Nonsymmetric curved beams within a symmetric caustic skeleton.

Nonsymmetric curved beams having a symmetric caustic skeleton are presented. They arise from a finite jump in the symmetric spectral phase that breaks the symmetry of the beam intensity without altering its associated caustic curve. These nonsymmetric beams can be represented as a superposition of two caustic beams whose wave fields have well-defined even and odd symmetries with weight coefficients dependent on the phase jump. In this approach, the phase jump acts as a measure of the beam asymmetry degree that can be easily controlled in experiments. This scheme is a promising step towards optical cryptography and quantum optics applications.

Structured light illumination for order sorting in Echelle spectrometers.

We report on the operation of an echelle spectrometer under structured light illumination. Each diffraction order of the spectrometer is encoded with a certain periodic structure allowing for order sorting by numerical analysis after detection. In contrast to cross-dispersed echelle spectrometers, in this approach the orders overlap at the detection plane so that the spectral calibration can be performed easily with a single reference wavelength. This operational simplification makes it possible to measure simultaneously the light source under study and the calibration wavelength giving rise to a self-calibrated echelle spectrometer. In this way the device compensates for the spectral drift due to temporal changes of environmental conditions in real time. Our proposal can be useful in a large number of applications requiring moderate, high or very high resolving power for a wide bandwidth in a non-isolated environment.

Characterization of digital dispersive spectrometers by low coherence interferometry.

We propose a procedure to determine the spectral response of digital dispersive spectrometers without previous knowledge of any parameter of the system. The method consists of applying the Fourier transform spectroscopy technique to each pixel of the detection plane, a CCD camera, to obtain its individual spectral response. From this simple procedure, the system-point spread function and the effect of the finite pixel width are taken into account giving rise to a response matrix that fully characterizes the spectrometer. Using the response matrix information we find the resolving power of a given spectrometer, predict in advance its response to any virtual input spectrum and improve numerically the spectrometer's resolution. We consider that the presented approach could be useful in most spectroscopic branches such as in computational spectroscopy, optical coherence tomography, hyperspectral imaging, spectral interferometry and analytical chemistry, among others.

Importance of tissue sampling, laboratory methods, and patient characteristics for detection of Pneumocystis in autopsied lungs of non-immunosuppressed individuals.

To understand the epidemiological significance of Pneumocystis detection in a lung tissue sample of non-immunosuppressed individuals, we examined sampling procedures, laboratory methodology, and patient characteristics of autopsy series reported in the literature. Number of tissue specimens, DNA-extraction procedures, age and underlying diagnosis highly influence yield and are critical to understand yield differences of Pneumocystis among reports of pulmonary colonization in immunocompetent individuals.

Portugal and Angola: similarities and differences in Toxoplasma gondii seroprevalence and risk factors in pregnant women.

In this study we determined the presence of IgM/IgG antibodies to Toxoplasma gondii in sera of 155 and 300 pregnant women from Lisbon (Portugal) and Luanda (Angola), respectively, and evaluated the potential risk factors associated with this infection. DNA detection was performed by PCR assays targeting T. gondii regions (RE/B1). Overall, 21·9% (10·9% IgG, 10·9% IgG/IgM) of the Lisbon women and 27·3% (23·7%, IgG, 2% IgM, 1·7% IgG/IgM) of the Luanda women had antibodies to T. gondii. Single variable and binary logistic regression analyses were conducted. Based on the latter, contacts with cats (family/friends), and having more than two births were identified as risk factors for Toxoplasma infection in Lisbon women. In Luanda, the risk factors for T. gondii infection suggested by the single variable analysis (outdoor contact with cats and consumption of pasteurized milk/dairy products) were not confirmed by binary logistic regression. This study shows original data from Angola, and updated data from Portugal in the study of infection by T. gondii in pregnant women, indicating that the prevalence of anti-Toxoplasma antibodies is high enough to alert the government health authorities and implement appropriate measures to control this infection.

Intensity-symmetric Airy beams.

