The Experts below are selected from a list of 276 Experts worldwide ranked by ideXlab platform
Ji Yoon Kang - One of the best experts on this subject based on the ideXlab platform.
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generalized Serial Dilution module for monotonic and arbitrary microfluidic gradient generators
Lab on a Chip, 2009Co-Authors: Rajagopal Panchapakesan, Anthony R Full, Ledum Nordee, Ji Yoon Kang, Kwang W OhAbstract:In this paper, we propose a generalized Serial Dilution module for universal microfluidic concentration gradient generators including N cascaded-mixing stages in a stepwise manner. Desired concentrations were generated by means of controlled volumetric mixing ratios of two merging solutions in each stage. The flow rates were adjusted by controlling channel length, which is proportional to fluidic resistance in each channel. A generalized mathematical model for generating any complex concentration and output flow rate gradients is presented based on the fact that there is an analogy between microfluidic circuits and electrical circuits. The pressure drop corresponds to a voltage drop, the flow rate to an electrical current, and the flow resistance to an electrical resistance. A simple equivalent electrical circuit model was generalized, and in the model each channel segment was represented by an electrical resistance. As a result of the mathematical modelling, the only variable parameter in the generalized Serial Dilution module was the channel length. By the use of the generalized Serial Dilution module with N = 4, three types of microfluidic gradient generators for linear, logarithmic and Gaussian gradients were successfully designed and tested. The proposed strategy is capable of generating universal monotonic gradients with a single module or arbitrary gradients with multiple modules ranging from linear to complex non-linear shapes of concentration gradients as well as arbitrary output flow rate gradients in a stepwise manner. The simple universal gradient generation technology using the generalized Serial Dilution module will find widespread use in the greater chemical and biological community, and address many challenges of gradient-dependent phenomena.
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A Serial Dilution microfluidic device using a ladder network generating logarithmic or linear concentrations.
Lab on a chip, 2008Co-Authors: Choong Kim, Kangsun Lee, Jong Hyun Kim, Kyeong-sik Shin, K. S. Lee, Tae Song Kim, Ji Yoon KangAbstract:In this paper, we propose a Serial Dilution microfluidic chip which is able to generate logarithmic or linear step-wise concentrations. These concentrations were generated via adjustments in the flow rate of two converging fluids at the channel junctions of the ladder network. The desired Dilution ratios are almost independent of the flow rate or diffusion length of molecules, as the Dilution device is influenced only by the ratio of volumetric flow rates. Given a set of necessary Dilution ratios, whether linear or logarithmic, a Serial Dilution chip can be constructed via the modification of a microfluidic resistance network. The design principle was suggested and both the logarithmic and linear Dilution chips were fabricated in order to verify their performance in accordance with the fluorescence intensity. The diluted concentrations of a fluorescein solution in the microfluidic device evidenced relatively high linearity, and the cytotoxicity test of MCF-7 breast cancer cellsvia the logarithmic Dilution chip was generally consistent with the results generated with manual Dilution.
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The Serial Dilution chip for cytotoxicity and cell differentiation test
2007 IEEE 20th International Conference on Micro Electro Mechanical Systems (MEMS), 2007Co-Authors: Kyung Sik Shin, Ji Yoon KangAbstract:This paper proposes two types of Serial Dilution devices for linear and logarithmic concentration gradient. The designs of Serial Dilution chips were based on the adjustment of flow rate to obtain desired Dilution ratio, so that they are not affected by molecular size, flow rate, and diffusion length. The performance of linear Dilution chip was verified by image analysis of diluted tryphane blue solution as well as by cytotoxicity test. The analysis of the color intensity indicated that the tryphane blue solution was diluted in linear scale, which was in good agreement with the theoretical value. The percentage of viable cells linearly increased with the concentration of PFA and the standard deviation was within 0.05%. Also, the experiment of logarithmic Dilution chip demonstrated that the concentrations of outlet was logarithmically linear, regardless of the variation of flow rates and was in accordance with that of Dilution by manual pipetting.
Sidnei Alves De Araújo - One of the best experts on this subject based on the ideXlab platform.
