Difference between revisions of "Team:Austin LASA/Human Practices"

Latest revision as of 03:57, 18 October 2018

h(g.Section, {title: 'Lindsey Dawson'},
    'Associate Director, HIV Policy',
    h('br'),
    'Kaiser Family Foundation',
    h('p', null, 'Ms. t will accompany our kit'),
    h('ul', null,
      h('li', null, 'She details on how understanding the importance of detection is important, but how it is equally important to consider the steps that should be taken to get treatment afterward (eg. antiretroviral treatment)'),
      h('li', null, 'Sent the following information (even though the CDC material is focused on US primarily)',
        h('ul', null,
          h('li', null, h('a', {href: 'https://stacks.cdc.gov/view/cdc/23447'}, 'CDC recommendations on Lab testing for HIV')),
          h('li', null, h('a', {href: 'https://www.cdc.gov/hiv/pdf/testing/hiv-tests-laboratory-use.pdf'}, 'Lab tests')),
          h('li', null, h('a', {href: 'https://www.cdc.gov/hiv/pdf/testing/rapid-hiv-tests-non-clinical.pdf'}, 'Rapid tests')),
          h('li', null, h('a', {href: 'https://www.cdc.gov/hiv/pdf/testing/hiv-tests-advantages-disadvantages_1.pdf   '}, 'Advantages/Disadvantages to different HIV tests')),
          h('li', null, h('a', {href: 'https://stacks.cdc.gov/view/cdc/50872'}, 'Recommended testing algorithm')),
          h('li', null, h('a', {href: 'https://www.cdc.gov/hiv/testing/laboratorytests.html'}, 'More info here (incl. all the above links)')),
          h('li', null, h('a', {href: 'http://www.oraquick.com/What-is-OraQuick/OraQuick-In-Home-HIV-Test'}, 'OraSure’s home test')),
          h('li', null, h('a', {href: 'http://aidsinfo.unaids.org/'}, 'To see hardest hit countries, including where share of people unaware of their HIV status is highest (i.e. undiagnosed)'))
        )
      )
    )
  ),

h(g.Section, {title: 'Christopher R Singh'},
    'Biological Safety Officer, MS, Ph.D.',
    h('br'),
    'The University of Texas at Austin',
    h('br'),
    'Environmental Health and Safety',
    h('p', null, 'Dr. Singh served as our guide for various safety concerns and was able to provide us information on various regulations as follows.'),
    h('ul', null,
      h('li', null, 'Based on the procedures and information provided, are there specific clearances or hazards that we need to be aware of?'),
      h('li', null, 'What is the best way to handle blood spots or DNA samples when using a detection kit? What are things that we should keep in mind for creating the most aseptic and safe kit?'),
      h('li', null, 'What are the best disposal or packaging methods when the goal is to use kits such as these overseas in non-lab environments?',
        h('ul', null,
          h('li', null, 'For the research side of things there would need to be approvals for working with human material, blood, cells etc. and working with HIV or the potential components, depending on the research there may be several groups that will look at the work including the IBC.  Research would need to be done in a BSL-2 space hopefully equipped with a biosafety cabinet.  The hazards with the research would of course be the human material as well as the virus or viral components. In the field there would be little opportunity for working aseptically unless the plan would be for a mobile lab to be in place. The best you can do there would be best practice or universal precautions, the idea being that you would treat all samples as potentially pathogenic or infectious, but there would likely not be an opportunity to set up a BSC or any type of clean work space.  You would want proper PPE which at a minimum would be clothes that cover skin (long sleeve etc.) gloves, eye protection and a lab coat.  Depending on how samples will be obtained there may be additional requirements needed.  All the waste should be hazardous material/biowaste, this means for the research side it will need to be autoclaved or disposed of in biohazard boxes.  For field work you would need to check country regulations since they often differ, but you would still want to consider it hazardous waste. Please let me know if I missed something or if anything needs clarification or if there is anything else I can help with.')
        )
      )
    )
  )

)
  ),

h(g.Section, {title: 'OUR APPROACH'},
    p('The reason why we chose to focus so heavily on education of younger students in our human practices is because we believe that a public educated in biotechnology and genetics starts at its roots. This meant attempting to spark some inspiration in younger students, which we believe we were successful in. They were so incredibly fascinated with the results of their experiments, and we believe that this is going to be a motivator for them the persue expanding their own knowledge.'),
    p('We focused on contacting people who have experience in diagnosing HIV-1 in the field because we knew that we would not have the opportunity to experience this ourselves, but the input from these individuals was still exceptionally valuable. We wanted to know what this diagnostic process was like and what the struggles were from someone who has spent time in that environment. We also contacted a people involved with policy and safety because HIV-1 is a dangerous disease and we realized that the kit and the process of using it (hypothetically) may have complications that we may not be able to see at first glance.')
