Electronics to Monitor Animal Behavior Remotely
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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
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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 chips
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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
Flexible chip for long-term antimicrobial resistance experiments
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
Flexible Membrane Chips for Drug Testing
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
Phenotyping paralysis in microscopic worms
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
Smartphone app for Skin Cancer Diagnostics
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
Folded Floating Gate CMOS Biosensor for Nano Charge Sensing
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
Paper based reconfigurable flow switch for paper microfluidics
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
Fast, reconfigurable switch for chemical sensors
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
Opening and Closing of Transmembrane Proteins in Single Cells
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 Membranes
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.
Electronic Ear Tag for Farm Animals
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
Magnetic Field to enhance ethanol production
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
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.
Parasite Nematode Egg Extraction and Counting
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
Extracting and counting of parasite eggs from soil
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 MicroChips
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
Sweat sensing - a comprehensive review
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.
Sweat sensors - a Review of latest technologies
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.
Worm sorting in Amplitude Modulated Microfluidic channels
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
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Antimicrobial resistance studies in low-cost microfluidic chips
Antimicrobial resistance studies in low-cost microfluidic chips
Flexible chip for long-term antimicrobial resistance experiments
Flexible chip for long-term antimicrobial resistance experiments
Folded Floating Gate CMOS Biosensor for Nano Charge Sensing
Folded Floating Gate CMOS Biosensor for Nano Charge Sensing
Paper based reconfigurable flow switch for paper microfluidics
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Opening and Closing of Transmembrane Proteins in Single Cells
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Ion Channel Fluctuations in Transmemembrane Proteins within Cell Membranes
Ion Channel Fluctuations in Transmemembrane Proteins within Cell Membranes
Magnetic field to improve fermentation kinetics for ethanol production
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Extracting and counting of parasite eggs from soil
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Effect of Static Magnetic Field on Parasitic Worms in MicroChips
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Worm sorting in Amplitude Modulated Microfluidic channels
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FIDO Alliance Osaka Seminar: Passkeys and the Road Ahead.pdf
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Neuro-symbolic is not enough, we need neuro-*semantic*
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Accelerate your Kubernetes clusters with Varnish Caching
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Electronics to Monitor Animal Behavior Remotely
- 1. Figure 1. Overall theme for behavioral health monitoring in pig farms: (a) the pig farm is equipped with technologies to monitor individual animals and populations with mobile devices, data computing and storage units, machine learning, decision support tools, clinical diagnosis, and treatment options; (b) our measurement setup is shown. The ear tag with sensor board is attached to the ear lobe of individual pigs to measure vital parameters and send the data through a smartphone app to the cloud. S. Pandey et al, Behavioral Monitoring Tool for Pig Farmers: Ear Tag Sensors, Machine Intelligence, and Technology Adoption Roadmap, Animals 2021, 11(9), 2665; https://doi.org/10.3390/ani11092665
- 2. Figure 2. Prototype design and assembly: (a) CAD layout of the electronic sensor board; (b) the fabricated PCB with soldered electronic chips; (c,d) inclined view and side view of an assembled sensor board sandwiched between the orange-colored ear tag.
- 3. Figure 3. Animal testing: (a) two growing pigs were used for testing the electronic sensor boards; (b) the ear tag with the sandwiched electronic sensor board was attached to the left ear of the pig. The sensors and ASIC chip were remotely controlled by predefined awake/sleep cycles.
- 4. Figure 4. Time-series data recorded from pig testing using the electronic sensor board. Sample data from the animals is shown here as obtained from the on- board (a) temperature sensor and (b) 3-axis accelerometer. The sound sensors collected the baseline curves, but there were no useful events (e.g., coughing or screaming) during the recorded time period.
- 5. Figure 5. Flowchart for metrics, behavioral outcomes, and indicators of poor well-being.
- 6. Figure 6. Process flow during machine intelligence involves data acquisition, preprocessing, feature set extraction, super- vised or unsupervised learning, class definitions, performance metrics, and decision support.