I was a Covid Virgin…until three weeks ago.

For more than three years, I’d masked, vaxed, boosted, quarantined. I once walked out of a New Hampshire restaurant where the owner refused to require masks despite a national mandate. (True confession: I also called him an idiot) I fended off Covidiots on Fresh Pond by running with a pool noodle across my shoulders, reminded folks of a $300 fine for non-maskers in Cambridge–and got cursed out for it.

I took Covid precautions very seriously: in the early days, my friend Jim Gewirtzman had died of Covid; a therapist I know got seriously impaired by brain fog and exhaustion– until finally, she had to retire. A 32-year old friend lost his mentor to Covid, then came down with it himself. Three years later, he has episodes of exhaustion and memory loss. Millions more died or can no longer work as a result of this wily virus.

Still, by this summer, President Biden had declared the pandemic over, most folks were no longer masking or bothering to schedule booster shots. An anti-vax acquaintance told me masks did not work and mocked me for wearing one; he said he believed in herd immunity. (Under that theory, used by Sweden early in the pandemic, the weak die of the illness and the rest survive; more recent evidence has shown that with so many quickly-developing virus mutations, that strategy did not–and will not end the pandemic.)

The last Sunday afternoon in August, when I hopped into Trader Joe’s to buy some wine for a picnic with my writers group. I realized I’d left my mask in the car but figured I’d only be inside for a few minutes. Three days later, after the picnic, I started sneezing but thought it was allergies. The next day, congestion built in my chest and sinuses; I decided to test just for the heck of it. Bam. Positive.

It would be 17 days until I tested negative –17 days of confusion, of not knowing how to protect myself and others due to conflicting information, uninformed medical guidance, and a lackadaisical attitude among friends and in the general public. This more than three years into Covid–and, with infections and hospitalizations rising in Cambridge and elswhere, still counting.

First, I called my doctor for Paxlovid.–the medicine said to help prevent serious illness and hospitalization. She said she’d put in a prescription and that I should ask someone pick it up for me but, living solo, I had to go myself.
Next morning, when I got to CVS at 9:30; I was the only one wearing in a mask. The pharmacy windows were shuttered, though they were supposed to open at 9; for some reason, I was told, the pharmacist had gone to the wrong CVS..not very reassuring for those seeking careful treatment. He would be there in ten minutes, a manager assured me.

Coughing into my surgical mask (I now know I should have used a more protective N95 or KN 95) I walked around the store checking for bargains, then went to the pharmacy window, waiting in line for it to open. Concerned that I might be infectious, I told people not to come near me and used my mobile phone in attempts to reach the manager to ask if there were some way they could contact me when my prescription had been filled. But each time I asked to speak the manager, the call was dropped: this happened not once, but four times. Still in line at 10:15, with no pharmacist available, I called another CVS; was told they couldn’t transfer the prescription and in any case I wasn’t to come inside.

Eventually, a CVS manager appeared near the growing pharmacy line. Alternating coughs and conversation, I explained that I was contagious and should go home; she agreed to call when the prescription was ready so I drove the mile-and-a-half back to my house. As soon as I got there, of course, she called, so I drove back, when I got to the pharmacy counter, the tech said the prescription was not ready, it would be 15 or 20 minutes…I protested, slamming my hand on the counter. The pharma tech said he would expedite it; so I hung around…probably spewing germs through my mask…for another 15 minutes. Before I left, I suggested to a clerk that someone might want to sanitize the coupon dispenser and the box of hair dye that I had touched.

Back home, I swallowed the first three Paxlovid pills as instructed and headed for the couch, where I spent most of that day coughing, sneezing and trying to work. My chest congestion deepened, making it painful to cough. As directed by the Centers for Disease Control, I spent the next few days pretty much in isolation.

Except that my cleaning person was scheduled to come on day three. I suggested postponing but she and her helper insisted they would be fine. I opened all of the windows and, when they arrived, offered masks, but the cleaners refused to wear them. “It’s not like in the past,” one said. ” Now, it’s like the flu; it’s curable; when you have the flu, you go to work.” (I wondered about going to work with the flu, and later thought perhaps I should have paid them not to come.

A neighbor also chose to visit–having already had Covid, she brought her own tea and was comfortable with our sitting on the balcony, so long as I was masked.

At some point I managed to find a number to call to report my positive test–but have no idea if that would count, or, as I was one of very few to do so, would make any difference at all.

I felt better on Day 4, and on Day 5 felt well enough to walk outside, wearing a mask. Two cousins from Chicago came by on their way to Cape Cod; we walked (only I was masked) to Fresh Pond and then for supper, outdoors, in Harvard Square. CDC guidelines said that after isolating for five days, it was unlikely that I was still contagious, so it would be fine to go out, masked, just in case. I’m not sure it was smart of me to walk 14K steps, because on Day 6, my congestion deepened, and, disappointingly, I tested positive. A friend on Facebook said he’d had something called “Covid rebound” after Paxlovid; I didn’t know what to do.

Meanwhile, First Lady Jill Biden had tested positive, but was negative after just three days. A friend who drove in to Boston from Provincetown for one night told me he’d picked up the virus—but had a light case, and within a few days was off on a trip to the opera, in New York.

