Strategies for Optimize Off-Lattice Aggregate Simulations

We review some computer algorithms for the simulation of off-lattice clusters grown from a seed, with emphasis on the diffusion-limited aggregation, ballistic aggregation and Eden models. Only those methods which can be immediately extended to distinct off-lattice aggregation processes are discussed. The computer efficiencies of the distinct algorithms are compared.Comment: 6 pages, 7 figures and 3 tables; published at Brazilian Journal of Physics 38, march, 2008 (http://www.sbfisica.org.br/bjp/files/v38_81.pdf

Cities: continuity, transformation, and emergence

Cities can be regarded as the quintessential example of complexity. Insofar as we can define a hidden hand determining their morphology, this is based on the glue that stitches together the actions of individuals and organizations who build the city from the ground-up, so-to-speak. When general systems theory entered the lexicon of science in the mid- 20th century, cities were regarded as being excellent examples of systems with interactions between basic elements that demonstrated the slogan of the field: the ‘whole is greater than the sum of the parts’. Since then, as complexity theory has evolved to embrace systems theory and as temporal dynamics has come onto the agenda, cities once again have been used to illustrate basic themes: global organization from local action, emergent morphology from simple spatial decision, temporal order at global levels from volatile, seemingly random change at the level of individual decision-making, evolution and progress through coevolution, competition, and endless variety. Here we will sketch these ideas with respect to cities illustrating particularly three key ideas which involve the tension between continuously changing systems, qualitative transformations, and radical change based on emergent properties of the whole. Our analysis has many implications for a new theory of urban planning which is built from the bottom up, rather than from the top down which is the traditional way in which such interventions are currently carried out in the name of making better cities. Contemporary problems such as ethnic segregation, urban sprawl, traffic congestion, urban decline, and regeneration are all informed by the perspective on complexity theory that we bring to bear here

Amplitude analysis of four-body decays using a massively-parallel fitting framework

The GooFit Framework is designed to perform maximum-likelihood fits for arbitrary functions on various parallel back ends, for example a GPU. We present an extension to GooFit which adds the functionality to perform time-dependent amplitude analyses of pseudoscalar mesons decaying into four pseudoscalar final states. Benchmarks of this functionality show a significant performance increase when utilizing a GPU compared to a CPU. Furthermore, this extension is employed to study the sensitivity on the $D^0 - \bar{D}^0$ mixing parameters $x$ and $y$ in a time-dependent amplitude analysis of the decay $D^0 \rightarrow K^+\pi^-\pi^+\pi^-$. Studying a sample of 50 000 events and setting the central values to the world average of $x = (0.49 \pm0.15) \%$ and $y = (0.61 \pm0.08) \%$, the statistical sensitivities of $x$ and $y$ are determined to be $\sigma(x) = 0.019 \%$ and $\sigma(y) = 0.019 \%$.Comment: Proceedings of the 22nd International Conference on Computing in High Energy and Nuclear Physics, CHEP 201

Considerations for optimizing photometric classification of supernovae from the Rubin Observatory

The Vera C. Rubin Observatory will increase the number of observed supernovae (SNe) by an order of magnitude; however, it is impossible to spectroscopically confirm the class for all SNe discovered. Thus, photometric classification is crucial, but its accuracy depends on the not-yet-finalized observing strategy of Rubin Observatory's Legacy Survey of Space and Time (LSST). We quantitatively analyze the impact of the LSST observing strategy on SNe classification using simulated multiband light curves from the Photometric LSST Astronomical Time-Series Classification Challenge (PLAsTiCC). First, we augment the simulated training set to be representative of the photometric redshift distribution per SNe class, the cadence of observations, and the flux uncertainty distribution of the test set. Then we build a classifier using the photometric transient classification library snmachine, based on wavelet features obtained from Gaussian process fits, yielding a similar performance to the winning PLAsTiCC entry. We study the classification performance for SNe with different properties within a single simulated observing strategy. We find that season length is important, with light curves of 150 days yielding the highest performance. Cadence also has an important impact on SNe classification; events with median inter-night gap 10 days) in light-curve observations do not impact performance if sufficient observations are available on either side, due to the effectiveness of the Gaussian process interpolation. This analysis is the first exploration of the impact of observing strategy on photometric SN classification with LSST

