Publications

@article{gerovasileiou_alien_2016,

title = {Alien biodiversity in Mediterranean marine caves},

author = {Vasilis Gerovasileiou and Eleni Voultsiadou and Yiannis Issaris and Argyro Zenetos},

doi = {10.1111/maec.12268},

issn = {14390485},

year  = {2016},

date = {2016-01-01},

journal = {Marine Ecology},

volume = {37},

pages = {239--256},

abstract = {The number of alien species in the Mediterranean Sea is increasing rapidly, but few attempts have been made to evaluate impacts on specific habitat types. The present study investigated alien biodiversity in Mediterranean marine caves, both by contributing new records of Eastern Mediterranean cave aliens, and by reviewing the scattered existing literature; the main goals were to highlight potential impacts and investigate the importance of cave environments for the expansion of alien species. Seven new alien species were found in marine caves of the Aegean and Ionian seas, raising the total number of aliens reported from Mediterranean marine caves to 56 species, classified as molluscs, cnidarians, bryozoans, polychaetes, crustaceans, macroalgae, fishes and tunicates. Most cave aliens (66%) were recorded from the Southeastern Levantine coasts, specifically from Lebanese caves. Shipping and Lessepsian migration have been suggested as the main pathways of alien introduction into caves of the Mediterranean Sea. The comparison of alien cave biodiversity with the updated Mediterranean alien inventory (32 species added to the latest inventory) showed similar patterns and trends for species richness, biogeographical origin and major introduction pathways, corroborating previous findings on the high local representativeness of Mediterranean cave biodiversity. Alien species seem to have invaded mostly the entrance and semi-dark zones of shallow and/or semi-submerged caves and tunnels, whereas only a few have reached the dark inner sectors or caves of the anchialine type; thus, the unfavourable cave environment seems to be naturally protected from impacts related to opportunistic invasive species, at least to a certain point. Currently there is no research confirming any direct impacts of alien biota on the native cavernicolous one. However, some issues have emerged, implying potential threats that need to be further explored: (i) the presence of a considerable proportion of aliens in most studied marine caves of the Southeastern Mediterranean basin, (ii) the recently observed population explosion of alien cave-dwelling fishes in the same area, (iii) several indications that alien diversity in marine caves is much higher than we know today. Quantitative surveys and monitoring schemes are needed in order to evaluate potential effects of alien diversity on cave community structure and the role of marine caves as stepping stones for its expansion in the Mediterranean.},

note = {ISBN: 1439-0485},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{koulouri_fish_2016,

title = {Fish and cephalopod assemblage structure of green alga Caulerpa prolifera (Chlorophyta) meadow in the eastern Mediterranean Sea (Elounda Bay, Crete Island)},

author = {P Koulouri and S Kalogirou and M Maidanou and D Koutsoubas and C Dounas},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84951094365&doi=10.1016%2fj.rsma.2015.12.002&partnerID=40&md5=327c2b4b5171a102b8d4cda066a5ad22},

doi = {10.1016/j.rsma.2015.12.002},

issn = {23524855},

year  = {2016},

date = {2016-01-01},

journal = {Regional Studies in Marine Science},

volume = {3},

pages = {33--41},

abstract = {The present study investigated for the first time in the eastern Mediterranean Sea species composition, density, wet biomass and body size of fish and cephalopod species associated with a Caulerpa prolifera meadow in a shallow semi-enclosed coastal marine ecosystem (Elounda Bay, Crete Island). Quantitative sampling with a local boat seine, revealed 34 fish species belonging to 22 families and three cephalopod taxa. The number and density of species peaked during the summer sampling period due to high numbers of juveniles, while the highest wet biomass was observed during the autumn sampling period. The fish species Boops boops, Spicara smaris, Mullus barbatus and the non-indigenous Siganus luridus were dominant, making up a high proportion of the total fish fauna of the studied area. The cephalopod Sepia officinalis was the most important species, in terms of wet biomass. The results of the study indicated that the semi-enclosed coastal marine ecosystem of Elounda Bay, characterized by a dense monospecific C. prolifera bed as well as specific abiotic and biotic features could be regarded as an important habitat for the development of fish and cephalopod species, thus contributing to the conservation and maintenance of marine biological resources of the area. © 2015 Elsevier B.V.},

note = {Publisher: Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{romero-ramirez_long-term_2016,

title = {Long-term (1998-2010) large-scale comparison of the ecological quality status of gulf of lions (NW Mediterranean) benthic habitats},

author = {A Romero-Ramirez and P Bonifácio and C Labrune and R Sardá and J M Amouroux and G Bellan and J C Duchêne and R Hermand and I Karakassis and C Dounas and A Grémare},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84956957240&doi=10.1016%2fj.marpolbul.2015.11.052&partnerID=40&md5=4a816b544ac0dcaee35ba40193d8fb38},

