A hallmark of bacterial populations cultured in vitro is their homogeneity of growth, where
the majority of cells display identical growth rate, cell size and content. Recent insights,
however, have revealed that even cells growing in exponential growth phase can be
heterogeneous with respect to variables typically used to measure cell growth. Bacterial
heterogeneity has important implications for how bacteria respond to environmental
stresses, such as antibiotics. The phenomenon of antimicrobial persistence, for example,
has been linked to a small subpopulation of cells that have entered into a state of dormancy
where antibiotics are no longer effective. While methods have been developed for identi-
fying individual non-growing cells in bacterial cultures, there has been less attention paid
to how these cells may influence growth in colonies on a solid surface. In response, we have
developed a low-cost, open-source platform to perform automated image capture and
image analysis of bacterial colony growth on multiple nutrient agar plates simultaneously.
The descriptions of the hardware and software are included, along with details about the
temperature-controlled growth chamber, high-resolution scanner, and graphical interface
to extract and plot the colony lag time and growth kinetics. Experiments were conducted
using a wild type strain of Escherichia coli K12 to demonstrate the feasibility and operation
of our setup. By automated tracking of bacterial growth kinetics in colonies, the system
holds the potential to reveal new insights into understanding the impact of microbial
heterogeneity on antibiotic resistance and persistence.
Flexible chip for long-term antimicrobial resistance experimentsIowa State University
By creating a low-cost, three-dimensional microfluidic platform, we have improved our ability to study bacterial cells at the single cell level. This technology allows for prolonged culturing of bacteria in a controlled environment, as well as high resolution observation and imaging of cells. We have used this platform to examine morphological changes in Escherichia coli exposed to ampicillin and to quantify the minimum inhibitory concentration of the antibiotic. Additionally, we demonstrated the potential for precise gene regulation using CRISPR interference (CRISPRi) in a concentration gradient. Ultimately, this engineering tool should be useful for uncovering new genetic factors that influence antibiotic susceptibility and evaluating the long-term effectiveness of antibiotics.
Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR Interference: Applications to Long-Term Bacterial Antibiotic Studies, Taejoon Kong, Nicholas Backes, Upender Kalwa, Christopher Legner, Gregory J. Phillips, and Santosh Pandey, ACS Sensors 2019 4 (10), 2638-2645
https://doi.org/10.1021/acssensors.9b01031
https://pubs.acs.org/doi/full/10.1021/acssensors.9b01031
Abstract:
New combinations of existing antibiotics are being investigated to combat bacterial resilience. This requires detection technologies with reasonable cost, accuracy, resolution, and throughput. Here, we present a multi -drug screening platform for bacterial cultures by combining droplet microfluidics, search algorithms, and imaging with a wide field of view. We remotely alter the chemical microenvironment around cells and test 12 combinations of resistant cell types and chemicals. Fluorescence intensity readouts allow us to infer bacterial resistance to specific antibiotics within 8 hours. The platform has potential to detect and identify parameters of bacterial resilience in cell cultures, biofilms, and microbial aggregates.
S. Pandey, T. Kong, N. Backes and G. J. Phillips, "Open Droplet Microfluidics for Testing Multi-Drug Resistance and Antibiotic Resilience in Bacteria," 2021 21st International Conference on Solid-State Sensors, Actuators and Microsystems (Transducers), 2021, pp. 988-991, doi: 10.1109/Transducers50396.2021.9495667.
"Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR Interference: Applications to Long-Term Bacterial Antibiotic Studies",
ACS Sens. 2019, 4, 10, 2638–2645
Publication Date:October 4, 2019
https://doi.org/10.1021/acssensors.9b01031
Open Droplet Microfluidics for Testing_Multi-Drug Resistance and Antibiotic R...Iowa State University
New combinations of existing antibiotics are being investigated to combat bacterial resilience. This requires detection technologies with reasonable cost, accuracy, resolution, and throughput. Here, we present a multi -drug screening platform for bacterial cultures by combining droplet microfluidics, search algorithms, and imaging with a wide field of view. We remotely alter the chemical microenvironment around cells and test 12 combinations of resistant cell types and chemicals. Fluorescence intensity readouts allow us to infer bacterial resistance to specific antibiotics within 8 hours. The platform has potential to detect and identify parameters of bacterial resilience in cell cultures, biofilms, and microbial aggregates.
Flexible chip for long-term antimicrobial resistance experimentsIowa State University
By creating a low-cost, three-dimensional microfluidic platform, we have improved our ability to study bacterial cells at the single cell level. This technology allows for prolonged culturing of bacteria in a controlled environment, as well as high resolution observation and imaging of cells. We have used this platform to examine morphological changes in Escherichia coli exposed to ampicillin and to quantify the minimum inhibitory concentration of the antibiotic. Additionally, we demonstrated the potential for precise gene regulation using CRISPR interference (CRISPRi) in a concentration gradient. Ultimately, this engineering tool should be useful for uncovering new genetic factors that influence antibiotic susceptibility and evaluating the long-term effectiveness of antibiotics.
Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR Interference: Applications to Long-Term Bacterial Antibiotic Studies, Taejoon Kong, Nicholas Backes, Upender Kalwa, Christopher Legner, Gregory J. Phillips, and Santosh Pandey, ACS Sensors 2019 4 (10), 2638-2645
https://doi.org/10.1021/acssensors.9b01031
https://pubs.acs.org/doi/full/10.1021/acssensors.9b01031
Abstract:
New combinations of existing antibiotics are being investigated to combat bacterial resilience. This requires detection technologies with reasonable cost, accuracy, resolution, and throughput. Here, we present a multi -drug screening platform for bacterial cultures by combining droplet microfluidics, search algorithms, and imaging with a wide field of view. We remotely alter the chemical microenvironment around cells and test 12 combinations of resistant cell types and chemicals. Fluorescence intensity readouts allow us to infer bacterial resistance to specific antibiotics within 8 hours. The platform has potential to detect and identify parameters of bacterial resilience in cell cultures, biofilms, and microbial aggregates.
S. Pandey, T. Kong, N. Backes and G. J. Phillips, "Open Droplet Microfluidics for Testing Multi-Drug Resistance and Antibiotic Resilience in Bacteria," 2021 21st International Conference on Solid-State Sensors, Actuators and Microsystems (Transducers), 2021, pp. 988-991, doi: 10.1109/Transducers50396.2021.9495667.
"Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR Interference: Applications to Long-Term Bacterial Antibiotic Studies",
ACS Sens. 2019, 4, 10, 2638–2645
Publication Date:October 4, 2019
https://doi.org/10.1021/acssensors.9b01031
Open Droplet Microfluidics for Testing_Multi-Drug Resistance and Antibiotic R...Iowa State University
New combinations of existing antibiotics are being investigated to combat bacterial resilience. This requires detection technologies with reasonable cost, accuracy, resolution, and throughput. Here, we present a multi -drug screening platform for bacterial cultures by combining droplet microfluidics, search algorithms, and imaging with a wide field of view. We remotely alter the chemical microenvironment around cells and test 12 combinations of resistant cell types and chemicals. Fluorescence intensity readouts allow us to infer bacterial resistance to specific antibiotics within 8 hours. The platform has potential to detect and identify parameters of bacterial resilience in cell cultures, biofilms, and microbial aggregates.
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data.
In this review, we focus on the hardware and software technologies used for the purpose of gastrointestinal tract monitoring in a safe and comfortable manner. We review the FDA guidelines for ingestible wireless telemetric medical devices, and the features incorporated in capsule systems such as microrobotics, closed-loop feedback, physiological sensing, nerve stimulation, sampling and delivery, panoramic imaging and rapid reading software. Both experimental and commercialized capsule systems with their sensors, devices, and circuits are discussed. Furthermore, the advances in biocompatible materials and batteries, edible electronics and alternative energy sources for ingestible capsule systems are presented. The clinical studies are reviewed to examine the safety and effectiveness of capsule procedures and the current challenges and outlook are summarized.
Design of MEMS Biosensor for Pathogenic Bacterial Disease DetectionAI Publications
In situations of a critical disease outbreak, any time delay in identifying the pathogen can prove to be risky and has its far-reaching effects on public health systems. There is a need for pathogenic bacteria detection at the point‐of‐care (POC) using a fast, sensitive, inexpensive, and easy‐to‐use method that does not require complex infrastructure and well‐trained technicians. For instance, detection of pneumonia, tuberculosis at acute infection stage has been challenging, since current antibody‐based POC technologies are not effective due to low concentration of antibodies. In this study, we demonstrated for the first time a label‐free electrical sensing method that can detect pathogenic bacteria, through MEMS cantilever technology. The presented method offers a rapid and portable tool that is MEMS biosensor, can be used as a bacteria detection technology at the hospital and primary care settings.
Video Capsule Endoscopy and Ingestible Electronics: Emerging Trends in Sensor...Iowa State University
Real-time monitoring of the gastrointestinal tract in a safe and comfortable manner is valuable for the diagnosis and therapy of many diseases. Within this realm, our review captures the trends in ingestible capsule systems with a focus on hardware and software technologies used for capsule endoscopy and remote patient monitoring. We introduce the structure and functions of the gastrointestinal tract, and the FDA guidelines for ingestible wireless telemetric medical devices. We survey the advanced features incorporated in ingestible capsule systems, such as microrobotics, closed-loop feedback, physiological sensing, nerve stimulation, sampling and delivery, panoramic imaging with adaptive frame rates, and rapid reading software. Examples of experimental and commercialized capsule systems are presented with descriptions of their sensors, devices, and circuits for gastrointestinal health monitoring. We also show the recent research in biocompatible materials and batteries, edible electronics, and alternative energy sources for ingestible capsule systems. The results from clinical studies are discussed for the assessment of key performance indicators related to the safety and effectiveness of ingestible capsule procedures. Lastly, the present challenges and outlook are summarized with respect to the risks to health, clinical testing and approval process, and technology adoption by patients and clinicians.
There are many characteristics of biological data. All these characteristics make the management of biological information a particularly challenging problem. Here mainly we will focus on characteristics of biological information and multidisciplinary field called bioinformatics. Bioinformatics, now a days has emerged with graduate degree programs in several universities.
Presentation in the "Whole genome sequencing for clinical microbiology:Translation into routine applications" Symposium , Basel , Switzerland, 2 Sep 2017
A Deep Learning Method for Plant Disease Diagnosis and Detection in Smart Agr...AakashRoy30
Creating and training a CNN model from scratch is a tedious process, this model can be used to detect and classification of other plant disease too, by simply training the model using respected datasets
BACTERIA IDENTIFICATION FROM MICROSCOPIC MORPHOLOGY USING NAÏVE BAYESijcseit
Great knowledge and experience on microbiology are required for accurate bacteria identification.
