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41.
Rupert A. Collins Giulia Trauzzi Katherine M. Maltby Thomas I. Gibson Frances C. Ratcliffe Jane Hallam Sophie Rainbird James Maclaine Peter A. Henderson David W. Sims Stefano Mariani Martin J. Genner 《Journal of fish biology》2021,99(4):1446-1454
The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib . 相似文献
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Tetralogy of Fallot is the most common cyanotic congenital heart disease, with a good outcome after total surgical correction. In spite of a low perioperative mortality and a good quality of life, late sudden death remains a significant clinical problem, mainly related to episodes of sustained ventricular tachycardia and ventricular fibrillation. Fibro-fatty substitution around infundibular resection, intraventricular septal scar, and patchy myocardial fibrosis, may provide anatomical substrates of abnormal depolarization and repolarization causing reentrant ventricular arrhythmias. Several non-invasive indices based on classical examination such as ECG, signal-averaging ECG, and echocardiography have been proposed to identify patients at high risk of sudden death, with hopeful results. In the last years other more sophisticated invasive and non-invasive tools, such as heart rate variability, electroanatomic mapping and cardiac magnetic resonance added a relevant contribution to risk stratification. Even if each method per se is affected by some limitations, a comprehensive multifactorial clinical and investigative examination can provide an accurate risk evaluation for every patient. 相似文献
44.
Luciano Pamplona de Góes Cavalcanti Lia Alves Martins Mota Gustavo Porto Lustosa Mayara Carvalho Fortes Davi Alves Martins Mota Ant?nio Afonso Bezerra Lima Ivo Castelo Branco Coelho Maria Paula Gomes Mour?o 《Memórias do Instituto Oswaldo Cruz》2014,109(1):93-98
In 2009, the World Health Organization (WHO) issued a new guideline that stratifies
dengue-affected patients into severe (SD) and non-severe dengue (NSD) (with or
without warning signs). To evaluate the new recommendations, we completed a
retrospective cross-sectional study of the dengue haemorrhagic fever (DHF) cases
reported during an outbreak in 2011 in northeastern Brazil. We investigated 84
suspected DHF patients, including 45 (53.6%) males and 39 (46.4%) females. The ages
of the patients ranged from five-83 years and the median age was 29. According to the
DHF/dengue shock syndrome classification, 53 (63.1%) patients were classified as
having dengue fever and 31 (36.9%) as having DHF. According to the 2009 WHO
classification, 32 (38.1%) patients were grouped as having NSD [4 (4.8%) without
warning signs and 28 (33.3%) with warning signs] and 52 (61.9%) as having SD. A
better performance of the revised classification in the detection of severe clinical
manifestations allows for an improved detection of patients with SD and may reduce
deaths. The revised classification will not only facilitate effective screening and
patient management, but will also enable the collection of standardised surveillance
data for future epidemiological and clinical studies. 相似文献
45.
Luciano Elias Da Cruz Perez Ana Lucia Machado Sebastião Vicente Canevarolo Carlos Eduardo Vergani Eunice Teresinha Giampaolo Ana Cláudia Pavarina 《Gerodontology》2010,27(1):62-69
doi:10.1111/j.1741‐2358.2009.00292.x Effect of reline material and denture base surface treatment on the impact strength of a denture base acrylic resin Objective: In this study, the effect of relining and surface treatment on the impact strength (IS) of a heat‐polymerising denture base acrylic resin (Lucitone 550‐L) was evaluated. Materials and methods: Rectangular bars of L were made (60 × 6 × 2 mm) and relined (2 mm) with the relining resins Ufi Gel Hard (UH) and Tokuso Rebase Fast (TR). Specimens relined with L and intact L, TR and UH specimens were also made (60 × 6 × 4 mm), for comparison. Before relining, the L surface was left untreated or wetted with methyl methacrylate monomer and/or the bonding agents (BA) supplied by manufacturers of the reline resins. V‐notches were machined at the midpoint of the length of all specimens. The notches were made either across the width (Nw) or across the thickness of the specimens (Nth). The Charpy impact test was performed using a 0.5‐J pendulum, which had been specially designed and constructed. Data were analysed separately for each notch position using one‐way analysis of variance and Tukey honestly significant difference post‐hoc test (p = 0.05). Results: The IS of L was similar to that of L/L. For the Nw notch, treating the denture base L with TR BA and relining with TR reline material produced the highest IS. Conclusion: The IS of specimens made from heat polymerising acrylic resin Lucitone 550 was increased after relining using the hard chairside reline resin TR with its proprietary BA. 相似文献
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47.
