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Data Rules: Looking Inside the Pandemic Prevention Institute with Kaitlyn Johnson

Inside Precision Medicine sits down with Kaitlyn Johnson, PhD, senior data analyst at The Rockefeller Foundation’s Pandemic Prevention Institute (PPI),…



Inside Precision Medicine sits down with Kaitlyn Johnson, PhD, senior data analyst at The Rockefeller Foundation’s Pandemic Prevention Institute (PPI), where her work leverages data analysis and modeling to provide real-time guidance to individuals and decision-makers to prevent and mitigate pandemics. Johnson is an interdisciplinary researcher passionate about developing quantitative solutions to improve public health and medicine.

Johnson completed her PhD in biomedical engineering at the University of Texas at Austin in April 2020, just as the COVID-19 pandemic was taking off. During her graduate work, she worked in a systems biology lab that developed genomic-based tools to better understand treatment of cancer cells. More specifically, they developed technologies to track cancer cell lineages, developing linkages between genotype and phenotype.

Johnson worked on the data analysis side—integrating the outputs from sequencing data with longitudinal data of cancer cell populations over time to understand how they responded to drugs and developed chemotherapy resistance.

She started working at the UT COVID-19 Modeling Consortium led by Lauren Ancel Meyers, PhD, for her postdoc, using models of infectious disease dynamics helping to provide situational awareness and scenario-based projections to help guide the pandemic response for UT and the city of Austin.

She joined PPI last year to build upon her previous work, and to develop it into tools so that others—outside of close-knit collaborators—could leverage it. Her goal was to combine the science with the product and technology side of the world—to make tools from some of the academic science she was immersed in.

We asked Johnson about her work, the PPI, COVID-19, and future pandemics.

This interview has been edited for clarity and length.


LeMieux: I know that your work revolves around data and decision making. Can you explain it in a bit more detail?

Kaitlyn Johnson, PhD
Senior Data Analyst
The Rockefeller Foundation Pandemic Prevention Institute

Johnson: Let me start by saying that we’re not developing policy. What we’re doing is analysis to help inform policy. That said, we are always considering policy in our work.

When I’m conceptualizing a data to action pipeline, I think of this question in terms of three different buckets.

The first bucket is “now casting” or understanding the current state. What state are we in and what are we dealing with? In the example of a new emerging pathogen, this includes questions such as, what is the basic reproductive number (Rº) of that pathogen? What is the effectiveness of vaccination? What are these properties that help us to be able to answer the policy questions? We need to have a baseline to dive into effects of policy on the epidemic context.

The second bucket is forecasting. Based on current trends, what do we think is going to happen? In pandemic forecasting, this is challenging because it is affected by human behavior, and it is hard to predict human behavior. So, forecasting tends to be only within the next two to three weeks—what do we think is going to happen based on what the data are telling us?

The last bucket, which is more on the side of informing policy, is the decision-making part of our analysis. This is where we might make scenario-based projections to assess the effect of different policies, where we try and mathematize what a policy is. One example would be analyzing different vaccine allocation strategies based on age, geography, or other factors— and the effects of the speed and timing of those rollouts on health outcomes. Another example, and something that was done at the PPI, was to analyze the difference between requiring COVID-19 rapid tests or COVID-19 vaccines at an event, to see what mitigation measures, or combination of measures, are better at preventing event attendees from arriving infected.

Again, we are not saying, this is what you should do. We’re saying, here is the evidence to empower you to decide.


LeMieux: How is your work communicated so that it can be implemented? How do you close that gap?

Johnson: In some cases, after we have built a tool, we write an accompanying blog post. In there, we can clarify what we recommend based on the analysis. Like writing a scientific paper… the results are separate from the interpretation. Both parts can empower the public to have the evidence basis to make the informed decision.

Having the quantitative evidence, we think, can enable someone to point to that tool when talking to friends and family. They can say, this is what the analysis shows and because of this, I’m going ask you to take a test before you come over to my holiday dinner.


LeMieux: How does the PPI communicate your findings?

