Parallelizing remote sensing image geometric correction

Remote sensing spatial, spectral, and temporal resolutions of images, acquired over a reasonably sized image extent, result in imagery that can be processed to represent land cover over large areas with an amount of spatial detail that is very attractive for monitoring, management, and scienti c activities. With Moore's Law alive and well, more and more parallelism is introduced into all computing platforms, at all levels of integration and programming to achieve higher performance and energy e ciency. Being the geometric calibration process one of the most time consuming processes when using remote sensing images, the aim of this work is to accelerate this process by taking advantage of new computing architectures and technologies, specially focusing in exploiting computation over shared memory multi-threading hardware. A parallel implementation of the most time consuming process in the remote sensing geometric correction has been implemented using OpenMP directives. This work compares the performance of the original serial binary versus the parallelized implementation, using several multi-threaded modern CPU architectures, discussing about the approach to nd the optimum hardware for a cost-e ective execution.

L'application de la spectroscopie Raman en criminalistique pour l'analyse du colorant des fibres textiles en acrylique, coton et laine

RESUME La méthode de la spectroscopie Raman est une technique d'analyse chimique basée sur l'exploitation du phénomène de diffusion de la lumière (light scattering). Ce phénomène fut observé pour la première fois en 1928 par Raman et Krishnan. Ces observations permirent à Raman d'obtenir le Prix Nobel en physique en 1930. L'application de la spectroscopie Raman a été entreprise pour l'analyse du colorant de fibres textiles en acrylique, en coton et en laine de couleurs bleue, rouge et noire. Nous avons ainsi pu confirmer que la technique est adaptée pour l'analyse in situ de traces de taille microscopique. De plus, elle peut être qualifiée de rapide, non destructive et ne nécessite aucune préparation particulière des échantillons. Cependant, le phénomène de la fluorescence s'est révélé être l'inconvénient le plus important. Lors de l'analyse des fibres, différentes conditions analytiques ont été testées et il est apparu qu'elles dépendaient surtout du laser choisi. Son potentiel pour la détection et l'identification des colorants imprégnés dans les fibres a été confirmé dans cette étude. Une banque de données spectrale comprenant soixante colorants de référence a été réalisée dans le but d'identifier le colorant principal imprégné dans les fibres collectées. De plus, l'analyse de différents blocs de couleur, caractérisés par des échantillons d'origine inconnue demandés à diverses personnes, a permis de diviser ces derniers en plusieurs groupes et d'évaluer la rareté des configurations des spectres Raman obtenus. La capacité de la technique Raman à différencier ces échantillons a été évaluée et comparée à celle des méthodes conventionnelles pour l'analyse des fibres textiles, à savoir la micro spectrophotométrie UV-Vis (MSP) et la chromatographie sur couche mince (CCM). La technique Raman s'est révélée être moins discriminatoire que la MSP pour tous les blocs de couleurs considérés. C'est pourquoi dans le cadre d'une séquence analytique nous recommandons l'utilisation du Raman après celle de la méthode d'analyse de la couleur, à partir d'un nombre de sources lasers le plus élevé possible. Finalement, la possibilité de disposer d'instruments équipés avec plusieurs longueurs d'onde d'excitation, outre leur pouvoir de réduire la fluorescence, permet l'exploitation d'un plus grand nombre d'échantillons. ABSTRACT Raman spectroscopy allows for the measurement of the inelastic scattering of light due to the vibrational modes of a molecule when irradiated by an intense monochromatic source such as a laser. Such a phenomenon was observed for the first time by Raman and Krishnan in 1928. For this observation, Raman was awarded with the Nobel Prize in Physics in 1930. The application of Raman spectroscopy has been undertaken for the dye analysis of textile fibers. Blue, black and red acrylics, cottons and wools were examined. The Raman technique presents advantages such as non-destructive nature, fast analysis time, and the possibility of performing microscopic in situ analyses. However, the problem of fluorescence was often encountered. Several aspects were investigated according to the best analytical conditions for every type/color fiber combination. The potential of the technique for the detection and identification of dyes was confirmed. A spectral database of 60 reference dyes was built to detect the main dyes used for the coloration of fiber samples. Particular attention was placed on the discriminating power of the technique. Based on the results from the Raman analysis for the different blocs of color submitted to analyses, it was possible to obtain different classes of fibers according to the general shape of spectra. The ability of Raman spectroscopy to differentiate samples was compared to the one of the conventional techniques used for the analysis of textile fibers, like UV-Vis Microspectrophotometry (UV-Vis MSP) and thin layer chromatography (TLC). The Raman technique resulted to be less discriminative than MSP for every bloc of color considered in this study. Thus, it is recommended to use Raman spectroscopy after MSP and light microscopy to be considered for an analytical sequence. It was shown that using several laser wavelengths allowed for the reduction of fluorescence and for the exploitation of a higher number of samples.

