A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

Batoid abundances, spatial distribution, and life history traits in the strait of sicily (Central mediterranean sea): Bridging a knowledge gap through three decades of survey

Batoid species play a key role in marine ecosystems but unfortunately they have globally declined over the last decades. Given the paucity of information, abundance data and the main life history traits for batoids, obtained through about three decades of bottom trawl surveys, are presented and discussed. The surveys were carried out in two areas of the Central Mediterranean (South of Sicily and Malta Island), in a timeframe ranging from 1990 to 2018. Excluding some batoids, the abundance trends were stable or increasing. Only R. clavata, R. miraletus, and D. oxyrinchus showed occurrence and abundance indexes notable enough to carry out more detailed analysis. In particular, spatial distribution analysis of these species highlighted the presence of two main hotspots in Sicilian waters whereas they seem more widespread in Malta. The lengths at first maturity (L50) were 695 and 860, 635 and 574, and 364 and 349 mm total length (TL), respectively, for females and males of D. oxyrinchus, R. clavata, and R. miraletus. The asymptotic lengths (L∞) and the curvature coefficients (K) were 1365 and 1240 (K = 0.11 and 0.26), 1260 and 1100 (K = 0.16 and 0.26), and 840 and 800 mm TL (K = 0.36 and 0.41), respectively, for females and males of D. oxyrinchus, R. clavata, and R. miraletus. The lack of detailed quantitative historical information on batoids of Sicily and Malta does not allow to analytically judge the current status of the stocks, although the higher abundance of some species within Malta raises some concern for the Sicilian counterpart. In conclusion, suitable actions to protect batoids in the investigated area are recommended

Reply to comment by C. Morhange, C. Flaux, P.A. Pirazzoli, M.B. Carre on \u201cHolocene Sea level Change in Malta\u201d

The pits of Birzebbugia are located near the present-day mean sea level, and some are partially submerged. They were dated using pottery discovered in an archaeological site close to the coast, dated to the Bronze Age (Zammit, 1928; Abela, 1999). As they have been interpreted as sites for the retting of flax, during their utilization they should have remained dry and the sea could not submerge them. This is the reason why these structures are not directly related to the sea level, as suggested by Biolchi et al. (2011), so they represent an upper limit.peer-reviewe

On consensus biomarker selection

<p>Abstract</p> <p>Background</p> <p>Recent development of mass spectrometry technology enabled the analysis of complex peptide mixtures. A lot of effort is currently devoted to the identification of biomarkers in human body fluids like serum or plasma, based on which new diagnostic tests for different diseases could be constructed. Various biomarker selection procedures have been exploited in recent studies. It has been noted that they often lead to different biomarker lists and as a consequence, the patient classification may also vary.</p> <p>Results</p> <p>Here we propose a new approach to the biomarker selection problem: to apply several competing feature ranking procedures and compute a consensus list of features based on their outcomes. We validate our methods on two proteomic datasets for the diagnosis of ovarian and prostate cancer.</p> <p>Conclusion</p> <p>The proposed methodology can improve the classification results and at the same time provide a unified biomarker list for further biological examinations and interpretation.</p

ONTOLOGY-BASED WEB TOOLS for RETRIEVING PHOTOGRAMMETRIC CULTURAL HERITAGE MODELS

International audienc

Underwater robots with sonar and smart tether for underground cistern mapping and exploration

This paper describes the application of using a submersible remotely operated vehicle (ROV) to map and explore underground water cisterns during a series of expeditions to Malta and Gozo. The purpose of this project was to create maps of ancient cisterns located under private homes, churches, and fortresses where passageways leading to the cisterns are too narrow and dangerous for humans to enter. These cisterns were used as water storage systems for hundreds of years, and many still contained water. The small ROV that was lowered into these cisterns was equipped with a sonar module to enable the creation of maps, two cameras to record live video, a grabber-arm for interacting with objects in the environment, and a Smart Tether to record additional positioning data of the ROV. Each of these components are discussed in terms of functionality and appropriateness for use by archaeologists wishing to explore and extract mapping information from narrow water-filled caverns. Additionally, three different mapping and localization techniques are presented including 1) Sonar image mosaics using stationary sonar scans, 2) Sonar image mosaics using stationary sonar scans with Smart Tether position data, and 3) Simultaneous Localization and Mapping (SLAM) using stationary sonar scans. Each of the algorithms used in this project have benefits in certain applications. During two expeditions in Malta and Gozo, 2-dimensional maps of 32 cisterns were successfully constructed.peer-reviewe

Archaeology via underwater robots : mapping and localization within Maltese cistern systems

This paper documents the application of several underwater robot mapping and localization techniques used during an archaeological expedition. The goal of this project was to explore and map ancient cisterns located on the islands of Malta and Gozo. The cisterns of interest acted as water storage systems for fortresses, private homes, and churches. They often consisted of several connected chambers, still containing water. A sonar-equipped Remotely Operated Vehicle (ROV) was deployed into these cisterns to obtain both video footage and sonar range measurements. Four different mapping and localization techniques were employed including 1) Sonar image mosaics using stationary sonar scans, and 2) Simultaneous Localization and Mapping (SLAM) while the vehicle was in motion, 3) SLAM using stationary sonar scans, and 4) Localization using previously created maps. Two dimensional maps of 6 different cisterns were successfully constructed. It is estimated that the cisterns were built as far back as 300 B.C.peer-reviewe

Correlations Between Parental Inbred Lines and Derived Hybrid Performance for Grain Filling Traits in Maize

Individual kernel weight (KW) is largely genetically determined, and its variability is achieved through different combinations of rate and duration of kernel growth. Genetic variability for grain-filling patterns has been observed among inbred lines and commercial hybrids, and there is current interest on dissecting its genetic basis. However, suitable grain filling phenotyping protocols are still to be determined, such as the value to study traits at the inbred or hybrid levels. The objective of our study was to evaluate the correlation between parental inbred line and derived hybrid performance for several grain-filling traits in maize (Zea mays L.). We hypothesized that there would be high correlations due to the relative high heritability of grainfilling traits. Three trials were conducted (two in Argentina and one in the United States) with commercial relevant germplasm (totaling 25 parental inbreds and 31 single-cross hybrids). Traits were KW, kernel growth rate (KGR), grainfilling duration (GFD), maximum water content (MWC), moisture concentration at physiological maturity (MCPM), and kernel desiccation rate (KDR) during the effective grain filling. Both heterosis and correlations between midparental value and hybrid performance were significant (p < 0.05) for all traits (r values of 0.63, 0.71, 0.81, 0.83, 0.61, and 0.71 for KW, KGR, GFD, MWC, KDR, and MCPM, respectively). Our results confirm that studying inbred lines for grain-filling traits generates valuable information for derived hybrid performanceFil: Alvarez Prado, Santiago. Universidad Nacional de Rosario. Facultad de Cs.agrarias. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gambin, Brenda Laura. Universidad Nacional de Rosario. Facultad de Cs.agrarias. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Novoa, A. Daniel. Nidera S. A; ArgentinaFil: Foster, Daniel. Syngenta Seeds; Estados UnidosFil: Senior, M. Lynn. Syngenta Biotechnology,; Estados UnidosFil: Zinselmeier, Christopher. Syngenta Seeds; Estados UnidosFil: Otegui, Maria Elena. Universidad de Buenos Aires. Facultad de Agronomía; ArgentinaFil: Borras, Lucas. Universidad Nacional de Rosario. Facultad de Cs.agrarias. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin