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Combining Multi-Shell Diffusion with Conventional MRI Improves Molecular Diagnosis of Diffuse Gliomas with Deep Learning
Get PDFThe WHO classification since 2016 confirms the importance of integrating molecular diagnosis for prognosis and treatment decisions of adult-type diffuse gliomas. This motivates the development of non-invasive diagnostic methods, in particular MRI, to predict molecular subtypes of gliomas before surgery. At present, this development has been focused on deep-learning (DL)-based predictive models, mainly with conventional MRI (cMRI), despite recent studies suggesting multi-shell diffusion MRI (dMRI) offers complementary information to cMRI for molecular subtyping. The aim of this work is to evaluate the potential benefit of combining cMRI and multi-shell dMRI in DL-based models. A model implemented with deep residual neural networks was chosen as an illustrative example. Using a dataset of 146 patients with gliomas (from grade 2 to 4), the model was trained and evaluated, with nested cross-validation, on pre-operative cMRI, multi-shell dMRI, and a combination of the two for the following classification tasks: (i) IDH-mutation; (ii) 1p/19q-codeletion; and (iii) three molecular subtypes according to WHO 2021. The results from a subset of 100 patients with lower grades gliomas (2 and 3 according to WHO 2016) demonstrated that combining cMRI and multi-shell dMRI enabled the best performance in predicting IDH mutation and 1p/19q codeletion, achieving an accuracy of 75 ± 9% in predicting the IDH-mutation status, higher than using cMRI and multi-shell dMRI separately (both 70 ± 7%). Similar findings were observed for predicting the 1p/19q-codeletion status, with the accuracy from combining cMRI and multi-shell dMRI (72 ± 4%) higher than from each modality used alone (cMRI: 65 ± 6%; multi-shell dMRI: 66 ± 9%). These findings remain when we considered all 146 patients for predicting the IDH status (combined: 81 ± 5% accuracy; cMRI: 74 ± 5%; multi-shell dMRI: 73 ± 6%) and for the diagnosis of the three molecular subtypes according to WHO 2021 (combined: 60 ± 5%; cMRI: 57 ± 8%; multi-shell dMRI: 56 ± 7%). Together, these findings suggest that combining cMRI and multi-shell dMRI can offer higher accuracy than using each modality alone for predicting the IDH and 1p/19q status and in diagnosing the three molecular subtypes with DL-based models
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Nuovi metodi di analisi di dati epigenetici per la previsione dell'età del paziente
Get PDFAnalizzeremo dati di metilazione di diversi gruppi di pazienti, mettendoli in relazione con le loro età, intesa in senso anagrafico e biologico. Adatteremo metodi di regressione che sono già stati usati in altri studi, in particolare di tipo statistico, cercando di migliorarli e proveremo ad applicare a questi dati anche dei metodi nuovi, non solo di tipo statistico. La nostra analisi vuole essere innovativa soprattutto perché, oltre a guardare i dati in maniera locale attraverso lo studio della metilazione di particolari sequenze genetiche più o meno note per essere collegate all’invecchiamento, andremo a considerare i dati anche in maniera globale, analizzando le proprietà della distribuzione di tutti i valori di metilazione di un paziente attraverso la trasformata di Fourier
Evolution of respiratory function in Duchenne muscular dystrophy from childhood to adulthood
No full textIn Duchenne muscular dystrophy (DMD), it is still to be determined if specific timepoints can be identified during the natural evolution of respiratory dysfunction from childhood to adulthood and if scoliosis, steroid therapy and nocturnal noninvasive mechanical ventilation (NIMV) have any effect on it.In a 7-year retrospective study performed on 115 DMD patients (6-24 years), evaluated once or twice per year, with 574 visits in total, evolution mean curves of spirometry, lung volumes, spontaneous breathing and thoraco-abdominal pattern (measured by optoelectronic plethysmography) parameters were obtained by nonlinear regression model analysis.While predicted values of forced vital capacity, forced expiratory volume in 1 s, and peak expiratory flow decline continuously since childhood, during spontaneous breathing the following parameters become significantly different than normal in sequence: abdominal contribution to tidal volume (lower after 14.8 years), tidal volume (lower after 17.2 years), minute ventilation (lower after 18.1 years) and respiratory rate (higher after 22.1 years). Restrictive lung pattern and diaphragmatic impairment are exacerbated by scoliosis severity, slowed by steroids treatment and significantly affected by NIMV.Spirometry, lung volumes, breathing pattern and thoraco-abdominal contributions show different evolution curves over time. Specific timepoints of respiratory impairment are identified during disease progression. These should be considered when defining outcome measures in clinical trials and treatment strategies in DMD
Non-parametric classification and regression techniques for the characterisation of the disease subtypes and the assessment of the temporal evolution of image-based biomarkers