Theoretical, numerical, and experimental research on a novel family of Airy beams in rectangular coordinates having a symmetric transverse pattern of light intensity is presented. The intensity-symmetric Airy beams include both the symmetric Airy beam whose field amplitude is an even function of the transverse coordinates and the antisymmetric Airy beam whose field amplitude is an odd function of such coordinates. The theoretical foundations are based on the relationship of the symmetries of the spectral phase with the cosine and sine Fourier transforms. These beams are analyzed in a propagation range also including the region preceding the Fourier plane. These beams exhibit autofocusing, collapse, self-bending, and reversal propagation. Moreover, the intensity distribution is strongly asymmetric with respect to the Fourier plane. All these peculiar features were not reported for other classes of paraxial beams in a rectangular frame. The experimental generation of intensity-symmetric Airy beams is demonstrated supporting the theoretical predictions. Possible applications in planar waveguide writing and optical trapping are also discussed.

(1-3)-beta-D-glucan in association with lactate dehydrogenase as biomarkers of Pneumocystis pneumonia (PcP) in HIV-infected patients.

Pneumocystis pneumonia (PcP) is a major HIV-related illness caused by Pneumocystis jirovecii. Definitive diagnosis of PcP requires microscopic detection of P. jirovecii in pulmonary specimens. The objective of this study was to evaluate the usefulness of two serum markers in the diagnosis of PcP. Serum levels of (1-3)-beta-d-glucan (BG) and lactate dehydrogenase (LDH) were investigated in 100 HIV-positive adult patients and 50 healthy blood donors. PcP cases were confirmed using indirect immunofluorescence with monoclonal anti-Pneumocystis antibodies and nested-PCR to amplify the large subunit mitochondrial rRNA gene of P. jirovecii in pulmonary specimens. BG and LDH levels in serum were measured using quantitative microplate-based assays. BG and LDH positive sera were statistically associated with PcP cases (P ≤ 0.001). Sensitivity, specificity, positive/negative predictive values (PPV/NPV), and positive/negative likelihood ratios (PLR/NLR) were 91.3 %, 61.3 %, 85.1 %, 79.2 %, 2.359, and 0.142, respectively, for the BG kit assay, and 91.3 %, 35.5 %, 75.9 %, 64.7 %, 1.415 and 0.245, respectively, for the LDH test. Serologic markers levels combined with the clinical diagnostic criteria for PcP were evaluated for their usefulness in diagnosis of PcP. The most promising cutoff levels for diagnosis of PcP were determined to be 400 pg/ml of BG and 350 U/l of LDH, which combined with clinical data presented 92.8 % sensitivity, 83.9 % specificity, 92.8 % PPV, 83.9 % NPV, 5.764 PLR and 0.086 NLR (P < 0.001). This study confirmed that BG is a reliable indicator for detecting P. jirovecii infection. The combination between BG/LDH levels and clinical data is a promising alternative approach for PcP diagnosis.

Femtosecond spatial pulse shaping at the focal plane.

Spatial shaping of ultrashort laser beams at the focal plane is theoretically analyzed. The description of the pulse is performed by its expansion in terms of Laguerre-Gaussian orthonormal modes. This procedure gives both a comprehensive interpretation of the propagation dynamics and the required signal to encode onto a spatial light modulator for spatial shaping, without using iterative algorithms. As an example, pulses with top-hat and annular spatial profiles are designed and their dynamics analyzed. The interference of top-hat pulses is also investigated finding potential applications in high precision pump-probe experiments (without using delay lines) and for the creation of subwavelength ablation patterns. In addition, a novel class of ultrashort pulses possessing non-stationary orbital angular momentum is also proposed. These exotic pulses provide additional degrees of freedom that open up new perspectives in fields such as laser-matter interaction and micro-machining.

Spatial dynamics of Amazonian commercial fisheries: an analysis of landscape composition and fish landings.

Amazonian commercial fishing is artisanal, and landings can be influenced by the flood pulse, the consumer market, the level of exploitation of species, habitat quality and vegetation cover. In this study, landscape variables and the river level were evaluated as possible drivers in the composition of catches landed in three regions of the Solimões-Amazon River. Fish landing data were collected in the upper and lower Solimões River and lower Amazon River. Fishing locations were mapped with information from fishers, civil defense departments and from the literature. Information related to river level and landscape was acquired from databases available online. Maps with the the radius of action of the fishing fleet and the quantification of landscape variables were made for periods of high and low-water, and non-metric multidimensional scaling analysis (nMDS) with catches by species, by region and hydrological period were performed. The largest operating radius of the fishing fleet was of 1,028 km and was identified in the lower Amazon River, which is probably due to the larger size of the consumer market, vessel characteristics and level of exploitation of the species near the landing center. The proportion of vegetation cover was reduced from 87% in the upper stretches of the Solimões River to 46% in the lower stretches. The upper and lower Solimões River regions presented a greater variety of species in the composition of landings. It was identified that the composition of landings between the three analyzed regions possibly varied according to the availability of habitats, indicating the importance of landscape variables for fish landings.

