3D printed microfluidic device with integrated optical sensing for particle analysis

The integration of particle counters within lab-on-chip (LOC) microfluidic devices creates a range of valuable tools for healthcare such as cell counting, and synthesis applications e.g. materials fabrication. Avoidance of long and/ or complex fabrication processes can aid the uptake of these devices, specially within resource-poor societies. We present an additively manufactured microfluidic particle counter. The device features a hydrodynamic focusing chamber to stream the particles past embedded optical fibres for their detection. The intensity of occluded light through the fibre was found to be related to the size of the particles, allowing particles of different sizes to be identified. The signal-to-noise ratio and reproducibility of the particle analysis was optimised to three objectives (pulse magnitude, uniformity and periodicity) via the use of a genetic algorithm (GA). Once optimised the device was able to count particles upto 5.5 × 104 particles ml-1, and size particles in a mixture

Rapid assessment of site specific DNA methylation through resistive pulse sensing

Many diseases are defined by patterns of DNA methylation which result in aberrant gene expression. We present a rapid assay based upon resistive pulse sensing, RPS, to characterize sequence specific DNA methylation sites in genomic DNA. We modify the surface of superparamagnetic beads, SPBs, with DNA (capture probe). The particles are added to solution where they bind to and extract sequence specific DNA (target DNA). The target loaded SPBs are then incubated with antibodies which bind to the methylation sites, and the velocity of the SPBs through the nanopore reveals the number and location of the epigenetic markers within the target. The approach is capable of distinguishing between different methylation sites within a DNA promoter region. Crucially the approach is not dependent on accurate sequencing of assayed DNA, with genomic regions targeted through complementary probes. As such the number of stages and reagents costs are low and the assay is complete in under 60 min which includes the incubation and run times. The format also allows simultaneous quantification of number of copies of methylated DNA, and we illustrate this with a dose response curve

A cluster analysis of Croatian counties as the base for an active demographic policy

This paper deals with Croatian counties cluster analysis as the base for developing a proactive demographic policy. Unfortunately, Croatia has no national demographic strategy and no national population policy is carried out. Some local governments are taking isolated policy measures but due to an unsystematic and distressed network at the national level it has to date given no significant effects. The Croatian nation is currently experiencing the initial process of demographic extinction. This process began even before the great emigration wave that started about a year and half ago. Since there are no financial resources for the simultaneous and complete implementation of an active demographic policy across the entire Croatian territory, this paper proposes a new approach. Namely, the main demographic indicators have been calculated and analyzed for each Croatian county. After that, using a multivariate methodology, fifteen demographic indicators that significantly differ from county to county were selected as criteria for clustering Croatian counties by k-means method. Clustering output defines several clusters consisting of a smaller number of counties with similar demographic characteristics. These clusters form a spatial county unit in which appropriate measures of an active demographic policy should be urgently implemented. In this way the process of active demographic policy can start with less financial resources and can be limited maybe only to spaces with poorest demographic characteristics. Moreover, the results of this study might very well stimulate "richer” government units to carry out the appropriate active demographic policy measures in their areas without waiting for the adoption of laws and regulations at the national state level

3D printed microfluidic device with integrated optical sensing for particle analysis

The integration of particle counters within lab-on-chip (LOC) microfluidic devices creates a range of valuable tools for healthcare such as cell counting, and synthesis applications e.g. materials fabrication. Avoidance of long and/ or complex fabrication processes can aid the uptake of these devices, specially within resource-poor societies. We present an additively manufactured microfluidic particle counter. The device features a hydrodynamic focusing chamber to stream the particles past embedded optical fibres for their detection. The intensity of occluded light through the fibre was found to be related to the size of the particles, allowing particles of different sizes to be identified. The signal-to-noise ratio and reproducibility of the particle analysis was optimised to three objectives (pulse magnitude, uniformity and periodicity) via the use of a genetic algorithm (GA). Once optimised the device was able to count particles upto 5.5 × 104 particles ml-1, and size particles in a mixture

Rapid assessment of site specific DNA methylation through resistive pulse sensing

Many diseases are defined by patterns of DNA methylation which result in aberrant gene expression. We present a rapid assay based upon resistive pulse sensing, RPS, to characterize sequence specific DNA methylation sites in genomic DNA. We modify the surface of superparamagnetic beads, SPBs, with DNA (capture probe). The particles are added to solution where they bind to and extract sequence specific DNA (target DNA). The target loaded SPBs are then incubated with antibodies which bind to the methylation sites, and the velocity of the SPBs through the nanopore reveals the number and location of the epigenetic markers within the target. The approach is capable of distinguishing between different methylation sites within a DNA promoter region. Crucially the approach is not dependent on accurate sequencing of assayed DNA, with genomic regions targeted through complementary probes. As such the number of stages and reagents costs are low and the assay is complete in under 60 min which includes the incubation and run times. The format also allows simultaneous quantification of number of copies of methylated DNA, and we illustrate this with a dose response curve

Rapid Assessment of Site Specific DNA Methylation through Resistive Pulse Sensing

Many diseases are defined by patterns of DNA methylation which result in aberrant gene expression. We present a rapid assay based upon resistive pulse sensing, RPS, to characterize sequence specific DNA methylation sites in genomic DNA. We modify the surface of superparamagnetic beads, SPBs, with DNA (capture probe). The particles are added to solution where they bind to and extract sequence specific DNA (target DNA). The target loaded SPBs are then incubated with antibodies which bind to the methylation sites, and the velocity of the SPBs through the nanopore reveals the number and location of the epigenetic markers within the target. The approach is capable of distinguishing between different methylation sites within a DNA promoter region. Crucially the approach is not dependent on accurate sequencing of assayed DNA, with genomic regions targeted through complementary probes. As such the number of stages and reagents costs are low and the assay is complete in under 60 min which includes the incubation and run times. The format also allows simultaneous quantification of number of copies of methylated DNA, and we illustrate this with a dose response curve

Effect of k-mer filtering (k-mer) / mapper subtraction (Map) and lowcomplexity filtering (LC) on post-assembly contig numbers.

<p>Effect of k-mer filtering (k-mer) / mapper subtraction (Map) and lowcomplexity filtering (LC) on post-assembly contig numbers.</p

Effect of k-mer filtering (K-mer)/ mapper subtraction (Map) on post-assembly contig number using multiple optimized assemblers with the HCV 9x mean coverage Illumina read dataset.

<p>Effect of k-mer filtering (K-mer)/ mapper subtraction (Map) on post-assembly contig number using multiple optimized assemblers with the HCV 9x mean coverage Illumina read dataset.</p

Human viral simulated dataset: effect of k-mer filtering (K-mer) & host mapping subtraction (Map) on post-assembly contig number.

<p>Human viral simulated dataset: effect of k-mer filtering (K-mer) & host mapping subtraction (Map) on post-assembly contig number.</p

Reports of novel animal virus species in PubMed over the last two decades.

<p>Reports of novel animal virus species in PubMed over the last two decades.</p