as the use of immunnutrition

    Alzheimer’s disease detection from magnetic resonance imaging: a deep learning perspective

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    Aim: Up to date many successful attempts to identify various types of lesions with machine learning (ML) were made, however, the recognition of Alzheimer’s disease (AD) from brain images and interpretation of the models is still a topic for the research. Here, using AD Imaging Initiative (ADNI) structural magnetic resonance imaging (MRI) brain images, the scope of this work was to find an optimal artificial neural network architecture for multiclass classification in AD, circumventing the dozens of images pre-processing steps and avoiding to increase the computational complexity. Methods: For this analysis, two supervised deep neural network (DNN) models were used, a three-dimensional 16-layer visual geometry-group (3D-VGG-16) standard convolutional network (CNN) and a three-dimensional residual network (ResNet3D) on the T1-weighted, 1.5 T ADNI MRI brain images that were divided into three groups: cognitively normal (CN), mild cognitive impairment (MCI), and AD. The minimal pre-processing procedure of the images was applied before training the two networks. Results: Results achieved suggest, that the network ResNet3D has a better performance in class prediction, which is higher than 90% in training set accuracy and arrives to 85% in validation set accuracy. ResNet3D also showed requiring less computational power than the 3D-VGG-16 network. The emphasis is also given to the fact that this result was achieved from raw images, applying minimal image preparation for the network. Conclusions: In this work, it has been shown that ResNet3D might have superiority over the other CNN models in the ability to classify high-complexity images. The prospective stands in doing a step further in creating an expert system based on residual DNNs for better brain image classification performance in AD detection

    30th European Congress on Obesity (ECO 2023)

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    This is the abstract book of 30th European Congress on Obesity (ECO 2023

    Towards the cross-identification of radio galaxies with machine learning and the effect of radio-loud AGN on galaxy evolution

