Improving resolution in multidimensional NMR using random quadrature detection with compressed sensing reconstruction

NMR spectroscopy is central to atomic resolution studies in biology and chemistry. Key to this approach are multidimensional experiments. Obtaining such experiments with sufficient resolution, however, is a slow process, in part since each time increment in every indirect dimension needs to be recorded twice, in quadrature. We introduce a modified compressed sensing (CS) algorithm enabling reconstruction of data acquired with random acquisition of quadrature components in gradient-selection NMR. We name this approach random quadrature detection (RQD). Gradient-selection experiments are essential to the success of modern NMR and with RQD, a 50 % reduction in the number of data points per indirect dimension is possible, by only acquiring one quadrature component per time point. Using our algorithm (CS_RQD), high quality reconstructions are achieved. RQD is modular and combined with non-uniform sampling we show that this provides increased flexibility in designing sampling schedules leading to improved resolution with increasing benefits as dimensionality of experiments increases, with particular advantages for 4- and higher dimensional experiments.

11-interval PFG pulse sequence for improved measurement of fast velocities of fluids with high diffusivity in systems with short T2(∗)

Magnetic resonance (MR) was used to measure SF6 gas velocities in beds filled with particles of 1.1 mm and 0.5 mm in diameter. Four pulse sequences were tested: a traditional spin echo pulse sequence, the 9-interval and 13-interval pulse sequence of Cotts et al. (1989) and a newly developed 11-interval pulse sequence. All pulse sequences measured gas velocity accurately in the region above the particles at the highest velocities that could be achieved (up to 0.1 ms(-1)). The spin echo pulse sequence was unable to measure gas velocity accurately in the bed of particles, due to effects of background gradients, diffusivity and acceleration in flow around particles. The 9- and 13-interval pulse sequence measured gas velocity accurately at low flow rates through the particles (expected velocity <0.06 ms(-1)), but could not measure velocity accurately at higher flow rates. The newly developed 11-interval pulse sequence was more accurate than the 9- and 13-interval pulse sequences at higher flow rates, but for velocities in excess of 0.1 ms(-1) the measured velocity was lower than the expected velocity. The increased accuracy arose from the smaller echo time that the new pulse sequence enabled, reducing selective attenuation of signal from faster moving nuclei.

Grain sizing in porous media using Bayesian magnetic resonance

We introduce a Bayesian inference approach to analyze magnetic resonance data of granular solids. To characterize structure using magnetic resonance, it is usual to acquire data in k space which are then Fourier transformed to obtain an image. An alternative approach, adopted here, is to utilize the Rayleigh distribution observed in the signal intensity for a given k when a random selection of grains is measured in k space, to define a likelihood function for Bayesian analysis. This Bayesian likelihood function is used to noninvasively characterize grains within a porous medium on length scales below the practical resolution of magnetic resonance imaging. A pore size distribution is then calculated from the measured grain size distribution using a Monte Carlo approach. We demonstrate this general technique with specific examples of water-saturated rock cores.

Extending the use of Earth's Field NMR using Bayesian methodology: application to particle sizing

There is currently much interest in extending the use of low-field magnetic resonance measurements and in particular, to obtain spatial information from these data. Here, we demonstrate the application of a Bayesian magnetic resonance approach for the sizing of objects using low magnetic field measurement technology, where there is insufficient signal-to-noise to allow a conventional imaging approach for structural characterisation. The method is illustrated in application to the sizing of spheres, in this case of radius 9.5mm, using an Earth's Field Nuclear Magnetic Resonance (EFNMR) spectrometer with pre-polarisation. Numerical simulations of the measurement at different signal-to-noise ratios and implementation of different k-space sampling schemes are considered to identify the optimal experimental protocol. In this example, the determination of sphere radius is found to be accurate to ±1mm. We confirm that the posterior distribution provides an accurate estimate of the uncertainty in the measurement.

