Constraining cosmological parameters with the clustering properties of galaxy clusters in optical and X-ray bands

(abridged) We use a theoretical model to predict the clustering properties of galaxy clusters. Our technique accounts for past light-cone effects on the observed clustering and follows the non-linear evolution of the dark matter correlation function and cluster bias factor. A linear treatment of redshift-space distortions is also included. We perform a maximum-likelihood analysis by comparing the theoretical predictions to a set of observational data, both in the optical (APM and EDCC catalogues) and X-ray band (RASS1 Bright Sample, BCS, XBACs, REFLEX). In the framework of CDM models, we compute the constraints on cosmological parameters. Our results show that X-ray data are more powerful than optical ones, allowing smaller regions in the parameter space. We find that the clustering properties of clusters are almost independent of the matter density parameter and of the presence of a cosmological constant, while they appear to be strongly dependent on the shape parameter. Using the X-ray data only, we obtain Gamma~0.1 and 0.4<sigma_8<1.1 for the Einstein-de Sitter model, while 0.14<Gamma<0.22 and 0.6<sigma_8<1.3 for open and flat models with Omega_0m=0.3. Finally, we use our model to make predictions on the correlation length of galaxy clusters expected in future surveys. In particular, we show the results for an optical catalogue with characteristics similar to the EIS project and for a very deep X-ray catalogue with the characteristics of the XMM/LSS survey. We find that clusters at high redshifts are expected to have larger a correlation length than local ones.Comment: 15 pages, Latex using MN style. Revised version accepted for publication in MNRA

Dermatophytes’ identification by Matrix-assisted laser desorption ionization-time of flight mass spectrometry. (MALDI-TOF MS) - the experience of a clinical laboratory

Objectives: Dermatophytes are a challenging group of fungi that infect the keratinized tissues. The taxonomy of these fungi has changed recently with the reclassification of some species and description of new ones. However, many clinical laboratories still base the identification of dermatophytes on their phenotype. Since dermatophytes are very pleomorphic, macro and micromorphology are often insufficient to reach a correct classification and may lead to misidentifications. The identification based on MALDI-TOF relies on the protein profile of the microorganism. Thus, this study aims to summarize our current laboratorial experience of dermatophyte identification using MALDI-TOF MS. Methods: From january to april 2018, 95 dermatophytes isolates, collected from human keratinized samples and also from quality control programs were characterized by phenotypic analysis, and by VITEK MS V3.2 bioMerieux. Before identification procedure, isolates were inoculated on Sabouraud Dextrose agar plates and incubated at 27°C during 5 to 10 days. Species were identified taking into account clinical features, as well as cultural, microscopic and physiological characteristics. Prior to MALDI-TOF MS analysis, the samples were pre-treated according to the manufacturer’s protocol for filamentous fungi. Molecular identification by sequencing of the internal transcribed spacer 1 (ITS1) was performed in 34 of those isolates Results: Through phenotypic analysis eight different species were identified (54 Trichophyton rubrum; 4 T.soudanense; 22 T.interdigitale; 1 T.mentagrophytes; 3 T.tonsurans; 7 Microsporum canis; 3 M.audouinii; 1 Microsporum spp.- (non canis or audouinii). MALDI-TOF analysis showed an identification agreement in 80 cases (84,2%) with a confidence level of 99,9%. Eight isolates showed divergent identification results: three T.rubrum were identified as T.violaceum, three T.soudanense were identified as T.rubrum, one T.mentagrophytes was identified as T.interdigitale and one T.tonsurans was identified as T.rubrum. In four cases MALDI-TOF analysis did not get a profile. The ITS sequencing analysis of discrepant results corroborated the MALDI-TOF identification in five of them. On the other hand, T.soudanense was only identified by phenotypic analysis since MALDI-TOF and ITS sequencing result was T.rubrum. MALDITOF identification of T.violaceum was not confirmed by ITS sequencing that identified T. rubrum instead, in accordance with the phenotypic identification. Conclusion: Correct identification of dermatophytes to species level requires sequencing of the ITS, LSU, and/or betatubulin regions. The implementation of this methodology in a clinical laboratory is expensive and time consuming. MALDI-TOF identification is a good option for dermatophytes’ identification performed in laboratory routine, since costs of consumables as well as time of sample preparation are lower than for PCR analysis and doesn’t require long training period as phenotypic identification does. In this study, however, both methods failed to identify some species variants like Trichophyton soudanense or T. violaceum. The combined use of both MALDI-TOF and phenotypic methods seems to be the better approach for dermatophytes’ identification since some species show significant phenotypic and clinical differences.info:eu-repo/semantics/publishedVersio

