Special issue on signal processing and machine learning for biomedical data

This Special Issue is focused on advanced techniques in signal processing, analysis, modelling, and classification, applied to a variety of medical diagnostic problems. Biomedical data play a fundamental role in many fields of research and clinical practice. Very often the complexity of these data and their large volume makes it necessary to develop advanced analysis techniques and systems. Furthermore, the introduction of new techniques and methodologies for diagnostic purposes, especially in the field of medical imaging, requires new signal processing and machine learning methods. The recent progress in machine learning techniques, and in particular deep learning, revolutionized various fields of artificial vision, significantly pushing the state of the art of artificial vision systems into a wide range of high-level tasks. Such progress can help address problems in the analysis of biomedical data.This Special Issue placed particular emphasis on contributions dealing with practical, applications-led research, on the use of methods and devices in clinical diagnosis. The works that make up this special issue show a remarkable variety of applications for the detection and classification of medical imaging problems. In particular, the aforementioned works can be divided on the basis of types of techniques used, into three categories—signal processing (SP) methods, traditional machine learning (ML) methods, and deep learning (DL) methods

Deep CNN for IIF Images Classification in Autoimmune Diagnostics

The diagnosis and monitoring of autoimmune diseases are very important problem in medicine. The most used test for this purpose is the antinuclear antibody (ANA) test. An indirect immunofluorescence (IIF) test performed by Human Epithelial type 2 (HEp-2) cells as substrate antigen is the most common methods to determine ANA. In this paper we present an automatic HEp-2 specimen system based on a convolutional neural network method able to classify IIF images. The system consists of a module for features extraction based on a pre-trained AlexNet network and a classification phase for the cell-pattern association using six support vector machines and a k-nearest neighbors classifier. The classification at the image-level was obtained by analyzing the pattern prevalence at cell-level. The layers of the pre-trained network and various system parameters were evaluated in order to optimize the process. This system has been developed and tested on the HEp-2 images indirect immunofluorescence images analysis (I3A) public database. To test the generalisation performance of the method, the leave-one-specimen-out procedure was used in this work. The performance analysis showed an accuracy of 96.4% and a mean class accuracy equal to 93.8%. The results have been evaluated comparing them with some of the most representative works using the same database

Sedimentation of halloysite nanotubes from different deposits in aqueous media at variable ionic strengths

Halloysite clay is a natural nanomaterial that is attracting a growing interest in colloidal science. The halloysite aqueous dispersion stability is a key aspect for the configuration of a purification protocol as well as to establish the durability of a formulation. A physico-chemical study demonstrated the role of ionic strength and nanotube characteristic sizes on the sedimentation behavior. We highlighted the importance of the electrostatic repulsions exercised between the particles in the settling process. A protocol for image analysis has been proposed to provide robust information from time resolved optical images on the suspensions. In conclusion, we managed to correlate microscopic aspect to the peculiar sedimentation process of halloysite nanotubes

Modifications in Chemical, Physical and Mechanical Properties of Nebbiolo (Vitis vinifera L.) Grape Berries Induced by Mixed Virus Infection

Modifications in grape quality parameters induced by mixed infection with GFLV and GFkV, GLRaV-1and GVA, and GLRaV-3 and GVA in three Nebbiolo clones were compared against healthy plants of thesame clones in two experimental vineyards in Piemonte, northwest Italy. The aim of the study was toevaluate the effect of virus infection on the mechanical properties of the berry skin and the whole berry asassessed by texture analysis tests, and on the amount and quality of berry skin phenols. Differences wereobserved in grapevine vigour, yield and juice composition, depending on the viral status of the plants. Theanthocyanin profile of the vines infected with GFV and GFkV and those infected with GLRaV-1 and GVAshowed a lower percentage of the more stable tri-substituted malvidin-3-glucoside and a higher percentageof cyanidin and peonidin-3-glucosides. Texture analysis showed that the viruses may increase berry-skinthickness and reduce phenol extractability. These effects carry practical implications for wine quality

diagnosis and treatment of bilateral respiratory epithelial adenomatoid hamartomas with and without sinonasal polyposis

n/

Altered Auditory and Multisensory Temporal Processing in Autism Spectrum Disorders

