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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Assarag, Bouchra; Dujardin, Bruno; Delamou, Alexandre; Meski, Fatima-Zahra; +1 Authors

    Background In Morocco, there is little information on the circumstances surrounding maternal near misses. This study aimed to determine the incidence, characteristics, and determinants of maternal near misses in Morocco. Method A prospective case-control study was conducted at 3 referral maternity hospitals in the Marrakech region of Morocco between February and July 2012. Near-miss cases included severe hemorrhage, hypertensive disorders, and prolonged obstructed labor. Three unmatched controls were selected for each near-miss case. Three categories of risk factors (sociodemographics, reproductive history, and delays), as well as perinatal outcomes, were assessed, and bivariate and multivariate analyses of the determinants were performed. A sample of 30 near misses and 30 non-near misses was interviewed. Results The incidence of near misses was 12‰ of births. Hypertensive disorders during pregnancy (45%) and severe hemorrhage (39%) were the most frequent direct causes of near miss. The main risk factors were illiteracy [OR = 2.35; 95% CI: (1.07 -5.15)], lack of antenatal care [OR = 3.97; 95% CI: (1.42-11.09)], complications during pregnancy [OR = 2.81; 95% CI: (1.26-6.29)], and having experienced a first phase delay [OR = 8.71; 95% CI: (3.97- 19.12)] and a first phase of third delay [OR = 4.03; 95% CI: (1.75-9.25)]. The main reasons for the first delay were lack of a family authority figure who could make a decision, lack of sufficient financial resources, lack of a vehicle, and fear of health facilities. The majority of near misses demonstrated a third delay with many referrals. The women's perceptions of the quality of their care highlighted the importance of information, good communication, and attitude. Conclusion Women and newborns with serious obstetric complications have a greater chance of successful outcomes if they are immediately directed to a functioning referral hospital and if the providers are responsive. info:eu-repo/semantics/published SCOPUS: ar.j

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    PLoS ONE
    Other literature type . Article . 2015 . Peer-reviewed
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    DI-fusion
    Article . 2015 . Peer-reviewed
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      Other literature type . Article . 2015 . Peer-reviewed
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      DI-fusion
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    Authors: Contreras, L.; Pross, J.; Bendle, J.A.; Schouten, S.; +8 Authors

    During IODP Expedition 318 (January–March 2010, Wellington to Hobart), ~2000 m of Eocene to Quaternary sediments were recovered from the Antarctic (Wilkes Land) margin, documenting the evolution of this margin from an ice-free “greenhouse Antarctica” to the present-day icehouse environment. Based on a bio- and magnetostratigraphically dated, late early to early middle Eocene record recovered at Site U1356, we have carried out palynological and organic geochemical analyses in order to gain insights into the terrestrial environmental dynamics on Antarctica under peak greenhouse conditions. Our preliminary palynological indicate that the vegetation along the Wilkes Land margin was highly diverse and contains thermophilous elements that today are widely distributed in the subtropics; along with our organic geochemical results, their presence suggests warm conditions at least in the coastal lowlands of the Wilkes Land margin. At the same time, taxa that today are typical for cool temperate settings are consistently present

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    Authors: Gonzalo Alvarez; Patricio A. Díaz; Marcos Godoy; Michael Araya; +7 Authors

    , it is very likely that the M. donacium population from Cucao Bay has not had a recurrent exposition to A. catenella and, consequently, that it has not been subjected to high selective pressure for PSP resistance. However, more research is needed to determine the effects of PSP toxins on behavioral and physiological responses, nerve sensitivity, and genetic/molecular basis for the resistance or sensitivity of M. donacium. 1 and with a toxin profile dominated by GTX3, GTX1, GTX2, GTX4, and neoSTX. Individuals were dissected into digestive gland (DG), foot (FT), adductor muscle (MU), and other body fractions (OBF), and histopathological and toxin analyses were carried out on the obtained fractions. Some pathological conditions were observed in gill and digestive gland of 40&ndash 1). The observed surf clam mortality seems to have been mainly due to the desiccation caused by the incapability of the clams to burrow. Considering the available information of the monitoring program and taking into account that this episode was the first detected along the open coast of the Pacific Ocean in southern Chiloé , leading to the banning of shellfish harvesting in an extended geographical area (~500 km). On April 24, 2016, this bloom produced a massive beaching (an accumulation on the beach surface of dead or impaired organisms which were drifted ashore) of surf clams Mesodesma donacium in Cucao Bay, Chiloé . To determine the effect of paralytic shellfish poisoning (PSP) toxins in M. donacium, samples were taken from Cucao during the third massive beaching detected on May 3, 2016. Whole tissue toxicity evidence a high interindividual variability with values which ranged from 1008 to 8763 &mu 50% of the individuals that correspond to hemocyte aggregation and haemocytic infiltration, respectively. The most toxic tissue was DG (2221 &mu In late February 2016, a harmful algal bloom (HAB) of Alexandrium catenella was detected in southern Chiloé 1), followed by OBF (710 &mu g STX eq 100 g&minus 1), and MU (314 &mu 1), FT (297 &mu

