Metabolic assessment of human liver transplants from biopsy samples at the donor and recipient stages using high-resolution magic angle spinning 1H NMR spectroscopy

This work presents the first application of high-resolution magic angle spinning (HR-MAS) 1H NMR spectroscopy to human liver biopsy samples, allowing a determination of their metabolic profiles before removal from donors, during cold perfusion, and after implantation into recipients. The assignment of peaks observed in the 1H HR-MAS NMR spectra was aided by the use of two-dimensional J-resolved, TOCSY and 1H-13C HMQC spectra. The spectra were dominated by resonances from triglycerides, phospholipids, and glycogen and from a variety of small molecules including glycerophosphocholine (GPC), glucose, lactate, creatine, acetate, amino acids, and nucleoside-related compounds such as uridine and adenosine. In agreement with histological data obtained on the same biopsies, two of the six livers were found to contain high amounts of triglycerides by NMR spectroscopy, which also indicated that these tissues contained a higher degree of unsaturated lipids and a lower proportion of phospholipids and low molecular weight compounds. Additionally, proton T2 relaxation times indicated two populations of lipids, a higher mobility triglyceride fraction and a lower mobility phospholipid fraction, the proportions of which changed according to the degree of fat content. GPC was found to decrease from the pretransplant to the posttransplant biopsy of all livers except for one with a histologically confirmed high lipid content, and this might represent a biomarker of liver function posttransplantation. NMR signals produced by the liver preservation solution were clearly detected in the cold perfusion stage biopsies of all livers but remained in the posttransplant spectra of only the two livers with a high lipid content and were prominent mainly in the graft that later developed primary graft dysfunction. This study has shown biochemical differences between livers used for transplants that can be related to the degree and type of lipid composition. This technology might therefore provide a novel screening approach for donor organ quality and a means to assess function in the recipient after transplantation.     

Vascular hemodynamics

The vascular system is a complex network transporting blood to and from all parts of the body. It distributes oxygenated and nutrient-rich blood to body tissue via arteries, arterioles, metarterioles, and capillaries. Venules and veins carry deoxygenated blood, cellular wastes, and carbon dioxide to the heart and lungs to be oxygenated or removed. The lymphatic system removes fluid left at the venous end of the capillaries and returns it to the circulatory system by way of the lymphatic ducts. Understanding the vascular system is basic to providing quality nursing care.     

Algorithmic Decision-Making and the Control Problem

Minds and Machines - The danger of human operators devolving responsibility to machines and failing to detect cases where they fail has been recognised for many years by industrial psychologists...     

Enabling computer models of the heart for high-performance computers and the grid

Although it is now feasible to compute multi-cellular models of the heart on a personal desktop or laptop computer, it is not feasible to undertake the detailed sweeps of high-dimensional parameter spaces required if we are to undertake in silico experimentation of the complex processes that constitute heart disease. For this research, modelling requirements move rapidly beyond the limit of commodity computers' resource both in terms of their memory footprint and the speed of calculation, so that multi-processor architectures must be considered. In addition, as such models have become more mature and have been validated against experimental data, there is increasing pressure for experimentalists to be able to make use of these models themselves as a key tool for hypothesis formulation and in planning future experimental studies to test those hypotheses.This paper discusses our initial experiences in a large-scale project (the Integrative Biology (IB) e-Science project) aimed at meeting these dual aims. We begin by putting the research in context by describing in outline the overall aims of the IB project, in particular focusing on the challenge of enabling novice users to make full use of high-performance resources without the need to gain detailed technical expertise in computing. We then discuss our experience of adapting one particular heart modelling package, Cellular Open Resource, and show how the solving engine of this code was dissected from the rest of the package, ported to C++ and parallelized using the Message-Passing Interface. We show that good parallel efficiency and realistic memory reduction can be achieved on simple geometries. We conclude by discussing lessons learnt in this process.     