Autism spectrum disorders (ASD) are characterized by deficits in social reciprocity and communication, as well as by repetitive behaviors and restricted interests. Unusual responses to sensory input and disruptions in the processing of both unisensory and multisensory stimuli also have been reported frequently. However, the specific aspects of sensory processing that are disrupted in ASD have yet to be fully elucidated. Recent published work has shown that children with ASD can integrate low-level audiovisual stimuli, but do so over an extended range of time when compared with typically developing (TD) children. However, the possible contributions of altered unisensory temporal processes to the demonstrated changes in multisensory function are yet unknown. In the current study, unisensory temporal acuity was measured by determining individual thresholds on visual and auditory temporal order judgment (TOJ) tasks, and multisensory temporal function was assessed through a cross-modal version of the TOJ task. Whereas no differences in thresholds for the visual TOJ task were seen between children with ASD and TD, thresholds were higher in ASD on the auditory TOJ task, providing preliminary evidence for impairment in auditory temporal processing. On the multisensory TOJ task, children with ASD showed performance improvements over a wider range of temporal intervals than TD children, reinforcing prior work showing an extended temporal window of multisensory integration in ASD. These findings contribute to a better understanding of basic sensory processing differences, which may be critical for understanding more complex social and cognitive deficits in ASD, and ultimately may contribute to more effective diagnostic and interventional strategies

Screening for Latent Tuberculosis Infection among Students of Healthcare Professions and Postgraduates of the Faculty of Medicine of the University of Palermo

Introduction and objective: Italy is a country with a low incidence of tuberculosis and in the last fifty years the annual number of TB cases decreased from 12,247 to 4,418, showing a reduction of approximately 64% in the number of cases and 71% in incidence. Despite of this encouraging trend, in the last years the epidemiology of tuberculosis changed and today it is a re-emerging infectious. The aim of this study is to measure the prevalence of positivity to tuberculosis infection (latent TB) in students, without any obvious manifestation of disease, attending degree courses of the health care professions and postgraduate medical courses of the School of Medicine of the University of Palermo, Italy. Materials and methods: A cross-sectional observational study in students of nursing, midwifery, dentistry degree courses and in resident physicians of postgraduate medical schools was carried out from January 2012 to July 2016. Mantoux test was performed and all positive cases were tested with Interferon-Gamma Release Assay (IGRA). Results: Of the 1,351 subjects evaluated, 25 (1.8%) resulted positive to Mantoux test; in 17 students (1.2%) the diagnosis was confirmed with IGRA. Positive cases were significantly more frequent among students attending Postgraduated Medical School Courses (p<0.001) and were older than negative cases (p<0.001). Conclusion: This study suggests that in our geographic area, latent TB shows a relatively low prevalence among students of medical schools. Despite of this evidence, and considering that several students have been found to be positive for TB, this infectious disease has to be considered a re-emerging biohazard that requires preventive strategies for the containment of the risk in exposed workers as well as in the general population