doi = {10.1016/j.marpolbul.2015.11.052},

issn = {0025326X},

year  = {2016},

date = {2016-01-01},

journal = {Marine Pollution Bulletin},

volume = {102},

number = {1},

pages = {102--113},

abstract = {A comprehensive Mediterranean data set has been used to address 3 questions associated with the use of sensitivity/tolerance based biotic indices to infer the Ecological Quality status (EcoQs) of benthic habitats. Our results showed: (1) a significant effect of the reference database on derived sensitivity/tolerance measure (ES500.05) as well as associated Benthic Quality Index values and derived EcoQs; (2) a lack of correlation neither between BQI and AZTI Marine Biotic Index values nor between BQI and Multivariate-AZTI Marine Biotic Index values; (3) a lack of correlation between the values of the Benthic Habitat Quality Index (index derived from Sediment Profile Imagery) and those of either of the 3 tested biotic indices; and (4) a general agreement between the 3 tested biotic indices in describing the lack of global trend for the EcoQs of the Gulf of Lions despite the occurrence of significant changes in benthic macrofauna composition between 1998 and 2010. © 2015 Elsevier Ltd.},

note = {Publisher: Elsevier Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wang_overview_2016,

title = {Overview of the interactive task in BioCreative V},

author = {Q Wang and S S Abdul and L Almeida and S Ananiadou and Y I Balderas-Martínez and R Batista-Navarro and D Campos and L Chilton and H -J Chou and G Contreras and L Cooper and H -J Dai and B Ferrell and J Fluck and S Gama-Castro and N George and G Gkoutos and A K Irin and L J Jensen and S Jimenez and T R Jue and I Keseler and S Madan and S Matos and P McQuilton and M Milacic and M Mort and J Natarajan and E Pafilis and E Pereira and S Rao and F Rinaldi and K Rothfels and D Salgado and R M Silva and O Singh and R Stefancsik and C -H Su and S Subramani and H D Tadepally and L Tsaprouni and N Vasilevsky and X Wang and A Chatr-Aryamontri and S J F Laulederkind and S Matis-Mitchell and J McEntyre and S Orchard and S Pundir and R Rodriguez-Esteban and K Van Auken and Z Lu and M Schaeffer and C H Wu and L Hirschman and C N Arighi},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009926974&doi=10.1093%2fdatabase%2fbaw119&partnerID=40&md5=402da6f94c190eed16badbee3f086daf},

doi = {10.1093/database/baw119},

issn = {17580463},

year  = {2016},

date = {2016-01-01},

journal = {Database},

volume = {2016},

abstract = {Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing predesigned tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development of the interactive task, from planning to execution and discuss major findings for the systems tested.},

note = {Publisher: Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sinclair_seqenv_2016,

title = {Seqenv: Linking sequences to environments through text mining},

author = {L Sinclair and U Z Ijaz and L J Jensen and M J L Coolen and C Gubry-Rangin and A Chroňáková and A Oulas and C Pavloudi and J Schnetzer and A Weimann and A Ijaz and A Eiler and C Quince and E Pafilis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85007364069&doi=10.7717%2fpeerj.2690&partnerID=40&md5=d6fb9302c27b05c3c656dcf2f8aa9512},

doi = {10.7717/peerj.2690},

issn = {21678359},

year  = {2016},

date = {2016-01-01},

journal = {PeerJ},

volume = {2016},

number = {12},

abstract = {Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts-if it is available-the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv. © 2016 Sinclair et al.},

note = {Publisher: PeerJ Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hoopen_value_2016,

title = {Value, but high costs in post-deposition data Curation},

author = {P T Hoopen and C Amid and P L Buttigieg and E Pafilis and P Bravakos and A M C O-Tárraga and R Gibson and T Kahlke and A Legaki and K N Murthy and G Papastefanou and E Pereira and M Rossello and A L Toribio and G Cochrane},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84969922176&doi=10.1093%2fdatabase%2fbav126&partnerID=40&md5=b3a55db8e3812454067026d468aa02dc},

doi = {10.1093/database/bav126},

issn = {17580463},

year  = {2016},

date = {2016-01-01},

journal = {Database},

volume = {2016},

abstract = {Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach. © The Author(s) 2016. Published by Oxford University Press.},

note = {Publisher: Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chatzifotis_effects_2016,

title = {Effects of dietary lecithin, nucleoside, and krill supplementation to a fishmeal based diet on growth and feed utilization of sharpsnout sea bream (Diplodus puntazzo)},

author = {S Chatzifotis and M Sala-Pérez and E Guerra and L Rodríguez and A Ruiz-Navarro},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84989961152&partnerID=40&md5=9c56a06e121779e1799a6acbec4c3bd7},