Automation of bacteria identification is required because there might be a shortage of skilled
microbiologists and clinicians at a time of great need. We propose an automatic bacteria identification
framework that can classify three famous classes of bacteria namely Cocci, Bacilli and Vibrio from
microscopic morphology using the Naïve Bayes classifier. The proposed bacteria identification framework
comprises two steps. In the first step, the system is trained using a set of microscopic images containing
Cocci, Bacilli, and Vibrio. The input images are normalized to emphasize the diameter and shape features.
Edge-based descriptors are then extracted from the input images. In the second step, we use theNaïve
Bayes classifier to performprobabilistic inference based on the input descriptors. 64 images for each class
of bacteria were used as the training setand 222 images consisting of the three classes of bacteria and
other random images such as humans and airplanes were used as the test set. There are no images
overlapped between the training set and the test set. The system was found to be able to accurately
discriminate the three classes of bacteria. Moreover, the system was also found to be able to reject images
that did not belong to any of the three classes of bacteria. The preliminary results demonstrate how a
simple machine learning classifier with a set of simple image-based features can result in high
classification accuracy. The preliminary results also demonstrate the efficacy and efficiency of our two-step
automatic bacteria identification approach and motivate us to extend this framework to identify a variety of
other types of bacteria.
Bacteria identification from microscopic morphology using naïve bayesijcseit
Great knowledge and experience on microbiology are required for accurate bacteria identification.
Automation of bacteria identification is required because there might be a shortage of skilled
microbiologists and clinicians at a time of great need. We propose an automatic bacteria identification
framework that can classify three famous classes of bacteria namely Cocci, Bacilli and Vibrio from
microscopic morphology using the Naïve Bayes classifier. The proposed bacteria identification framework
comprises two steps. In the first step, the system is trained using a set of microscopic images containing
Cocci, Bacilli, and Vibrio. The input images are normalized to emphasize the diameter and shape features.
Edge-based descriptors are then extracted from the input images. In the second step, we use theNaïve
Bayes classifier to performprobabilistic inference based on the input descriptors. 64 images for each class
of bacteria were used as the training setand 222 images consisting of the three classes of bacteria and
other random images such as humans and airplanes were used as the test set. There are no images
overlapped between the training set and the test set. The system was found to be able to accurately
discriminate the three classes of bacteria. Moreover, the system was also found to be able to reject images
that did not belong to any of the three classes of bacteria. The preliminary results demonstrate how a
simple machine learning classifier with a set of simple image-based features can result in high
classification accuracy. The preliminary results also demonstrate the efficacy and efficiency of our two-step
automatic bacteria identification approach and motivate us to extend this framework to identify a variety of
other types of bacteria.
A deep learning-based mobile app system for visual identification of tomato p...IJECEIAES
Tomato is one of many horticulture crops in Indonesia which plays a vital role in supplying public food needs. However, tomato is a very susceptible plant to pests and diseases caused by bacteria and fungus. The infected diseases should be isolated as soon as it was detected. Therefore, developing a reliable and fast system is essential for controlling tomato pests and diseases. The deep learning-based application can help to speed up the identification of tomato disease as it can perform direct identification from the image. In this research, EfficientNetB0 was implemented to perform multi-class tomato plant disease classification. The model was then deployed to an android-based application using machine learning (ML) kit library. The proposed system obtained satisfactory results, reaching an average accuracy of 91.4%.
A comparative study of mango fruit pest and disease recognitionTELKOMNIKA JOURNAL
Mango is a popular fruit for local consumption and export commodity. Currently, Indonesian mango export at 37.8 M accounted for 0.115% of world consumption. Pest and disease are the common enemies of mango that degrade the quality of mango yield. Specialized treatment in export destinations such as gamma-ray in Australia, or hot water treatment in Korea, demands pest-free and high-quality products. Artificial intelligence helps to improve mango pest and disease control. This paper compares the deep learning model on mango fruit pests and disease recognition. This research compares Visual Geometry Group 16 (VGG16), residual neural network 50 (ResNet50), InceptionResNet-V2, Inception-V3, and DenseNet architectures to identify pests and diseases on mango fruit. We implement transfer learning, adopt all pre-trained weight parameters from all those architectures, and replace the final layer to adjust the output. All the architectures are re-train and validated using our dataset. The tropical mango dataset is collected and labeled by a subject matter expert. The VGG16 model achieves the top validation and testing accuracy at 89% and 90%, respectively. VGG16 is the shallowest model, with 16 layers; therefore, the model was the smallest size. The testing time is superior to the rest of the experiment at 2 seconds for 130 testing images.
In this review, we focus on the hardware and software technologies used for the purpose of gastrointestinal tract monitoring in a safe and comfortable manner. We review the FDA guidelines for ingestible wireless telemetric medical devices, and the features incorporated in capsule systems such as microrobotics, closed-loop feedback, physiological sensing, nerve stimulation, sampling and delivery, panoramic imaging and rapid reading software. Both experimental and commercialized capsule systems with their sensors, devices, and circuits are discussed. Furthermore, the advances in biocompatible materials and batteries, edible electronics and alternative energy sources for ingestible capsule systems are presented. The clinical studies are reviewed to examine the safety and effectiveness of capsule procedures and the current challenges and outlook are summarized.
Dylan Miley*, Leonardo Bertoncello Machado*, Calvin Condo, Albert E. Jergens, Kyoung-Jin Yoon, Santosh Pandey, “Video Capsule Endoscopy and Ingestible Electronics: Emerging Trends in Sensors, Circuits, Materials, Telemetry, Optics, and Rapid Reading Software“, Advanced Devices & Instrumentation, (Science Partner Journal), Volume 2021, Article ID 9854040, 2021. https://spj.science.org/doi/10.34133/2021/9854040?permanently=true
https://doi.org/10.34133/2021/9854040
Antimicrobial resistance studies in low-cost microfluidic chipsIowa State University
By utilizing a low-cost engineering tool, we have created a microfluidic platform to study bacteria at the single cell level, allowing us to unlock insights into microbial physiology and genetics that would otherwise not be possible. The platform is composed of 3D devices made of adhesive tapes, an agarose membrane as the resting substrate, a temperature-controlled environmental chamber, and an autofocusing module. With this technology, we have been able to observe Escherichia coli morphological changes during ampicillin exposure and measure the minimum inhibitory concentration of the antibiotic. Additionally, we have been able to use CRISPR interference (CRISPRi) to evaluate gene regulation in a concentration gradient. Overall, our microfluidic platform provides a powerful, low-cost tool to uncover new genetic determinants of antibiotic susceptibility and assess the long-term effectiveness of antibiotics in bacterial cultures.
Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR Interference: Applications to Long-Term Bacterial Antibiotic Studies, Taejoon Kong, Nicholas Backes, Upender Kalwa, Christopher Legner, Gregory J. Phillips, and Santosh Pandey, ACS Sensors 2019 4 (10), 2638-2645
https://doi.org/10.1021/acssensors.9b01031
https://pubs.acs.org/doi/full/10.1021/acssensors.9b01031
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Similar to Low-cost, open-source bacterial colony tracking over large areas and extended incubation times
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data.
In this review, we focus on the hardware and software technologies used for the purpose of gastrointestinal tract monitoring in a safe and comfortable manner. We review the FDA guidelines for ingestible wireless telemetric medical devices, and the features incorporated in capsule systems such as microrobotics, closed-loop feedback, physiological sensing, nerve stimulation, sampling and delivery, panoramic imaging and rapid reading software. Both experimental and commercialized capsule systems with their sensors, devices, and circuits are discussed. Furthermore, the advances in biocompatible materials and batteries, edible electronics and alternative energy sources for ingestible capsule systems are presented. The clinical studies are reviewed to examine the safety and effectiveness of capsule procedures and the current challenges and outlook are summarized.
Design of MEMS Biosensor for Pathogenic Bacterial Disease DetectionAI Publications
In situations of a critical disease outbreak, any time delay in identifying the pathogen can prove to be risky and has its far-reaching effects on public health systems. There is a need for pathogenic bacteria detection at the point‐of‐care (POC) using a fast, sensitive, inexpensive, and easy‐to‐use method that does not require complex infrastructure and well‐trained technicians. For instance, detection of pneumonia, tuberculosis at acute infection stage has been challenging, since current antibody‐based POC technologies are not effective due to low concentration of antibodies. In this study, we demonstrated for the first time a label‐free electrical sensing method that can detect pathogenic bacteria, through MEMS cantilever technology. The presented method offers a rapid and portable tool that is MEMS biosensor, can be used as a bacteria detection technology at the hospital and primary care settings.
Video Capsule Endoscopy and Ingestible Electronics: Emerging Trends in Sensor...Iowa State University
Real-time monitoring of the gastrointestinal tract in a safe and comfortable manner is valuable for the diagnosis and therapy of many diseases. Within this realm, our review captures the trends in ingestible capsule systems with a focus on hardware and software technologies used for capsule endoscopy and remote patient monitoring. We introduce the structure and functions of the gastrointestinal tract, and the FDA guidelines for ingestible wireless telemetric medical devices. We survey the advanced features incorporated in ingestible capsule systems, such as microrobotics, closed-loop feedback, physiological sensing, nerve stimulation, sampling and delivery, panoramic imaging with adaptive frame rates, and rapid reading software. Examples of experimental and commercialized capsule systems are presented with descriptions of their sensors, devices, and circuits for gastrointestinal health monitoring. We also show the recent research in biocompatible materials and batteries, edible electronics, and alternative energy sources for ingestible capsule systems. The results from clinical studies are discussed for the assessment of key performance indicators related to the safety and effectiveness of ingestible capsule procedures. Lastly, the present challenges and outlook are summarized with respect to the risks to health, clinical testing and approval process, and technology adoption by patients and clinicians.
There are many characteristics of biological data. All these characteristics make the management of biological information a particularly challenging problem. Here mainly we will focus on characteristics of biological information and multidisciplinary field called bioinformatics. Bioinformatics, now a days has emerged with graduate degree programs in several universities.
Presentation in the "Whole genome sequencing for clinical microbiology:Translation into routine applications" Symposium , Basel , Switzerland, 2 Sep 2017
A Deep Learning Method for Plant Disease Diagnosis and Detection in Smart Agr...AakashRoy30
Creating and training a CNN model from scratch is a tedious process, this model can be used to detect and classification of other plant disease too, by simply training the model using respected datasets
BACTERIA IDENTIFICATION FROM MICROSCOPIC MORPHOLOGY USING NAÏVE BAYESijcseit
Great knowledge and experience on microbiology are required for accurate bacteria identification.
