Scale-adaptive surface modeling of vascular structures

Background  

The effective geometric modeling of vascular structures is crucial for diagnosis, therapy planning and medical education. These applications require good balance with respect to surface smoothness, surface accuracy, triangle quality and surface size.     

High-resolution ex vivo magnetic resonance angiography: a feasibility study on biological and medical tissues

Background  

In biomedical sciences, ex vivo angiography is a practical mean to elucidate vascular structures three-dimensionally with simultaneous estimation of intravascular volume. The objectives of this study were to develop a magnetic resonance (MR) method for ex vivo angiography and to compare the findings with computed tomography (CT). To demonstrate the usefulness of this method, examples are provided from four different tissues and species: the human placenta, a rice field eel, a porcine heart and a turtle.     

Effect of non-linearity in predicting doppler waveforms through a novel model

Background  

In pregnancy, the uteroplacental vascular system develops de novo locally in utero and a systemic haemodynamic & bio-rheological alteration accompany it. Any abnormality in the non-linear vascular system is believed to trigger the onset of serious morbid conditions like pre-eclampsia and/or intrauterine growth restriction (IUGR). Exact Aetiopathogenesis is unknown. Advancement in the field of non-invasive doppler image analysis and simulation incorporating non-linearities may unfold the complexities associated with the inaccessible uteroplacental vessels. Earlier modeling approaches approximate it as a linear system.     

CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks

Background  

One-dimensional protein structures such as secondary structures or contact numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of the sequence-structure relationship. Accurate prediction methods will serve as a basis for these and other purposes.     

Immunohistochemical study of N-epsilon-carboxymethyl lysine (CML) in human brain: relation to vascular dementia

Background  

Advanced glycation end-products (AGEs) and their receptor (RAGE) occur in dementia of the Alzheimer's type and diabetic microvascular disease. Accumulation of AGEs relates to risk factors for vascular dementia with ageing, including hypertension and diabetes. Cognitive dysfunction in vascular dementia may relate to microvascular disease resembling that in diabetes. We tested if, among people with cerebrovascular disease, (1) those with dementia have higher levels of neuronal and vascular AGEs and (2) if cognitive dysfunction depends on neuronal and/or vascular AGE levels.     

Modelling the development and arrangement of the primary vascular structure in plants

Background and Aims

The process of vascular development in plants results in the formation of a specific array of bundles that run throughout the plant in a characteristic spatial arrangement. Although much is known about the genes involved in the specification of procambium, phloem and xylem, the dynamic processes and interactions that define the development of the radial arrangement of such tissues remain elusive.

Methods

This study presents a spatially explicit reaction–diffusion model defining a set of logical and functional rules to simulate the differentiation of procambium, phloem and xylem and their spatial patterns, starting from a homogeneous group of undifferentiated cells.

Key Results

Simulation results showed that the model is capable of reproducing most vascular patterns observed in plants, from primitive and simple structures made up of a single strand of vascular bundles (protostele), to more complex and evolved structures, with separated vascular bundles arranged in an ordered pattern within the plant section (e.g. eustele).

Conclusions

The results presented demonstrate, as a proof of concept, that a common genetic–molecular machinery can be the basis of different spatial patterns of plant vascular development. Moreover, the model has the potential to become a useful tool to test different hypotheses of genetic and molecular interactions involved in the specification of vascular tissues.     

Impact of environmental inputs on reverse-engineering approach to network structures

Background  

Uncovering complex network structures from a biological system is one of the main topic in system biology. The network structures can be inferred by the dynamical Bayesian network or Granger causality, but neither techniques have seriously taken into account the impact of environmental inputs.     

A method for aligning RNA secondary structures and its application to RNA motif detection

Background  

Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure alignment. However, existing tools either require a large number of prealigned structures or suffer from high time complexities. This makes it difficult for the tools to process RNAs whose prealigned structures are unavailable or process very large RNA structure databases.     

A mathematical model of venous neointimal hyperplasia formation

Background  

In hemodialysis patients, the most common cause of vascular access failure is neointimal hyperplasia of vascular smooth muscle cells at the venous anastomosis of arteriovenous fistulas and grafts. The release of growth factors due to surgical injury, oxidative stress and turbulent flow has been suggested as a possible mechanism for neointimal hyperplasia.     

Columba: an integrated database of proteins,structures, and annotations

Background  

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures.     

Shift from facilitative to neutral interactions by the cushion plant Silene acaulis along a primary succession gradient

Background

The stress‐gradient hypothesis predicts a shift from facilitative to competitive plant interactions with decreasing abiotic stress. This has been supported by studies along elevation and temperature gradients, but also challenged by the hypothesis of a facilitation collapse at extremely harsh sites. Although facilitation is known to be important in primary succession, few studies have examined these hypotheses along primary succession gradients.