The familial hypercholesterolaemia phenotype: Monogenic familial hypercholesterolaemia, polygenic hypercholesterolaemia and other causes

Familial Hypercholesterolaemia (FH) is a monogenic disorder characterised by high LDL-C concentrations and increased cardiovascular risk. However, in clinically defined FH cohorts worldwide, an FH-causing variant is only found in 40-50% of the cases. The aim of this work was to characterise the genetic cause of the FH phenotype in Portuguese clinical FH patients. Methods and Results Between 1999 and 2017, 731 index patients (311 children and 420 adults) who met the Simon Broome diagnostic criteria had been referred to our laboratory. LDLR, APOB, PCSK9, APOE, LIPA, LDLRAP1, ABCG5/8 genes were analysed by PCR amplification and Sanger sequencing. The 6-SNP LDL-C genetic risk score (GRS) for polygenic hypercholesterolaemia was validated in the Portuguese population and cases with a GRS over the 25th percentile were considered to have a high likelihood of polygenic hypercholesterolaemia. An FH-causing mutation was found in 39% of patients (94% in LDLR, 5% APOB and 1% PCSK9), while at least 29% have polygenic hypercholesterolaemia and 1% have other lipid disorders. A genetic cause for the FH phenotype was found in 503 patients (69%). All known causes of the FH phenotype should be investigated in FH cohorts to ensure accurate diagnosis and appropriate management. This article is protected by copyright. All rights reserved

Exploring the physiological role of transthyretin in glucose metabolism in the liver

Transthyretin (TTR), a 55 kDa evolutionarily conserved protein, presents altered levels in several conditions, including malnutrition, inflammation, diabetes, and Alzheimer’s Disease. It has been shown that TTR is involved in several functions, such as insulin release from pancreatic ß-cells, recovery of blood glucose and glucagon levels of the islets of Langerhans, food intake, and body weight. Here, the role of TTR in hepatic glucose metabolism was explored by studying the levels of glucose in mice with different TTR genetic backgrounds, namely with two copies of the TTR gene, TTR+/+; with only one copy, TTR+/-; and without TTR, TTR-/-. Results showed that TTR haploinsufficiency (TTR+/-) leads to higher glucose in both plasma and in primary hepatocyte culture media and lower expression of the influx glucose transporters, GLUT1, GLUT3, and GLUT4. Further, we showed that TTR haploinsufficiency decreases pyruvate kinase M type (PKM) levels in mice livers, by qRT-PCR, but it does not affect the hepatic production of the studied metabolites, as determined by 1H NMR. Finally, we demonstrated that TTR increases mitochondrial density in HepG2 cells and that TTR insufficiency triggers a higher degree of oxidative phosphorylation in the liver. Altogether, these results indicate that TTR contributes to the homeostasis of glucose by regulating the levels of glucose transporters and PKM enzyme and by protecting against mitochondrial oxidative stress.This work was supported by Norte-01-0145-FEDER-000008-Porto Neurosciences and Neurologic Disease Research Initiative at I3S, and Pest-OE/SAU/UI0215/2014 at UMIB, supported by Norte Portugal Regional Operational Programme (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, by COMPETE 2020—Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020, through the European Regional Development Fund (FEDER), by Portuguese funds through FCT—Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Ensino Superior in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274), and by a grant from Fundação Millennium bcp. Alemi M was a recipient of fellowship by Norte-01-0145-FEDER-000008. Oliveira  was a recipient of fellowship by Norte-01-0145-FEDER-000008. Cardoso I, Oliveira PF, and Alves MG work under the Investigator FCT Program, which is financed by national funds through the Foundation for Science and Technology and co-financed by the European Social Fund (ESF) through the Human Potential Operational Programme (HPOP), type 4.2—Promotion of Scientific Employment

