Molecular phylogenetic analysis of a known and a new hydrothermal vent octopod:Their relationships with the genus Benthoctopus (Cephalopoda: Octopodidae)

The resolution of evolutionary relationships among deep-sea incirrate octopuses has been hindered by the paucity of individuals available for morphological studies and by the lack of tissue samples preserved using fixatives compatible with simple DNA extraction techniques. Evolutionary relationships from 11 species of deep-sea incirrate octopuses were investigated using 2392 base pairs (bp) of DNA from four mitochondrial genes (12S rDNA, 16S rDNA, cytochrome c oxidase subunit III, and cytochrome b) and the nuclear gene, rhodopsin. Morphological examination of these species was also undertaken. Molecular analyses distinguish a species of octopus from hydrothermal vents at Manus Basin from the vent octopodid Vulcanoctopus hydrothermalis known from vents on the East Pacific Rise. Both are herein considered members of the clade currently assigned the name Benthoctopus, although taxonomic implications preclude formally naming Vulcanoctopus as a junior synonym. Morphological investigations led to the conclusion that Benthoctopus macrophallus is a junior synonym of Benthoctopus yaquinae. An amended diagnosis of Benthoctopus is provided with additional information on male reproductive characteristics. Copyright © 2009 · Magnolia Press.

Probing confinement resonances by photoionizing Xe inside a C60+ molecular cage

Double photoionization accompanied by loss of n C atoms (n=0, 2, 4, 6) was investigated by merging beams of Xe@C60+ ions and synchrotron radiation and measuring the yields of product ions. The giant 4d dipole resonance of the caged Xe atom has a prominent signature in the cross section for these product channels, which together account for 6.2 ± 1.4 of the total Xe 4d oscillator strength of 10. Compared to that for a free Xe atom, the oscillator strength is redistributed in photon energy due to multipath interference of outgoing Xe 4d photoelectron waves that may be transmitted or reflected by the spherical C60+ molecular cage, yielding so-called confinement resonances. The data are compared with an earlier measurement and with theoretical predictions for this single-molecule photoelectron interferometer system. Relativistic R-matrix calculations for the Xe atom in a spherical potential shell representing the fullerene cage show the sensitivity of the interference pattern to the molecular geometry. © 2013 American Physical Society.

M Dwarf Flare Continuum Variations on One-second Timescales: Calibrating and Modeling of ULTRACAM Flare Color Indices

We present a large data set of high-cadence dMe flare light curves obtained with custom continuum filters on the triple-beam, high-speed camera system ULTRACAM. The measurements provide constraints for models of the near-ultraviolet (NUV) and optical continuum spectral evolution on timescales of ≈1 s. We provide a robust interpretation of the flare emission in the ULTRACAM filters using simultaneously obtained low-resolution spectra during two moderate-sized flares in the dM4.5e star YZ CMi. By avoiding the spectral complexity within the broadband Johnson filters, the ULTRACAM filters are shown to characterize bona fide continuum emission in the NUV, blue, and red wavelength regimes. The NUV/blue flux ratio in flares is equivalent to a Balmer jump ratio, and the blue/red flux ratio provides an estimate for the color temperature of the optical continuum emission. We present a new “color-color” relationship for these continuum flux ratios at the peaks of the flares. Using the RADYN and RH codes, we interpret the ULTRACAM filter emission using the dominant emission processes from a radiative-hydrodynamic flare model with a high nonthermal electron beam flux, which explains a hot, T ≈ 104 K, color temperature at blue-to-red optical wavelengths and a small Balmer jump ratio as observed in moderate-sized and large flares alike. We also discuss the high time resolution, high signal-to-noise continuum color variations observed in YZ CMi during a giant flare, which increased the NUV flux from this star by over a factor of 100. Based on observations obtained with the Apache Point Observatory 3.5 m telescope, which is owned and operated by the Astrophysical Research Consortium, based on observations made with the William Herschel Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofsica de Canarias, and observations, and based on observations made with the ESO Telescopes at the La Silla Paranal Observatory under programme ID 085.D-0501(A).