  ),

h(g.Section, {title: 'INTEGRATION'},
    p('When conducting any research, it is important to understand the extent of its repercussions on various groups in society. In the planning stages of the project, we had a plan for the type of protocols we wanted to test, but we were looking for the correct purpose to use it for. With the tools in hand, we had discussed various diseases that we could target, but agreed upon focusing on HIV-1 detection in infants specifically. The reason was simple. HIV is a global health problem that affects millions all over the world. Its impact is especially prevalent over disadvantaged groups in low and middle-income countries. Thereby, we decided to improve the already existing tests available in these locations, by creating one better suited to the needs of the patients.'),
    p('The current antibody tests are not suited to testing newborn infants for HIV. In order to create a more accurate test, we used a different method of detection. Our proposed kit relies on HIV viral DNA and utilizes protocols that can be replicated in low resource environments as well. In order to better understand the currents testing protocols in rural locations, we discussed with Dr. Leautaud (who works with Rice Global Health) and a research fellow, Jessie Anderson on the current conditions. After reviewing the issues faced by patients in these locations, we were better able to focus our project to handle the problems. We learned that the hospitals were regularly understaffed, and the hospitals in the area (district hospitals) did not have adequate resources in the lab either. According to Dr. Leautaud’s experience, “In Malawi, there is no lab. They had a separate room with a fridge, centrifuge, agar plates, did not have pipettes or a vortexer; Eppendorf tubes and gloves were scarce.” In order to corroborate her statements, we discussed with Jessie who stated, “The neonatal wards for both QECH and KCH seemed understaffed, even for this season which is not the busiest of the year. There were two short (10-30 seconds long) power outages within 20 minutes in the KCH ward. KCH had more equipment available to them than QECH (much more incubators, radiant warmers, blue-lights, etc; I think also a higher proportion of the room heaters was working), but the flow and size of space available seemed better at QECH. Still not ideal at either location.” Throughout our conversations, it became increasingly clear that local hospitals did not have any substantial equipment.'),
    p('Additionally, when discussing with Dr. Leautaud, she mentioned that “One major problem in Africa or Malawi is that there is no communication and follow up with patients and the hospital, so even if a child is diagnosed the parent will not know. The hospitals don’t have the manpower to do that.” The mother’s that came to the hospitals often left soon after delivery, hence any testing results may not reach the mother, nor any future precautionary measures.  On top of short-staffed hospitals, many of the nurses or lab technicians that ran the test were not trained adequately. During discussions with Dr. Leautaud, she mentioned, “The nurse or lab technician, who is not as highly trained as they are in America. Instead, they have technical degrees. You need to teach them to not contaminate the test.” Upon learning of these various problems, we began integrating it into our project.'),
    p('Taking this into consideration, challenged ourselves to design a detection protocol that would utilize the least parts and would be able to withhold the most severe conditions. This would accommodate for the lack of resources that was discussed earlier with Dr. Leautaud. In order to integrate her advice into our lab work, we designed protocols utilizing lyophilized cellular reagents and decided to use LAMP for amplification purposes. The lyophilized reagents are stable as they do not need to be frozen, and LAMP amplification would only need a constant water bath, not a thermocycler like with PCR. Not only would this take the hospital’s capabilities into consideration, but it would offer our kit a competitive edge in the market as advised by Ms. Dawson. She recommended that in creating our kit to take into consideration the comfort level of the patient, but also to ensure that the kit is unique. The reason being, it would increase the chances for the kit to be sponsored by organizations, allowing the kit to be used by a larger clientele.'),
    p('Previously, Dr. Leautaud stated that “The test needs to be under 3 or 4 hours for the mother to stay in the hospital. In order to integrate this into our project, we designed a protocol that would fit this limit. The final protocol we decided upon would take about 3 hours to complete, allowing the mother to receive the results before her exit from the hospital. This would allow the hospital to provide additional information and would aid in the treatment of the infant.'),
    p('In terms of sterility, we created an educational training protocol to include with the kit which would help equalize any differences in training. In order to do so successfully, we reached out to a safety officer for advice (Dr. Singh) and consulted with an NGO official (Ms. Dawson) who offered information regarding HIV kits. Dr. Singh recommended that “ The best you can do there would be best practice or universal precautions, the idea being that you would treat all samples as potentially pathogenic or infectious, but there would likely not be an opportunity to set up a BSC or any type of clean workspace.  You would want proper PPE which at a minimum would be clothes that cover skin (long sleeve etc.) gloves, eye protection, and a lab coat. All the waste should be hazardous material/biowaste, this means for the research side it will need to be autoclaved or disposed of in biohazard boxes.”  This information proved valuable when creating our sample training protocol. Ms. Dawson provided us comparisons of HIV tests in order to differentiate ours and sent us example home tests that were on the market. After reviewing these existing solutions, we were able to clearly define the differences and advantages in our kit. With the information procured from the human practices part of the project, we were able to adapt our research to best suit the needs of the target group.')