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automatic segmentation method for cfu counting in single plate Serial Dilution
Chemometrics and Intelligent Laboratory Systems, 2019Co-Authors: Dimitria T. Boukouvalas, Cintia Raquel Lima Leal, Renato Araujo Prates, Sidnei Alves De AraújoAbstract:Abstract Quantification of colony forming units (CFU) on microbial cultures prepared according to the standard spread plate technique is a daily laboratory routine that requires significant resources. On the other hand, SP-SDS (Single Plate Serial Dilution Spotting) is a widely used technique that allows a great reduction in the use of material resources and time. However, previous approaches for automatic quantification are based on images of standard spread plate Petri dishes with low variation of CFU features and captured under controlled lighting conditions. In this paper, we propose a novel approach that automatically separates each Dilution in images of Petri dishes prepared in the SP-SDS technique and counts total CFU per Dilution, which most approaches are unable to perform. The proposed approach employs region-based shape descriptors for quantification of isolated CFU and cross-correlation granulometry for the quantification of CFU in agglomerates. For the experiments, we composed two image datasets and used images from two publicly available datasets. The images from our datasets were acquired under real laboratory ambient conditions and show variation in lighting, background noise, low contrast between bacterial colonies and background, and high variation in CFU features. Overall, the results obtained by our approach in terms of accuracy, precision, and sensitivity were superior to those of two other approaches recently proposed in the literature used for comparison in this study, especially for high-definition images. In addition, our results present greater or similar accuracy to various approaches found in the literature, most of which are not able to count CFU in images obtained from Petri dishes prepared in the SP-SDS technique and low control of ambient conditions. Our composed datasets are publicly available for download as a contribution to further research.
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CIARP - Automated Colony Counter for Single Plate Serial Dilution Spotting
Progress in Pattern Recognition Image Analysis Computer Vision and Applications, 2019Co-Authors: Dimitria T. Boukouvalas, Peterson Adriano Belan, Cintia Raquel Lima Leal, Renato Araujo Prates, Sidnei Alves De AraújoAbstract:This paper discusses the automated visual identification and quantification of colony forming units (CFU) in Single Plate Serial Dilution Spotting (SP-SDS) through correlation-based granulometry under uncontrolled lighting conditions. There are many different approaches in the literature based on images captured under controlled conditions, which is not the real life situation of laboratories that present high variation in illuminating conditions resulting in low contrast between bacterial colonies and background, background noise, and in addition, high variation in CFU features. Furthermore, SP-SDS has been widely used due to its reduction in the use of resources, but most of previous approaches are not capable of counting separately the number of CFU present in each Dilution zone. In that sense, our study focuses on analyzing real images taken at laboratory day-to-day conditions and proposes an approach suitable for real laboratory practice with high accuracies.
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automated colony counter for single plate Serial Dilution spotting
Iberoamerican Congress on Pattern Recognition, 2018Co-Authors: Dimitria T. Boukouvalas, Peterson Adriano Belan, Cintia Raquel Lima Leal, Renato Araujo Prates, Sidnei Alves De AraújoAbstract:This paper discusses the automated visual identification and quantification of colony forming units (CFU) in Single Plate Serial Dilution Spotting (SP-SDS) through correlation-based granulometry under uncontrolled lighting conditions. There are many different approaches in the literature based on images captured under controlled conditions, which is not the real life situation of laboratories that present high variation in illuminating conditions resulting in low contrast between bacterial colonies and background, background noise, and in addition, high variation in CFU features. Furthermore, SP-SDS has been widely used due to its reduction in the use of resources, but most of previous approaches are not capable of counting separately the number of CFU present in each Dilution zone. In that sense, our study focuses on analyzing real images taken at laboratory day-to-day conditions and proposes an approach suitable for real laboratory practice with high accuracies.
Ya-tang Yang - One of the best experts on this subject based on the ideXlab platform.