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    Toxins
    Other literature type . Article . 2019 . Peer-reviewed
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    Toxins
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    Toxins
    Article . 2019
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      Toxins
      Other literature type . Article . 2019 . Peer-reviewed
      License: CC BY
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      Toxins
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      Toxins
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    Authors: ANTONINI, Dario; MOLLO, MARIA ROSARIA; MISSERO, Caterina;

    Long noncoding RNAs (lncRNAs) are a functionally heterogeneous and abundant class of RNAs acting in all cellular compartments that can form complexes with DNA, RNA, and proteins. Recent advances in high-throughput sequencing and techniques leading to the identification of DNA-RNA, RNA-RNA, and RNA-protein complexes have allowed the functional characterization of a small set of lncRNAs. However, characterization of the full repertoire of lncRNAs playing essential roles in a number of normal and dysfunctional cellular processes remains an important goal for future studies. Here we describe the most commonly used techniques to identify lncRNAs, and to characterize their biological functions. In addition, we provide examples of these techniques applied to cutaneous research in healthy skin, that is, epidermal differentiation, and in diseases such as cutaneous squamous cell carcinomas and psoriasis. As with protein-coding RNA transcripts, lncRNAs are differentially regulated in disease, and can serve as novel biomarkers for the diagnosis and prognosis of skin diseases.

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    Journal of Investigative Dermatology
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      Journal of Investigative Dermatology
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    Authors: Yasser B. Ruiz-Blanco; Guillermin Agüero-Chapin; Enrique García-Hernández; Orlando Álvarez; +2 Authors

    Background: Computational prediction of protein function constitutes one of the more complex problems in Bioinformatics, because of the diversity of functions and mechanisms in that proteins exert in nature. This issue is reinforced especially for proteins that share very low primary or tertiary structure similarity to existing annotated proteomes. In this sense, new alignment-free (AF) tools are needed to overcome the inherent limitations of classic alignment-based approaches to this issue. We have recently introduced AF protein-numerical-encoding programs (TI2BioP and ProtDCal), whose sequence-based features have been successfully applied to detect remote protein homologs, post-translational modifications and antibacterial peptides. Here we aim to demonstrate the applicability of 4 AF protein descriptor families, implemented in our programs, for the identification enzyme-like proteins. At the same time, the use of our novel family of 3D-structure-based descriptors is introduced for the first time. The Dobson & Doig (D&D) benchmark dataset is used for the evaluation of our AF protein descriptors, because of its proven structural diversity that permits one to emulate an experiment within the twilight zone of alignment-based methods (pair-wise identity <30%). The performance of our sequence-based predictor was further assessed using a subset of formerly uncharacterized proteins which currently represent a benchmark annotation dataset. Results: Four protein descriptor families (sequence-composition-based (0D), linear-topology-based (1D), pseudo-fold-topology-based (2D) and 3D-structure features (3D), were assessed using the D&D benchmark dataset. We show that only the families of ProtDCal's descriptors (0D, 1D and 3D) encode significant information for enzymes and non-enzymes discrimination. The obtained 3D-structure-based classifier ranked first among several other SVM-based methods assessed in this dataset. Furthermore, the model leveraging 1D descriptors, showed a higher success rate than EzyPred on a benchmark annotation dataset from the Shewanella oneidensis proteome. Conclusions: The applicability of ProtDCal as a general-purpose-AF protein modelling method is illustrated through the discrimination between two comprehensive protein functional classes. The observed performances using the highly diverse D&D dataset, and the set of formerly uncharacterized (hard-to-annotate) proteins of Shewanella oneidensis, places our methodology on the top range of methods to model and predict protein function using alignment-free approaches. © 2017 The Author(s). Acknowledgements The authors thank Dr. Reinaldo Molina-Ruiz for his assistance in obtaining the latest version of TI2BioP program. GACh acknowledges Dr. Federico Pallardo’s support, Dean of Medicine and Dentistry Faculty, University of Valencia (UV) in regards to the access to the UV’s facilities during part of this work. Funding YBRB is financed by a Postdoc Fellowship in the Chemistry Institute of the UNAM (DGAPA-UNAM [PAPIIT-IN200115]). GACh was funded by a Postdoc fellowship (SFRH/BPD/92978/2013) granted by the Portuguese Fundação para a Ciência e a Tecnologia (FCT). AA was partially supported by the Strategic Funding UID/Multi/04423/2013 through national funds provided by FCT and the European Regional Development Fund (ERDF) in the framework of the program PT2020, by the European Structural and Investment Funds (ESIF) through the Competitiveness and Internationalization Operational Program – COMPETE 2020 and by National Funds through the FCT under the project PTDC/AAG-GLO/6887/2014 (POCI-01-0124-FEDER-016845), and by the Structured Programs of R&D&I INNOVMAR (NORTE-01-0145-FEDER-000035 – NOVELMAR) and CORAL NORTE (NORTE- 01–0145-FEDER-000036), and funded by the Northern Regional Operational Program (NORTE2020) through the ERDF. The funding sources were not involved with the design of the study, analysis and interpretation of data or in the writing of the manuscript.

