Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis.

BACKGROUND: Whole mitochondrial genomes are quickly becoming markers of choice for the exploration of within-species genealogical and among-species phylogenetic relationships. Most often, 'primer walking' or 'long PCR' strategies plus Sanger sequencing or low-pass whole genome sequencing using Illumina short reads are used for the assembling of mitochondrial chromosomes. In this study, we first confirmed that mitochondrial genomes can be sequenced from long reads using nanopore sequencing data exclusively. Next, we examined the accuracy of the long-reads assembled mitochondrial chromosomes when comparing them to a 'gold' standard reference mitochondrial chromosome assembled using Illumina short-reads sequencing. RESULTS: Using a specialized bioinformatics tool, we first produced a short-reads mitochondrial genome assembly for the silky shark C. falciformis with an average base coverage of 9.8x. The complete mitochondrial genome of C. falciformis was 16,705 bp in length and 934 bp shorter than a previously assembled genome (17,639 bp in length) that used bioinformatics tools not specialized for the assembly of mitochondrial chromosomes. Next, low-pass whole genome sequencing using a MinION ONT pocket-sized platform plus customized de-novo and reference-based workflows assembled and circularized a highly accurate mitochondrial genome in the silky shark Carcharhinus falciformis. Indels at the flanks of homopolymer regions explained most of the dissimilarities observed between the 'gold' standard reference mitochondrial genome (assembled using Illumina short reads) and each of the long-reads mitochondrial genome assemblies. Although not completely accurate, mitophylogenomics and barcoding analyses (using entire mitogenomes and the D-Loop/Control Region, respectively) suggest that long-reads assembled mitochondrial genomes are reliable for identifying a sequenced individual, such as C. falciformis, and separating the same individual from others belonging to closely related congeneric species. CONCLUSIONS: This study confirms that mitochondrial genomes can be sequenced from long-reads nanopore sequencing data exclusively. With further development, nanopore technology can be used to quickly test in situ mislabeling in the shark fin fishing industry and thus, improve surveillance protocols, law enforcement, and the regulation of this fishery. This study will also assist with the transferring of high-throughput sequencing technology to middle- and low-income countries so that international scientists can explore population genomics in sharks using inclusive research strategies. Lastly, we recommend assembling mitochondrial genomes using specialized assemblers instead of other assemblers developed for bacterial and/or nuclear genomes.

[Ethics in health technology assessment. Review]. / Ética y evaluación de tecnologías sanitarias. Revisión.

INTRODUCTION: Bioethics and the health technologies assessment emerged to help make decisions. The objective of the work was to know, with respect to the health technologies assessment, the scientific production on its ethical issues, the degree of incorporation of these in practice, the inclusion of the values in the deliberative processes and the most relevant approaches to ethical analysis. METHODOLOGY: A narrative review was made, based on a systematic search of literature in both natural and hierarchical language, using the terms technology assessment biomedical, ethics and deliberation (and its related terms). All types of papers published between May 2007 and April 2017 in Spanish, French, English or Italian that included both ethical aspects and health technology assessment were included. The PUBMED, OVID-Medline, Scopus databases and secondary searches were explored from the identified works. The information was extracted by a single researcher and managed with Mendeley and EPIINFO 7.2. RESULTS: A total of 141 papers were identified, including 85 after revision by title and summary, with the following characteristics: 29 reviews (5 systematic), 16 frameworks, 18 methodological works and 29 with description of experiences. Multiple frameworks, approaches and methods in ethical analysis were identified. CONCLUSION: The health technologies assessment has an approach excessively mechanistic, and can be improved by incorporating the values of the stakeholder, through deliberative processes. The methods of ethical analysis that seem most suitable are the axiological ones and those developed specifically for the health technologies assessment.

Management of Chronic Hand Eczema.

Management of hand eczema is complex because of the broad range of different pathogeneses, courses, and prognoses. Furthermore, the efficacy of most available treatments is not well established and the more severe forms can have a major impact on the patient's quality of life. Patient education, preventive measures, and the use of emollients are the mainstays in the management of hand eczema. High-potency topical corticosteroids are the treatment of choice, with calcineurin inhibitors used for maintenance. Phototherapy or systemic treatments are indicated in patients who do not respond to topical treatments. Switching from topical treatments should not be delayed to avoid sensitizations, time off work, and a negative impact on quality of life. Alitretinoin is the only oral treatment approved for use in chronic hand eczema.