But I kept testing positive and feeling miserable, for the next five days. Dr. Google said you are likely most contagious two days before and after symptoms…CDC said it was OK to go out masked after isolating for 5 days if you’ve had no fever for 24 hours…the only time I had a temperature over 98 was on day two–so I did.

On Day 6, at Henrietta’s Kitchen, no one masked. At an art opening on Day 8, no one masked. Over the next few days, behind my mask, I was coughing and sneezing, my chest was still congested, and I felt awful.

After testing positive on Sunday, Day 9, I wondered if I was having that Covid rebound, which in Covid recurs in some folks who take Paxlovid (evidently, the drug slows the growth of the virus, but doesn’t always wipe it out). I called the doctor to ask what I should do. The nurse on call said she wasn’t familiar with the latest protocols; she suggested that I stay inside, “better safe than sorry”–and that I contact my doctor the next day to request a chest x-ray.

On Day 10, the doc said my symptoms were not due to Covid rebound, which takes longer to present. They were likely caused by allergies, exacerbated by Covid. She told me to take certain over the counter pills and nasal spray, both of which made me woozy.

For five more days, I felt congested, tired, with no energy to write. A friend who called told me, “You sound like you’re under water.” I put on a mask and went to the library (no one masked); and to an art opening (only one other person masked). Finally, on Day 17, I tested negative.

On Day 20–three weeks in, I was feeling better; though still congested and tired. I found a story on NPR that suggested the label “medium” Covid. It’s different from “long Covid,” which is used to describe Covid symptoms that go on for more than a month. In “medium Covid,” the reporter suggested, symptoms last for weeks, and those who have it “are caught in a gray area of recovery with little support.” Yup, I thought.

I walked my 4k steps on the river (where, usually, I run). And, having tested negative, went unmasked to a party on the anti-vax/masker’s porch. There, a former dentist whose mother had died of Covid insisted that masks and Paxlovid do not work. A woman who had contracted Covid the same weekend I did said she’d isolated for the five days and was fine after that.

The next morning, a coffee pal at Henrietta’s who consults to international pharma companies told me he did not know if he’d ever had Covid but insisted that there’s no reason to wear a mask. (He also proclaimed that US policy of shutting down stores and schools was misguided because the disease supposedly only kills old people–and more young people have died of suicide due to isolation than have died of Covid). The bartender said that despite the current uptick in cases, he will not wear a protective mask: “If you wear a mask, people think you are sick and stay away.”

Given the vehemence and mockery with which many anti-maskers expressed their views, I wondered if I were overdoing the masking thing–and emailed to ask a renowned scientist friend who was involved in inventing the vaccines what he thought.

He responded:
I don’t think anyone knows for sure. I think it works some , but not perfectly.  But one should wear k 95 ideally. Or kn 95. But it’s important to fit correctly. I always wear them in crowds or crowded places. 

That settled it for me. I wrote back:

I’m concerned that there’s is so much misinformation and people are being so careless…even reckless!  And ridiculing others for taking precautions.

He wrote:
I’m not sure any conclusive studies have been done. Also terrible and repeatedly inconsistent and contradictory info from the World Health Organization and the Centers for Disease Control. That said, I see no harm and I think there is definitely possible good. 

So–supposedly I’m immune from Covid for three months. After that, I’ll get the latest booster (out this week) and mask in crowded spaces. I’m grateful for the vaccines, the boosters, and the medicines that have helped get this nasty illness under control. Though I was laid low for three weeks, I am very grateful not have been laid even lower–like, in a grave.

I remain concerned that after all this time, no one seems sure about what works and what does not. But given the contradictory guidance, guesswork, and nonchalance about an illness that seems to affect each of us differently, I ask, “Why not mask and vax? What do you have to lose?

–Anita M. Harris

Anita Harris is a writer, photographer and communications consultant in Cambridge, Mass. Earlier in her career, she covered health, science and technology for the “MacNeil-Lehrer Report” (now the “NewsHour” of PBS), served as public affairs director for the Harvard School of Public Health.

New Cambridge Observer is a publication of the Harris Communications Group, also in Cambridge, Mass.

On June 7, 2023, I was privileged to cover the convention of the Biotechnology Industry Organization (BIO) International Convention–my first time attending the meeting since 2018, when the 25th anniversary of the gathering was held here in Boston. The excitement was back–with 9144 companies registered to attend, many with booths, tables or pavilions–and, according to Stat News, some 15, 000 investors, executives and promoters.

On the afternoon of its third day, the convention, headlined “Stand Up for Science,” had a more fun and friendly vibe than I’d noticed at past BIO conventions.

Short on time, I wandered around the exhibition floor–chatting with exhibitors and attendees, snagging a latte, dark chocolate squares, a small nylon backpack advertising New York State Life Sciences, and a large mousepad.