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    BMC Bioinformatics
    Article . 2017
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    Authors: Dany Domínguez-Pérez; Armando Rodríguez; Hugo Osório; Joana Azevedo; +3 Authors

    Cnidarian constitutes a great source of bioactive compounds. However, research involving peptides from organisms belonging to the order Zoanthidea has received very little attention, contrasting to the numerous studies of the order Actiniaria, from which hundreds of toxic peptides and proteins have been reported. In this work, we performed a mass spectrometry analysis of a low molecular weight (LMW) fraction previously reported as lethal to mice. The low molecular weight (LMW) fraction was obtained by gel filtration of a Zoanthus sociatus (order Zoanthidea) crude extract with a Sephadex G‐50, and then analyzed by matrix‐assisted laser desorption/ionization time‐of‐flight/time‐of‐flight (MALDI‐TOF/TOF) mass spectrometry (MS) in positive ion reflector mode from m/z 700 to m/z 4000. Afterwards, some of the most intense and representative MS ions were fragmented by MS/MS with no significant results obtained by Protein Pilot protein identification software and the Mascot algorithm search. However, microcystin masses were detected by mass‐matching against libraries of non‐ribosomal peptide database (NORINE). Subsequent reversed‐phase C18 HPLC (in isocratic elution mode) and mass spectrometry analyses corroborated the presence of the cyanotoxin Microcystin‐LR (MC‐LR). To the best of our knowledge, this finding constitutes the first report of MC‐LR in Z. sociatus, and one of the few evidences of such cyanotoxin in cnidarians.

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    Toxins
    Other literature type . Article . 2017 . Peer-reviewed
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    Toxins
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      Toxins
      Other literature type . Article . 2017 . Peer-reviewed
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      Toxins
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    Authors: M I, Quiroga; M J, Redondo; A, Sitjà-Bobadilla; O, Palenzuela; +6 Authors

    An epidemiological cohort study of Enteromyxum scophthalmi in cultured turbot was performed on a farm in North Western Spain. Four different ongrowing stocks (A, B, C, D) were monitored monthly until market size. Fish from stocks C and D were divided into 2 subgroups, receiving filtered (CF and DF) or unfiltered (CUF and DUF) water. The lack of water filtration was positively associated with infection prevalence, as all fish kept in filtered water remained uninfected. Parasite abundance varied seasonally (P<0·05) in stock B and subgroup CUF. Infection was also associated (P<0·05) with host weight, and the highest prevalences and intensities were detected in 101-200 g and 201-300 g fish. Distribution pattern of E. scophthalmi in subgroups CUF and DUF had a variance higher than the mean, indicating overdispersion. The minimum period necessary for the first detection of the parasite and for the appearance of disease symptoms and mortality, varied depending on the stock and introduction date, although a long pre-patent period was always observed. Several factors, such as host density, parasite recruitment and parasite-induced fish mortality can contribute to the observed distribution pattern. Risk factors found to be associated with E. scophthalmi infection, including water quality and accumulation of infective stages in the culture tanks, should be considered when designing control strategies to prevent the introduction and spread of infective stages in the facilities. © 2006 Cambridge University Press. Funding for this study was provided by the EU and the Spanish Ministerio de Ciencia y Tecnología through research grants FEDER 1FD97-0679-C02-01 and AGL2001-2241-C02-01. Additional support was obtained from Stolt Sea Farm S. A. We are grateful to J. Monfort from IATS and C. M. Carreira from the School of Veterinary Medicine of Lugo for histological processing.