Automation of bacteria identification is required because there might be a shortage of skilled
microbiologists and clinicians at a time of great need. We propose an automatic bacteria identification
framework that can classify three famous classes of bacteria namely Cocci, Bacilli and Vibrio from
microscopic morphology using the Naïve Bayes classifier. The proposed bacteria identification framework
comprises two steps. In the first step, the system is trained using a set of microscopic images containing
Cocci, Bacilli, and Vibrio. The input images are normalized to emphasize the diameter and shape features.
Edge-based descriptors are then extracted from the input images. In the second step, we use theNaïve
Bayes classifier to performprobabilistic inference based on the input descriptors. 64 images for each class
of bacteria were used as the training setand 222 images consisting of the three classes of bacteria and
other random images such as humans and airplanes were used as the test set. There are no images
overlapped between the training set and the test set. The system was found to be able to accurately
discriminate the three classes of bacteria. Moreover, the system was also found to be able to reject images
that did not belong to any of the three classes of bacteria. The preliminary results demonstrate how a
simple machine learning classifier with a set of simple image-based features can result in high
classification accuracy. The preliminary results also demonstrate the efficacy and efficiency of our two-step
automatic bacteria identification approach and motivate us to extend this framework to identify a variety of
other types of bacteria.
Bacteria identification from microscopic morphology using naïve bayesijcseit
Great knowledge and experience on microbiology are required for accurate bacteria identification.
Automation of bacteria identification is required because there might be a shortage of skilled
microbiologists and clinicians at a time of great need. We propose an automatic bacteria identification
framework that can classify three famous classes of bacteria namely Cocci, Bacilli and Vibrio from
microscopic morphology using the Naïve Bayes classifier. The proposed bacteria identification framework
comprises two steps. In the first step, the system is trained using a set of microscopic images containing
Cocci, Bacilli, and Vibrio. The input images are normalized to emphasize the diameter and shape features.
Edge-based descriptors are then extracted from the input images. In the second step, we use theNaïve
Bayes classifier to performprobabilistic inference based on the input descriptors. 64 images for each class
of bacteria were used as the training setand 222 images consisting of the three classes of bacteria and
other random images such as humans and airplanes were used as the test set. There are no images
overlapped between the training set and the test set. The system was found to be able to accurately
discriminate the three classes of bacteria. Moreover, the system was also found to be able to reject images
that did not belong to any of the three classes of bacteria. The preliminary results demonstrate how a
simple machine learning classifier with a set of simple image-based features can result in high
classification accuracy. The preliminary results also demonstrate the efficacy and efficiency of our two-step
automatic bacteria identification approach and motivate us to extend this framework to identify a variety of
other types of bacteria.
A deep learning-based mobile app system for visual identification of tomato p...IJECEIAES
Tomato is one of many horticulture crops in Indonesia which plays a vital role in supplying public food needs. However, tomato is a very susceptible plant to pests and diseases caused by bacteria and fungus. The infected diseases should be isolated as soon as it was detected. Therefore, developing a reliable and fast system is essential for controlling tomato pests and diseases. The deep learning-based application can help to speed up the identification of tomato disease as it can perform direct identification from the image. In this research, EfficientNetB0 was implemented to perform multi-class tomato plant disease classification. The model was then deployed to an android-based application using machine learning (ML) kit library. The proposed system obtained satisfactory results, reaching an average accuracy of 91.4%.
A comparative study of mango fruit pest and disease recognitionTELKOMNIKA JOURNAL
Mango is a popular fruit for local consumption and export commodity. Currently, Indonesian mango export at 37.8 M accounted for 0.115% of world consumption. Pest and disease are the common enemies of mango that degrade the quality of mango yield. Specialized treatment in export destinations such as gamma-ray in Australia, or hot water treatment in Korea, demands pest-free and high-quality products. Artificial intelligence helps to improve mango pest and disease control. This paper compares the deep learning model on mango fruit pests and disease recognition. This research compares Visual Geometry Group 16 (VGG16), residual neural network 50 (ResNet50), InceptionResNet-V2, Inception-V3, and DenseNet architectures to identify pests and diseases on mango fruit. We implement transfer learning, adopt all pre-trained weight parameters from all those architectures, and replace the final layer to adjust the output. All the architectures are re-train and validated using our dataset. The tropical mango dataset is collected and labeled by a subject matter expert. The VGG16 model achieves the top validation and testing accuracy at 89% and 90%, respectively. VGG16 is the shallowest model, with 16 layers; therefore, the model was the smallest size. The testing time is superior to the rest of the experiment at 2 seconds for 130 testing images.
Similar to Low-cost, open-source bacterial colony tracking over large areas and extended incubation times (20)
In this review, we focus on the hardware and software technologies used for the purpose of gastrointestinal tract monitoring in a safe and comfortable manner. We review the FDA guidelines for ingestible wireless telemetric medical devices, and the features incorporated in capsule systems such as microrobotics, closed-loop feedback, physiological sensing, nerve stimulation, sampling and delivery, panoramic imaging and rapid reading software. Both experimental and commercialized capsule systems with their sensors, devices, and circuits are discussed. Furthermore, the advances in biocompatible materials and batteries, edible electronics and alternative energy sources for ingestible capsule systems are presented. The clinical studies are reviewed to examine the safety and effectiveness of capsule procedures and the current challenges and outlook are summarized.
Dylan Miley*, Leonardo Bertoncello Machado*, Calvin Condo, Albert E. Jergens, Kyoung-Jin Yoon, Santosh Pandey, “Video Capsule Endoscopy and Ingestible Electronics: Emerging Trends in Sensors, Circuits, Materials, Telemetry, Optics, and Rapid Reading Software“, Advanced Devices & Instrumentation, (Science Partner Journal), Volume 2021, Article ID 9854040, 2021. https://spj.science.org/doi/10.34133/2021/9854040?permanently=true
https://doi.org/10.34133/2021/9854040
Antimicrobial resistance studies in low-cost microfluidic chipsIowa State University
By utilizing a low-cost engineering tool, we have created a microfluidic platform to study bacteria at the single cell level, allowing us to unlock insights into microbial physiology and genetics that would otherwise not be possible. The platform is composed of 3D devices made of adhesive tapes, an agarose membrane as the resting substrate, a temperature-controlled environmental chamber, and an autofocusing module. With this technology, we have been able to observe Escherichia coli morphological changes during ampicillin exposure and measure the minimum inhibitory concentration of the antibiotic. Additionally, we have been able to use CRISPR interference (CRISPRi) to evaluate gene regulation in a concentration gradient. Overall, our microfluidic platform provides a powerful, low-cost tool to uncover new genetic determinants of antibiotic susceptibility and assess the long-term effectiveness of antibiotics in bacterial cultures.
Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR Interference: Applications to Long-Term Bacterial Antibiotic Studies, Taejoon Kong, Nicholas Backes, Upender Kalwa, Christopher Legner, Gregory J. Phillips, and Santosh Pandey, ACS Sensors 2019 4 (10), 2638-2645
https://doi.org/10.1021/acssensors.9b01031
https://pubs.acs.org/doi/full/10.1021/acssensors.9b01031
In this paper, we explore the use of microfluidic paper-based analytical devices (PADs) to study the behavior of Caenorhabditis elegans. We show how these devices can be fabricated on paper and plastic substrates, as well as how to load, visualize, and transfer single and multiple nematodes. We also demonstrate the use of anthelmintic drug, levamisole, to perform chemical testing on C. elegans. Furthermore, we provide a custom program that is able to recognize individual worms on the PADs in real-time and extract their locomotion parameters. This combination of PADs and the nematode tracking program creates a low-cost, easy-to-fabricate imaging and screening assay that is superior to standard agarose plates or polymeric microfluidic devices for non-microfluidic, nematode laboratories.
Zach Njus, Taejoon Kong, Upender Kalwa, Christopher Legner, Matthew Weinstein, Shawn Flanigan, Jenifer Saldanha, and Santosh Pandey, "Flexible and disposable paper- and plastic-based gel micropads for nematode handling, imaging, and chemical testing", APL Bioengineering 1, 016102 (2017)
https://doi.org/10.1063/1.5005829
https://aip.scitation.org/doi/10.1063/1.5005829
The resistance of parasites to existing drugs and the availability of better technology platforms has driven the discovery of new drugs. Microfluidic devices have been used to facilitate faster screening of compounds, controlled sampling/sorting of whole animals, and automated behavioral pattern recognition. In most cases, drug effects on small creatures (e.g., Caenorhabditis elegans) are measuredelegant by a single parameter such as worm velocity or stroke frequency. We present a multi-parameter extraction method to characterize modes of paralysis in C. elegans over a longer duration. This was done using a microfluidic device featuring real-time imaging, exposing worms to four anthelmintic drugs at EC75, where 75% of the worm population is affected. We monitored the worms' behavior with metrics such as curls per second, types of paralyzation, mode frequency, and number/duration of active/immobilization periods. Differences were observed in how the worms paralyzed in the various drug environments at equivalent concentrations. This study highlights the importance of assessing drug effects on small animals with multiple parameters, measured at regular intervals over a prolonged period, to accurately detect resistance and adaptability in chemical environments.
Roy Lycke, Archana Parashar, and Santosh Pandey, "Microfluidics-enabled method to identify modes of Caenorhabditis elegans paralysis in four anthelmintics", Biomicrofluidics 7, 064103 (2013).
https://doi.org/10.1063/1.4829777
https://aip.scitation.org/doi/10.1063/1.4829777
Melanoma is a particularly dangerous type of skin cancer and is hard to treat in its later stages. Therefore, early detection is key in reducing mortality rates. In order to assist dermatologists in doing this, computer-aided systems have been designed for desktop computers. However, there is a desire for the development of mobile, at-home diagnostics for melanoma risk assessment. Here, we introduce a smartphone application that captures images and extracts ABCD features to classify skin lesions as either malignant or benign. The algorithms used are adaptive to make the process light and user-friendly, as well as reliable in diagnosis. Images can be taken with the phone's camera or imported from public datasets. The entire process of taking the image, performing preprocessing, segmentation and classification is completed on an Android smartphone in a short time. Our application is evaluated on a dataset of 200 images, and achieved either comparable or better performance metrics than other methods. Additionally, it is easy-to-download and easy-to-navigate for the user, which is important for the widespread use of such diagnostics.
Kalwa, U.; Legner, C.; Kong, T.; Pandey, S. Skin Cancer Diagnostics with an All-Inclusive Smartphone Application. Symmetry 2019, 11, 790. https://doi.org/10.3390/sym11060790
https://www.mdpi.com/2073-8994/11/6/790
A CMOS biosensor with a folded floating-gate is created to detect charged biochemical molecules. It contains a FET, a control-gate and a sensing area. The floating-gate spans the whole device, allowing the sensing area to be placed on top of the FET, resulting in a decrease of the device's total area. The device is sensitive to the polarity and quantity of charged poly amino acids and could be used for electronic recognition of temporal and spatial migration of charges, such as in biological phenomena.