A Bayesian approach to characterising multi-phase flows using magnetic resonance: application to bubble flows

Magnetic Resonance (MR) imaging is difficult to apply to multi-phase flows due to both the inherently short T₂* characterising such systems and the relatively long time taken to acquire the data. We develop a Bayesian MR approach for analysing data in k-space that eliminates the need for image acquisition, thereby significantly extending the range of systems that can be studied. We demonstrate the technique by measuring bubble size distributions in gas-liquid flows. The MR approach is compared with an optical technique at a low gas fraction (∼2%), before being applied to a system where the gas fraction is too high for optical measurements (∼15%).

Magnetic resonance measurements of high-velocity particle motion in a three-dimensional gas-solid spouted bed

Magnetic resonance imaging has been used to measure particle velocities, exceeding 1 m s⁻¹ in a two-phase granular system, namely, a spouted bed. The measurements are complicated due to the high voidage, i.e., low particle density, in the region of the highest particle velocity. However, applying gradient shapes which allow fast switching and, thus, short encoding and observation times in combination with a short echo time enable these measurements. It was found that the profile of the particle velocity is nonparabolic. Based on these measurements it was possible to confirm observations made in numerical simulations that there must be a continuous momentum exchange between the annulus region and the spout along the entire length of the spout.

Reducing data acquisition times in phase-encoded velocity imaging using compressed sensing

We present a method for accelerating the acquisition of phase-encoded velocity images by the use of compressed sensing (CS), a technique that exploits the observation that an under-sampled signal can be accurately reconstructed by utilising the prior knowledge that it is sparse or compressible. We present results of both simulated and experimental measurements of liquid flow through a packed bed of spherical glass beads. For this system, the best image reconstruction used a spatial finite-differences transform. The reconstruction was further improved by utilising prior knowledge of the liquid distribution within the image. Using this approach, we demonstrate that for a sampling fraction of approximately 30% of the full k-space data set, the velocity can be recovered with a relative error of 11%, which is below the visually detectable limit. Furthermore, the error in the total flow measured using the CS reconstruction is <3% for sampling fractions > or = 30%. Thus, quantitative velocity images were obtained in a third of the acquisition time required using conventional imaging. The reduction in data acquisition time can also be exploited in acquiring images at a higher spatial resolution, which increases the accuracy of the measurements by reducing errors arising from partial volume effects. To illustrate this, the CS algorithm was used to reconstruct gas-phase velocity images at a spatial resolution of 230 microm x 230 microm. Images at this spatial resolution are prohibitively time-consuming to acquire using full k-space sampling techniques.

Magnetic resonance velocity imaging of liquid and gas two-phase flow in packed beds

Single-phase liquid flow in porous media such as bead packs and model fixed bed reactors has been well studied by MRI. To some extent this early work represents the necessary preliminary research to address the more challenging problem of two-phase flow of gas and liquid within these systems. In this paper, we present images of both the gas and liquid velocities during stable liquid-gas flow of water and SF(6) within a packing of 5mm spheres contained within columns of diameter 40 and 27 mm; images being acquired using (1)H and (19)F observation for the water and SF(6), respectively. Liquid and gas flow rates calculated from the velocity images are in agreement with macroscopic flow rate measurements to within 7% and 5%, respectively. In addition to the information obtained directly from these images, the ability to measure liquid and gas flow fields within the same sample environment will enable us to explore the validity of assumptions used in numerical modelling of two-phase flows.

Pulse wave analysis is a reproducible technique for measuring central blood pressure during hemodynamic perturbations induced by exercise

BACKGROUND

Central blood pressure (BP) and markers of wave reflection (augmentation index; AIx) measured by radial tonometry have prognostic value independent from brachial BP. The measurement of the central waveform is increasingly used during altered hemodynamics, including exercise, but reliability of the test has not been reported under changed loading conditions. This study aimed to test the technique's reproducibility during major hemodynamic perturbations induced by exercise.

METHODS

Radial waveforms were recorded (SphygmoCor) in 28 healthy subjects (aged 53 +/- 11 years) at rest, during submaximal exercise (cycling at 50, 60, and 70% of maximal age-predicted heart rate (HR)) and immediately after maximal treadmill exercise on two occasions separated by 9 +/- 5 days. Data were compared between testing days. Waveforms were calibrated with brachial BP measured using a mercury sphygmomanometer. Pulse pressure amplification (PPAmp) was defined as the ratio of brachial to central pulse pressure.