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    Parasitology
    Article . 2006 . Peer-reviewed
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      Parasitology
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    Authors: Galpert, Deborah; del Río, Sara; Herrera, Francisco; Ancede-Gallardo, Evys; +2 Authors

    Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles) are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiaeSchizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification. national funds through FCT PEst-C/MAR/LA0015/2013 PTDC/AAC-AMB/121301/2010 FCOMP-01-0124-FEDER-019490 Portuguese Foundation for Science and Technology SFRH/BPD/92978/2013 Regional Andalusian Research P11-TIC-7765 P10-TIC-6858 Spanish Government TIN2014-57251-P European Union (EU)

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    BioMed Research International
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    Authors: Jaya Kumari Swain; Yamila Carpio; Lill-Heidi Johansen; Janet Velázquez; +4 Authors

    AbstractInfection with parasitic copepod salmon louse Lepeophtheirus salmonis, represents one of the most important limitations to sustainable Atlantic salmon (Salmo salar L.) farming today in the North Atlantic region. The parasite exerts negative impact on health, growth and welfare of farmed fish as well as impact on wild salmonid populations. It is therefore central to ensure continuous low level of salmon lice with the least possible handling of the salmon and drug use. To address this, vaccination is a cost-effective and environmentally friendly control approach. In this study, efficacy of a vaccine candidate, containing a peptide derived from ribosomal protein P0, was validated post infestation with L. salmonis, at the lab-scale. The sampling results showed good potential of the vaccine candidate when administered intraperitoneally in the host, in reducing the ectoparasite load, through reduction of adult female lice counts and fecundity and with greater presumptive effect in F1 lice generation. The sampling results correlated well with the differential modulation of pro-inflammatory, Th1, Th2 and T regulatory mediators at the transcript level at different lice stages. Overall, the results supports the effectiveness of the vaccine candidate in controlling salmon lice infestation load. However, further validation is necessary under field conditions.

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    PLoS ONE
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    DOAJ; PLoS ONE
    Article . 2020
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    PLoS ONE
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      Article . 2020
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      PLoS ONE
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    Authors: Charles W. Fox; C. Sean Burns; Anna D. Muncy; Jennifer A. Meyer;

    Summary Peer review is the primary method by which journals evaluate the quality and importance of scientific papers. To help editors find suitable reviewers, many journals allow or require authors to suggest names of preferred and nonpreferred reviewers. Though authors should know best who is qualified to review their papers, they also have a strong incentive to suggest reviewers that they expect to review their paper positively. In this study, we examine the reviewers that are suggested as preferred and nonpreferred by authors, the use of these author suggestions by editors, and the influence of author suggestions on the peer review process and outcomes at the journal Functional Ecology. In particular, we examined how gender of the participants (author, editor and reviewer) influences the role of preferred reviewers in the peer review process. Even when not required by the journal, most authors suggest preferred reviewers, but few suggest nonpreferred reviewers. Most author‐preferred reviewers are male, but the proportion of women among author suggestions increased over the 11 years, from a low of 15% in 2004 to a high of 25% in 2014. Male and female authors did not differ in how likely they were to suggest preferred reviewers, but the proportion of women among author suggestions was higher for female authors (~28%, averaged across years) than for male authors (~21%). Women that were suggested as author‐preferred reviewers were more likely to be selected by editors than were men suggested by authors. There was no evidence that editor gender, seniority or length of service as an editor for Functional Ecology affected the probability that they used author suggestions. Of reviewers invited to review, those that were author‐suggested were more likely to respond to the editors' review invitations but were not more likely to agree to review. Most strikingly, author‐preferred reviewers rated papers more positively than did editor‐selected reviewers, and papers reviewed by author‐preferred reviewers were much more likely to be invited for revision than were papers reviewed by editor‐selected reviewers. This difference was not influenced by the gender of the participants in the process. Suggesting preferred reviewers benefits authors because preferred reviewers rate papers significantly more positively than do editor‐selected reviewers, improving the chances that a paper will be published. Journals and journal editors should recognize that preferred reviewers rate manuscripts differently than do editor‐selected reviewers, and be aware that this difference can have large effects on editor decisions. A Lay Summary is available for this article.