  ),

h(g.Section, {title: 'END RESULT'},
    h('p', null, 'Our project targets an expansive disease and provides an opportunity for the most vulnerable groups to receive effective care, increasing their chances of survival. In many rural areas, disease, lack of food, and stable living conditions hinder the ability of forthcoming generations to prosper. With proper detection technology like our project, the future of these individuals can be secured, allowing them to live out their lives with one less hindrance. Not only do we aim to affect society, but society plays a large role in our project. By interacting with and understanding the problems that affect others in less fortunate locations, we can create more influential projects. Listening to the issues with communication brought forth other useful solutions such as the development of an app to serve as a mediator between the individual and the hospital. It is only by interacting with the community that we are able to understand their needs and devise solutions and projects that benefit the most people. Even a simple change in plan, like the addition of a training guide, could mean a world of difference to those who go through these problems every day.'),
    h('p', null, 'It is idealistic to think that simply conducting research will result in the development of a detection kit. Even with our research, there is still much that would need to be tested and implemented. Additionally, in order to implement these kits, we would require the financial backing of individuals. Thereby, even with functioning equipment, the cost and marketability of such products are equally important. When conversing with the NGO official on HIV detection kits, a recurring point that was brought up, was how is this kit different from the market and what is the cost. In this manner, the cost is especially important because our kit was developed to target those in the rural location who have a higher risk of HIV. Thereby, in order for this kit to be able to reach its target audience, the cost must be competitive with other existing models. Creating a kit with an idealistic purpose, but in reality, using the kit for those that can afford it undermine both the purpose and the ethics of such a project. In an effort to keep costs low, we utilized methods to efficiently organize the materials such as aliquoting to prevent contamination and only provide the necessary quantities. Similarly, the protocols for our kit do not require expensive machinery like other tests. This helps to not only keep the overall price low but allows us to use the kit in laboratories without much equipment. Throughout our project we have kept the protocols minimalistic but efficient, with the majority of material including cellular reagents and CRISPR complexes that are combined in microcentrifuge tubes; we have devised a protocol that suits our target audience and all others involved.')
  )
);

@@ Line 1: / Line 1: @@
 {{Austin_LASA}}
 <html>
+<head>
+<style>
+li {
+  line-height: normal;
+}
+.link {
+  padding: 0 !important;
+}
+</style>
+</head>
 <textarea id='page'>
+const p = t => h('p', null, t);
 h(g.Page, {title: 'Integrated Human Practices', prev: 'https://2018.igem.org/Team:Austin_LASA/Safety', next: 'https://2018.igem.org/Team:Austin_LASA/Model', selector: [5, 0]},
-   h('p', null, 'The LASA iGEM Team accomplished and carried out the following activities to count towards to Silver Medal Human Practices criterion and Best Integrated Human Practices Award:'),
+   h(g.Section, {title: 'SILVER MEDAL CRITERIA'},
-   h('br'),
+    p('We believe that our work is a positive impact because early detection of HIV-1 can lead to a reduction in mortality of up to 75%. Currently, the detection methods for HIV in resource deficient areas are time consuming or require a lot of resources and expertise. We have detailed this in the “Why HIV Detection in Infants” section of our Description page further. After realizing this problem, we wanted to make a quick and low resource method of detection, which led to our current project. The possibility of such a method reducing infant mortality is a possibility, which is nothing but a positive impact.'),
+    p('We investigated the struggles of HIV diagnosis by talking to someone who had traveled to Malawi and had experienced that environment. In our opinion, her direct experience was one of the best ways to investigate the issue. She discussed how the device must be relatively simple to use and be fast, as often people leave the clinic before they get the results back. The more we spoke to people, the more evident it was that a quick and simple kit was something that was an actual necessity. More details on these investigations can be found in the “Engaging with Experts” section of this page.'),
+    p('We also engaged with people who are vital to the process of HIV-1 diagnosis and an integral part of that community. We spoke to someone involved in HIV policy in order to help us understand the complexities of building a kit and how to ensure that it was truly beneficial in diagnosis. We also spoke to a biological safety officer in order to understand the disposal techniques and packaging methods in order to ensure that our kit would be used responsibly and have no negative effects that were preventable. More details on this HIV and safety community engagement can be found in the “Engaging with Experts” section of this page.'),
+    p('We chose this approach of interviewing people who had actually traveled to locations where our kit was needed because we thought that it would be the best way to get feedback that was personal and genuine. We feel as if we were successful in this, as the information they provided us was seemed much more personal than information gained from papers or other resources. We also interviewed safety and policy officials, as we felt like they would be able to provide a fresh perspective on our project. The team ourselves would not be able to catch every single minute detail that may have a negative impact considering we are not experts in the field. Therefore, we talked to experts who were able to make sure that our work was truly responsible and would have a positive impact.')
+  ),
+  h(g.Section, {title: 'GOLD MEDAL CRITERIA'},
+    p('Utilizing the information that we gained from various experts, we were able to finalize our laboratory protocols and decided to focus on protocols that did not require specific machinery. By doing so, we were able to divert from depending on large central labs, to doing detection within small rural hospitals, thereby increasing communication between the technicians and family. In response to sterility, we created a resource to establish a standard for universal precautions. To see a more detailed description of the designing and implementation please refer to the Integration section.')
+  ),
+   h(g.Section, {title: 'BEST INTEGRATED HUMAN PRACTICES SPECIAL PRIZE'},
+    p('Our project directly targets one of the most vulnerable groups to the HIV infection, infants in rural countries, and aims to provide a seamless solution to detecting this infection early on by using synthetic biology techniques. In doing so, we not only familiarize ourselves with local hospitals in order to understand common issues and better adapt, but we have considered implementation of our project from the viewpoint of a stakeholder. Thereby, all the protocols and materials used in this project were chosen with a specific goal in mind, more information on how our project best integrates the interest of all parties can be found in the “End Result” section.')