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    It is now well established that active galactic nuclei (AGN) play a fundamental role in galaxy evolution. On cosmic scales, the evolution over cosmic time of the star-formation rate density and black hole accretion rate appear to be closely related, and on galactic scales, the mass of the stellar bulge is tightly correlated to the mass of the black hole. In particular, radio-loud AGN, which are characterised by powerful jets extending hundreds of kiloparsecs from the galaxy, make a significant contribution to the evolution of the most massive galaxies. There exists a correlation between the prevalence of radio-loud AGN and the stellar and black hole masses, with the stellar mass being the stronger driver of AGN activity. Furthermore, essentially all of the most massive galaxies host a radio-loud AGN. AGN feedback is the strongest candidate for driving the quenching of star-formation activity, in particular at galaxies at the highest masses, as it is capable of maintaining these galaxies as "red and dead". However, the precise mechanisms by which AGN influence galaxy evolution remain poorly understood. The anticipation of the Square Kilometre Array (SKA) brought radio astronomy into a revolutionary new era. New-generation radio telescopes have been built to develop and test new technologies while addressing different scientific questions. These have already detected a large number of sources and many previously unknown galaxies. One of these telescopes is the Low Frequency Array (LOFAR), which has been conducting an extensive survey across the entire northern sky called the LOFAR Two-Metre Sky Survey (LoTSS). In LoTSS, the source density is higher than in any existing large-area radio survey, and in less than a third of the survey, LoTSS already detected more than 4 million radio sources. The large size of the LoTSS samples already allows the separation of the AGNs into bins of stellar mass, environment, black hole mass, star formation rate, and morphology independently, thus enabling the breaking of degeneracies between the different parameters. The radio, long used to identify and study AGNs, is a powerful tool when radio sources are matched to their optically identified host galaxies. This "cross-matching" process typically depends on a combination of statistical approaches and visual inspection. For compact sources, cross-matching is traditionally achieved using statistical methods. The task becoms significantly more difficult when the radio emission is extended, split into multiple radio components, or when the host galaxy is not detected in the optical. In these cases, sources need to be inspected, radio components need to be eventually associated together into physical sources, and then radio sources need to be cross-matched with their optical and/or infrared counterparts. With recent radio continuum surveys growing massively in size, it is now extremely laborious to visually cross-match more than a small fraction of the total sources. The new high-sensitivity radio telescopes are also better at detecting complex radio structures, resulting in an increase in the number of radio sources whose radio emission is separated into different radio components. In addition, due to a higher density of objects, more compact sources can be randomly positioned close enough to resemble extended sources. Consequently, the cross-matching of radio galaxies with their optical counterparts is becoming increasingly difficult. It is crucial to minimise the extent of unnecessary inspection, with the present cross-matching systems demanding improvement. In this thesis, I use Machine Learning (ML) to investigate solutions to improve the cross-matching process. ML is a rapidly evolving technique that has recently benefited from a vast increase in data availability, increased computing power, and significantly improved algorithms. ML is gaining popularity in the field of astronomy, and it is undoubtedly the most promising technique for managing the large radio astronomy datasets, while having available at the same time the amount of data required to train ML algorithms. Part of the work in this thesis was indeed focused on creating a dataset based on visual inspections of the first data release of the LoTSS survey (LoTSS DR1) in order to train and cross-validate the ML models, and apply the results to the second data release (LoTSS DR2). I trained tree-based ML models using this dataset to determine whether a statistical match is reliable. In particular, I implemented a classifier to identify the sources for which a statistical match to optical and infrared catalogues by likelihood ratio is not reliable in order to select radio sources for visual inspection. I used the properties of the radio sources, the Gaussians that compose a source, the neighbouring radio sources, as well as the optical counterparts. The best model, a gradient boosting classifier, achieves an accuracy of 95% on a balanced dataset and 96% on real unbalanced data after optimising the classification threshold. The results were incorporated in the cross-matching of LoTSS DR2. I further present a deep learning classifier for identifying sources that require radio component association. In order to improve spatial and local information about the radio sources, I create a multi-modal model that makes use of different types of input data, with a convolutional network component of the model receiving radio images as input and a neural network component using parameters measured from the radio source and its near neighbours. The model helps to recover 94% of the sources with multiple components in balanced dataset and has an accuracy of 97% on real unbalanced data. The method has already been applied with success to properly identify sources that require component association in order to get the correct radio fluxes for AGN population studies. The ML techniques used in this work can be adapted to other radio surveys. Furthermore, ML will be crucial to dealing with the next radio surveys, in particular for source detection, identification and cross-matching, where only with reliable source identification is it possible to combine radio data with other data at different wavelengths and maximally exploit the scientific potential of the radio data. The use of deep learning, in particular testing ways of combining different data types, can bring further advantages, as it may help with the comprehension of data with different origins. This is particularly important for any upcoming data integration within the SKA. Finally, I used the results of cross-matching the LoTSS DR2 data to understand the interaction between radio-loud AGN, the host galaxy, and the surrounding environment. Specifically, the investigation focused on the properties of the hosts of radio-loud AGN, such as stellar mass, bulge mass, and black hole mass, as well as morphology and environmental factors. The results consistently support the significant influence of stellar mass on radio-AGN activity. It was found that galaxy morphology (i.e. ellipticals vs. spirals) has a negligible dependence on AGN activity unless at higher masses, but those correlate with stellar mass as well as with the environment. The most relevant factor for radio AGN prevalence, after controlling for stellar mass, emerged as higher-density environments, in particular on a global scale. These outcomes provide valuable insights into the triggering and fuelling mechanisms of radio-loud AGN, aligning with cooling flow models and improving our understanding of the phenomenon

    Novel Analytical Methods in Food Analysis

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    This reprint provides information on the novel analytical methods used to address challenges occurring at academic, regulatory, and commercial level. All topics covered include information on the basic principles, procedures, advantages, limitations, and applications. Integration of biological reagents, (nano)materials, technologies, and physical principles (spectroscopy and spectrometry) are discussed. This reprint is ideal for professionals of the food industry, regulatory bodies, as well as researchers

    Temporal dynamics of natural sound categorization

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    While extensive research has elucidated the brain’s processing of semantics from speech sound waves and their mapping onto the auditory cortex, the temporal dynamics of how meaningful non-speech sounds are processed remain less examined. Understanding these dynamics is key to resolving the debate between cascaded and parallel hierarchical processing models, both plausible given the anatomical evidence. This study investigates how semantic category information from environmental sounds is processed in the temporal domain, using electroencephalography (EEG) collected from 25 participants and representational similarity analysis (RSA) along with models of acoustic and semantic information. We examined information extracted by the brain from 80 onesecond natural sounds across four categories. The results revealed a cascaded temporal hierarchy of processing of information towards identifying the sound category, which supports the well established anatomical hierarchy. Low-level information is decodable at ~ 30 ms, and semantic information begins to emerge ~ 40 ms later. We conclude that basic information transforms to more complex information over time, while semantic representations are more stable over time than representations of acoustic information