I was sorry to miss many fascinating discussions: “Realizing the Promise of Gene Therapy and Gene Editing: Current Challenges, Opportunities and Trends; ” “A Price Control Odyssey: The Inflation Reduction Act’s Effects on the Innovation Ecosystem;” ” Belonging in Biotech: How to Advance Greater Inclusion Across the Biotech Workforce;” “Launching Successful Gene Therapies; Fighting Antimicrobial Resistance with Vaccine Innovation; ” “New Approaches to Oncology Drug Discovery;’ Re-imagining Drug Development and Regulatory Submissions through Cloud-Based Technologies;” “The Intersection of Cancer and Mental Health”; “Women and their Health: Fueling an Ecosystem of Scientific Innovation to Address Unmet Needs”. All of the above (and more) took place in the same hour as my first chosen panel discussion of the day: “Psychedelics…the Trip Continues.” (I viewed a streaming version because the main conference room was packed full.)

Psychedelics…the Trip Continues

Freelance journalist and broadcaster David Cox led Jeff Rolx, venture partner and portfolio CEO at 02h Ventures; Kurt Rasmussen, Chief Scientific Officer at Delix Therapeutics, Inc., and Peter Silverstone, CEO and Director of Zylorian Health in a wide-ranging discussion of the future an evolving industry projected to be worth billions of dollars, one day.

The panelists described the variety of challenges faced by the fledgling industry as it evolves from what the official writeup termed “a stigmatized counterculture” to a scientifically robust industry.

Among the challenges:

• Navigating the wide variety of regulatory systems in the US and abroad as well as attitudes of different states and national governments
• Issues involved in clinical trials given potentially dangerous side effects; measuring efficacy of treatments when placebos are not an option
• Whether the pharmaceutical industry will invest in a field with a “hippy” reputation
• Whether non-hallucinognic forms will be likelier to be used therapeutically before hallocinogenics
• How psychedelic therapeutics will get to market given the difficulty small developers may have in getting funding
• Determining what the therapy is and how it can be standardized.

“We are completely blind right now, ” said Silverstone, of Zylorian Health. “Our AI [artificial intelligence] overlords may soon tell us [what to expect]…but we are just at the beginning.” Silverstone predicted that the next three or four years will be telling for the industry, and suggested that 2024 could possibly be “a big year” for psychedelics.

Roix, of 02 Ventures described the current mental health situation as a “public health emergency,” with huge numbers of patients struggling with depression and post traumatic stress disorder. There are complex protocols and treatments and too few resources, he said. He also wondered how anyone will make money–especially if psychedlics work after just a few treatments and are not given as pills to be taken every day.

According to Silverstone, science is moving to the point where “the opportunity to deliver something novel in the field of neuroimmunology is huge.”

He predicted that the field may need to be “reformatted” to interest big pharma–“which will jump in when it’s ‘de-risked’ from safety concerns, reimbursement issues and questions about whether non-hallucinogens will work.

Rassumen of Delix Therapeutics expressed optimism that non -hallucinatory forms are possibilities. He pointed out that that compounds that enhance structural nerve plasticity are “starting to uncover how the brain changes over time”–which could, perhaps in conjunction with stem cell therapies, lead to getting back some functions in patients with dementia and other diseases of the aging brain.

He also said that treatment forms which resemble what in past would have been called “tripping” may diminish because depressed patients now seem to be more secure in carefully monitored medical settings.

When Rasmussen suggested possibly rebranding the field–that is, ” don’t call it psychedics,” Silverstone quipped, “That won’t happen.”

Life Science and the Gun Violence Epidemic

I next attended “The Life Sciences Industry: Taking a Public Health Approach to Ending the Gun Violence Epidemic,” moderated by Steve Usdin, Washington Editor and Head of Policy and Regulation at BioCentury.

The panelists included (left to right) Paul Hastings, President and CEO of Nkarta, a clinical stage biotechnology company in California; Juan Carter, outreach manager at the Giffords Center for Violence Intervention, headquartered in San Francisco and Washington, DC. [moderator Steve Usdin] ; Angus Mcquilken, co-founder of Life Sciences to End Gun Violence Epidemic and Industry Relationship Executive for Life Sciences at Boston Law Firm McDermott Will and Emery; Sharon Barber-Lui, a life sciences leader and BIO board member; and BIO CEO Rachel King.

All of the panelists said they strongly believe in gun control; King and Barber-Lui both said they had attended the Million Mom March to call for stricter gun control some twenty years ago. But most agreed that corporate lobbying for what has become a volatile political issue presents difficulties–and that individual commitment is called for.

King said that though she personally supports ending gun violence, she must adhere to the BIO directors’ decision to limit activities to those directly concerning the biotechnology industry.

Mcquilken urged attendees to join the organization he cofounded– “Life Sciences to End the Violence Epidemic”–which lobbies for stronger gun control laws. He pointed out that biotech seeks evidence-based solutions to problems–and that there is strong evidence that Massachusetts’ strict gun control laws, which require considerable training before guns may be purchased, account for the commonwealth’s relatively low rate of shooting deaths.

Hastings said that as a CE0 he has held events supporting gun control measures–but that he has been reticent to publicize photos of participants due to the negative backlash he would expect.

Carter said that it is important for health care and other professionals who work with victims of gun violence and their families to be supportive and accepting of them, lest they become dejected and hopeless when they return to troubled communities, and do not return for needed help.

Also suggested was that companies seeking to recruit youthful employees find ways to encourage activism.

An audience member who did not give his name pointed out that the Second Amendment to the Constitution, which grants certain rights to bear arms , was meant to prevent imperialism but it is now being used to promote terrorism.