Johnson: That is one of the major challenges that we face as a broader public health community. We must make these tools so useful that everyone is willing and wants to use them. There’s always a tension between the complexity of the scientific message and the need for something that is easily communicated and interpretable.

One of the analogies that we think about is the weather app. People use it daily; it helps guide their daily decision-making. Because people are so reliant on weather forecasts, it encourages the collection and submission of data to the system. The idea that we have, as an Institute, is to have that type of desire for these tools within both the public and among decision makers. And that requires us working with them, answering the questions that they are most interested in, and presenting it all in a user-friendly way.

We think a lot about how to make our findings interpretable to the public so that they will be more easily accessed and how we can make them more widely available to people across the globe. It will be more impactful with a wider reach.


LeMieux: How do you feel when the evidence-based measures that you recommend are not implemented, or totally disregarded? 

Johnson: What motivates me, and keeps me going, is the science.

The challenge is finding how we can meet the person or the community that we’re trying to serve where they are, and how to figure out the key questions that they’re interested in. Instead of sitting at our desk and presuming we know what people need.

For example, I did a lot of work in my postdoc supporting university policies. We found that the university had differing concerns outside of the realms of a pure health perspective. We were focused on the level of infection while they were more interested in absenteeism, quarantine time, and the costs of testing that we had not originally considered. So, we incorporated those into our analysis.


LeMieux: The pandemic is changing all the time. How do you factor in the constant change?

Johnson: The PPI has partnerships that allow us to work directly with people. And we are looking to develop tools for not just high-income countries, but also lower- and middle-income countries. We need to figure out what are the questions that they need answered? What are the types of tools that they’re looking for? We must make sure that the policy options that we are trying to mathematize, and demonstrate, are relevant to them. For example, emphasizing COVID-19 testing is not useful if tests are not readily available. So, we need to think about other policy options that we can think about incorporating. And when their needs and questions change, so too must our methods adapt to reflect this.


LeMieux: What have you learned over the past year? And what do you think about, going forward?

Johnson: We have learned the importance of interdisciplinary collaboration across sectors. That is, taking the pandemic science of academia, incorporating cost effectiveness and economic modeling, putting the communications aspect at the forefront, adding in the user center design, and then making that all into something that is production ready and scalable.

Because SARS-CoV-2 was a novel virus, those tools were not in place at the start of the pandemic. What we are trying to do is to set up those systems for currently circulating

pathogens and for novel pathogens. We want to be able to pipe in new data, answer those questions quickly, and then communicate quickly.

In general, the scientific community struggles to communicate uncertainty. So, we need to be able to say that this is what we think might happen, based on these sets of assumptions, and with a lot of uncertainty in how this could play out. Because all of it is dynamic and constantly changing. Being adaptable, while also being clear on your message, is important.


LeMieux: Do you anticipate a break after COVID-19? Or do you prepare for one new emerging pathogen after another, going forward?

Johnson: There are so many other pathogens, including endemic viruses, that could use better response tools. We’re hoping to build from what is currently circulating to be able to respond to, and have early detection of, new pathogens too.

That is some of the work that we’ve been doing in wastewater surveillance. It is multi-pathogen testing so that we could have a better idea of the baseline levels of these circulating pathogens from wastewater, and readily modify them for novel or re-emerging pathogens.


LeMieux: What keeps you up at night?

Johnson: The effect of climate change and its interaction with zoonotic spillover. In the past, we had a major respiratory pandemic every hundred years. But will that rate accelerate? And will we start to see more novel emerging pathogens because of changes in the environment that are driving movement of species into different regions?


LeMieux: I just read a Nature paper on exactly this. It is entitled, “Climate change increases cross-species viral transmission risk.”

Johnson: One of the other data analysts on our team worked closely with that first author (Carlson et al.). We’ve been thinking about it a lot. What keeps me up at night is how we are going to handle this moving forward as a society.


