MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular data. We provide an open-source software pipeline, which we call MS-DIAL, for DIA-based identification and quantification of small molecules by mass spectral deconvolution. For a reversed-phase LC-MS/MS analysis of nine algal strains, MS-DIAL using an enriched LipidBlast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between the algal strains

4D-PET reconstruction using a spline-residue model with spatial and temporal roughness penalties

4D reconstruction of dynamic positron emission tomography (dPET) data can improve the signal-to-noise ratio in reconstructed image sequences by fitting smooth temporal functions to the voxel time-activity-curves (TACs) during the reconstruction, though the optimal choice of function remains an open question. We propose a spline-residue model, which describes TACs as weighted sums of convolutions of the arterial input function with cubic B-spline basis functions. Convolution with the input function constrains the spline-residue model at early time-points, potentially enhancing noise suppression in early time-frames, while still allowing a wide range of TAC descriptions over the entire imaged time-course, thus limiting bias. 
 Spline-residue based 4D-reconstruction is compared to that of a conventional (non-4D) maximum a posteriori (MAP) algorithm, and to 4D-reconstructions based on adaptive-knot cubic B-splines, the spectral model and an irreversible two-tissue compartment ('2C3K') model. 4D reconstructions were carried out using a nested-MAP algorithm including spatial and temporal roughness penalties. The algorithms were tested using Monte-Carlo simulated scanner data, generated for a digital thoracic phantom with uptake kinetics based on a dynamic [18F]-Fluromisonidazole scan of a non-small cell lung cancer patient. For every algorithm, parametric maps were calculated by fitting each voxel TAC within a sub-region of the reconstructed images with the 2C3K model. 
 Compared to conventional MAP reconstruction, spline-residue-based 4D reconstruction achieved >50% improvements for 5 of the 8 combinations of the 4 kinetics parameters for which parametric maps were created with the bias and noise measures used to analyse them, and produced better results for 5/8 combinations than any of the other reconstruction algorithms studied, while spectral model-based 4D reconstruction produced the best results for 2/8. 2C3K model-based 4D reconstruction generated the most biased parametric maps. Inclusion of a temporal roughness penalty function improved the performance of 4D reconstruction based on the cubic B-spline, spectral and spline-residue models.&#13

Numerical simulation of fully nonlinear interaction between steep waves and 2D floating bodies using the QALE-FEM method

This paper extends the QALE-FEM (quasi arbitrary Lagrangian–Eulerian finite element method) based on a fully nonlinear potential theory, which was recently developed by the authors [Q.W. Ma, S. Yan, Quasi ALE finite element method for nonlinear water waves, J. Comput. Phys, 212 (2006) 52–72; S. Yan, Q.W. Ma, Application of QALE-FEM to the interaction between nonlinear water waves and periodic bars on the bottom, in: 20th International Workshop on Water Waves and Floating Bodies, Norway, 2005], to deal with the fully nonlinear interaction between steep waves and 2D floating bodies. In the QALE-FEM method, complex unstructured mesh is generated only once at the beginning of calculation and is moved to conform to the motion of boundaries at other time steps, avoiding the necessity of high cost remeshing. In order to tackle challenges associated with floating bodies, several new numerical techniques are developed in this paper. These include the technique for moving mesh near and on body surfaces, the scheme for estimating the velocities and accelerations of bodies as well as the forces on them, the method for evaluating the fluid velocity on the surface of bodies and the technique for shortening the transient period. Using the developed techniques and methods, various cases associated with the nonlinear interaction between waves and floating bodies are numerically simulated. For some cases, the numerical results are compared with experimental data available in the public domain and good agreement is achieved

A high-speed tunable beam splitter for feed-forward photonic quantum information processing

We realize quantum gates for path qubits with a high-speed, polarization-independent and tunable beam splitter. Two electro-optical modulators act in a Mach-Zehnder interferometer as high-speed phase shifters and rapidly tune its splitting ratio. We test its performance with heralded single photons, observing a polarization-independent interference contrast above 95%. The switching time is about 5.6 ns, and a maximal repetition rate is 2.5 MHz. We demonstrate tunable feed-forward operations of a single-qubit gate of path-encoded qubits and a two-qubit gate via measurement-induced interaction between two photons