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A nanoliter microfluidic Serial Dilution bioreactor
Biomicrofluidics, 2015Co-Authors: Yi-wei Lee, Chih-chung Chiang, Ya-tang YangAbstract:Bacterial culture is a basic technique in both fundamental and applied microbiology. The excessive reagent consumption and laborious maintenance of bulk bioreactors for microbial culture have prompted the development of miniaturized on-chip bioreactors. With the minimal choice of two compartments (N = 2) and discrete time, periodic Dilution steps, we realize a microfluidic bioreactor that mimics macroscopic Serial Dilution transfer culture. This device supports automated, long-term microbial cultures with a nanoliter-scale working volume and real-time monitoring of microbial populations at single-cell resolution. Because of the high surface-to-volume ratio, the device also operates as an effective biofilm-flow reactor to support cogrowth of planktonic and biofilm populations. We expect that such devices will open opportunities in many fields of microbiology.
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Theory of a microfluidic Serial Dilution bioreactor for growth of planktonic and biofilm populations
Journal of mathematical biology, 2015Co-Authors: Sze-bi Hsu, Ya-tang YangAbstract:We present the theory of a microfluidic bioreactor with a two-compartment growth chamber and periodic Serial Dilution. In the model, coexisting planktonic and biofilm populations exchange by adsorption and detachment. The criteria for coexistence and global extinction are determined by stability analysis of the global extinction state. Stability analysis yields the operating diagram in terms of the Dilution and removal ratios, constrained by the plumbing action of the bioreactor. The special case of equal uptake function and logistic growth is analytically solved and explicit growth curves are plotted. The presented theory is applicable to generic microfluidic bioreactors with discrete growth chambers and periodic Dilution at discrete time points. Therefore, the theory is expected to assist the design of microfluidic devices for investigating microbial competition and microbial biofilm growth under Serial Dilution conditions.
Dimitria T. Boukouvalas - One of the best experts on this subject based on the ideXlab platform.
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automatic segmentation method for cfu counting in single plate Serial Dilution
Chemometrics and Intelligent Laboratory Systems, 2019Co-Authors: Dimitria T. Boukouvalas, Cintia Raquel Lima Leal, Renato Araujo Prates, Sidnei Alves De AraújoAbstract:Abstract Quantification of colony forming units (CFU) on microbial cultures prepared according to the standard spread plate technique is a daily laboratory routine that requires significant resources. On the other hand, SP-SDS (Single Plate Serial Dilution Spotting) is a widely used technique that allows a great reduction in the use of material resources and time. However, previous approaches for automatic quantification are based on images of standard spread plate Petri dishes with low variation of CFU features and captured under controlled lighting conditions. In this paper, we propose a novel approach that automatically separates each Dilution in images of Petri dishes prepared in the SP-SDS technique and counts total CFU per Dilution, which most approaches are unable to perform. The proposed approach employs region-based shape descriptors for quantification of isolated CFU and cross-correlation granulometry for the quantification of CFU in agglomerates. For the experiments, we composed two image datasets and used images from two publicly available datasets. The images from our datasets were acquired under real laboratory ambient conditions and show variation in lighting, background noise, low contrast between bacterial colonies and background, and high variation in CFU features. Overall, the results obtained by our approach in terms of accuracy, precision, and sensitivity were superior to those of two other approaches recently proposed in the literature used for comparison in this study, especially for high-definition images. In addition, our results present greater or similar accuracy to various approaches found in the literature, most of which are not able to count CFU in images obtained from Petri dishes prepared in the SP-SDS technique and low control of ambient conditions. Our composed datasets are publicly available for download as a contribution to further research.
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CIARP - Automated Colony Counter for Single Plate Serial Dilution Spotting
Progress in Pattern Recognition Image Analysis Computer Vision and Applications, 2019Co-Authors: Dimitria T. Boukouvalas, Peterson Adriano Belan, Cintia Raquel Lima Leal, Renato Araujo Prates, Sidnei Alves De AraújoAbstract:This paper discusses the automated visual identification and quantification of colony forming units (CFU) in Single Plate Serial Dilution Spotting (SP-SDS) through correlation-based granulometry under uncontrolled lighting conditions. There are many different approaches in the literature based on images captured under controlled conditions, which is not the real life situation of laboratories that present high variation in illuminating conditions resulting in low contrast between bacterial colonies and background, background noise, and in addition, high variation in CFU features. Furthermore, SP-SDS has been widely used due to its reduction in the use of resources, but most of previous approaches are not capable of counting separately the number of CFU present in each Dilution zone. In that sense, our study focuses on analyzing real images taken at laboratory day-to-day conditions and proposes an approach suitable for real laboratory practice with high accuracies.