Julianna LeMieux, has been a science writer at GEN/IPM for four years where she covers synthetic biology genomics infectious disease, genome editing, and more. Previously, she spent years training at the bench while studying pathogenic bacteria during her PhD and postdoc. She has a passion for explaining complicated scientific concepts to a wide variety of audiences.

The post Data Rules: Looking Inside the Pandemic Prevention Institute with Kaitlyn Johnson appeared first on Inside Precision Medicine.

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Nonprofit Blood Donation Service Starts Matching Unvaccinated Patients With Donors

Nonprofit Blood Donation Service Starts Matching Unvaccinated Patients With Donors

Authored by Allan Stein via The Epoch Times (emphasis ours),




Nonprofit Blood Donation Service Starts Matching Unvaccinated Patients With Donors

Authored by Allan Stein via The Epoch Times (emphasis ours),

Swiss naturopathic physician George Della Pietra believes people worldwide should be free to choose whether to get a COVID-19 vaccine injection or not.

He believes the same should hold for those receiving transfusions with “vaccinated” blood.

“The problem is right now we have no choice,” said Della Pietra, founder of the nonprofit Safe Blood Donation service in 2021, matching unvaccinated blood recipients with donors in 65 countries.

“It was very clear from the beginning that the COVID hype was way out of control,” Della Pietra said. “It was not as dangerous as they say it was.

“As a naturopath, I can make no sense of this pandemic, which was never really a pandemic. It leaves space for so many explanations.”

Della Pietra believes that an mRNA injection is more dangerous than the pharmaceutical companies are willing to admit. He said the growing numbers of adverse reactions are reason to question their safety and effectiveness.

Data from the Centers for Disease Control and Prevention (CDC) showed that vaccinated and boosted people made up 58.6 percent (6,512) of the COVID-19 deaths in August—up from 41 percent in January.

We can no longer say this is a pandemic of the unvaccinated,” Cynthia Cox, the Vice President of the Kaiser Family Foundation told The Washington Post in an article on Nov. 23.

Nearly 70 percent of the world’s 8 billion people have received at least one mRNA injection for COVID-19 since the vaccines began rolling out in 2021 at the height of the virus’s spread.

Each of the three primary mRNA COVID-19 vaccines contains COVID-19 “spike protein” fragments, which bind at the cellular level to stimulate an immune response to the virus.

Della Pietra believes these spike proteins produce “classic symptoms”—namely blood clots—that “horrified” him.

“I’ve never seen anything similar—and I’m not talking only about spike proteins,” Della Pietra told The Epoch Times in a phone interview.

It’s unbelievable because we never had this problem before. It’s been only two years. They want to keep the narrative [that an mRNA vaccine] is not dangerous.”

A man looks at his phone while donating blood at Vitalant blood donation center in San Francisco on Jan. 11, 2022. (Justin Sullivan/Getty Images)

Although donated blood and plasma must undergo a cleansing process before transfusion, Safe Blood Donation says this is not enough to remove all mRNA ingredients.

“I’m talking about graphene oxide and non-declared inorganic components in the vaccine, which we can see in the blood. When I see them, I have no idea how we can get rid of them again,” Della Pietra said.

Looking at the abnormalities in vaccinated blood, he said, “OK, we have a problem.” People are receiving the vaccine “more or less through the back door.”

“You can not avoid it anymore.”

In the United States alone, there are approximately 16 million units of donated blood annually. Of those units, about 643,000 are “autologous”—self-donated—and the number is increasing yearly, according to

Della Pietra said that, to his knowledge, Safe Blood Donation, based in Switzerland, is the first unvaccinated blood donation service of its kind.

“So, there is no blood bank with mRNA-free blood yet, not even with us,” Safe Blood Donation states on its website.

“And, although we have already asked hundreds of clinics, at the moment—at least in Europe—all of them still refuse to allow the human right of free blood choice with them—or at least do not want to be mentioned because otherwise, they fear reprisals.”

