0000000000009898
AUTHOR
Ignazio Fontana
Identifying small pelagic Mediterranean fish schools from acoustic and environmental data using optimized artificial neural networks
Abstract The Common Fisheries Policy of the European Union aims to exploit fish stocks at a level of Maximum Sustainable Yield by 2020 at the latest. At the Mediterranean level, the General Fisheries Commission for the Mediterranean (GFCM) has highlighted the importance of reversing the observed declining trend of fish stocks. In this complex context, it is important to obtain reliable biomass estimates to support scientifically sound advice for sustainable management of marine resources. This paper presents a machine learning methodology for the classification of pelagic species schools from acoustic and environmental data. In particular, the methodology was tuned for the recognition of an…
Pelagic species identification by using a PNN neural network and echo-sounder data
For several years, a group of CNR researchers conducted acoustic surveys in the Sicily Channel to estimate the biomass of small pelagic species, their geographical distribution and their variations over time. The instrument used to carry out these surveys is the scientific echo-sounder, set for different frequencies. The processing of the back scattered signals in the volume of water under investigation determines the abundance of the species. These data are then correlated with the biological data of experimental catches, to attribute the composition of the various fish schools investigated. Of course, the recognition of the fish schools helps to produce very good results, that is very clo…
Candida parapsilosis Infection:A Multilocus Microsatellite Genotyping-Based Survey Demonstrating an Outbreak in Hospitalized Patients
Microsatellite analysis identifies specific genotypes and the genetic relationship between strains. Our objective was to analyze the genotypes of C. parapsilosis strains isolated on different wards of aTertiary- Referral University Center. We evaluated 70 C. parapsilosis strains in total, isolated from samples of patients admitted to five different wards over two years (January 2015-December 2016). Eight microsatellite markers were selected, and two multiplex PCR assays were set up for microsatellite analysis. The 70 strains, examined at eight microsatellite loci, showed 46 different multilocus genotypes profiles. A total of 74 alleles were detected, with an average of 9.25 alleles per locu…
Artificial neural networks for fault tollerance of an air-pressure sensor network
A meteorological tsunami, commonly called Meteotsunami, is a tsunami-like wave originated by rapid changes in barometric pressure that involve the displacement of a body of water. This phenomenon is usually present in the sea cost area of Mazara del Vallo (Sicily, Italy), in particular in the internal part of the seaport canal, sometimes making local population at risk. The Institute for Coastal Marine Environment (IAMC) of the National Research Council in Italy (CNR) have already conducted several studies upon meteotsunami phenomenon. One of the project has regarded the creation of a sensors network composed by micro-barometric sensors, located in 4 different stations close to the seaport …
Pattern Classification from Multi-beam Acoustic Data Acquired in Kongsfjorden
Climate change is causing a structural change in Arctic ecosystems, decreasing the effectiveness that the polar regions have in cooling water masses, with inevitable repercussions on the climate and with an impact on marine biodiversity. The Svalbard islands under study are an area greatly influenced by Atlantic waters. This area is undergoing changes that are modifying the composition and distribution of the species present. The aim of this work is to provide a method for the classification of acoustic patterns acquired in the Kongsfjorden, Svalbard, Arctic Circle using multibeam technology. Therefore the general objective is the implementation of a methodology useful for identifying the a…
Automatic classification of acoustically detected krill aggregations: A case study from Southern Ocean
Acoustic surveys represent the standard methodology to assess the spatial distribution and abundance of pelagic organisms characterized by aggregative behaviour. The species identification of acoustically observed aggregations is usually performed by taking into account the biological sampling and according to expert-based knowledge. The precision of survey estimates, such as total abundance and spatial distribution, strongly depends on the efficiency of acoustic and biological sampling as well as on the species identification. In this context, the automatic identification of specific groups based on energetic and morphological features could improve the species identification process, allo…
Unsupervised Classification of Acoustic Echoes from Two Krill Species in the Southern Ocean (Ross Sea)
This work presents a computational methodology able to automatically classify the echoes of two krill species recorded in the Ross sea employing scientific echo-sounder at three different frequencies (38, 120 and 200 kHz). The goal of classifying the gregarious species represents a time-consuming task and is accomplished by using differences and/or thresholds estimated on the energy features of the insonified targets. Conversely, our methodology takes into account energy, morphological and depth features of echo data, acquired at different frequencies. Internal validation indices of clustering were used to verify the ability of the clustering in recognizing the correct number of species. Th…