RESULTS

There was very good reproducibility between visits at all exercise intensities for all waveform measures, including AIx, central pulse pressure, and PPAmp (intraclass correlations at 50% exercise were 0.93, 0.89, and 0.89, respectively; P < 0.001). The mean difference between tests at this intensity was 0 +/- 4% for AIx, 4 +/- 6 mm Hg for central pulse pressure, and -0.02 +/- 0.09 for PPAmp. There were no significant differences between visits for HR, PPAmp, or AIx at rest or with exercise (P > 0.05 for all).

CONCLUSIONS

Radial tonometry is a reproducible technique for measurement of central waveform indices during perturbations induced by exercise. It should, therefore, be suitable for use in intervention studies in which hemodynamics are altered.

Determining NMR flow propagator moments in porous rocks without the influence of relaxation

Flow propagators, used for the study of advective motion of brine solution in porous carbonate and sandstone rocks, have been obtained without the influence of Nuclear Magnetic Resonance (NMR) relaxation times, T1 and T2. These spin relaxation mechanisms normally result in a loss of signal that varies depending on the displacement zeta of the flowing spins, thereby preventing the acquisition of quantitative propagator data. The full relaxation behaviour of the system under flow needs to be characterised to enable the implementation of a true quantitative measurement. Two-dimensional NMR correlations of zeta-T2 and T1-T2 are used in combination to provide the flow propagators without relaxation weighting. T1-zeta correlations cannot be used due to the loss of T1 information during the displacement observation time Delta. Here the moments of the propagators are extracted by statistical analysis of the full propagator shape. The measured displacements (first moments) are seen to correlate with the expected mean displacements for long observation times Delta. The higher order moments of the propagators determined by this method indicate those obtained previously using a correction were overestimated.

Spatially resolved quantification of metal ion concentration in a biofilm-mediated ion exchanger

A bioremediation process to remove Co(2+) from aqueous solution is investigated in this study using a magnetic resonance imaging (MRI) protocol to rapidly obtain multiple 2D spatially resolved Co(2+) ion concentration maps. The MRI technique is described in detail and its ability to determine the evolution in both axial and radial concentration profiles demonstrated, from which total column capacity can be determined. The final ion exchange column design allows operation in the 'plug flow' regime, hence making use of its full capacity before breakthrough. Conventional techniques for such process optimization are either restricted to the analysis of the exchanger outlet, which provides no information on the spatial heterogeneity of the system, or are invasive and need a variety of sample points to obtain 1D concentration information. To the best of our knowledge, our results represent the first concentration maps describing the bioremediation of metal ion contaminated water.

Time-of-flight variant to image mixing of granular media in a 3D fluidized bed

This paper describes a variant of time-of-flight magnetic resonance (MR) imaging that provides a method of measuring the inherent mixing in a fluidized bed without the introduction of tracer particles. The modifications to conventional time-of-flight imaging enable the measurement of the axial mixing of a precisely controlled initial particle distribution, thereby providing measurements suitable for a direct comparison with models of solids mixing in granular systems. The imaging sequence is applied to characterize mixing, over time scales of 25-1000 ms, in a gas-fluidized bed of Myosotis seed particles; mixing over short timescales, inaccessible using conventional tracer techniques, is studied using this technique. The mixing pattern determined by this pulse sequence is used in conjunction with MR velocity images of the motion of the particles to provide new insight into the mechanism of solids mixing in granular systems.

Rapid two-dimensional imaging of bubbles and slugs in a three-dimensional, gas-solid, two-phase flow system using ultrafast magnetic resonance

Ultrafast magnetic resonance has been applied to measure the geometry of bubbles and slugs in a three-dimensional gas-solid two-phase flow. A bed of particles of diameter 0.5 mm were fluidized with gas velocities in the range of 0.08-0.26 m/s. Bubbles were imaged in transverse as well as vertical planes with an acquisition time of down to 25 ms and a spatial resolution down to 1.7 mm. Owing to the ultrafast character of these measurements, it is not only possible to evaluate correlations, e.g., for the bubble diameter, but also evaluate models of complex hydrodynamic phenomena, such as the splitting and coalescence of bubbles.