A nurse works as employees donate blood during a blood drive held in a bloodmobile in Los Angeles on March 19, 2020. (Mario Tama/Getty Images)

Della Pietra said the main goal of Safe Blood Donation is not to start an mRNA-free blood bank. Rather, it is to make it possible to match unvaccinated blood donors and unvaccinated recipients, “which we bring together in a clinic (medical partner) that allows the choice of blood donor.”

Medical website Seed Scientific said that blood banks and biotech companies will offer as much as $1,000 monthly for blood donations.

While Della Pietra said there are no unvaccinated blood banks, he sees the demand for unvaccinated blood rising.

This is why I decided to do [SafeBlood Donation]. I wanted to make a network for unvaccinated people looking for a blood donor because they need it—whether they have scheduled surgery or an emergency,” he said.

Safe Blood Donation began working in the United States about a month ago, building an infrastructure of medical partners.

However, in the current medical environment, central blood banks such as the Red Cross do not segregate their blood donations based on their vaccinated or unvaccinated status.

Rendering of SARS-CoV-2 spike proteins binding to ACE2 receptors. (Shutterstock)

“The American Red Cross does not facilitate designated donations for standard blood needs, as this process often takes longer and is more resource intensive than obtaining a blood product through our normal process,” the Red Cross told The Epoch Times in an email.

In a small number of situations, there is an exception for rare blood types where compatible blood types are extremely difficult to find. A rare blood type is defined as one that is present in less than 1/1000 people.

“We want to emphasize that the Red Cross adheres to all donor and product requirements as determined by the FDA to ensure the safety of the blood supply and is committed to continuing to provide life-saving blood products for patients across the country.”

The National Library of Medicine said that “across study sites, the average hospital cost per unit transfused was $155 and the average charge per patient was $219.”

Still, the Red Cross, which provides 40 percent of the nation’s blood donations, said “no studies” demonstrate adverse outcomes from transfusions of blood products collected from vaccinated donors.

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Tyler Durden Sun, 12/04/2022 - 20:55

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Pedestrians choose healthy obstacles over boring pavements, study finds

Up to 78% of walkers would take a more challenging route featuring obstacles such as balancing beams, steppingstones and high steps, research has found….



Up to 78% of walkers would take a more challenging route featuring obstacles such as balancing beams, steppingstones and high steps, research has found. The findings suggest that providing ‘Active Landscape’ routes in urban areas could help tackle an “inactivity pandemic” and improve health outcomes.

Credit: Anna Boldina

Up to 78% of walkers would take a more challenging route featuring obstacles such as balancing beams, steppingstones and high steps, research has found. The findings suggest that providing ‘Active Landscape’ routes in urban areas could help tackle an “inactivity pandemic” and improve health outcomes.

[A copy of the paper and images can be downloaded here]

Millions of people in the UK are failing to meet recommended targets for physical activity. Exercising “on the go” is key to changing this but while walking along a pavement is better than nothing it causes no significant increase in heart rate so only qualifies as mild exercise. Walking also fails to significantly improve balance or bone density, unless it includes jumping, balancing, and stepping down.

But would adults opt for such ‘fun’ routes if given the choice? A University of Cambridge-led study published today in the journal Landscape Research suggests that with the right design, most would.

Previous research on ‘healthy route choices’ has focused on people’s likelihood of walking instead of using transport. But this study examined how likely people are to pick a more challenging route over a conventional one and which design characteristics influenced their choices.

Lead author, Anna Boldina, from the University of Cambridge’s Department of Architecture, said: “Even when the increase in level and extent of activity level is modest, when millions of people are using cityscapes every day, those differences can have a major positive impact on public health.”

“Our findings show that pedestrians can be nudged into a wider range of physical activities through minor changes to the urban landscape. We want to help policy makers and designers to make modifications that will improve physical health and wellbeing.”

Boldina began this research after moving from Coimbra in Portugal – where she found herself climbing hills and ancient walls – to London, which she found far less physically challenging.

Working with Dr Paul Hanel from the Department of Psychology at the University of Essex, and Prof. Koen Steemers from Cambridge, Boldina invited almost 600 UK residents to compare photorealistic images of challenging routes – variously incorporating steppingstones, balancing beams, and high steps – with conventional pavements.