Novel critical phenomena in optimization driven processes on networks

The work presented in this Ph.D thesis was developed in the context of complex network theory, from a statistical physics standpoint. We examine two distinct problems in this research field, taking a special interest in their respective critical properties. In both cases, the emergence of criticality is driven by a local optimization dynamics. Firstly, a recently introduced class of percolation problems that attracted a significant amount of attention from the scientific community, and was quickly followed up by an abundance of other works. Percolation transitions were believed to be continuous, until, recently, an 'explosive' percolation problem was reported to undergo a discontinuous transition, in [93]. The system's evolution is driven by a metropolis-like algorithm, apparently producing a discontinuous jump on the giant component's size at the percolation threshold. This finding was subsequently supported by number of other experimental studies [96, 97, 98, 99, 100, 101]. However, in [1] we have proved that the explosive percolation transition is actually continuous. The discontinuity which was observed in the evolution of the giant component's relative size is explained by the unusual smallness of the corresponding critical exponent, combined with the finiteness of the systems considered in experiments. Therefore, the size of the jump vanishes as the system's size goes to infinity. Additionally, we provide the complete theoretical description of the critical properties for a generalized version of the explosive percolation model [2], as well as a method [3] for a precise calculation of percolation's critical properties from numerical data (useful when exact results are not available). Secondly, we study a network flow optimization model, where the dynamics consists of consecutive mergings and splittings of currents flowing in the network. The current conservation constraint does not impose any particular criterion for the split of current among channels outgoing nodes, allowing us to introduce an asymmetrical rule, observed in several real systems. We solved analytically the dynamic equations describing this model in the high and low current regimes. The solutions found are compared with numerical results, for the two regimes, showing an excellent agreement. Surprisingly, in the low current regime, this model exhibits some features usually associated with continuous phase transitions.

Assessment of reserve effect in a marine protected area: the case study of the Professor Luiz Saldanha Marine Park (Portugal)

Dissertação de mest., Biologia Marinha (Ecologia e Conservação Marinhas), Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2011

Estrutura de comunidades de peixes, amostradas por SVSI - sistema de vídeo subaquático iscado, na Costa Sul de Portugal

Desenvolveu-se um Sistema de Vídeo Submerso Iscado (SVSI) viavelmente adaptado para caracterizar comunidades de peixes do substrato rochoso subtidal (forma não-destrutiva e não-invasiva), entre 5 e 50 metros, na costa sul de Portugal (Algarve). Entre Junho e Julho de 2013, amostraram-se 15 pontos na zona Greta (Praia de Faro), divididos em 3 Amostragens (A1, A2, A3) com isco sardinha, mexilhão e sem isco. Captaram-se foto-sequências de intervalo 1 segundo durante 60 minutos e as imagens resultantes processadas qualitativa e quantitativamente para obtenção de resultados. Registaram-se 32 espécies no total. Os tempos de entrada do 1º indivíduo de cada espécie permitiram aferir 30 minutos máximos de filmagem SVSIs para resultados viáveis, enquanto abundâncias por número de indivíduos comprovaram o isco sardinha como mais eficaz e com maior poder atrativo (do que mexilhão). As espécies Coris julis, Diplodus vulgaris, Diplodus cervinus, Diplodus sargus e Serranus cabrilla foram as mais interventivas no estudo, cujo intervalo de tempo entre contagens se adequou em 30 segundos. O estudo de índices de abundâncias e Nmax mostraram não existirem diferenças entre as comunidades ictiológicas de cada tipo de iscagem, contudo existem diferenças dentro da comunidade geral em si do substrato rochoso. A análise alimentar pelo menor tempo de 1ª alimentação indicou Coris julis, Diplodus vulgaris, Serranus cabrilla e Octopus vulgaris como as espécies mais rápidas a morder os iscos. No geral, 69% das espécies preferiram isco sardinha. Comportamentos como a passagem esporádica, territorialidade e interações com a câmara foram as ações dominantes na análise comportamental. Esta técnica e respetiva metodologia foram o primeiro estudo do género nesta região, que de forma simples, se mostrou uma boa ferramenta metodológica para estudos marinhos sobre comunidades, suas preferências alimentares, abundâncias e tempos de reação, aconselhando-se o seu desenvolvimento tecnológico e melhoramento metodológico analítico dos resultados no futuro.