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    Functional Ecology
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    Functional Ecology
    Article . 2016 . Peer-reviewed
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      Functional Ecology
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    Authors: Assarag, Bouchra; Dujardin, Bruno; Delamou, Alexandre; Meski, Fatima-Zahra; +1 Authors

    Background In Morocco, there is little information on the circumstances surrounding maternal near misses. This study aimed to determine the incidence, characteristics, and determinants of maternal near misses in Morocco. Method A prospective case-control study was conducted at 3 referral maternity hospitals in the Marrakech region of Morocco between February and July 2012. Near-miss cases included severe hemorrhage, hypertensive disorders, and prolonged obstructed labor. Three unmatched controls were selected for each near-miss case. Three categories of risk factors (sociodemographics, reproductive history, and delays), as well as perinatal outcomes, were assessed, and bivariate and multivariate analyses of the determinants were performed. A sample of 30 near misses and 30 non-near misses was interviewed. Results The incidence of near misses was 12‰ of births. Hypertensive disorders during pregnancy (45%) and severe hemorrhage (39%) were the most frequent direct causes of near miss. The main risk factors were illiteracy [OR = 2.35; 95% CI: (1.07 -5.15)], lack of antenatal care [OR = 3.97; 95% CI: (1.42-11.09)], complications during pregnancy [OR = 2.81; 95% CI: (1.26-6.29)], and having experienced a first phase delay [OR = 8.71; 95% CI: (3.97- 19.12)] and a first phase of third delay [OR = 4.03; 95% CI: (1.75-9.25)]. The main reasons for the first delay were lack of a family authority figure who could make a decision, lack of sufficient financial resources, lack of a vehicle, and fear of health facilities. The majority of near misses demonstrated a third delay with many referrals. The women's perceptions of the quality of their care highlighted the importance of information, good communication, and attitude. Conclusion Women and newborns with serious obstetric complications have a greater chance of successful outcomes if they are immediately directed to a functioning referral hospital and if the providers are responsive. info:eu-repo/semantics/published SCOPUS: ar.j

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    PLoS ONE
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    DI-fusion
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    Authors: Contreras, L.; Pross, J.; Bendle, J.A.; Schouten, S.; +8 Authors

    During IODP Expedition 318 (January–March 2010, Wellington to Hobart), ~2000 m of Eocene to Quaternary sediments were recovered from the Antarctic (Wilkes Land) margin, documenting the evolution of this margin from an ice-free “greenhouse Antarctica” to the present-day icehouse environment. Based on a bio- and magnetostratigraphically dated, late early to early middle Eocene record recovered at Site U1356, we have carried out palynological and organic geochemical analyses in order to gain insights into the terrestrial environmental dynamics on Antarctica under peak greenhouse conditions. Our preliminary palynological indicate that the vegetation along the Wilkes Land margin was highly diverse and contains thermophilous elements that today are widely distributed in the subtropics; along with our organic geochemical results, their presence suggests warm conditions at least in the coastal lowlands of the Wilkes Land margin. At the same time, taxa that today are typical for cool temperate settings are consistently present

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    Authors: Gonzalo Alvarez; Patricio A. Díaz; Marcos Godoy; Michael Araya; +7 Authors

    , it is very likely that the M. donacium population from Cucao Bay has not had a recurrent exposition to A. catenella and, consequently, that it has not been subjected to high selective pressure for PSP resistance. However, more research is needed to determine the effects of PSP toxins on behavioral and physiological responses, nerve sensitivity, and genetic/molecular basis for the resistance or sensitivity of M. donacium. 1 and with a toxin profile dominated by GTX3, GTX1, GTX2, GTX4, and neoSTX. Individuals were dissected into digestive gland (DG), foot (FT), adductor muscle (MU), and other body fractions (OBF), and histopathological and toxin analyses were carried out on the obtained fractions. Some pathological conditions were observed in gill and digestive gland of 40&ndash 1). The observed surf clam mortality seems to have been mainly due to the desiccation caused by the incapability of the clams to burrow. Considering the available information of the monitoring program and taking into account that this episode was the first detected along the open coast of the Pacific Ocean in southern Chiloé , leading to the banning of shellfish harvesting in an extended geographical area (~500 km). On April 24, 2016, this bloom produced a massive beaching (an accumulation on the beach surface of dead or impaired organisms which were drifted ashore) of surf clams Mesodesma donacium in Cucao Bay, Chiloé . To determine the effect of paralytic shellfish poisoning (PSP) toxins in M. donacium, samples were taken from Cucao during the third massive beaching detected on May 3, 2016. Whole tissue toxicity evidence a high interindividual variability with values which ranged from 1008 to 8763 &mu 50% of the individuals that correspond to hemocyte aggregation and haemocytic infiltration, respectively. The most toxic tissue was DG (2221 &mu In late February 2016, a harmful algal bloom (HAB) of Alexandrium catenella was detected in southern Chiloé 1), followed by OBF (710 &mu g STX eq 100 g&minus 1), and MU (314 &mu 1), FT (297 &mu

