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.

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.

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.

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.

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.

Serological diagnosis of pneumocystosis: production of a synthetic recombinant antigen for immunodetection of Pneumocystis jirovecii.

Diagnosis of Pneumocystis pneumonia (PcP) relies on the detection of P. jirovecii in respiratory specimens obtained by invasive techniques. Thus, the development of a serological test is urgently needed as it will allow the diagnosis of PcP using blood, an inexpensive and non-invasive specimen. This study aims to combine the production of a multi-epitope synthetic recombinant antigen (RSA) and an ELISA test for detection of anti-P. jirovecii antibodies, in order to develop a new approach for PcP diagnosis. The RSA was selected and designed based on the study of the immunogenicity of the carboxyl-terminal domain of the major surface glycoprotein. This antigen was purified and used as an antigenic tool in an ELISA technique for detection of Ig, IgG and IgM antibodies anti-P. jirovecii (patent-pending no. PT109078). Serum specimens from 88 patients previously categorized in distinct clinical subgroups and 17 blood donors, were analysed. The IgM anti-P. jirovecii levels were statistically increased in patients with PcP (p = 0.001) and the ELISA IgM anti-P. jirovecii test presented a sensitivity of 100% and a specificity of 80.8%, when associated with the clinical diagnosis criteria. This innovative approach, provides good insights about what can be done in the future serum testing for PcP diagnosis.

Multicentre study highlighting clinical relevance of new high-throughput methodologies in molecular epidemiology of Pneumocystis jirovecii pneumonia.

Pneumocystis jirovecii causes severe interstitial pneumonia (PcP) in immunosuppressed patients. This multicentre study assessed the distribution frequencies of epidemiologically relevant genetic markers of P. jirovecii in different geographic populations from Portugal, the USA, Spain, Cuba and Mozambique, and the relationship between the molecular data and the geographical and clinical information, based on a multifactorial approach. The high-throughput typing strategy for P. jirovecii characterization consisted of DNA pooling using quantitative real-time PCR followed by multiplex-PCR/single base extension. The frequencies of relevant P. jirovecii single nucleotide polymorphisms (mt85, SOD110, SOD215, DHFR312, DHPS165 and DHPS171) encoded at four loci were estimated in ten DNA pooled samples representing a total of 182 individual samples. Putative multilocus genotypes of P. jirovecii were shown to be clustered due to geographic differences but were also dependent on clinical characteristics of the populations studied. The haplotype DHFR312T/SOD110C/SOD215T was associated with severe AIDS-related PcP and high P. jirovecii burdens. The frequencies of this genetic variant of P. jirovecii were significantly higher in patients with AIDS-related PcP from Portugal and the USA than in the colonized patients from Portugal, and Spain, and children infected with P. jirovecii from Cuba or Mozambique, highlighting the importance of this haplotype, apparently associated with the severity of the disease and specific clinical groups. Patients from the USA and Mozambique showed higher rates of DHPS mutants, which may suggest the circulation of P. jirovecii organisms potentially related with trimethoprim-sulfamethoxazole resistance in those geographical regions. This report assessed the worldwide distribution of P. jirovecii haplotypes and their epidemiological impact in distinct geographic and clinical populations.

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.

Diagnosis of Pneumocystis pneumonia: evaluation of four serologic biomarkers.

The diagnosis of Pneumocystis pneumonia (PCP) relies on microscopic visualization of Pneumocystis jirovecii organisms or DNA detection in pulmonary specimens. This study aimed to assess the usefulness of (1-3)-ß-d-glucan (BG), Krebs von den Lungen-6 antigen (KL-6), lactate dehydrogenase (LDH) and S-adenosyl methionine (SAM) as serologic biomarkers in the diagnosis of PCP. Serum levels of BG, KL-6, LDH and SAM were investigated in 145 Portuguese patients, 50 patients from the Netherlands, 25 Spanish patients and 40 Portuguese blood donors. Data on clinical presentation, chest imaging and gasometry tests were available. PCP cases were confirmed by microscopy and PCR techniques. A cost-effectiveness analysis was performed. BG was found to be the most reliable serologic biomarker for PCP diagnosis, followed by KL-6, LDH and SAM. The BG/KL-6 combination test was the most accurate serologic approach for PCP diagnosis, with 94.3% sensitivity and 89.6% specificity. Although less sensitive/specific than the reference standard classic methods based on bronchoalveolar lavage followed by microscopic or molecular detection of P. jirovecii organisms, the BG/KL-6 test may provide a less onerous procedure for PCP diagnosis, as it uses a minimally invasive and inexpensive specimen (blood), which may be also a major benefit for the patient's care. The BG/KL-6 combination test should be interpreted within the clinical context, and it may be used as a preliminary screening test in patients with primary suspicion of PCP, or as an alternative diagnostic procedure in patients with respiratory failure or in children, avoiding the associated risk of complications by the use of bronchoscopy.

(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.

Unusual coexistence of opportunistic lung infections in a human immunodeficiency virus positive patient suffering from persistent Pneumocystis jirovecii pneumonia: a case report.

It is well established that HIV patients are at high risk of opportunistic infections (OI), like the ones caused by Pneumocystis jirovecii, a worldwide pathogen implicated in interstitial pneumonia (PcP). We present a case of a newly diagnosed HIV-1 patient with multiple OI, including a persistent form of PcP, an invasive aspergillosis (IA), cytomegalovirus and Mycobacterium xenopi lung infection. We describe the combination of laboratorial screening, surgery and antimicrobial therapy that were crucial for patient recovery.