The validity and reliability of the exposure index as a metric for estimating the radiation dose to the patient

Introduction With the introduction of digital radiography, the feedback between image quality and over-exposure has been partly lost which in some cases has led to a steady increase in dose. Over the years the introduction of exposure index (EI) has been used to resolve this phenomenon referred to as ‘dose creep’. Even though EI is often vendor specific it is always a related of the radiation exposure to the detector. Due to the nature of this relationship EI can also be used as a patient dose indicator, however this is not widely investigated in literature. Methods A total of 420 dose-area-product (DAP) and EI measurements were taken whilst varying kVp, mAs and body habitus on two different anthropomorphic phantoms (pelvis and chest). Using linear regression, the correlation between EI and DAP were examined. Additionally, two separate region of interest (ROI) placements/per phantom where examined in order to research any effect on EI. Results When dividing the data into subsets, a strong correlation between EI and DAP was shown with all R-squared values > 0.987. Comparison between the ROI placements showed a significant difference between EIs for both placements. Conclusion This research shows a clear relationship between EI and radiation dose which is dependent on a wide variety of factors such as ROI placement, body habitus. In addition, pathology and manufacturer specific EI’s are likely to be of influence as well. Implications for practice The combination of DAP and EI might be used as a patient dose indicator. However, the influencing factors as mentioned in the conclusion should be considered and examined before implementation

Consumption of resistant starch decreases postprandial lipogenesis in white adipose tissue of the rat

Chronic consumption of diets high in resistant starch (RS) leads to reduced fat cell size compared to diets high in digestible starch (DS) in rats and increases total and meal fat oxidation in humans. The aim of the present study was to examine the rate of lipogenesis in key lipogenic organs following a high RS or DS meal. Following an overnight fast, male Wistar rats ingested a meal with an RS content of 2% or 30% of total carbohydrate and were then administered an i.p bolus of 50 μCi (3)H(2)O either immediately or 1 hour post-meal. One hour following tracer administration, rats were sacrificed, a blood sample collected, and the liver, white adipose tissue (WAT), and gastrocnemius muscle excised and frozen until assayed for total (3)H-lipid and (3)H-glycogen content. Plasma triglyceride and NEFA concentrations and (3)H-glycogen content did not differ between groups. In all tissues, except the liver, there was a trend for the rate of lipogenesis to be higher in the DS group than the RS group which reached significance only in WAT at 1 h (p < 0.01). On a whole body level, this attenuation of fat deposition in WAT in response to a RS diet could be significant for the prevention of weight gain in the long-term

Alteration of Gene Expression Signatures of Cortical Differentiation and Wound Response in Lethal Clear Cell Renal Cell Carcinomas

Clear cell renal cell carcinoma (ccRCC) is the most common malignancy of the adult kidney and displays heterogeneity in clinical outcomes. Through comprehensive gene expression profiling, we have identified previously a set of transcripts that predict survival following nephrectomy independent of tumor stage, grade, and performance status. These transcripts, designated as the SPC (supervised principal components) gene set, show no apparent biological or genetic features that provide insight into renal carcinogenesis or tumor progression. We explored the relationship of this gene list to a set of genes expressed in different anatomical segments of the normal kidney including the cortex (cortex gene set) and the glomerulus (glomerulus gene set), and a gene set expressed after serum stimulation of quiescent fibroblasts (the core serum response or CSR gene set). Interestingly, the normal cortex, glomerulus (part of the normal renal cortex), and CSR gene sets captured more than 1/5 of the genes in the highly prognostic SPC gene set. Based on gene expression patterns alone, the SPC gene set could be used to sort samples from normal adult kidneys by the anatomical regions from which they were dissected. Tumors whose gene expression profiles most resembled the normal renal cortex or glomerulus showed better survival than those that did not, and those with expression features more similar to CSR showed poorer survival. While the cortex, glomerulus, and CSR signatures predicted survival independent of traditional clinical parameters, they were not independent of the SPC gene list. Our findings suggest that critical biological features of lethal ccRCC include loss of normal cortical differentiation and activation of programs associated with wound healing

