Discriminative feature domains for reverberant acoustic environments

Several speech processing and audio data-mining applications rely on a description of the acoustic environment as a feature vector for classification. The discriminative properties of the feature domain play a crucial role in the effectiveness of these methods. In this work, we consider three environment iden- tification tasks and the task of acoustic model selection for speech recognition. A set of acoustic parameters and Ma- chine Learning algorithms for feature selection are used and an analysis is performed on the resulting feature domains for each task. In our experiments, a classification accuracy of 100% is achieved for the majority of tasks and the Word Er- ror Rate is reduced by 20.73 percentage points for Automatic Speech Recognition when using the resulting domains. Ex- perimental results indicate a significant dissimilarity in the parameter choices for the composition of the domains, which highlights the importance of the feature selection process for individual applications

Host range and symptomatology of Pepino mosaic virus strains occurring in Europe

Pepino mosaic virus (PepMV) has caused great concern in the greenhouse tomato industry after it was found causing a new disease in tomato in 1999. The objective of this paper is to investigate alternative hosts and compare important biological characteristics of the three PepMV strains occurring in Europe when tested under different environmental conditions. To this end we compared the infectivity and symptom development of three, well characterized isolates belonging to three different PepMV strains, EU-tom, Ch2 and US1, by inoculating them on tomato, possible alternative host plants in the family Solanaceae and selected test plants. The inoculation experiments were done in 10 countries from south to north in Europe. The importance of alternative hosts among the solanaceous crops and the usefulness of test plants in the biological characterization of PepMV isolates are discussed. Our data for the three strains tested at 10 different European locations with both international and local cultivars showed that eggplant is an alternative host of PepMV. Sweet pepper is not an important host of PepMV, but potato can be infected when the right isolate is matched with a specific cultivar. Nicotiana occidentalis 37B is a useful indicator plant for PepMV studies, since it reacts with a different symptomatology to each one of the PepMV strains.Ravnikar, M.; Blystad, D.; Van Der Vlugt, R.; Alfaro Fernández, AO.; Del Carmen Cordoba, M.; Bese, G.; Hristova, D.... (2015). Host range and symptomatology of Pepino mosaic virus strains occurring in Europe. European Journal of Plant Pathology. 143(1):43-56. doi:10.1007/s10658-015-0664-1S43561431Alfaro-Fernández, A., Córdoba-Sellés, M. C., Herrera-Vásquez, J. A., Cebrián, M. C., & Jordá, C. (2009). Transmission of Pepino mosaic virus by the fungal vector Olpidium virulentus. Journal of Phytopathology, 158, 217–226.Charmichael, D. J., Rey, M. E. C., Naidoo, S., Cook, G., & van Heerden, S. W. (2011). First report of Pepino mosaic virus infecting tomato in South Africa. Plant Disease, 95(6), 767.2.Córdoba, M. C., Martínez-Priego, L., & Jordá, C. (2004). New natural hosts of Pepino mosaic virus in Spain. Plant Disease, 88, 