Generalized collisional radiative model for light elements: C: Data for the B isonuclear sequence

A first stage collision database is assembled which contains electron-impact excitation, ionization,\r and recombination rate coefficients for B, B + , B 2+ , B 3+ , and B 4+ . The first stage database\r is constructed using the R-matrix with pseudostates, time-dependent close-coupling, and perturbative\r distorted-wave methods. A second stage collision database is then assembled which contains\r generalized collisional-radiative ionization, recombination, and power loss rate coefficients as a\r function of both temperature and density. The second stage database is constructed by solution of\r the collisional-radiative equations in the quasi-static equilibrium approximation using the first\r stage database. Both collision database stages reside in electronic form at the IAEA Labeled Atomic\r Data Interface (ALADDIN) database and the Atomic Data Analysis Structure (ADAS) open database.

Generalized collisional radiative model for light elements. Part B: Data for the Be isonuclear sequence

A first-stage collision database is assembled which contains electron-impact excitation, ionization, and recombination rate coefficients for Be, Be+, Be2+, and Be3+. The first-stage database is constructed using the R-matrix with pseudo-states, time-dependent close-coupling, and perturbative, distorted-wave methods. A second-stage collision database is then assembled which contains generalized collisional-radiative and radiated power loss coefficients. The second-stage database is constructed by solution of collisional-radiative equations in the quasi-static equilibrium approximation using the first-stage database. Both collision database stages reside in electronic form at the ORNL Controlled Fusion Atomic Data Center and in the ADAS database, and are easily accessed over the worldwide internet. © 2007 Elsevier Inc. All rights reserved.

Generalised collisional-radiative model for light elements. A: Data for the Li isonuclear sequence

A first stage collision database is assembled which contains electron-impact effective collision strengths, and ionization and recombination rate coefficients for Li, Li+, and Li2+. The first stage database is constructed using the R-matrix with pseudo-states, time-dependent close-coupling, converged close-coupling, and perturbative distorted-wave methods. A second stage collision database is then assembled which contains generalized collisional-radiative and radiated power loss coefficients. The second stage database is constructed by solution of collisional-radiative equations in the quasi-static equilibrium approximation using the first stage database. Both collision database stages reside in electronic form at the ORNL Controlled Fusion Atomic Data Center and in the ADAS database, and are easily accessed over the worldwide internet. ?? 2006 Elsevier Inc. All rights reserved.

Sequence and expression of complement factor H gene cluster variants and their roles in age-related macular degeneration risk

Purpose: To investigate how potentially functional genetic variants are coinherited on each of four common complement factor H (CFH) and CFH-related gene haplotypes and to measure expression of these genes in eye and liver tissues.

Methods: We sequenced the CFH region in four individuals (one homozygote for each of four common CFH region haplotypes) to identify all genetic variants. We studied associations between the haplotypes and AMD phenotypes in 2157 cases and 1150 controls. We examined RNA-seq profiles in macular and peripheral retina and retinal pigment epithelium/choroid/sclera (RCS) from eight eye donors and three liver samples.

Results: The haplotypic coinheritance of potentially functional variants (including missense variants, novel splice sites, and the CFHR3–CFHR1 deletion) was described for the four common haplotypes. Expression of the short and long CFH transcripts differed markedly between the retina and liver. We found no expression of any of the five CFH-related genes in the retina or RCS, in contrast to the liver, which is the main source of the circulating proteins.

Conclusions: We identified all genetic variants on common CFH region haplotypes and described their coinheritance. Understanding their functional effects will be key to developing and stratifying AMD therapies. The small scale of our expression study prevented us from investigating the relationships between CFH region haplotypes and their expression, and it will take time and collaboration to develop epidemiologic-scale studies. However, the striking difference between systemic and ocular expression of complement regulators shown in this study suggests important implications for the development of intraocular and systemic treatments.

