The role of intravascular ultrasound imaging in vascular brachytherapy

Intracoronary brachytherapy has recently emerged as a new therapy to prevent restenosis. Initial experimental work was achieved in animal models and the results were assessed by histomorphometry. Initial clinical trials used angiography to guide dosimetry and to assess efficacy. Intravascular ultrasound (IVUS) permits tomographic examination of the vessel wall, elucidating the true morphology of the lumen and transmural components, which cannot be investigated on the lumenogram obtained by angiography. This paper reviews the use of IVUS in the clinical studies of brachytherapy conducted to date. IVUS allows clinicians to make a thorough assessment of the remodeling of the vessel and appears to have a major role to play in facilitating understanding of the underlying mechanisms of action in this emerging field. The authors propose that state-of-the-art IVUS techniques should be employed to further knowledge of the mechanisms of action of brachytherapy in atherosclerotic human coronary arteries.     

Improving model construction of profile HMMs for remote homology detection through structural alignment

Background  

Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance.     

Taxonomic,functional, and phylogenetic dimensions of rodent biodiversity along an extensive tropical elevational gradient

Relationships among taxonomic, functional, and phylogenetic dimensions of biodiversity provide insight about the relative contributions of ecological and evolutionary processes in structuring local assemblages. We used data for rodent species distributions from an extensive tropical elevational gradient to 1) describe elevational gradients for each of three dimensions of biodiversity, 2) evaluate the sufficiency of species richness as a surrogate for other dimensions, and 3) quantify the relative support for mechanisms that increase or decrease phylogenetic or functional dispersion. Taxonomic biodiversity was quantified by species richness, as well as by richness, evenness, diversity, dominance, and rarity at generic and familial levels. Morphological and categorical traits were used to estimate functional biodiversity, and an ultrametric mammalian supertree was used as the basis for estimating phylogenetic biodiversity. Elevational gradients of each dimension of biodiversity were strong, with significant linear and non‐linear components based on orthogonal polynomial regression. Empirical linear and non‐linear regression components were consistently different than those expected based on species richness for generic, familial, and phylogenetic biodiversity, but not for functional biodiversity. Nevertheless, the congruence of dimensions of biodiversity based on correlation analyses indicated that any one dimension is a useful surrogate for the other dimensions for rodents at Manu. Given variation in species richness, assemblages from lowland rainforests comprised more biodiversity than expected, whereas assemblages from cloud and elfin forests represented less biodiversity than expected. Warm temperatures, vertical complexity of the vegetation, and high productivity likely facilitate niche differentiation in rainforests, whereas cricetid rodents are competitively superior to other clades in the less structurally complex, less productive, and colder, high elevation habitats.     

Myelin basic protein-dependent plasma membrane reorganization in the formation of myelin

During vertebrate development, oligodendrocytes wrap their plasma membrane around axons to produce myelin, a specialized membrane highly enriched in galactosylceramide (GalC) and cholesterol. Here, we studied the formation of myelin membrane sheets in a neuron-glia co-culture system. We applied different microscopy techniques to visualize lipid packing and dynamics in the oligodendroglial plasma membrane. We used the fluorescent dye Laurdan to examine the lipid order with two-photon microscopy and observed that neurons induce a dramatic lipid condensation of the oligodendroglial membrane. On a nanoscale resolution, using stimulated emission depletion and fluorescence resonance energy transfer microscopy, we demonstrated a neuronal-dependent clustering of GalC in oligodendrocytes. Most importantly these changes in lipid organization of the oligodendroglial plasma membrane were not observed in shiverer mice that do not express the myelin basic protein. Our data demonstrate that neurons induce the condensation of the myelin-forming bilayer in oligodendrocytes and that MBP is involved in this process of plasma membrane rearrangement. We propose that this mechanism is essential for myelin to perform its insulating function during nerve conduction.     

Variation in nutrient characteristics of surface soils from the Luquillo Experimental Forest of Puerto Rico: A multivariate perspective

We assessed the effects of landscape features (vegetation type and topography), season, and spatial hierarchy on the nutrient content of surface soils in the Luquillo Experimental Forest (LEF) of Puerto Rico. Considerable spatial variation characterized the soils of the LEF, and differences between replicate sites within each combination of vegetation type (tabonuco vs. palo colorado vs. dwarf vs. pasture) and topographic position (ridge vs valley) accounted for 11–60% of the total variation in soil properties. Nevertheless, mean soil properties differed significantly among vegetation types, between topographic positions, and between seasons (wet vs dry). Differences among vegetation types reflected soil properties (e.g., bulk density, soil moisture, Na, P, C, N, S) that typically are related to biological processes and inputs of water. In forests, differences between topographic positions reflected elements (e.g., Ca, Mg, K, and Al) that typically are associated with geochemical processes; however, the nutrients and elements responsible for topographic differences in dwarf forest were different from those in other forest types. In pastures, differences between topographic positions were associated with the same soil properties responsible for differences among the other vegetation types. Pastures also had reduced N levels and different soil characteristics compared to undisturbed tabonuco forest. The only soil parameter that differed significantly between seasons was soil moisture. Soils of the LEF do not support the contention that N becomes limiting with an increase in elevation, and suggest that absolute pool sizes of N and P are not responsible for the reduction in productivity with elevation.     

Mammals from the Caatinga: an updated list and summary of recent research

The taxonomic status of Caatinga mammals, considered by Mares et al. (1981), is updated herein and a checklist of extant mammals is included. A brief survey of recent contributions to the scientific literature on Caatinga mammals is also provided.     

Short‐Term Responses of Birds to Forest Gaps and Understory: An Assessment of Reduced‐Impact Logging in a Lowland Amazon Forest1

We studied physiognomy‐specific (i.e., gaps vs. understory) responses of birds to low harvest (18.7 m³/ha), reduced‐impact logging by comparing 3500 mist net captures in control and cut blocks of an Amazonian terra firme forest in Brazil at 20–42 mo postharvest. Species richness did not differ significantly between control (92 species) and cut (85) forest based on rarefaction to 1200 captures. Fifty‐six percent of all species were shared between control and cut forest, compared to the 64 percent shared between control blocks. Higher captures of nectarivores and frugivores in cut forest likely occurred as a consequence of postharvest resource blooms. Higher captures of some insectivores in cut as compared to control forest were unexpected, attributable to increased wandering or shifts from association with midstory to understory as a consequence of habitat alteration. Logging influenced capture rates for 21 species, either consistently, or via positive interaction with physiognomy or time (13 species higher in cut forest and 8 species higher in control forest). Cut understory sites had lower diversity (H′) and scaled dominance than understory and gap sites in control forest. Temporal changes in captures may have resulted from successional dynamics in cut forest: two guilds and three species increased in abundance. Increases in abundances of guilds and particular species were more prevalent in control than in cut forest, suggesting that logging displaced birds to control forest. In general, the effects of logging were relatively minor; low harvest rates and reduced‐impact methods may help to retain aspects of avian biodiversity in Amazon forest understories.