+  ),
+  h(g.Section, {title: 'CONSIDERED TOPICS'},
+    p('Our project was related to the detection of HIV-1 in infants. This gave us a lot of room to work with human practices topics. One of the major topics we wanted to look at was the education of the general public about synthetic biology. We considered numerous educational opportunities about synthetic biology and genetics with younger children, which we followed through with. Another topic we considered was informing ourselves about how people diagnosed with HIV in the United States feel about the process and general experience. We pursued the option of going to HIV-1 clinics, but unfortunately this was not possible for us due to the sensitive circumstances surrounding such an institution. Along with this, we wanted to focus on the topic of the struggles of HIV diagnosis and other low resource diagnoses. This led us talking to experts who have experience diagnosing HIV in the field and safety protocols, since we wanted to make sure that our kit would be safe.')
+  ),
+  h(g.Section, {title: 'ACTIVITIES'},
    h(g.Section, {title: 'Education and Outreach'},
      h('p', null, 'Our team was very active in reaching out to our local community, particularly to younger children. We’ve listed out below everything we’ve done.'),
@@ Line 17: / Line 42: @@
          h('ul', null,
            h('li', null, 'Members led 3-4 hour workshops in the Thinkery Museum, a children’s museum created to  help the new generation of innovators and creative problem solvers.'),
-           h('li', null, 'Workshops included the following the ', h('a', {href: 'https://www.genome.gov/pages/education/modules/strawberryextractioninstructions.pdf'}, 'procedure'), ' of the classic Strawberry DNA Lab')
+           h('li', null, 'Workshops included the following the ', h('a', {href: 'https://www.genome.gov/pages/education/modules/strawberryextractioninstructions.pdf', className: 'link'}, 'procedure'), ' of the classic Strawberry DNA Lab'),
+          h('li', null, 'During the lab, members discussed basic science concepts with children and parents and mentioned the field of synthetic biology to adults. This event was extremely successful as there were over 30 participants each session. The LASA iGEM team volunteered here for a total of about 8 hours each.'),
          )
+      ),
+      h('li', null, 'The LASA iGEM Team volunteered at the Summer Mad Science Camps in Austin (8/6/18-8/7/18)',
+        h('ul', null,
+          h('li', null, 'Austin Mad Science is a well known establishment with the goal of delivering unique, hands-on science experiences to children.'),
+          h('li', null, 'From 1:30 p.m. to 4:30 p.m. members of the LASA iGEM team helped the camp run by facilitating activities with kids and interacting with them about synthetic biology.'),
+          h('li', null, 'Activities are attached ', h('a', {href: 'https://austin.madscience.org/locations/austin/pdf/SummerCamp2018IAAAustin.pdf', className: 'link'}, 'here'), '.')
+        )
+      ),
+      h('li', null, 'The LASA iGEM Team conducted a short lab experiment with Clayton Elementary School on (10/5/18)',
+        h('ul', null,
+          h('li', null, 'LASA iGEM members went to Clayton Elementary and met with an afterschool science group to perform a simple DNA lab. Students had a great time learning about new scientific concepts and having hands-on experience with scientific tools.'),
+          h('li', null, 'Workshops included the following the ', h('a', {href: 'https://www.genome.gov/pages/education/modules/strawberryextractioninstructions.pdf', className: 'link'}, 'procedure'), ' of the classic Strawberry DNA Lab')
+        )
+      ),
+      h('li', null, 'The LASA iGEM Team went to a local elementary school, Laurel Mountain Elementary and talked about DNA, genetics and did the strawberry DNA extraction activity (the protocol in one of the sections above). The kids were super enthusiastic about the activity and even knew what the acronym DNA stands for at the end.',
+        h(g.Image, {src: 'https://static.igem.org/mediawiki/2018/1/1f/T--Austin_LASA--Strawberry1.jpg', position: 'center'},
+          h('p', null, 'Here’s some of our team members in the classroom, before performing the experiment with the class.')
+        ),
+        h(g.Image, {src: 'https://static.igem.org/mediawiki/2018/5/50/T--Austin_LASA--Strawberry2.jpg', position: 'center'},
+          h('p', null, 'Will helping a student filter their mixture in order to remove chunks. The kids enjoyed seeing the DNA form after rubbing alcohol was added.')
+        )
+      )
+    )
+  ),
+  h(g.Section, {title: 'Engaging with Experts'},
+    p('In order to learn more about the diagnosis of HIV and biosafety, we interviewed several experts in the field and have included the information they gave us below.'),
+  h(g.Section, {title: 'Dr. Veronica Leautaud, Ph. D.'},
+    'Director of Education',
+    h('br'),
+    'Rice 360 Institute for Global Health',
+    h('p', null, 'Dr. Leautaud is a professor at the Rice 360 Institute for Global Health and was able to provide the following feedback on our project and kit.'),
+    h('ul', null,
+      h('li', null, 'Discussion Regarding Blood Sample to LAMP Procedures',
+        h('ul', null,
+          h('li', null, 'Dr. Leautaud recommends that for the LAMP assay to start with white blood cells. If we begin with plasma, after lysing we will still want to have white blood cells present, but she adds that “The good thing about LAMP is that it is a robust amplification so you can still get away with lysing the WBC with a small amount of detergent or high temperature or some other mechanical approach without killing the LAMP enzymes. And without having to purify so much, normally [compared]  with PCR you need to clean it so much before the Taq polymerase works.”'),
+          h('li', null, 'Overall the initial starting point would be to start with whole blood, with both red and white cells, then lyse the white blood cells (what we are after for the double-stranded DNA template)')
+        )
+      ),
+      h('li', null, 'Blood Sample to Amplification Procedures/Advice',
+        h('ul', null,
+          h('li', null, 'Dr. Leautaud’s advice, “It is not trivial, but there are papers… There is one professor, David Kelso, he takes whole blood, takes a finger prick on a wet mount, flushes it with a bit of sodium hydroxide (diluted) which destroys the cells and even denatures the DNA a bit, but in the end results in clean DNA for easy sample prep.”'),
+          h('li', null, 'Overall, the means of procuring a blood sample and processing it until it is usable in amplification studies has its own challenges. In terms of our team, it would be in our best interest to focus on one part of the planned kit. Generally, in a larger lab, different individuals would work on various parts of such a kit, so it is not realistic to plan on developing a fully functional kit (in theory) with such limited resources and time. This part is best suited for a collaboration with another lab.')