B. Chen, A. Parashar and S. Pandey, "Folded Floating-Gate CMOS Biosensor for the Detection of Charged Biochemical Molecules," IEEE Sensors Journal, vol. 11, no. 11, pp. 2906-2910, Nov. 2011, doi: 10.1109/JSEN.2011.2149514.
https://ieeexplore.ieee.org/document/5762313
We attempt to offer an innovative solution to the issues of long response times, large volumes of actuation fluid, and external control circuitry that have been associated with past approaches in creating switches in paper microfluidics. Our method consists of a device created from chromatography paper and featuring folds which, when selectively wetted with an actuation fluid, will either raise or lower the actuator's tip and thus engage or break the desired fluidic connections. As a result, response time is drastically reduced (2 seconds) and the volume of actuation fluid consumed is extremely small (4 microliters). We have tested this approach with six switch configurations, ranging from single-pole single-throw (normally OFF and normally ON) to single-pole double-throw (with single and double break). We further demonstrate its potential with a colorimetric assay involving six actuators in parallel, which can detect the presence of three analytes (glucose, protein, and nitrite) in artificial saliva. Finally, this work brings in the concept of origami to paper microfluidics, combining multiple-fold geometries for programmable switching of fluidic connections.
"A fast, reconfigurable flow switch for paper
microfluidics based on selective wetting of folded
paper actuator strips",
Lab on Chip, 2017, 17, 3621
A method to create smart and flexible switches for the regulation of liquid flow across multiple channels is essential in paper microfluidics. Prior approaches are hampered by long response times, high actuation fluid volumes, and external control circuitry. To diminish these problems, we designed a distinctive actuator device fashioned entirely from chromatography paper and featuring folds. The fold can be selectively wetted by an actuation fluid at either the crest or trough, resulting in the raising or lowering of the actuator's tip and thus bringing about the connection or severance of fluidic channels. This actuation principle reduces the response time to only two seconds and the amount of fluid used to merely four microliters. We have also added six switch arrangements which can be divided into single-pole single-throw (normally OFF and normally ON) and single-pole double-throw (with single and double break). The utilization of six actuators in a parallel system allowed us to construct an autonomous colorimetric assay for the detection of three analytes - glucose, protein, and nitrite - in artificial saliva. This study has brought the concept of origami to paper microfluidics, allowing the use of multiple-fold geometries for the programmable switching of fluidic connections.
Taejoon Kong et al, "A fast, reconfigurable flow switch for paper
microfluidics based on selective wetting of folded
paper actuator strips", Lab on Chip, 2017, 17, 3621
The transmembrane proteins known as ion channels play a role in controlling and preserving the ionic concentrations across the cell membrane. Modeling the flux of ions in and out of these channels on an atomic level is essential for understanding several neurological diseases and related pharmaceutical discoveries. Recent experimental research has provided information on the channel's physical structure which can be used to create realistic ion transport models. Different trajectories exist for the ions entering the channel, each having its own probability of occurrence. Variables that measure these trajectories are the translocation and return probabilities, average lifetime, and spectral density of the ion number fluctuations. Theoretical analysis of ion transport has been restricted to low-resolution continuum diffusion-based or kinetic-based models which do not consider important factors that have an effect on ionic conduction. This paper extends previous models by an electro-diffusion model which takes into account the effects of electric fields, energy barriers, and rate-limited association/dissociation of ions with surface charges present inside the channel. Derived from the analytical model are the survival probability and spectral density.
:Analytical Modeling of the Ion Number Fluctuations in Biological Ion Channels"
Journal of Nanoscience and Nanotechnology; Vol. 12, 2489–2495, 2012
Ion Channel Fluctuations in Transmemembrane Proteins within Cell MembranesIowa State University
The transmembrane proteins known as ion channels play a role in controlling and preserving the ionic concentrations across the cell membrane. Modeling the flux of ions in and out of these channels on an atomic level is essential for understanding several neurological diseases and related pharmaceutical discoveries. Recent experimental research has provided information on the channel's physical structure which can be used to create realistic ion transport models. Different trajectories exist for the ions entering the channel, each having its own probability of occurrence. Variables that measure these trajectories are the translocation and return probabilities, average lifetime, and spectral density of the ion number fluctuations. Theoretical analysis of ion transport has been restricted to low-resolution continuum diffusion-based or kinetic-based models which do not consider important factors that have an effect on ionic conduction. This paper extends previous models by an electro-diffusion model which takes into account the effects of electric fields, energy barriers, and rate-limited association/dissociation of ions with surface charges present inside the channel. Derived from the analytical model are the survival probability and spectral density.
This paper presents a remote monitoring tool for the objective measurement of behavioral indicators that can help in assessing the health and welfare of pigs in precision swine production. The multiparameter electronic sensor board can measure posture, gait, vocalization, and external temperature, and has been characterized through laboratory measurements and animal tests. Machine learning algorithms and decision support tools can be implemented to detect animal lameness, lethargy, pain, injury, and distress. The adoption of this technology could lead to more efficient management of farm animals, better targeting of sick animals, lower medical costs, and fewer antibiotics being used. Challenges and a road map for technology adoption are discussed, along with suggestions for future improvements.
Animals 2021, 11(9), 2665; https://doi.org/10.3390/ani11092665
We propose a remote monitoring device for measuring behavioral indicators like posture, gait, vocalization, and external temperature which can help in evaluating the health and welfare of pigs. The multiparameter electronic sensor board was tested in a laboratory and on animals. Machine learning algorithms and decision support tools can be used to detect lameness, lethargy, pain, injury, and distress. The roadmap for technology adoption, potential benefits, and further challenges are discussed. This technology could help in efficient management of farm animals, providing targeted attention to sick animals, saving medical costs, and reducing the use of antibiotics.
"Behavioral Monitoring Tool for Pig Farmers: Ear Tag Sensors,
Machine Intelligence, and Technology Adoption Roadmap",
Animals 2021, 11, 2665.
https://doi.org/10.3390/ani11092665
In this study, two sets of experiments were conducted in order to investigate the impact of static magnetic fields on the growth and ethanol production of Saccharomyces cerevisiae. The first experiment ran for 25 hours with a 2% dextrose loading rate, while the second ran for 30 hours with a 6% dextrose loading rate. The magnetic fields used were homogeneous and non-homogeneous, with strengths of 100 mT and 200 mT, respectively. The results showed that the homogenous magnetic field had no significant effect on cell growth, whilst the non-homogeneous field yielded an increase of approximately 8% in peak ethanol concentration compared to the control.
Deutmeyer, A. , Raman, R. , Murphy, P. and Pandey, S. (2011) Effect of magnetic field on the fermentation kinetics of Saccharomyces cerevisiae. Advances in Bioscience and Biotechnology, 2, 207-213.
doi: 10.4236/abb.2011.24031.
https://www.scirp.org/journal/paperinformation.aspx?paperid=6857
Magnetic field to improve fermentation kinetics for ethanol production Iowa State University
Two experiments were conducted to analyze the influence that magnetic fields have on cell growth and ethanol production during fermentation. The first experiment was conducted for 25 hours at a 2% dextrose loading rate with a homogeneous and non-homogeneous static magnetic field of 100 mT and 200 mT, respectively. The second experiment was conducted for 30 hours at a 6% dextrose loading rate with a non-homogeneous static magnetic field of 200 mT. The results indicated that homogeneous magnetic fields did not have a significant effect on the yeast cell growth. However, the non-homogeneous static magnetic field resulted in about 8% more peak ethanol concentration than the control for the 2% dextrose loading rate.
To evaluate the severity of SCN infections in the field, population densities of nematode eggs must be calculated. A method utilizing OptiPrep as a density gradient medium has been shown to provide more effective separation and recovery of extracted eggs compared to sucrose centrifugation. Furthermore, computerized processes have been established to facilitate the discernment and enumeration of eggs from processed samples. A high-resolution scanner was employed to capture static images of eggs and debris on filter papers, and a deep learning network was trained to distinguish and count the eggs from the debris. Additionally, a lensless imaging setup was established using standard components, and the egg samples were allowed to pass through a microfluidic flow chip created from double-sided adhesive tape. Holographic videos were then recorded of the eggs and debris as they moved through, which were reconstructed and processed by a custom software program to obtain the egg counts. The software programs' efficacy for egg counting was validated using soil samples obtained from two farms, and the results were compared to those obtained through manual counting.
Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10): e0223386.
https://doi.org/10.1371/journal.pone.0223386
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
To evaluate the level of infestation of the soybean cyst nematode (SCN), Heterodera glycines, in the field, egg population densities are determined from soil samples. Sucrose centrifugation is a common technique for separating debris from the extracted SCN eggs. We have developed a procedure, however, that employs OptiPrep as a density gradient medium, with improved extraction and recovery of the eggs compared to the sucrose centrifugation technique. Also, we have built computerized methods to automate the identification and counting of the nematode eggs from the processed samples. One approach uses a high-resolution scanner to capture static images of the eggs and debris on filter papers and a deep learning network is trained to detect and count the eggs. The second approach utilizes a lensless imaging setup with off-the-shelf components and the egg samples flow through a microfluidic flowchip. Holographic videos are taken of the passing eggs and debris, which are then reconstructed and processed by a custom software program to calculate egg counts. To evaluate the performance of the software programs, SCN-infested soils were collected from two farms and the results were compared with manual counts.
Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019), New methods of removing debris and high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10): e0223386.
https://doi.org/10.1371/journal.pone.0223386
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
Effect of Static Magnetic Field on Parasitic Worms in MicroChipsIowa State University
This study uses the model organism, C. elegans, to investigate its sensitivity and response to static magnetic fields. Wild-type C. elegans are put into microfluidic channels and exposed to permanent magnets for five cycles of thirty-second time intervals at field strengths ranging from 5 milli Tesla to 120 milli Tesla. Recorded and analyzed with custom software, the results of the worm's movement - the average velocity, turning and curling percentage - were compared to control experiments. Surprisingly, the results did not show any significant difference, indicating that C. elegans may not be able to sense static magnetic fields at the range of field strengths tested.
Njus, Z. , Feldmann, D. , Brien, R. , Kong, T. , Kalwa, U. and Pandey, S. (2015) Characterizing the Effect of Static Magnetic Fields on C. elegans Using Microfluidics. Advances in Bioscience and Biotechnology, 6, 583-591.
doi: 10.4236/abb.2015.69061.
https://www.scirp.org/journal/paperinformation.aspx?paperid=59434
The integration of physical and chemical sensing mechanisms found in nature has been harnessed to enable the development of wearable devices that can track the biochemical and physiological signals of the human body. Numerous consumer electronics have been developed to measure activity, posture, heart rate, respiration rate, and blood oxygen level. Sweat sampling provides a source of biomarkers that is accessible in a continuous, on-the-go, and non-invasive way, allowing for unique developments in wearable sweat sensing. This review focuses on recent trends in material science, device development, sensing mechanisms, power generation, and data management related to these devices. Additionally, exemplary wearable sweat sensors and commercialization efforts in this area are discussed, with an emphasis on the multifunctional sensing platforms that integrate data from both physical and biochemical sweat sensors.