Upper palaeozoic stratigraphy and palynology of OMZ, NW and SW Portugal

Neste trabalho descreve-se e interpreta-se a estratigrafia e palinologia de rochas sedimentares e metassedimentos de idade devónica e carbónica aflorantes ao longo da zona de cisalhamento Porto-Tomar, a Sul na Bacia de Santa Susana e em vários locais onde afloram os Calcários de Odivelas. Existe um registo de sedimentação descontínuo possivelmente associado a esta zona de cisalhamento desde o Devónico Superior até ao Pennsylvaniano. Desde o Devónico Superior até ao Mississippiano esta sedimentação é marinha, de carácter essencialmente turbiditico com uma tendência geral para se tornar mais proximal. A maturação térmica atingida por estas rochas (Unidade de Albergaria-a-Velha) é alta e a unidade é considerada pós-madura em termos de potencial gerador de hidrocarbonetos. O metamorfismo incipiente é acompanhado por intensa deformação. A bacia do Buçaco é inteiramente terrestre e tem a sua idade restrita ao Gjeliano (Pennsylvaniano superior). O controlo da sedimentação pela actividade da zona de cisalhamento Porto-Tomar é evidente. A sua maturação térmica é relativamente baixa (dentro da catagénese) e a deformação menos intensa, contrastando com a Unidade de Albergaria-a-Velha com a qual parece ter uma relação geométrica complexa, de origem tectónica. As relações de campo e dados da maturação térmica permitem inferir um evento térmico e de deformação à escala regional entre o Serpukoviano e o Gjeliano e outro, essencialmente de deformação, entre o Gjeliano e o Carniano (Triássico Superior). A bacia de Santa Susana tem características semelhantes à do Buçaco, visto estar enquadrada também numa zona de cisalhamento importante que neste caso separa a Zona de Ossa-Morena da Zona Sul Portuguesa. A sua idade é kasimoviana, possivelmente também moscoviana (Pennsylvaniano médio). A evolução térmica da bacia e a relação estrutural com as unidades circundantes permite inferir um evento térmico e de deformação regionalmente importante entre o Viseano e o (?)Moscoviano-Kasimoviano. O estudo detalhado de vários locais onde afloram os Calcários de Odivelas permite desenhar uma paleogeografia regional durante o intervalo Emsiano terminal-Givetiano (fim do Devónico Inferior – Devónico Médio) para o sector Oeste da Zona de Ossa-Morena: Actividade vulcânica em regime marinho (e talvez subaéreo), formando edifícios vulcânicos no topo dos quais (e possivelmente também em altos fundos estruturais) se instalaram recifes, tendo a comunidade recifal, em termos de diversidade, persistido durante todo ou grande parte deste intervalo de tempo. O evento Choteč basal é observável num destes locais.

Molecular cloning, full-length sequence and preliminary characterization of a 56-kDa protein induced by human interferons

Among the various proteins which are induced when human cells are are treatened with interferon, a predominant protein of unknown function, with molecular mass 56 kDa, has been observed. With the aim of exploring the molecular basis of the regulation of this protein and of its mRNA, in order to understand its biological functionand its possible contribution to the various antiviral and non-antiviral actions exerted by interferons.

O repertório cerâmico da sala nº 1(Vidigueira), na sequência Neolítico final e Calcolítico do Alentejo Médio

O trabalho aqui proposto tem como objectivo central, a realização de análises ao conjunto dos recipientes cerâmicos pertencentes ao povoado da Sala nº1. Repertório esse, que se baseou no acervo retirado do sítio arqueológico Sala nº1, intervencionado pelo Professor Victor S. Gonçalves (1988, 1989 e 1995). As análises e descrições efectuadas foram sempre norteadas para a tentativa de estabelecer uma sequência de formas que se pudesse verificar quanto à sua normalização e frequência nos contextos presentes ao povoado da Sala nº1. Traduzindo nessa realidade, a diacronia transversal entre os estratos arqueológicos pertencentes ao Neolítico final e os estratos pertencentes ao Calcolítico. Tendo sempre como parâmetros de análise, as metodologias e critérios descritivos dos recipientes cerâmicos, presentes nos trabalhos publicados sobre as realidades cronológicas semelhantes no Sul de Portugal. O próprio conjunto de recipientes cerâmicos aqui analisado foi submetido a essas metodologias, com fim de obter primordialmente as formas e as tipologias a que pertencem. Nesse sentido procurei criar um quadro de referência local e regional, e posteriormente coloca-lo num enquadramento geral do Neolítico final e início do Calcolítico do Alentejo Médio, tentando verificar as similitudes nos quadros tipológicos existentes, como os estabelecidos por Carlos Tavares da Silva e Joaquina Soares. Sendo este um estudo que abrange um tempo cronológico de praticamente 1500 anos, premiei através da amplitude dos contornos que moldaram esta análise, algumas perspectivas possíveis. Quer ao nível das tipologias, quer ao nível das estratégias de ocupação do território, aplicáveis para o espaço e o tempo em análise. Verificando a realidade escassa nos contextos alentejanos (publicados), em que a cultura material se integra numa estratigrafia e cronologias com uma diacronia semelhante à do povoado da Sala nº1. Tentei integrar este povoado num estudo que não sendo comparativo, tivesse essa componente em relação às tipologias e formas cerâmicas identificadas. Procurou-se dar enfase à realidade artefactual das taças carenadas, e à sua possível evolução para formas mais adaptáveis ao uso e consumo quotidiano das comunidades contemporâneas das fases Calcolíticas do povoado.