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    Toxins
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    Authors: ANTONINI, Dario; MOLLO, MARIA ROSARIA; MISSERO, Caterina;

    Long noncoding RNAs (lncRNAs) are a functionally heterogeneous and abundant class of RNAs acting in all cellular compartments that can form complexes with DNA, RNA, and proteins. Recent advances in high-throughput sequencing and techniques leading to the identification of DNA-RNA, RNA-RNA, and RNA-protein complexes have allowed the functional characterization of a small set of lncRNAs. However, characterization of the full repertoire of lncRNAs playing essential roles in a number of normal and dysfunctional cellular processes remains an important goal for future studies. Here we describe the most commonly used techniques to identify lncRNAs, and to characterize their biological functions. In addition, we provide examples of these techniques applied to cutaneous research in healthy skin, that is, epidermal differentiation, and in diseases such as cutaneous squamous cell carcinomas and psoriasis. As with protein-coding RNA transcripts, lncRNAs are differentially regulated in disease, and can serve as novel biomarkers for the diagnosis and prognosis of skin diseases.

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    Journal of Investigative Dermatology
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      Journal of Investigative Dermatology
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    Authors: Yasser B. Ruiz-Blanco; Guillermin Agüero-Chapin; Enrique García-Hernández; Orlando Álvarez; +2 Authors

    Background: Computational prediction of protein function constitutes one of the more complex problems in Bioinformatics, because of the diversity of functions and mechanisms in that proteins exert in nature. This issue is reinforced especially for proteins that share very low primary or tertiary structure similarity to existing annotated proteomes. In this sense, new alignment-free (AF) tools are needed to overcome the inherent limitations of classic alignment-based approaches to this issue. We have recently introduced AF protein-numerical-encoding programs (TI2BioP and ProtDCal), whose sequence-based features have been successfully applied to detect remote protein homologs, post-translational modifications and antibacterial peptides. Here we aim to demonstrate the applicability of 4 AF protein descriptor families, implemented in our programs, for the identification enzyme-like proteins. At the same time, the use of our novel family of 3D-structure-based descriptors is introduced for the first time. The Dobson & Doig (D&D) benchmark dataset is used for the evaluation of our AF protein descriptors, because of its proven structural diversity that permits one to emulate an experiment within the twilight zone of alignment-based methods (pair-wise identity <30%). The performance of our sequence-based predictor was further assessed using a subset of formerly uncharacterized proteins which currently represent a benchmark annotation dataset. Results: Four protein descriptor families (sequence-composition-based (0D), linear-topology-based (1D), pseudo-fold-topology-based (2D) and 3D-structure features (3D), were assessed using the D&D benchmark dataset. We show that only the families of ProtDCal's descriptors (0D, 1D and 3D) encode significant information for enzymes and non-enzymes discrimination. The obtained 3D-structure-based classifier ranked first among several other SVM-based methods assessed in this dataset. Furthermore, the model leveraging 1D descriptors, showed a higher success rate than EzyPred on a benchmark annotation dataset from the Shewanella oneidensis proteome. Conclusions: The applicability of ProtDCal as a general-purpose-AF protein modelling method is illustrated through the discrimination between two comprehensive protein functional classes. The observed performances using the highly diverse D&D dataset, and the set of formerly uncharacterized (hard-to-annotate) proteins of Shewanella oneidensis, places our methodology on the top range of methods to model and predict protein function using alignment-free approaches. © 2017 The Author(s). Acknowledgements The authors thank Dr. Reinaldo Molina-Ruiz for his assistance in obtaining the latest version of TI2BioP program. GACh acknowledges Dr. Federico Pallardo’s support, Dean of Medicine and Dentistry Faculty, University of Valencia (UV) in regards to the access to the UV’s facilities during part of this work. Funding YBRB is financed by a Postdoc Fellowship in the Chemistry Institute of the UNAM (DGAPA-UNAM [PAPIIT-IN200115]). GACh was funded by a Postdoc fellowship (SFRH/BPD/92978/2013) granted by the Portuguese Fundação para a Ciência e a Tecnologia (FCT). AA was partially supported by the Strategic Funding UID/Multi/04423/2013 through national funds provided by FCT and the European Regional Development Fund (ERDF) in the framework of the program PT2020, by the European Structural and Investment Funds (ESIF) through the Competitiveness and Internationalization Operational Program – COMPETE 2020 and by National Funds through the FCT under the project PTDC/AAG-GLO/6887/2014 (POCI-01-0124-FEDER-016845), and by the Structured Programs of R&D&I INNOVMAR (NORTE-01-0145-FEDER-000035 – NOVELMAR) and CORAL NORTE (NORTE- 01–0145-FEDER-000036), and funded by the Northern Regional Operational Program (NORTE2020) through the ERDF. The funding sources were not involved with the design of the study, analysis and interpretation of data or in the writing of the manuscript.