Clinical relevance of multiple single-nucleotide polymorphisms in Pneumocystis jirovecii Pneumonia: development of a multiplex PCR-single-base-extension methodology.

Pneumocystis jirovecii pneumonia (PcP) is a major cause of respiratory illness in patients with AIDS. The identification of multiple single-nucleotide polymorphisms (SNPs) at three distinct P. jirovecii loci encoding dihydrofolate reductase (DHFR), mitochondrial large-subunit rRNA (mtLSU rRNA), and superoxide dismutase (SOD) was achieved using multiplex-PCR (MPCR) followed by direct sequencing and two single-base extension (SBE) techniques. Four SNPs (DHFR312, mt85, SOD215, and SOD110), correlated previously with parameters of disease, were amplified and genotyped simultaneously. The concordance of results between the standard sequencing technique (direct sequencing) and SBE analysis was 96.9% for the acrylamide gel electrophoresis and 98.4% for the capillary electrophoresis. The cross-genetic analysis established several statistical associations among the SNPs studied: mt85C-SOD110T, SOD110T-SOD215C, and SOD110C-SOD215T. These results were confirmed by cluster analysis. Data showed that among the isolates with low to moderate parasite burden, the highest percentages of DHFR312C, mt85C, SOD110T, and SOD215C were detected, whereas for high parasite burden cases the highest frequencies were observed among isolates with DHFR312T, mt85T, SOD110C, and SOD215T. The polymorphisms studied were shown to be suitable genetic targets potentially correlated with PcP clinical data that can be used as predictors of outcome in further studies to help clinical decision-making in the management of PcP. The MPCR/SBE protocol described for the first time in the present study was shown to be a rapid, highly accurate method for genotyping P. jirovecii SNPs encoded by different loci that could be used for epidemiological studies and as an additional procedure for the prognostic classification and diagnosis of PcP.

Characterization of holographically generated beams via phase retrieval based on Wigner distribution projections.

In this work, we propose a robust and versatile approach for the characterization of the complex field amplitude of holographically generated coherent-scalar paraxial beams. For this purpose we apply an iterative algorithm that allows recovering the phase of the generated beam from the measurement of its Wigner distribution projections. Its performance is analyzed for beams of different symmetry: Laguerre-Gaussian, Hermite-Gaussian and spiral ones, which are obtained experimentally by a computer generated hologram (CGH) implemented on a programmable spatial light modulator (SLM). Using the same method we also study the quality of their holographic recording on a highly efficient photopolymerizable glass. The proposed approach is useful for the creation of adaptive CGH that takes into account the peculiarities of the SLM, as well as for the quality control of the holographic data storage.

Femtosecond spectral pulse shaping with holographic gratings recorded in photopolymerizable glasses.

The majority of the applications of ultrashort laser pulses require a control of its spectral bandwidth. In this paper we show the capability of volume phase holographic gratings recorded in photopolymerizable glasses for spectral pulse reshaping of ultrashort laser pulses originated in an Amplified Ti: Sapphire laser system and its second harmonic. Gratings with high laser induce damage threshold (LIDT) allowing wide spectral bandwidth operability satisfy these demands. We have performed LIDT testing in the photopolymerizable glass showing that the sample remains unaltered after more than 10 million pulses with 0,75 TW/cm2 at 1 KHz repetition rate. Furthermore, it has been developed a theoretical model, as an extension of the Kogelnik's theory, providing key gratings design for bandwidth operability. The main features of the diffracted beams are in agreement with the model, showing that non-linear effects are negligible in this material up to the fluence threshold for laser induced damage. The high versatility of the grating design along with the excellent LIDT indicates that this material is a promising candidate for ultrashort laser pulses manipulations.