906.Córdoba-Sellés, M. C., García-Rández, A., Alfaro-Fernández, A., & Jordá-Gutiérrez, C. (2007). Seed transmission of pepino mosaic virus and efficacy of tomato seed disinfection treatments. Plant Disease, 91, 1250–1254.Efthimiou, K. E., Gatsios, A. P., Aretakis, K. C., Papayannis, L. C., & Katis, N. I. (2011). First report of Pepino mosaic virus infecting greenhouse cherry tomato in Greece. Plant Disease, 95(1), 78.2.Fakhro, A., von Bargen, S., Bandte, M., Büttner, C., Franken, P., & Schwarz, D. (2011). Susceptibility of different plant species and tomato cultivars to two isolates of Pepino mosaic virus. European Journal of Plant Pathology, 129, 579–590.Gómez, P., Sempere, R. N., Elena, S. F., & Aranda, M. A. (2009). Mixed infections of Pepino mosaic virus strains modulate the evolutionary dynamics of this emergent virus. Journal of Virology, 83, 12378–12387.Hanssen, I. M., Paeleman, A., Wittemans, L., Goen, K., Lievens, B., Bragard, C., Vanachter, A. C. R. C., & Thomma, B. P. H. J. (2008). Genetic characterization of Pepino mosaic virus isolates from Belgian greenhouse tomatoes reveals genetic recombination. European Journal of Plant Pathology, 121, 131–146.Hanssen, I. M., Paeleman, A., Vandewoestijne, E., Van Bergen, L., Bragard, C., Lievens, B., Vanachter, A. C. R. C., & Thomma, B. P. H. J. (2009). Pepino mosaic virus isolates and differential symptomatology in tomato. Plant Pathology, 58, 450–460.Hanssen, I. M., Mumford, R., Blystad, D.-G., Cortez, I., Hasiów-Jaroszewska, B., Hristova, D., Pagán, I., Pereira, A.-M., Peters, J., Pospieszny, H., Ravnikar, M., Stijger, I., Tomassoli, L., Varveri, C., van der Vlugt, R., & Nielsen, S. L. (2010). Seed transmission of Pepino mosaic virus in tomato. European Journal of Plant Pathology, 126, 145–152.Hasiów-Jaroszewska, B., Borodynko, N., Jackowiak, P., Figlerowicz, M., & Pospieszny, H. (2010a). Pepino mosaic virus – a pathogen of tomato crops in Poland: biology, evolution and diagnostics. Journal of Plant Protection Research, 50, 470–476.Hasiów-Jaroszewska, B., Jackowiak, P., Borodynko, N., Figlerowicz, M., & Pospieszny, H. (2010b). Quasispecies nature of Pepino mosaic virus and its evolutionary dynamics. Virus Genes, 41, 260–267.Jeffries, C. J. (1998). FAO/IPGRI technical guidelines for the safe movement of germplasm no. 19. Potato. Food and agriculture organization of the United Nations, Rome/International Plant Genetic Resources Institute, Rome pp 177Jones, R. A. C., Koenig, R., & Lesemann, D. E. (1980). Pepino mosaic virus, a new potexvirus from pepino (Solanum muricatum). Annals of Applied Biology, 94, 61–68.Jordá, C., Lázaro Pérez, A., & Martínez Culebras, P. (2001). First report of Pepino mosaic virus on natural hosts. Plant Disease, 85, 1292.King, A. M. Q., Adams, M. J., Carstens, E. B., Lefkowitz, E. J., (eds). (2012). potexvirus, pp 912–915, in virus taxonomy, classification and nomenclature of viruses; ninth report of the international committee on taxonomy of viruses (p 1327) London, UK: Elsevier Academic PressLing, K.