Data Science newsletter – April 15, 2020

GROUP CURATION: N/A

A number of universities are beginning to consider the possibility that in-person classes may not resume until 2021.

Boston University has already canceled all “in-person summer activities” on its primary campus. But the school’s coronavirus recovery plan includes protocols should officials deem it not safe to return in-person for the fall semester, and says classes would continue to be held remotely through the fall semester.

“The Recovery Plan recognizes that if, in the unlikely event that public health officials deem it unsafe to open in the fall of 2020, then the University’s contingency plan envisions the need to consider a later in-person return, perhaps in January 2021,” the university said in an online statement.

Newsha Ghaeli wants to turn the sewer system into a public health observatory.

“Urine and stool contain a lot of information about human health and well-being,” said Ghaeli, a former MIT researcher who co-founded Somerville startup Biobot Analytics with Mariana Matus in 2017.

Biobot scours wastewater for the stuff we excrete, like bacteria or drug byproducts.

“Every time we flush the toilet we’re actually flushing this valuable information away and it’s aggregating in our city sewers,” said Ghaeli. [audio, 4:03]

To get a better sense of the COVID-19 challenges facing leagues and organizations and the possible effectiveness of proposed workarounds, Hreal Sports spoke to Zach Binney, an epidemiologist at Emory University who wrote his dissertation on injuries in the National Football League. … Hreal Sports: Let’s start with a soccer match in Italy. The now-infamous Champions League match that took place in Milan on Feb. 19 between Atalanta, an Italian team, and Valencia, a Spanish team, and since has been identified as a likely super-spreader event for the coronavirus, with 40,000-plus fans exposing themselves to infection and helping carry it back to other parts of Spain and Italy. There’s a famous quote from an Italian doctor calling it a “biological bomb.”

Some apps highlight when a person is online — and then share that information with their followers. When a user logs in to a website or app that uses online status indicators, a little green (or orange or blue) dot pops up to alert their followers that they’re currently online.

Researchers at the University of Washington wanted to know if people recognize that they are sharing this information and whether these indicators change how people behave online.
A graphic showing the online status of four people — Alice who is online at work, Bob who is offline, Carol who is online but has changed her status to appear offline to avoid Malory, and Malory who is waiting for Carol to get online to ask for a favor.

After surveying smartphone users, the team found that many people misunderstand online status indicators but still carefully shape their behavior to control how they are displayed to others. More than half of the participants reported that they had suspected that someone had noticed their status. Meanwhile, over half reported logging on to an app just to check someone else’s status. And 43% of participants discussed changing their settings or behavior because they were trying to avoid one specific person.

The scientists believe knowing where polar bears currently set up their dens may help humans find better ways to help and manage the bears as their habitat changes and, in some cases, is destroyed.

Researchers said they were intrigued by gaps that emerged as the map was completed.

“Most coastal regions in northern Canada supported denning, but large areas exist where denning is unreported,” the 10 scientists wrote in an abstract of their work, published in the journal Polar Biology.

Changes in the ability of rivers to hold and convey floodwaters downstream (river conveyance capacity) do not affect the amount of water that flows through river systems during floods, but they do alter the probability of floods overtopping riverbanks or flood defenses [Slater et al., 2015]. These changes in river capacity are driven by interactions among hydrology, landscape, and climate and by the interdependencies of processes at different spatial and temporal scales. Humans are also inextricably linked to water resources and are now, more than ever, active participants in complex flood–river systems.

While studies attributing flood events to individual drivers can be valuable, ignoring interdependencies among these drivers as well as the effects of changing river morphology implicitly promotes simplified views of the challenges inherent to flood management. Further research must account for these interdependencies, study flooding from a transdisciplinary perspective, and make use of remote sensing and emerging technologies to overcome these simplified depictions to adapt effectively to future flood hazards.

Yet rainforest destruction continues unabated, not just in the South American Amazon, but also in Sub-Saharan Africa and Southeast Asia, to clear land for the cultivation of beef, timber, and oil crops like soy and oil palm. And deforestation doesn’t just impact species on the tracts that are directly burned—it’s also harmful to neighboring forestland still left standing in ways that scientists are only beginning to understand. In a study published this week in the Proceedings of the National Academy of Sciences, Elsa Ordway, a postdoctoral fellow at the Harvard University Center for the Environment, and co-author Greg Asner of Arizona State University mapped and measured these “edge effects” on rainforests that border oil-palm plantations in Malaysian Borneo. Forestland that was within about 100 meters of a boundary with a plantation, they found, showed a 22 percent decline in above-ground carbon compared to forest interiors, reflecting a reduced ability for trees there to store carbon.

It’s a critical moment for a species on the brink of collapse. The monarch butterfly population in eastern North America dropped by half from last year, and the fragile insects are now winging north from Mexico toward Minnesota.

Crews with the Monarch Joint Venture, a national conservation organization based in St. Paul, are eager to head south to research the migration to determine what conservation work can keep the beloved orange butterfly from disappearing.

They will have to wait. The nonprofit has delayed its field work as the nation fights to outwit the novel coronavirus. The monarch research is one of a host of environmental projects across the state delayed, suspended or thrown into uncertainty by the pandemic.

