About 16 years ago, I stood on the warning track and held my then one-year old son high in my arms above the blue, outfield fence in right center field of the old Yankee Stadium. We asked him to extend his glove as if he had leapt in the air to catch a home run.
Now, as he prepares to graduate from high school, my wife and I are pondering the end of an era filled with the numerous triumphs and challenges of youth sports.
In the last few weeks, while we have awaited the time outs, batting glove adjustments, pauses to look for signs from the catcher, and warm up tosses by each pitcher, we have been replaying our own montage from his years on a baseball field.
A few years after his Yankee Stadium debut, our son donned a baggy uniform that hung from his slight four-year old frame, standing with his left arm out, hoping to catch a ball I tossed with a slight arc toward him.
As the years advanced, his skill set and intensity for the game grew more rapidly than the developmental rules of the sport.
Station-to-station baseball was an abomination for him. When he was six, he caught a ball at shortstop, tagged the runner jogging from second and stepped on third for, what he considered, an unassisted triple play. He tossed the ball to the mound and jogged off the field, only to hear that everyone hadn’t batted so he had to stay on the field. I can still see the disappointed look on his face as all the runners moved to the next base.
Every moment wasn’t athletic heaven. He struggled to find the strike zone when he was pitching, swung and missed at pitches he knew he could hit and suffered through the inconsistent coaching and advice of everyone from his father to the parents of his teammates to semi-professionals eager to give back to the community.
Despite playing a game of failure, he continued to venture to fields close and far for another opportunity to compete, get some exercise and join teammates who have become long-time friends.
He learned how to pick up his friends after their moment in the spotlight didn’t end the way they wanted.
He took us to places way off a tour guide’s map of the eastern United States, as we drove from single traffic-light towns, with their one gas station and one diner, all the way up to Cooperstown.
We paced along frigid sidelines, hoping darkness or snow would grant us a reprieve from frozen bleachers and numb toes. We drove on roads in which the car thermometer read 113 degrees.
When he was old enough, he stood on a 90-foot diamond, looking from third to first as if he needed binoculars to see his teammate and a strong wind to help his throw reach the target.
As he got taller and stronger, the distance became more manageable.
As parents, we made our share of errors on the sidelines and in the stands. While we told him it was the effort that mattered, not the result, he could see the joy in our faces after a win and the slumped shoulders after a tough loss.
While he’ll undoubtedly play other games down the road, that road won’t be as close as the ones we’ve traveled together.
In a recent game, our son raced back and caught a ball against the wall, in a place on the field similar to the one where he extended his tiny glove at Yankee Stadium. We have shared such a long and inspired journey between those two mirrored moments.
Stony Brook, NY; Stony Brook University: School of Medicine 2018 Convocation Photo by Arthur Fredericks
Stony Brook, NY; Stony Brook University Medical Center: The White Coat Ceremony in the Student Activities Center. (8/14/2016)
Stony Brook, NY; Stony Brook University MART & Children's Hospital Pavilion: MART ribbon cutting, November 1, 2018. Left to right: New York State Assemblyman Steve Englebright; SUNY Trustee and Stony Brook Foundation board member Cary Staller; Stony Brook University President Samuel L. Stanley Jr., MD; New York State Senator Kenneth P. LaValle; SUNY Chancellor Kristina Johnson; Jim and Marilyn Simons; New York State Senate Majority Leader John Flanagan; Kevin Law, President of the Long Island Association and Chair of the Stony Brook Council; Kenneth Kaushansky, MD, Senior Vice President for Health Sciences and Dean of the School of Medicine; Director of the Stony Brook University Cancer Center Yusuf Hannun, MD; representing Governor Andrew Cuomo, Marta Santiago-Jones, Consultant Nurse Hospital Services Administrator at the New York State Department of Health.
Stony Brook, NY; Stony Brook University Medical Center: Donors David and Cynthia Lippe and Dean, School of Medicine and Senior Vice President of Health Sciences Ken Kaushansky outside of the garden area of the MART/Hospital Pavilion
Stony Brook, NY; Stony Brook University Hospital: Stony Brook Medicine rolled out new Mobile Stroke Units on March 18, 2019, to treat people who are having a stroke.
Left to right: Kimberly Noel, MD, Director, Telehealth, Stony Brook Medicine, Michael Guido III, MD, Neurologist, Director, Stony Brook Neurology Stroke Program, Ken Kaushansky, MD, Dean, Renaissance School of Medicine at Stony Brook University, David Fiorella, MD, PhD, Neurointerventionalist, Director, Stony Brook Cerebrovascular Center, Trevor Marshall, MD and Eric Niegelberg, Associate Director, Operations, Emergency Services and Internal Medicine
Stony Brook, NY; Stony Brook University: Chancellor Jim Malatras and Stony Brook University President McInnis Announce Partnership with SUNY Upstate Medical University to Launch Pooled Surveillance Testing for COVID-19.
Stony Brook to Test 5200 Students Each Week. Testing Expansion Follows FDA Approval of Groundbreaking Saliva Swab Test Developed at Upstate Medical University
By Daniel Dunaief
Like so many others, Ken Kaushansky had to alter his plans when the pandemic hit last March. Kaushansky had expected to retire after over 10 years as Dean of the Renaissance School of Medicine at Stony Brook University and the Senior Vice President of Health Sciences, but the public health needs of the moment, particularly on Long Island which became an early epicenter for the disease, demanded his attention.