Recent developments in wearable physical sensors have enabled the development of a number of consumer electronics products which measure parameters related to activity, posture, heart rate, respiration rate, and blood oxygen level. However, progress in the development of wearable chemical sensors has been slower due to the inherent challenges in retrieving and processing bodily fluids. Sweat is a valuable source of biomarkers which can be accessed continuously, on-the-go, and non-invasively. This review provides an overview of recent trends in the area of wearable sweat sensing, looking at topics such as material science, device development, sensing mechanisms, power generation, and data management. Examples of wearable sweat sensors published in recent years, as well as commercialization efforts in this field are also presented. The review highlights the trends in multifunctional sensing platforms which incorporate flexible electronics to integrate data from both physical and biochemical sensors.
This paper explores how the adaptability of Caenorhabditis elegans locomotion behavior can be assessed through a movement-based assay. This assay is set up with a series of sinusoidal microchannels, featuring a fixed wavelength and modulating amplitude. These channels are comparable to the body diameter of the organism, and worms are allowed to travel from the input port to the output port. In regions that closely fit the worms' natural undulations, progress is quick and steady. As the channel amplitude changes along the device, the worm struggles to generate propulsive force, slows down, and eventually is unable to move forward. An array of locomotion parameters (average forward velocity, number and duration of pauses, range of contact angle, and cut-off region) are generated from the recorded videos to measure how the worm moves in the modulated sinusoidal channels. The device is tested on wild-type (N2) and two mutant (lev-8 and unc-38) C. elegans. We suggest that this passive, movement-based assay can be used to differentiate between nematodes with distinct locomotion phenotypes.
"Amplitude-modulated sinusoidal microchannels
for observing adaptability in C. elegans locomotion",
Biomicrofluidics 5, 024112 (2011)
https://doi.org/10.1063/1.3604391
Recomendações da OMS sobre cuidados maternos e neonatais para uma experiência pós-natal positiva.
Em consonância com os ODS – Objetivos do Desenvolvimento Sustentável e a Estratégia Global para a Saúde das Mulheres, Crianças e Adolescentes, e aplicando uma abordagem baseada nos direitos humanos, os esforços de cuidados pós-natais devem expandir-se para além da cobertura e da simples sobrevivência, de modo a incluir cuidados de qualidade.
Estas diretrizes visam melhorar a qualidade dos cuidados pós-natais essenciais e de rotina prestados às mulheres e aos recém-nascidos, com o objetivo final de melhorar a saúde e o bem-estar materno e neonatal.
Uma “experiência pós-natal positiva” é um resultado importante para todas as mulheres que dão à luz e para os seus recém-nascidos, estabelecendo as bases para a melhoria da saúde e do bem-estar a curto e longo prazo. Uma experiência pós-natal positiva é definida como aquela em que as mulheres, pessoas que gestam, os recém-nascidos, os casais, os pais, os cuidadores e as famílias recebem informação consistente, garantia e apoio de profissionais de saúde motivados; e onde um sistema de saúde flexível e com recursos reconheça as necessidades das mulheres e dos bebês e respeite o seu contexto cultural.
Estas diretrizes consolidadas apresentam algumas recomendações novas e já bem fundamentadas sobre cuidados pós-natais de rotina para mulheres e neonatos que recebem cuidados no pós-parto em unidades de saúde ou na comunidade, independentemente dos recursos disponíveis.
É fornecido um conjunto abrangente de recomendações para cuidados durante o período puerperal, com ênfase nos cuidados essenciais que todas as mulheres e recém-nascidos devem receber, e com a devida atenção à qualidade dos cuidados; isto é, a entrega e a experiência do cuidado recebido. Estas diretrizes atualizam e ampliam as recomendações da OMS de 2014 sobre cuidados pós-natais da mãe e do recém-nascido e complementam as atuais diretrizes da OMS sobre a gestão de complicações pós-natais.
O estabelecimento da amamentação e o manejo das principais intercorrências é contemplada.
Recomendamos muito.
Vamos discutir essas recomendações no nosso curso de pós-graduação em Aleitamento no Instituto Ciclos.
Esta publicação só está disponível em inglês até o momento.
Prof. Marcus Renato de Carvalho
www.agostodourado.com
New Directions in Targeted Therapeutic Approaches for Older Adults With Mantl...i3 Health
i3 Health is pleased to make the speaker slides from this activity available for use as a non-accredited self-study or teaching resource.
This slide deck presented by Dr. Kami Maddocks, Professor-Clinical in the Division of Hematology and
Associate Division Director for Ambulatory Operations
The Ohio State University Comprehensive Cancer Center, will provide insight into new directions in targeted therapeutic approaches for older adults with mantle cell lymphoma.
STATEMENT OF NEED
Mantle cell lymphoma (MCL) is a rare, aggressive B-cell non-Hodgkin lymphoma (NHL) accounting for 5% to 7% of all lymphomas. Its prognosis ranges from indolent disease that does not require treatment for years to very aggressive disease, which is associated with poor survival (Silkenstedt et al, 2021). Typically, MCL is diagnosed at advanced stage and in older patients who cannot tolerate intensive therapy (NCCN, 2022). Although recent advances have slightly increased remission rates, recurrence and relapse remain very common, leading to a median overall survival between 3 and 6 years (LLS, 2021). Though there are several effective options, progress is still needed towards establishing an accepted frontline approach for MCL (Castellino et al, 2022). Treatment selection and management of MCL are complicated by the heterogeneity of prognosis, advanced age and comorbidities of patients, and lack of an established standard approach for treatment, making it vital that clinicians be familiar with the latest research and advances in this area. In this activity chaired by Michael Wang, MD, Professor in the Department of Lymphoma & Myeloma at MD Anderson Cancer Center, expert faculty will discuss prognostic factors informing treatment, the promising results of recent trials in new therapeutic approaches, and the implications of treatment resistance in therapeutic selection for MCL.
Target Audience
Hematology/oncology fellows, attending faculty, and other health care professionals involved in the treatment of patients with mantle cell lymphoma (MCL).
Learning Objectives
1.) Identify clinical and biological prognostic factors that can guide treatment decision making for older adults with MCL
2.) Evaluate emerging data on targeted therapeutic approaches for treatment-naive and relapsed/refractory MCL and their applicability to older adults
3.) Assess mechanisms of resistance to targeted therapies for MCL and their implications for treatment selection
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NVBDCP.pptx Nation vector borne disease control programSapna Thakur
NVBDCP was launched in 2003-2004 . Vector-Borne Disease: Disease that results from an infection transmitted to humans and other animals by blood-feeding arthropods, such as mosquitoes, ticks, and fleas. Examples of vector-borne diseases include Dengue fever, West Nile Virus, Lyme disease, and malaria.
Report Back from SGO 2024: What’s the Latest in Cervical Cancer?bkling
Are you curious about what’s new in cervical cancer research or unsure what the findings mean? Join Dr. Emily Ko, a gynecologic oncologist at Penn Medicine, to learn about the latest updates from the Society of Gynecologic Oncology (SGO) 2024 Annual Meeting on Women’s Cancer. Dr. Ko will discuss what the research presented at the conference means for you and answer your questions about the new developments.
Ozempic: Preoperative Management of Patients on GLP-1 Receptor Agonists Saeid Safari
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- Video recording of this lecture in English language: https://youtu.be/lK81BzxMqdo
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micro teaching on communication m.sc nursing.pdfAnurag Sharma
Microteaching is a unique model of practice teaching. It is a viable instrument for the. desired change in the teaching behavior or the behavior potential which, in specified types of real. classroom situations, tends to facilitate the achievement of specified types of objectives.
Lung Cancer: Artificial Intelligence, Synergetics, Complex System Analysis, S...Oleg Kshivets
RESULTS: Overall life span (LS) was 2252.1±1742.5 days and cumulative 5-year survival (5YS) reached 73.2%, 10 years – 64.8%, 20 years – 42.5%. 513 LCP lived more than 5 years (LS=3124.6±1525.6 days), 148 LCP – more than 10 years (LS=5054.4±1504.1 days).199 LCP died because of LC (LS=562.7±374.5 days). 5YS of LCP after bi/lobectomies was significantly superior in comparison with LCP after pneumonectomies (78.1% vs.63.7%, P=0.00001 by log-rank test). AT significantly improved 5YS (66.3% vs. 34.8%) (P=0.00000 by log-rank test) only for LCP with N1-2. Cox modeling displayed that 5YS of LCP significantly depended on: phase transition (PT) early-invasive LC in terms of synergetics, PT N0—N12, cell ratio factors (ratio between cancer cells- CC and blood cells subpopulations), G1-3, histology, glucose, AT, blood cell circuit, prothrombin index, heparin tolerance, recalcification time (P=0.000-0.038). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and PT early-invasive LC (rank=1), PT N0—N12 (rank=2), thrombocytes/CC (3), erythrocytes/CC (4), eosinophils/CC (5), healthy cells/CC (6), lymphocytes/CC (7), segmented neutrophils/CC (8), stick neutrophils/CC (9), monocytes/CC (10); leucocytes/CC (11). Correct prediction of 5YS was 100% by neural networks computing (area under ROC curve=1.0; error=0.0).
CONCLUSIONS: 5YS of LCP after radical procedures significantly depended on: 1) PT early-invasive cancer; 2) PT N0--N12; 3) cell ratio factors; 4) blood cell circuit; 5) biochemical factors; 6) hemostasis system; 7) AT; 8) LC characteristics; 9) LC cell dynamics; 10) surgery type: lobectomy/pneumonectomy; 11) anthropometric data. Optimal diagnosis and treatment strategies for LC are: 1) screening and early detection of LC; 2) availability of experienced thoracic surgeons because of complexity of radical procedures; 3) aggressive en block surgery and adequate lymph node dissection for completeness; 4) precise prediction; 5) adjuvant chemoimmunoradiotherapy for LCP with unfavorable prognosis.
Title: Sense of Taste
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
Ethanol (CH3CH2OH), or beverage alcohol, is a two-carbon alcohol
that is rapidly distributed in the body and brain. Ethanol alters many
neurochemical systems and has rewarding and addictive properties. It
is the oldest recreational drug and likely contributes to more morbidity,
mortality, and public health costs than all illicit drugs combined. The
5th edition of the Diagnostic and Statistical Manual of Mental Disorders
(DSM-5) integrates alcohol abuse and alcohol dependence into a single
disorder called alcohol use disorder (AUD), with mild, moderate,
and severe subclassifications (American Psychiatric Association, 2013).