By analyzing data from nearly all US PhD recipients and their dissertations across three decades, this paper finds demographically underrepresented students innovate at higher rates than majority students, but their novel contributions are discounted and less likely to earn them academic positions. The discounting of minorities’ innovations may partly explain their underrepresentation in influential positions of academia.

The team at the Harvard School of Public Health used what’s known about Covid-19 and other coronaviruses to create possible scenarios of the current pandemic.

“Intermittent distancing may be required into 2022 unless critical care capacity is increased substantially or a treatment or vaccine becomes available,” they wrote in their report. “Even in the event of apparent elimination, SARS-CoV-2 surveillance should be maintained since a resurgence in contagion could be possible as late as 2024.”

The Harvard team’s projections also indicate that the virus would come roaring back fairly quickly once restrictions were lifted.

An unpublished study went viral after a research team warned that respiratory droplets may travel more than 6 feet during exercise. But that’s not the whole story.

Stanford Medicine researchers and their collaborators, Fitbit and Scripps Research, are launching a new effort that aims to detect early signs of viral infection through data from smartwatches and other wearable devices.

By using wearable devices to measure things such as heart rate and skin temperature, which are known to elevate when the body is fighting off an infection, the team seeks to train a series of algorithms that indicates when your immune system is acting up.

If the algorithms succeed, the team hopes they could help curb the spread of viral infections, such as COVID-19.

NYU scientists: Largest US study of COVID-19 finds obesity the single biggest ‘chronic’ factor in New York City’s hospitalizations

At our annual Summer School in 2019, there were two young physicists (Jonathan Gorard and Max Piskunov) who were like, “You just have to pursue this!” Physics had been my great passion when I was young, and in August 2019 I had a big birthday and realized that, yes, after all these years I really should see if I can make something work.

So—along with the two young physicists who’d encouraged me—I began in earnest in October 2019. It helped that—after a lifetime of developing them—we now had great computational tools. And it wasn’t long before we started finding what I might call “very interesting things”. We reproduced, more elegantly, what I had done in the 1990s. And from tiny, structureless rules out were coming space, time, relativity, gravity and hints of quantum mechanics.

We were doing zillions of computer experiments, building intuition. And gradually things were becoming clearer. We started understanding how quantum mechanics works. Then we realized what energy is. We found an outline derivation of my late friend and mentor Richard Feynman’s path integral. We started seeing some deep structural connections between relativity and quantum mechanics. Everything just started falling into place. All those things I’d known about in physics for nearly 50 years—and finally we had a way to see not just what was true, but why.

As the coronavirus pandemic leads to anxiety over the strength of the world’s food supply chains, everyone from governments to banks are turning to the skies for help.

Orbital Insight, a California-based Big Data company that uses satellites, drones, balloons and cell phone geolocation data to track what’s happening on Earth, has seen inquiries about monitoring food supplies double in the past two months, according to James Crawford, founder and chief executive officer of the company.

“We’re helping supply chain managers, financial institutions, and government agencies answer questions they never thought they would have to ask,” Crawford said in a phone interview.

Online April 22, starting at 12:30 p.m. EDT. Speaker: Tamas Rudas, Eotvos Lorand University. [free]

Online June 18, starting at 9 a.m. EDT. The conference “explores the impact of technology and big data on the ways in which people come together to communicate, combine knowledge and get work done.” [$$]

“We’re introducing OpenAI Microscope, a collection of visualizations of every significant layer and neuron of eight vision “model organisms” which are often studied in interpretability. Microscope makes it easier to analyze the features that form inside these neural networks, and we hope it will help the research community as we move towards understanding these complicated systems.”

“Johns Hopkins University has launched a data-rich, U.S.-focused coronavirus tracking map, adding to existing efforts that have made the university a go-to global resource for tracking confirmed cases of COVID-19 and related data over the past three months.”

“Created through a multidisciplinary collaboration by experts from across Johns Hopkins, the new map features county-level infection and population data, allowing policymakers, the media, and the public to find specific, up-to-date information about the outbreak and how it is affecting communities across the nation.”

“Recognizing the evolving data management needs of its diverse user community, the National Energy Research Scientific Computing Center (NERSC) at the U.S. Department of Energy’s (DOE) Lawrence Berkeley National Laboratory recently unveiled the Community File System (CFS), a long-term data storage tier developed in collaboration with IBM that is optimized for capacity and manageability.”

“The CFS replaces NERSC’s Project File System, a data storage mainstay at the center for years that was designed more for performance and input/output than capacity or workflow management. But as high performance computing edges closer to the exascale era, the data storage and management landscape is changing, especially in the science community, noted Glenn Lockwood, acting group lead of NERSC’s Storage Systems Group. In the next few years, the explosive growth in data coming from exascale simulations and next-generation experimental detectors will enable new data-driven science across virtually every domain. At the same time, new nonvolatile storage technologies are entering the market in volume and upending long-held principles used to design the storage hierarchy.”

The virus is having enormous direct health impacts on our society as well as other major indirect social and economic impacts. The full scientific research community and its rich set of tools are key to responding to these challenges. … The website provides links to various information sources on COVID-19 related research, resources and research projects. We are also actively engaged through discussion in the Slack channel and periodic meetings in building further connections and enabling related discussions.