Holographic Fabry-Perot spectrometer.

We propose a spectrum analyzer based on the properties of a hologram recorded with the field transmitted by a Fabry-Perot etalon. The spectral response of this holographic Fabry-Perot spectrometer (HFPS) is analytically investigated in the paraxial approximation and compared with a conventional Fabry-Perot etalon of similar characteristics. We demonstrate that the resolving power is twice increased and the free spectral range (FSR) is reduced to one-half. The proposed spectrometer could improve the operational performance of the etalon because it can exhibit high efficiency and it would be insensible to environmental conditions such as temperature and vibrations. Our analysis also extends to another variant of the HFPS based on holographic multiplexing of the transmitted field of a Fabry-Perot etalon. This device increases the FSR, keeping the same HFPS performance.

Generation of femtosecond paraxial beams with arbitrary spatial distribution.

We present an approach to generate paraxial laser beams with arbitrary spatial distribution in the femtosecond time regime. The proposed technique is based upon a pair of volume phase holographic gratings working in parallel arrangement. It exploits the spatial coherence properties of the incoming laser beam in a compact and robust setup that mitigates angular and spatial chirp. The gratings were recorded in a photopolymerizable glass with a high optical damage threshold and a large optical throughput. Setup performance is studied and experimentally demonstrated by generating Laguerre-Gaussian femtosecond pulses.

Structure of the dielectric tensor in nematic liquid crystals with topological charge.

A q-plate is a stratified medium composed of a uniaxial nematic liquid crystal with an inhomogeneous orientation of the optical axis possessing a topological charge q, which looks promising as a switching device. This work reports an approach to diagonalizing the dielectric tensor in q-plates, giving a detailed study of nontrivial tensor coordinate transformations. The relationship between the diagonal dielectric tensor and the topological charge of the plate is established. From that, the dielectric tensor for a given q-plate can be explicitly calculated in a convenient frame, and hence the field propagation equations can be derived. These studies establish a theoretical basis that could further deepen the research on these particular structures for nonconventional manipulation of the light.

Epidemiology and clinical relevance of Pneumocystis jirovecii Frenkel, 1976 dihydropteroate synthase gene mutations.

A review was conducted to examine the published works that studied the prevalence of Pneumocystis jirovecii dihydropteroate synthase (DHPS) mutations in patients with P. jirovecii pneumonia (PcP), in develop and developing countries, and that focused the problem of the possible association of these mutations with exposure to sulpha or sulphone drugs and their influence in the PcP outcome. Studies conducted in United States of America presented higher P. jirovecii mutations rates, in comparison with European countries, and in developing countries, lower rates of DHPS mutations were reported, due to limited use of sulpha drugs. A significant association was reported between the use of sulpha or sulphone agents for PcP prophylaxis in HIV-infected patients and the presence of DHPS mutations. However these mutations were also detected in PcP patients who were not currently receiving sulpha or sulphone agents. The outcome and mortality of HIV-infected patients with PcP harbouring DHPS gene mutations were related primarily to the underlying severity of illness and the initial severity of PcP, more than to the presence of mutations.

Implementation of a systematic approach to diabetes in primary care in Bahia, Brazil improves metabolic outcomes: PRODIBA-Programa de Interiorização da Assistência ao Diabetes na Bahia (Project for Dissemination of Diabetes Care in the State of Bahia).

BACKGROUND: Staged Diabetes Management (SDM) improves glycaemic control and reduces diabetes-related complications in primary care. METHODS: An 18-month randomized controlled cohort study was conducted in two municipalities in the state of Bahia, Brazil, involving 100 patients with Type 2 diabetes in each municipality. In one municipality, healthcare professionals were trained to use SDM customized protocols for clinical decisions and, in the other municipality, no protocols for diabetes care were implemented. We hypothesized that, in the municipality with SDM trained professionals, patients would have better outcomes, including a fall in glycated haemoglobin (HbA(1c)). RESULTS: Improvements in some metabolic parameters were observed in the SDM group, including a 22% decrease in mean random glucose, a significant 15% decrease in mean HbA(1c), a 6% decrease in systolic blood pressure and an 11% decrease in diastolic blood pressure. There were no differences in body mass index and lipid profile. CONCLUSIONS: SDM customized algorithms are effective, practical and easy to use in primary healthcare teams with very limited resources.