Higher education and national identity : Polish student activism in Russia 1832-1863

Doctoral dissertation, University of Helsinki

FAM161A, associated with retinitis pigmentosa, is a component of the cilia-basal body complex and interacts with proteins involved in ciliopathies.

Retinitis pigmentosa (RP) is a retinal degenerative disease characterized by the progressive loss of photoreceptors. We have previously demonstrated that RP can be caused by recessive mutations in the human FAM161A gene, encoding a protein with unknown function that contains a conserved region shared only with a distant paralog, FAM161B. In this study, we show that FAM161A localizes at the base of the photoreceptor connecting cilium in human, mouse and rat. Furthermore, it is also present at the ciliary basal body in ciliated mammalian cells, both in native conditions and upon the expression of recombinant tagged proteins. Yeast two-hybrid analysis of binary interactions between FAM161A and an array of ciliary and ciliopathy-associated proteins reveals direct interaction with lebercilin, CEP290, OFD1 and SDCCAG8, all involved in hereditary retinal degeneration. These interactions are mediated by the C-terminal moiety of FAM161A, as demonstrated by pull-down experiments in cultured cell lines and in bovine retinal extracts. As other ciliary proteins, FAM161A can also interact with the microtubules and organize itself into microtubule-dependent intracellular networks. Moreover, small interfering RNA-mediated depletion of FAM161A transcripts in cultured cells causes the reduction in assembled primary cilia. Taken together, these data indicate that FAM161A-associated RP can be considered as a novel retinal ciliopathy and that its molecular pathogenesis may be related to other ciliopathies.

Study of the variability in chemical composition of bark layers of Quercus Suber L. from different production areas

Cork is the bark of the cork oak tree (Quercus suber L), a renewable and biodegradable raw bioresource concentrated mainly in the Mediterranean region. Development of its potential uses as a biosorbent will require the investigation of its chemical composition; such information can be of help to understand its interactions with organic pollutants. The present study investigates the summative chemical composition of three bark layers (back, cork, and belly) of five Spanish cork samples and one cork sample from Portugal. Suberin was the main component in all the samples (21.1 to 53.1%), followed by lignin (14.8 to 31%), holocellulose (2.3 to 33.6%), extractives (7.3 to 20.4%), and ash (0.4 to 3.3%). The Kruskal-Wallis test was used to determine whether the variations in chemical composition with respect to the production area and bark layers were significant. The results indicate that, with respect to the bark layer, significant differences were found only for suberin and holocellulose contents: they were higher in the belly and cork than in the back. Based on the results presented, cork is a material with a lot of potential because of its heterogeneity in chemical composition

A Variant of Higher-Order Anti-Unification

We present a rule-based Huet’s style anti-unification algorithm for simply-typed lambda-terms in ɳ long β normal form, which computes a least general higher-order pattern generalization. For a pair of arbitrary terms of the same type, such a generalization always exists and is unique modulo α equivalence and variable renaming. The algorithm computes it in cubic time within linear space. It has been implemented and the code is freely available

Trophic dynamics in the northern Humboldt Current system: insights from stable isotopes and stomach content analyses