    Spatio-temporal analysis of coastal sediment erosion in Cape Town through remote sensing and geoinformation science

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    Coastal erosion can be described as the landward or seaward propagation of coastlines. Coastal processes occur over various space and time scales, limiting in-situ approaches of monitoring change. As such it is imperative to take advantage of multisensory, multi-scale and multi-temporal modern spatial technologies for multi-dimensional coastline change monitoring. The research presented here intends to showcase the synergy amongst remote sensing techniques by showcasing the use of coastal indicators towards shoreline assessment over the Kommetjie and Milnerton areas along the Cape Town coastline. There has been little progress in coastal studies in the Western Cape that encompass the diverse and dynamic aspects of coastal environments and in particular, sediment movement. Cape Town, in particular; is socioeconomically diverse and spatially segregated, with heavy dependence on its 240km of coastline. It faces sea level rise intensified by real-estate development close to the high-water mark and on reclaimed land. Spectral indices and classification techniques are explored to accommodate the complex bio-optical properties of coastal zones. This allows for the segmentation of land and ocean components to extract shorelines from multispectral Landsat imagery for a long term (1991-2021) shoreline assessment. The DSAS tool used these extracted shorelines to quantify shoreline change and was able to determine an overall averaged erosional rate of 2.56m/yr. for Kommetjie and 2.35m/yr. for Milnerton. Beach elevation modelling was also included to evaluate short term (2016-2021) sediment volumetric changes by applying Differential Interferometry to Sentinel-1 SLC data and the Waterline method through a combination of Sentinel -1 GRD and tide gauge data. The accuracy, validation and correction of these elevation models was conducted at the pixel level by comparison to an in-field RTK GPS survey used to capture the current state of the beaches. The results depict a sediment deficit in Kommetjie whilst accretion is prevalent along the Milnerton coastline. Shoreline propagation and coastal erosion quantification leads to a better understanding of geomorphology, hydrodynamic and land use influences on coastlines. This further informs climate adaptation strategies, urban planning and can support further development of interactive coastal information systems

    Re-emergence of Neglected Tropical Diseases amid the COVID-19 Pandemic : Epidemiology, Transmission, Mitigation Strategies, and Recent Advances in Chemotherapy and Vaccines

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    The current re-emergence of neglected tropical diseases (NTD) amid the global COVID-19 pandemic requires increased attention. These include communicable and vector-borne diseases caused by various fungi, bacteria (e.g. tuberculosis), viruses (e.g. dengue, Chikungunya fever, monkeypox, Marburg and Ebola virus disease, poliomyelitis, rabies), and parasites (e.g. filariasis, malaria, trypanosomiasis, leishmaniasis, schistosomiasis, onchocerciasis). Whilst the vast majority of such diseases remain endemic to specific regions of the world (e.g. tropical Africa), some - like those caused by the Ebola virus, the Marburg virus, and more recently the Monkeypox virus - have been reported elsewhere (e.g. Europe and America), forcing public health boards in various countries to take all necessary precautions to control such a spread. The Department for Control of Neglected Tropical Disease was created in 2005 by the World Health Organization (WHO) to tackle NTD. In 2021, the 74th World Health Assembly proposed a 9-year plan (2021-2030) intended to eradicate neglected diseases. Over the past three years, COVID-19 has had a significant impact on socio-economic activities and healthcare systems worldwide. With the WHO recently declaring the global monkeypox outbreak a Public Health Emergency of International Concern, a coordinated effort among high-income and low/middle-income countries is now more than ever recommended to address the threat posed by the worldwide re-emergence of some NTD. There is currently a lack of knowledge on understanding how such diseases are transmitted and what mitigation strategies should be put in place to control their spread. Better availability of diagnostic tests, vaccines, and drugs in affected countries is also required. In this Research Topic, we wish to address how to best tackle the re-emergence of NTD in the context of the COVID-19 pandemic. This collection welcomes a range of articles including opinion, commentary, systematic reviews, and original research articles on epidemiology, transmission, mitigation strategies, and recent advances in chemotherapy and vaccines for these NTD
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