Team:Rochester/Human Practices

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Introduction
Initial Research and Meetings
Solidifying our Project
Future of Our Device
Wetlab Considerations
Hardware Considerations
Integration of our efforts into the community
Stop Animations

Integrated Human Practices

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Activity Development Feedback and Implementation Synthetic Biology Lessons

Introduction

Sepsis is an excessive immune response to an infection, which eventually leads to very low blood pressure, organ failure and rapid deterioration of the patient. Sepsis makes up for 20% of deaths worldwide and is the cause of 1 in 3 deaths in the US hospitals!1 Even though it is extremely common, less than 30% of people are knowledgeable about this condition and its early symptoms.[2]. There are three stages of sepsis: sepsis, severe sepsis, and septic shock. One of the main sources of information and advocacy in the field of sepsis is the Sepsis Alliance organization. It was established in 2007 with a mission to “save lives and reduce suffering by improving sepsis awareness and care”. They conduct studies about sepsis awareness and care worldwide, lead outreach projects, help create new policies to improve sepsis care, and collect survivor stories as part of their initiatives. The touching stories of survivors motivated us to choose sepsis diagnostics as a focus of our project and later provided many resources for research. Once the problem of high mortality due to sepsis was established, we set out to find a solution.

Throughout our preliminary research stages, the literature we read and healthcare professionals we had the pleasure of talking to strongly emphasized the lack of a proper diagnostic tool for sepsis. The explanation for the high deaths from sepsis was that it was not diagnosed quickly or accurately enough to administer the right treatments in time. One contributing factor for high mortality is that sepsis symptoms are heterogeneous with other critical illness conditions. For example, chest pain could be a symptom of a heart attack, but it could also be a sign of sepsis onset. Physicians are faced with a difficult task of trusting their intuition to prescribe the right treatment. Currently, the most accurate diagnostic tool available to hospitals are bacterial blood cultures to see if there is any bacterial infection present in the blood.[3] However, these take a long time to provide results (24 hours), which is much longer than the time in which early sepsis can develop into full blown septic shock (as quickly as an hour after first symptoms). The accurate and early administration of antibiotics is key in preventing the negative implications of sepsis. If not treated early enough, the patient is at a very high risk of organ failure, amputations, brain damage and death.[4]

While designing and developing the diagnostic, we took into consideration the advice of researchers, physicians, other point of care workers and health policy makers to design a product that best serves the purpose of diagnosing sepsis risk earlier and with more accuracy.

Initial Research and Meetings

In this section, we describe the advice of professionals we spoke to directly and that has impacted our solution to the problem of inaccurate and slow sepsis detection tools.

Dr. Jeffrey Yaeger

Pediatrician at the University of Rochester Medical Center ICU

Figure 1: Screenshot of Our Meeting with Dr. Yaegar.

Dr. Yaeger told us about how difficult it is to diagnose sepsis because most of its symptoms are homogeneous with symptoms for many other conditions. He also introduced us to distinct terminology to use when discussing sepsis.

  • Systemic Inflammatory Response syndrome (SIRS): condition of fever, high heart rate, high respiratory rate, high white blood cell count.
  • Sepsis: occurs when SIRS is present due to an infection – there are three distinct stages of sepsis.
    1. Sepsis: immune response to infection starts.
    2. Severe Sepsis: immune response intensifies, patient experiences severe SIRS symptoms.
    3. Septic Shock: as infection spreads, it causes organ failure and a drop in blood pressure.

Dr. Yaeger also suggested that we try to predict if someone will develop sepsis/go into septic shock before it happens, rather than trying to explain symptoms that are already present. Physicians aim to administer treatment as soon as possible and prevent patients from entering severe sepsis and septic shock, so a predictive tool would be more useful than a diagnostic one.

He also advised us on how to make our device as accessible as possible. To make the device more equitable and accessible to as many people as possible, we need to make sure that there is as little extra equipment as possible, and does not require extensive training. Both of these considerations will reduce the cost of implementation and improve accessibility.

Dr. Yaeger’s advice contributed a lot to our initial idea of making a biosensor for sepsis diagnosis. After meeting with him, we recognized that when a patient experiences severe sepsis or septic shock, it can be diagnosed more easily by physicians, however it is often too late for treatments at that point. Instead, Dr. Yaeger suggested we create a diagnostic device that can predict the development of sepsis before there are any clear clinical symptoms. At this point in our research, we started brainstorming quantitative methods of diagnosing sepsis risk.

Sepsis Alliance

Non-Profit Organization

Their Mission: “Save lives and reduce suffering by improving sepsis awareness and care.”

The Sepsis Alliance was established in 2007, due to a large push from the community throughout the US to prevent sepsis deaths. When we spoke with Jill Gress, a Board Member of Sepsis Alliance, she told us that a very important prevention tactic is patient awareness. The idea is that the more an individual knows about the symptoms of sepsis risk, the more likely they are to seek medical help and advocate for themselves in the hospital. For example, if Krista cuts her finger and then goes outside to play with the kids in the grass, her wound may accidentally get infected. As time goes on, the wound may become more swollen and start hurting. Krista may not suspect it, but the infection is rapidly spreading through her body and causing inflammation until she starts feeling extremely ill. At that stage, it may be too late to go to the hospital and she risks losing her limbs due to organ failure. However, according to Ms. Gress, this turn of events can be avoided if the symptoms are recognized early on by Krista herself and she goes to the hospital. Recognizing that public awareness of sepsis symptoms is crucial in preventing deaths, a large portion of our efforts were aimed at empowering the public with knowledge of risks and treatment options in the case of sepsis.

In addition, Sepsis Alliance promotes equity research and has given us insight into the health disparities worldwide, but most importantly the implications it has for the population here in Rochester, NY. Studies done by affiliated institutions show not only the prevalence but also the inequality of successful treatment of sepsis in the US. Specifically, Black patients bear nearly twice the number of sepsis deaths, relative to the size of the Black population, as compared to whites (80%-92% higher).2 This data is especially important to the development of our product because Rochester, NY has a majority black population, accounting for 40% of the city’s population. Because of this, our solution includes equity considerations and a push towards increasing awareness among the underserved Rochester population.