Frequency and molecular epidemiology of Aspergillus isolated from patients with suspicion of respiratory fungal infection

Objective: The aim of this study was to determine the frequency of Aspergillus detected in respiratory samples from a cohort of patients with suspicion of fungal infection of the respiratory tract as well as to determine the susceptibility to azoles of the isolates from the Fumigati section. Methods: A retrospective study was performed involving samples obtained from 16 hospitals covering different districts of continental Portugal and Azores islands. One hundred and eighty-seven respiratory samples (101 bronchoalveolar lavage fluids, 52 bronchial lavages, 27 bronchial secretions, 6 expectorations and 1 bronchial aspirate) were collected between November 2011 and December 2017 from a cohort of 146 patients with suspicion of respiratory fungal infection (ages ranging from 20 to 87 years old). Demographic and clinical data were recorded. Detection of Aspergillus was done by culture, immunoenzimatic assay and/or molecular techniques. Aspergillus molecular identification to species level was performed by sequencing of the calmodulin and β-tubulin genes. To detect possible resistance to azoles, isolates belonging to section Fumigati were inoculated into Sabouraud dextrose agar media supplemented with 1 µg/ml or 4 µg/ml of voriconazole, 4 µg/ml of itraconazole and 0.5 µg/ml of posaconazole and their growth was observed and recorded after 7 days of incubation at 27ºC. Doubtful results were confirmed when possible by E-test and by real-time multiplex PCR for the detection of mutations in the Cyp51A gene. Results: Fifty-seven (39.0%) of the studied patients were positive for Aspergillus. From the cases with a positive culture (n=58) the species were identified by sequencing and belonged to six different sections. The most frequently isolated was the section Nigri (42.1%) followed by the Fumigati (33.3%) and Flavi sections (8.6%). Regarding the species, the most frequent was A. niger sensu stricto (33.9%) followed by A. fumigatus sensu stricto (32.1%). Nine cryptic species were also identified which frequency was 21.4%. In order to study the frequency of azole resistance in Fumigati isolates collected from the samples of this cohort as well from other biological products, 52 isolates - Aspergillus fumigatus sensu stricto (n=45), A. lentulus (n=4), A. udagawae (n=2) and A. pseudofelis (n=1) – were tested. The tested A. fumigatus sensu stricto isolates did not show resistance to azoles. An A. udagawae strain revealed low susceptibility to voriconazole (MIC was not determined due to loss of strain viability). An A. pseudofelis strain also showed decreased susceptibility to voriconazole (MIC =1 μg/ml) as well as to and itraconazole (MIC = 2 μg/ml). Conclusion: In this study, the genus Aspergillus was frequently isolated in the respiratory samples tested and a high number of cryptic species was detected. Although resistance to azoles was not a problem identified in the tested isolates, determination of the in vitro susceptibility profile and molecular identification of the Aspergillus species is essential to improve the diagnosis and management of aspergillosis since several cryptic species have intrinsic resistance to antifungal drugs.info:eu-repo/semantics/publishedVersio