Genetic characterization of the UCS and Kex1 loci of Pneumocystis jirovecii.

Nucleotide variation in the Pneumocystis jirovecii upstream conserved sequence (UCS) and kexin-like serine protease (Kex1) loci was studied in pulmonary specimens from Portuguese HIV-positive patients. DNA was extracted and used for specific molecular sequence analysis. The number of UCS tandem repeats detected in 13 successfully sequenced isolates ranged from three (9 isolates, 69%) to four (4 isolates, 31%). A novel tandem repeat pattern and two novel polymorphisms were detected in the UCS region. For the Kex1 gene, the wild-type (24 isolates, 86%) was the most frequent sequence detected among the 28 sequenced isolates. Nevertheless, a nonsynonymous (1 isolate, 3%) and three synonymous (3 isolates, 11%) polymorphisms were detected and are described here for the first time.

Occurrence of Cryptosporidium and Giardia genotypes and subtypes in raw and treated water in Portugal.

AIMS: Waterborne outbreaks of diarrhoeal illness reported worldwide are mostly associated with Cryptosporidium spp. and Giardia spp. Their presence in aquatic systems makes it essential to develop preventive strategies for water and food safety. This study was undertaken to monitor the presence of Cryptosporidium and Giardia in a total of 175 water samples, including raw and treated water from both surface and ground sources in Portugal. METHODS AND RESULTS: The samples were processed according to USEPA Method 1623 for immunomagnetic separation (IMS) of Cryptosporidium oocysts and Giardia cysts, followed by detection of oocysts/cysts by immunofluorecence (IFA) microscopy, PCR-based techniques were done on all water samples collected. Out of 175 samples, 81 (46.3%) were positive for Cryptosporidium and 67 (38.3%) for Giardia by IFA. Cryptosporidium spp. and G. duodenalis genotypes were identified by PCR in 37 (21.7%) and 9 (5.1%) water samples, respectively. C. parvum was the most common species (78.9%), followed by C. hominis (13.2%), C. andersoni (5.3%), and C. muris (2.6%). Subtype IdA15 was identified in all C. hominis-positive water samples. Subtyping revealed the presence of C. parvum subtypes IIaA15G2R1, IIaA16G2R1 and IIdA17G1. Giardia duodenalis subtype A1 was identified. CONCLUSIONS: The results of the present study suggest that Cryptosporidium spp. and Giardia spp. were widely distributed in source water and treated water in Portugal. Moreover, the results obtained indicate a high occurrence of human-pathogenic Cryptosporidium genotypes and subtypes in raw and treated water samples. SIGNIFICANCE AND IMPACT OF THE STUDY: Thus, water can be a potential vehicle in the transmission of cryptosporidiosis, and giardiasis of humans and animals in Portugal.

Pneumocystis jirovecii multilocus genotyping profiles in patients from Portugal and Spain.

Pneumonia caused by the opportunistic organism Pneumocystis jirovecii is a clinically important infection affecting AIDS and other immunocompromised patients. The present study aimed to compare and characterise the frequency pattern of DNA sequences from the P. jirovecii mitochondrial large-subunit rRNA (mtLSU rRNA) gene, the dihydropteroate synthase (DHPS) gene and the internal transcribed spacer (ITS) regions of the nuclear rRNA operon in specimens from Lisbon (Portugal) and Seville (Spain). Total DNA was extracted and used for specific molecular sequence analysis of the three loci. In both populations, mtLSU rRNA gene analysis revealed an overall prevalence of genotype 1. In the Portuguese population, genotype 2 was the second most common, followed by genotype 3. Inversely, in the Spanish population, genotype 3 was the second most common, followed by genotype 2. The DHPS wild-type sequence was the genotype observed most frequently in both populations, and the DHPS genotype frequency pattern was identical to distribution patterns revealed in other European studies. ITS types showed a significant diversity in both populations because of the high sequence variability in these genomic regions. The most prevalent ITS type in the Portuguese population was Eg, followed by Cg. In contrast to other European studies, Bi was the most common ITS type in the Spanish samples, followed by Eg. A statistically significant association between mtLSU rRNA genotype 1 and ITS type Eg was revealed.