The effect of conservation measures on the spatial and temporal variation of rocky fish assemblages in the Arrábida Marine Park

Marine protected areas (MPAs) have been widely proposed for conservation purposes and as a tool for fisheries management. The Arrábida Marine Park is the first MPA in continental Portugal having a management plan, fully implemented since 2009. The main objective of this study was to evaluate the effect of protection measures on rocky reef fish assemblages and target invertebrates through before-after and control-effect (no-take vs. fished areas) underwater visual surveys and analysis of landings trends. Second, we used surveys before, during and after implementation of the management plan to understand fishers‟ preferences for fishing grounds and adaptation to the new rules, and evaluated the reserve effect through analysis of both ecological responses and fishing effort density. Third, we identified the main oceanographic drivers influencing the structure of reef fish assemblages and predicted the community structure for the last 50 years, in light of climatic change. Overall results suggest positive responses in biomass but not yet in numbers of some commercial species, with no effects on non-target species. The reserve effect is reinforced by the increase in landings of commercial species, despite increased fishing effort density in some areas, especially with octopus traps. Fishing grounds are mainly chosen based on the distribution of target species and associated habitats, but distance to port, weather conditions and safety also influence fishers‟ choices. Moreover, different fisheries respond differently to the protection measures, and within each fishery, individual fishers show distinct strategies, with some operating in a broader area whereas others keep preferred territories. Our results also show that wind stress and temperature are the main oceanographic drivers for rocky reef fish assemblages, with tropicalization of assemblages and polewards movements of species over the last 50 years consistent with temperature trends. We believe this study provides significant lessons for marine conservation and management of coastal systems.

Molecular determinants of the cellular internalization of crotamine-derived peptides

Tese de doutoramento, Ciências Biomédicas (Bioquímica Médica), Universidade de Lisboa, Faculdade de Medicina, 2014

Comportamento à fadiga de juntas soldadas de aços tipo 460M com fios fluxados

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecânica

Critical reappraisal of Late Mesozoic-Cenozoic Central and North Atlantic, Caribbean and Mediterranean evolution