Multidimensional Quasi-Monte Carlo Malliavin Greeks

We investigate the use of Malliavin calculus in order to calculate the Greeks of multidimensional complex path-dependent options by simulation. For this purpose, we extend the formulas employed by Montero and Kohatsu-Higa to the multidimensional case. The multidimensional setting shows the convenience of the Malliavin Calculus approach over different techniques that have been previously proposed. Indeed, these techniques may be computationally expensive and do not provide flexibility for variance reduction. In contrast, the Malliavin approach exhibits a higher flexibility by providing a class of functions that return the same expected value (the Greek) with different accuracies. This versatility for variance reduction is not possible without the use of the generalized integral by part formula of Malliavin Calculus. In the multidimensional context, we find convenient formulas that permit to improve the localization technique, introduced in Fourni\'e et al and reduce both the computational cost and the variance. Moreover, we show that the parameters employed for variance reduction can be obtained \textit{on the flight} in the simulation. We illustrate the efficiency of the proposed procedures, coupled with the enhanced version of Quasi-Monte Carlo simulations as discussed in Sabino, for the numerical estimation of the Deltas of call, digital Asian-style and Exotic basket options with a fixed and a floating strike price in a multidimensional Black-Scholes market.Comment: 22 pages, 6 figure

On cosmological observables in a swiss-cheese universe

Photon geodesics are calculated in a swiss-cheese model, where the cheese is made of the usual Friedmann-Robertson-Walker solution and the holes are constructed from a Lemaitre-Tolman-Bondi solution of Einstein's equations. The observables on which we focus are the changes in the redshift, in the angular-diameter--distance relation, in the luminosity-distance--redshift relation, and in the corresponding distance modulus. We find that redshift effects are suppressed when the hole is small because of a compensation effect acting on the scale of half a hole resulting from the special case of spherical symmetry. However, we find interesting effects in the calculation of the angular distance: strong evolution of the inhomogeneities (as in the approach to caustic formation) causes the photon path to deviate from that of the FRW case. Therefore, the inhomogeneities are able to partly mimic the effects of a dark-energy component. Our results also suggest that the nonlinear effects of caustic formation in cold dark matter models may lead to interesting effects on photon trajectories.Comment: 25 pages, 21 figures; replaced to fit the version accepted for publication in Phys. Rev.

Light-cone averages in a swiss-cheese universe

We analyze a toy swiss-cheese cosmological model to study the averaging problem. In our model, the cheese is the EdS model and the holes are constructed from a LTB solution. We study the propagation of photons in the swiss-cheese model, and find a phenomenological homogeneous model to describe observables. Following a fitting procedure based on light-cone averages, we find that the the expansion scalar is unaffected by the inhomogeneities. This is because of spherical symmetry. However, the light-cone average of the density as a function of redshift is affected by inhomogeneities. The effect arises because, as the universe evolves, a photon spends more and more time in the (large) voids than in the (thin) high-density structures. The phenomenological homogeneous model describing the light-cone average of the density is similar to the concordance model. Although the sole source in the swiss-cheese model is matter, the phenomenological homogeneous model behaves as if it has a dark-energy component. Finally, we study how the equation of state of the phenomenological model depends on the size of the inhomogeneities, and find that the equation-of-state parameters w_0 and w_a follow a power-law dependence with a scaling exponent equal to unity. That is, the equation of state depends linearly on the distance the photon travels through voids. We conclude that within our toy model, the holes must have a present size of about 250 Mpc to be able to mimic the concordance model.Comment: 20 pages, 14 figures; replaced to fit the version accepted for publication in Phys. Rev.