Identification of a Novel Recycling Sequence in the C-tail of FPR2/ALX Receptor: Association with Cell Protection from Apoptosis

Formyl-peptide receptor type 2 (FPR2; also called ALX because it is the receptor for lipoxin A4) sustains a variety of biological responses relevant to the development and control of inflammation, yet the cellular regulation of this G-protein-coupled receptor remains unexplored. Here we report that, in response to peptide agonist activation, FPR2/ALX undergoes β-arrestin-mediated endocytosis followed by rapid recycling to the plasma membrane. We identify a transplantable recycling sequence that is both necessary and sufficient for efficient receptor recycling. Furthermore, removal of this C-terminal recycling sequence alters the endocytic fate of FPR2/ALX and evokes pro-apoptotic effects in response to agonist activation. This study demonstrates the importance of endocytic recycling in the anti-apoptotic properties of FPR2/ALX and identifies the molecular determinant required for modulation of this process fundamental for the control of inflammation.

IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

A physical packing sequence algorithm for the container loading problem with static mechanical equilibrium conditions

The container loading problem (CLP) is a combinatorial optimization problem for the spatial arrangement of cargo inside containers so as to maximize the usage of space. The algorithms for this problem are of limited practical applicability if real-world constraints are not considered, one of the most important of which is deemed to be stability. This paper addresses static stability, as opposed to dynamic stability, looking at the stability of the cargo during container loading. This paper proposes two algorithms. The first is a static stability algorithm based on static mechanical equilibrium conditions that can be used as a stability evaluation function embedded in CLP algorithms (e.g. constructive heuristics, metaheuristics). The second proposed algorithm is a physical packing sequence algorithm that, given a container loading arrangement, generates the actual sequence by which each box is placed inside the container, considering static stability and loading operation efficiency constraints.

SDAR: a package for plotting and analyzing stratigraphy data in R

Stratigraphic Columns (SC) are the most useful and common ways to represent the eld descriptions (e.g., grain size, thickness of rock packages, and fossil and lithological components) of rock sequences and well logs. In these representations the width of SC vary according to the grain size (i.e., the wider the strata, the coarser the rocks (Miall 1990; Tucker 2011)), and the thickness of each layer is represented at the vertical axis of the diagram. Typically these representations are drawn 'manually' using vector graphic editors (e.g., Adobe Illustrator®, CorelDRAW®, Inskape). Nowadays there are various software which automatically plot SCs, but there are not versatile open-source tools and it is very di cult to both store and analyse stratigraphic information. This document presents Stratigraphic Data Analysis in R (SDAR), an analytical package1 designed for both plotting and facilitate the analysis of Stratigraphic Data in R (R Core Team 2014). SDAR, uses simple stratigraphic data and takes advantage of the exible plotting tools available in R to produce detailed SCs. The main bene ts of SDAR are: (i) used to generate accurate and complete SC plot including multiple features (e.g., sedimentary structures, samples, fossil content, color, structural data, contacts between beds), (ii) developed in a free software environment for statistical computing and graphics, (iii) run on a wide variety of platforms (i.e., UNIX, Windows, and MacOS), (iv) both plotting and analysing functions can be executed directly on R's command-line interface (CLI), consequently this feature enables users to integrate SDAR's functions with several others add-on packages available for R from The Comprehensive R Archive Network (CRAN).

Product quality judgments in a two-sequence cue environment

Previous research demonstrated that the sequence of informational cues and the level of distraction have an impact on the judgment of a product’s quality. This study investigates the influence of the force behind the processing of these cues, working memory (WM). The results indicate that without distraction, consumers with low and high WM capacity (WMC) equally base their product evaluation on the first sequential cue. In the presence of a distractor, however, low WM individuals are no longer able to recall the initial cue, and thus derive their product judgment from the final cue. Moreover, evidence of intercultural differences in the perception of product related cues, and their aptitude for signaling a favorable product quality is provided.