Gli uccelli delle isole circumsiciliane

Gli autori sintetizzano tutte le informazioni bibliografiche e inedite sulle specie che sino al 30 agosto 2015 sono state contattate almeno una volta nelle 14 isole circumsiciliane (Eolie, Ustica, Egadi, Pantelleria e Pelagie), confrontando alla fine la lista complessiva con quella delle isole Maltesi. In totale sono ad oggi note 434 specie (isole Maltesi incluse); molte di esse hanno mostrato nel corso dei secoli una notevole capacità di colonizzazione, fluttuando nel tempo o addirittura estinguendosi e ricolonizzando alcune isole. Questi piccoli territori in mezzo al mare rappresentano ottimi siti di controllo dell’andamento delle migrazioni nel corso dei decenni; alcune specie hanno chiaramente cambiato il loro status rispetto al passato, aumentando o diminuendo. Nel corso di circa 15 anni in alcune di queste isole (Ustica, Marettimo, Lampedusa e Linosa) sono stati condotti dei campi di inanellamento sia primaverili sia autunnali che hanno permesso di inanellare 102.208 uccelli, in gran parte Passeriformes; ciò ha consentito di raccogliere una notevole mole di dati sulle strategie migratorie, che vengono qui brevemente presentati. Le piccole isole sono davvero importanti per gli uccelli migratori transahariani, che devono sostare durante i loro lunghi viaggi per recuperare energie; la disponibilità di risorse sotto forma di frutti selvatici o di insetti (a seconda delle specie) consente a queste masse di migratori di continuare il loro viaggio. La conservazione degli uccelli è dettata dalla Direttiva Uccelli e l’istituzione delle Zone di Protezione Speciale ha proprio lo scopo di salvaguardare alcune specie in determinati territori. Questo è un impegno preso da parte di tutti i Paesi dell’Unione Europea, proprio perché le popolazioni di uccelli non conoscono confini amministrativi e la loro tutela va al di là delle competenze e degli interessi di un singolo Paese. Per quanto riguarda le specie nidificanti, è risultata un’elevata correlazione negativa (r=-0,746), altamente significativa (P=0,002) tra la capacità dispersiva media delle specie e la superficie in km2 delle isole. Le specie con minore capacità dispersiva hanno colonizzato le isole di maggiori dimensioni, ma non quelle più piccole; questo con molta probabilità dipende dalla eterogeneità ambientale, a sua volta legata alla dimensione delle isole ed alla loro posizione geografica. Nel caso delle isole circumsiciliane, sembra che non sia tanto la distanza dalla costa a determinare il numero di specie, quanto le condizioni ambientali e la posizione geografica; indubbiamente la posizione tirrenica delle isole settentrionali rappresenta un vantaggio per la presenza di habitat differenziati e la conseguente colonizzazione di specie ad essi legate, mentre la posizione meridionale, influenzata dall’aridità africana, riduce alcune possibilità colonizzatrici da parte di alcune specie di uccelli e rende altresì problematica la stessa esistenza di habitat diversificati. Il numero delle specie nidificanti in un’isola è variabile nel tempo, essendovi specie che vi nidificano in modo irregolare. La correlazione area/N° specie nelle isole circumsiciliane è pari a 0,58, ma se si esclude l’isola di Pantelleria, sale a 0,86; essa è pari a 0,92 per le sole isole settentrionali (Eolie, Ustica ed Egadi), mentre risulta 0,99 per le sole tre isole meridionali del Canale di Sicilia.Authors summarize all bibliographic and unpublished information on bird species that have been detected at least one time up to 30th August 2015 in the 14 circum-sicilian islands (Eolian, Ustica, Egadi, Pantelleria and Pelagian Is.). The Appendix 1 compares overall lists with that of the Maltese Is., also lying in the Sicilian waters. On the whole, 434 species are known till now (Maltese Is. included); many of them showed a high colonizing capacity along the centuries, fluctuating or even becoming extinct and re-colonising some islands. These small territories in the middle of the Mediterranean sea are very good check-control sites of long-term migration trend; compared to the past, some species changed their status, increasing or declining. Additionally, during the last 15 years in some of these islands (Ustica, Marettimo, Lampedusa and Linosa) bird ringing activity has been carried out, both in spring and in autumn; it allowed to ring 102,208 birds, mainly Passeriformes; this opportunity allowed to collect a remarkable amount of data on migration strategy, here presented. The small islands are very important stop-over sites for transsaharan migratory birds, that must rest during their long journey to recover fuel in the form of fat; the availability of natural resources, such as wild fruits or insects, allows these masses of migrant birds to continue their trip. The conservation of birds has been established by the Bird Directive and the institution of Zones of Special Protection has the aim to safeguard some species in some territories. This agreement was signed by all countries of the EU, because bird populations do not know administrative borders and their conservation lies beyond the interests and authorities of a single country. Concerning breeding birds, a high negative correlation (r=-0.746, P=0.002) has been found between the average dispersal power of species and the area in km2 of islands. Species with minor dispersal power colonized the biggest but not the smallest islands; this, very probably depended on habitat heterogeneity of islands, in turn linked to the size of them and to the geographical position, more than to the distance from the continental land. Tyrrhenian position of northern islands is certainly an advantage for the presence of diversified habitats and birds inhabiting them, whereas southern position of Pantelleria and Pelagian Is., as well as Maltese Is., affected by African dryness, decreases colonizing probabilities of some bird species and the same existence of diversified habitats. The number of breeding species in each island varied along the time and some species bred irregularly. The correlation area/No. species in the islands surrounding Sicily resulted to be 0.58, but if we exclude Pantelleria Is., it grows to 0.86; besides, it grows to 0.92 if we consider only northern islands (Eolian, Ustica and Egadi Is.), and to 0.99 if we consider only southern islands