Optimization of spatial resolution for peripheral magnetic resonance angiography.

RATIONALE AND OBJECTIVES: To determine optimum spatial resolution when imaging peripheral arteries with magnetic resonance angiography (MRA). MATERIALS AND METHODS: Eight vessel diameters ranging from 1.0 to 8.0 mm were simulated in a vascular phantom. A total of 40 three-dimensional flash MRA sequences were acquired with incremental variations of fields of view, matrix size, and slice thickness. The accurately known eight diameters were combined pairwise to generate 22 "exact" degrees of stenosis ranging from 42% to 87%. Then, the diameters were measured in the MRA images by three independent observers and with quantitative angiography (QA) software and used to compute the degrees of stenosis corresponding to the 22 "exact" ones. The accuracy and reproducibility of vessel diameter measurements and stenosis calculations were assessed for vessel size ranging from 6 to 8 mm (iliac artery), 4 to 5 mm (femoro-popliteal arteries), and 1 to 3 mm (infrapopliteal arteries). Maximum pixel dimension and slice thickness to obtain a mean error in stenosis evaluation of less than 10% were determined by linear regression analysis. RESULTS: Mean errors on stenosis quantification were 8.8% +/- 6.3% for 6- to 8-mm vessels, 15.5% +/- 8.2% for 4- to 5-mm vessels, and 18.9% +/- 7.5% for 1- to 3-mm vessels. Mean errors on stenosis calculation were 12.3% +/- 8.2% for observers and 11.4% +/- 15.1% for QA software (P = .0342). To evaluate stenosis with a mean error of less than 10%, maximum pixel surface, the pixel size in the phase direction, and the slice thickness should be less than 1.56 mm2, 1.34 mm, 1.70 mm, respectively (voxel size 2.65 mm3) for 6- to 8-mm vessels; 1.31 mm2, 1.10 mm, 1.34 mm (voxel size 1.76 mm3), for 4- to 5-mm vessels; and 1.17 mm2, 0.90 mm, 0.9 mm (voxel size 1.05 mm3) for 1- to 3-mm vessels. CONCLUSION: Higher spatial resolution than currently used should be selected for imaging peripheral vessels.

High-resolution selective three-dimensional magnetic resonance coronary angiography with navigator-echo technique: segment-by-segment evaluation of coronary artery stenosis.

PURPOSE: To investigate the feasibility of high-resolution selective three-dimensional (3D) magnetic resonance coronary angiography (MRCA) in the evaluation of coronary artery stenoses. MATERIALS AND METHODS: In 12 patients with coronary artery stenoses, MRCA of the coronary artery groups, including the coronary segments with stenoses of 50% or greater based on conventional x-ray coronary angiography (CAG), was performed with double-oblique imaging planes by orienting the 3D slab along the major axis of each right coronary artery-left circumflex artery (RCA-LCX) group and each left main trunk-left anterior descending artery (LMT-LAD) group. Ten RCA-LCX and five LMT-LAD MR angiograms were obtained, and the results were compared with those of conventional x-ray angiography. RESULTS: Among 70 coronary artery segments expected to be covered, a total of 49 (70%) segments were fully demonstrated in diagnostic quality. The identification of segmental location of stenoses showed as high an accuracy as 96%. The retrospective analysis for stenosis of 50% or greater yielded the sensitivity, specificity, and accuracy of 80%, 85%, and 84%, respectively. CONCLUSION: Selective 3D MRCA has the potential for segment-by-segment evaluation of major portions of the right and left coronary arteries with high accuracy.

Active Learning of Very-High Resolution Optical Imagery with SVM: Entropy vs Margin Sampling

An active learning method is proposed for the semi-automatic selection of training sets in remote sensing image classification. The method adds iteratively to the current training set the unlabeled pixels for which the prediction of an ensemble of classifiers based on bagged training sets show maximum entropy. This way, the algorithm selects the pixels that are the most uncertain and that will improve the model if added in the training set. The user is asked to label such pixels at each iteration. Experiments using support vector machines (SVM) on an 8 classes QuickBird image show the excellent performances of the methods, that equals accuracies of both a model trained with ten times more pixels and a model whose training set has been built using a state-of-the-art SVM specific active learning method

Ultra-high pressure liquid chromatography-mass spectrometry for plant metabolomics: a systematic comparison of high-resolution quadrupole-time-of-flight and single stage Orbitrap mass spectrometers.