The northern Humboldt Current system (NHCS) off Peru is one of the most productive world marine regions. It represents less than 0.1% of the world ocean surface but presently sustains about 10% of the world fish catch, with the Peruvian anchovy or anchoveta Engraulis ringens as emblematic fish resource. Compared with other eastern boundary upwelling systems, the higher fish productivity of the NHCS cannot be explained by a corresponding higher primary productivity. On another hand, the NHCS is the region where El Niño, and climate variability in general, is most notable. Also, surface oxygenated waters overlie an intense and extremely shallow Oxygen Minimum Zone (OMZ). In this context, the main objective of this study is to better understand the trophic flows in the NHCS using both stomach content and stable isotope analyses. The study focuses on a variety of organisms from low trophic levels such as zooplankton to top predators (seabirds and fur seals). The approach combines both long-term and specific studies on emblematic species such as anchoveta, and sardine Sardinops sagax and a more inclusive analysis considering the 'global' food web in the recent years (2008 – 2012) using stable isotope analysis. Revisiting anchovy and sardine we show that whereas phytoplankton largely dominated anchoveta and sardine diets in terms of numerical abundance, the carbon content of prey items indicated that zooplankton was by far the most important dietary component. Indeed for anchovy euphausiids contributed 67.5% of dietary carbon, followed by copepods (26.3%). Selecting the largest prey, the euphausiids, provide an energetic advantage for anchoveta in its ecosystem where oxygen depletion imposes strong metabolic constrain to pelagic fish. Sardine feed on smaller zooplankton than do anchoveta, with sardine diet consisting of smaller copepods and fewer euphausiids than anchoveta diet. Hence, trophic competition between sardine and anchovy in the northern Humboldt Current system is minimized by their partitioning of the zooplankton food resource based on prey size, as has been reported in other systems. These results suggest an ecological role for pelagic fish that challenges previous understanding of their position in the foodweb (zooplanktophagous instead of phytophagous), the functioning and the trophic models of the NHCS. Finally to obtain a more comprehensive vision of the relative trophic position of NHCS main components we used stable isotope analyses. For that purpose we analyzed the δ13C and δ15N stable isotope values of thirteen taxonomic categories collected off Peru from 2008 - 2011, i.e., zooplankton, fish, squids and air-breathing top predators. The δ15N isotope signature was strongly impacted by the species, the body length and the latitude. Along the Peruvian coast, the OMZ get more intense and shallow south of ~7.5ºS impacting the baseline nitrogen stable isotopes. Employing a linear mixed-effects modelling approach taking into account the latitudinal and body length effects, we provide a new vision of the relative trophic position of key ecosystem components. Also we confirm stomach content-based results on anchoveta Engraulis ringens and highlight the potential remarkable importance of an often neglected ecosystem component, the squat lobster Pleuroncodes monodon. Indeed, our results support the hypothesis according to which this species forage to some extent on fish eggs and larvae and can thus predate on the first life stages of exploited species. However, the δ13C values of these two species suggest that anchoveta and squat lobster do not exactly share the same habitat. This would potentially reduce some direct competition and/or predation.

André spectral sequences for Baues-Wirsching cohomology of categories

We construct spectral sequences in the framework of Baues-Wirsching cohomology and homology for functors between small categories and analyze particular cases including Grothendieck fibrations. We also give applications to more classical cohomology and homology theories including Hochschild-Mitchell cohomology and those studied before by Watts, Roos, Quillen and others

Higher CNS penetration-effectiveness of long-term combination antiretroviral therapy is associated with better HIV-1 viral suppression in cerebrospinal fluid.

OBJECTIVES: To determine HIV-1 RNA in cerebrospinal fluid (CSF) of successfully treated patients and to evaluate if combination antiretroviral treatments with higher central nervous system penetration-effectiveness (CPE) achieve better CSF viral suppression. METHODS: Viral loads (VLs) and drug concentrations of lopinavir, atazanavir, and efavirenz were measured in plasma and CSF. The CPE was calculated using 2 different methods. RESULTS: The authors analyzed 87 CSF samples of 60 patients. In 4 CSF samples, HIV-1 RNA was detectable with 43-82 copies per milliliter. Median CPE in patients with detectable CSF VL was significantly lower compared with individuals with undetectable VL: CPE of 1.0 (range, 1.0-1.5) versus 2.3 (range, 1.0-3.5) using the method of 2008 (P = 0.011) and CPE of 6 (range, 6-8) versus 8 (range, 5-12) using the method of 2010 (P = 0.022). The extrapolated CSF trough levels for atazanavir (n = 12) were clearly above the 50% inhibitory concentration (IC50) in only 25% of samples; both patients on atazanavir/ritonavir with detectable CSF HIV-1 RNA had trough levels in the range of the presumed IC50. The extrapolated CSF trough level for lopinavir (n = 42) and efavirenz (n = 18) were above the IC50 in 98% and 78%, respectively, of samples, including the patients with detectable CSF HIV-1 RNA. CONCLUSIONS: This study suggests that treatment regimens with high intracerebral efficacy reflected by a high CPE score are essential to achieve CSF HIV-1 RNA suppression. The CPE score including all drug components was a better predictor for treatment failure in the CSF than the sole concentrations of protease inhibitor or nonnucleoside reverse transcriptase inhibitor in plasma or CSF.

