Measuring Image Resolution in Ultrasound Localization Microscopy.

The resolution of an imaging system is usually determined by the width of its point spread function and is measured using the Rayleigh criterion. For most system, it is in the order of the imaging wavelength. However, super resolution techniques such as localization microscopy in optical and ultrasound imaging can resolve features an order of magnitude finer than the wavelength. The classical description of spatial resolution no longer applies and new methods need to be developed. In optical localization microscopy, the Fourier Ring Correlation has showed to be an effective and practical way to estimate spatial resolution for Single Molecule Localization Microscopy data. In this work, we wish to investigate how this tool can provide a direct and universal estimation of spatial resolution in Ultrasound Localization Microscopy. Moreover, we discuss the concept of spatial sampling in Ultrasound Localization Microscopy and demonstrate how the Nyquist criterion for sampling drives the spatial/temporal resolution tradeoff. We measured spatial resolution on five different datasets over rodent's brain, kidney and tumor finding values between [Formula: see text] and [Formula: see text] for precision of localization between [Formula: see text] and [Formula: see text]. Eventually, we discuss from those in vivo datasets how spatial resolution in Ultrasound Localization Microscopy depends on both the localization precision and the total number of detected microbubbles. This study aims to offer a practical and theoretical framework for image resolution in Ultrasound Localization Microscopy.

Exploitation of blood non-Newtonian properties for ultrasonic measurement of hematocrit.

New processing techniques for manipulating blood and its components at a microfluidic scale are currently implemented. As for extracorporeal circulation, the in-line evaluation and monitoring of blood properties during these microfluidic techniques is a challenging task. Here, we show that the blood hematocrit can be measured non-invasively in a sub-millimeter medical tube using the non-Newtonian behavior of blood velocity profile. This hematocrit measurement is demonstrated on human blood with a simple Doppler ultrasound system. Results show a mean measurement error of 4.6 ± 1.3%Hct for hematocrit up to 52% and for 5 s-long ultrasonic signals. The simplicity and the measurement scale of the approach make it highly valuable for measuring hematocrit in new blood separation techniques. The approach may have an impact on in-vitro blood processing in general.

A versatile and robust microfluidic device for capillary-sized simple or multiple emulsions production.

Ultrasound-vaporizable microdroplets can be exploited for targeted drug delivery. However, it requires customized microfluidic techniques able to produce monodisperse, capillary-sized and biocompatible multiple emulsions. Recent development of microfluidic devices led to the optimization of microdroplet production with high yields, low polydispersity and well-defined diameters. So far, only few were shown to be efficient for simple droplets or multiple emulsions production below 5 µm in diameter, which is required to prevent microembolism after intravenous injection. Here, we present a versatile microchip for both simple and multiple emulsion production. This parallelized system based on microchannel emulsification was designed to produce perfluorocarbon in water or water within perfluorocarbon in water emulsions with capillary sizes (<5 µm) and polydispersity index down to 5% for in vivo applications such as spatiotemporally-triggered drug delivery using Ultrasound. We show that droplet production at this scale is mainly controlled by interfacial tension forces, how capillary and viscosity ratios influence droplet characteristics and how different production regimes may take place. The better understanding of droplet formation and its relation to applied pressures is supported by observations with a high-speed camera. Compared to previous microchips, this device opens perspectives to produce injectable and biocompatible droplets with a reasonable yield in order to realize preclinical studies in mice.

Use of bioinformatic SNP predictions in differentially expressed genes to find SNPs associated with Salmonella colonization in swine.

Asymptomatic Salmonella-carrier pigs present a major problem in preharvest food safety, with a recent survey indicating >50% of swine herds in the United States have Salmonella-positive animals. Salmonella-carrier pigs serve as a reservoir for contamination of neighbouring pigs, abattoir pens and pork products. In addition, fresh produce as well as water can be contaminated with Salmonella from manure used as fertilizer. Control of Salmonella at the farm level could be through genetic improvement of porcine disease resistance, a potentially powerful method of addressing preharvest pork safety. In this research, we integrate gene expression profiling data and sequence alignment-based prediction of single nucleotide polymorphisms (SNPs) to successfully identify SNPs in functional candidate genes to test for the associations with swine response to Salmonella. A list of 2527 genes that were differentially regulated in porcine whole blood in response to infection with Salmonella enterica serovar Typhimurium were selected. In those genes, SNPs were predicted using ANEXdb alignments based on stringent clustering of all publically available porcine cDNA and expressed sequence tag (EST) sequences. A set of 30 mostly non-synonymous SNPs were selected for genotype analysis of four independent populations (n = 750) with Salmonella faecal shedding or tissue colonization phenotypes. Nine SNPs segregated with minor allele frequency ≥15% in at least two populations. Statistical analysis revealed SNPs associated with Salmonella shedding, such as haptoglobin (HP, p = 0.001, q = 0.01), neutrophil cytosolic factor 2 (NCF2 #2, p = 0.04, q = 0.21) and phosphogluconate dehydrogenase (p = 0.066, q = 0.21). These associations may be useful in identifying and selecting pigs with improved resistance to this bacterium.