Targeting Success: 3 MIT Thought Leaders on Innovation

At my third panel discussion of the afternoon, MIT’s Angela Koehler, associate professor of biological engineering; Robert Langer, David H. Koch Institute Professor, and Giovanni Traverso, associate professor, delved into questions and challenges for scientists in academic and research institutions who seek to bring their innovations to market.

In a discussion moderated by Joshua Fox of the Mintz law firm, Langer [second from left]–who is well- known as a co-founder of Moderna pharmaceuticals and has more than 400 patents licensed or sub-licensed by a myriad of companies–said that spinning a successful company out of academe requires a “breakthrough technology platform”; a really good CE0; and raising enough money. (Full disclosure: Bob is a personal friend of mine).

Koehler [left] emphasized the importance of building “connections” to raise funds and recruit a great team–and that a CEO has to be willing to “plug in a fridge”–that is, be willing to do everything.

According to Travers [second from right], ” it’s important to have a management team as outstanding as the scientific team.” When Langer’s warned not to try to leave the academic setting too early lest you wind up in “the valley of death” (unable to raise enough money), Travers recommended seeking grants and non-traditional investors such as insurance companies to take the science through clinical trials. Koehler suggested looking for disease-oriented foundations for funding.

All-in-all, BIO 2023 a fascinating convention; next time I’ll try to go to everything–which is, of course, impossible.

—Anita M. Harris
Anita Harris is a writer, photographer and communications consultant. She has authored three non-fiction books.
New Cambridge Observer is a publication of the Harris Communications Group, a PR and digital media firm based in Cambridge, Mass.

Once again, the Lacoste Keane gallery in Concord MA presents a stunning new show–in which ceramicist Ani Kasten uses the concept of visual poems to reflect on issues such as environmental collapse, social collapse, and inner and outer strife. 

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In the show, Kasten creates sculptural compositions from fragments and debris. While some vessels are quite large, other, smaller pieces Kasten calls “poems,” are three-dimensional objects which she likens to written verse. A poem, says the one-time literature major, ” shears away everything but the most essential, evoking an emotional response through the sparest communication, constructing concepts and feelings into a hewn verbal form, without engaging narrative or logic.”

Kasten uses earth materials like clay and rocks as a metaphor to explore ideas of decay, disintegration and renewal. “Working in clay is about the search for balance between the natural tendencies of the materials and the craft that is brought about by contact with the human hand,” according to the gallery writeup. “Faced with monumental forces of nature and entropy, a sadness and feeling of futility is provoked with the notion that human hubris seeks to create lasting structure and survival in the face of decimation by forces outside of our control—earthquakes, tsunamis, volcanoes, tornadoes, violence and war. “

In this work, Kasten “reveals emerging structures and constructs under stress, made by the human hand but fighting against collapsing infrastructure. They show the cracking, warping and erosion that are natural expressions of the material, and explore the beauty and sadness in building from wreckage, such as a little robot made from scavenged shards of something former, with two little ears made from fossilized hornets’ nests.

Kasten says that “In the act of scavenging, building and creating the visual poems, ” she is “searching for beauty and harmony in the act of piecing back together what may seem like meaningless detritus of a collapsing world, reclaiming a tenuous and fragile feeling of meaning and purpose.”

In my view, she is successful in doing so. The pieces look delicate–as if they could fall apart at any second. But with their pastel colors and seemingly -haphazard-yet-powerful shapes reaching out in many directions, they exude tremendous energy–inviting the viewer to enter into Kasten’s exploration and expression of the tenuous-yet-enduring relationships of natural and human forces.

At Lacoste Keane Gallery, 25 Main St Concord MA 01742, through February 8, 2020.

—Anita M. Harris

Anita Harris is a writer and communications consultant based in Cambridge, MA. New Cambridge Observer is a publication of the Harris Communications Group, an award-winning public relations and digital marketing agency, also in Cambridge.

Artificial intelligence is likely to transform the public sector by automating many government tasks—including making combat decisions. But, according to experts at a recent symposium held  at Harvard University, this “over-the-horizon” technology can only guide and inform government leaders. There will always be a need for human decision making—and for clear ethical standards to prevent harmful intentions.

At the September 20 conference, “AI-Government and AI Arms Races and Norms,” organized by the Michael Dukakis Institute (MDI), Professor Marc Rotenberg underscored the growing gap between informed government decision-making and the reality of our technology-driven world. “Governments may ultimately lose control of these systems if they don’t take action,” he told some 60 attendees.

Rosenberg, who teaches at Georgetown University Law School, is President of the Electronic Privacy Information Center (EPIC), and a member of the AI World Society Standards and Practice Committee,

Prof. Matthias Scheutz, Director of the Human-Robot Interaction Laboratory at Tufts University, said the greatest risk caused by AI and robotics technologies is when unconstrained machine learning is out of control. This can happen when AI systems acquire knowledge and start to pursue goals that were not intended by their human designers, he said. For example, “If an AI program operating the power grid decides to cut off energy in certain areas for better power utilization overall, it will leave millions of people without electricity, which consequently turns out to be an AI accidental failure.”