Mathematical models in physiology

Computational modelling of biological processes and systems has witnessed a remarkable development in recent years. The search-term (modelling OR modeling) yields over 58000 entries in PubMed, with more than 34000 since the year 2000: thus, almost two-thirds of papers appeared in the last 5-6 years, compared to only about one-third in the preceding 5-6 decades. The development is fuelled both by the continuously improving tools and techniques available for bio-mathematical modelling and by the increasing demand in quantitative assessment of element inter-relations in complex biological systems. This has given rise to a worldwide public domain effort to build a computational framework that provides a comprehensive theoretical representation of integrated biological function-the Physiome. The current and next issues of this journal are devoted to a small sub-set of this initiative and address biocomputation and modelling in physiology, illustrating the breadth and depth of experimental data-based model development in biological research from sub-cellular events to whole organ simulations.     

Resistance, capacitance, and electrode kinetic effects in Fourier-transformed large-amplitude sinusoidal voltammetry: emergence of powerful and intuitively obvious tools for recognition of patterns of behavior

Large-amplitude sinusoidal ac voltammetric techniques, when analyzed in the frequency domain using the Fourier transform-inverse Fourier transform sequence, produce the expected dc and fundamental harmonic ac responses in addition to very substantial second, third, and higher ac harmonics that arise from the presence of significant nonlinearity. A full numerical simulation of the process, Red right arrow over left arrow Ox + e(-), incorporates terms for the uncompensated resistance (R(u)), capacitance of the double layer (C(dl)), and slow electron transfer kinetics (in particular, the reversible potential (E degrees ), rate constant (k(0)), and charge transfer coefficient (alpha) from the Butler-Volmer model). Identification of intuitively obvious patterns of behavior (with characteristically different sensitivity regimes) in dc, fundamental, and higher harmonic terms enables simple protocols to be developed to estimate R(u), C(dl), E degrees , k(0), and alpha. Thus, if large-amplitude sinusoidal cyclic voltammograms are obtained for two concentrations of the reduced species, data obtained from analysis of the recovered signals provide initial estimates of parameters as follows: (a) the dc cyclic component provides an estimate of E degrees (because the R(u) and k(0) effects are minimized); (b) the fundamental harmonic provides an estimate of C(dl) (because it has a high capacitance-to-faradaic current ratio); and (c) the second harmonic provides an estimate of R(u), k(0), and alpha (because the C(dl) effect is minimized). Methods of refining the initial estimates are then implemented. As a check on the fidelity of the parameters (estimated on the basis of an essentially heuristic approach that solely utilizes the dc, fundamental, and second harmonic voltammograms), comparison of the predicted simulated and experimental third (or higher) harmonic voltammograms can be made to verify that agreement between theory and experiment has been achieved at a predetermined level. The use of the heuristic pattern recognition approach to evaluate the oxidation of ferrocene at a platinum electrode (a reversible process) in the very high resistance solvent dichloromethane (0.1 M Bu(4)NPF(6)) and the reduction of [Fe(CN(6))](3)(-) at a glassy carbon electrode (a quasi-reversible process) in much lower resistance but higher capacitance conditions found in aqueous (0.5 M KCl) media is described and verifies the inherent advantages of employing large-amplitude sinusoidal techniques in quantitative studies of electrode processes.     

Predicting tumor location by modeling the deformation of the breast

Breast cancer is one of the biggest killers in the western world, and early diagnosis is essential for improved prognosis. The shape of the breast varies hugely between the scenarios of magnetic resonance (MR) imaging (patient lies prone, breast hanging down under gravity), X-ray mammography (breast strongly compressed) and ultrasound or biopsy/surgery (patient lies supine), rendering image fusion an extremely difficult task. This paper is concerned with the use of the finite-element method and nonlinear elasticity to build a 3-D, patient-specific, anatomically accurate model of the breast. The model is constructed from MR images and can be deformed to simulate breast shape and predict tumor location during mammography or biopsy/surgery. Two extensions of the standard elasticity problem need to be solved: an inverse elasticity problem (arising from the fact that only a deformed, stressed, state is known initially), and the contact problem of modeling compression. The model is used for craniocaudal mediolateral oblique mammographic image matching, and a number of numerical experiments are performed.     