issn = {0792156X},

year  = {2016},

date = {2016-01-01},

journal = {Israeli Journal of Aquaculture - Bamidgeh},

volume = {68},

abstract = {The aim of this 96 day feeding trial was to investigate the effects of the addition of different combinations of dietary lecithin, nucleosides, and krill to a fishmeal-based diet on the growth, feed utilization, feed consumption, and body composition of sharpsnout sea bream (Diplodus puntazzo). Six hundred (600) fish (average weight 21.21 ± 0.06SD g) were divided into 8 groups (triplicate treatments) and fed eight isoenergetic fishmeal-based diets, (C-control, L-lecithin, N-nucleosides, K-krill, L+N-lecithin+nucleosides, N+K-nucleosides+krill, L+K-lecithin+krill, L+N+K-lecithin+nucleosides+krill). The effects of the dietary regimes were evaluated in terms of specific growth rate (SGR), feed conversion ratio (FCR), daily feed intake (DFI), and whole body chemical composition (moisture, crude ash, crude protein and crude lipid). At the end the trial the fish had tripled their initial weight. SGR, FCR and DFI were 1.17-1.24 %, 0.95-1.01, and 1.03-1.14% respectively. Although differences were observed between some groups, none of the tested feed additives improved SGR, FCR, and DFI, compared to the control diet. Analysis of whole body proximate composition showed that moisture, crude ash, crude protein, and crude lipid ranged 61.45-64.00%, 3.96-4.26%, 15.44-17.26% and 14.87-18.82% respectively. Crude lipid concentration was higher in whole body of fish fed the nucleoside supplemented diet compared to control, lecithin, and krill groups. No other effects of the dietary regime on the whole body composition of sharpshout sea bream were observed. © 2016, Israeli Journal of Aquaculture - Bamidgeh. All rights reserved.},

note = {Publisher: Israeli Journal of Aquaculture - Bamidgeh},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{buttigieg_environment_2016,

title = {The environment ontology in 2016: Bridging domains with increased scope, semantic density, and interoperation},

author = {P L Buttigieg and E Pafilis and S E Lewis and M P Schildhauer and R L Walls and C J Mungall},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84988625177&doi=10.1186%2fs13326-016-0097-6&partnerID=40&md5=c65c1deb2752ddedfe277e0968752111},

doi = {10.1186/s13326-016-0097-6},

issn = {20411480},

year  = {2016},

date = {2016-01-01},

journal = {Journal of Biomedical Semantics},

volume = {7},

number = {1},

abstract = {Background: The Environment Ontology (ENVO; http://www.environmentontology.org/), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications. Methods: We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO. Results: Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl. Conclusions: ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, 'omics, and socioeconomic development. Through continued interactions with our users and partners, particularly those performing data archiving and sythesis, we anticipate that ENVO's growth will accelerate in 2017. As always, we invite further contributions and collaboration to advance the semantic representation of the environment, ranging from geographic features and environmental materials, across habitats and ecosystems, to everyday objects in household settings. © 2016 The Author(s).},

note = {Publisher: BioMed Central Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gasco_tenebrio_2016,

title = {Tenebrio molitor meal in diets for European sea bass (Dicentrarchus labrax L.) juveniles: Growth performance, whole body composition and in vivo apparent digestibility},

author = {L Gasco and M Henry and G Piccolo and S Marono and F Gai and M Renna and C Lussiana and E Antonopoulou and P Mola and S Chatzifotis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84995467750&doi=10.1016%2fj.anifeedsci.2016.07.003&partnerID=40&md5=31b52a5867163311a054ffd4f7e540db},

doi = {10.1016/j.anifeedsci.2016.07.003},

issn = {03778401},

year  = {2016},

date = {2016-01-01},

journal = {Animal Feed Science and Technology},

volume = {220},

pages = {34--45},

abstract = {Two trials were carried out on European sea bass (Dicentrarchus labrax L.) juveniles to evaluate the effects of dietary inclusion of a full-fat Tenebrio molitor (TM) larvae meal. A first growth trail was performed on 450 European sea bass using three isonitrogenous and isolipidic experimental diets (3 tanks/diet, 50 fish/tank) formulated to contain increasing levels of TM meal inclusion and precisely: 0 (TM0), 25 (TM25) and 50% (TM50) as fed basis. The performances, proximate body composition and fatty acid (FA) profile of whole fish fed the experimental diets were evaluated. A digestibility trial was then conducted on 180 fish to evaluate the in vivo apparent digestibility coefficient (ADC) of diets having 25% of TM inclusion in absence (TMD) or presence of exogenous enzymes (Carbohydrases, TM-Carb; Proteases, TM-Prot) compared to a fish meal based control diet (CD). The growth trial results showed that the highest inclusion level (TM50) led to a worsening of final body weight, weight gain, specific growth rate, and feeding rate if compared to the control diet (TM0). Regarding the whole body composition, crude protein and ether extract were not significantly influenced by the use of TM, while changes were observed in the FA profile. In particular, C18:2 n6 increased (+91% and +173% in TM25 and TM50, respectively vs TM0) with the inclusion of TM while sharp decreases of C20:5 n3 (−30% and −58% in TM25 and TM50, respectively vs TM0) and C22:6 n3 (−35% and −67% respectively vs TM0) were highlighted. Consequently, the ∑ n3/∑ n6 FA ratio showed a significant decrease (−63% and −84% in TM25 and TM50, respectively vs TM0). As far as digestibility trial is concerned, the crude protein ADC of the fish fed TMD was significantly higher than that of the fish fed CD (92.31 vs 89.97, respectively). The supplementation of digestive enzymes did not improve the protein and ADF digestibility. © 2016 Elsevier B.V.},