Scheutz also said that common preventive solutions inside and outside the system are largely insufficient to safeguard AI and robotics technologies. Even with “emergency buttons,” the system itself might finally set its own goal to prevent a shutdown previously set up by humans.

The best way to safeguard AI systems is to build ethical provisions directly into the learning, reasoning, recognition and other algorithms. In his presentation, he demonstrated “ethical testing” to catch and handle ethical violations.

Here’s a link to video of Scheutz’s talk. https://youtu.be/66EeYzkTxwA

Prof. Joseph Nye, emeritus of Harvard University, who created the concept of “Soft Power” diplomacy, focused on the expansion of Chinese firms in the US market and their ambition to surpass the US in AI. Nye said the notion of an AI arms race and geopolitical competition in AI can have profound effects on our society. However, he added, predictions that China will overtake the US in AI by 2030 are “uncertain” and “indeterminate” because China’s only advantage is having more data and little concern about privacy.

Nye also point out that as people unleash AI, which is leading to warfare and autonomous offensives, we should have treaties in place to control the technology, managed perhaps by international institutions that will monitor AI programs in various countries.

During the symposium, Tuan Nguyen and Michael Dukakis, cofounders of the Michael Dukakis Institute (MDI), announced MDI’s cooperation with AI World–the industry’s largest conference and expo covering the business and technology of enterprise AI, to be held in Boston December 3-5, 2018.

Nguyen said, “Our cooperation marks the determination between two organizations toward achieving the goal of developing, measuring, and tracking the progress of ethical AI policy-making and solution adoption by governments and corporations.” Nguyen also introduced Eliot Weinman – Chairman of AI World Conference and Expo as a new member of AIWS Standards and Practice Committee.

Conference details are published in the current issue of AIWS Weekly.
–Dick Pirozzolo

New Cambridge Observer is a publication of the Harris Communications Group, a PR, content and digital marketing firm based in Cambridge, MA.

Dick Pirozzolo is a member of the Group; the Michael Dukakis Institute, formed by Boston Global Forum, is his client. 

I recently interviewed Bob Langer–MIT biotech guru extraordinaire–on behalf of the EBD Group, which holds international partnering conferences for the life sciences six times a year.  Here’s the opening…and a link to the rest, on the EBD Site. The piece will also  appear in xconomy shortly. Full disclosure…Bob is a personal friend, former classmate, and a member of the Harris Communications Group advisory board…so this should be considered a sponsored post.

–Anita M. Harris

 

When Bob Langer joined the MIT faculty in 1977 he had a rocky start. Trained as a chemical engineer and working on drug delivery systems, many of his ideas went against conventional wisdom. “I had people write the most insulting things about my knowledge of biology and medicine. Many thought my ideas were crazy. A number of professors wanted me to leave and my first nine grant proposals were turned down.”

Eventually, after numerous academic scientists and companies repeated and used his work Langer was able to get grant funding from the NIH. He also turned to companies for research funding—in return for licensing his patents—which, at that time, also went against the conventional grain.

Today, Langer is one of 13 Institute Professors (being an Institute Professor is MIT’s highest honor) at Massachusetts Institute of Technology. With more than 1,400 articles to his credit, he is the ninth most cited individual in history, according to Google scholar. (Sigmund Freud is first). His 1,300 patents, licensed or sublicensed to more than 350 companies in pharmaceutical, chemical, biotechnology and medical device fields, have led to more than 100 products currently in use or in clinical trials. He has received more than 220 major professional awards including the Queen Elizabeth Prize for Engineering, Priestly Medal, National Medal of Science, National Medal of Technology and Innovation, the Charles Stark Draper Prize (considered the equivalent of the Nobel Prize for engineers), and the Lemelson-MIT prize for being “one of history’s most prolific inventors in medicine.” In June 2018, he was named a US international envoy for science by the US State Department.

Despite his success, Langer remains well aware of his early setbacks, and, as a scientific advisor to some 200 companies over the past 40 years, is highly cognizant of what can go wrong.

“You can have bad animal results, failed trials, or patent problems. I’ve seen partners pull out, companies take bad loans, and the FDA create delays. Stumbling blocks can arise anywhere along the way,” he says.

One of the most difficult problems can occur early on “when a researcher has good findings but is not far enough along for investors or companies to want to spend a lot of money.” In that situation, known as “the valley of death,” Langer says, “the question is how to get enough data so that will change.”

More: 

 

Anita M. Harris is a writer and communications consultant based in Cambridge, MA.

New Cambridge Observer is a publication of the Harris Communications Group, also in Cambridge.

Spent an interesting Wednesday afternoon, last week,  visiting exhibitors at the Bio-IT World Conference & Expo –several of whom won “Best of Show” Awards later that day.

The judges, listed below,  named winners in six categories: Data Integration & Management; Analysis & Data Computing; Genomic Data Services; Data Visualization & Exploration; Storage Infrastructure & Hardware; and the Judges’ Prize.  Attendees also voted on the People’s Choice Award, selecting products that they believed measurably improve workflow or capacity, enabling better research.