Contribution of major cardiovascular risk factors to familial premature coronary artery disease : the GENECARD project

Résumé Objectifs: Cette étude relève la prévalence des principaux facteurs de risque cardiovasculaire dans les coronaropathies précoces (P-CAD) familiales, survenant chez au moins deux frères et/ou soeurs d'une même fratrie. Méthodes: Nous avons recruté 213 survivants atteints de P-CAD, issus de 103 fratries, diagnostiqués avant l'âge de 50 ans chez les hommes et 55 ans chez les femmes. La présence ou non d'hypertension, d'hypercholestérolémie, d'obésité et de tabagisme a été documentée au moment de l'événement chez 163 de ces patients (145 hommes et 18 femmes). Chaque patient a été comparé à deux individus de même âge et sexe, chez qui un diagnostic de P-CAD «sporadique» (non familiale) était posé, et à trois individus choisis au hasard parmi la population générale. Résultats: En comparaison de la population générale, les patients atteints de P-CAD sporadique avaient une prévalence supérieure pour l 'hypertension (29% vs. 14%, p<0.001), le cholestérol (54% vs. 33%, p<0.001), l'obésité (20% vs. 13%, p<0.001) et le tabagisme (76% vs. 39%, p<0.001). Ces facteurs de risque étaient de prévalences similaires, voire supérieures chez les patients atteints de P-CAD familiale (43% [p0.05 vs. P-CAD sporadiques], 58% [p=0.07], 21% et 72% respectivement). Seulement 7 (4%) des 163 patients atteints de P-CAD familiale et 22 (7%) des 326 patients atteints de P-CAD sporadique, ne présentaient aucun facteur de risque cardiovasculaire, comparés à 167 (34%) des 489 patients issus de la population générale. Conclusions: Les facteurs de risque cardiovasculaire classiques et réversibles ont une haute prévalence chez les patients atteints de P-CAD familiale. Ce fait rend improbable une contribution génétique prédominante, agissant en l'absence de facteurs de risque. Summary Objectives: This study was designed to assess the prevalence of major cardiovascular risk factors in familial premature coronary artery disease (P-CAD), affecting two or more siblings within one sibship. Background: Premature CAD has a genetic component. It remains to be established whether familial P-CAD is due to genes acting independently from major cardiovascular risk factors. Methods: We recruited 213 P-CAD survivors from 103 sibships diagnosed before age ?50 (men) or ?55 (women) years old. Hypertension, hypercholesterolemia, obesity, and smoking were documented at the time of the event in 163 patients (145 men and 18 women). Each patient was compared with two individuals of the same age and gender, diagnosed with sporadic (nonfamilial) P-CAD, and three individuals randomly sampled from the general population. Result: Compared with the general population, patients with sporadic P-CAD had a higher prevalence of hypertension (29% vs. 14%, p < 0.001), hypercholesterolemia (54% vs. 33%, p < 0.001), obesity (20% vs. 13%, p < 0.01), and smoking (76% vs. 39%, p < 0.001). These risk factors were equally or even more prevalent in patients with familial P-CAD (43% [p < 0.05 vs. sporadic P-CAD], 58% [p = 0.07], 21% and 72%, respectively). Overall, only 7 (4%) of 163 of patients with familial P-CAD and 22 (7%) of 326 of patients with sporadic P-CAD had none of these conditions, as compared with 167 (34%) of 489 patients in the general population. Conclusions: Classic, remediable risk factors are highly prevalent in patients with familial P-CAD. Accordingly, a major contribution of genes acting in the absence of these risk factors is unlikely.

Corticosterone mediates the condition-dependent component of melanin-based coloration