note = {Publisher: Elsevier B.V.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{grigorakis_chemical_2016,

title = {Chemical quality and sensory profile of the mediterranean farmed fish shi drum (Umbrina cirrosa) as affected by its dietary protein/fat levels},

author = {K Grigorakis and N Alexi and A Vasilaki and I Giogios and E Fountoulaki},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84996565541&doi=10.1080%2f1828051X.2016.1222890&partnerID=40&md5=991fee64ac8d2146e822844d0c584c62},

doi = {10.1080/1828051X.2016.1222890},

issn = {15944077},

year  = {2016},

date = {2016-01-01},

journal = {Italian Journal of Animal Science},

volume = {15},

number = {4},

pages = {681--688},

abstract = {Two groups of identically-reared shi drum,having received different diets (Group A: 45% protein and 16% fat and Group B: 48% protein and 12% fat),were compared for their yields and their chemical and sensory quality. They exhibited similar dressing and filleting yields,fat deposit and fillet composition. Differences were observed in the fillet fatty acids,with group B exhibiting higher 16:1ω-7,16:1ω-9,16:0,18:0,and total saturate contents. Their fillet volatile compounds also differed (group A,in particular,contained higher levels of carbonyl-compounds). A triangle test revealed that the two shi drum groups were perceived as sensory different. A Check-All-That-Apply (CATA) test showed that group A (high dietary lipids) was perceived as having a significantly higher ‘fish oil’ aroma,hardness and elasticity,while group B was characterised mainly by higher ‘sweet taste’,higher ‘hay’ and ‘fresh seaweed’ aroma and ‘crab/prawn’ flavour. © 2016 The Author(s).},

note = {Publisher: Taylor and Francis Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{musk_first_2016,

title = {First record of Streptosyllis nunezi Faulwetter et al., 2008 (Annelida, Syllidae) from the United Kingdom, and amendment to the genus streptosyllis Webster & Benedict, 1884},

author = {W Musk and S Faulwetter and P McIlwaine},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84964311552&doi=10.3897%2fzookeys.582.8006&partnerID=40&md5=d5f016914c3665b0f2a7a43068e145e2},

doi = {10.3897/zookeys.582.8006},

issn = {13132989},

year  = {2016},

date = {2016-01-01},

journal = {ZooKeys},

volume = {2016},

number = {582},

pages = {1--11},

abstract = {During a benthic survey of a Marine Conservation Zone located on the Skerries Bank in the English Channel off the south-west coast of England, three specimens of Streptosyllis nunezi Faulwetter et al., 2008 were found. This is the second ever record of the species after its original description, and the first record from waters around the U.K. and a significant northerly range extension for a species previously only recorded from the Canary Islands and the Mediterranean Sea. A single simple ventral chaeta in each of the two posterior-most segments was discovered in this and two other species of Streptosyllis Webster & Benedict, 1884. The generic definition of Streptosyllis is emended to include this feature previously unknown for the genus, and an updated key to the Streptosyllis found in UK waters is provided. © Will Musk et al.},

note = {Publisher: Pensoft Publishers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mylonas_enhancement_2016,

title = {Enhancement of oogenesis/spermatogenesis in meagre Argyrosomus regius using a combination of temperature control and GnRHa treatments},

author = {C C Mylonas and S Salone and T Biglino and P H de Mello and I Fakriadis and I Sigelaki and N Duncan},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84978193838&doi=10.1016%2fj.aquaculture.2016.07.006&partnerID=40&md5=33e0a7321455743f1b6c84fcc8aedb38},