Quantitative magnetic resonance imaging of urea and lysozyme in protein chromatography

Magnetic resonance imaging (MRI) techniques have been implemented to enable quantitative imaging of protein and urea within a 5 ml HiTrap size-exclusion chromatography desalting column, without introduction of contrast agents. One-, two- and three-dimensional images of urea injected at concentrations of 2, 4, 6 and 8 M were acquired. One-dimensional profiles of lysozyme at concentrations between 5 and 25 mg ml(-1) were also obtained. All data were accurate to within +/- 15% when compared to the known amount injected. Quantitative MRI elution profiles of both urea and lysozyme were then obtained in real-time during a desalting separation.

Applications of fast diffusion measurement using Difftrain

Novel applications of fast self-diffusion measurement are presented. Difftrain (Diffusion train), which uses successive stimulated echoes from a single excitation pulse where a portion of the available magnetisation is recovered for each echo, is used to measure self-diffusion by varying the observation time. It is applied to produce the droplet size distribution of an oil-in-water emulsion in less than 4s. This is verified by comparison with the droplet size distribution produced by a standard pulsed field gradient (PFG) technique. Difftrain is also extended to enable the application of incremental gradients, in addition to varying the observation time. This is used to produce propagators or displacement probabilities of water flowing through a packed bed for a range of 16 observation times in under 10 min. Again verification is provided by acquisition of the same propagators using a conventional PFG technique.

Operative field contamination by the sweating surgeon

BACKGROUND

There are a number of factors relating to the host, bacteria and wound that are important in the development of wound infection. The effect of the surgeon sweating has not been previously reported.

METHODS

Ten surgeons performed a mock total hip joint operation under sterile conditions while not sweating and then repeated the operation while sweating. Settle plates were used to quantify the bacterial counts in the operative field in both phases.

RESULTS

For each subject a mean of 3.3 colony forming units (c.f.u.) were present in the non-sweating phase and 6.9 c.f.u. were present in the sweating phase (P < 0.05). Organisms grown were normal skin flora.

CONCLUSION

The sweating surgeon may be more likely to contaminate the surgical field than the non-sweating surgeon. It is important for orthopaedic surgeons, especially those performing joint replacement surgery, to be aware of this and to take measures to minimize sweating in the operating theatre.

Anterograde transport of herpes simplex virus type 1 in cultured, dissociated human and rat dorsal root ganglion neurons

The mechanism of anterograde transport of herpes simplex virus was studied in cultured dissociated human and rat dorsal root ganglion neurons. The neurons were infected with HSV-1 to examine the distribution of capsid (VP5), tegument (VP16), and glycoproteins (gC and gB) at 2, 6, 10, 13, 17, and 24 h postinfection (p.i.) with or without nocodazole (a microtubule depolymerizer) or brefeldin A (a Golgi inhibitor). Retrogradely transported VP5 was detected in the cytoplasm of the cell body up to the nuclear membrane at 2 h p.i. It was first detected de novo in the nucleus and cytoplasm at 10 h p.i., the axon hillock at 13 h p.i., and the axon at 15 to 17 h p.i. gC and gB were first detected de novo in the cytoplasm and the axon hillock at 10 h p.i. and then in the axon at 13 h p.i., which was always earlier than the detection of VP5. De novo-synthesized VP16 was first detected in the cytoplasm at 10 to 13 h p.i. and in the axon at 16 to 17 h p.i. Nocodazole inhibited the transport of all antigens, VP5, VP16, and gC or gB. The kinetics of inhibition of VP5 and gC could be dissociated. Brefeldin A inhibited the transport of gC or gB and VP16 but not VP5 into axons. Transmission immunoelectron microscopy confirmed that there were unenveloped nucleocapsids in the axon with or without brefeldin A. These findings demonstrate that glycoproteins and capsids, associated with tegument proteins, are transported by different pathways with slightly differing kinetics from the nucleus to the axon. Furthermore, axonal anterograde transport of the nucleocapsid can proceed despite the loss of most VP16.