Finalizing our Project

Medical Setting Considerations

Sepsis Survivors (Katy Grainger)

We listened to sepsis survivor stories, hundreds of which are posted on the Sepsis Alliance website and heard from Jill Gress, who is an advocate and a survivor herself. Hearing the personal accounts of these individuals was a source of inspiration for our efforts for a better sepsis diagnostic tool One of the most impressive and shocking experiences was shared by Katy Grainger, who is now an avid advocate for sepsis awareness. Her sepsis story started with a finger cut. She did not think much of it, but two days passed and the wound became more swollen and leaky. Katy went to the hospital where the medical professionals gave her some oral antibiotics and sent her home. A day later, she ended up in the emergency room, with a very low blood pressure, extremely pale skin and numb limbs. She was already experiencing septic shock. Katy was transferred to the ICU and treated for sepsis for nearly two weeks.

1 in 3 people in the US hospitals develop sepsis, and about 20% of patients who develop sepsis are post-surgery patients. The stories on the Sepsis Alliance website helped our team understand the severity of this condition and the impact it has on families. The sincere wish of all of the survivors is to prevent any further deaths due to sepsis. To integrate the benefits of our project into the public, we spread awareness to the local Rochester population by hosting the Sepsis Symposium and distributing flyers with the symptoms of sepsis. Our efforts will be discussed in a later section on this page.

Advice From Medical Professionals

Dr. Anthony Pietropaoli, MD

Director of the Medical Intensive Care Unit, the Respiratory Therapy Department, and the Pulmonary Rehabilitation Program at the University of Rochester Medical Center.

We reached out to Dr.Pietropaoli because he is not only knowledgeable in the condition of sepsis but also could give us a very accurate account of the administrative side of procedures related to the diagnosis and treatment of sepsis.

Takeaways

  • NY state and Center for Medicare and Medicaid Services (CMS) have set standards for hospitals. In NY state, sepsis is definitely a priority. However, one of the challenges is that there is not a lot of agreement about when time 0 is. Protocols lay out when to do what (in 1 hour, 2 hours, etc.) but it is hard to determine exactly at what instant to start counting those hours.
  • He explained the hospital approval process for biomedical diagnostic devices.
  • For post-surgical ICU’s sepsis is probably the 2nd most common diagnosis.
  • Early detection is the most important step, because that will allow to start accurate treatment earlier.
  • Currently, the fastest test is a blood culture and take 24 hours and is not always accurate.
  • Dr. Pietropaoli was able to direct us to paper where researchers discuss cytokine levels in blood.

Adjustments Made

  • Sweat Cytokine Levels Model: blood cytokine levels from papers that Dr. Pietropaoli suggested allowed us to more accurately present the sweat cytokine level by creating a model that related sweat cytokine levels to blood cytokine levels. This model makes it easier for medical professionals to interpret the data.
  • Continuous monitoring of sweat biomarkers is what we should strive for.
  • We established the time zero as being the second that the patient gets the first reading of biomarker concentrations from our device.

Dr. Pietropaoli informed us that in order for our device to be approved, we first have to get it approved by the FDA, which would most definitely require clinical trials. This led us to seek out advice from a former FDA employee to learn more about the entrepreneurship requirements of our project . In addition, we found out that a single intensive care unit usually holds around 70 nurses and 20 advanced practice professionals. Dr. Pietropaoli stressed the importance of providing training resources that are easy to reference. For this reason, we decided to create a video tutorial for our device, also taking into account the neurodiverse professionals and making it as clear as possible. In addition, we realized how important our diagnostic device is and that we should apply it to post-surgical patients as soon as they leave the operating room to maximize data.

Finally, the papers on blood cytokine levels that Dr. Pietropaoli sent us were invaluable in portraying data in a way that is familiar to professionals. Clinicians are accustomed to reading cytokine levels in blood and it would be easier for them to use our device if the software showed blood levels instead of cytokine levels, which is exactly what our model accomplished.

Dr. David Nagel

Pulmonary and Critical Care physician at the Strong Hospital

Dr. Nagel sees patients in the Intensive Care Unit at Strong Hospital. He was our most important advisor specifically on the topic of sepsis and the details of the condition.

Takeaways

  • He shared the University of Rochester Medical Center Sepsis Detection and Treatment Protocol: a protocol of how to treat a patient that is suspected to have sepsis which has been adapted in 2019.
  • Dr. Nagel explained to us that in sepsis, physicians should be worried about damage in organs due to infection spread. Low blood pressure is temporary and can be cured with fluids. The primary concern of low blood pressure is that other organs, kidneys especially, are not getting enough oxygen, which leads to organ failure.
  • He is concerned that many biomarkers are not as specific to infection, but increase during any inflamatory response.
  • For this reason, applying our novel device to the post-surgical patients is a good idea, because the time of possible sepsis infection is more controlled and medical professionals know that few other possible conditions are possible other than sepsis.
  • Biomarkers are definitely the way to go for detecting sepsis, because this approach will make the diagnosis more accurate. He encouraged us by saying that the biomarker tracking approach has succeeded in detecting other diseases, such as Hepatitis B.
  • It is important to distinguish sepsis from other conditions because the necessary administration of antibiotics against sepsis could lead to antibiotic resistance if the individual does not actually have an infection. Furthermore, a broad spectrum of antibiotics can be detrimental to the kidneys in the case where patients do not have an infection. Patients can also develop secondary bacterial infections, due to possible gut flora changes, or develop antibiotic resistance so it is harder to treat later infections.

Adjustments Made

  • Knowing from Dr. Nagels comments that there is a new protocol in the University of Rochester Medical Center, we knew that modifications to sepsis detection protocols are crucial to improving care. We decided to look at the prevalence of sepsis in countries around the world and learned that sepsis is the cause of 20% of deaths worldwide.
  • Based on this need, we made our own sepsis diagnosis guide, based on the guidelines Dr. Nagel shared with us, that suggests various ways that countries can standardise their hospital policies to improve their care for patients in danger of getting septic shock.
  • Since a single biomarker cannot determine whether the condition is sepsis or something else, we decided to use multiple pro- and anti-inflammatory biomarkers to get a complete picture of the patient's condition.

Dr. Nagel’s continuous mentoring has been very helpful to the development of our device. We were also able to better understand the point-of-care perspective through a very precise URMC Sepsis Detection and Treatment Protocol that Dr. Nagel shared with us. This protocol shows the exact time that patient samples need to be taken, what tests should be conducted and what personnel should be involved in the process of detecting and managing patients at risk of worsening sepsis. He assured us that after the implementation of this protocol, patient survival improved and severe sepsis and septic shock were prevented more often.