doi = {10.1016/j.aquaculture.2016.07.006},

issn = {00448486},

year  = {2016},

date = {2016-01-01},

journal = {Aquaculture},

volume = {464},

pages = {323--330},

abstract = {A multiple GnRHa injection method for inducing spawning of high fecundity and quality in meagre was optimized. Specifically, the study (a) examined how long females would continue spawning in response to consecutive, weekly GnRHa injections, if maintained at the natural spawning temperature, and (b) evaluated whether males can produce adequate amounts of good quality sperm for the same period, with the assistance of a GnRHa therapy. Combined with stable temperatures (19–20 °C) that are prevalent during the early spawning season (April–May) in the Mediterranean Sea, each weekly GnRHa injection induced 2 consecutive spawns per week for a period of 17 weeks. Fish spawned consistently 2 days after treatment and produced high fecundity and egg quality (i.e. fertilization, hatching and early larval development). Maximum mean total fecundity (± S.D.) obtained was 1,415,000 ± 149,000 eggs kg− 1 in 32 spawns, being the highest total season fecundity reported for meagre, and significantly higher than the estimated maximum potential fecundity for the species. At the same time, sperm of consistently high quality (i.e. initial motility, duration of motility and storage survival) was produced in response to treatment with multiple GnRHa implants, though towards the end of the experiment a significant reduction (ANOVA, P ≤ 0.05) in spermatozoa density was observed. This protocol is expected to enhance greatly commercial production of meagre. Statement of relevance The present study reports on an optimized protocol for the induction of consistent and repeated spawning in meagre, based on the use of weekly GnRHa injections combined with stable temperatures that are prevalent at the early spawning season in the Mediterranean Sea. This protocol produced eggs of high fecundity and quality (i.e. fertilization, hatching and early larval development) for a period of > 4 months, and it is expected to enhance greatly commercial production of meagre. © 2016},

note = {Publisher: Elsevier B.V.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{davies_simulating_2016,

title = {Simulating social-ecological systems: The Island Digital Ecosystem Avatars (IDEA) consortium},

author = {N Davies and D Field and D Gavaghan and S J Holbrook and S Planes and M Troyer and M Bonsall and J Claudet and G Roderick and R J Schmitt and L A Zettler and V Berteaux and H C Bossin and C Cabasse and A Collin and J Deck and T Dell and J Dunne and R Gates and M Harfoot and J L Hench and M Hopuare and P Kirch and G Kotoulas and A Kosenkov and A Kusenko and J J Leichter and H Lenihan and A Magoulas and N Martinez and C Meyer and B Stoll and B Swalla and D M Tartakovsky and H T Murphy and S Turyshev and F Valdvinos and R Williams and S Wood},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84991529168&doi=10.1186%2fs13742-016-0118-5&partnerID=40&md5=8cee8d8941e5eaf5d39db97438c349a6},

doi = {10.1186/s13742-016-0118-5},

issn = {2047217X},

year  = {2016},

date = {2016-01-01},

journal = {GigaScience},

volume = {5},

number = {1},

abstract = {Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions. © 2016 Davies et al.},

note = {Publisher: BioMed Central Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rizzo_kolumbo_2016,

title = {Kolumbo submarine volcano (Greece): An active window into the Aegean subduction system},

author = {A L Rizzo and A Caracausi and V Chavagnac and P Nomikou and P N Polymenakou and M Mandalakis and G Kotoulas and A Magoulas and A Castillo and D Lampridou},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84975454736&doi=10.1038%2fsrep28013&partnerID=40&md5=e24dc2fa03414abaf410e586529f758d},

doi = {10.1038/srep28013},

issn = {20452322},

year  = {2016},

date = {2016-01-01},

journal = {Scientific Reports},

volume = {6},

abstract = {Submarine volcanism represents ∼80% of the volcanic activity on Earth and is an important source of mantle-derived gases. These gases are of basic importance for the comprehension of mantle characteristics in areas where subaerial volcanism is missing or strongly modified by the presence of crustal/atmospheric components. Though, the study of submarine volcanism remains a challenge due to their hazardousness and sea-depth. Here, we report 3He/4He measurements in CO2-dominated gases discharged at 500 m below sea level from the high-temperature (∼220 °C) hydrothermal system of the Kolumbo submarine volcano (Greece), located 7 km northeast off Santorini Island in the central part of the Hellenic Volcanic Arc (HVA). We highlight that the mantle below Kolumbo and Santorini has a 3He/4He signature of at least 7.0 Ra (being Ra the 3He/4He ratio of atmospheric He equal to 1.39×10-6), 3 Ra units higher than actually known for gases-rocks from Santorini. This ratio is also the highest measured across the HVA and is indicative of the direct degassing of a Mid-Ocean-Ridge-Basalts (MORB)-like mantle through lithospheric faults. We finally highlight that the degassing of high-temperature fluids with a MORB-like 3He/4He ratio corroborates a vigorous outgassing of mantle-derived volatiles with potential hazard at the Kolumbo submarine volcano.},

note = {Publisher: Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bravakos_polyphasic_2016,

title = {A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece},

author = {P Bravakos and G Kotoulas and K Skaraki and A Pantazidou and A Economou-Amilli},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84959209388&doi=10.1016%2fj.ympev.2016.02.009&partnerID=40&md5=e4f85b36c7ffd4404af7ca17e083364e},

doi = {10.1016/j.ympev.2016.02.009},

issn = {10557903},

year  = {2016},

date = {2016-01-01},

journal = {Molecular Phylogenetics and Evolution},

volume = {98},

pages = {147--160},

abstract = {Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S-23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes. © 2016 Elsevier Inc.},