Anterograde transport of herpes simplex virus proteins in axons of peripheral human fetal neurons: an immunoelectron microscopy study

Herpes simplex virus (HSV) reactivates from latency in the neurons of dorsal root ganglia (DRG) and is subsequently transported anterogradely along the axon to be shed at the skin or mucosa. Although we have previously shown that only unenveloped nucleocapsids are present in axons during anterograde transport, the mode of transport of tegument proteins and glycoproteins is not known. We used a two-chamber culture model with human fetal DRG cultivated in an inner chamber, allowing axons to grow out and penetrate an agarose barrier and interact with autologous epidermal cells in the outer chamber. After HSV infection of the DRG, anterograde transport of viral components could be examined in the axons in the outer chamber at different time points by electron and immunoelectron microscopy (IEM). In the axons, unenveloped nucleocapsids or focal collections of gold immunolabel for nucleocapsid (VP5) and/or tegument (VP16) were detected. VP5 and VP16 usually colocalized in both scanning and transmission IEM. In contrast, immunolabel for glycoproteins gB, gC, and gD was diffusely distributed in axons and was rarely associated with VP5 or VP16. In longitudinal sections of axons, immunolabel for glycoprotein was arrayed along the membranes of axonal vesicles. These findings provide evidence that in DRG axons, virus nucleocapsids coated with tegument proteins are transported separately from glycoproteins and suggest that final assembly of enveloped virus occurs at the axon terminus.

The axonal transmission of herpes simplex virus to epidermal cells: a novel use of the freeze substitution technique applied to explant cultures retained on cover slips

Retaining the ultrastructural arrangement of a mixed-cell culture on a solid support while processing for immunocytochemical study is a technical challenge. We developed a technique to study the axonal transport of the Herpes simplex virus from dorsal root ganglia sensory neurones to epidermal cells. Autologous explants of human foetal dorsal root ganglia and skin were cultured on plastic cover slips. Axon fascicles grew from the ganglia to the epidermal cells and the ganglia were inoculated selectively with virus. The whole preparation, retained on the cover slip, was fixed with formaldehyde 4% (freshly prepared from paraformaldehyde)/glutaraldehyde 0.1%, processed by freeze substitution, and embedded in Lowicryl HM20 resin. The edges of the cover slip in the block were trimmed, allowing clean and complete separation from the resin block, which retained the tissue. The resin block was placed in fresh HM20 and repolymerized. The polymerizing resin bonded strongly to the existing block. After trimming, serial sections were easily obtained and successfully immunolabelled for viral proteins. This is a convenient technique for immunolabelling tissue grown on cover slips in which the preservation of the ultrastructural interactions between different cells is important. It should be adaptable to a number of cell-culture applications and has a number of advantages over other techniques.

Emerging viruses

An emerging virus is a term applied to a newly discovered virus, one that is increasing in incidence or with the potential to increase in incidence. Many viruses fit into this definition. HIV is the clearest example of a previously unknown virus that has now produced one of the largest pandemics in history. Recent advances have occurred in the identification and understanding of new hantaviruses in the Americas, causing an acute respiratory disease. The possible causal role of human herpesvirus 8 in Kaposi's sarcoma has gained support, whereas that of a newly discovered flavivirus in causing hepatitis has not been confirmed. A major advance has been evidence showing that the bovine spongiform encephalopathy agent is almost certainly the cause of a new variant of Creutzfeldt-Jakob disease. Although new viruses are discovered almost yearly (e.g., Australian bat lyssavirus), other "older" viruses (e.g., dengue) are reemerging, infecting millions of people every year with significant mortality.