This protocol allowed us to then research the various approaches that different locations have and recommend a similar protocol, considering the resources that are available. Regardless of the time, the "Golden Hour" rule prevails. It states that a patient who is suspected to have sepsis must receive definitive treatment 60 minutes after the appearance of symptoms. For this reason, we adjusted our device to read out sepsis related biomarkers levels continuously, to catch a change in changes of the concentrations as soon as possible. The Golden Hour standard gives further incentive to medical professionals to obtain a faster and more accurate diagnosis of sepsis, which is what our device aims to achieve.

Kate Valcin

Director of Adult Critical Care Nursing at the University of Rochester Medical Center

Figure 2: Screenshot of Our Meeting with Kate Valcin.

Kate Vlacin, DNP, RN, CCRN-K, NEA-BC, CNL, has an enormous amount of experience in the administrative as well as the patient care settings. We reached out to her in order to get the point of care perspective and know how to best adjust our device to best fit the needs of the medical staff.

Takeaways

  • We should collaborate with the Sepsis Alliance organization to increase public awareness about sepsis.
  • Ms. Valcin suggested the sleeve should be flexible and go on to the forearm or the forehead. Feet are not an ideal location, because they are not as sanitary and tend to have compression socks on them.
  • The sleeve should be transparent to allow monitoring of irritation, flexible, and stretchable to fit all sizes.
  • Most hospitals use General Electric or Phillips MindRay Monitors to display the data from other devices, measuring vital pressure signs,for the medical staff.
  • The sleeve can be put on the patient as soon as they exit the operating room.
  • In order to see how the clinical care setting looks, we were able to visit the Intensive Care Unit (ICU) under her supervision.

Adjustments Made

  • We decided to use silicon for the sleeve because it is a stretchy and transparent material. Kate showed us some patches and sanitary methods that were used on patients. We took inspiration from the combination of their properties (stickiness, transparency, flexibility) to build our sleeve device.
  • We talked to the Sepsis Alliance and collaborated with them to organize the Sepsis Awareness Symposium for the general public.
  • We created Sepsis Symptom informational sheets that were distributed throughout the hospital and Rochester neighborhoods in physical and digital forms, aiming to increase awareness of the public, encouraging people to reach out for medical help earlier.

The ICU visit was valuable for the hardware side of our project as well as for implementation of modifications of our device to fit into the point of care sepsis. We obtained samples of materials that were regularly used on patients and that minimized irritation. These wound patches and brain wave stickers were later incorporated into our device. We also realized that the ICU setting is the best use for our device, because it is a more controlled environment and the condition of the patients can be monitored more easily. Kate’s expertise once more reinforced our decision to target our aptasensor device to post-surgery patients.

Future Improvements for Our Device to Benefit as Many People as Possible

Based on the suggestions of medical professionals we met with so far, we knew that our device should be implemented in a more controlled setting that would allow medical professionals to be more certain that the changes in biomarkers actually indicate sepsis onset. Because of this advice, we decided to adapt our device to post - surgical patients first. However, we are aware that about 80% of patients develop sepsis outside of the hospital.3 These patients come into the Emergency Room (ER) where their symptoms are much harder to establish as sepsis, since, as was mentioned earlier, sepsis symptoms are very similar to symptoms of other conditions, such as a heart attack. Adjusting our device to the emergency room setting is one of our future directions as a way of decreasing deaths of sepsis even further. Dr. Barbash advised us on the details of implementing our device into the emergency room setting.

Dr. Ian Barbash, MD

Physician-researcher at the University of Pittsburgh Medical Center

Figure 3: Screenshot of Our Meeting with Dr. Barbash.

Dr. Barbash has a significant knowledge base about sepsis policy. We reached out in order to learn more about how our product could fit into the everyday workings of the ICU and to gain a deeper understanding of how sepsis was currently defined, diagnosed, and treated. Currently, sepsis definitions are variable, and steps to making a diagnosis consist of physical history, lab tests (X-ray or CT), and blood and urine culture (which both take 24 to 48 hours to grow and obtain results and are therefore often not helpful for initial diagnosis and treatment).

Takeaways

  • We need to ask ourselves how practical is our device to deploy broadly and how much new information does it provide to a clinician on top of what already exists.
  • 80% of sepsis cases occur in the Emergency Room and so focusing efforts here would have a large public health impact.
  • It would be useful to combine our device with the EKG reading and pulse oximetry monitors to provide more meaningful data to detect infections in an ER setting.
  • Integrating our device and the pulse oximeter would also enable for less cords and parts to worry about in the chaotic Emergency Room setting.

Adjustments Made

  • In order to assess the practicality of our device, Dr. Barbash’s advice encouraged us to reach out to nurses and more physicians to get further information on the types of patients that would benefit the most from our device.
  • Dr. Barbash provided us with suggestions that we will include in our project’s future directions. Specifically, he emphasized that developing a device that combines the functionality of ours with that of an EKG and pulse oximetry monitor will allow for a more comprehensive look at the patient. This consolidation of data will enable physicians to make more informed decisions.

Dr. Barbash told us about an important challenge faced by physicians in the ER setting.

“The symptoms for many acute medical conditions are heterogenous - It is very difficult to determine whether a patient is sick due to an infection or from a different illness, such as a heart attack or pulmonary embolism.”

Therefore, Dr. Barbash stressed the necessity for a quantitative approach to provide a more definitive diagnosis for sepsis. He provided insight on the progress of current sepsis diagnostics and where he believes it needs to be improved -- towards an early diagnosis of whether one is sick due to an infection or a separate cause, as well as early determination of the severity of illness. Practically speaking, there is an absence of a gold standard algorithm for sepsis detection, and a need for a faster and better method than obtaining a blood culture. Dr. Barbash also informed us that after developing our device to detect biomarkers, the ultimate goal would be combining it with an EKG reading and pulse oximetry monitor to allow for more meaningful data for diagnosis. Additionally, this would increase ease of distribution to hospitals if we could offer them one device that can single-handedly cover multiple needs. We have added this to our future directions.