note = {Publisher: Academic Press Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sarropoulou_transcriptomic_2016,

title = {Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata)},

author = {E Sarropoulou and A Tsalafouta and A Y M Sundaram and G D Gilfillan and G Kotoulas and N Papandroulakis and M Pavlidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84984849269&doi=10.1186%2fs12864-016-2874-0&partnerID=40&md5=0cba8ed79f3200cb9be9e48551ecc2e7},

doi = {10.1186/s12864-016-2874-0},

issn = {14712164},

year  = {2016},

date = {2016-01-01},

journal = {BMC Genomics},

volume = {17},

number = {1},

abstract = {Background: Teleosts are exposed to a broad range of external stimuli, which may be either of acute or chronic nature. The larval phase of certain fish species offer a unique opportunity to study the interactions between genes and environmental factors during early life. The present study investigates the effects of early-life events, applied at different time points of early ontogeny (first feeding, flexion and development of all fins; Phase 1) as well as on the subsequent juvenile stage after the application of an additional acute stressor (Phase 2) in the gilthead sea bream (Sparus aurata), a commercially important European aquaculture species. Animal performance, the cortisol response and gene expression patterns during early development as well as on the subsequent phases (juveniles) after the application of additional acute stressors were investigated. Results: Significant differences on fish performance were found only for juveniles exposed to early-life events at the phase of the formation of all fins. On the transcriptome level distinct expression patterns were obtained for larvae as well as for juveniles with the most divergent expression pattern found to be again at the phase of the development of all fins, which showed to have also an impact later on in the acute stress response of juveniles. Conclusions: The present study showed that applying an early-life protocol, characterized by the unpredictable, variable and moderate intensity of the applied stimuli provides a relative realistic model to evaluate the impact of daily aquaculture practices on fish performance. In addition, the power of investigating global gene expression patterns is shown, providing significant insights regarding the response of early-life events during development and as juveniles after the application of extra acute stressors. © 2016 The Author(s).},

note = {Publisher: BioMed Central Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{georgiou_transient_2016,

title = {Transient up- and down-regulation of expression of myosin light chain 2 and myostatin mRNA mark the changes from stratified hyperplasia to muscle fiber hypertrophy in larvae of gilthead sea bream (Sparus aurata L.)},

author = {S Georgiou and H Alami-Durante and D M Power and E Sarropoulou and Z Mamuris and K A Moutou},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84956950356&doi=10.1007%2fs00441-015-2254-0&partnerID=40&md5=e35128d4a27fb8161b4a2ef30b1c3b19},

doi = {10.1007/s00441-015-2254-0},

issn = {0302766X},

year  = {2016},

date = {2016-01-01},

journal = {Cell and Tissue Research},

volume = {363},

number = {2},

pages = {541--554},

abstract = {Hyperplasia and hypertrophy are the two mechanisms by which muscle develops and grows. We study these two mechanisms, during the early development of white muscle in Sparus aurata, by means of histology and the expression of structural and regulatory genes. A clear stage of stratified hyperplasia was identified early in the development of gilthead sea bream but ceased by 35 dph when hypertrophy took over. Mosaic recruitment of new white fibers began as soon as 60 dph. The genes mlc2a and mlc2b were expressed at various levels during the main phases of hyperplasia and hypertrophy. The genes myog and mlc2a were significantly up-regulated during the intensive stratified formation of new fibers and their expression was significantly correlated. Expression of mstn1 and igf1 increased at 35 dph, appeared to regulate the hyperplasia-to-hypertrophy transition, and may have stimulated the expression of mlc2a, mlc2b and col1a1 at the onset of mosaic hyperplasia. The up-regulation of mstn1 at transitional phases in muscle development indicates a dual regulatory role of myostatin in fish larval muscle growth. © 2015, Springer-Verlag Berlin Heidelberg.},

note = {Publisher: Springer Verlag},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{samaras_repeatability_2016,

title = {Repeatability of cortisol stress response in the European sea bass (Dicentrarchus labrax) and transcription differences between individuals with divergent responses},

author = {A Samaras and A Dimitroglou and E Sarropoulou and L Papaharisis and L Kottaras and M Pavlidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84990048823&doi=10.1038%2fsrep34858&partnerID=40&md5=2f8fdd5e3716b42be506c888bf96f144},