In the DSM-5, all types of substance abuse and dependence have been
combined into a single substance use disorder (SUD) on a continuum
from mild to severe. A diagnosis of AUD requires that at least two of
the 11 DSM-5 behaviors be present within a 12-month period (mild
AUD: 2–3 criteria; moderate AUD: 4–5 criteria; severe AUD: 6–11 criteria).
The four main behavioral effects of AUD are impaired control over
drinking, negative social consequences, risky use, and altered physiological
effects (tolerance, withdrawal). This chapter presents an overview
of the prevalence and harmful consequences of AUD in the U.S.,
the systemic nature of the disease, neurocircuitry and stages of AUD,
comorbidities, fetal alcohol spectrum disorders, genetic risk factors, and
pharmacotherapies for AUD.
Low-cost, open-source bacterial colony tracking over large areas and extended incubation times
1. Scan4CFU: Low-cost, open-source bacterial colony tracking
over large areas and extended incubation times
Santosh Pandey a,⇑
, Yunsoo Park a
, Ankita Ankita a
, Gregory J. Phillips b,⇑
a
Electrical and Computer Engineering, Iowa State University, Ames, IA, USA
b
Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
a r t i c l e i n f o
Article history:
Received 31 July 2021
Received in revised form 1 November 2021
Accepted 21 November 2021
Keywords:
Antimicrobial resistance
Antibiotics
Incubation chamber
Scanner
Phenotype
Image analysis
Bacteria imaging
a b s t r a c t
A hallmark of bacterial populations cultured in vitro is their homogeneity of growth, where
the majority of cells display identical growth rate, cell size and content. Recent insights,
however, have revealed that even cells growing in exponential growth phase can be
heterogeneous with respect to variables typically used to measure cell growth. Bacterial
heterogeneity has important implications for how bacteria respond to environmental
stresses, such as antibiotics. The phenomenon of antimicrobial persistence, for example,
has been linked to a small subpopulation of cells that have entered into a state of dormancy
where antibiotics are no longer effective. While methods have been developed for identi-
fying individual non-growing cells in bacterial cultures, there has been less attention paid
to how these cells may influence growth in colonies on a solid surface. In response, we have
developed a low-cost, open-source platform to perform automated image capture and
image analysis of bacterial colony growth on multiple nutrient agar plates simultaneously.
The descriptions of the hardware and software are included, along with details about the
temperature-controlled growth chamber, high-resolution scanner, and graphical interface
to extract and plot the colony lag time and growth kinetics. Experiments were conducted
using a wild type strain of Escherichia coli K12 to demonstrate the feasibility and operation
of our setup. By automated tracking of bacterial growth kinetics in colonies, the system
holds the potential to reveal new insights into understanding the impact of microbial
heterogeneity on antibiotic resistance and persistence.
Ó 2021 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY
license (http://creativecommons.org/licenses/by/4.0/).
Specifications Table
Hardware name Bacterial Growth, Imaging, and Analysis Station (Scan4CFU)
Subject area Biological Sciences (Microbiology)
Environmental, Planetary and Agricultural Sciences
Hardware type Imaging tools
Closest commercial analog QuebecTM
Dark-Field Colony Counter, IncuCountTM
Colony Counter, Corning Cell
Counter, and Bel-ArtTM
SP SciencewareTM
Plate Reader
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https://doi.org/10.1016/j.ohx.2021.e00249
2468-0672/Ó 2021 The Authors. Published by Elsevier Ltd.
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
⇑ Corresponding authors.
E-mail addresses: pandey@iastate.edu (S. Pandey), yunsoopk@iastate.edu (Y. Park), ankita@iastate.edu (A. Ankita), gregory@iastate.edu (G.J. Phillips).
HardwareX 10 (2021) e00249
Contents lists available at ScienceDirect
HardwareX
journal homepage: www.elsevier.com/locate/ohx
2. a (continued)
Hardware name Bacterial Growth, Imaging, and Analysis Station (Scan4CFU)
Open Source License CC-BY-SA 4.0
Cost of Hardware $306.40
Source File Repository Zenodo Data Repository Pandey, Santosh (2021), ‘‘ScanCFU: Low-cost, open-source
bacterial colony tracking over large areas and extended incubation times ”, Zenodo,
V1, /https://doi.org/10.5281/zenodo.5636769
Hardware in context
Counting bacterial colonies that form on nutrient agar plates (i.e., plate counting) is a standard practice in microbiology in
order to quantify the number of individual bacteria within a culture, and is based on reporting on the number of colony
forming units (CFU)/mL of culture. However, this method is not designed to measure growth kinetics of bacteria as they form
visible colonies [1]. There are multiple studies, however, that would benefit from the ability to monitor growth kinetics of
bacterial colonies over prolonged time scales. For example, since bacteria growing in broth culture encounter different envi-
ronmental conditions than those growing on a solid substrate, such as spatial limitations and oxygen availability, measuring
the impact of these differences would be valuable. It is also now clear that even bacteria growing in exponential growth
phases, under so called ‘‘balanced” growth conditions can exhibit heterogeneity with respect to growth rate, cell size and
content [2–4]. Importantly, these cells have been linked to the phenomenon of antibiotic persistence, where a small subpop-
ulation of cells reside in a state of dormancy causing them to be less susceptible to the lethal action of antibiotics [4–6].
Because persistence is associated with the emergence of antibiotic resistance and reoccurrence of bacterial infections [3],
new methods are needed to understand the contribution of persister cells, and cells that have entered into an asynchronous
growth phase in general, to overall bacterial growth and adaptation [7,8]. For example, the impact that cells (that are not in a
state of synchronous growth) have on the formation of individual colonies is not known [7,9,10].
Automated counting of bacterial colonies has been pursued by researchers in both academics and industry to improve the
experimental throughput, reproducibility, processing time, and documentation [7–12]. Commercialized products for bacte-
rial enumeration include optical density counters (e.g., spectrophotometer), digital colony counters (e.g., Neutec Group’s
Sphere Flash Colony Counter), and automated image analysis systems (e.g., BD Kiestra System). Some other examples are
the QuebecTM
Dark-Field Colony Counter, IncuCountTM
Colony Counter, Corning Cell Counter, and Bel-ArtTM
SP SciencewareTM
Plate Reader. These commercialized products are expensive, typically priced between $1000 to $10,000 USD per system.
The commercialized image processing software are usually proprietary and restrictive, and do not fully support user mod-
ification or sharing within communities.
As an alternative to commercialized products, there is a need to democratize microbiology tools for bacterial image cap-
ture and image analysis [9]. Previous researchers have recorded digital images of Petri dish using webcams, DSLR cameras,
smartphones, and flatbed scanners [7]. For example, a recent study used a Canon EOS 500D 15 MP SLR Camera to record dig-
ital plate images in grayscale and RGB color at 300 and 800 dpi resolution, respectively [11]. Another recent study employed
the Canon EOS 1200D reflex camera triggered by an Arduino controller to record plate images [2]. In addition, a number of
open source software have been released for this application [7,9–13]. Over the years, image processing and analysis tech-
niques have significantly refined to improve robustness, versatility, and user-friendliness. Various algorithms and plug-ins
have been added to overcome the common artifacts and imperfections during image capture, background, color, contrast,
edge effects, and colonies amongst agar plates. One example is the open-source ImageJ software originally developed by
Wayne Rasband at the National Institutes of Health [14]. In recent years, GitHub has emerged as the public repository for
open-source software for bacterial counting from images of plates, such as the DDot Counter based on the watershed algo-
rithm [13].
While significant improvements have been made in image recognition and analysis, there is a dearth of open-source hard-
ware for incubating bacterial colonies and tracking their growth on multiple agar plates in parallel and over several hours. In
this work, we address this need by presenting an open-source station to study the growth kinetics and lag time of bacterial
colonies. The image capture is conducted inside a temperature-controlled acrylic chamber by placing multiple nutrient agar
plates with seeded cells on a high-resolution flatbed scanner (resolution of 2400 dpi or higher). The scanned images of every
plate are automatically recorded at fixed intervals and stored in a designated folder through the course of the experiment.
The image analysis is performed on the recorded images to extract various growth parameters of single colonies within each
plate. A graphical user interface (GUI) is developed to navigate through the various steps of image processing. The hardware
and software for image capture and image analysis are described, along with the bill of materials, and instructions for build-
ing and operating the system. Lastly, the limitations of the presented technology and future directions are discussed. The
hardware and software are open-source and made available in the online Zenodo Data Repository at /https://doi.org/10.
5281/zenodo.5636769
S. Pandey, Y. Park, A. Ankita et al. HardwareX 10 (2021) e00249
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3. Fig. 1. Open-source hardware to track the growth and imaging of bacterial colonies on agar plates. (A) The enclosure for housing the scanner is shown,
along with the heating unit, thermostat to monitor the internal temperature, ventilation tubing, and desktop computer. (B) Four nutrient agar plates are
placed on the EPSON flatbed scanner. Scanned image of the four agar plates are displayed on the monitor. The inset shows the temperature within the
enclosure as a function of time.
S. Pandey, Y. Park, A. Ankita et al. HardwareX 10 (2021) e00249
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4. Hardware description
Our bacterial growth and imaging hardware consists of two chambers (i.e., interior and exterior chambers) to enclose a
high-resolution scanner, a side chamber with an attachable heater/fan unit, and a vent system to regulate the air flow
through the chambers (Fig. 1). The interior chamber has 1-inch diameter holes to avoid direct air flow over the scanner.
The chambers were custom-built using acrylic material, but other durable materials can also be used. The heater/fan unit
was low cost and purchased from an outside vendor. Other vendors for a portable heater and fan are available at local hard-
ware stores. The main imaging module is the Epson Perfection V750 Pro Scanner having a 6400 dpi scan resolution and a
maximum scan area of 21.6 cm 29.7 cm. A cheaper option is the Epson V19 Flatbed Scanner that has a resolution of
4800 dpi which is sufficient for the imaging experiments. The system described here builds upon our previous work on single
cell imaging studies that employed an acrylic incubation chamber to house a student upright microscope [8].
For plating and growing the bacteria, nutrient agar plates (3-inch diameter) have been used (Fig. 1B). One imaging exper-
iment can image up to six such nutrient agar plates. Other sizes of agar plates can be used, provided that all the plates fit
within the maximum scanning area (21.6 cm 29.7 cm). For plating cells on the agar surface, our goal was to have less than
250 colonies in the entire plate. This is because an appropriate colony count is between 25 and 250 colony forming units (CFU)
per plate, according to the U.S. Food and Drug Administration (FDA) [15]. If the colonies are over 250 CFUs, the growth may
be inhibited for some bacteria [15]. On the other hand, plates with less than 25 CFUs are not considered statistically repre-
sentative of the test sample [15]. Each CFU on the plate is assumed to have emerged from a single cell or a small group of
cells. We tried to reduce occurrence of colony clusters during initial plating of cells by appropriately shaking the cell pop-
ulations and choosing a suitable dilution before seeding.
