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MOTIVATION Rapid advances in next-generation sequencing (NGS) technology have led to exponential increase in the amount of genomic information. However, NGS reads contain far more errors than data from traditional sequencing methods, and downstream genomic analysis results can be improved by correcting the errors. Unfortunately, all the previous error(More)
Evaporation is a critical problem when handling submicroliter volumes of fluids. This paper characterizes this problem as it applies to microfluidic cell culture in poly(dimethylsiloxane) (PDMS) devices and provides a practical solution. Evaporation-mediated osmolality shifts through PDMS membranes with varying thicknesses (10, 1, 0.2, or 0.1 mm) were(More)
The ideal cryopreservation protocol would combine the benefits of slow freezing with the benefits of vitrification. This report describes a method for the ultra-rapid vitrification of oocytes using slush nitrogen in quartz capillaries. The approach minimizes the thermal mass of the vitrification vessel by using open microcapillaries made of highly(More)
BACKGROUND Despite advances in in vitro manipulation of preimplantation embryos, there is still a reduction in the quality of embryos produced leading to lower pregnancy rates compared with embryos produced in vivo. We hypothesized that a dynamic microfunnel embryo culture system would enhance outcomes by better mimicking the fluid-mechanical and(More)
The homozygous deletion allele of the angiotensin-converting enzyme gene (ACE/DD), homozygous threonine allele of the angiotensinogen gene (AGN/TT), and the ɛ4 allele of the apolipoprotein E gene (apoE/ɛ4) are reported to be associated with ischemic heart disease. Cerebral infarction (CI) is another atherosclerotic disease, and the effects of these(More)
Microfluidic bioreactors fabricated from highly gas-permeable poly(dimethylsiloxane) (PDMS) materials have been observed, somewhat unexpectedly, to give rise to heterogeneous long term responses along the length of a perfused mammalian cell culture channel, reminiscent of physiologic tissue zonation that arises at least in part due to oxygen gradients. To(More)
Oocyte cryopreservation has become an essential tool in the treatment of infertility by preserving oocytes for women undergoing chemotherapy. However, despite recent advances, pregnancy rates from all cryopreserved oocytes remain low. The inevitable use of the cryoprotectants (CPAs) during preservation affects the viability of the preserved oocytes and(More)
With the cost reduction of the next-generation sequencing (NGS) technologies, genomics has provided us with an unprecedented opportunity to understand fundamental questions in biology and elucidate human diseases. De novo genome assembly is one of the most important steps to reconstruct the sequenced genome. However, most de novo assemblers require enormous(More)
UNLABELLED The most important features of error correction tools for sequencing data are accuracy, memory efficiency and fast runtime. The previous version of BLESS was highly memory-efficient and accurate, but it was too slow to handle reads from large genomes. We have developed a new version of BLESS to improve runtime and accuracy while maintaining a(More)
Correcting errors in DNA sequencing data is an important process that can improve the quality of downstream analysis using the data. Even though many error-correction methods have been proposed for Illumina reads, their throughput is not high enough to process data from large genomes. The current paper describes the first FPGA-based error-correction tool,(More)