+        )
+      ),
+      h('li', null, 'Dr. Leautaud’s Experience in Malawi',
+        h('ul', null,
+          h('li', null, 'Dr. Leautaud was developing a detection assay for HIV RNA in 2012 in which she focused on plasma (since it dealt with RNA).'),
+          h('li', null, 'She describes the workspace as follows, “In Malawi, there is no lab. They had a separate room with a fridge, centrifuge, agar plates, did not have pipettes or a vortexer; Eppendorf tubes and gloves were scarce.”',
+            h('ul', null,
+              h('li', null, '“There are centralized locations that will look at PCR, made out of blood spots that will be taken when a baby is born, it is analyzed by a large microbiology lab with all the staff and materials needed. Two types of locations, local labs with no or minimal resources and large centralized national lab.”'),
+              h('li', null, '“One major problem in Africa or Malawi is that there is no communication and follow up with patients and the hospital, so even if a child is diagnosed the parent will not know. The hospitals don’t have the manpower to do that.”')
+            )
+          ),
+          h('li', null, 'She describes various parameters that should be considered, “The test needs to be under 3 or 4 hours for the mother to stay in the hospital.',
+            h('ul', null,
+              h('li', null, ' You also need to keep in mind cost.'),
+              h('li', null, 'The third parameter is your user which would be the nurse or lab technician, who is not as highly trained as they are in America. Instead, they have technical degrees. You need to teach them to not contaminate the test. You need to be aware of the level of literacy and skill of the user. My test in Malawi was a fail, it was too sensitive and was always contaminated.'),
+              h('li', null, 'Dr. Leautaud sent materials with visiting staff to Malawi, used lyophilized reagents.',
+                h('ul', null,
+                  h('li', null, 'She mentions considering that most products will be kept at room temperature, so to keep that in mind when designing the project.')
+                )
+              ),
+              h('li', null, '“Be aware of the resources: whether you need electricity or will use battery powered machines?”',
+                h('ul', null,
+                  h('li', null, 'One research fellow that works with Dr. Leautaud mentions that she is planning on conducting a usability study to see if people in the area are willing to take time out of their schedule to learn how to use the technology/ device she created.'),
+                  h('li', null, 'important to consider public interest and involvement')
+                )
+              )
+            )
+          )
+        )
+      ),
+      h('li', null, 'Precautionary Measures to Prevent Contamination (Other than sending material directly)',
+        h('ul', null,
+          h('li', null, 'Dr. Leautaud mentions, “A good option is to aliquot your products or enzymes. You also need to make sure that when you are running your tests that you have a negative control, positive control, and sample.”'),
+          h('li', null, 'When she conducted her tests, Dr. Leautaud used synthetic oligos as a positive control  and plasma as the negative control. She would follow through the entire process with the controls, not just add it in at a certain step to make sure there was no contamination of the data.')
+        )
+      ),
+      h('li', null, 'Advice for Project Planning',
+        h('ul', null,
+          h('li', null, 'Dr. Leautaud recommended ordering LAMP immediately as it will take a while to arrive.'),
+          h('li', null, 'She recommends to focus on the sensitivity of assays (explains method on how to do so).',
+            h('ul', null,
+              h('li', null, '“Start from the beginning, when you are receiving a blood sample from a baby you most likely will do a heel prick which is no more than 50 microliters on a good day, if you do a venous draw, no doctor will allow you to have more than 0.1 mL. So how many white blood cells will be present? Assume that there will be 10 HIV copies in that 50 microliters of the blood sample, then you must look at LAMP; you have 20 microliter LAMP reaction and 50 microliters, so you can identify how much the HIV copies are present. From there you can identify how many copies you will need for the CRISPR assay to work and how many for the fluoresce to work (find the limit of detection of the LAMP assay).”')