Software description
Our custom software is designed to convert a group of scanned plate images into a video file for easy visualization, to
remotely control the operation of the EPSON scanner, to effectively subtract background from the scanned plate images,
to isolate and detect individual bacterial colonies, and to plot the increasing area of different colonies as a function of time.
The software is written as a collection of Matlab Files with instructions in the readme file. Upon downloading and running
the files according to the instructions, a new window pops up as shown in Fig. 2. A number of colonies are automatically
selected with unique color codes, and some of them can be de-selected if they are touching or merging with one another.
An X-Y cursor is used to select the background area. Thereafter, the background is subtracted from the images, and all
the individual colonies are found and tracked by their respective area and centroid position. A plot of the tracked bacterial
colony area is then generated as a function of the recording time.
Design files
Design files summary
The Design files correspond to the CAD files to build the acrylic chamber housings around the scanner and heater/fan unit,
.exe files for automated image capture from the scanner (zip file folder: Automated Image Capture). and MatLab files (zip file
Fig. 2. Open-source software to track the growth and imaging of bacterial colonies on agar plates. The graphical interface is shown on the left that has
clickable buttons to select image files and de-select colonies that are merged or touching one another. An X-Y cursor is used to select the background area
for subsequent background subtraction and identification of bacterial colonies. Thereafter, a number of parameters can be plotted, such as colony area,
diameter, and emergence. The data is exported to Microsoft Excel for further analysis. A representative image of the nutrient agar plate is shown on the right
with and y slide bars.
S. Pandey, Y. Park, A. Ankita et al. HardwareX 10 (2021) e00249
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5. folder name: MATLAB_Files_for_Bacteria_Tracking) to automatically detect bacterial colonies from a sequence of images and
track the colony area as a function of time. The source files mentioned below are posted in the Zenodo Data Repository, V1, /
https://doi.org/10.5281/zenodo.5636769
Design file name File type Open source
license
Location of the file
Exterior Chamber CAD file (.dwg) CC-BY-SA 4.0 available with the article
Interior Chamber CAD file (.dwg) CC-BY-SA 4.0 available with the article
Heater Chamber CAD file (.dwg) CC-BY-SA 4.0 available with the article
Automated Image Capture Executable Files (.exe) CC-BY-SA 4.0 available with the article
Readme(Scanner) Instructions for Scanner Use (.docx) CC-BY-SA 4.0 available with the article
BacteriaTrackerFiles Matlab files (.m) CC-BY-SA 4.0 available with the article
Readme(BacteriaTrackingSteps) Instructions for Bacteria Tracking (.docx) CC-BY-SA 4.0 available with the article
Bill of materials
The Bill of Materials correspond to the acrylic sheets, tubing, and hinges to construct the chambers for the scanner and
heater unit. There is an aluminum duct that provide the passage for steady air flow and a constant pre-set temperature
through the chambers.
Bill of materials
Designator Component # Cost per
unit –USD
Total
cost -USD
Source of materials Material
type
Incubator (all-in-
one digital
thermostat,
heater, fan
control)
IncuKitTM
XL for
Reptile Incubators
1 $85.99 $86 https://
incubatorwarehouse.com/
incukit-xlrk.html
Electrical
Units,
Sensors
Acrylic sheets for
incubation
chamber
1200
x 9.500
x 3/800
2 $90 $90 https://countryplasticsia.com/
homepage/shop/
Acrylic
1200
x 1200
x 3/800
1
11.2500
x 9.500
x 3/800
2
17.7500
x 9.500
x 3/800
2
2500
x 9.500
x 3/8 2
2500
x 17.7500
x 3/800
1
2700
x 10.500
x 3/800
2
2000
x 10.500
x 3/800
2
27.7500
x 2000
x 3/800
1
Acrylic Hinges Hinges 4 $3 $12 https://countryplasticsia.com/
homepage/shop/
Acrylic
Acrylic tubing Tubing (diameter 40
’
and length 20
’)
4 $6 $24 https://countryplasticsia.com/
homepage/shop/
Acrylic
Aluminum Duct 4-in. 8 ft. flexible
dryer vent duct
1 $10 $10 http://homedepot.com Aluminum
Screws/Nails 1/4 in.-20 1/2 in.
Combo Round Head
Zinc Plated Machine
Screw
48 $0.30 $14.40 http://homedepot.com Stainless
Steel
EPSON Perfection
V19
Flatbed Scanner
(4800 dpi)
1 $69.99 $69.99 http://adorama.com Imaging
Unit
Build instructions
To build the bacterial growth and imaging hardware, the acrylic sheets are received from a machine shop and sorted
according to their dimensions listed in Bill of Materials. First, the structure of the side enclosure is assembled as shown
in Fig. 3A. To hold the structure in place, holes are drilled at the wall junctions of the side enclosure using an electric drill
S. Pandey, Y. Park, A. Ankita et al. HardwareX 10 (2021) e00249
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6. and screws are inserted in the holes to construct the side enclosure. Then, the heater/fan unit and acrylic tubing are manually
put in the opening of the side enclosure as shown in Fig. 3B. Next, the structure of the interior scanner enclosure is assem-
bled, holes are drilled in the interior scanner enclosure, and screws are inserted in the holes to construct the interior scanner
enclosure. Thereafter, the interior scanner enclosure is attached to the side enclosure as shown in Fig. 3C. Next, the structure
Fig. 3. CAD model assembly of the open-source hardware. (A) Hold the side enclosure in the upright position shown here. (B) Affix the heater/fan unit to the
side enclosure. (C) Connect and install the interior scanner enclosure to the side enclosure as shown in the image. (D) Install the exterior scanner enclosure
over the perforated interior enclosure.
S. Pandey, Y. Park, A. Ankita et al. HardwareX 10 (2021) e00249
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7. of the exterior scanner chamber is assembled, holes are drilled in the exterior scanner chamber, screws are inserted in the
holes to construct the exterior scanner chamber. The exterior scanner chamber is then placed over to the interior scanner
enclosure as shown in Fig. 3C. Two aluminum ducts are cut to suitable size and connected between the two openings of
the side enclosure and those of the exterior scanner chamber for air flow as shown in Fig. 1A. The EPSON Perfection V750
Pro Scanner (or the EPSON Perfection V850 Pro Scanner) is placed within the interior scanner chamber and connected to
a desktop computer. The power supply is connected to the heater/fan unit and scanner. Two cheaper versions of the EPSON
scanner with a 4800 dpi resolution are the Epson Perfection V19 and V39 Flatbed scanner that cost $70 and $100,
respectively.
Operation instructions
At the start of the experiment, the chambers and scanner are ensured to be clear of any unnecessary items, such as plates
from previous experiments. The nutrient agar plates are prepared. The bacterial cultures (Escherichia coli wild-type), previ-
ously grown overnight, are diluted to approximately 50 to 100 CFU per mL. The controller of the heater/fan unit is turned on
and the desired temperature is set for 37 °C. The temperature probe is placed inside the interior scanner enclosure. The
chamber temperature reaches 37 °C after a wait time of around 35 to 40 min. The wild-type (mg1655) E. coli cells are plated
as a cell suspension separately on six 3-inch nutrient agar plates using a pipette, and placed on the scanner. A custom .exe
program is run, along with the Epson Scan Utility software, to automatically repeat the scanning operation every 5, 15 or
30 min for a total of 20 h, while saving the recorded image of six plates to a file folder. The .exe program allows users to
select specific areas in the scanned A4-size image of six plates, and save them separately into a destination folder as six sep-
arate images of individual plates. This .exe custom program is written using the ‘AutoIt’ scripting language and available in a
zip folder (‘‘Automated Image Capture”). At the end of the experiment, the heater unit is turned off. Thereafter, the agarose
plates are removed from the scanner, opened off their lids, sprayed with 70% ethanol to kill the bacteria, and disposed of in a
bio-waste disposal unit. It is important to turn off the scanner and heater/fan unit immediately after the experiment to min-
imize equipment burn out. The heater/fan unit may break down after prolonged use, but affordable replacements are readily
available from the manufacturer (mentioned in the Bill of Materials).
There are potential safety concerns with the hardware components. It is advisable not to physically touch or come close to
the heater/fan unit or the vent system during or after its operation because its hot surface may damage the skin. The elec-
trical wiring must be securely taped outside the chambers and away from the common space for handling. It is advised to
open/close the acrylic chamber slowly and carefully to avoid physical injuries. All biosafety protocols should be followed
while handling the nutrient agar plates with bacterial colonies. For working with nonpathogenic strain of E. coli, Biosafety
Level 1 (BSL-1) protocols need to be followed. Key points to consider here are: (i) cleaning and disposing the agar plates after
the experiments, (ii) turning off the heater and/or scanner after the experiments, and (iii) frequently checking that the image
files are being saved properly and the scanner operations are working well.
Validation and characterization
After constructing the chamber housing, the heater/fan unit was set at 37 °C. The internal temperature within the cham-
bers was observed monitored every few minutes for three separate days (Fig. 1 B). We found that the internal temperature
was maintained at the pre-set temperature throughout the monitoring period. The heater fan ensured that the temperature
was uniform throughout the two chambers. Trial runs were conducted to determine the optimum concentration of bacteria
required for seeding on the plates. Time-scanned images of representative nutrient agar plates comprising the wild-type
E. coli are shown in Fig. 4. The saved images of agarose plates were run through our custom MatLab programs (listed in
Fig. 4. Growth and imaging of wild-type E. coli with our system. The colonies are noticeable within less than 8 h and the colony area grows with time for
five different sets of experimental runs (N = 5).
S. Pandey, Y. Park, A. Ankita et al. HardwareX 10 (2021) e00249
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8. Design Files Summary) to extract the area of different bacterial colonies at different time points. Almost all the wild-type
colonies emerge within 5 to 8 h of plating on agarose plates (Fig. 5).
Limitations and future scope
Our open-source station can be constructed with minimal costs to conduct experiments in microbiology where auto-
mated tracking the growth of bacterial colonies is made possible. Purchasing commercial setups for this purpose may not
be cost-effective and are often closed source for any system modifications. However, there are certain limitations of the pre-
sented technology. As with most experiments in bacteriology, the natural heterogeneity in different cell populations makes it
challenging to standardize the image processing steps for all experiments [3]. At the start of experiment, it is difficult to esti-
mate the optimal dilution to start with, but we have seen that a low to mid CFU per mL (i.e. 50 to 100) helps to prevent
grouping of cells or merging of colonies. Only a finite number of bacterial colonies (less than250 CFU per mL [15]) can be
tracked over time within the maximum scanning area, and the imaging has to be completed before the colonies merge or
start competing for nutrients. It is difficult to ascertain the actual number of cells in each colony by scanning plate images.