One of my favorites was Nanome, which won best in show for Data Visualization and Exploration.
Nanome uses virtual reality to improve the drug discovery process, according to its award application. The company offers applications for experimentation, collaborattion, and learning at the nano-scale– leveraging  VR hardware such as the Oculus Rift and HTC Vive to create immersive virtual workspaces allowing users to visualize, design, and simulate molecules, proteins, and more.

At  Nanom’se i BIO–IT World booth, Marketing Director Jarrell James handed me a pair of VR goggles and two joysticks (?) with which  I could explore within a molecule–by seeming to make components larger, smaller or revolve.

A more sophisticated user might be able to:

• -Import molecular structures from a local machine or an online database such as RCSB or DrugBank.
• – Manipulate molecular structures by literally grabbing, rotating, or enlarging the area of interest with their hands.
• – Apply different representations to their selection of Atoms, Residues, Chains, or Proteins such as Stick, Wire, Ball & Stick, or Van der Waals.
• – Measure distances and angles between atoms.
• – Mutate amino acids and cycle through rotamer libraries.
• – Design small molecules by building with any element from the periodic table.
• – Minimize manipulated molecules to prevent clashes and provide a local energy minimum conformation.
• – Duplicate or Split any selected area of your structure to modify or export independently.
• – Export your molecular structures to PDB.
• – Join a virtual reality session as a guest with or without virtual reality hardware.

• – Present and collaborate in the same virtual environment with colleagues to demonstrate proposals or compare before and after results.

Nanome plans next to enter the education space. The company’s VR technology wil help high school and college students , likely already proficient in gaming technology,  better understqand biologic processes, James said.

 

 

The Hyve 

I also spent some time with the folks at Hyve…whose fake robot ( that is, a “robot inhabited” by a human) did make me  curious about Hyve’s work.

RADAR-base
radar-cns.org

As described in the company’s award submission,  the company’s RADAR-base, developed in the framework of the IMI RADAR-CNS project, is an open source platform designed to securely collect, store and share readings from wearable devices and smartphone sensors to enable remote monitoring. The RADAR-base platform consists of three major categories of components:

 

• Data ingestion: Recognizing and registering data-sources (including smartphones and wearable devices), collecting the data via a direct Bluetooth connection or through a 3rd party API and streaming in near real time to the server (green box in the figure). Using Apache Kafka, the collected data is streamed to dedicated topics in real-time where the data is optimally schematized using Apache Avro;
• Data storage and management: Consists of two centralized storage systems behind an authorized security layer. A cold-storage based on HDFS that is scalable and fault-tolerant focusing on storing large volumes of high frequency raw-data, and a hot-storage based on MongoDB storing aggregated data to provide a near real-time overview of the raw-data. (blue box in the figure);
• Data sharing: Visualizing aggregated data in a live dashboard and exporting raw data for further analyses in various formats including AVRO, JSON and CSV (yellow box in the figure).

The platform is highly secured by a centralized management system of users and their authorities, participants, allowed devices and their specifications. RADAR-Base platform is distributed as Docker containers with associated scripts and configuration files to enable easy installation.

 

 

 In addition, I  visited Sinequa, which took the prize in the Analysis & Data Computing category. 

 

 

 

 

Sinequa ES v10
sinequa.com

The Sinequa Cognitive Search and Analytics platform handles all structured and unstructured data sources and uses Natural Language Processing (NLP), statistical analysis and Machine Learning (ML) in order to create an enriched “Logical Data Warehouse” (LDW). This LDW is optimized for performance in delivering rapid responses to users’ information needs. Users can ask questions in their native language or ask that relevant information be “pushed” to them in a timely fashion when it emerges.

More than 180 connectors ready for use “out of the box” make the process of connecting multiple data sources fast and seamless. Company and industry-specific dictionaries and ontologies can be easily integrated, putting specific knowledge “under the hood” of the Sinequa platform, making it an intelligent partner for anyone in search of relevant subject information.

 

Other awards, as descrbed in company literature: :

Genomic Data Services

Diploid
Moon 1.0
diploid.com/moon

Moon is the first software to autonomously diagnose rare diseases from WES/WGS data. By applying AI to the domain of rare disease diagnostics, Moon brings speed and scalability to the genome interpretation process.

The software only requires the patient’s gender, age of onset and his/her symptoms – in addition to the genetic data. Moon then goes from whole genome variant data (VCF) to pinpointing the causal variant in less than 5 minutes.

The software highlights one or a few variants that could explain the patient’s phenotype. For every variant, Moon displays an extensive list of annotations that it mined from the literature, allowing geneticists to easily verify decisions from the AI algorithms. Moon’s speed does not only save a lot of time and money, it also saves lives: Moon has already proven its utility in the NICU at Rady Children’s Hospital (San Diego): https://goo.gl/7TDrQD.

Unfortunately, about 50% of rare disease patients remain undiagnosed, even after whole genome sequencing and expert interpretation. Most hospitals don’t have the resources to keep analyzing negative cases even though new correlations between genes and disorders are published every day. Moon changes all this: as the software autonomously mines the literature and analyses samples, it can reanalyze older, negative cases in the background. Only when new information that might lead to a diagnosis becomes available, the assigned geneticist is notified. That way, hospitals can frequently reanalyze thousands of cases with minimal labor, providing a perspective to undiagnosed patients.