Urgent need for preservation of grapevine (Vitis vinifera L. Subsp. vinifera) germplasm from small circum-Sicilian islands as revealed by SSR markers and traditional use investigations
Since the last decades grapevine germplasm is undergoing a process of rapid genetic erosion. This process is of particular concern in minor circum-Sicilian islands, because of the sharp reduction of the cultivated surfaces and the shift of their economy from agriculture to tourism. Aiming at valorising and preserving the surviving varieties we collected 185 accessions during several surveys since 2007. Six nuclear microsatellite markers were used for germplasm characterization, yielding 75 different genetic profiles. We found out that most genetic profiles (39) were not listed in national and international grapevine databases, confirming that the Sicilian minor islands represent underexplor…
Phylogenetic Relationship Among Wild and Cultivated Grapevine in Sicily: A Hotspot in the Middle of the Mediterranean Basin
Grapevine (Vitis vinifera ssp. sativa) is a perennial crop especially important for wine and fruit production. The species is highly polymorphic with thousands of different varieties selected by farmers and clonally propagated. However, it is still debated whether grapevine domestication from its wild ancestor (V. vinifera ssp. sylvestris) has been a single event or rather it occurred on multiple occasions during the diffusion of its cultivation across the Mediterranean. Located in the center of the Basin, Sicily is its largest island and has served as a hotspot for all civilizations that have crossed the Mediterranean throughout history. Hundreds of unique grapevine cultivars are still cul…
A novel method to simulate the 3D chlorophyll distribution in marine oligotrophic waters
Abstract A 3D advection-diffusion-reaction model is proposed to investigate the abundance of phytoplankton in a difficult-to-access ecosystem such as the Gulf of Sirte (southern Mediterranean Sea) characterized by oligotrophic waters. The model exploits experimentally measured environmental variables to reproduce the dynamics of four populations that dominate phytoplankton community in the studied area: Synechococcus, Prochlorococcus HL, Prochlorococcus LL and picoeukaryotes. The theoretical results obtained for phytoplankton abundances are converted into chl-a and Dvchl-a concentrations, and the simulated vertical chlorophyll profiles are compared to the corresponding experimentally acquir…
A pattern recognition approach to identify biological clusters acquired by acoustic multi-beam in Kongsfjorden
The Svalbardsis one of the most intensively studied marine regions in the Artic; here the composition and distribution of marine assemblages are changing under the effect of global change, and marine communities are monitored in order to understand the long-term effects on marine biodiversity. In the present work, acoustic data collected in the Kongsfjorden using multi-beam technology was analyzed to develop a methodology for identifying and classifying 3D acoustic patterns related to fish aggregations. In particular, morphological, energetic and depth features were taken into account to develop a multi-variate classification procedure allowing to discriminate fish species. The results obta…
Hybridization in Capparis spinosa L.: Molecular and morphological evidence from a Mediterranean island complex
Inter-Simple Sequence Repeat (ISSR) molecular markers and morphological analysis were used in order to characterize wild populations and cultivated forms of orphan crop species Capparis spinosa L. in a Mediterranean island complex. Nineteen wild populations belonging to two different subspecies, C. spinosa subsp. spinosa and subsp. rupestris, were sampled in different environments in Sicily and the surrounding islets Lampedusa, Pantelleria and Salina. Different biotypes cultivated in Pantelleria and Salina were analyzed. Six ISSR primers were selected for genetic characterization, and all clear and reproducible bands were scored and analyzed. Among the 47 ISSR bands obtained, 97.5% were pol…
Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value.
AbstractCaper (Capparis spinosa L.) is a xerophytic shrub cultivated for its flower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classification of the genus Capparis has been hampered so far by the lack of reliable genetic information and molecular markers. Here, we present the first genomic resource for C. spinosa, generated by transcriptomic approach and de novo assembly. The sequencing effort produced nearly 80 million clean reads assembled into 124,723 unitranscripts. Careful annotation and comparison with public databases revealed homologs to genes with a key role in important metabolic pathways linked to abiotic stress t…
Distribution and spatial structure of pelagic fish schools in relation to the nature of the seabed in the Sicily Channel (Central Mediterranean).
Hydroacoustic data collected during two echosurveys carried out in the Sicily Channel in 1998 and 2002 were analysed to investigate the distribution and spatial structure of small pelagic fish species in relation to the sedimentological nature of the sea bottom. The study was carried out on two contiguous areas (labelled ZONE 1 and ZONE 2) of the continental shelf off the southern coast of Sicily, characterised by different dominant texture, ‘sand’ for ZONE 1 and ‘clayey-silt’ for ZONE 2. Simultaneous information on small pelagic fish schools and the seabed was obtained using a quantitative echo-sounder (SIMRAD EK500) that measures echoes due to the scattering from both fish schools and the…