The response of Arabidopsis to stress caused by mechanical wounding was chosen as a model to compare the performances of high resolution quadrupole-time-of-flight (Q-TOF) and single stage Orbitrap (Exactive Plus) mass spectrometers in untargeted metabolomics. Both instruments were coupled to ultra-high pressure liquid chromatography (UHPLC) systems set under identical conditions. The experiment was divided in two steps: the first analyses involved sixteen unwounded plants, half of which were spiked with pure standards that are not present in Arabidopsis. The second analyses compared the metabolomes of mechanically wounded plants to unwounded plants. Data from both systems were extracted using the same feature detection software and submitted to unsupervised and supervised multivariate analysis methods. Both mass spectrometers were compared in terms of number and identity of detected features, capacity to discriminate between samples, repeatability and sensitivity. Although analytical variability was lower for the UHPLC-Q-TOF, generally the results for the two detectors were quite similar, both of them proving to be highly efficient at detecting even subtle differences between plant groups. Overall, sensitivity was found to be comparable, although the Exactive Plus Orbitrap provided slightly lower detection limits for specific compounds. Finally, to evaluate the potential of the two mass spectrometers for the identification of unknown markers, mass and spectral accuracies were calculated on selected identified compounds. While both instruments showed excellent mass accuracy (<2.5ppm for all measured compounds), better spectral accuracy was recorded on the Q-TOF. Taken together, our results demonstrate that comparable performances can be obtained at acquisition frequencies compatible with UHPLC on Q-TOF and Exactive Plus MS, which may thus be equivalently used for plant metabolomics.

A New Year's Resolution - be smart about your drinking!

Now 2012 has arrived, the Public Health Agency is encouraging people to make a New Year's resolution to know their limits when it comes to alcohol, not to drink excessively and to cut back for a while, especially if the festive period led to a little too much consumption.Owen O'Neill, PHA Health and Social Wellbeing Improvement Manager and drugs and alcohol lead, explained: "The New Year is a great opportunity for us to be positive about our health, making resolutions that make us look and feel better. If people choose to drink, staying within the safe drinking limits is important. Excessive and binge drinking can have lasting effects on health, such as damage to the liver, heart, brain and stomach. Drinking too much can also increase the risk of accidents and antisocial behaviour as well as sexually transmitted infections and unplanned pregnancy. And it doesn't have to be drinking to extremes - regularly drinking over the recommended limits can have a damaging effect."Remember that for each unit you drink over the daily limit, the risk to your health increases. It's important to spread the units throughout the week and not 'save' them for the weekend and to drink plenty of water, ideally matching the amount of alcohol you have consumed."For those who have consumed a lot of alcohol over the festive season, cutting back in the New Year and being careful can have immediate, positive effects particularly on helping you to look and feel better, being less tired during the day, feeling fitter and perhaps losing weight. Longer term, the benefits include improved mood, sleep, memory and general health, particularly improving liver function, immunity to illness and preventing any damage caused by any excessive drinking getting any worse."Daily alcohol limits are recommended by the government to avoid the dangers of excessive and binge drinking in any one session. These are:MenNo more than 3 to 4 units of alcohol a day and no more than 21 units over the course of the week.WomenNo more than 2 to 3 units of alcohol a day and no more than 14 units over the course of the week.Examples of units:Can of extra strong lager - 4 unitsBottle of lager - 1.5 unitsSmall pub bottle of wine - 2.25 unitsPub measure of spirits - 1.5 unitsPint of stout - 2.5 unitsPint of cider - 3 unitsFor further information on sensible drinking and alcohol units visit the Public Health Agency's website www.knowyourlimits.info

Real-time dual-wavelength digital holographic microscopy for extended measurement range with enhanced axial resolution

We report on advanced dual-wavelength digital holographic microscopy (DHM) methods, enabling single-acquisition real-time micron-range measurements while maintaining single-wavelength interferometric resolution in the nanometer regime. In top of the unique real-time capability of our technique, it is shown that axial resolution can be further increased compared to single-wavelength operation thanks to the uncorrelated nature of both recorded wavefronts. It is experimentally demonstrated that DHM topographic investigation within 3 decades measurement range can be achieved with our arrangement, opening new applications possibilities for this interferometric technique. ©2008 COPYRIGHT SPIE

The feasibility of 350 μm spatial resolution coronary magnetic resonance angiography at 3 T in humans.