<i>Vibrio communis</i> sp. nov., isolated from the marine animals <i>Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis</i> and <i>Litopenaeus vannamei</i>

Eight Vibrio isolates originating from the marine corals Mussismilia hispida and Phyllogorgia dilatata and the zoanthids Palythoa caribaeorum and Palythoa variabilis in Brazil and the Pacific white shrimp (Litopenaeus vannamei) in Ecuador were studied by means of a polyphasic approach. The novel isolates formed a tight monophyletic group in the genus Vibrio and were closely related to species of the Vibrio harveyi group, to which they showed more than 99?% 16S rRNA gene sequence similarity. Analysis based on concatenated sequences of the following seven genes, 16S rRNA, gyrB, recA, rpoA, topA, pyrH and mreB (5633 bp in length), showed clear separation between the isolates and species of the V. harveyi group. Amplified fragment length polymorphism (AFLP) analysis, performed previously, revealed that a representative isolate of this group, LMG 20370, was clearly separate from known Vibrio species (it belonged to the so-called AFLP cluster A31). DNA–DNA hybridization (DDH) experiments with representative isolates and type strains of the V. harveyi species group revealed high DDH between the novel isolates (more than 74?%) and less than 70?% DDH towards type strains of related Vibrio species, proving the novel species status of the isolates. Phenotypically, the novel species belongs to the arginine dihydrolase (A)-negative, lysine decarboxylase (L)-positive and ornithine decarboxylase (O)-positive (A-/L+/O+) cluster reported previously. Most species of the V. harveyi group (i.e. Vibrio rotiferianus, V. harveyi, V. parahaemolyticus and V. alginolyticus) also belong to this A-/L+/O+ cluster. However, several phenotypic features can be used for the identification of the novel species. In contrast to its closest phylogenetic neighbours, the novel species exhibits esterase (C4) and N-acetyl-ß-glucosaminidase activities, but it does not produce acetoin, does not use citrate, a-ketoglutaric acid or propionic acid and does not ferment melibiose. The novel species can also be differentiated on the basis of the presence of the fatty acids C17?:?0, C17?:?1?8c, iso-C17?:?0 and iso-C13?:?0 and the absence of the fatty acid C18?:?0. The name Vibrio communis sp. nov. is proposed for this taxon. Strain R-40496T (=LMG 25430T =CAIM 1816T) is the type strain

Chitosan-based scaffolds for tissue regeneration: preparation and microstructure characterization

Scaffolds are porous three-dimensional supports, designed to mimic the extracellular environment and remain temporarily integrated into the host tissue while stimulating, at the molecular level, specific cellular responses to each type of body tissues. The major goal of the research work entertained herein was to study the microstructure of scaffolds made from chitosan (Ch), blends of chitosan and sodium alginate (Ch/NaAlg), blends of chitosan, sodium alginate and calcium chloride (Ch/NaAlg/CaCl2) and blends of chitosan, sodium alginate and hydroxyapatite (Ch/NaAlg/HA). Scaffolds possessing ideal physicochemical properties facilitate cell proliferation and greatly increase the rate of recovery of a damaged organ tissue. Using CT three-dimensional images of the scaffolds, it was observed that all scaffolds had a porosity in the range 64%-92%, a radius of maximum pore occurrence in the range 95m-260m and a permeability in the range 1×10-10-18×10-10 m2. From the results obtained, the scaffolds based on Ch, Ch/NaAlg and Ch/NaAlg/CaCl2 would be most appropriate both for the growth of osteoid and for bone tissue regeneration, while the scaffold made with a blend of Ch/NaAlg/HA, by possessing larger pores size, might be used as a support for fibrovascular tissue.Project funding by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, São Paulo, Brazil) (FAPESP Refs. No. 2012/21219-5, 2012/15651-4, 2013/03181-6, 2013/19300-4, and 2014/21122-0), is hereby gratefully acknowledged. This work received support from CNPq, National Council for Scientific and Technological Development – Brazil, in the form of Research Productivity (PQ) fellowships granted to Victor M. Balcão and Marco V. Chaud