The Teggiolo zone: a key to the Helvetic-Penninic connection (stratigraphy and tectonics in the Val Bavona, Ticino, Central Alps)

The Teggiolo zone is the sedimentary cover of the Antigorio nappe, one of the lowest tectonic units of the Penninic Central Alps. Detailed mapping, stratigraphic and structural analyses, and comparisons with less metamorphic series in several well-studied domains of the Alps, provide a new stratigraphic interpretation. The Teggiolo zone is comprised of several sedimentary cycles, separated by erosive surfaces and large stratigraphic gaps, which cover the time span from Triassic to Eocene. At Mid-Jurassic times it appears as an uplifted, partially emergent block, marking the southern limit of the main Helvetic basin (the Limiting South-Helvetic Rise LSHR). The main mass of the Teggiolo calcschists, whose base truncates the Triassic-Jurassic cycles and can erode the Antigorio basement, consists of fine-grained clastic sediments analogous to the deep-water flyschoid deposits of Late Cretaceous to Eocene age in the North-Penninic (or Valais s.l.) basins. Thus the Antigorio-Teggiolo domain occupies a crucial paleogeographic position, on the boundary between the Helvetic and Penninic realms: from Triassic to Early Cretaceous its affinity is with the Helvetic; at the end of Cretaceous it is incorporated into the North-Penninic basins. An unexpected result is the discovery of the important role played by complex formations of wildflysch type at the top of the Teggiolo zone. They contain blocks of various sizes. According to their nature, three different associations are distinguished that have specific vertical and lateral distributions. These blocks give clues to the existence of territories that have disappeared from the present-day level of observation and impose constraints on the kinematics of early folding and embryonic nappe emplacement. Tectonics produced several phases of superimposed folds and schistosities, more in the metasediments than in the gneissic basement. Older deformations that predate the amplification of the frontal hinge of the nappe generated the dominant schistosity and the km-wide Vanzèla isoclinal fold.

Are there two species of Pygmy Shrews (Sorex)? Revisiting the question using DNA sequence data

Pygmy Shrews in North America have variously been considered to be one species (Sorex hoyi) or two species (S. hoyi and S. thompsoni). Currently, only S. hoyi is recognized. In this study, we examine mitochondrial DNA sequence data for the cytochrome b gene to evaluate the level of differentiation and phylogeographic relationships among eleven samples of Pygmy Shrews from across Canada. Pygmy Shrews from eastern Canada (i.e., Ontario, Quebec, New Brunswick, Nova Scotia, and Prince Edward Island) are distinct from Pygmy Shrews from western Canada (Alberta, Yukon) and Alaska. The average level of sequence divergence between these clades (3.3%) falls within the range of values for other recognized pairs of sister species of shrews. A molecular clock based on third position transversion substitutions suggests that these two lineages diverged between 0.44 and 1.67 million years ago. These molecular phylogenetic data. combined with a reinterpretation of previously published morphological data, are suggestive of separate species status for S. hoyi and S. thompsoni as has been previously argued by others. Further analysis of specimens from geographically intermediate areas (e.g., Manitoba. northern Ontario) is required to determine if there is secondary contact and/or introgression between these two putative species.

Representation of motor habit in a sequence of repetitive reach and grasp movements performed by macaque monkeys: evidence for a contribution of the dorsolateral prefrontal cortex.

In the context of an autologous cell transplantation study, a unilateral biopsy of cortical tissue was surgically performed from the right dorsolateral prefrontal cortex (dlPFC) in two intact adult macaque monkeys (dlPFC lesioned group), together with the implantation of a chronic chamber providing access to the left motor cortex. Three other monkeys were subjected to the same chronic chamber implantation, but without dlPFC biopsy (control group). All monkeys were initially trained to perform sequential manual dexterity tasks, requiring precision grip. The motor performance and the prehension's sequence (temporal order to grasp pellets from different spatial locations) were analysed for each hand. Following the surgery, transient and moderate deficits of manual dexterity per se occurred in both groups, indicating that they were not due to the dlPFC lesion (most likely related to the recording chamber implantation and/or general anaesthesia/medication). In contrast, changes of motor habit were observed for the sequential order of grasping in the two monkeys with dlPFC lesion only. The changes were more prominent in the monkey subjected to the largest lesion, supporting the notion of a specific effect of the dlPFC lesion on the motor habit of the monkeys. These observations are reminiscent of previous studies using conditional tasks with delay that have proposed a specialization of the dlPFC for visuo-spatial working memory, except that this is in a different context of "free-will", non-conditional manual dexterity task, without a component of working memory.