PURPOSE: The purposes of this study were to (1) develop a high-resolution 3-T magnetic resonance angiography (MRA) technique with an in-plane resolution approximate to that of multidetector coronary computed tomography (MDCT) and a voxel size of 0.35 × 0.35 × 1.5 mm³ and to (2) investigate the image quality of this technique in healthy participants and preliminarily in patients with known coronary artery disease (CAD). MATERIALS AND METHODS: A 3-T coronary MRA technique optimized for an image acquisition voxel as small as 0.35 × 0.35 × 1.5 mm³ (high-resolution coronary MRA [HRC]) was implemented and the coronary arteries of 22 participants were imaged. These included 11 healthy participants (average age, 28.5 years; 5 men) and 11 participants with CAD (average age, 52.9 years; 5 women) as identified on MDCT. In addition, the 11 healthy participants were imaged using a method with a more common spatial resolution of 0.7 × 1 × 3 mm³ (regular-resolution coronary MRA [RRC]). Qualitative and quantitative comparisons were made between the 2 MRA techniques. RESULTS: Normal vessels and CAD lesions were successfully depicted at 350 × 350 μm² in-plane resolution with adequate signal-to-noise ratio (SNR) and contrast-to-noise ratio. The CAD findings were consistent among MDCT and HRC. The HRC showed a 47% improvement in sharpness despite a reduction in SNR (by 72%) and in contrast-to-noise ratio (by 86%) compared with the regular-resolution coronary MRA. CONCLUSION: This study, as a first step toward substantial improvement in the resolution of coronary MRA, demonstrates the feasibility of obtaining at 3 T a spatial resolution that approximates that of MDCT. The acquisition in-plane pixel dimensions are as small as 350 × 350 μm² with a 1.5-mm slice thickness. Although SNR is lower, the images have improved sharpness, resulting in image quality that allows qualitative identification of disease sites on MRA consistent with MDCT.

Nitric oxide and the resolution of inflammation: implications for atherosclerosis

The ubiquitous free radical, nitric oxide (NO), plays an important role in many biological processes including the regulation of the inflammatory response. Alterations in NO synthesis by endogenous systems likely influence inflammatory processes occurring in a wide range of diseases including many in the cardiovascular system (e.g. atherosclerosis). Progression of inflammatory conditions depends not only upon the recruitment and activation of inflammatory cells but also upon their subsequent removal from the inflammatory milieu. Apoptosis, or programmed cell death, is a fundamental process regulating inflammatory cell survival and is critically involved in ensuring the successful resolution of an inflammatory response. Apoptosis results in shutdown of secretory pathways and renders effete, but potentially highly histotoxic, cells instantly recognisable for non-inflammatory clearance by phagocytes (e.g., macrophages). However, dysregulation of apoptosis and phagocytic clearance mechanisms can have drastic consequences for development and resolution of inflammatory processes. In this review we highlight the complexities of NO-mediated regulation of inflammatory cell apoptosis and clearance by phagocytes and discuss the molecular mechanisms controlling these NO mediated effects. We believe that manipulation of pathways involving NO may have previously unrecognised therapeutic potential for limiting or resolving inflammatory and cardiovascular disease.

Attaining the minimum target of resolution WHA 54.19 for schistosomiasis control in the Rainforest Zone of the state of Pernambuco, Northeastern Brazil

Resolution 19 of the 54th World Health Assembly (WHA-54.19) urged member nations to promote preventive measures, ensure treatment and mobilize resources for control of schistosomiasis and soil-transmitted helminthiases (STH). The minimum target is to attend 75% of all school-age children at risk by year 2010. The Brazilian Ministry of Health (MoH) recommends biennial surveys of whole communities and treatment of the positives through the Schistosomiasis Control Program within the Unified Health System (PCE-SUS). However, by 2004 the PCE-SUS had covered only 8.4% of the 1.2 million residents in the Rainforest Zone of Pernambuco (ZMP). Six of the 43 municipalities still remained unattended. Only three of the municipalities already surveyed reached coverage of 25% or more. At least 154 thousand children in the 7-14 years old range have to be examined (and treated if positive) within the next five years to attend the minimum target of the WHA 54.19 for the ZMP. To make this target feasible, it is suggested that from 2006 to 2010 the PCE-SUS actions should be complemented with school-based diagnosis and treatment, involving health and educational organs as well as community associations to include both children in schools and non-enrolled school-age children.