The mechanism of the amine-catalysed isomerizationof dialkyl maleate: A computational study

DFT at B3LYP/6-31G (d,p) level calculation results for the amine-catalysed isomerization of dimethyl maleate revealed that the mechanism proceeds via foursteps: (1) a concerted proton transfer from one amine molecule to another which subsequently enhances the addition of the adduct thus formed to the C-C double bond to yield INT1. (2) Abstraction of a proton from the -carbon of INT1 by a second amine molecule to give intermediate INT2. (3) Rotation about the C-C single bond followed by proton abstraction by an amine molecule to yield unstable INT3, and (4) an elimination of an amine molecule to yield the trans isomer, dimethyl fumarate. Furthermore, it was found that step 1 is the rate limiting step. However, the activation energy difference between steps 1 and 2 was significantly low and its value depends on the amine catalyst used. The activation energy was found to be lower in water when compared to that calculated in the gas phase. In addition, linear correlation was found between the amine-catalysed isomerization experimental rate and the pKa of the amine catalyst on one hand and the enthalpic and free activation energies on the other hand. The calculations also confirmed that the reaction is first order in dimethyl maleate, second order in the amine catalyst and overall third order. This study disproves three of the four different intermediates that were previously suggested to explain the amine catalysed isomerization of dialkyl maleates. The study verifies the intermediate suggested by Rappopor

Screening of cryptic species among clinical Aspergillus isolates collected during one year period in a Portuguese reference laboratory

Objectives: Correct identification of Aspergillus species is important given that sibling species may show variable susceptibilities to multiple antifungal drugs and also because sharper definition of species may facilitate epidemiological studies. Thus, we screened Aspergillus clinical isolates from Portuguese hospitals to determine which, if any, of the cryptic species of Aspergillus were involved in patient infections. Methods: Over a one year period, Aspergillus isolates from Portuguese health institutions were collected. These isolates were identified on the basis of microscopic morphology and through the use of molecular tools. Genomic DNA was prepared from each isolate and the sequencing of the Internal Transcribed Spacers (ITS) regions, specifically the ITS1 and ITS2 non-coding regions flanking the 5.8S rDNA was used to determine the species complex, whereas β-tubulin and calmodulin sequencing was done to achieve the correct species identification. Results: Over the study period, 57 Aspergillus isolates from clinical samples were collected from 10 Portuguese health institutions. According to the morphological observations, 29 isolates were identified as Aspergillus fumigatus, 11 A. flavus, 8 A. niger, 3 A. nidulans, 2 A. terreus, 2 A. candidus and 2 Aspergillus sp. Among those isolates, six species-complexes were detected by ITS sequencing, and were distributed as follows: fumigati (50.1%), flavi (21.0%), nigri (15.8%), terrei (5.3%), nidulantes (3.6%) and versicolores (3.6%). β-tubulin and calmodulin sequencing resulted in ten (17.5%) cryptic species being identified among the 57 isolates. Six of those isolates belonged to the nigri complex (A. brasiliensis, A. awamorii and A. tubigensis), two to the versicolores complex (A. sidowii and A. fructus), one to the fumigati complex (A. lentulus) and one to the nidulantes complex (Emmericella echinulata). Conclusion: With rigorous application of molecular tools, cryptic species of Aspergillus are not uncommon in the clinic. The identification of cryptic species among the collected clinical isolates of Aspergillus alerts the clinician to isolates with reduced susceptibilities to antifungal drugs and emphasizes a correct identification to species level

Tinea Corporis Causada por Trichophyton Benhamiae de Transmissão Canina: Primeiro Relato em Portugal

Dermatophytoses are superficial and contagious infections caused by dermatophyte fungi. They are the most fre-quent infectious dermatosis in clinical practice, and can affect the skin, hair and nails. Its correct diagnosis allows the understanding of clinical, ecological and epidemiological aspects associated with these microorganisms. Clinical presentation is variable and depends on the habitat (human, animal or soil origin), virulence of the fungus and on the host’s immune status.We report the clinical case of a 62-year-old man with tinea corporis, which stands out for its exuberant clinical pres-entation and by the isolated agent, Trichophyton benhamiae (formerly known as Arthroderma benhamiae), an etiologi-cal agent of dermatophytosis that has not been scientifically reported in Portugal yet.info:eu-repo/semantics/publishedVersio