Paulo J. Oliveira

Land-Use Allocation Protects the Peruvian Amazon

Disturbance and deforestation have profound ecological and socioeconomic effects on tropical forests, but their diffuse patterns are difficult to detect and quantify at regional scales. We expanded the Carnegie forest damage detection system to show that, between 1999 and 2005, disturbance and deforestation rates throughout the Peruvian Amazon averaged 632 square kilometers per year and 645 square kilometers per year, respectively. However, only 1 to 2% occurred within natural protected areas, indigenous territories contained only 11% of the forest disturbances and 9% of the deforestation, and recent forest concessions effectively protected against clear-cutting. Although the region shows recent increases in disturbance and deforestation rates and leakage into forests surrounding concession areas, land-use policy and remoteness are serving to protect the Peruvian Amazon.

Condition and fate of logged forests in the Brazilian Amazon

The long-term viability of a forest industry in the Amazon region of Brazil depends on the maintenance of adequate timber volume and growth in healthy forests. Using extensive high-resolution satellite analyses, we studied the forest damage caused by recent logging operations and the likelihood that logged forests would be cleared within 4 years after timber harvest. Across 2,030,637 km2 of the Brazilian Amazon from 1999 to 2004, at least 76% of all harvest practices resulted in high levels of canopy damage sufficient to leave forests susceptible to drought and fire. We found that 16 ± 1% of selectively logged areas were deforested within 1 year of logging, with a subsequent annual deforestation rate of 5.4% for 4 years after timber harvests. Nearly all logging occurred within 25 km of main roads, and within that area, the probability of deforestation for a logged forest was up to four times greater than for unlogged forests. In combination, our results show that logging in the Brazilian Amazon is dominated by highly damaging operations, often followed rapidly by deforestation decades before forests can recover sufficiently to produce timber for a second harvest. Under the management regimes in effect at the time of our study in the Brazilian Amazon, selective logging would not be sustained.

Diabetes and the impairment of reproductive function: possible role of mitochondria and reactive oxygen species.

Diabetes Mellitus (DM), a state of chronic hyperglycemia, is a major cause of serious micro and macrovascular diseases, affecting, therefore, nearly every system in the body. Growing evidence indicates that oxidative stress is increased in diabetes due to overproduction of reactive oxygen species (ROS) and decreased efficiency of antioxidant defences, a process that starts very early and worsens over the course of the disease. During the development of diabetes, oxidation of lipids, proteins and DNA increase with time. Mitochondrial DNA mutations have also been reported in diabetic tissues, suggesting oxidative stress-related mitochondrial damage. Diabetes-related oxidative stress may also be the trigger for many alterations on sexual function, which can also include decreased testicular mitochondrial function. Although sexual disorders have been extensively studied in diabetic men, possible changes in the sexual function of diabetic women have only recently received attention. The prevalence of sexual dysfunction in diabetic men approaches 50%, whereas in diabetic women it seems to be slightly lower. Testicular dysfunction, impotence, decreased fertility potential and retrograde ejaculations are conditions that have been described in diabetic males. Diabetes is also the most common cause of erectile dysfunction in men. Poor semen quality has also been reported in diabetic men, including decreased sperm motility and concentration, abnormal morphology and increased seminal plasma abnormalities. In addition, diabetic men may have decreased serum testosterone due to impaired Leydig cell function. Among diabetic women neuropathy, vascular impairment and psychological complaints have been implicated in the pathogenesis of decreased libido, low arousability, decreased vaginal lubrication, orgasmic dysfunction, and dyspareunia. An association between the production of excess radical oxygen species and disturbed embryogenesis in diabetic pregnancies has also been suggested. In fact, maternal diabetes during pregnancy is associated with an increased risk of complications in the offspring, such as altered fetal growth, polyhydramnios, fetal loss and congenital malformations. In addition, hypocalemia and reduced bone mineral content are found in neonates of diabetic mothers. Abnormalities in gametogenesis and sexual function have also been documented in animal models for both types of Diabetes, which thus constitute an important research tool to both study the effects of the disease, and to test novel therapeutical interventions. Because sexuality and fertility are important aspects in the lives of individuals and couples, and considering that over 124 million individuals worldwide suffer from Diabetes, this review highlights the impact of Diabetes and associated oxidative stress on sexual function.