Clinical pharmacogenomic testing of KRAS, BRAF and EGFR mutations by high resolution melting analysis and ultra-deep pyrosequencing

BACKGROUND: Epidermal growth factor receptor (EGFR) and its downstream factors KRAS and BRAF are mutated in several types of cancer, affecting the clinical response to EGFR inhibitors. Mutations in the EGFR kinase domain predict sensitivity to the tyrosine kinase inhibitors gefitinib and erlotinib in lung adenocarcinoma, while activating point mutations in KRAS and BRAF confer resistance to the anti-EGFR monoclonal antibody cetuximab in colorectal cancer. The development of new generation methods for systematic mutation screening of these genes will allow more appropriate therapeutic choices. METHODS: We describe a high resolution melting (HRM) assay for mutation detection in EGFR exons 19-21, KRAS codon 12/13 and BRAF V600 using formalin-fixed paraffin-embedded samples. Somatic variation of KRAS exon 2 was also analysed by massively parallel pyrosequencing of amplicons with the GS Junior 454 platform. RESULTS: We tested 120 routine diagnostic specimens from patients with colorectal or lung cancer. Mutations in KRAS, BRAF and EGFR were observed in 41.9%, 13.0% and 11.1% of the overall samples, respectively, being mutually exclusive. For KRAS, six types of substitutions were detected (17 G12D, 9 G13D, 7 G12C, 2 G12A, 2 G12V, 2 G12S), while V600E accounted for all the BRAF activating mutations. Regarding EGFR, two cases showed exon 19 deletions (delE746-A750 and delE746-T751insA) and another two substitutions in exon 21 (one showed L858R with the resistance mutation T590M in exon 20, and the other had P848L mutation). Consistent with earlier reports, our results show that KRAS and BRAF mutation frequencies in colorectal cancer were 44.3% and 13.0%, respectively, while EGFR mutations were detected in 11.1% of the lung cancer specimens. Ultra-deep amplicon pyrosequencing successfully validated the HRM results and allowed detection and quantitation of KRAS somatic mutations. CONCLUSIONS: HRM is a rapid and sensitive method for moderate-throughput cost-effective screening of oncogene mutations in clinical samples. Rather than Sanger sequence validation, next-generation sequencing technology results in more accurate quantitative results in somatic variation and can be achieved at a higher throughput scale.

Use of high-resolution geophysical data to characterize heterogeneous aquifers: influence of data integration method on hydrological predictions

The integration of geophysical data into the subsurface characterization problem has been shown in many cases to significantly improve hydrological knowledge by providing information at spatial scales and locations that is unattainable using conventional hydrological measurement techniques. The investigation of exactly how much benefit can be brought by geophysical data in terms of its effect on hydrological predictions, however, has received considerably less attention in the literature. Here, we examine the potential hydrological benefits brought by a recently introduced simulated annealing (SA) conditional stochastic simulation method designed for the assimilation of diverse hydrogeophysical data sets. We consider the specific case of integrating crosshole ground-penetrating radar (GPR) and borehole porosity log data to characterize the porosity distribution in saturated heterogeneous aquifers. In many cases, porosity is linked to hydraulic conductivity and thus to flow and transport behavior. To perform our evaluation, we first generate a number of synthetic porosity fields exhibiting varying degrees of spatial continuity and structural complexity. Next, we simulate the collection of crosshole GPR data between several boreholes in these fields, and the collection of porosity log data at the borehole locations. The inverted GPR data, together with the porosity logs, are then used to reconstruct the porosity field using the SA-based method, along with a number of other more elementary approaches. Assuming that the grid-cell-scale relationship between porosity and hydraulic conductivity is unique and known, the porosity realizations are then used in groundwater flow and contaminant transport simulations to assess the benefits and limitations of the different approaches.