Get PDFIn questa tesi, si presentano alcuni modelli e metodi statistici non parametrici, sviluppati e adattati per gestire diversi tipi di biomarcatori. In particolare, si descrive la stima dell'evoluzione della funzione respiratoria dalla fanciullezza all'età adulta di pazienti affetti dalla Distrofia Muscolare di Duchenne, dove le misurazioni sono state acquisite longitudinalmente a tempi irregolari e specifici per ogni soggetto. In questo caso, si adotta un modello di regressione a effetti misti basato su spline cubiche, che permette di identificare specifici istanti temporali di peggioramento della funzione respiratoria durante la progressione della malattia, e di investigare possibili effetti della scoliosi, della ventilazione meccanica notturna non invasiva e della terapia steroidea. Nel seguito della tesi, si caratterizzano i sottotipi della malattia di Creutzfeldt-Jakob sporadica con biomarcatori da imaging medico, acquisiti con campionamento cross-sectional. In questo caso, i biomarcatori considerati sono le iper-intensità del segnale di diffusione tramite imaging a risonanza magnetica, le quali sono misurate con un sistema semi-qualitativo in alcune regioni cerebrali. Quindi, si classificano i pazienti nel sottotipo più compatibile della malattia di Creutzfeldt-Jakob sporadica, secondo le loro misurazioni dei biomarcatori, attraverso un metodo basato sugli alberi di classificazione. Inoltre, si descrive la progressione della malattia in ognuno di tali sottotipi, identificando la sequenza delle regioni cerebrali che diventano distinguibilmente iperintense nelle immagini di risonanza magnetica pesate in diffusione. Per raggiungere tale obiettivo, si adatta il cosiddetto "event-based model" recentemente introdotto in letteratura, che consiste in un modello statistico data-driven che stima l'evoluzione della malattia in termini dei suoi biomarcatori caratterizzanti, senza basarsi su un dataset longitudinale. Nella parte finale della tesi, si delinea un lavoro che vuole sviluppare un modello di regressione "function-on-function", che possa gestire biomarcatori con dipendenza temporale (ad esempio, immagini ottenute tramite risonanza magnetica funzionale). A tale scopo, si modellizza la risposta funzionale in termini di diverse covariate funzionali e si propone un test basato su permutazioni per identificare sotto-regioni che esibiscono differenze statistiche simili. Inoltre, nel caso di test multipli effettuati in diversi punti dello stesso dominio (ad esempio, i voxel dell'immagine cerebrale ottenuta mediante risonanza magnetica), si estende a un contesto tridimensionale il "closure multiplicity adjustment method" per controllare il family-wise error rate della procedura proposta.In this thesis, we present some non-parametric statistical models and methods that have been developed and adapted to deal with different types of biomarker. In particular, we describe the assessment of the respiratory function evolution of Duchenne Muscular Dystrophy (DMD) patients from childhood to adulthood, where measurements are collected longitudinally at irregular and subject-specific times. We adopt here a regression model based on natural cubic splines with mixed effects, that allows to identify specific time points of respiratory impairment during disease progression, and to investigate possible effects of scoliosis, nocturnal non-invasive mechanical ventilation and steroid therapy. Then, we characterise the sybtypes of the sporadic Creutzfeldt-Jakob disease (sCJD) with imaging biomarkers collected in a cross-sectional design. In this case, the considered biomarkers are the signal hyperintensities of diffusion magnetic resonance imaging (dMRI), that are measured with a semi-quantitative scoring system devised to visually assess the images in different brain regions. We classify the sCJD patients into their most compatible subtype according to their biomarker measurements, with a classification tree-based method. Moreover, we describe the disease progression in each sCJD subtype by finding the sequence of brain regions that become detectably hyperintense on the diffusion images. We adapt the recently introduced event-based model, a data-driven statistical model that assess the disease evolution in terms of its characterising biomarkers, without relying on a longitudinal dataset. Finally, we outline a work aimed at developing a function-on-function regression model that can deal with temporal dependent biomarkers (e.g., from functional magnetic resonance imaging data). We model a functional response in terms of several functional covariates, and we propose a permutation test to identify sub-regions that exhibit similar statistical differences. Moreover, in case of multiple tests performed at different locations in the same domain (e.g., the voxels of the brain MR image), we extend to a three-dimensional setting the closure multiplicity adjustment method to control the family-wise error rate of the proposed procedure.DIPARTIMENTO DI MATEMATICA30LUCCHETTI, ROBERTOSABADINI, IRENE MARI
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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