Participants were shown images of challenging and conventional tarmac routes and asked which route they would choose. The researchers tested out a range of encouraging / discouraging parameters in different scenarios, including crossing water, shortcuts, unusual sculptures and the presence / absence of a handrail and other people. Participants were asked to score how challenging they thought the route would be from 1 (as easy as walking on level tarmac) to 7 (I would not be able to do it).

Eighty per cent of the study’s participants opted for a challenging route in at least one of the scenarios, depending on perceived level of difficulty and design characteristics. Where a challenging option was shorter than a conventional route, this increased the likelihood of being chosen by 10%. The presence of handrails achieved a 12% rise.

Importance for health

The WHO and NHS recommend at least 150 minutes of ‘moderate’ or 75 minutes of ‘vigorous’ activity spread over a week, including a variety of activities aimed at enhancing bones, muscles, and agility to stay healthy. In addition, adults over 65 are advised to perform strength, flexibility, and balance exercises.

Boldina said: “The human body is a very complex machine that needs a lot of things to keep working effectively. Cycling and swimming are great for your heart and for your leg muscles but do very little for your bone density.”

“To improve cardiovascular health, bone density and balance all at once, we need to add a wider range of exercises into our routine daily walks.”

Psychology of choice

Co-author Dr Paul Hanel said: “Children don’t need much encouragement to try out a balance beam but we wanted to see how adults would respond, and then identify design modifications which made them more likely to choose a challenging route.”

“We found that while embarrassment, anxiety, caution and peer pressure can put some adults off, the vast majority of people can be persuaded to take a more challenging route by paying careful attention to design, safety, difficulty level, location and signage.”

The proportion of participants who were willing to pick a more challenging route varied from 14% for a particular balance beam route to 78% for a route involving wide, low stepping stones and a log with a handrail. The least intimidating routes were found to be those with wide, steady-looking balancing beams and wide steppingstones, especially with the presence of handrails.

The researchers suggest that routes that incorporate more difficult challenges, such as obstacle courses and narrow balancing beams, should be placed in areas more likely to be frequented by younger users.

The participants expressed a range of reasons for picking challenging routes. Unsurprisingly, the study found that challenging routes which also acted as short cuts appealed. Up to 55% of participants chose such routes. The researchers also found that the design of pavements, lighting and flowerbeds, as well as signage helped to nudge participants to choose more challenging routes. Many participants (40%) said the sight of other people taking a challenging route encouraged them to do the same.

The participants who picked conventional routes often had concerns about safety but the introduction of safety measures, such as handrails, increased uptake of some routes. Handrails next to one steppingstones route increased uptake by 12%.

To test whether tendency to choose challenging routes was linked to demographic and personality factors, participants were asked to answer questions about their age, gender, habits, health, occupation, and personality traits (such as sensation seeking or general anxiety).

The researchers found that people of all levels of activity are equally likely to pick a challenging route. But for the most difficult routes, participants who regularly engaged in strength and balancing exercises were more likely to choose them.

Older participants were as supportive of the concept as younger ones but were less likely to opt for the more challenging routes for themselves. Nevertheless, across all age groups, only a small percentage of participants said they would avoid adventurous options completely.

The study applies the idea of “Choice Architecture” (making good choices easier and less beneficial choices harder) plus “Fun theory”, a strategy whereby physical activity is made more exciting; as well as some of the key principles of persuasion: social proof, liking, authority, and consistency.

Future work

The researchers hope to run experiments in physical test sites to see how intentions convert into behaviour, and to measure how changes in habits improve health. In the meantime, Dr Boldina continues to present her findings to policy makers.

Critics might question the affordability and cost effectiveness of introducing ‘Active landscape routes’ in the current economic environment.

In response, the researchers argue that installing stepping stones in a turfed area can be cheaper than laying and maintaining conventional tarmac pavements. They also point out that these measures could save governments far greater sums by reducing demand for health care related to lack of exercise.