-S., & Zhang, W. (2011). First report of Pepino mosaic virus infecting tomato in Mexico. Plant Disease, 95(8), 1035.Martin, J., & Mousserion, C. (2002). Potato varieties which are sensitive to the tomato strains of Pepino mosaic virus (PepMV). Phytoma Défence Végétaux, 552, 26–28.Mehle, N., Gutierrez-Aguirre, I., Prezelj, N., Delić, D., Vidic, U., & Ravnikar, M. (2014). Survival and transmission of potato virus Y, pepino mosaic virus, and potato spindle tuber viroid in water. Applied and Environmental Microbiology, 80(4), 1455–1462.Moreno-Pérez, M. G., Pagán, I., Aragón-Caballero, L., Cáceres, F., Aurora Fraile, A., & García-Arenal, F. (2014). Ecological and genetic determinants of Pepino mosaic virus emergence. Journal of Virology, 88(6), 3359–3368.Noël, P., Hance, T., & Bragard, C. (2014). Transmission of the pepino mosaic virus by whitefly. European Journal of Plant Pathology, 138, 23–27.Pagan, I., Cordoba-Selles, M. D., Martinez-Priego, L., Fraile, A., Malpica, J. M., Jorda, C., & Garcia-Arenal, F. (2006). Genetic structure of the population of pepino mosaic virus infecting tomato crops in Spain. Phytopathology, 96, 274–279.Papayiannis, L. C., Kokkinos, C. D., & Alfaro-Fernández, A. (2012). Detection, characterization and host range studies of Pepino mosaic virus in Cyprus. European Journal of Plant Pathology, 132, 1–7.Pospieszny, H., Haslow, B., & Borodynko, N. (2008). Characterization of two Polish isolates of Pepino mosaic virus. European Journal of Plant Pathology, 122, 443–445.Salomone, A., & Roggero, P. (2002). Host range, seed transmission and detection by ELISA and lateral flow of an Italian isolate of Pepino mosaic virus. Journal of Plant Pathology, 84, 65–68.Samson, R. G., Allen, T. C., & Whitworth, J. L. (1993). Evaluation of direct tissue blotting to detect potato viruses. American Potato Journal, 70, 257–265.Schwarz, D., Beuch, U., Bandte, M., Fakhro, A., Büttner, C., & Obermeier, C. (2010). Spread and interaction of pepino mosaic virus (PepMV) and pythium aphanidermatum in a closed nutrient solution recirculation system: effects on tomato growth and yield. Plant Pathology, 59(3), 443–452.Shipp, J. L., Buitenhuis, R., Stobbs, L., Wang, K., Kim, W. S., & Ferguson, G. (2008). Vectoring of pepino mosaic virus by bumble-bees in tomato greenhouses. Annals of Applied Biology, 153, 149–155.Van der Vlugt, R. A. A. (2009). Pepino mosaic virus (review). Hellenic Plant Protection Journal, 2, 47–56.Van der Vlugt, R. A. A., & Stijger, C. C. M. M. (2008). Pepino mosaic virus. In B. W. J. Mahy & M. H. V. Van Regenmortel (Eds.), Encyclopedia of virology (5th ed., pp. 103–108). Wageningen: Oxford Elsevier.Van der Vlugt, R. A. A., Stijger, C. C. M. M., Verhoeven, J. T. J., & Lesemann, D.-E. (2000). First report of Pepino mosaic virus on tomato. Plant Disease, 84, 103.Van der Vlugt, R. A. A., Cuperus, C., Vink, J., Stijger, I. C. M. M., Lesemann, D.-E., Verhoeven, J. T. J., & Roenhorst, J. W. (2002). Identification and characterization of Pepino mosaic potexvirus in tomato. Bulletin EPPO/EPPO Bulletin, 32, 503–508.Verchot-Lubicz, J., Chang-Ming, Y., & Bamunusinghe, D. (2007). Molecular biology of potexviruses: recent advances. Journal of General Virology, 88(6), 1643–1655.Verhoeven, J. T. H. J., van der Vlugt, R., & Roenhorst, J. W. (2003). High similarity between tomato isolates of pepino mosaic virus suggests a common origin. European Journal of Plant Pathology, 109, 419–425.Werkman, A.W., & Sansford, C.E. (2010). Pest risk analysis for pepino mosaic virus for the EU. Deliverable Report 4.3. EU Sixth Framework project PEPEIRA. http:// www.pepeira.com .Wright, D., & Mumford, R. (1999). Pepino mosaic potexvirus (PepMV): first records in tomato in the United Kingdom. Plant disease notice (89th ed.). York, UK: Central Science Laboratory