Numerical simulation of non-linear elastic flows with a general collocated finite-volume method

This paper reports the development and application of a finite-volume based methodology for the calculation of the flow of fluids which follow differential viscoelastic constitutive models. The novelty of the method lies on the use of the non-staggered grid arrangement, in which all dependent variables are located at the center of the control volumes, thus greatly simplifying the adoption of general curvilinear coordinates. The pressure‐velocity‐stress decoupling was removed by the development of a new interpolation technique inspired on that of Rhie and Chow, AIAA 82 (1982) 998. The differencing schemes are second order accurate and the resulting algebraic equations for each variable are solved in a segregated way (decoupled scheme). The numerical formulation especially designed for the interpolation of the stress field was found to work well and is shown to be indispensable for accurate results. Calculations have been carried out for two problems: the entry flow problem of Eggleton et al., J. Non-Newtonian Fluid Mech. 64 (1996) 269, with orthogonal and non-orthogonal meshes; and the bounded and unbounded flows around a circular cylinder. The results of the simulations compare favourably with those in the literature and iterative convergence has been attained for Deborah and Reynolds numbers similar to, or higher than, those reported for identical flow problems using other numerical methods. The application of the method with non-orthogonal coordinates is demonstrated. The entry flow problem is studied in more detail and for this case differences between Newtonian and viscoelastic fluids are identified and discussed. Viscoelasticity is shown to be responsible for the development of very intense normal stresses, which are tensile in the wall region. As a consequence, the viscoelastic fluid is more intensely decelerated in the wall region than the Newtonian fluid, thus reducing locally the shear rates and the role of viscosity in redeveloping the flow. A layer of high stress-gradients is formed at the wall leading edge and is convected below and away from the wall; its effect is to intensify the aforementioned deviation of elastic fluid from the wall.

Doxorubicin-induced cardiotoxicity: from bioenergetic failure and cell death to cardiomyopathy.

Doxorubicin (DOX) is an anticancer anthracycline that presents a dose‐dependent and cumulative cardiotoxicity as one of the most serious side effects. Several hypotheses have been advanced to explain DOX cardiac side effects, which culminate in the development of life‐threatening cardiomyopathy. One of the most studied mechanisms involves the activation of DOX molecule into a more reactive semiquinone by mitochondrial Complex I, resulting in increased oxidative stress. The present review describes and critically discusses what is known about some of the potential mechanisms of DOX‐induced cardiotoxicity including mitochondrial oxidative damage and loss of cardiomyocytes. We also discuss alterations of mitochondrial metabolism and the unique characteristics of DOX delayed toxicity, which can also interfere on how the cardiac muscle handles a “second‐hit stress.” We also present pharmaceutical and nonpharmaceutical approaches that may decrease DOX cardiac alterations in animal models and humans and discuss the limitations of each strategy.