Mariana Morando Luciano J. Avila Cristian H.F. Perez Monty A. Hawkins Jack W. Sites 《Molecular phylogenetics and evolution》2013,66(3):694-714
The lizard genus Phymaturus is widely distributed in Argentina and along the eastern edge of Chile between 25° and 45° south. We sampled 27 of the 38 currently recognized species plus 22 candidate species using two mitochondrial genes (cytb and 12S), four protein coding nuclear genes and seven anonymous nuclear loci, and present the first comprehensive molecular phylogenetic hypothesis for the clade. We recovered two large clades (the palluma or northern group and patagonicus or southern group) previously recognized on the basis of morphological and mitochondrial sequence evidence, and compared results obtained from concatenated-gene analyses with results of a coalescent-based species-tree approach (BEST). With both methods we identified four main clades within the palluma group (mallimaccii, roigorum, verdugo, and vociferator) and five main clades within the patagonicus group (calcogaster, indistinctus, payuniae, somuncurensis, and spurcus). We found several instances of non-monophyly with cytb and cases of incongruence between mitochondrial vs nuclear data for which we discuss alternative hypotheses. Although with lower support values, combined BEST results are more congruent with concatenated nuclear data than with combined concatenated analyses, suggesting that BEST is less influenced by demographic processes than combined concatenated analyses. We discuss the taxonomic, biogeographic and conservation implications of these results and how the future integration of phylogeographic and morphological approaches will allow the further testing of demographic and biogeographic hypotheses. 相似文献
48.
Emanuele Lombardo Cristian Sabellico Jan Hájek Veronika Staňková Tomá? Filipsky Valentina Balducci Paolo De Vito Stefano Leone Eugenia I. Bavavea Ilaria Proietti Silvestri Giuliana Righi Paolo Luly Luciano Saso Paolo Bovicelli Jens Z. Pedersen Sandra Incerpi 《PloS one》2013,8(4)
Natural polyphenol compounds are often good antioxidants, but they also cause damage to cells through more or less specific interactions with proteins. To distinguish antioxidant activity from cytotoxic effects we have tested four structurally related hydroxyflavones (baicalein, mosloflavone, negletein, and 5,6-dihydroxyflavone) at very low and physiologically relevant levels, using two different cell lines, L-6 myoblasts and THP-1 monocytes. Measurements using intracellular fluorescent probes and electron paramagnetic resonance spectroscopy in combination with cytotoxicity assays showed strong antioxidant activities for baicalein and 5,6-dihydroxyflavone at picomolar concentrations, while 10 nM partially protected monocytes against the strong oxidative stress induced by 200 µM cumene hydroperoxide. Wide range dose-dependence curves were introduced to characterize and distinguish the mechanism and targets of different flavone antioxidants, and identify cytotoxic effects which only became detectable at micromolar concentrations. Analysis of these dose-dependence curves made it possible to exclude a protein-mediated antioxidant response, as well as a mechanism based on the simple stoichiometric scavenging of radicals. The results demonstrate that these flavones do not act on the same radicals as the flavonol quercetin. Considering the normal concentrations of all the endogenous antioxidants in cells, the addition of picomolar or nanomolar levels of these flavones should not be expected to produce any detectable increase in the total cellular antioxidant capacity. The significant intracellular antioxidant activity observed with 1 pM baicalein means that it must be scavenging radicals that for some reason are not eliminated by the endogenous antioxidants. The strong antioxidant effects found suggest these flavones, as well as quercetin and similar polyphenolic antioxidants, at physiologically relevant concentrations act as redox mediators to enable endogenous antioxidants to reach and scavenge different pools of otherwise inaccessible radicals. 相似文献
49.