doi = {10.1038/srep34858},

issn = {20452322},

year  = {2016},

date = {2016-01-01},

journal = {Scientific Reports},

volume = {6},

abstract = {Understanding the stress responses of organisms is of importance in the performance and welfare of farmed animals, including fish. Especially fish in aquaculture commonly face stressors, and better knowledge of their responses may assist in proper husbandry and selection of breeding stocks. European sea bass (Dicentrarchus labrax), a species with high cortisol concentrations, is of major importance in this respect. The main objectives of the present study were to assess the repeatability and consistency of cortisol stress response and to identify differences in liver transcription profiles of European sea bass individuals, showing a consistent low (LR) or high (HR) cortisol response. The progeny of six full sib families was used, and sampled for plasma cortisol after an acute stress challenge once per month, for four consecutive months. Results suggest that cortisol responsiveness was a repeatable trait with LR and HR fish showing low or high resting, free and post-stress cortisol concentrations respectively. Finally, the liver transcription profiles of LR and HR fish showed some important differences, indicating differential hepatic regulation between these divergent phenotypes. These transcription differences were related to various metabolic and immunological processes, with 169 transcripts being transcribed exclusively in LR fish and 161 exclusively in HR fish. © 2016 The Author(s).},

note = {Publisher: Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{leese_dnaqua-net_2016,

title = {DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe},

author = {Florian Leese and Florian Altermatt and Agnès Bouchez and Torbjørn Ekrem and Daniel Hering and Kristian Meissner and Patricia Mergen and Jan Pawlowski and Jeremy Piggott and Frédéric Rimet and Dirk Steinke and Pierre Taberlet and Alexander Weigand and Kessy Abarenkov and Pedro Beja and Lieven Bervoets and Snaedís Björnsdóttir and Pieter Boets and Angela Boggero and Atle Bones and Ángel Borja and Kat Bruce and Vojislava Bursić and Jens Carlsson and Fedor Čiampor and Zuzana Čiamporová-Zatovičová and Eric Coissac and Filipe Costa and Marieta Costache and Simon Creer and Zoltán Csabai and Kristy Deiner and Ángel DelValls and Stina Drakare and Sofia Duarte and Tina Eleršek and Stefano Fazi and Cene Fišer and Jean-François Flot and Vera Fonseca and Diego Fontaneto and Michael Grabowski and Wolfram Graf and Jóhannes Guðbrandsson and Micaela Hellström and Yaron Hershkovitz and Peter Hollingsworth and Bella Japoshvili and John Jones and Maria Kahlert and Belma Kalamujic Stroil and Panagiotis Kasapidis and Martyn Kelly and Mary Kelly-Quinn and Emre Keskin and Urmas Kõljalg and Zrinka Ljubešić and Irena Maček and Elvira Mächler and Andrew Mahon and Marketa Marečková and Maja Mejdandzic and Georgina Mircheva and Matteo Montagna and Christian Moritz and Vallo Mulk and Andreja Naumoski and Ion Navodaru and Judit Padisák and Snæbjörn Pálsson and Kristel Panksep and Lyubomir Penev and Adam Petrusek and Martin Pfannkuchen and Craig Primmer and Baruch Rinkevich and Ana Rotter and Astrid Schmidt-Kloiber and Pedro Segurado and Arjen Speksnijder and Pavel Stoev and Malin Strand and Sigitas Šulčius and Per Sundberg and Michael Traugott and Costas Tsigenopoulos and Xavier Turon and Alice Valentini and Berry Van Der Hoorn and Gábor Várbíró and Marlen Vasquez Hadjilyra and Javier Viguri and Irma Vitonytė and Alfried Vogler and Trude Vrålstad and Wolfgang Wägele and Roman Wenne and Anne Winding and Guy Woodward and Bojana Zegura and Jonas Zimmermann},

url = {http://riojournal.com/articles.php?id=11321},

doi = {10.3897/rio.2.e11321},

issn = {2367-7163},

year  = {2016},

date = {2016-01-01},

urldate = {2023-03-03},

journal = {Research Ideas and Outcomes},

volume = {2},

pages = {e11321},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rigos_application_2016,

title = {Application of compound mixture of caprylic acid, iron and mannan oligosaccharide against Sparicotyle chrysophrii (Monogenea: Polyopisthocotylea) in gilthead sea bream, Sparus aurata},

author = {G Rigos and I Mladineo and C Nikoloudaki and A Vrbatovic and D Kogiannou},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85019231071&doi=10.14411%2ffp.2016.027&partnerID=40&md5=5b741f866a7cc8a0e42e3efe344fce51},