Digital tomosynthesis in breast cancer: A systematic review.

OBJECTIVE: To estimate and compare the diagnostic validity of tomosynthesis and digital mammography for screening and diagnosing breast cancer. MATERIAL AND METHODS: We systematically searched MedLine, EMBASE, and Web of Science for the terms breast cancer, screening, tomosynthesis, mammography, sensitivity, and specificity in publications in the period comprising June 2010 through February 2013. We included studies on diagnostic tests and systematic reviews. Two reviewers selected and evaluated the articles. We used QUADAS 2 to evaluate the risk of bias and the NICE criteria to determine the level of evidence. We compiled a narrative synthesis. RESULTS: Of the 151 original studies identified, we selected 11 that included a total of 2475 women. The overall quality was low, with a risk of bias and follow-up and limitations regarding the applicability of the results. The level of evidence was not greater than level II. The sensitivity of tomosynthesis ranged from 69% to 100% and the specificity ranged from 54% to 100%. The negative likelihood ratio was good, and this makes tomosynthesis useful as a test to confirm a diagnosis. One-view tomosynthesis was no better than two-view digital mammography, and the evidence for the superiority of two-view tomosynthesis was inconclusive. CONCLUSIONS: The results for the diagnostic validity of tomosynthesis in the diagnosis of breast cancer were inconclusive and there were no results for its use in screening.

Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy.

The family Mugilidae comprises mainly coastal marine species that are widely distributed in all tropical, subtropical and temperate seas. Mugilid species are generally considered to be ecologically important and they are a major food resource for human populations in certain parts of the world. The taxonomy and systematics of the Mugilidae are still much debated and based primarily on morphological characters. In this study, we provide the first comprehensive molecular systematic account of the Mugilidae using phylogenetic analyses of nucleotide sequence variation at three mitochondrial loci (16S rRNA, cytochrome oxidase I, and cytochrome b) for 257 individuals from 55 currently recognized species. The study covers all 20 mugilid genera currently recognized as being valid. The family comprises seven major lineages that radiated early on from the ancestor to all current forms. All genera that were represented by two species or more, except Cestraeus, turned out to be paraphyletic or polyphyletic. Thus, the present phylogenetic results generally disagree with the current taxonomy at the genus level and imply that the anatomical characters used for the systematics of the Mugilidae may be poorly informative phylogenetically. The present results should provide a sound basis for a taxonomic revision of the mugilid genera. A proportion of the species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) appear to consist of cryptic species, thus warranting further taxonomic and genetic work at the infra-generic level.

Global phylogeography of the dolphinfish (Coryphaena hippurus): the influence of large effective population size and recent dispersal on the divergence of a marine pelagic cosmopolitan species.

Pelagic fish that are distributed circumtropically are characterised by a low population structure level as a result of a high capacity for dispersion and large population sizes. Nevertheless, historical and contemporary processes, including past demographic and/or range expansions, secondary contact, dispersal, gene flow, and the achievement of large effective population sizes, may play a part in the detection of divergence signals, especially in the case of tropical pelagic species, whose distribution range depends strongly on the sea surface temperature. The connectivity and historical demography of Atlantic, Indian, Pacific and Mediterranean populations of dolphinfish (Coryphaena hippurus) was studied using partial sequences of the mitochondrial DNA NADH dehydrogenase subunit 1 (ND1). AMOVA analyses revealed significant inter-oceanic divergence with three phylogroups located in the Indo-Pacific, Eastern Atlantic, and Mediterranean Sea, the last one being the most divergent. However, it was not possible to clearly observe any genetic differentiation between the Indo-Pacific and Atlantic populations, as has been reported for most tropical pelagic species of tuna and billfishes. This supports the assumption of recent dispersal among basins facilitated by the actual continuous distribution of dolphinfish populations. Moreover, the lack of a divergence signal for populations separated by the Panamanian Isthmus reveals that genetic drift does not exert a strong influence on tropical pelagic species with large effective population sizes.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009-30 September 2009.

This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.

Local adaptation and pronounced genetic differentiation in an extremophile fish, Poecilia mexicana, inhabiting a Mexican cave with toxic hydrogen sulphide.