(l) The Pacific basin (Pacific area) may be regarded as moving eastwards like a double zip fastener relative to the continents and their respective plates (Pangaea area): opening in the East and closing in the West. This movement is tracked by a continuous mountain belt, the collision ages of which increase westwards. (2) The relative movements between the Pacific area and the Pangaea area in the W-E/E-W direction are generated by tidal forces (principle of hypocycloid gearing), whereby the lower mantle and the Pacific basin or area (Pacific crust = roof of the lower mantle?) rotate somewhat faster eastwards around the Earth's spin axis relative to the upper mantle/crust system with the continents and their respective plates (Pangaea area) (differential rotation). (3) These relative West to East/East to West displacements produce a perpetually existing sequence of distinct styles of opening and closing ocean basins, exemplified by the present East to West arrangement of ocean basins around the globe (Oceanic or Wilson Cycle: Rift/Red Sea style; Atlantic style; Mediterranean/Caribbean style as eastwards propagating tongue of the Pacific basin; Pacific style; Collision/Himalayas style). This sequence of ocean styles, of which the Pacific ocean is a part, moves eastwards with the lower mantle relative to the continents and the upper-mantle/crust of the Pangaea area. (4) Similarly, the collisional mountain belt extending westwards from the equator to the West of the Pacific and representing a chronological sequence of collision zones (sequential collisions) in the wake of the passing of the Pacific basin double zip fastener, may also be described as recording the history of oceans and their continental margins in the form of successive Wilson Cycles. (5) Every 200 to 250 m.y. the Pacific basin double zip fastener, the sequence of ocean styles of the Wilson Cycle and the eastwards growing collisional mountain belt in their wake complete one lap around the Earth. Two East drift lappings of 400 to 500 m.y. produce a two-lap collisional mountain belt spiral around a supercontinent in one hemisphere (North or South Pangaea). The Earth's history is subdivided into alternating North Pangaea growth/South Pangaea breakup eras and South Pangaea growth/North Pangaea breakup eras. Older North and South Pangaeas and their collisional mountain belt spirals may be reconstructed by rotating back the continents and orogenic fragments of a broken spiral (e.g. South Pangaea, Gondwana) to their previous Pangaea growth era orientations. In the resulting collisional mountain belt spiral, pieced together from orogenic segments and fragments, the collision ages have to increase successively towards the West. (6) With its current western margin orientated in a West-East direction North America must have collided during the Late Cretaceous Laramide orogeny with the northern margin of South America (Caribbean Andes) at the equator to the West of the Late Mesozoic Pacific. During post-Laramide times it must have rotated clockwise into its present orientation. The eastern margin of North America has never been attached to the western margin of North Africa but only to the western margin of Europe. (7) Due to migration eastwards of the sequence of ocean styles of the Wilson Cycle, relative to a distinct plate tectonic setting of an ocean, a continent or continental margin, a future or later evolutionary style at the Earth's surface is always depicted in a setting simultaneously developed further to the West and a past or earlier style in a setting simultaneously occurring further to the East. In consequence, ahigh probability exists that up to the Early Tertiary, Greenland (the ArabiaofSouth America?) occupied a plate tectonic setting which is comparable to the current setting of Arabia (the Greenland of Africa?). The Late Cretaceous/Early Tertiary Eureka collision zone (Eureka orogeny) at the northern margin of the Greenland Plate and on some of the Canadian Arctic Islands is comparable with the Middle to Late Tertiary Taurus-Bitlis-Zagros collision zone at the northern margin of the Arabian Plate.

Patologia e parâmetros oculares em doentes com infeção pelo VIH - Avaliação antes e após Terapêutica Antirretrovirica combinada

INTRODUÇÃO: As complicações oculares do VIH/SIDA são comuns e podem afetar qualquer tecido do olho. Na era da terapêutica antirretroviral combinada (TARc), houve uma redução drástica nas infeções oportunistas oculares. O impacto da terapêutica em outras alterações na visão de doentes VIH+ sem retinopatia infecciosa, como alterações na sensibilidade ao contraste (SC), visão cromática (VC) e nos campos visuais, sinal de uma disfunção microvascular retiniana, não está totalmente esclarecido. OBJETIVOS: Determinar os efeitos da TARc em parâmetros e patologia oculares de doentes VIH+ que vão iniciar ou reiniciar TARc MÉTODOS: Foi realizado um estudo observacional, longitudinal, transversal e prospetivo com a inclusão de 31 doentes VIH+ sem infeções oculares oportunistas, que iam iniciar ou reiniciar TARc. Após serem recolhidos alguns dados da história clínica, foi feita uma avaliação oftalmológica completa que incluiu: biomicroscopia do segmento anterior, acuidade visual com a escala de ETDRS, pressão intra-ocular com a tonometria de aplanação de Goldmann, SC com o CSV-1000E, VC com o Farnsworth- Munsell 100 e perimetria com o programa 24-2 do Octopus® 900. Após midríase farmacológica foram realizadas fotografias do segmento posterior, avaliação da espessura da camada de fibras nervosas (CFN) e macular com o OCT Stratus™ e avaliação da densidade do cristalino e do ângulo irido-corneano pelo Pentacam®. Cerca de 9 meses após o início da TARc, foi realizada uma segunda observação oftalmológica usando os mesmos métodos. Procuraram-se associações estatísticas entre vários parâmetros da infeção pelo VIH e a avaliação oftalmológica. RESULTADOS: Na primeira observação, encontraram-se 15 olhos (24%) com complicações anteriores do VIH, 10 olhos (16%) com retinopatia do VIH, 15 (24%) com alterações vasculares retinianas e 6 (10%) com defeitos na CFN; nenhuma destas alterações estava relacionada com o nível de linfócitos CD4+ ou carga viral. A SC, VC e perimetria estavam alteradas em 45%, 68% e 76% dos olhos, respetivamente. Encontrou-se uma correlação positiva entre valores mais elevados de linfócitos T CD4+ e melhor SC, sobretudo nos 6 e 12 ciclos por grau e no valor soma da SC (p<0,01). A avaliação pelo OCT revelou que os doentes com CFN fina tinham tendencialmente infeção mais antiga, níveis mais baixos de linfócitos CD4+ (p<0,05) e pior SC (p<0,05). Foi possível realizar segunda observação em 16 doentes (52%). Após 9 meses de TARc as alterações encontradas na primeira avaliação mantiveram-se, com exceção da retinopatia do VIH que regrediu. As alterações na SC, VC, perimetria e na espessura da CFN mantiveram-se; a densidade do cristalino não se alterou com a reconstituição imunitária após TARc. CONCLUSÕES: Foram detetadas alterações na avaliação oftalmológica de doentes VIH+ sem retinopatia infecciosa e que parecem estar relacionadas com a existência de microvasculopatia e disfunção neurorretiniana associada. A reconstituição imunitária com a TARc não parece levar a uma melhoria desta disfunção apesar da recuperação da imunidade para valores normais.