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automated colony counter for single plate Serial Dilution spotting
Iberoamerican Congress on Pattern Recognition, 2018Co-Authors: Dimitria T. Boukouvalas, Peterson Adriano Belan, Cintia Raquel Lima Leal, Renato Araujo Prates, Sidnei Alves De AraújoAbstract:This paper discusses the automated visual identification and quantification of colony forming units (CFU) in Single Plate Serial Dilution Spotting (SP-SDS) through correlation-based granulometry under uncontrolled lighting conditions. There are many different approaches in the literature based on images captured under controlled conditions, which is not the real life situation of laboratories that present high variation in illuminating conditions resulting in low contrast between bacterial colonies and background, background noise, and in addition, high variation in CFU features. Furthermore, SP-SDS has been widely used due to its reduction in the use of resources, but most of previous approaches are not capable of counting separately the number of CFU present in each Dilution zone. In that sense, our study focuses on analyzing real images taken at laboratory day-to-day conditions and proposes an approach suitable for real laboratory practice with high accuracies.
Toshiyuki Kanamori - One of the best experts on this subject based on the ideXlab platform.
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microfluidic Serial Dilution cell based assay for analyzing drug dose response over a wide concentration range
Analytical Chemistry, 2010Co-Authors: Shinji Sugiura, Koji Hattori, Toshiyuki KanamoriAbstract:In this paper we report a perfusion culture microchamber array chip with a Serial Dilution microfluidic network for analyzing drug dose response over a concentration range spanning 6 orders of magnitude, which is required for practical drug discovery applications. The microchamber array chip was equipped with a pressure-driven interface, in which medium and drug solution were added with a micropipet and delivered into the microfluidic network by pneumatic pressure. We demonstrated that the microchamber array chip could be used to estimate the 50% growth inhibitory concentration using the model anticancer drug paclitaxel and the model cancer cell line HeLa. The results obtained by using the microchamber array chip were consistent with those obtained by a conventional assay using microplates. The microchamber array chip, with its simple interface and well-designed microfluidic network, has potential as an efficient platform for high-throughput dose response assays in drug discovery applications.
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generation of arbitrary monotonic concentration profiles by a Serial Dilution microfluidic network composed of microchannels with a high fluidic resistance ratio
Lab on a Chip, 2009Co-Authors: Koji Hattori, Shinji Sugiura, Toshiyuki KanamoriAbstract:This paper reports a Serial Dilution microfluidic network composed of microchannels with a high fluidic-resistance ratio for generating linear concentration profiles as well as logarithmic concentration profiles spanning 3 and 6 orders of magnitude. The microfluidic networks were composed of thin fluidic-resistance microchannels with 160 to 730 µm2 cross-sectional areas and thick diffusion-mixing microchannels with 3,600 to 17,000 µm2 cross-sectional areas, and were fabricated from polydimethylsiloxane by multilayer photolithography and replica molding. We proposed a design algorithm of the microfluidic network for an arbitrary monotonic concentration profile by means of a hydrodynamic calculation. Because of the high fluidic-resistance ratio of the fluidic-resistance microchannels to the diffusion-mixing microchannels, appropriate geometry and dimensions of the fluidic-resistance microchannels allowed us to obtain desired concentration profiles. The fabricated microfluidic network was compact, occupying a 8 × 18 to 21.0 × 13.5 mm2 area on the microchip. Both the linear and the logarithmic concentration profiles were successfully generated with the error less than 15% for the linear concentration profile, 22% and 35% for the logarithmic concentration profiles of 3 and 6 orders of magnitude, respectively. The generated linear concentration profiles of the small molecule, calcein, were independent of the flow rate within the range of 0.009 to 0.23 µL/min. The concentration profiles of the large molecules, dextrans, depended on the flow rate and molecular weight. The required residence time of large molecules in the diffusion-mixing microchannel was correlated with dimensionless diffusion time, Fick number, and was discussed based on the scaling law. These compact, stable Serial Dilution microfluidic networks are expected to be applied to various integrated on-chip analyses.