We investigated genetic differentiation and migration patterns in a small livebearing fish, Poecilia mexicana, inhabiting a sulfidic Mexican limestone cave (Cueva del Azufre). We examined fish from three different cave chambers, the sulfidic surface creek draining the cave (El Azufre) and a nearby surface creek without the toxic hydrogen sulphide (Arroyo Cristal). Using microsatellite analysis of 10 unlinked loci, we found pronounced genetic differentiation among the three major habitats: Arroyo Cristal, El Azufre and the cave. Genetic differentiation was also found within the cave between different pools. An estimation of first-generation migrants suggests that (i) migration is unidirectional, out of the cave, and (ii) migration among different cave chambers occurs to some extent. We investigated if the pattern of genetic differentiation is also reflected in a morphological trait, eye size. Relatively large eyes were found in surface habitats, small eyes in the anterior cave chambers, and the smallest eyes were detected in the innermost cave chamber (XIII). This pattern shows some congruence with a previously proposed morphocline in eye size. However, our data do not support the proposed mechanism for this morphocline, namely that it would be maintained by migration from both directions into the middle cave chambers. This would have led to an increased variance in eye size in the middle cave chambers, which we did not find. Restricted gene flow between the cave and the surface can be explained by local adaptations to extreme environmental conditions, namely H2S and absence of light. Within the cave system, habitat properties are patchy, and genetic differentiation between cave chambers despite migration could indicate local adaptation at an even smaller scale.

Micro- and macroevolutionary decoupling of cichlid jaws: a test of Liem's key innovation hypothesis.

The extent to which elements of functional systems can change independently (modularity) likely influences the diversification of lineages. Major innovations in organismal design, like the pharyngeal jaw in cichlid fishes, may be key to a group's success when they relax constraints on diversification by increasing phenotypic modularity. In cichlid fishes, pharyngeal jaw modifications that enhanced the ability to breakdown prey may have freed their oral jaws from serving their ancestral dual role as a site of both prey capture and prey processing. This functional decoupling that allowed the oral jaws to become devoted solely to prey capture has been hypothesized to have permitted the two sets of cichlid jaws to evolve independently. We tested the hypothesis that oral and pharyngeal jaw mechanics are evolutionarily decoupled both within and among Neotropical Heroine cichlids. In the trophically polymorphic species Herichthys minckleyi, molariforms that exhibit enlarged molarlike pharyngeal jaw teeth were found to have approximately 400% greater lower jaw mass compared to H. minckleyi with the alternative papilliform pharyngeal morphology. However, oral jaw gape, lower jaw velocity ratios, anterior jaw linkage mechanics, and jaw protrusion did not differ between the morphotypes. In 40 other Heroine species, there was a weak correlation between oral jaw mechanics and pharyngeal jaw mass when phylogenetic history was ignored. Yet, after expansion of the cytochrome b phylogeny for Heroines, change in oral jaw mechanics was found to be independent of evolutionary change in pharyngeal jaw mass based on independent contrasts. Evolutionary decoupling of oral and pharyngeal jaw mechanics has likely played a critical role in the unparalleled trophic diversification of cichlid fishes.

[Idiopathic thrombocytopenic purpura as an extraintestinal manifestation of Crohn's disease]. / Púrpura trombocitopénica idiopática como manifestación extraintestinal de la enfermedad de Crohn.

Idiopathic thrombocytopenic purpura is an infrequent extraintestinal manifestation of inflammatory bowel disease. It is particularly rare in association with Crohn's disease. In these cases it presents certain peculiarities with respect to its normal clinical features, occurring more frequently when Crohn's disease is mainly colonic and usually appearing after the diagnosis of Crohn's disease has been made. Moreover, it usually complicates the clinical course of both diseases. We present a case of idiopathic thrombocytopenic purpura in a 14-year-old girl in whom the two diseases first presented simultaneously. The clinical course was poor and both diseases were refractory to habitual treatment.

Convergence among cave catfishes: long-branch attraction and a Bayesian relative rates test.

Convergence has long been of interest to evolutionary biologists. Cave organisms appear to be ideal candidates for studying convergence in morphological, physiological, and developmental traits. Here we report apparent convergence in two cave-catfishes that were described on morphological grounds as congeners: Prietella phreatophila and Prietella lundbergi. We collected mitochondrial DNA sequence data from 10 species of catfishes, representing five of the seven genera in Ictaluridae, as well as seven species from a broad range of siluriform outgroups. Analysis of the sequence data under parsimony supports a monophyletic Prietella. However, both maximum-likelihood and Bayesian analyses support polyphyly of the genus, with P. lundbergi sister to Ictalurus and P. phreatophila sister to Ameiurus. The topological difference between parsimony and the other methods appears to result from long-branch attraction between the Prietella species. Similarly, the sequence data do not support several other relationships within Ictaluridae supported by morphology. We develop a new Bayesian method for examining variation in molecular rates of evolution across a phylogeny.