Quality control and conduct of genome-wide association meta-analyses.

Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association meta-analyses (GWAMAs) of statistics aggregated across multiple genome-wide association studies. This protocol provides guidelines for (i) organizational aspects of GWAMAs, and for (ii) QC at the study file level, the meta-level across studies and the meta-analysis output level. Real-world examples highlight issues experienced and solutions developed by the GIANT Consortium that has conducted meta-analyses including data from 125 studies comprising more than 330,000 individuals. We provide a general protocol for conducting GWAMAs and carrying out QC to minimize errors and to guarantee maximum use of the data. We also include details for the use of a powerful and flexible software package called EasyQC. Precise timings will be greatly influenced by consortium size. For consortia of comparable size to the GIANT Consortium, this protocol takes a minimum of about 10 months to complete.

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.

Circulating levels of adiponectin, a hormone produced predominantly by adipocytes, are highly heritable and are inversely associated with type 2 diabetes mellitus (T2D) and other metabolic traits. We conducted a meta-analysis of genome-wide association studies in 39,883 individuals of European ancestry to identify genes associated with metabolic disease. We identified 8 novel loci associated with adiponectin levels and confirmed 2 previously reported loci (P = 4.5×10(-8)-1.2×10(-43)). Using a novel method to combine data across ethnicities (N = 4,232 African Americans, N = 1,776 Asians, and N = 29,347 Europeans), we identified two additional novel loci. Expression analyses of 436 human adipocyte samples revealed that mRNA levels of 18 genes at candidate regions were associated with adiponectin concentrations after accounting for multiple testing (p<3×10(-4)). We next developed a multi-SNP genotypic risk score to test the association of adiponectin decreasing risk alleles on metabolic traits and diseases using consortia-level meta-analytic data. This risk score was associated with increased risk of T2D (p = 4.3×10(-3), n = 22,044), increased triglycerides (p = 2.6×10(-14), n = 93,440), increased waist-to-hip ratio (p = 1.8×10(-5), n = 77,167), increased glucose two hours post oral glucose tolerance testing (p = 4.4×10(-3), n = 15,234), increased fasting insulin (p = 0.015, n = 48,238), but with lower in HDL-cholesterol concentrations (p = 4.5×10(-13), n = 96,748) and decreased BMI (p = 1.4×10(-4), n = 121,335). These findings identify novel genetic determinants of adiponectin levels, which, taken together, influence risk of T2D and markers of insulin resistance.