 

Storage Infrastructure & Hardware

PetaGene
PetaSuite Cloud Edition – Version 1.2
petagene.com

Launching at Bio-IT World 2018, PetaSuite Cloud Edition (CE) combines two innovations: (i) the ability for a user’s software tools and pipelines to seamlessly integrate with a wide variety of cloud platforms without modification, and (ii) significantly improved, high-performance, scalable PetaSuite genomic compression technology. 

For example, users can now directly run, without modification, their custom BWA-mem, GATK, Python, Java, shell scripts, and other POSIX-based software/pipelines streaming directly to/from AWS, Google Cloud, Azure, and private cloud storage, as though they were local filestores. PetaSuite CE supports each platform’s object encryption during transfer and at rest. User applications can connect to multiple cloud platforms, buckets and regions as desired, transparently, and on demand, in user-mode, without needing to modify their pipelines, setup mounts, or have administrator privileges.

Whether running on bare-metal, in VMs, or within Docker containers, for public, private or hybrid cloud, PetaSuite CE enables organizations to unlock the power of distributed object storage seamlessly from their POSIX-compliant tools and pipelines.

PetaSuite CE is built from the ground-up for the extremely high performance streaming and random-access workloads demanded by genomics applications. The integrated, transparent PetaGene compression has been significantly improved to deliver even faster compression and greater reductions of up to 6x of both BAM and FASTQ.GZ files, enabling large costs savings in cloud storage and data transfer times. Moreover, PetaGene compression can also preserve the MD5 checksum of the original BAM or FASTQ.GZ file and not just the internal raw SAM/FASTQ data.

 

The Judges’ Prize went to 

 Linguamatics and its iScite 2.0 (iscite.com) provide a Software-as-a-Service search application that puts the power of text analytics directly into scientists’ hands, according to the company writeup.

Using Linguamatics’ Award-winning Natural Language Processing
Researchers can extract and analyze relevant data to rapidly answer business-critical questions. iScite utilizes Linguamatics’ award-winning Natural Language  L(NLP) based blend of analytical methods. By understanding the semantics and structure of text, iScite handles the variety of ways people express the same information, ensuring searches are comprehensive and accurate.

Easy to use on any device
iScite’s intuitive HTML interface includes a simple search box and auto-complete suggestions. The innovative answer-routing engine lets users answer simple or complex questions using puzzle-piece building blocks – simplifying access to powerful queries that extract concepts, relationships, numerical data such as drug dosages, mutations and more.

Get answers to questions, not just documents
Data sources include Linguamatics’ cloud-hosted content. MEDLINE, Clinical Trials.gov, FDA Drug Labels, PubMed Central, and Patent Abstracts are annotated with curated terminologies for diseases, drugs, genes and organizations. Scientists can answer questions such as:

• What genes are involved in breast cancer?
• What protocol designs have been used for immuno-oncology trials?
• What are the adverse events for kinase inhibitors?

Actionable results
Results are presented in structured form, with bar chart facets for dynamic, visual results-filtering, a document viewer that highlights key terms and relationships, and relevant link-outs. Users can curate, save, and export their results.

iScite allows users across drug discovery and development to cut through the vast information landscape and discover the most valuable insights.

 

The People’s Choice award went to 

OnRamp BioInformatics, Inc. and itsROSALIND™ platform:  the first-ever genomics analysis platform specifically designed for life science researchers to  analyze and interpret datasets, while freeing up more time for bioinformaticians.

Named in honor of pioneering researcher Rosalind Franklin, who made a major contribution to the discovery of the double-helix structure of DNA with her famous photograph 51, OnRamp’s ROSALIND platform aims to simplify the practice of genomic data interpretation. According to the company’s writeup,  ROSALIND puts the researcher into the driver’s seat of data analysis and democratizes bioinformatics by broadly expanding access to genomic and proteomic technologies for cancer research, precision medicine and sustainable agriculture.

While many open-source tools remain the lifeline of genomic analysis, a simplified and innovative user experience for the biologist can empower them to run their own analyses, while utilizing these tools without the need for typing any command-line instructions.

ROSALIND is powered in partnership with Google Cloud and features scalable compute power and economical cloud-based storage. ROSALIND is a swarming docker-based genomic analysis solution incorporating the industry’s most trusted open-source tools and algorithms, with an angular front-end and secure RESTful API. ROSALIND is also deployable on-premise.

On Ramp technololgists believe that empowering biologists with “an intuitive and comprehensive platform” to explore their data and collaborate with colleagues and bioinformaticians, they  can help accelerate their industry and the widespread adoption of genomic technologies by dramatically lowering costs, reducing  complexity and, ultimately, focus more on what what to do with results, rather than on how to get to them.

 

In the words of Allison Profitt, BIO-IT World’s editor,” The awards program recognizes the best of the innovative product solutions for the life sciences industry on display at the conference,

“It’s always a treat to explore what’s new in our industry.

” The innovation on display by Bio-IT World exhibitors never disappoints, and we are excited to shine a spotlight on the best life sciences has to offer.”

Judges
“The Best of Show program relies on a panel of expert judges from academia and industry who screen eligible new products and hear presentations from a list of finalists on site. This year our judges considered 46 new products and viewed presentations on site from 18 finalists.”