Wetlab Considerations

Making Graphne Oxide

Ram Surya Gona

Materials Science PhD student in Dr. Anne S. Meyer’s Lab, at the University of Rochester

Physician-researcher at the University of Pittsburgh Medical Center

Figure 4: Screenshot of Our Meeting with Ram Gona.

Ram Surya Gona is working on 3D printing of engineered living materials, who worked on graphene production in the past. He was a hardware Teaching Assistant for last year’s (2020) University of Rochester iGEM team: Team UteRus, where he gave valuable technical advice. We reached out in order to understand which electrical property of reduced graphene oxide would be best to measure for our purposes, as well as for experimental advice on making and quantifying the conductivity of graphene oxide (GO).

Takeaways

  • We can measure conductance with a 4-probe system setup, and the University of Rochester Nanocenter has the necessary equipment. Unfortunately, we were not able to use it because of limited availability.
  • He reminded us that oxidation of graphite is a quite dangerous reaction, and very tight temperature control is needed. Ram Gona supervised us during our initial attempts to make graphene oxide.

Adjustments Made

  • After the supervised synthesis of GO, we decided that the reaction was too time consuming, resource intensive, and unsafe without intensive precuations to be a viable path for us. We approached Graphenea, who generously sponsored us by providing us with graphene oxide. LINK
  • We researched the various ways of measuring conductance of graphene oxide, including impedance.

Ram Surya Gona encouraged us to explore the aptasensor field more, and read papers not only about rGO-based biosensors but also about sensors based on multiple other materials. He gave us a lot of small technical suggestions, such as using acetone to help the surface shrink more. He helped us produce GO for the first time, teaching us how to conduct the synthesis carefully and safely.

Reducing GO and Attaching Aptamers

Dr. Benjamin Lehner

Project portfolio manager for scientific and engineering innovation at the Dutch Marine Energy Center.

Figure 5: Screenshot of Our Meeting with Dr. Lehner.

Dr. Benjamin Lehner is a project portfolio manager for scientific and engineering innovation at the Dutch Marine Energy Center. During his Ph.D. at TU Delft , under the supervision of our very own PI Dr. Anne Meyer, he worked extensively on the modification and production of graphene and its derivatives. We reached out to him for his expertise on alternative ways to produce reduced graphene oxide.

Takeaways

  • Dr. Lehner shared his protocol on how to make bacterially reduced graphene oxide (rGO) and gave us advice on difficult experimental steps.
  • He advised us to think about the level of reduction of the graphene oxide, as more reduction increases the electrochemical change across the rGO sheet when the biomarker binds, but allows fewer aptamers to be bound due to fewer functional groups.
  • He proposed pi-pi stacking as the easiest method to attach our aptamers to rGO, but pointed out that aptamers could be washed off through this method, which would reduce the signal and lead to inaccuracies.

Adjustments Made

  • This meeting not only provided us with a detailed protocol on how to bacterially reduce graphene oxide, but especially gave us advice on difficult steps and potential problems that could arise and how to solve them. For example, he told us to make sure we carefully control the temperature to an accuracy of 0.5°C when oxidizing graphite, since temperature changes could easily affect the outcome and purity of the resulting graphene oxide.
  • To account for this, we came up with a feedback-enabled heating plate, which maintains the temperature within the 0.5°C threshold, as recommended.
  • Due to Dr. Lehner’s advice, we confirmed that we wanted to attempt to produce rGO with bacteria to increase the reduction capabilities through synthetic biology.
  • We learned much more about the implications of reducing graphene oxide on its electrochemical properties. Our idea of using rGO as the base for our aptasensor was supported, but we also learned that we had to account for the degree of reduction. We decided to determine the optimal degree of reduction through Modeling.
  • Prior to this meeting, we were considering more complicated and expensive options such as EDC-NHS linking or the use of gold nanoparticles. After our meeting with Dr. Lehner, we focused on pi-pi stacking to attach the aptamers to rGO.
  • We learned that it’s very hard to detect conductance changes because rGO is highly conductive, so we realized we have to use impedance instead.
  • Finally, he suggested using AFM to visualize whether aptamers attached to rGO properly.

The meeting with Dr. Lehner gave us valuable insight into simpler methods rGO production. Although we had read papers about bacterially reduced materials, it was very helpful to receive a full protocol and advice on what could go wrong and why. In addition, Dr. Lehner gave us the final confirmation we needed to decide on rGO as our aptasensor foundation, as opposed to other conductive materials, such as GO and gold nanoparticles. Aptamers would be attached to rGO, which will enable us to measure electrochemical changes associated with biomarker-aptamer binding. Dr. Lehner explained to us the exact differences between graphene, graphene oxide, and reduced graphene oxide and the implications for our aptasensor. This led to our modeling team to start a new model to determine how many aptamers could attach to rGO at varying levels of graphene oxide reduction. Throughout the modeling process, we had to keep in mind that the more reduced the GO becomes the better its electrical properties are but the fewer aptamers can be attached. Lastly, he talked to us about attaching aptamers to the rGO and suggested pi-pi stacking as a simple but robust method that would not require special, expensive linker particles. Precise attachment of aptamers is crucial to the sensitivity of our aptasensor, since the concentration of biomarkers in the sweat of a patient is quantified by an electrochemical signal from the biomarker-aptamer binding to the rGO film to the electrode, and displayed to the medical professionals through our software. Dr. Lehner’s advice allowed us to finalize the planning for our wetlab team and to get started with the production of rGO and attachment of aptamers.

Hardware Considerations

Microfluidics

Dr. James McGrath

Professor of Engineering at the University of Rochester, NY, USA

Figure 6: Screenshot of Our Meeting with Dr. McGrath.

Dr. James McGrath teaches a class focused on microfluidics and additionally leads research in the field of biosensors. He was one of our first contacts to learn more about microfluidics and how to best approach building our own microfluidic device.

Takeaways

  • Dr. McGrath suggested designing an inverted, branched, tree-like structure for the collection of sweat, in which the capillaries slowly increase in volume to promote passive flow.
  • The actual channels can only be 0.5 mm or larger in diameter. Using photolithography would be an option, but it is expensive and will require a clean room. An alternative would be to use a 3D printer to create a mold for the microfluidic device.
  • He introduced us to materials used in microfluidics and recommended using either PDMS or silicone for our channels.
  • He suggested using two different materials to close the channels in the microfluidic device - one permeable to sweat for the collection of sweat and one impermeable to sweat for the transport of sweat.
  • He pointed out that protein adsorption to capillary walls as they travel could be a potential problem that could then be solved by coating the channels from the inside with an anti-stick material.
  • He taught us about engineering design and how we should first aim for a simple version and then add modularity and complexity later once tests are successful.