A comparison of chemical dipsticks read visually or by photometry in the routine screening of urine specimens in the clinical microbiology laboratory

Two different commercially available urine dipsticks were evaluated to determine their usefulness as a screening test for the detection of non-infected urine specimens. The reactions of both dipstick strips were read visually and, in addition, one was read by semi-automated reflectance photometry. 2928 consecutive routine urine specimens received by the microbiology laboratory during normal working hours underwent testing by the conventional method of microscopy and culture and the results were compared with those obtained by dipstick testing. There were poor correlations between microscopy for red and white blood cells and dipstick results for blood and leucocyte esterase respectively. The dipsticks had a low positive predictive value (PPV) in identifying infected urines. In contrast, dipsticks had a very high negative predictive value (NPV) of 98.6-99.5% and correctly identified a significant proportion (about 1/3) of non-infected urines as reported by the conventional method. Introduction of dipstick testing of urine specimens in our hospital has led to significant time saving as dipstick-negative urines are not processed further (except for specific clinical indications) and there has also been a significant decrease (25%) in the number of specimens submitted to the laboratory. Further efficiencies may be obtainable with increased automation.

Mycobacterium neoaurum infection of a Hickman catheter in an immunosuppressed patient

Mycobacterium neoaurum is a rapidly growing mycobacterium that has only once before been reported as a cause of bacteremia in an immunocompromised patient. We report on a patient who developed bacteremia after an allogeneic bone marrow transplantation and from whose blood (taken via a Hickman catheter) M. neoaurum was isolated on three separate occasions. There was a clinical response to therapy with ticarcillin/clavulanate and tobramycin, and the organism appeared to be susceptible to the former in vitro. The Hickman catheter was removed because of persistence of the organism in cultures of blood taken from the catheter. M. neoaurum may be a rare cause of infections in immunocompromised patients and should not be dismissed as an environmental contaminant.

Antimicrobial therapy and prevention of spontaneous bacterial peritonitis

Spontaneous bacterial peritonitis is a frequent and serious infection in cirrhotic patients with ascites. A high index of suspicion is required for early diagnosis and rapid institution of treatment. The common micro-organisms involved in SBP are the aerobic Gram-negative bacilli and Gram-positive cocci that inhabit the intestine. Empiric antibiotic therapy active against these organisms should be instituted as soon as possible to improve survival. Third generation cephalosporins are very effective and safe as the initial empiric antibiotic regimen. Alternatives include beta-lactam-clavulanic acid combinations and other broad-spectrum antibiotics, although cost benefit considerations are important in selection. If cultures and susceptibility tests allow, antibiotic therapy should be altered to provide optimum narrow-spectrum and cost-effective treatment. Recent evidence suggests that (at least in the case of cefotaxime), 5-day treatment is equally effective as 10-day treatment. Except in patients awaiting liver transplantation, antibiotic prophylaxis of SBP is not recommended at present, as the few trials performed have not been able to demonstrate superior results for survival, hospital admissions or cost-effectiveness, over prompt diagnosis and therapy of individual episodes of SBP.

H Uptake and Extrusion by Nitella clavata

Very high rates of H(+) extrusion by internodal cells of Nitella clavata Kutz were measured after acid loading at pH 4.6. The highest rate observed, 160 picomoles per square centimeter per second, was more than twice the rate of photosynthetic bicarbonate utilization under saturating light. These results are consistent with the recently proposed hypothesis that bicarbonate is not taken in directly but is protonated at the exterior surface; the CO(2) thereby formed diffuses preferentially into the cell because of the asymmetric concentration gradient.The H(+) taken up, about 150 nanomoles per square centimeter in 2 hours, was distributed in three fractions: 30% in the cell wall, 40% in the cytoplasm, and 30% in the vacuole. This was concluded from the kinetics of the H(+) release by intact cells and isolated walls, and from the pH decrease of the vacuolar sap.The cytoplasmic H(+) was extruded rapidly, with a half-time of about 2 minutes when the external pH was 5.7 or higher. The extrusion of the vacuolar H(+) only proceeded at a measurable rate when the [K(+)] in the medium was raised to 20 millimolar; the half-time was about 100 minutes. There was little H(+) extruded when the external pH was 5.0.