Micro-Electro-Mechanical Systems (MEMS), Nov 5, 2000
The absence of turbulence and the difficulty associated with introducing moving stirrers into mic... more The absence of turbulence and the difficulty associated with introducing moving stirrers into microfluidic systems make the mixing problem in microdevices challenging. We studied theoretically steady, laminar, incompressible flow through a sequence of conduits with rectangular cross-sections aligned to form 90° with each other. The feasibility of taking advantage of bend-induced vortices to stir the fluid and enhance the mixing process was evaluated. Since at very low Reynolds numbers the bend-induced vortices decay rapidly, it was necessary to utilize a large number of bends to achieve the desired effects. Since it is not practical to directly simulate the flow through a large number of bends, we borrowed Jones et. al.’s (1989) idea of constructing a two-dimensional map to project fluid particles from a cross-section upstream of the bend to a cross-section downstream of the bend. This map was then applied repetitively to trace particle trajectories in various bend arrangements. Under certain conditions, chaotic advection was observed.
An experimental investigation of fluid flow in extremely small channels is presented. Potential a... more An experimental investigation of fluid flow in extremely small channels is presented. Potential applications for such channels include cooling of electronic circuits, and reactors for modification and separation of biological cells. The immediate goal is to determine at what length ...
In what case do you like reading so much? What about the type of the symbolic computation in flui... more In what case do you like reading so much? What about the type of the symbolic computation in fluid mechanics and heat transfer heat transfer division volume 105 and applied mechanics division volume 97 book? The needs to read? Well, everybody has their own reason why should read some books. Mostly, it will relate to their necessity to get knowledge from the book and want to read just to get entertainment. Novels, story book, and other entertaining books become so popular this day. Besides, the scientific books will also be the best reason to choose, especially for the students, teachers, doctors, businessman, and other professions who are fond of reading.
Liquid biopsy is a highly promising method for non-invasive detection of tumor-associated nucleic... more Liquid biopsy is a highly promising method for non-invasive detection of tumor-associated nucleic acid fragments in body fluids but is challenged by the low abundance of nucleic acids of clinical interest and their sequence homology with the vast background of nucleic acids from healthy cells. Recently, programmable endonucleases such as clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas) and prokaryotic Argonautes have been successfully used to remove background nucleic acids and enrich mutant allele fractions, enabling their detection with deep next generation sequencing (NGS). However, the enrichment level achievable with these assays is limited by futile binding events and off-target cleavage. To overcome these shortcomings, we conceived a new assay (Programmable Enzyme-Assisted Selective Exponential Amplification, PASEA) that combines the cleavage of wild type alleles with concurrent polymerase amplification. While PASEA increases the numbers of both wild type and mutant alleles, the numbers of mutant alleles increase at much greater rates, allowing PASEA to achieve an unprecedented level of selective enrichment of targeted alleles. By combining CRISPR-Cas9 based cleavage with recombinase polymerase amplification, we converted samples with 0.01% somatic mutant allele fractions (MAFs) to products with 70% MAFs in a single step within 20 min, enabling inexpensive, rapid genotyping with such as Sanger sequencers. Furthermore, PASEA’s extraordinary efficiency facilitates sensitive real-time detection of somatic mutant alleles at the point of care with custom designed Exo-RPA probes. Real-time PASEA’ performance was proved equivalent to clinical amplification refractory mutation system (ARMS)-PCR and NGS when testing over hundred cancer patients’ samples. This strategy has the potential to reduce the cost and time of cancer screening and genotyping, and to enable targeted therapies in resource-limited settings. We devised a new assay dubbed Programmable Enzyme-Assisted Selective Exponential Amplification (PASEA) that concurrently amplifies both wild type and mutant alleles in the presence of guided endonuclease that targets only the wild type allele, enabling point-of-care genotyping and inexpensive rare mutant allele detection.
Sensitive, specific and rapid molecular diagnosis of respiratory diseases in animals and humans i... more Sensitive, specific and rapid molecular diagnosis of respiratory diseases in animals and humans is critical to facilitate appropriate control measures and treatment.
The porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porci... more The porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV) are coronaviruses (CoVs) of neonatal pigs that cause great economic losses to pig farms and pork processors.
The 2019 novel coronavirus (COVID-19) is a newly emerged strain that has never been found in huma... more The 2019 novel coronavirus (COVID-19) is a newly emerged strain that has never been found in humans before. At present, the laboratory-based reverse transcription-polymerase chain reaction (RT-PCR) is the main method to confirm COVID-19 infection. The intensification of the COVID-19 epidemic overwhelms limited clinical resources in particular, but not only, in developing countries, resulting in many patients not being tested for the infection and in large queues of potentially infected individuals waiting to be tested while providing a breeding ground for the disease. We describe here a rapid, highly sensitive, point-of-care, molecular test amenable for use at home, in the clinic, and at points of entry by minimally trained individuals and with minimal instrumentation. Our test is based on loop mediated isothermal amplification (COVID-19 LAMP) and for higher sensitivity on nested nucleic acid, two stage isothermal amplification (COVID-19 Penn-RAMP). Both tests can be carried out in ...