Adjustments Made

  • This meeting helped us create our initial design for our microfluidics component of the aptasensor. We were able to decide on the necessary and optimal materials and plan the channel geometry design. Dr. McGrath confirmed that microfluidics would be a good approach to collect and transport sweat for our aptasensor.
  • We also learned about the engineering design process in more detail and began to automatically incorporate cycles of testing and readjusting to our planning and designing process.
  • We learned about potential difficulties we could have, especially regarding passive fluid flow and protein adsorption that we weren’t aware of before, such that we could account for them and have various possible solutions at hand if we happen to encounter them.
  • Although photolithography for production and soft-lithography for creating subtle shapes is the most common way of producing microfluidic devices, the meeting made us realize that we need another method in order to avoid clean room technology and expensive micromachining equipment. We thus chose an iterative cycle of shrinking and casting, to create smaller and smaller molds for our final device.
  • Our initial plan was to make a modular biosensor that can be adjusted according to the patient's needs and condition. However after the meeting we decided to take a step back and work on a simpler version first to not get stuck on complicated or irrelevant details from the beginning. Instead, we decided to pursue a more step by step approach with many future directions and possible adaptations

The meeting with Dr. McGrath had the main purpose of helping us better understand microfluidics and what we need to take into account for our purposes. We were able to confirm that a microfluidic approach to collecting and transporting sweat would work well. The information and resources he provided us with helped us better understand the underlying fundamentals which were necessary to start the design of our microfluidic device. He gave us many examples of different designs and what they do so we could then figure out which parts we would need for our microfluidic device. Furthermore, his experience as an engineer helped us think about the entire design process more specifically and make many prototypes first before attempting to make the perfect design. He encouraged us to incorporate different testing points for a proof of concept of individual components into our design and overall plan and to first simplify everything. This approach helped us get individual, but fundamental, steps to function. We then built upon these fundamental steps to make the device more complex and modular. It thus was a great meeting to help us figure out how to best structure our plan of action for hardware.

Combining Microfluidics and Electrodes

Dr. Richard Janissen

Lecturer in the Department of Bionanosciences at TU Delft

Figure 8: Screenshot of Our Meeting with Dr. Janissen.

Dr. Janissen works on biocompatible graphene oxide nanosheets, functionalized with biologically active molecules for biosensing applications. We reached out in order to ask about the best ways to detect binding of biomarkers to our aptamer receptors through electrical signals, as well as how to attach aptamers to reduced graphene oxide, how to deposit reduced graphene oxide on the electrode, and how to design the microfluidic channels.

Takeaways

  • Placing the electrodes in series will require less total sweat than placing them in parallel.
  • The flow rate of sweat will influence how much non-specific binding we have. The slower the flow rate, the better, because non-stable interactions have more time to disappear.
  • Bovine Serum Albumin is a good agent to use to passivate the surface. In other words, to prevent the biological materials from sticking to the microfluidic surface as they travel down the channels.

Adjustments Made

  • We modified the shape of the microfluidics channels, from parallel to in series, based on Dr. Janissen’s advice.
  • We used drop casting for attaching graphene oxide (GO) to the electrode, as suggested. According to Dr. Jenissen, this method is most cost effective as it requires virtually no equipment except for the electrode, water and GO.

The meeting with Dr. Janissen was a tremendous help for our project, because he has vast experience in biosensing using graphene-based materials. He not only encouraged us to consider carbon nanofibers and other materials instead of rGO and realize their advantages, but he also provided us with a lot of research articles that describe novel protocols for creating a microfluidic device or depositing graphene materials on electrodes were described. He also guided our modelling team by highlighting the most important parameters, such as number of oxygen groups and and ability to form pi bonds, when thinking about flow rate and aptamer-biomarker dissociation, as well as understanding how the amount of aptamers that can be attached to rGO depends on the different degrees of reduction. Moreover, Dr. Janissen put us in contact with Prof. Dr. Cecilia de Carvalho Castro e Silva and Prof. Dr. Antonio Riul Junior, who were both an invaluable source for our hardware team.

Dr. Cecilia de Carvalho Castro e Silva

Researcher at Mackenzie Presbyterian University, São Paulo, Brazil

Figure 9: Screenshot of Our Meeting with Dr. Silva.

Dr. Cecilia, PhD is a Brazilian researcher who has experience in reduced graphene oxide (rGO) modifications and the biosensor aspect of our device. She advised us on the deposition of rGO onto the electrodes, provided us with a procedure to produce screen-printed electrodes, and advised on testing resistance of the electric signal with silver ink. Dr. Cecilia’s advice was based on her experience with other types of biosensors, so we had to adjust it when applying it to our system. For example, the biosensors she has worked with before were not sweat based and did not require electrodes to be embedded within the microfluidics channel. For this reason, we had to be creative with the solutions we came up with. The microfluidics and the electrode modifications are the biggest areas of advice that we received from her.

Takeaways

  • GO is exceptionally stable in water, so we can do drop casting on the surface of the electrode. Drop casting means dropping the GO onto the electrode, so it sticks. Drop casting involves dropping the GO solution onto the electrode and letting the solvent evaporate, so it sticks.
  • After drop casting, dry for 3 hours . This should result in a homogeneous film on the surface of the electrode. Next, reduce the GO into rGO using Shewanella oneidensis MR-1 or electrochemical reduction.
  • Microfluidics: Dr. Cecilia suggested to use PDMS to make the channels through 3D printing.PDMS is a flexible material when it solidifies. It can be poured into a 3D mold and then pealed off to reveal our microfluidics channels. She suggested we Use Onshape and COMSOL to design the microfluidics device (these softwares can be easily connected to a 3D printer to make our molds).

Adjustments Made

  • We decided to use drop casting to modify the electrodes with GO because that method is more reproducible and will be easier to repeat by others who want to replicate our results.
  • We 3D printed a plastic master mold of the microfluidics channels, which was then used to pour PDMS to make the microfluidics channels themselves.
  • Electrodes were attached to a glass slide so that they adhere well.