The handicap principle of sexual selection theory states that colourful phenotypic traits signal aspects of individual quality because only individuals in prime condition can afford to produce and bear conspicuous traits. Melanin-based pigments participate in the elaboration of many secondary sexual characters and, given their role in sexual selection, melanin-based coloration may therefore honestly reject individual quality. Although the expression of melanism is usually under genetic control, in some species it is condition dependent. However, the underlying physiological mechanism is yet unknown. Based on the negative feedback link between corticosterone and melanogenesis ( melanocortins, tyrosinase) in response to stressful environmental factors, we hypothesize that corticosterone mediates the condition-dependent component of melanism. This hypothesis predicts that stressful factors induce a rise in circulating corticosterone which inhibits the secretion of melanocortins and tyrosinase and in turn melanin production. We tested this prediction by manipulating the level of corticosterone at the time of melanin production in nestling barn owls, Tyto alba, a species showing heritable variation in the degree of phaeomelanism from reddish-brown to white. The finding that corticosterone-implanted nestlings produced feathers with less phaeomelanic coloration than placebo-implanted nestlings is consistent with the hypothesis that the environment-mediated reduction in the degree of melanism is, at least in part, caused by a rise in corticosterone. In species in which the expression of melanin-based coloration is condition dependent, we now need a test showing that individuals with less corticosterone and more melanin-based signals are individuals in better condition.

Effects of aerobic fitness on oxygen uptake kinetics in heavy intensity swimming.

This study aimed to characterise both the [Formula: see text] kinetics within constant heavy-intensity swimming exercise, and to assess the relationships between [Formula: see text] kinetics and other parameters of aerobic fitness, in well-trained swimmers. On separate days, 21 male swimmers completed: (1) an incremental swimming test to determine their maximal oxygen uptake [Formula: see text], first ventilatory threshold (VT), and the velocity associated with [Formula: see text] [Formula: see text] and (2) two square-wave transitions from rest to heavy-intensity exercise, to determine their [Formula: see text] kinetics. All the tests involved breath-by-breath analysis of freestyle swimming using a swimming snorkel. [Formula: see text] kinetics was modelled with two exponential functions. The mean values for the incremental test were 56.0 ± 6.0 ml min(-1) kg(-1), 1.45 ± 0.08 m s(-1); and 42.1 ± 5.7 ml min(-1) kg(-1) for [Formula: see text], [Formula: see text] and VT, respectively. For the square-wave transition, the time constant of the primary phase (τ(p)) averaged 17.3 ± 5.4 s and the relevant slow component (A'(sc)) averaged 4.8 ± 2.9 ml min(-1) kg(-1) [representing 8.9% of the end-exercise [Formula: see text] (%A'(sc))]. τ(p) was correlated with [Formula: see text] (r = -0.55, P = 0.01), but not with either [Formula: see text] (r = 0.05, ns) or VT (r = 0.14, ns). The %A'(sc) did not correlate with either [Formula: see text] (r = -0.14, ns) or [Formula: see text] (r = 0.06, ns), but was inversely related with VT (r = -0.61, P < 0.01). This study was the first to describe the [Formula: see text] kinetics in heavy-intensity swimming using specific swimming exercise and appropriate methods. As has been demonstrated in cycling, faster [Formula: see text] kinetics allow higher aerobic power outputs to be attained. The slow component seems to be reduced in swimmers with higher ventilatory thresholds.

Secretory component delays the conversion of secretory IgA into antigen-binding competent F(ab')2: a possible implication for mucosal defense.

Secretory component (SC) represents the soluble ectodomain of the polymeric Ig receptor, a membrane protein that transports mucosal Abs across epithelial cells. In the protease-rich environment of the intestine, SC is thought to stabilize the associated IgA by unestablished molecular mechanisms. To address this question, we reconstituted SC-IgA complexes in vitro by incubating dimeric IgA (IgAd) with either recombinant human SC (rSC) or SC isolated from human colostral milk (SCm). Both complexes exhibited an identical degree of covalency when exposed to redox agents, peptidyl disulfide isomerase, and temperature changes. In cross-competition experiments, 50% inhibition of binding to IgAd was achieved at approximately 10 nM SC competitor. Western blot analysis of IgAd digested with intestinal washes indicated that the alpha-chain in IgAd was primarily split into a 40-kDa species, a phenomenon delayed in rSC- or SCm-IgAd complexes. In the same assay, either of the SCs was resistant to degradation only if complexed with IgAd. In contrast, the kappa light chain was not digested at all, suggesting that the F(ab')2 region was left intact. Accordingly, IgAd and SC-IgAd digestion products retained functionality as indicated by Ag reactivity in ELISA. Size exclusion chromatography under native conditions of digested IgAd and rSC-IgAd demonstrates that SC exerts its protective role in secretory IgA by delaying cleavage in the hinge/Fc region of the alpha-chain, not by holding together degraded fragments. The function of integral secretory IgA and F(ab')2 is discussed in terms of mucosal immune defenses.