Micro-Electro-Mechanical Systems (MEMS), Nov 5, 2000
The absence of turbulence and the difficulty associated with introducing moving stirrers into mic... more The absence of turbulence and the difficulty associated with introducing moving stirrers into microfluidic systems make the mixing problem in microdevices challenging. We studied theoretically steady, laminar, incompressible flow through a sequence of conduits with rectangular cross-sections aligned to form 90° with each other. The feasibility of taking advantage of bend-induced vortices to stir the fluid and enhance the mixing process was evaluated. Since at very low Reynolds numbers the bend-induced vortices decay rapidly, it was necessary to utilize a large number of bends to achieve the desired effects. Since it is not practical to directly simulate the flow through a large number of bends, we borrowed Jones et. al.’s (1989) idea of constructing a two-dimensional map to project fluid particles from a cross-section upstream of the bend to a cross-section downstream of the bend. This map was then applied repetitively to trace particle trajectories in various bend arrangements. Under certain conditions, chaotic advection was observed.
An experimental investigation of fluid flow in extremely small channels is presented. Potential a... more An experimental investigation of fluid flow in extremely small channels is presented. Potential applications for such channels include cooling of electronic circuits, and reactors for modification and separation of biological cells. The immediate goal is to determine at what length ...
In what case do you like reading so much? What about the type of the symbolic computation in flui... more In what case do you like reading so much? What about the type of the symbolic computation in fluid mechanics and heat transfer heat transfer division volume 105 and applied mechanics division volume 97 book? The needs to read? Well, everybody has their own reason why should read some books. Mostly, it will relate to their necessity to get knowledge from the book and want to read just to get entertainment. Novels, story book, and other entertaining books become so popular this day. Besides, the scientific books will also be the best reason to choose, especially for the students, teachers, doctors, businessman, and other professions who are fond of reading.
Liquid biopsy is a highly promising method for non-invasive detection of tumor-associated nucleic... more Liquid biopsy is a highly promising method for non-invasive detection of tumor-associated nucleic acid fragments in body fluids but is challenged by the low abundance of nucleic acids of clinical interest and their sequence homology with the vast background of nucleic acids from healthy cells. Recently, programmable endonucleases such as clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas) and prokaryotic Argonautes have been successfully used to remove background nucleic acids and enrich mutant allele fractions, enabling their detection with deep next generation sequencing (NGS). However, the enrichment level achievable with these assays is limited by futile binding events and off-target cleavage. To overcome these shortcomings, we conceived a new assay (Programmable Enzyme-Assisted Selective Exponential Amplification, PASEA) that combines the cleavage of wild type alleles with concurrent polymerase amplification. While PASEA increases the numbers of both wild type and mutant alleles, the numbers of mutant alleles increase at much greater rates, allowing PASEA to achieve an unprecedented level of selective enrichment of targeted alleles. By combining CRISPR-Cas9 based cleavage with recombinase polymerase amplification, we converted samples with 0.01% somatic mutant allele fractions (MAFs) to products with 70% MAFs in a single step within 20 min, enabling inexpensive, rapid genotyping with such as Sanger sequencers. Furthermore, PASEA’s extraordinary efficiency facilitates sensitive real-time detection of somatic mutant alleles at the point of care with custom designed Exo-RPA probes. Real-time PASEA’ performance was proved equivalent to clinical amplification refractory mutation system (ARMS)-PCR and NGS when testing over hundred cancer patients’ samples. This strategy has the potential to reduce the cost and time of cancer screening and genotyping, and to enable targeted therapies in resource-limited settings. We devised a new assay dubbed Programmable Enzyme-Assisted Selective Exponential Amplification (PASEA) that concurrently amplifies both wild type and mutant alleles in the presence of guided endonuclease that targets only the wild type allele, enabling point-of-care genotyping and inexpensive rare mutant allele detection.
Sensitive, specific and rapid molecular diagnosis of respiratory diseases in animals and humans i... more Sensitive, specific and rapid molecular diagnosis of respiratory diseases in animals and humans is critical to facilitate appropriate control measures and treatment.
The porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porci... more The porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV) are coronaviruses (CoVs) of neonatal pigs that cause great economic losses to pig farms and pork processors.
The 2019 novel coronavirus (COVID-19) is a newly emerged strain that has never been found in huma... more The 2019 novel coronavirus (COVID-19) is a newly emerged strain that has never been found in humans before. At present, the laboratory-based reverse transcription-polymerase chain reaction (RT-PCR) is the main method to confirm COVID-19 infection. The intensification of the COVID-19 epidemic overwhelms limited clinical resources in particular, but not only, in developing countries, resulting in many patients not being tested for the infection and in large queues of potentially infected individuals waiting to be tested while providing a breeding ground for the disease. We describe here a rapid, highly sensitive, point-of-care, molecular test amenable for use at home, in the clinic, and at points of entry by minimally trained individuals and with minimal instrumentation. Our test is based on loop mediated isothermal amplification (COVID-19 LAMP) and for higher sensitivity on nested nucleic acid, two stage isothermal amplification (COVID-19 Penn-RAMP). Both tests can be carried out in ...
Uploads
Papers