The 3D printing approach with PDMS was chosen by our team because it is easily reproducible. The designs for 3D printing are saved on the Onshape and COMSOL softwares and can be easily printed on any 3D printer. In addition, it is cheap to print, since the 3D printer utilizes plastic. Furthermore, we plan on making a kit for our device, which will include the mold itself and will enable others to replicate our device, even if they do not have access to a 3D printer.

We developed the S. oneidensis reduction method as a more environmentally friendly and efficient solution to obtaining reduced graphene oxide for our project. You can read more about the efficiency of this technique on the wetlab page.

Dr. Antonio Riul

Researcher and Professor at the Universidade Estadual de Campinas, Brazil

Figure 10: Screenshot of Our Meeting with Dr. Riul and Dr. Janissen.

Dr. Antonio Riul’s research is in the field of materials sciences with a specific focus on impedance measurements in sensors. He was recommended to us by Dr. Janissen to talk about how we could best incorporate our electrodes into the microfluidic device and what property to use to measure the concentrations of biomarkers.

Takeaways

  • We should focus on impedance measurements using a potentiostat (an instrument used to control and measure the voltage in electrodes) to measure the varying concentrations of our biomarkers in sweat.
  • To incorporate the electrodes in the microfluidic device, we can directly insert them into the microfluidics channels and seal the sides to let sweat flow over the electrodes through capillary action. In sealed channels, the sweat is able to flow from the point of highest (small diameter channels) to lowest pressure (highest diameter channels), as intended by our design.
  • He suggested the use of screen-printed electrodes and the alternative of directly printing the electrodes onto the microfluidic device.

Adjustments Made

  • The meeting provided us with new design ideas in which the electrodes are attached to the sealing layer of our device such that the working electors are centered in the main channel and do not hinder fluid flow.
  • We started looking more specifically into printed interdigitated and standard screen printed electrodes for our device. We decided on screen printed electrodes after thorough research.
  • We chose impedance measurements as electrical signal for our readout using a potentiostat. As a consequence, we looked more into potentiostats and decided to build our own.

The meeting with Dr. Riul was very useful to provide us with an overview on how to use electrodes to measure the electrochemical changes in rGO and how to incorporate them into a microfluidic device without hindering fluid flow. He gave us different examples of the microfluidics devices he has designed and the various ways he has embedded the electrodes into them. He specifically talked about printing interdigitated electrodes onto a glass slide and sealing it to the microfluidic device, to avoid sealing problems that could arise when using standard screen printed electrodes. He explained what property we could best measure with each type of electrode, eventually leading us to pick screen printed electrodes, and highly recommended looking into impedance measurements using a potentiostat. This led to us looking more into potentiostats and eventually resulted in us building our own, much cheaper and accessible potentiostat. His expertise in biosensors was incredibly useful and supported our efforts to build one for the detection of sepsis.

Now that all the parts of our aptasensor were fabricated - the microfluidic channels, the rGO modified electrodes, the aptamers specific for the biomarkers - we could start testing our prototypes. We were not able to conduct a clinical trial study due to strict regulations and time constraints for experiments on humans. However, even without testing we knew that the patients in the ICU produce very little sweat. Therefore, sweat induction is very important to consider as a potential requirement for the device to work optimally. In order to find out about how to best do that, we reached out to professionals who have worked on sweat stimulation in the past.

Sweat Stimulation

Emma Moonen

PhD candidate at the Toonder lab at the Eindhoven University of Technology

Figure 11: Screenshot of Our Meeting with Emma Moonen.

Emma J.M. Moonen is working towards developing a hybrid patch for monitoring patients by measuring biomarkers in sweat. We reached out in order to discuss challenges in sweat collection for patient monitoring, ask a few questions about the microfluidics part of our device, and get more advice on developing flexible skin devices for disease detection.

Takeaways

  • For collecting sweat, it is a good idea to use the palm of the hand, but sweat induction is still necessary.
  • PDMS is a good material choice for our sleeve because it is flexible and has low surface energy.
  • Cytokines concentration in sweat might be sweat rate independent, and most cytokines have correlation to blood concentrations.

Adjustments Made

  • We realized that we need to do COMSOL calculations in order to understand how the sweat rate would influence flow within the microfluidic device and how that is impacted by the channel sizes.
  • After these calculations, we would be able to tell how strongly we need to induce sweat in order for it to flow properly through the channels and contain a sufficient amount of biomarkers for detection.
  • We realized how important it is to clean the skin before putting our aptasensor device on. Each sweat gland produces sebum, which is a complex mixture of fatty acids, sugars, waxes and other chemicals, meant to protect the skin from water evaporation. Thus, sebum is quite hydrophobic and if it is present near the collection channel, it would cause sweat to “stick” to the skin surface.
  • Iontophoresis is a procedure where an electrical current is passed through skin soaked with water/saline at a certain pH, which causes glands to secrete sweat faster. Emma confirmed that, although unsafe, this is pretty much the only way to induce sweat locally, but more research and testing is needed for other methods.
    • Pilocarpine is a safe induction substance. However, it requires reapplication every 30 minutes, which is not ideal for our device application, where it would be on the patient for a longer time.
    • We would want to conduct further experiments around seat induction with candidate chemicals, such as charbacol, that have been proven to induce sweat for a longer time, but have not yet passed safety checks for use on humans.
    • Because of safety concerns and inability for our team to test sweat induction on human subjects, we decided to rely on pilocarpine as our induction chemical for now, leaving more robust methods of induction for our future directions.

The meeting with Emma encouraged us to think deeply about the technical difficulties of our device, more specifically how we would enable sweat to flow into our channels in the first place, and why it would not start flowing on the skin. These questions were the starting point of our final inverted-tree hardware design. She also made us realize the need for COMSOL calculations first, in order to find the proper channel sizes for the desired sweat rate. Lastly, Emma’s view helped us realize that even though the correlation of sweat cytokine concentration to blood cytokine concentration is still debatable, most research shows that a strong correlation exists. Moreover, she encouraged us to pursue our project because there is a huge need to be able to detect low concentrations of biomarkers in sweat.

Because of safety concerns and inability for our team to test sweat induction on human subjects, we decided to rely on pilocarpine as our induction chemical for now, leaving more robust methods of induction for our future directions.