End-to-end classification of reverberant rooms using DNNs

Reverberation is present in our workplaces, ourhomes, concert halls and theatres. This paper investigates howdeep learning can use the effect of reverberation on speechto classify a recording in terms of the room in which it wasrecorded. Existing approaches in the literature rely on domainexpertise to manually select acoustic parameters as inputs toclassifiers. Estimation of these parameters from reverberantspeech is adversely affected by estimation errors, impacting theclassification accuracy. In order to overcome the limitations ofpreviously proposed methods, this paper shows how DNNs canperform the classification by operating directly on reverberantspeech spectra and a CRNN with an attention-mechanism isproposed for the task. The relationship is investigated betweenthe reverberant speech representations learned by the DNNs andacoustic parameters. For evaluation, AIRs are used from theACE-challenge dataset that were measured in 7 real rooms. Theclassification accuracy of the CRNN classifier in the experimentsis 78% when using 5 hours of training data and 90% when using10 hours

Insects and mites feeding on berries of Juniperus foetidissima Willd. on the Mediterranean island of Cyprus

Endemic forests with Juniperus spp. in the Mediterranean are listed as a priority habitat in the EU Habitats Directive, with the stinking juniper tree (Juniperus foetidissima Willd.) a key constituent. Within the EU, the island of Cyprus represents the southernmost range of distribution of J. foetidissima with clumps of the tree located mostly on the rocky and steep slopes of the Troodos National Forest Park (NFP) between 1.500–1.950 m above sea level. The reproductive potential of J. foetidissima may be at risk, partly because of berry attacks by arthropods. To identify the arthropod species that infest J. foetidissima berries we sampled trees biweekly for one year at three elevations (1.950 m, 1.800 m, and 1.650 m). We identified four microlepidoptera species attacking berries: Pammene mariana (Zerny), P. juniperana (Millière), P. blockiana (Herrich-Schäffer) (Lepidoptera: Torticidae) and Argyresthia aurulentella Stainton (Lepidoptera: Yponomeutidae). Eriophyid mites were also recorded to feed on berries. All insect species are recorded for the first time in Cyprus. Infestation during the maturation period of berries collected by cutting varied from an average of 16% at the medium elevation (1.800 m) to 11% at the low elevation (1.650 m). Infestation of berries collected by beating remained above 30% during the berry maturation period

Insects and mites feeding on berries of Juniperus foetidissima Willd. on the Mediterranean island of Cyprus

Endemic forests with Juniperus spp. in the Mediterranean are listed as a priority habitat in the EU Habitats Directive, with the stinking juniper tree (Juniperus foetidissima Willd.) a key constituent. Within the EU, the island of Cyprus represents the southernmost range of distribution of J. foetidissima with clumps of the tree located mostly on the rocky and steep slopes of the Troodos National Forest Park (NFP) between 1.500–1.950 m above sea level. The reproductive potential of J. foetidissima may be at risk, partly because of berry attacks by arthropods. To identify the arthropod species that infest J. foetidissima berries we sampled trees biweekly for one year at three elevations (1.950 m, 1.800 m, and 1.650 m). We identified four microlepidoptera species attacking berries: Pammene mariana (Zerny), P. juniperana (Millière), P. blockiana (Herrich-Schäffer) (Lepidoptera: Torticidae) and Argyresthia aurulentella Stainton (Lepidoptera: Yponomeutidae). Eriophyid mites were also recorded to feed on berries. All insect species are recorded for the first time in Cyprus. Infestation during the maturation period of berries collected by cutting varied from an average of 16% at the medium elevation (1.800 m) to 11% at the low elevation (1.650 m). Infestation of berries collected by beating remained above 30% during the berry maturation period

Molecular typing of cyst-forming nematodes globodera pallida and G.rostochiensis, using real-time PCR and evaluation of five methods for template preparation