+            )
+          ),
+          h('li', null, 'Dr. Leautaud recommends doing the experiment with the fluorophore specifically because even if it says that it is visible to the naked eye, it is important to identify the concentration that must be present for it to be visible?'),
+          h('li', null, 'She recommends to focus on the CRISPR assay with a really clear limit of detection and characterize the assay (do a dilution series of the assay).'),
+          h('li', null, 'Dr. Leautaud adds that we can consider a paper test instead of a test tube if that is better suited to our goal.'),
+        )
+      )
+    )
+  ),
+  h(g.Section, {title: 'Jessie Anderson'},
+    'Research Fellow',
+    h('br'),
+    'Rice 360 Institute for Global Health',
+    h('p', null, 'Ms. Anderson visited Malawi as preparation for her own validation study but was able to provide valuable insight into the conditions of the hospital and staff in other parts of the world. She was able to provide insight into the functionality the neonatal wards at two tertiary, referral hospitals and was able to give us the following feedback.'),
+    h('ul', null,
+      h('li', null, 'Would you be able to describe the setting of the hospitals that you visited? What were the conditions? How many staff and how well trained were they?',
+        h('ul', null,
+          h('li', null, 'The neonatal wards for both QECH and KCH seemed understaffed, even for this season which is not the busiest of the year. There were two short (10-30 seconds long) power outages within 20 minutes in the KCH ward. KCH had more equipment available to them than QECH (much more incubators, radiant warmers, blue-lights, etc; I think also a higher proportion of the room heaters was working), but the flow and size of space available seemed better at QECH. Still not ideal at either location. Both wards were segmented off into low-risk, high-risk, and isolation/quarantine areas or rooms. Every 2 hours the mothers come for feeding at both sites, and once every morning nurses go on rounds to check up on every patient (a doctor accompanies at QECH; they only come if called at KCH).'),
+          h('li', null, 'Overall the initial starting point would be to start with whole blood, with both red and white cells, then lyse the white blood cells (what we are after for the double-stranded DNA template)')
+        )
+      ),
+      h('li', null, 'Blood Sample to Amplification Procedures/Advice',
+        h('ul', null,
+          h('li', null, 'Dr. Leautaud’s advice, “It is not trivial, but there are papers… There is one professor, David Kelso, he takes whole blood, takes a finger prick on a wet mount, flushes it with a bit of sodium hydroxide (diluted) which destroys the cells and even denatures the DNA a bit, but in the end results in clean DNA for easy sample prep.”'),
+          h('li', null, 'As far as training, I am not able to know how well-trained the nurses are; every nurse in Malawi must go through a training provided by the COIN Manual, but I don’t know how often (if ever) it is repeated. For diagnosing of jaundice, talking with two different nurses at KCH yielded two different procedures in using the transcutaneous bilirubinometer (one answered us “I think everyone should be trained on it now..” and when asked how often it was calibrated “I have never seen it calibrated” – if it is supposed to be used the same as a very similar device, t is supposed to be calibrated every use).'),
+          h('li', null, 'KCH is better staffed 24/7. At QECH, there are 3-4 nurses during the weekday, and 2 overnight and on weekends. The study nurse who was there told us 75% of deaths occur overnight.')
+        )
+      ),
+      h('li', null, 'Are the hospitals equipped to handle diagnostic studies? How knowledgeable were the staff or patients on diagnostic testing/ how willing are they to get them done?',
+        h('ul', null,
+          h('li', null, 'Both of these central hospitals have partnered with various universities and organizations throughout the years to complete studies. Rice itself has primarily partnered with the neonatal and maternity wards of QECH over the past 10 years (starting with bubble CPAP), and other organizations (like Baylor and UNC-Chapel Hill) have done some work at KCH, though I’m not sure exactly what studies they’ve done. UNC has a permanent building at KCH, as does Rice and the Liverpool Welcome Trust at QECH. There is also currently a sepsis diagnostic study occurring at KCH as with another group funded by Greater Challenges Canada.'),
+          h('li', null, 'The staff is knowledgeable at both locations of diagnostic tests; both QECH and KCH are very supportive of the BiliSpec jaundice-diagnostic study (we’ve met with the department heads of both locations as well as other clinicians). Also, because the grant that funds our study provides stipends for the nurses who work with us, they are willing to work beyond their normal work hours to have another source of income.'),
+          h('li', null, 'Are there any problems with sanitation, resources, or communication that is present?',
+            h('ul', null,
+              h('li', null, 'The sanitation and resources at both central hospitals are not the same that’s present in the US (or most western) hospitals. That being said, nurses are supposed to use available hand sanitizer before and after each time they interact/touch a patient, and gloves and biohazard bins are used when drawing blood or performing heelpricks. As far as communication, the data management is not consistent or as thorough as in western hospitals. I think that is one of the biggest obstacles in performing studies in such an environment. For the BiliSpec study (and most studies should do this anyway), we will be providing all our material resources (i.e. devices, consumables like gloves and needles among other, computer, desk/chair, wifi dongle as wifi is not available, etc).')