Bahía de Coishco, Chimbote, Perú: una visión integral de sus recursos vivos y su ambiente. 2001 - 2005

Se ha recorrido la Bahía de Coishco a fin de conocer las actividades artesanal e industrial que se desarrollan en esta área, y se han revisado los informes sobre las actividades y proyectos que ejecuta el Laboratorio Costero de Chimbote como parte del Plan Anual de Trabajo Institucional. Se presenta una descripción de la morfología, topografía y sedimentología de la Bahía de Coishco, así como de las características físicas, químicas y biológicas de sus masas de agua. Se hace una descripción de las fuentes y niveles de contaminación, producto del vertimiento de aguas de diferentes tipo de uso: industrial, pesquero, doméstico; de escorrentía y producto de actividades de las embarcaciones que operan en esta bahía. Se mencionan las especies que sustentan la pesca artesanal e industrial, los instrumentos y áreas de pesca, los bancos naturales de invertebrados marinos, los tonelajes de extracción a nivel artesanal y de procesamiento a nivel industrial por cada una de las fábricas que operan en esta bahía. La bahía de Coishco, con un área aproximada de 11.655 km2 es una bahía abierta, rodeada por las islas Santa y Moñaque; en sus profundidades predominan las isóbatas desde 12 a 16 m y en el centro de la bahía existe alta concentración de materia orgánica. Las masas de agua son generalmente Aguas Costeras Frias, de 15 a 20 ºC; la salinidad cerca de la línea litoral es menor a 35 ups, en cambio en el sur de la balúa las salinidades son en promedio del orden de 35,1ups. El vertimiento de aguas de uso industrial pesquero y doméstico influye en el contenido de oxígeno tanto superficial como de fondo, habiéndose detectado situaciones de anoxia; igualmente se afectan los nutrientes, tal es así que los niveles de fosfatos se incrementan durante la época de intensa actividad pesquera y disminuyen durante la época de veda. Se ha identificado 60 especies de organismos planctónicos, destacando las diatomeas de afloramiento Chaetoceros decipiens, Thalassiosira rotula y Skeletonema costatum. Los peces constituyen la principal fuente de pesca artesanal (82% de las capturas), destacando: "lorna" Sciaena deliciosa, "pejerrey" Odonthestes regia regia, "machete" Etmidium maculatum, "cachema" Cynoscion analis, "cabinza" Isacia conceptionís. La anchoveta es la principal materia prima para la elaboración de harina y aceite de pescado. Entre los invertebrados, destacaron "caracol" Stramoníta chocolata, "almeja" Semele spp., "concha de abanico" Argopecten purpu­ratus, "pulpo" Octopus mimus.

El calamar gigante en el mar peruano. Crucero B/P Hakurei Maru Nº 8. Primavera 2010 y Verano 2011

El crucero se desarrolló en dos etapas, la primera en primavera 2010, de 4° a 11°25’S y la segunda en verano 2011, de 10°10’ a 17°23’S, entre 50 a 200 mn de la costa. La captura del recurso en la primera etapa fue 35.079,6 kg (25.669,1 kg de producción) y en la segunda 165.955,7 kg (123.229,5 kg de producción). La captura por unidad de esfuerzo por día de trabajo fluctuó de 2,9 a 4.292,6 kg/hora; 0,68 a 948,4 kg/línea; 0,07 a 99,8 kg/ línea*hora y 0,0017 a 2,4957 kg/pot*hora. La longitud del manto varió de 17 a 119 cm. Se registró hembras en estadio desovante III (51,5%), madurante II (21,6%); y machos en estadio evacuación III (85,1%) y virginales I (9,7%). Los grupos tróficos más importantes fueron: cefalópodos (% IRI= 66,4), crustáceos (% IRI= 23,7), peces (% IRI= 9,9). Las hembras presentaron: L∞ =111,233 cm LM, K=0,016, t0= 235 y los machos L∞ =99,718 cm LM, K=0,167 y t0=228,4; esta especie tiene una longevidad próxima o poco mayor a un año.