Giovannetti M Sbrana C Strani P Agnolucci M Rinaudo V Avio L 《Applied and environmental microbiology》2003,69(1):616-624
We detected, for the first time, the occurrence of vegetative incompatibility between different isolates of the arbuscular mycorrhizal fungal species Glomus mosseae. Vegetative compatibility tests performed on germlings belonging to the same isolate showed that six geographically different isolates were capable of self-anastomosing, and that the percentage of hyphal contacts leading to fusions ranged from 60 to 85%. Successful anastomoses were characterized by complete fusion of hyphal walls, protoplasm continuity and occurrence of nuclei in the middle of hyphal bridges. No anastomoses could be detected between hyphae belonging to different isolates, which intersected without any reaction in 49 to 68% of contacts. Microscopic examinations detected hyphal incompatibility responses in diverse pairings, consisting of protoplasm retraction from the tips and septum formation in the approaching hyphae, even before physical contact with neighboring hyphae. Interestingly, many hyphal tips showed precontact tropism, suggesting that specific recognition signals may be involved during this stage. The intraspecific genetic diversity of G. mosseae revealed by vegetative compatibility tests was confirmed by total protein profiles and internal transcribed spacer-restriction fragment length polymorphism profiles, which evidenced a higher level of molecular diversity between the two European isolates IMA1 and BEG25 than between IMA1 and the two American isolates. Since arbuscular mycorrhizal fungi lack a tractable genetic system, vegetative compatibility tests may represent an easy assay for the detection of genetically different mycelia and an additional powerful tool for investigating the population structure and genetics of these obligate symbionts. 相似文献
50.
Kagawa HK Yaoi T Brocchieri L McMillan RA Alton T Trent JD 《Molecular microbiology》2003,49(1):143-156
The hyperthermoacidophilic archaeon Sulfolobus shibatae contains group II chaperonins, known as rosettasomes, which are two nine-membered rings composed of three different 60 kDa subunits (TF55 alpha, beta and gamma). We sequenced the gene for the gamma subunit and studied the temperature-dependent changes in alpha, beta and gamma expression, their association into rosettasomes and their phylogenetic relationships. Alpha and beta gene expression was increased by heat shock (30 min, 86 degrees C) and decreased by cold shock (30 min, 60 degrees C). Gamma expression was undetectable at heat shock temperatures and low at normal temperatures (75-79 degrees C), but induced by cold shock. Polyacrylamide gel electrophoresis indicated that in vitro alpha and beta subunits form homo-oligomeric rosettasomes, and mixtures of alpha, beta and gamma form hetero-oligomeric rosettasomes. Transmission electron microscopy revealed that beta homo-oligomeric rosettasomes and all hetero-oligomeric rosettasomes associate into filaments. In vivo rosettasomes were hetero-oligomeric with an average subunit ratio of 1alpha:1beta:0.1gamma in cultures grown at 75 degrees C, a ratio of 1alpha:3beta:1gamma in cultures grown at 60 degrees C and a ratio of 2alpha:3beta:0gamma after 86 degrees C heat shock. Using differential scanning calorimetry, we determined denaturation temperatures (Tm) for alpha, beta and gamma subunits of 95.7 degrees C, 96.7 degrees C and 80.5 degrees C, respectively, and observed that rosettasomes containing gamma were relatively less stable than those with alpha and/or beta only. We propose that, in vivo, the rosettasome structure is determined by the relative abundance of subunits and not by a fixed geometry. Furthermore, phylogenetic analyses indicate that archaeal chaperonin subunits underwent multiple duplication events within species (paralogy). The independent evolution of these paralogues raises the possibility that chaperonins have functionally diversified between species. 相似文献