doi = {10.14411/fp.2016.027},

issn = {00155683},

year  = {2016},

date = {2016-01-01},

journal = {Folia Parasitologica},

volume = {63},

abstract = {We have evaluated the therapeutic effect of a compound mixture of caprylic acid (200 mg/kg fish), organic iron (0.2% of diet) and mannan oligosaccharide (0.4% of diet) in gilthead sea bream, Sparus aurata Linnaeus, infected with Sparicotyle chrysophrii Beneden et Hesse, 1863 in controlled conditions. One hundred and ten reared and S. chrysophrii-free fish (197 g) located in a cement tank were infected by the parasite two weeks following the addition of 150 S. chrysophrii-infected fish (70 g). Growth parameters and gill parasitic load were measured in treated against control fish after a ten-week-period. Differences in final weight, feed conversion ratio, specific growth rate and feed efficiency were not statistically significant between the experimental groups, suggesting no evident effect with respect to fish growth during the study period. Although the prevalence of S. chrysophrii was not affected by the mixture at the end of the experiment, the number of adults and larvae was significantly lower. The mean intensity encompassing the number of adults and larvae was 8.1 in treated vs 17.7 in control fish. Individual comparisons of gill arches showed that the preferred parasitism site for S. chrysophrii it the outermost or fourth gill arch, consistently apparent in fish fed the modified diet and in control fish. In conclusion, the combined application of caprylic acid, organic iron and mannan oligosaccharide can significantly affect the evolution of infection with S. chrysophrii in gilthead sea bream, being capable of reducing adult and larval stages of the monogenean. However, no difference in growth improvement was observed after the trial period, potentially leaving space for further optimisation of the added dietary compounds. © Institute of Parasitology, Biology Centre CAS.},

note = {Publisher: Czech Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kentouri_behaviour_1982,

title = {Behaviour and prey selection of striped sea bream Lithognathus mormyrus ( Sparidae) larvae reared in polyspecific and pluridimensional food conditions.},

author = {M Kentouri and P Divanach},

url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0020401751&partnerID=40&md5=77c3818f6f7c57ac0f66fe44d712b5ea},

year  = {1982},

date = {1982-01-01},

journal = {Comptes Rendus des Seances, Academie des Sciences, Serie III},

volume = {294},

number = {17},

pages = {859 -- 861},

abstract = {Striped sea bream larvae select, in order of preference, ciliata and veligers (2.9-3.5mm), rotifers (4-7mm), small pelagic crustacea up to 7mm. Digestibility of each prey class is very different. Veligers, barnacles and the rotifer Cephalodella remain alive in the gut.-from English summary},

note = {Original title (in French): Comportement et regime alimentaire des larves de marbre Lithognathus mormyrus (Poisson, Teleost., Sparidae) elevees dans des conditions de choix trophique polyspecifique et pluridimensionnel.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kentouri_differences_1982,

title = {Differences and similarities in the genesis of the locomotor and trophic behaviour of the prelarval stages of Sparus auratus, Diplodus vulgaris and Diplodus sargus},

author = {M Kentouri and P Divanach},

url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0020220374&partnerID=40&md5=ca25fa5468ce2d956d97645d687678ad},

year  = {1982},

date = {1982-01-01},

journal = {Aquaculture},

volume = {27},

pages = {355 -- 376},

abstract = {The behaviour of the prelarval stages of Sparus auratus, Diplodus vulgaris and Diplodus sargus was studied in 570-l tanks at a temperature of 19°C. The different stages in swimming from hatching to the age of 4 days are as follows; period of dominating immobility (1st day); passive vertical migration (2nd day); first oblique swimming (3rd day); first horizontal swimming (4th day). The different speeds of swimming and the distances covered are calculated; the specific differences are mentioned. The predation training period is described and food selectivity at this stage is demonstrated. Aquacultural implications are discussed. © 1982.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kentouri_preliminary_1980,

title = {Preliminary data in behavior, growth and survival of reared sea bream Diplodus sargus L.},

author = {M Kentouri and P Divanach and M Cantou},

url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0019237286&partnerID=40&md5=0f8ae0457204d44480d1358711cdee9e},

year  = {1980},

date = {1980-01-01},

journal = {Mediterranean Studies Review - General Fisheries Council},

volume = {57},

pages = {33--51},

abstract = {For larvae, the survival rate ranges from 3-8% after 54 days and rises to 77% for juveniles after 14 months’ farming. Growth is fast during summer but drops from September to May. The specimens reach 34 g in the 1st year, and 123 g by the end of 17 months of culture.-from Sport Fishery Abstracts},

note = {Original title (in French): Donnees preliminaires sur le comportement, la croissance et la survie du sar Diplodus sargus L. en elevage},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{frankle_nutrition_1976,

title = {Nutrition education in the medical school curriculum: a proposal for action: a curriculum design},

author = {R T Frankle},

doi = {10.1093/ajcn/29.1.105},

issn = {0002-9165},

year  = {1976},

date = {1976-01-01},

journal = {The American Journal of Clinical Nutrition},

volume = {29},

number = {1},

pages = {105--109},

abstract = {Nutrition has been traditionally taught in medical schools with emphasis on clinical management of disease states with modified diets. However, the science of nutrition can no longer be considered only in terms of the diagnosis and treatment of nutritional deficiency diseases. Prevention of disease-care rather than cure-must be emphasized. Using the nutrition concepts that evolved from the 1972 Williamsburg Conference encompassing the science and the sociology of nutrition, the author offers a proposal for action-a sequential nutrition curriculum design for years, I, II, and III of undergraduate medical education based on the experiences of the Nutrition Division, Department of Community Medicine, Mount Sinai School of Medicine-City University of New York.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}