+            )
+          )
+        )
+      )
+    )
+  ),
+  h(g.Section, {title: 'Lindsey Dawson'},
+    'Associate Director, HIV Policy',
+    h('br'),
+    'Kaiser Family Foundation',
+    h('p', null, 'Ms. t will accompany our kit'),
+    h('ul', null,
+      h('li', null, 'She details on how understanding the importance of detection is important, but how it is equally important to consider the steps that should be taken to get treatment afterward (eg. antiretroviral treatment)'),
+      h('li', null, 'Sent the following information (even though the CDC material is focused on US primarily)',
+        h('ul', null,
+          h('li', null, h('a', {href: 'https://stacks.cdc.gov/view/cdc/23447'}, 'CDC recommendations on Lab testing for HIV')),
+          h('li', null, h('a', {href: 'https://www.cdc.gov/hiv/pdf/testing/hiv-tests-laboratory-use.pdf'}, 'Lab tests')),
+          h('li', null, h('a', {href: 'https://www.cdc.gov/hiv/pdf/testing/rapid-hiv-tests-non-clinical.pdf'}, 'Rapid tests')),
+          h('li', null, h('a', {href: 'https://www.cdc.gov/hiv/pdf/testing/hiv-tests-advantages-disadvantages_1.pdf   '}, 'Advantages/Disadvantages to different HIV tests')),
+          h('li', null, h('a', {href: 'https://stacks.cdc.gov/view/cdc/50872'}, 'Recommended testing algorithm')),
+          h('li', null, h('a', {href: 'https://www.cdc.gov/hiv/testing/laboratorytests.html'}, 'More info here (incl. all the above links)')),
+          h('li', null, h('a', {href: 'http://www.oraquick.com/What-is-OraQuick/OraQuick-In-Home-HIV-Test'}, 'OraSure’s home test')),
+          h('li', null, h('a', {href: 'http://aidsinfo.unaids.org/'}, 'To see hardest hit countries, including where share of people unaware of their HIV status is highest (i.e. undiagnosed)'))
+        )
+      )
+    )
+  ),
+  h(g.Section, {title: 'Christopher R Singh'},
+    'Biological Safety Officer, MS, Ph.D.',
+    h('br'),
+    'The University of Texas at Austin',
+    h('br'),
+    'Environmental Health and Safety',
+    h('p', null, 'Dr. Singh served as our guide for various safety concerns and was able to provide us information on various regulations as follows.'),
+    h('ul', null,
+      h('li', null, 'Based on the procedures and information provided, are there specific clearances or hazards that we need to be aware of?'),
+      h('li', null, 'What is the best way to handle blood spots or DNA samples when using a detection kit? What are things that we should keep in mind for creating the most aseptic and safe kit?'),
+      h('li', null, 'What are the best disposal or packaging methods when the goal is to use kits such as these overseas in non-lab environments?',
+        h('ul', null,
+          h('li', null, 'For the research side of things there would need to be approvals for working with human material, blood, cells etc. and working with HIV or the potential components, depending on the research there may be several groups that will look at the work including the IBC.  Research would need to be done in a BSL-2 space hopefully equipped with a biosafety cabinet.  The hazards with the research would of course be the human material as well as the virus or viral components. In the field there would be little opportunity for working aseptically unless the plan would be for a mobile lab to be in place. The best you can do there would be best practice or universal precautions, the idea being that you would treat all samples as potentially pathogenic or infectious, but there would likely not be an opportunity to set up a BSC or any type of clean work space.  You would want proper PPE which at a minimum would be clothes that cover skin (long sleeve etc.) gloves, eye protection and a lab coat.  Depending on how samples will be obtained there may be additional requirements needed.  All the waste should be hazardous material/biowaste, this means for the research side it will need to be autoclaved or disposed of in biohazard boxes.  For field work you would need to check country regulations since they often differ, but you would still want to consider it hazardous waste. Please let me know if I missed something or if anything needs clarification or if there is anything else I can help with.')
+        )
        )
      )
+  )
+  )
+  ),
+  h(g.Section, {title: 'OUR APPROACH'},
+    p('The reason why we chose to focus so heavily on education of younger students in our human practices is because we believe that a public educated in biotechnology and genetics starts at its roots. This meant attempting to spark some inspiration in younger students, which we believe we were successful in. They were so incredibly fascinated with the results of their experiments, and we believe that this is going to be a motivator for them the persue expanding their own knowledge.'),
+    p('We focused on contacting people who have experience in diagnosing HIV-1 in the field because we knew that we would not have the opportunity to experience this ourselves, but the input from these individuals was still exceptionally valuable. We wanted to know what this diagnostic process was like and what the struggles were from someone who has spent time in that environment. We also contacted a people involved with policy and safety because HIV-1 is a dangerous disease and we realized that the kit and the process of using it (hypothetically) may have complications that we may not be able to see at first glance.')
+  ),
+  h(g.Section, {title: 'INTEGRATION'},
+    p('When conducting any research, it is important to understand the extent of its repercussions on various groups in society. In the planning stages of the project, we had a plan for the type of protocols we wanted to test, but we were looking for the correct purpose to use it for. With the tools in hand, we had discussed various diseases that we could target, but agreed upon focusing on HIV-1 detection in infants specifically. The reason was simple. HIV is a global health problem that affects millions all over the world. Its impact is especially prevalent over disadvantaged groups in low and middle-income countries. Thereby, we decided to improve the already existing tests available in these locations, by creating one better suited to the needs of the patients.'),
+    p('The current antibody tests are not suited to testing newborn infants for HIV. In order to create a more accurate test, we used a different method of detection. Our proposed kit relies on HIV viral DNA and utilizes protocols that can be replicated in low resource environments as well. In order to better understand the currents testing protocols in rural locations, we discussed with Dr. Leautaud (who works with Rice Global Health) and a research fellow, Jessie Anderson on the current conditions. After reviewing the issues faced by patients in these locations, we were better able to focus our project to handle the problems. We learned that the hospitals were regularly understaffed, and the hospitals in the area (district hospitals) did not have adequate resources in the lab either. According to Dr. Leautaud’s experience, “In Malawi, there is no lab. They had a separate room with a fridge, centrifuge, agar plates, did not have pipettes or a vortexer; Eppendorf tubes and gloves were scarce.” In order to corroborate her statements, we discussed with Jessie who stated, “The neonatal wards for both QECH and KCH seemed understaffed, even for this season which is not the busiest of the year. There were two short (10-30 seconds long) power outages within 20 minutes in the KCH ward. KCH had more equipment available to them than QECH (much more incubators, radiant warmers, blue-lights, etc; I think also a higher proportion of the room heaters was working), but the flow and size of space available seemed better at QECH. Still not ideal at either location.” Throughout our conversations, it became increasingly clear that local hospitals did not have any substantial equipment.'),