Optimized molecular resolution of cross-contamination alerts in clinical mycobacteriology laboratories

BACKGROUND. The phenomenon of misdiagnosing tuberculosis (TB) by laboratory cross-contamination when culturing Mycobacterium tuberculosis (MTB) has been widely reported and it has an obvious clinical, therapeutic and social impact. The final confirmation of a cross-contamination event requires the molecular identification of the same MTB strain cultured from both the potential source of the contamination and from the false-positive candidate. The molecular tool usually applied in this context is IS6110-RFLP which takes a long time to provide an answer, usually longer than is acceptable for microbiologists and clinicians to make decisions. Our purpose in this study is to evaluate a novel PCR-based method, MIRU-VNTR as an alternative to assure a rapid and optimized analysis of cross-contamination alerts. RESULTS. MIRU-VNTR was prospectively compared with IS6110-RFLP for clarifying 19 alerts of false positivity from other laboratories. MIRU-VNTR highly correlated with IS6110-RFLP, reduced the response time by 27 days and clarified six alerts unresolved by RFLP. Additionally, MIRU-VNTR revealed complex situations such as contamination events involving polyclonal isolates and a false-positive case due to the simultaneous cross-contamination from two independent sources. CONCLUSION. Unlike standard RFLP-based genotyping, MIRU-VNTR i) could help reduce the impact of a false positive diagnosis of TB, ii) increased the number of events that could be solved and iii) revealed the complexity of some cross-contamination events that could not be dissected by IS6110-RFLP.

Three-dimensional high-resolution fast spin-echo coronary magnetic resonance angiography.

Due to SNR constraints, current "bright-blood" 3D coronary MRA approaches still suffer from limited spatial resolution when compared to conventional x-ray coronary angiography. Recent 2D fast spin-echo black-blood techniques maximize signal for coronary MRA at no loss in image spatial resolution. This suggests that the extension of black-blood coronary MRA with a 3D imaging technique would allow for a further signal increase, which may be traded for an improved spatial resolution. Therefore, a dual-inversion 3D fast spin-echo imaging sequence and real-time navigator technology were combined for high-resolution free-breathing black-blood coronary MRA. In-plane image resolution below 400 microm was obtained. Magn Reson Med 45:206-211, 2001.

High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization.

We created a high-throughput modality of photoactivated localization microscopy (PALM) that enables automated 3D PALM imaging of hundreds of synchronized bacteria during all stages of the cell cycle. We used high-throughput PALM to investigate the nanoscale organization of the bacterial cell division protein FtsZ in live Caulobacter crescentus. We observed that FtsZ predominantly localizes as a patchy midcell band, and only rarely as a continuous ring, supporting a model of "Z-ring" organization whereby FtsZ protofilaments are randomly distributed within the band and interact only weakly. We found evidence for a previously unidentified period of rapid ring contraction in the final stages of the cell cycle. We also found that DNA damage resulted in production of high-density continuous Z-rings, which may obstruct cytokinesis. Our results provide a detailed quantitative picture of in vivo Z-ring organization.

Plasmid-based controls to detect rpoB mutations in Mycobacterium tuberculosis by quantitative polymerase chain reaction-high-resolution melting

Quantitative polymerase chain reaction-high-resolution melting (qPCR-HRM) analysis was used to screen for mutations related to drug resistance in Mycobacterium tuberculosis. We detected the C526T and C531T mutations in the rifampicin resistance-determining region (RRDR) of the rpoB gene with qPCR-HRM using plasmid-based controls. A segment of the RRDR region from M. tuberculosis H37Rv and from strains carrying C531T or C526T mutations in the rpoB were cloned into pGEM-T vector and these vectors were used as controls in the qPCR-HRM analysis of 54 M. tuberculosis strains. The results were confirmed by DNA sequencing and showed that recombinant plasmids can replace genomic DNA as controls in the qPCR-HRM assay. Plasmids can be handled outside of biosafety level 3 facilities, reducing the risk of contamination and the cost of the assay. Plasmids have a high stability, are normally maintained in Escherichia coli and can be extracted in large amounts.