Integration of our efforts into the community

After taking into consideration the valuable advice from professionals in the field of medicine, wetlab experiments and hardware engineering, we implemented policies and practices that made our device more robust and in agreement with the needs of the patients and hospitals. In addition to the adjustments made throughout our process to our device, we made our efforts accessible to the public.

The integration of efforts into our society are listed in detail below:

Sepsis Symposium

On Saturday, September 18, 2021, we hosted the Sepsis Awareness Symposium, which we organized and prepared for throughout the months of August and September. Given the huge rate of fatalities, high costs, and associated patient and relatives’ suffering because of sepsis it has been our goal to raise awareness about sepsis, so that symptoms can be recognized, the condition taken seriously, and medical aid be sought sooner. Our goal was to reach the underserved Rochester population to improve their knowledge and ability to advocate for themselves at the hospital if they suspect sepsis.

Throughout the year we have spoken to many professionals in diverse fields that work with sepsis and septic patients one way or another. This has helped us understand that not only a diagnostic device that could continuously measure a patient's condition in light of sepsis, but also that awareness about sepsis is largely missing in the field. Sepsis is a serious medical condition occurring all over the world and yet some populations are at higher risk than others. Especially in the United States, African Americans are twice as likely to die from sepsis as compared to the Caucasian population. Here in Rochester, New York, 42% of the population is African American and it thus was especially important for us to lead a public awareness event. We decided to create a Sepsis Awareness Symposium that was open to everyone and provided background about sepsis, point of care, and included experience stories and resources.

We invited Kate Valcin, the director of adult critical care at the University of Rochester Medical Center, to talk about sepsis from a medical and point of care perspective. Her presentation was followed by videos provided by the Sepsis Alliance on sepsis survivor stories and a presentation by Jill Gress, a member of the Board of Directors of the Sepsis Alliance. Gress was able to talk about resources and advocacy for sepsis, for patients, doctors, family members and anyone interested in making a difference. Each section was followed by time for questions from the participants. Finally, the symposium ended with our team presenting about our iGEM project on the diagnosis of sepsis and the Ohio State University iGEM team presenting on their project on the treatment of sepsis.

The symposium was a large success. We were able to reach a wide range of people by advertising our event on the global iGEM slack, social media, and via flyers and posters locally. We had members from different iGEM teams join, undergraduate, graduate, and medical students, friends and family members, and anyone in the community interested in learning more about sepsis. We had a total of 45 attendees and have received overwhelmingly positive feedback from them! It is our hope that all participants can now share their knowledge on sepsis and help save lives by passing on the word!

Anonymous Feedback:

“I never knew a person can die from a scratch, I will definitely be more mindful of this now”

“I think I actually saved myself from septic shock after attending your symposium! I came to the hospital with an infected wound that had only been getting worse. The physicians were about to send me home, but I insisted on them giving me broad spectrum antibiotics because I was not feeling too well and the wound did not heal. I advocated for myself and I think that saved me from further complications.”

This feedback is exactly what we hoped to achieve! We are very glad that the symposium was a success in educating the Rochester community and decreasing the number of sepsis complications through our informative event.

Sepsis Book is now available for free on Amazon!

We collaborated with the Ohio State University iGEM team to create a children's book and improve awareness of sepsis starting from a younger age. Sepsis is even more dangerous in children than in adults, because it can become deadly even faster than in adults. More than 75,000 children are treated for sepsis every year.[7] To increase awareness of this risk for children, we decided to create a children's book that improves their understanding of the risks, but most importantly, prevention measures for sepsis that can be implemented daily. (link to collaboration page). This book is completely free and available on Amazon.

Sepsis Awareness Posters

As yet another awareness effort to reach the wider Rochester community, we designed and distributed porters that outlined the most prevalent symptoms of sepsis and when to see a physician. We advertised these porters throughout the Medical Center waiting areas, so patients of all kinds can view this information. In addition, we hung the pamphlets around our university’s campus and in parks around Rochester.

Integration of the Aptasensor into the Hospital

In addition to spreading awareness, we realize that a big part of making a difference in the field of sepsis detection is through making a device that is usable in the hospitals. As mentioned above, our considerations for integrating our aptasensor device into the ICU rooms is supported by our consultations with the administrative heads of the ICU at the University of Rochester Medical Center as well as an actual tour of the ICU. We saw for ourselves the current setup of the rooms and the conditions in which the medical professionals as well as patients are in. We recognized that post-surgical patients should be our target population. We took all of these factors into account and created policies and guidelines that will enable the proper use of our device as well as the best outcome for patients. Although all the technical adjustments made to our aptasensor are described in the sections above, we would like to go more into detail about the policies that our team created and distributed, because we truly believe they will make a difference in the equity and quality of care that is delivered to patients!

Policy for sepsis detection in hospitals

In order to go even further and improve the actual outcomes of hospitalized sepsis patients with the current available tools, we decided to write and distribute an up to date version of the Sepsis Detection and Treatment Policy that has been proven to provide better outcomes in patients at the University of Rochester Medical Center. Based on the guidance of Dr. Nagel and the policy he provided us with, we were able to not only create a comprehensive guideline for all hospitals, but also created recommendations for various countries for the improvements they can make to their current policies around sepsis detection and treatment.

Sepsis Detection and Treatment Policy:

The Sepsis Alert Standard Operating Procedure, graciously provided to us by the UR Strong Memorial Hospital, is their policy describing the process for “pharmacist attendance on code sepsis alerts.” It follows the Sepsis 2 and ICD-10 Coding definitions for severe sepsis and septic shock. This document outlines the criteria for vitals for one to be determined to have severe sepsis or septic shock. It also outlines the sepsis team members and the criteria for “code sepsis” alerts. The policy then moves into discussing the exact procedure for response to these alerts. Some major timestamps include ensuring two sets of blood cultures have been drawn within 24 hours prior or no more than 3 hours after criteria for severe sepsis are met. Additionally, antibiotics should be administered in this same time period, but ideally, the administration should be within 1 hour of meeting severe sepsis criteria. Specifics as to which antibiotics should be recommended are included. This procedure walks through all the steps of responding to a sepsis alert to ensure thoroughness and quality of care. In the University of Rochester Medical Center, there is a designated Sepsis Team that makes sure the protocol gets implemented accurately. The hospital pharmacist is a crucial link in this procedure.