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    BMC Bioinformatics
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    Authors: Dany Domínguez-Pérez; Armando Rodríguez; Hugo Osório; Joana Azevedo; +3 Authors

    Cnidarian constitutes a great source of bioactive compounds. However, research involving peptides from organisms belonging to the order Zoanthidea has received very little attention, contrasting to the numerous studies of the order Actiniaria, from which hundreds of toxic peptides and proteins have been reported. In this work, we performed a mass spectrometry analysis of a low molecular weight (LMW) fraction previously reported as lethal to mice. The low molecular weight (LMW) fraction was obtained by gel filtration of a Zoanthus sociatus (order Zoanthidea) crude extract with a Sephadex G‐50, and then analyzed by matrix‐assisted laser desorption/ionization time‐of‐flight/time‐of‐flight (MALDI‐TOF/TOF) mass spectrometry (MS) in positive ion reflector mode from m/z 700 to m/z 4000. Afterwards, some of the most intense and representative MS ions were fragmented by MS/MS with no significant results obtained by Protein Pilot protein identification software and the Mascot algorithm search. However, microcystin masses were detected by mass‐matching against libraries of non‐ribosomal peptide database (NORINE). Subsequent reversed‐phase C18 HPLC (in isocratic elution mode) and mass spectrometry analyses corroborated the presence of the cyanotoxin Microcystin‐LR (MC‐LR). To the best of our knowledge, this finding constitutes the first report of MC‐LR in Z. sociatus, and one of the few evidences of such cyanotoxin in cnidarians.

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    Toxins
    Other literature type . Article . 2017 . Peer-reviewed
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    Authors: M I, Quiroga; M J, Redondo; A, Sitjà-Bobadilla; O, Palenzuela; +6 Authors

    An epidemiological cohort study of Enteromyxum scophthalmi in cultured turbot was performed on a farm in North Western Spain. Four different ongrowing stocks (A, B, C, D) were monitored monthly until market size. Fish from stocks C and D were divided into 2 subgroups, receiving filtered (CF and DF) or unfiltered (CUF and DUF) water. The lack of water filtration was positively associated with infection prevalence, as all fish kept in filtered water remained uninfected. Parasite abundance varied seasonally (P<0·05) in stock B and subgroup CUF. Infection was also associated (P<0·05) with host weight, and the highest prevalences and intensities were detected in 101-200 g and 201-300 g fish. Distribution pattern of E. scophthalmi in subgroups CUF and DUF had a variance higher than the mean, indicating overdispersion. The minimum period necessary for the first detection of the parasite and for the appearance of disease symptoms and mortality, varied depending on the stock and introduction date, although a long pre-patent period was always observed. Several factors, such as host density, parasite recruitment and parasite-induced fish mortality can contribute to the observed distribution pattern. Risk factors found to be associated with E. scophthalmi infection, including water quality and accumulation of infective stages in the culture tanks, should be considered when designing control strategies to prevent the introduction and spread of infective stages in the facilities. © 2006 Cambridge University Press. Funding for this study was provided by the EU and the Spanish Ministerio de Ciencia y Tecnología through research grants FEDER 1FD97-0679-C02-01 and AGL2001-2241-C02-01. Additional support was obtained from Stolt Sea Farm S. A. We are grateful to J. Monfort from IATS and C. M. Carreira from the School of Veterinary Medicine of Lugo for histological processing.