Consecuencias psicopatológicas de las catástrofes y desastres: el síndrome del estrés postraumático / Psychopathological consequences in catastrophes and disasters: The post traumatic stress syndrome

Vivimos en una sociedad de riesgo creciente en la que los desastres y catástrofes van a ser cada vez más frecuentes y masivos, requiriendo una intervención interdisciplinaria especialmente psicológica y psiquiátrica, dadas las consecuencias psicopatológicas en las víctimas de estos eventos, en sus familias e, incluso, en los profesionales y voluntarios que intervengan. En este marco, tras analizar genéricamente los grandes cuadros sindrómicos que pueden generar las catástrofes y desastres, presentamos una revisión en profundidad del Síndrome del Estrés Postraumático, conceptualizándolo y describiendo su psicopatología, incidencia y factores de vulnerabilidad etiológicos exponiendo, asimismo, su evolución, pronóstico y tratamiento, apelando a la intervención psicológica precoz en estos casos, todo ello con un tono que no debe ser totalmente de tragedia, puesto que la aplicación a estos casos del nuevo concepto de RESILENCIA, con sus componentes, nos trae una luz de esperanza" (AU)

[Warning systems: a priority in epidemiological surveillance]. / Sistemas de alerta: una prioridad en vigilancia epidemiológica.

One of the functions of public health is to reduce the impact of emergency situations; hence the need to establish an early warning and response system. Community reactions to emerging and reemerging diseases, exposure to environmental risks, and potential terrorist acts are the factors that have that have mainly contributed to the instauration of warning systems based on mathematical models. Information is obtained from diverse sources (for example, laboratory data, sentinel physicians, or visits to particular websites). Once the data are gathered, and the situation provoking the alert is detected, control measures to reduce risks and minimize damage are taken at the earliest.

Intervención y prevención del estrés laboral / Intervention and prevention in labour stress

Hemos analizado distintas estrategias y técnicas que se pueden poner en práctica para la prevención e intervención ante el estrés laboral encada uno de los tres niveles considerados (organizacional, individual y de interfaz individuo-organización) y para cada uno de los objetivos planteados (control de los estresores, procesos de apreciación de las demandas y de los recursos para satisfacerlas y estrategias de afrontamiento del estrés una vez que éste ha aparecido). Nosotros recomendamos las intervenciones a nivel organizacional orientadas al control de los estresores. Las revisiones mencionadas ponen de manifiesto que esas intervenciones son las que menos se llevan a cabo, aunque por razones ajenas a su eficacia en la solución de este problema (AU)

Influencia de las creencias religiosas en las actitudes en el personal sanitario (P.S.) ante la muerte / Influence of religious beliefs on the attitudes of health professionals (H.P.) in the face of death

Fundamento: Las creencias religiosas son una variable psicosocial de gran importancia para una proporción considerable de la población, entre la que se encuentran los Profesionales Sanitarios y, por consiguiente, influye en las actitudes que estos tienen hacia los demás. Por ello, es deseable investigar dichas influencias, sobre todo en situaciones críticas de la vida, entre las que se incluye la muerte por su trascendencia a la hora de la atención al enfermo terminal. Objetivos y Metodología: Analizar las influencias de las creencias religiosas en las actitudes ante la muerte en el P.S. estableciendo su prevalencia y correlacionándolas con variables psicosociales y personalísticas, con otros aspectos religiosos, así como con la experiencia con moribundos; mediante técnicas psicométricas y un inventario de creencia religiosa, siguiendo un diseño observacional-transversal, sobre una muestra representativa de la población del P.S. de un Hospital Universitario. Resultados y Conclusiones: La mayoría del P.S. que componen la muestra resultan creyentes religiosos (con un nivel medio de práctica "moderado"). Las mujeres se muestran más religiosas que los hombres y los jóvenes resultan menos religiosos que las personas mayores. De los dos grupos extremos bien diferenciados que aparecen (creyentes practicantes y no creyentes, por un lado y creyentes no practicantes, tibios en su fe, agnósticos, etc., por otro) los que menos ansiedad ante la muerte manifiestan son los creyentes practicantes y no creyentes. El P.S., en general, presenta baja ansiedad (Estado y Rasgo) y baja ansiedad ante la muerte (AU)