Sepsis Detection and Treatment Policy Procedure: carried out by the pharmacist
  1. Pharmacy ED and pharmacy Critical Care pagers will be paged.
  2. Pharmacist needs to respond ASAP.
  3. Identify the adult sepsis team leader
  4. Introduce yourself to the team
  5. Encourage sepsis order panel to guide orders cultures, lactate, fluids, and antibiotics
  6. Make sure two sets of blood cultures have been drawn within the proper time frame

    --> Within 24 hours prior or up to 3 hours after meeting severe sepsis criteria--ideally within 1 hour*

  7. Make sure lactate was drawn within the proper time frame

    --> Within 6 hours prior or up to 3 hours after meeting severe sepsis criteria-- ideally within 1 hour*

  8. Make sure IV fluid bolus has been given within the proper time period

    --> 30 mL/kg IV within 6 hours prior or 3 hours-- ideally within 1 hour-- after initial hypotension or septic shock criteria are met*

  9. Review the patient chart for the current antibiotic region and optimize dose and frequency. If the patient is not on antibiotics, make antibiotic recommendations.
  10. Facilitate antibiotic administration.

    --> Antibiotics need to be given in 24 hours prior or within 3 hours-- ideally within 1 hour-- after meeting severe sepsis criteria*

  11. Evaluate which fluids and how much are being given

    --> Chloride restrictive fluids are preferred over 0.9% sodium chloride*

  12. If the team requests it, facilitate vasopressors administration

    --> Ideally within 6 hours of meeting septic shock criteria*

  13. Help facilitate any other medication that the team needed during patient evaluation.

    --> RSI meds, sedatives/analgesics, corticosteroids, etc.*

  14. Leave a telephone/pager number so that team can contact if more pharmacy help is needed
  15. Document all the recommendations and interventions made
  16. Re-evaluate response in chart 4-6 hours later

    --> Review cultures, determine whether more or different antibiotics are needed, and ensure that repeat lactate is drawn and a repeat volume status is assessed and documented.

This policy guide that we sent out to hospitals in the region and which has been approved by Dr. Nagel, upon review, will help hospitals monitor patients at risk of sepsis and improve the outcomes of the efforts, which depend highly on the promptness and accuracy of diagnosis and treatment. Our aptasensor will enable medical professionals to determine if the patient is septic with more accuracy and speed. However, as we learned from both Kate Valcin and Dr. Pietropaoli, the organization of the medical team is also extremely important in ensuring that every patient is cared for properly. Because we recognize that sepsis is a global concern, we conducted more research and came up with the following insights and recommendations:

Implementation of the Sepsis Detection and Treatment Policy worldwide

There are some specific challenges that together compound the global burden of sepsis.

A lot of the data and guidelines that are available on sepsis come from high-income countries. This can be particularly problematic because the data does not transfer nicely to what is actually happening in low and middle-income countries (LMICs). In these countries, there are multiple factors increasing the risk of sepsis-- poverty, overcrowding, poor hygiene, and inadequate healthcare-- and so generalizing the data results in inaccuracies in morbidity and mortality numbers. Furthermore, in low-income areas, many deaths and sepsis cases could occur in the home because healthcare facilities were inaccessible. These cases are often left undocumented and can further the fallacies in the data. [8] Not only is there an issue with obtaining representative data as explained above, but also with vague definitions for what constitutes sepsis and septic shock. This is not merely a discussion of semantics; a clear definition is in fact essential to the comparability of patients in research studies and data collection, as well as for clarity in guideline-driven treatment.

Other important contributors to the global burden are the numerous insufficiencies in low-income countries with healthcare and accessing it. Risk factors in these countries span multiple arenas, including healthcare facilities, transportation, capacity, and antimicrobials.

Healthcare facilities can many times be understaffed for the amount of sepsis patients they need to see. 83 countries in Latin America, Africa, and Asia, do not meet the health care worker-to-population ratios that are set out by WHO. Additionally, there are knowledge gaps to be considered when it comes to specialized care, such as pediatric sepsis cases. On top of a lack of healthcare workers, facilities themselves are often in poor conditions which can result in the infections spread from patient to patient or during health care. Transportation to a facility can also raise a problem for patients who live too far away.

Capacity- Many facilities do not have the necessary supplies, medications, nurses, and doctors to allow access for surgery to all that need it. Startlingly, 67% of the world’s population-- specifically those in South Asia and sub-Saharan Africa-- do not have access to surgery![9] Further, beds in critical care units are often filled to the maximum, and this results in severely ill patients having to be treated outside the ICU.

Inadequate antimicrobials- As one of the major first courses of treatment for sepsis patients is antibiotics, having access to these medications is essential. In many countries however, there is not only a lack of these drugs, but also-- because of no monitoring-- some are counterfeit or ineffective. Additionally, because in some countries the antibiotics can just be purchased over-the-counter without a prescription, antibiotic resistance resulting from unregulated self-medicating for past illness could impede on the antibiotics efficacy in septic individuals.

In addition, it is important to note that sepsis care in high-income countries may not be the same care necessary for those in low-income countries. This is a result of the potential difference in hosts and difference in pathogens between the two.

Low and middle income countries have challenges that make sepsis diagnosis and treatment significantly more difficult, and these varying circumstances lead to differences in presentation of the condition. While obtaining accurate data and catering treatment and resources towards these LMICs may be difficult, the work is essential as about 85% of sepsis cases and related deaths in the world happen in these countries.

Final Remarks

Our solution has evolved and improved enormously throughout the past months! We encountered challenges in the design of our product and overcame them through troubleshooting and creative solutions. We engaged in the design and perfection of the wetlab and hardware components to make a prototype of our aptasensor. In addition, our product is integrated into the local and international community through sepsis awareness efforts, policies that will improve treatment, and a device that will be easy to use, targeted to post-surgical patients, and drastically decrease the world-wide suffering due to sepsis!

References

  1. Centers for Disease Control and Prevention. (2021, August 17). What is sepsis? Centers for Disease Control and Prevention. Retrieved October 17, 2021, from https://www.cdc.gov/sepsis/what-is-sepsis.html.
  2. Kempker, J. A., Kramer, M. R., Waller, L. A. and Martin, G. S. (2018) Risk Factors for Septicemia Deaths and Disparities in a Longitudinal US Cohort, Open Forum Infectious Diseases, 5(12), ofy305.
  3. Get Ahead of Sepsis, CDC.org