The 2018 judging panel included Joe Cerro, BostonCIO; Chris Dwan, Bridgeplate; Richard Holland, New Forest Ventures; Eleanor Howe, Diamond Age Data Science; Phillips Kuhl, Cambridge Healthtech Institute; Steve Marshall, Marshall Data Solutions; Michael Miller, Genentech; Art Morales, Analgesic Solutions; Nanguneri Nirmala, Tufts University School of Medicine; Alexander Sherman, Massachusetts General Hospital; Subi Subramanian, Vertex Pharmaceuticals; Bill Van Etten, BioTeam; and Proffitt.

 

–Anita M. Harris
Anita Harris is a science writer based in Cambridge, MA. 
New Cambridge Observer is a publication of the Harris Commmunications Group, also in Cambridge, ma.  

Links to
Part I Overview, Watson, analytics
Part II digital devices, long term care.
Part III Apps, devices, roadblocks

Behavioral and Population Health; Roadblocks to change

Can mobile apps really improve mental health? Cut the costs of health care? Help professionals track and care for patients? At a day-long conference sponsored  on health systems innovation organized the MIT/Sloan MIT  Initiative for Health Systems Innovation (HSI), experts from a variety of fields attempted to answer those and other questions aimed at furthering a transformation of  the US healthcare system.  Part III of a series about the conference describes apps and devices for behavioral health, personalized and long-distance care. It also discusses new state models to integrate community, health and social systems aimed at tracking and caring for patients and points out that no matter how sophisticated the technology, it is still up to human beings to make it work.

Behavioral Health

Dan Mordecai, MD, National Leader, Mental Health and Wellness at the managed care consortium Kaiser Permanente described:

• Promising mobile apps aimed at helping people prevent or overcome eating disorders, addiction, or suicide; remain on diets or exercise plans; or connect them with treating providers or coaches.
• Wearables that can measure how much people move or perform text and voice analysis to help professionals understand who needs care, months or years before it is needed.
• Predictive analytics to help prevent self-harm

While many of the above technologies have yet to be proven effective, Mordecai said, telehealth technology has been shown to be helpful in supporting and promoting long-distance health care for areas with shortages of medical personnel.  Telehealth may be carried out through videoconferencing, store-and-forward imaging, streaming media, and terrestrial and wireless communication.  

Mordecai also pointed out that with digital advances, “we are moving from individual doctor patient relationships” to a “personalized’” system, which relies increasingly on data, but that “there is a long way to go.”    Mordecai plans to use what he termed “crowd sourcing” to analyze the effectiveness of apps and other new health technologies, based on the electronic health records of Kaiser Permanente’s   nearly 12 million patients.

 

State models and population health
Analysis like that used at Kaiser Permanente is crucial for assessing treatment and cutting costs, but it is more challenging to perform outside of managed care programs, which have access to a vast array of patient records, according to Michael Wilkening, the California Undersecretary for Health and Human Services.  Analysis to records for care funded by government or private insurance is hampered by fragmented  social, health provider and  insurance systems and by legal and technical challenges of sharing patient data among those systems,

The New York State Medicaid director, Jason Helgerson, pointed out that for state Medicaid systems,  which serve mainly low-income populations,  it can be difficult to simply keep track of patients,  much less co-ordinate and evaluate their care or reduce their treatment costs.  As an example, he described a city homeless shelter that serves breakfast and dinner, but not lunch. Hungry residents regularly go to the fire station next door and complain of chest pain; they are taken by ambulance to a hospital emergency room, where they are evaluated, at high cost, given lunch, and then transported back to the homeless shelter in time for dinner.

Medicaid systems in at least several states are working on projects to prevent such situations by better integrating social services with medical and behavioral health care. Some are starting to employ analytics to recommend, monitor and measure the success of treatments, and to pay for performance rather than service.  As a result, Helgerson said, “Medicaid may be in the best position to drive change” in health delivery systems.

Roadblocks to change
Still, as a variety of speakers pointed out, despite the promise of digital innovation, there are many roadblocks to change.   Such roadblocks include: reluctance to replace or augment human decision-making with digital solutions;  complex reimbursement systems  and the need for insurer “buy-in” to pay for new technologies;  disparate stakeholders with different goals;  issues of privacy and security;   the  tendency of legislators and other policymakers to view health problems as individual rather than societal;   failure to address the lack of food and shelter that leads to poor health and expensive repeat hospital visits;  and, last but not least, cost.

In the words of Vocera’s Elizabeth Boehm, regarding systemic change, “it takes more than technology to get it done.“

And, as Restef Levi, of the Sloan School, put it: “Technology is important but…at the end of the day, health is about humans.”

 

LINKS TO:

Part I Overview, Watson, analytics
Part II digital devices, long term care.
Part III Apps, devices, roadblocks

Videotapes and photos of the conference, held November 29, 2017, are available at http://mitsloan.mit.edu/alumni/events/2017-cambridge-health-conference/

–Anita M. Harris

Anita Harris is a writer and communications consultant specializing in health science and technology.

New Cambridge Observer is a publication of the Harris Communications Group, a content and digital marketing firm based in Cambridge, MA.