Measurement of Internal Acyl Migration Reaction Kinetics Using Directly Coupled HPLC-NMR: Application for the Positional Isomers of Synthetic (2-Fluorobenzoyl)-d-glucopyranuronic Acid

Ester glucuronides (1-O-acyl-β-d-glucopyranuronates) of many drugs may undergo internal acyl migration reactions, resulting in the formation of new positional isomers with both α- and β-anomers. We illustrate here a novel approach for the direct investigation of the acyl migration kinetics of ester glucuronides and show the application with respect to the isomers of synthetic (2-fluorobenzoyl)-d-glucopyranuronic acid. Individual isomers were separated from an equilibrium mixture containing the β-1-O-acyl, α- and β-2-O-acyl, α- and β-3-O-acyl, and α- and β-4-O-acyl isomers at pH 7.4 in 20 mM phosphate buffer. The interconverting isomers were separated using reversed-phase HPLC and pumped directly into a dedicated on-line NMR flow probe in a 600 MHz NMR spectrometer. The flow was stopped with each isomer in the NMR flow probe, and sequential NMR spectra were collected at 25 °C, allowing direct measurement of the production of positional isomers from each selectively isolated glucuronide isomer. All of the positional isomers and anomers were characterized, and relative quantities determined, and a kinetic model describing the rearrangement reactions was constructed. The acyl migration reaction kinetics were simulated using a theoretical approach using nine first-order rate constants determined for the acyl migration reactions and six first-order rate constants describing the mutarotation each of the 2-, 3-, and 4-positional isomers. The rate constants (in h(-)(1)) for the rearrangement reactions of the 2-fluorobenzoyl glucuronide isomers were as follows: β-1-O-acyl, 0.29 ± 0.01; α-2-O-acyl, 0.11 ± 0.01; β-2-O-acyl, 0.07 ± 0.01; α-3-O-acyl, 0.10 ± 0.01; β-3-O-acyl, 0.09 ± 0.01; α-4-O-acyl, 0.09 ± 0.01; and β-4-O-acyl, 0.06 ± 0.01. The α- and β-anomerization rates were estimated on the basis of the kinetics model; the anomerization rates of the 4-O-acyl isomers were additionally determined experimentally using directly coupled HPLC-NMR. The fitted anomerization rates for the 4-O-acyl isomer were 0.80 (α → β) and 0.50 h(-)(1) (β → α), whereas the experimentally estimated anomerization rates were 0.89 ± 0.1 and 0.52 ± 0.1 h(-)(1), respectively. The dynamic stop-flow HPLC-NMR approach allows unique kinetic information to be obtained relating to glucuronide reactivity, and this approach will be useful in future structure-reactivity studies on drug ester glucuronides and their properties.     

Chaste: using agile programming techniques to develop computational biology software

Cardiac modelling is the area of physiome modelling where the available simulation software is perhaps most mature, and it therefore provides an excellent starting point for considering the software requirements for the wider physiome community. In this paper, we will begin by introducing some of the most advanced existing software packages for simulating cardiac electrical activity. We consider the software development methods used in producing codes of this type, and discuss their use of numerical algorithms, relative computational efficiency, usability, robustness and extensibility. We then go on to describe a class of software development methodologies known as test-driven agile methods and argue that such methods are more suitable for scientific software development than the traditional academic approaches. A case study is a project of our own, Cancer, Heart and Soft Tissue Environment, which is a library of computational biology software that began as an experiment in the use of agile programming methods. We present our experiences with a review of our progress thus far, focusing on the advantages and disadvantages of this new approach compared with the development methods used in some existing packages. We conclude by considering whether the likely wider needs of the cardiac modelling community are currently being met and suggest that, in order to respond effectively to changing requirements, it is essential that these codes should be more malleable. Such codes will allow for reliable extensions to include both detailed mathematical models--of the heart and other organs--and more efficient numerical techniques that are currently being developed by many research groups worldwide.