A. Boldina et al., ‘Active Landscape and Choice Architecture: Encouraging the use of challenging city routes for fitness’, Landscape Research (2022). DOI: 10.1080/01426397.2022.2142204

Media contact

Tom Almeroth-Williams, Communications Manager (Research), University of Cambridge: / tel: +44 (0) 7540 139 444

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Apple Accelerates Plans To Shift Production Out Of China

Apple Accelerates Plans To Shift Production Out Of China

Apple has accelerated plans to shift some of its production outside of China, the…



Apple Accelerates Plans To Shift Production Out Of China

Apple has accelerated plans to shift some of its production outside of China, the Wall Street Journal reports, citing insiders.

The company has been reportedly telling suppliers to 'actively' plan on assembling Apple products elsewhere in Asia - primarily India and Vietnam, as the company looks to reduce dependence on Taiwanese assemblers spearheaded by Foxconn.

The company's goal is to ship 40-45% of iPhones from India, vs the current single-digit percentage, according to TF International Securities analyst, Ming-chi Kuo. Vietnam is also expected to shoulder more of the manufacturing of other Apple products, such as AirPods, smartwatches and laptops.

A worker is shown disinfecting equipment.

The decision was sparked by turmoil at "iPhone City" inside Zhengzhou (a 'city-within-a-city'), where as many as 300,000 workers assemble iPhones and other Apple products as a Foxconn-run factory, which produces roughly 85% of the iPhone Pro lineup, according to Counterpoint Research.

In November, violent protests hit the Zhengzhou factory - as workers upset over wages and Covid-19 restrictions began rioting and throwing things at the police. All of this poses a risk to Apple, which has relied on the factory as a stable manufacturing center.

Zhengzhou is home to a giant Foxconn facility known as iPhone City, where a worker is shown at right disinfecting equipment. (Shang Ji/Future Publishing/Getty Images)

"Apple no longer feels comfortable having so much of its business tied up in one place," according to the report.

So no, Apple isn't moving production out of concerns over human rights abuses, censorship, or other types of oppression.

"In the past, people didn’t pay attention to concentration risks," said former US-based Foxconn executive, Alan Yeung. "Free trade was the norm and things were very predictable. Now we’ve entered a new world."

One response, say the people involved in Apple’s supply chain, is to draw from a bigger pool of assemblers—even if those companies are themselves based in China. Two Chinese companies that are in line to get more Apple business, they say, are Luxshare Precision Industry Co. and Wingtech Technology Co. 

On calls with investors earlier this year, Luxshare executives said some consumer-electronics clients, which they didn’t name, were worried about Chinese supply-chain snafus caused by Covid-19 prevention measures, power shortages and other issues. They said these clients wanted Luxshare to help them do more work outside China. -WSJ

The concerns over production revolve around new product introduction (NPI), which requires teams to work with contractors to translate blueprints and prototypes into a detailed manufacturing plan. According to the report, Apple has put its manufacturing partners on notice to start trying to do more of this outside of China.

That said, unless places like Vietnam and India can excel at NPI as well, they will 'remain stuck playing second fiddle' according to supply chain specialists.

For now, consumers doing Christmas shopping are stuck with some of the longest wait times for high-end iPhones in the product’s 15-year history, stretching until after Christmas. Apple issued a rare midquarter warning in November that shipments of the Pro models would be hurt by Covid-19 restrictions at the Zhengzhou facility. -WSJ

The shift marks a massive change in the relationship between Apple and China - which for decades have been engaged in a mutually beneficial relationship.

According to Kup, the supply-chain analyst, iPhone shipments in the fourth quarter of this year were likely to reach between 70 and 75 million units - around 10 million fewer than market projections before the Zhengzhou riots.

"Apple is going to have to find multiple places to replace iPhone City," said Dan Panzica, a former Foxconn executive who now advises companies on supply-chain issues. "They’re going to have to spread it around and make more villages instead of big cities."

Tyler Durden Sun, 12/04/2022 - 13:55

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