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    Parasitology
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    Authors: Galpert, Deborah; del Río, Sara; Herrera, Francisco; Ancede-Gallardo, Evys; +2 Authors

    Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles) are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiaeSchizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification. national funds through FCT PEst-C/MAR/LA0015/2013 PTDC/AAC-AMB/121301/2010 FCOMP-01-0124-FEDER-019490 Portuguese Foundation for Science and Technology SFRH/BPD/92978/2013 Regional Andalusian Research P11-TIC-7765 P10-TIC-6858 Spanish Government TIN2014-57251-P European Union (EU)

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      BioMed Research International
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    Authors: Jaya Kumari Swain; Yamila Carpio; Lill-Heidi Johansen; Janet Velázquez; +4 Authors

    AbstractInfection with parasitic copepod salmon louse Lepeophtheirus salmonis, represents one of the most important limitations to sustainable Atlantic salmon (Salmo salar L.) farming today in the North Atlantic region. The parasite exerts negative impact on health, growth and welfare of farmed fish as well as impact on wild salmonid populations. It is therefore central to ensure continuous low level of salmon lice with the least possible handling of the salmon and drug use. To address this, vaccination is a cost-effective and environmentally friendly control approach. In this study, efficacy of a vaccine candidate, containing a peptide derived from ribosomal protein P0, was validated post infestation with L. salmonis, at the lab-scale. The sampling results showed good potential of the vaccine candidate when administered intraperitoneally in the host, in reducing the ectoparasite load, through reduction of adult female lice counts and fecundity and with greater presumptive effect in F1 lice generation. The sampling results correlated well with the differential modulation of pro-inflammatory, Th1, Th2 and T regulatory mediators at the transcript level at different lice stages. Overall, the results supports the effectiveness of the vaccine candidate in controlling salmon lice infestation load. However, further validation is necessary under field conditions.

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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    PLoS ONE
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    DOAJ; PLoS ONE
    Article . 2020
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    PLoS ONE
    Article . 2020 . Peer-reviewed
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      DOAJ; PLoS ONE
      Article . 2020
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      PLoS ONE
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    Authors: Charles W. Fox; C. Sean Burns; Anna D. Muncy; Jennifer A. Meyer;

    Summary Peer review is the primary method by which journals evaluate the quality and importance of scientific papers. To help editors find suitable reviewers, many journals allow or require authors to suggest names of preferred and nonpreferred reviewers. Though authors should know best who is qualified to review their papers, they also have a strong incentive to suggest reviewers that they expect to review their paper positively. In this study, we examine the reviewers that are suggested as preferred and nonpreferred by authors, the use of these author suggestions by editors, and the influence of author suggestions on the peer review process and outcomes at the journal Functional Ecology. In particular, we examined how gender of the participants (author, editor and reviewer) influences the role of preferred reviewers in the peer review process. Even when not required by the journal, most authors suggest preferred reviewers, but few suggest nonpreferred reviewers. Most author‐preferred reviewers are male, but the proportion of women among author suggestions increased over the 11 years, from a low of 15% in 2004 to a high of 25% in 2014. Male and female authors did not differ in how likely they were to suggest preferred reviewers, but the proportion of women among author suggestions was higher for female authors (~28%, averaged across years) than for male authors (~21%). Women that were suggested as author‐preferred reviewers were more likely to be selected by editors than were men suggested by authors. There was no evidence that editor gender, seniority or length of service as an editor for Functional Ecology affected the probability that they used author suggestions. Of reviewers invited to review, those that were author‐suggested were more likely to respond to the editors' review invitations but were not more likely to agree to review. Most strikingly, author‐preferred reviewers rated papers more positively than did editor‐selected reviewers, and papers reviewed by author‐preferred reviewers were much more likely to be invited for revision than were papers reviewed by editor‐selected reviewers. This difference was not influenced by the gender of the participants in the process. Suggesting preferred reviewers benefits authors because preferred reviewers rate papers significantly more positively than do editor‐selected reviewers, improving the chances that a paper will be published. Journals and journal editors should recognize that preferred reviewers rate manuscripts differently than do editor‐selected reviewers, and be aware that this difference can have large effects on editor decisions. A Lay Summary is available for this article.

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    Functional Ecology
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Functional Ecology
    Article . 2016 . Peer-reviewed
    License: Wiley Online Library User Agreement
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      Functional Ecology
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