Methods for transcriptomic analyses of the porcine host immune response: application to Salmonella infection using microarrays.

Technological developments in both the collection and analysis of molecular genetic data over the past few years have provided new opportunities for an improved understanding of the global response to pathogen exposure. Such developments are particularly dramatic for scientists studying the pig, where tools to measure the expression of tens of thousands of transcripts, as well as unprecedented data on the porcine genome sequence, have combined to expand our abilities to elucidate the porcine immune system. In this review, we describe these recent developments in the context of our work using primarily microarrays to explore gene expression changes during infection of pigs by Salmonella. Thus while the focus is not a comprehensive review of all possible approaches, we provide links and information on both the tools we use as well as alternatives commonly available for transcriptomic data collection and analysis of porcine immune responses. Through this review, we expect readers will gain an appreciation for the necessary steps to plan, conduct, analyze and interpret the data from transcriptomic analyses directly applicable to their research interests.

A method for differentiating targeted microbubbles in real time using subharmonic micro-ultrasound and interframe filtering.

This study introduces a new method for differentiating targeted microbubbles in the presence of flowing microbubbles and tissue using micro-ultrasound. The method relies on subharmonic (SH) imaging for segmenting microbubble signals from tissue signals, and low-pass interframe filtering for segmenting bound targeted microbubbles from flowing microbubbles. The method is evaluated with 30 frames per second SH B-mode imaging in vitro, using a wall-less vessel flow phantom. The SH B-mode cineloops were postprocessed using an interframe moving average filter to segment the regions of bound microbubbles on the inner surface of the vessel phantom. The bound bubbles were then disrupted with sufficiently high ultrasound pressures, so that the dynamic process of targeted microbubble binding under flowing conditions could be observed. These preliminary results show that the proposed method is a feasible solution to the challenge of differentiating targeted microbubbles in the presence of tissue and freely flowing microbubbles at high frequencies, which in turn should improve the specificity of targeted microbubble detection.

Computational integration of structural and functional genomics data across species to develop information on the porcine inflammatory gene regulatory pathway.

We are investigating the porcine gut immune response to infection through gene expression profiling. Porcine Affymetrix GeneChip data was obtained from RNA prepared from mesenteric lymph node of swine infected with either Salmonella enterica serovar Typhimurium (ST) or S. Choleraesuis (SC) for 0, 8, 24, 48 or 504 hours post-inoculation (hpi). In total, 2365 genes with statistical evidence for differential expression (DE; p < 0.01, q < 0.26, fold-change > 2) between at least two time-points were identified. Comparative Gene Ontology analyses revealed that a high proportion of annotated DE genes in both infections are involved in immune and defence responses. Hierarchical clustering of expression patterns and annotations showed that 22 of the 83 genes upregulated from 8-24 hpi in the SC infection are known NF-kappaB targets. The promoter sequences of human genes orthologous to the DE genes were collected and TFM-Explorer was used to identify a set of 72 gene promoters with significant over-representation of NF-kappaB DNA-binding motifs. All 22 known NF-kappaB target genes are in this list; we hypothesize that the remaining 51 genes are un-recognized NF-kappaB targets. Integration of these results and verification of putative target genes will increase our understanding of the porcine response pathways responding to bacterial infection.

In vitro characterization of the subharmonic ultrasound signal from Definity microbubbles at high frequencies.

Ultrasound microbubble contrast agents have been demonstrated to scatter subharmonic energy at one-half the driving frequency. At ultrasound frequencies in the 20-40 MHz range, the subharmonic offers the potential to differentiate the blood in the microcirculation from the surrounding tissue. It is unknown whether current contrast agents, manufactured to be resonant between 2 and 12 MHz, are ideal for subharmonic imaging at higher frequencies. We performed numerical simulations of the Keller-Miksis model for the behavior of a single bubble and experimental investigations of Definity microbubbles in water. The results supported the hypothesis that off-resonant bubbles, excited at their second harmonic, may be primarily responsible for the observed subharmonic energy. For frequencies between 20 and 32 MHz and 32 and 40 MHz, the optimal bubble diameters for the generation of subharmonics in vitro were determined experimentally to be 1.2-5 microm and less than 1.2 microm, respectively. Definity may be a suitable ultrasound contrast agent for subharmonic imaging at 20 MHz with peak-negative pressures between 380 and 590 kPa and pulses greater than or equal to four cycles in duration.

Model for the ultrasound reflection from micro-beads and cells distributed in layers on a uniform surface.

A model predicting the reflection of ultrasound from multiple layers of small scattering spheres is developed. Predictions of the reflection coefficient, which takes into account the interferences between the different sphere layers, are compared to measurements performed in the 10-80 MHz and 15-35 MHz frequency range with layers of glass beads and spherical acute myeloid leukemia (AML) cells, respectively. For both types of scatterers, the reflection coefficient increases as a function of their density on the surface for less than three superimposed layers, at which point it saturates at 0.38 for glass beads and 0.02 for AML cells. Above three layers, oscillations of the reflection coefficient due to constructive or destructive interference between layers are observed experimentally and are accurately predicted by the model. The use of such a model could lead to a better understanding of the structures observed in layered tissue images.