Globodera pallida and G.rostochiensis are two cyst-forming nematodes known to infest potato crops, causing severe economic losses worldwide. In this study, a real-time TaqMan PCR assay was developed and optimized for the simultaneous detection of G.pallida and G. rostochiensis. The assay's analytical and diagnostic sensitivity and specificity were evaluated using reference isolates. Four different DNA extraction methods and one rapid crude template-preparation procedure were compared in terms of extraction purity, efficiency for PCR applications, utility and cost. Extraction methods A and B included two commercially available kits that utilize silica columns and magnetic beads, respectively. Method C was based on DNA isolation using Chelex resin, and method D was a standard chemistry in-house protocol. Procedure E included the direct use of crude mixture composed of disrupted cysts in Tris-EDTA buffer. The multiplex TaqMan PCR assay successfully discriminated the two nematode species from all reference cyst samples and its recorded diagnostic sensitivity (Dse) and specificity (Dsp) was 100%. On the contrary, in conventional (Co) PCR tests, the overall Dsp and Dse were lower and estimated at 94 and 87% for G. pallida, and 97 and 88% for G. rostochiensis, respectively. Spectrophotometric results showed that DNA extraction methods A, B and C yielded the purest DNA and gave the lowest mean Ct values as well as the most consistent results in Co PCR. Alternative crude preparation method E resulted in statistically similar and Ct values consistent with those obtained with methods A to C when tested by TaqMan PCR. The developed assay, using crude template-preparation E, allows the simple, accurate and cost-effective testing of a large number of cyst samples and can be applied in surveys and certification schemes

Molecular characterization of Citrus tristeza virus isolates from Cyprus on the basis of the coat protein gene

Within the context of a program in Cyprus for the control of Citrus tristeza virus (CTV), the coat protein (CP) genes of 12 local isolates of the virus that induced different symptoms on host trees, were compared to those of known isolates. The CP genes were reverse-transcribed (RT) and amplified by polymerase chain reaction (PCR) and the resulting amplicons were cloned and sequenced. Nucleotide sequence analysis revealed no signs of geographic speciation. All the sequences obtained clustered close to those of previously known isolates of worldwide origin that are in five distinct groups. The nucleotide diversity was high compared to that found using a worldwide database of CP gene sequences. These data support the existence of different CTV introductions into Cyprus or an introduction from a location in which CTV is relatively diverse. Some of the isolates induced stem pitting on branches of grapefruit and sweet orange. Such isolates have not been noted often in the Mediterranean basin. They were close in CP sequence to isolate B249 from Venezuela, which induces stem pitting, and are of particular concern for the whole region

Molecular typing of cyst-forming nematodes globodera pallida and G.rostochiensis, using real-time PCR and evaluation of five methods for template preparation

Globodera pallida and G.rostochiensis are two cyst-forming nematodes known to infest potato crops, causing severe economic losses worldwide. In this study, a real-time TaqMan PCR assay was developed and optimized for the simultaneous detection of G.pallida and G. rostochiensis. The assay's analytical and diagnostic sensitivity and specificity were evaluated using reference isolates. Four different DNA extraction methods and one rapid crude template-preparation procedure were compared in terms of extraction purity, efficiency for PCR applications, utility and cost. Extraction methods A and B included two commercially available kits that utilize silica columns and magnetic beads, respectively. Method C was based on DNA isolation using Chelex resin, and method D was a standard chemistry in-house protocol. Procedure E included the direct use of crude mixture composed of disrupted cysts in Tris-EDTA buffer. The multiplex TaqMan PCR assay successfully discriminated the two nematode species from all reference cyst samples and its recorded diagnostic sensitivity (Dse) and specificity (Dsp) was 100%. On the contrary, in conventional (Co) PCR tests, the overall Dsp and Dse were lower and estimated at 94 and 87% for G. pallida, and 97 and 88% for G. rostochiensis, respectively. Spectrophotometric results showed that DNA extraction methods A, B and C yielded the purest DNA and gave the lowest mean Ct values as well as the most consistent results in Co PCR. Alternative crude preparation method E resulted in statistically similar and Ct values consistent with those obtained with methods A to C when tested by TaqMan PCR. The developed assay, using crude template-preparation E, allows the simple, accurate and cost-effective testing of a large number of cyst samples and can be applied in surveys and certification schemes