Single cell studies are not possible with this method but can be performed using microfluidic chips at a lower dilution
(Fig. 6). Finally, considering that each image file may be over 10 Mb, there is a finite number of high-resolution images that
can realistically be captured by the scanner during each experiment.
Fig. 5. Lag time and growth kinetics of bacterial colonies. (A, B) The colonies of wild-type E. coli emerge within 5 to 8 h of plating with an exponential rise
and eventual saturation phase.
Fig. 6. Microfluidic chips to quantify elongation and division of single bacterial cells. (A) Microfluidic channels were fabricated to hold multiple discrete
rows of single cells with slow perfusion of nutrient media. (B) Snapshots of different sections of the microfluidic chip, showing the elongation and cell
division with adequate resolution. These single cell studies complement the population-scale quantification of colony growth and lag time.
S. Pandey, Y. Park, A. Ankita et al. HardwareX 10 (2021) e00249
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9. In the near future, there is scope to expand the imaging functionalities to unravel new phenotypic traits and characterize
the natural heterogeneity in bacterial populations. For example, our method can be adapted to probe other characteristics of
bacterial colonies, such as their morphology, organization, and/or color for addressing unanswered questions in biofilm for-
mation and antibiotic resistance. Persistence is still poorly understood and there are many attributes that could be quantified
by the measuring the lag time and growth kinetics of different persistors under different stressful conditions. The results
obtained from our scanner-based imaging method can further be validated with conventional tools in microbiology, such
as flow cytometry, optical plate readers, turbidity measurements, and single cell analysis. An example of open source hard-
ware and software for the automated counting of bacterial colonies showed that high-resolution images from flatbed scan-
ners (1200 dpi and higher) were superior than those from digital cameras for bacterial enumeration [16]. Besides
applications in microbiology, our bacterial enumeration system can be diversified for imaging, counting, and tracking other
microorganisms on agar plates, such as C. elegans and parasitic nematodes [17–20]. For this purpose, a number of open
source image processing and analysis techniques are freely available through the ImageJ software and the scientific imaging
community [14,21,22]. Finally, the presented system offers a range of possibilities for STEM education and direct hands-on
training for undergraduate and graduate students who want to tinker with the system and methods to optimize its perfor-
mance and throughout at a low costsomething that is difficult with commercial cell trackers. For example, students can
learn to prepare microbiology experiments, construct incubation chambers from CAD drawings and off-the-shelf compo-
nents, and write open source software to control the scanner operations and track colonies over time.
CRediT authorship contribution statement
Santosh Pandey: Conceptualization, Methodology, Validation, Investigation, Writing – review editing, Funding acqui-
sition, Software, Writing – original draft, Visualization, Data curation, Supervision, Resources. Yunsoo Park: Conceptualiza-
tion, Methodology, Validation, Investigation, Writing – review editing, Funding acquisition, Software, Writing – original
draft, Visualization, Data curation, Supervision, Resources. Ankita Ankita: Conceptualization, Methodology, Validation,
Investigation, Writing – review editing, Funding acquisition, Software, Writing – original draft, Visualization, Data cura-
tion, Supervision, Resources. Gregory J. Phillips: Conceptualization, Methodology, Writing – review editing, Funding
acquisition, Writing – original draft, Investigation, Visualization, Resources.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have
appeared to influence the work reported in this paper.
Acknowledgements
This work was partially supported by the U.S. Defense Threat Reduction Agency (HDTRA1-15-1-0053) and U.S. National
Science Foundation (NSF IDBR-1556370). We are grateful to all our past graduate students who worked on the bacterial
imaging system, including Zach Njus, Upender Kalwa, Taejoon Kong, Nicholas Backes, Augustine Beeman, Jared Jensen, Eliz-
abeth Wlezien, and Christopher Legner. We also thank Dr. Gregory Tylka and his laboratory personnel for improving the sys-
tem functions to image populations of soybean cyst nematodes.
References
[1] L.M. Young, D.J. Rieman, L. Walden, V.A. Motz, In search of a counter you can count on: relative efficacy of human visual and automated colony
counting, Lett. Appl. Microbiol. 66 (2018) 188–193. /10.1111/lam.12851.
[2] J. Bär, M. Boumasmoud, R.D. Kouyos, A.S. Zinkernagel, C. Vulin, Efficient microbial colony growth dynamics quantification with ColTapp, an automated
image analysis application, Sci. Rep. 10 (2020) 16084. /10.1038/s41598-020-72979-4.
[3] F. Goormaghtigh, L. Van Melderen, Single-cell imaging and characterization of Escherichia coli persister cells to ofloxacin in exponential cultures, Sci.
Adv. 5 (2019) eaav9462. /10.1126/sciadv.aav9462.
[4] R.A. Fisher, B. Gollan, S. Helaine, Persistent bacterial infections and persister cells, Nat. Rev. Microbiol. 15 (2017) 453–464. /10.1038/nrmicro.2017.42.
[5] N.R. Cohen, M.A. Lobritz, J.J. Collins, Microbial persistence and the road to drug resistance, Cell Host Microbe. 13 (2013) 632–642. 10.1016/
j.chom.2013.05.009.
[6] A. Jo~ers, N. Kaldalu, T. Tenson, The frequency of persisters in Escherichia coli reflects the kinetics of awakening from dormancy, J. Bacteriol. 192 (13)
(2010) 3379–3384.
[7] I. Levin-Reisman, O. Gefen, O. Fridman, I. Ronin, D. Shwa, H. Sheftel, N.Q. Balaban, Automated imaging with ScanLag reveals previously undetectable
bacterial growth phenotypes, Nat. Methods. 7 (2010) 737–739. /10.1038/nmeth.1485.
[8] T. Kong, N. Backes, U. Kalwa, C. Legner, G.J. Phillips, S. Pandey, Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR
Interference: Applications to Long-Term Bacterial Antibiotic Studies, ACS Sensors. 4 (2019) 2638–2645. /10.1021/acssensors.9b01031.
[9] Q. Geissmann, OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects, PLoS One. 8 (2013). /10.1371/journal.
pone.0054072.
[10] M. Putman, R. Burton, M.H. Nahm, Simplified method to automatically count bacterial colony forming unit, J. Immunol. Methods. 302 (2005) 99–102. /
10.1016/j.jim.2005.05.003.
[11] L. Hogekamp, S.H. Hogekamp, M.R. Stahl, Experimental setup and image processing method for automatic enumeration of bacterial colonies on agar
plates, PLoS One. 15 (2020) e0232869. /10.1371/journal.pone.0232869.
S. Pandey, Y. Park, A. Ankita et al. HardwareX 10 (2021) e00249
9
10. [12] S.D. Brugger, C. Baumberger, M. Jost, W. Jenni, U. Brugger, K. Mühlemann, S. Bereswill, Automated Counting of Bacterial Colony Forming Units on Agar
Plates, PLoS One. 7 (3) (2012) e33695.
[13] D. Johnston, DDot Counter, GitHub. (2019). https://github.com/microbialman/DDotCounter.
[14] C.A. Schneider, W.S. Rasband, K.W. Eliceiri, NIH Image to ImageJ: 25 years of image analysis, Nat. Methods. 9 (2012) 671–675. /10.1038/nmeth.2089.
[15] J.T.P. Larry Maturin, B.A.M. Chapter, 3: Aerobic Plate Count, U.S, Food Drug Adm. (2001). https://www.fda.gov/food/laboratory-methods-food/bam-
chapter-3-aerobic-plate-count.
[16] M.L. Clarke, R.L. Burton, A.N. Hill, M. Litorja, M.H. Nahm, J. Hwang, Low-cost, high-throughput, automated counting of bacterial colonies, Cytom. Part A.
77A (2010) 790–797. /10.1002/CYTO.A.20864.
[17] S. Pandey, A. Joseph, R. Lycke, A. Parashar, Decision-making by nematodes in complex microfluidic mazes, Adv. Biosci. Biotechnol. 02 (2011) 409–415. /
10.4236/abb.2011.26060.
[18] A.Q. Beeman, Z.L. Njus, S. Pandey, G.L. Tylka, Chip technologies for screening chemical and biological agents against plant-parasitic nematodes,
Phytopathology. 106 (12) (2016) 1563–1571.
[19] A.Q. Beeman, Z.L. Njus, S. Pandey, G.L. Tylka, The effects of ILeVO and VOTiVO on root penetration and behavior of the soybean cyst nematode,
heterodera glycines, Plant Dis. 103 (3) (2019) 392–397.
[20] J.P. Jensen, A.Q. Beeman, Z.L. Njus, U. Kalwa, S. Pandey, G.L. Tylka, Movement and motion of soybean cyst nematode heterodera glycines populations
and individuals in response to abamectin, Phytopathology. 108 (7) (2018) 885–891.
[21] Z. Njus, T. Kong, U. Kalwa, C. Legner, M. Weinstein, S. Flanigan, J. Saldanha, S. Pandey, Flexible and disposable paper- A nd plastic-based gel micropads
for nematode handling, imaging, and chemical testing, APL Bioeng. 1 (2017) 16102. /10.1063/1.5005829.
[22] U. Kalwa, C. Legner, E. Wlezien, G. Tylka, S. Pandey, New methods of removing debris and highthroughput counting of cyst nematode eggs extracted
from field soil, PLoS One. 14 (2019) e0223386. /10.1371/journal.pone.0223386.
Santosh Pandey is an Associate Professor in the Department of Electrical and Computer Engineering at Iowa State University. He
supervises the Micro/Nano Systems Laboratory in Coover Hall where research projects are conducted in experimental areas of
sensors, microfluidics, instrumentation, imaging, and software processing, and data analytics.
Yunsoo Park is a Master Student at Iowa State University. His research interests include machine learning, imaging, sensors,
low-powered PCB design and low-powered wireless communication. He participated in the Micro/Nano Systems Laboratory in
Coover Hall.
Ankita is a Ph.D. student at Iowa State University. She works in the Micro/Nano Systems Laboratory in Coover Hall. Her research
interests include bioengineering, machine learning, low-power PCB design, video analytics and image processing.
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11. Gregory Phillips is a Professor in Veterinary Microbiology and Preventive Medicine at Iowa State University. His research
interests are in genomics and metagenomics, microbiome/host interactions, antibiotic persistence in bacterial pathogens, and
bacterial membrane protein localization. He received the Pfizer award for research excellence in veterinary medicine. He is in
the editorial board of Plasmid, Journal of Bacteriology, and EcoSal.
S. Pandey, Y. Park, A. Ankita et al. HardwareX 10 (2021) e00249
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