Study of relationship between osteoarthritis, postural changes and osteoporosis in postmenopausal women / Estudios de la relación entre osteoartritis, las alteraciones posturales y osteoporosis en mujeres posmenopáusicas

Objectives. To verify the relationship between postural changes, osteoarthritis, and bone mineral density in women with osteoporosis in a research group of participants in this area. Methods. Seventy four Brazilian women aged 50 years or older with osteoporosis sent to Clinical Hospital were assessed. After anamnesis the subjects were evaluated in posture with a postural framework. The experimental protocol consisted of two groups: control group (without postural changes) and study group (with postural changes). Results. The age average in the study group was greater than in the control group. In the joint changes, 65 subjects showed osteoarthritis in some part of the body. In the whole group assessed, 19 showed change in posture and all of them have osteoarthritis too. Conclusion. This research showed that posture changes are direct relationship with advanced age. It concluded that posture assessment is essential to prescribe the most objective and efficient exercise program, with understanding of the biomechanical incidence forces, but not forgetting to strengthen the muscles to maintain the corporal posture(AU)

Objetivos. Verificar la relación entre los cambios posturales, la osteoartritis y la densidad mineral ósea en mujeres con osteoporosis en un grupo de investigación de los participantes en esta área. Métodos. Se evaluó a setenta y cuatro mujeres brasileñas de 50 años o mayores con osteoporosis en el Hospital Clínico. Después de anamnesis las mujeres fueron evaluadas respecto a la postura con una cuadrícula postural. El protocolo experimental consistió en dos grupos: grupo control (sin cambios posturales) y el grupo de estudio (con los cambios posturales). Resultados. El promedio de edad en el grupo de estudio fue mayor que en el grupo control. En los cambios en las articulaciones, 65 mujeres mostraron osteoartritis en alguna parte del cuerpo. En todo el grupo evaluado, 19 mostraron un cambio en la postura y todas ellas tenían osteoartritis también. Conclusión. Esta investigación mostró que los cambios posturales tienen relación directa con la edad avanzada. Concluye que la evaluación de la postura es esencial para prescribir el programa de ejercicios más objetivo y eficiente, con la comprensión de las fuerzas biomecánicas de incidencia, pero sin olvidar fortalecer los músculos para mantener la postura corporal(AU)

Pneumocystis jirovecii multilocus genotyping in pooled DNA samples: a new approach for clinical and epidemiological studies.

Specific single-nucleotide polymorphisms (SNPs) are recognized as important DNA sequence variations influencing the pathogenesis of Pneumocystis jirovecii and the clinical outcome of Pneumocystis pneumonia, which is a major worldwide cause of illness among immunocompromised patients. Genotyping platforms for pooled DNA samples are promising methodologies for genetic characterization of infectious organisms. We have developed a new typing strategy for P. jirovecii, which consisted of DNA pools prepared according to clinical data (HIV diagnosis, microscopic and molecular detection of P. jirovecii, parasite burden, clinical diagnosis and follow-up of infection) from individual samples using quantitative real-time PCR followed by multiplex-PCR/single base extension (MPCR/SBE). The frequencies of multiple P. jirovecii SNPs (DHFR312, mt85, SOD215 and SOD110) encoded at three distinct loci, the dihydrofolate reductase (DHFR), the mitochondrial large-subunit rRNA (mtLSU rRNA) and the superoxide dismutase (SOD) loci, were estimated in seven DNA pooled samples, representing a total of 100 individual samples. The studied SNPs were confirmed to be associated with distinct clinical parameters of infection such as parasite burden and follow-up. The MPCR/SBE-DNA pooling methodology, described in the present study, was demonstrated to be a useful high-throughput procedure for large-scale P. jirovecii SNPs screening and a powerful tool for evaluation of clinically relevant SNPs potentially related to parasite burden, clinical diagnosis and follow-up of P. jirovecii infection. In further studies, the candidate SNPs mt85, SOD215 and SOD110 may be used as molecular markers in association with MPCR/SBE-DNA pooling to generate useful information for understanding the patterns and causes of Pneumocystis pneumonia.

Antioxidant and antibacterial activity of essential oil and extracts of bay laurel Laurus nobilis Linnaeus (Lauraceae) from Portugal.

Laurus nobilis L. is an aromatic plant frequently used as a spice in Mediterranean cookery and as a traditional medicine for the treatment of several infectious diseases. The aim of this study was to characterise the antibacterial and antioxidant activities of bay laurel essential oil (EO), ethanolic extract (EE) and hot/cold aqueous extract (AE). The major components detected in bay laurel EO were eucalyptol (27.2%), α-terpinenyl acetate (10.2%), linalool (8.4%), methyleugenol (5.4%), sabinene (4.0%) and carvacrol (3.2%). The EO exhibited strong antibacterial activity against all tested foodborne spoilage and pathogenic bacteria, whereas this activity was less pronounced or even nonexistent in the EE and AE. In contrast, EO exhibited low antioxidant activity compared to extracts (EX), and among the EX, the hot AE revealed the highest antioxidant ability. The results show that bay laurel EO and its EX have potential as natural alternatives to synthetic food preservatives, in order to enhance food safety and increase food shelf life.

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.

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.

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.

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.