+    p('Additionally, when discussing with Dr. Leautaud, she mentioned that “One major problem in Africa or Malawi is that there is no communication and follow up with patients and the hospital, so even if a child is diagnosed the parent will not know. The hospitals don’t have the manpower to do that.” The mother’s that came to the hospitals often left soon after delivery, hence any testing results may not reach the mother, nor any future precautionary measures.  On top of short-staffed hospitals, many of the nurses or lab technicians that ran the test were not trained adequately. During discussions with Dr. Leautaud, she mentioned, “The nurse or lab technician, who is not as highly trained as they are in America. Instead, they have technical degrees. You need to teach them to not contaminate the test.” Upon learning of these various problems, we began integrating it into our project.'),
+    p('Taking this into consideration, challenged ourselves to design a detection protocol that would utilize the least parts and would be able to withhold the most severe conditions. This would accommodate for the lack of resources that was discussed earlier with Dr. Leautaud. In order to integrate her advice into our lab work, we designed protocols utilizing lyophilized cellular reagents and decided to use LAMP for amplification purposes. The lyophilized reagents are stable as they do not need to be frozen, and LAMP amplification would only need a constant water bath, not a thermocycler like with PCR. Not only would this take the hospital’s capabilities into consideration, but it would offer our kit a competitive edge in the market as advised by Ms. Dawson. She recommended that in creating our kit to take into consideration the comfort level of the patient, but also to ensure that the kit is unique. The reason being, it would increase the chances for the kit to be sponsored by organizations, allowing the kit to be used by a larger clientele.'),
+    p('Previously, Dr. Leautaud stated that “The test needs to be under 3 or 4 hours for the mother to stay in the hospital. In order to integrate this into our project, we designed a protocol that would fit this limit. The final protocol we decided upon would take about 3 hours to complete, allowing the mother to receive the results before her exit from the hospital. This would allow the hospital to provide additional information and would aid in the treatment of the infant.'),
+    p('In terms of sterility, we created an educational training protocol to include with the kit which would help equalize any differences in training. In order to do so successfully, we reached out to a safety officer for advice (Dr. Singh) and consulted with an NGO official (Ms. Dawson) who offered information regarding HIV kits. Dr. Singh recommended that “ The best you can do there would be best practice or universal precautions, the idea being that you would treat all samples as potentially pathogenic or infectious, but there would likely not be an opportunity to set up a BSC or any type of clean workspace.  You would want proper PPE which at a minimum would be clothes that cover skin (long sleeve etc.) gloves, eye protection, and a lab coat. All the waste should be hazardous material/biowaste, this means for the research side it will need to be autoclaved or disposed of in biohazard boxes.”  This information proved valuable when creating our sample training protocol. Ms. Dawson provided us comparisons of HIV tests in order to differentiate ours and sent us example home tests that were on the market. After reviewing these existing solutions, we were able to clearly define the differences and advantages in our kit. With the information procured from the human practices part of the project, we were able to adapt our research to best suit the needs of the target group.')
+  ),
+  h(g.Section, {title: 'END RESULT'},
+    h('p', null, 'Our project targets an expansive disease and provides an opportunity for the most vulnerable groups to receive effective care, increasing their chances of survival. In many rural areas, disease, lack of food, and stable living conditions hinder the ability of forthcoming generations to prosper. With proper detection technology like our project, the future of these individuals can be secured, allowing them to live out their lives with one less hindrance. Not only do we aim to affect society, but society plays a large role in our project. By interacting with and understanding the problems that affect others in less fortunate locations, we can create more influential projects. Listening to the issues with communication brought forth other useful solutions such as the development of an app to serve as a mediator between the individual and the hospital. It is only by interacting with the community that we are able to understand their needs and devise solutions and projects that benefit the most people. Even a simple change in plan, like the addition of a training guide, could mean a world of difference to those who go through these problems every day.'),
+    h('p', null, 'It is idealistic to think that simply conducting research will result in the development of a detection kit. Even with our research, there is still much that would need to be tested and implemented. Additionally, in order to implement these kits, we would require the financial backing of individuals. Thereby, even with functioning equipment, the cost and marketability of such products are equally important. When conversing with the NGO official on HIV detection kits, a recurring point that was brought up, was how is this kit different from the market and what is the cost. In this manner, the cost is especially important because our kit was developed to target those in the rural location who have a higher risk of HIV. Thereby, in order for this kit to be able to reach its target audience, the cost must be competitive with other existing models. Creating a kit with an idealistic purpose, but in reality, using the kit for those that can afford it undermine both the purpose and the ethics of such a project. In an effort to keep costs low, we utilized methods to efficiently organize the materials such as aliquoting to prevent contamination and only provide the necessary quantities. Similarly, the protocols for our kit do not require expensive machinery like other tests. This helps to not only keep the overall price low but allows us to use the kit in laboratories without much equipment. Throughout our project we have kept the protocols minimalistic but efficient, with the majority of material including cellular reagents and CRISPR complexes that are combined in microcentrifuge tubes; we have devised a protocol that suits our target audience and all others involved.')
    )
 );
 </textarea>
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