Cyanobacterial H2 production — a comparative analysis

Several unicellular and filamentous, nitrogen-fixing and non-nitrogen-fixing cyanobacterial strains have been investigated on the molecular and the physiological level in order to find the most efficient organisms for photobiological hydrogen production. These strains were screened for the presence or absence of hup and hox genes, and it was shown that they have different sets of genes involved in H2 evolution. The uptake hydrogenase was identified in all N2-fixing cyanobacteria, and some of these strains also contained the bidirectional hydrogenase, whereas the non-nitrogen fixing strains only possessed the bidirectional enzyme. In N2-fixing strains, hydrogen was mainly produced by the nitrogenase as a by-product during the reduction of atmospheric nitrogen to ammonia. Therefore, hydrogen production was investigated both under non-nitrogen-fixing conditions and under nitrogen limitation. It was shown that the hydrogen uptake activity is linked to the nitrogenase activity, whereas the hydrogen evolution activity of the bidirectional hydrogenase is not dependent or even related to diazotrophic growth conditions. With regard to large-scale hydrogen evolution by N2-fixing cyanobacteria, hydrogen uptake-deficient mutants have to be used because of their inability to re-oxidize the hydrogen produced by the nitrogenase. On the other hand, fermentative H2 production by the bidirectional hydrogenase should also be taken into account in further investigations of biological hydrogen production.

Benchmark solutions for the flow of Oldroyd-B and PTT fluids in planar contractions

The paper presents very accurate numerical results for the vortex size, the vortex intensity and the Couette correction, in planar contraction flows of Oldroyd-B and PTT fluids ( e = 0.25) with both the linear and the exponential stress function, and with a solvent viscosity ratio equal to 1/9. The accuracy of these results is quantified, being generally below 1% (0.3% for most results), and the finest mesh employed had over 1 million degrees of freedom. Such degree of mesh fineness is shown to be required for accurate results with the Oldroyd-B fluid, especially at high Deborah numbers, but the shear-thinning PTT fluid in general does not require the finest meshes. In terms of level of elasticity, steady results for the PTT fluid could be obtained for values of the Deborah number in excess of 100 (linear PTT) and 10,000 (exponential PTT).

Synthetic Biology in Cyanobacteria: Engineering and Analyzing Novel Functions

Cyanobacteria are the only prokaryotes capable of using sunlight as their energy, water as an electron donor, and air as a source of carbon and, for some nitrogen-fixing strains, nitrogen. Compared to algae and plants, cyanobacteria are much easier to genetically engineer, and many of the standard biological parts available for Synthetic Biology applications in Escherichia coli can also be used in cyanobacteria. However, characterization of such parts in cyanobacteria reveals differences in performance when compared to E. coli, emphasizing the importance of detailed characterization in the cellular context of a biological chassis. Furthermore, cyanobacteria possess special characteristics (e.g., multiple copies of their chromosomes, high content of photosynthetically active proteins in the thylakoids, the presence of exopolysaccharides and extracellular glycolipids, and the existence of a circadian rhythm) that have to be taken into account when genetically engineering them. With this chapter, the synthetic biologist is given an overview of existing biological parts, tools and protocols for the genetic engineering, and molecular analysis of cyanobacteria for Synthetic Biology applications.

Fully developed laminar flow of purely viscous non-Newtonian liquids through annuli, including the effects of eccentricity and inner-cylinder rotation

The results are presented of extensive numerical calculations, carried out using a highly accurate finite-volume method, for the fully developed laminar flow of an inelastic shear-thinning power-law fluid through an eccentric annulus with inner cylinder rotation. Additional calculations are reported for more complex rheological models, including Cross, Carreau and Herschel–Bulkley, which we relate systematically to the power-law model. Comparisons are made with the results of other recent numerical studies. An extensive bibliography is appended of 100 papers additional to those specifically referenced and concerned with theoretical and numerical investigations of laminar flow of non-Newtonian fluids through annular channels. 2002 Elsevier Science Inc. All rights reserved.

Analytical solution for fully developed channel and Pipe Flow of Phan-Thien/Tanner Fluids

Analytical expressions are derived for the velocity vector, the stress components and the viscosity function in fully developed channel and pipe flow of Phan-Thien–Tanner (PTT) fluids; both the linearized and the exponential forms of the PTT equation are considered. The solution shows that the wall shear stress of a PTT fluid is substantially smaller than the corresponding value for a Newtonian or upper-convected Maxwell fluid, with implications for comparing predicted and measured values in a non-dimensional form.