Camera motion estimation through planar deformation determination

In this paper, we propose a global method for estimating the motion of a camera which films a static scene. Our approach is direct, fast and robust, and deals with adjacent frames of a sequence. It is based on a quadratic approximation of the deformation between two images, in the case of a scene with constant depth in the camera coordinate system. This condition is very restrictive but we show that provided translation and depth inverse variations are small enough, the error on optical flow involved by the approximation of depths by a constant is small. In this context, we propose a new model of camera motion, that allows to separate the image deformation in a similarity and a ``purely'' projective application, due to change of optical axis direction. This model leads to a quadratic approximation of image deformation that we estimate with an M-estimator; we can immediatly deduce camera motion parameters.Comment: 21 pages, version modifi\'ee accept\'e le 20 mars 200

Post-mortem culture of Balamuthia mandrillaris from the brain and cerebrospinal fluid of a case of granulomatous amoebic meningoencephalitis, using human brain microvascular endothelial cells

The first isolation in the UK of Balamuthia mandrillaris amoebae from a fatal case of granulomatous amoebic meningoencephalitis is reported. Using primary cultures of human brain microvascular endothelial cells (HBMECs), amoebae were isolated from the brain and cerebrospinal fluid (CSF). The cultures showed a cytopathic effect at 20–28 days, but morphologically identifiable B. mandrillaris amoebae were seen in cleared plaques in subcultures at 45 days. The identification of the organism was later confirmed using PCR on Chelex-treated extracts. Serum taken while the patient was still alive reacted strongly with slide antigen prepared from cultures of the post-mortem isolate, and also with those from a baboon B. mandrillaris strain at 1 : 10 000 in indirect immunofluorescence, but with Acanthamoeba castellanii (Neff) at 1 : 160, supporting B. mandrillaris to be the causative agent. If the presence of amoebae in the post-mortem CSF reflects the condition in life, PCR studies on CSF and on biopsies of cutaneous lesions may also be a valuable tool. The role of HBMECs in understanding the interactions of B. mandrillaris with the blood–brain barrier is discussed

First report of NDM-1-producing acinetobacter baumannii in East Africa

Background: The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) was observed in a Kenyan hospital from 2009 to 2010. Further investigation of the dissemination of CRAB isolates and the molecular characterization of associated resistance determinants were therefore performed. Methods: Antibiotic susceptibilities were determined by broth microdilution and Etest. Metallo-blactamases were detected by Etest method. Clonal relationships were studied by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). b-Lactam and aminoglycoside resistance determinants and the clonal relatedness to widespread European clones were studied by PCR and sequencing. Results: Sixteen CRAB isolates from 10 patients possessed six pulsotypes; half of the isolates belonged to the European clone II (ECII) lineage. ECII strains were typed as MLST sequence type 2 (ST2) and ST109, and non-ECII strains as ST25 and ST113. All isolates harbored ISAba1–blaOXA-23, blaOXA-51-like, blaADC, and class 1 integron, including one that also harbored blaNDM-1. ADC-57 and two integron cassettes (arr-2- cmlA5 and aadB-aadA2-cmlA6-aadA15) were newly-identified. Non-ECII isolates, designated non-ECII clone, carried armA and integron cassette arr-2-cmlA5. Conclusions: Two distinct clones of CRAB – ECII and non-ECII epidemic clones – were disseminated in Kenya. The concomitance of ISAba1–blaOXA-23 was the major mechanism contributing to CRAB. The first identification of ECII CRAB and New Delhi metallo-b-lactamase 1 (NDM-1) extensively drug-resistant A. baumannii in East Africa is of concern