Aim

To examine whether there is a relationship between the presence of the circumpolar cushion plant Silene acaulis and other species, and if so, whether there is a shift between positive and negative interactions along a primary succession gradient in a glacier foreland.

Location

Finse, southern Norway.

Methods

We examined the performance of the common alpine forb Bistorta vivipara, species richness of vascular plants, bryophytes and lichens, and the number of seedlings and fertile vascular plants in S. acaulis cushions, and control plots without S. acaulis, along a succession gradient with increasing distance from a glacier front, and thus decreasing abiotic stress. To examine if S. acaulis cushions modify the abiotic environment, we recorded soil temperature, moisture, organic content and pH in cushions and control plots.

Results

Bistorta vivipara performed better, as shown by bigger leaves in S. acaulis cushions compared to control plots in the harshest part of the gradient close to the glacier. There were few differences in B. vivipara performance between cushion and control plots in the more benign environment further away from the glacier. This suggests a shift from facilitative to mainly neutral interactions by S. acaulis on the performance of B. vivipara with decreasing abiotic stress. A trend, although not significant, of higher vascular species richness and fertility inside S. acaulis cushions along the whole gradient, suggests that S. acaulis also facilitates community‐level species richness. The causal mechanism of this facilitation is likely that the cushions buffer extreme temperatures.

Conclusions

Our results support the stress‐gradient hypothesis for the relationship between the cushion plant S. acaulis and the performance of a single species along a primary succession gradient in a glacier foreland. S. acaulis also tended to increase vascular plant species richness and fertility regardless of stress level along the gradient, suggesting facilitation at the community level. We found no collapse of facilitation at the most stressful end of the gradient in this alpine glacier foreland.     

Edge detection in microscopy images using curvelets

Background  

Despite significant progress in imaging technologies, the efficient detection of edges and elongated features in images of intracellular and multicellular structures acquired using light or electron microscopy is a challenging and time consuming task in many laboratories.     

A knowledge-based structure-discriminating function that requires only main-chain atom coordinates

Background  

The use of knowledge-based potential function is a powerful method for protein structure evaluation. A variety of formulations that evaluate single or multiple structural features of proteins have been developed and studied. The performance of functions is often evaluated by discrimination ability using decoy structures of target proteins. A function that can evaluate coarse-grained structures is advantageous from many aspects, such as relatively easy generation and manipulation of model structures; however, the reduction of structural representation is often accompanied by degradation of the structure discrimination performance.     

Alignment of protein structures in the presence of domain motions

Background  

Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of domains or subdomains with respect to each other. Such movements can impede the identification of structural equivalences when rigid aligners are used.     

A novel FRET pair for detection of parallel DNA triplexes by the LightCycler

Background  

Melting temperature of DNA structures can be determined on the LightCycler using quenching of FAM. This method is very suitable for pH independent melting point (Tm) determination performed at basic or neutral pH, as a high throughput alternative to UV absorbance measurements. At acidic pH quenching of FAM is not very suitable, since the fluorescence of FAM is strongly pH dependent and drops with acidic pH.     

Cα-H···O=C hydrogen bonds contribute to the specificity of RGD cell-adhesion interactions

Background  

The Arg-Gly-Asp (RGD) cell adhesion sequence occurs in several extracellular matrix molecules known to interact with integrin cell-surface receptors. Recently published crystal structures of the extracellular regions of two integrins in complex with peptides containing or mimicking the RGD sequence have identified the Arg and Asp residues as key specificity determinants for integrin recognition, through hydrogen bonding and metal coordination interactions. The central Gly residue also appears to be in close contact with the integrin surface in these structures.     

An image processing approach to computing distances between RNA secondary structures dot plots

Background  

Computing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA structure of interest in a database of structures. Several methods are available for computing distances between RNAs represented as strings or graphs, but none utilize the RNA representation with dot plots. Since dot plots are essentially digital images, there is a clear motivation to devise an algorithm for computing the distance between dot plots based on image processing methods.     

Analysis of xylem sap proteins from Brassica napus

Background  

Substance transport in higher land plants is mediated by vascular bundles, consisting of phloem and xylem strands that interconnect all plant organs.     

Using molecular principal axes for structural comparison: determining the tertiary changes of a FAB antibody domain induced by antigenic binding

Background  

Comparison of different protein x-ray structures has previously been made in a number of different ways; for example, by visual examination, by differences in the locations of secondary structures, by explicit superposition of structural elements, e.g. α-carbon atom locations, or by procedures that utilize a common symmetry element or geometrical feature of the structures to be compared.