“Now that COVID hopefully is coming under control, it seems more logical” to retire this year, Kaushansky said in a wide-ranging interview about the pandemic, his career, and the medical school. In January, he stepped down as the dean, while he plans to retire as Senior Vice President of Health Sciences at the end of June.
Views on the Pandemic
Dr. Kenneth Kaushansky
Looking back at the immediate challenges in the first few months, Kaushansky said SBU did “extremely well” in caring for patients who were battling COVID-19 and was gratified by the school’s effort to catalog and understand the disease. “I’m very proud that we’ve been able to study this infection on all sorts of levels and make a real impact that has helped others,” he said.
Early on, as the medical team at Stony Brook met, Kaushansky urged the hospital to study COVID “to the hilt” and to “extract every little bit of data we can. We must keep all that data on all these patients.”
Indeed, Stony Brook has created a database that continues to grow of close to 10,000 people, which includes 3,000 inpatients, 4,000 who weren’t sick enough for hospital admission, and around 3,000 who thought they had the disease, but had other illnesses. “We’ve learned a ton from that, and it’s not just learning for learning’s sake,” Kaushansky said. The demand for the use of the database is so high that a steering committee is reviewing proposals.
Stony Brook had heard from doctors in Italy that COVID patients were having problems with blood clotting. This symptom was particularly meaningful to Kaushansky, who is a hematologist.
SBU studied the symptoms and “did a trial to see if aggressive anticoagulants would produce better outcomes” than the standard of care at the time, he said. “Our [intensive care unit] patients who were on this more aggressive anticoagulation protocols had half the mortality” of other patients, so the hospital “quickly adopted all of our care” to the more effective approach.
The hospital preemptively used biomarkers to determine who should and should not get aggressive anticoagulation. A subsequent study using the database confirmed the school’s early conclusion. Stony Brook published over 150 papers on the structure of the virus, clinical observations, sociological interventions, and a host of other areas, according to Kaushansky.
Carol Gomes, Chief Executive Officer of Stony Brook University Hospital, appreciated Kaushansky’s hands on approach, which included participating in daily calls as part of the hospital incident command center.
She likened Kaushansky to an orchestra leader, coordinating the research and patient care, making sure there was “no duplication of effort.”
Kaushansky believes federal research funding agencies and policy makers will recognize the importance of gathering information about this pandemic to treat future patients who might battle against variants and to provide a playbook for other health threats. “We really do need to prepare for the next one” as this is the third and deadliest of three coronaviruses, including SARS and MERS, he said.
Vaccines
As for vaccines, Kaushansky said Stony Brook was making it as “convenient as we can” to get a vaccination for health care workers. As of about a month ago, over 80 percent of Stony Brook’s health care workers had been vaccinated.
The black and brown communities have benefited from seeing leaders and role models receiving the vaccine. “This is beginning to erode the mistrust,” said Kaushansky, which developed as a byproduct of the infamous Tuskegee experiment, in which black men with syphilis did not receive penicillin despite its availability as an effective treatment.
Kaushansky added that a concern he’s heard from a range of people is that the vaccine was developed too quickly and that the side effects could be problematic. He cited the simultaneous steps doctors, pharmaceutical companies and others took to accelerate a process that didn’t leave out any of those steps.
Kaushansky participates in a group email interaction with prominent European hematologists. Looking at the data for the Astrazeneca vaccine, these researchers have calculated that anywhere from one in 500,000 to one in a million have developed blood clots.
“Not a single person on this mass email believes that they should stop the Astrazeneca vaccines for that kind of incident,” he said.
What He Helped Build
Kaushansky has been such a supporter of expanding the facilities and expertise at Stony Brook that he said the campus developed a joke about him.
“What’s the dean’s favorite bird?” he asked. “A crane.”
Fixtures on the campus for years, those cranes — the construction vehicles, not the birds — have changed the university, adding new teaching, research and clinical space on the campus.
That includes the Medical and Research Translational building and Bed Tower, which started in 2013 and opened in 2018, and the Hospital Pavilion, which has an additional 150 beds. Those extra beds were especially important a year after the pavilion opened, providing much-needed space for patients battling against COVID.
Gomes appreciated what Kaushansky built physically, as well as the interactive collaborations among different parts of the university. “An active collaboration and communication between researchers, clinicians and academics is a very different model” from the typical separation among those groups, she said. The work “reaped great rewards on the front end with the ability to collaborate to bring new ideas forward.”
As for the type of care patients received at Stony Brook, Kaushansky recalled a discussion over six years ago about central line infections. The data came from a 12 month period, starting six months prior to the meeting and going back to 18 months earlier.
“How are we going to know why all those central line infections occurred by looking at data” from so much earlier, Kaushansky recalled asking. The hospital created real time dashboards, which is an effort that has “paid huge dividends.”
Kaushansky cited the hospitals’ top 100 health grade for three years running. These grades assess whether patients survive a procedure, have complications or need to be readmitted.
“You’re going to get the best care possible when you come to Stony Brook,” Kaushansky said, as the top 100 rating puts Stony Brook in the top 2 percent of hospitals in the country.
Apart from the buildings Kaushansky helped develop, he’s proud of the program he helped build for medical school students.
About six years ago, Stony Brook instituted a new medical school curriculum that had translational pillars. The school starts students in the clinical realm considerably earlier than the classic program that involves two years of basic studies, followed by two years of clinical work.
Stony Brook provides basic science, followed by earlier exposure to the clinic, with a return to basic science after that
“It’s much more effective if you teach the basic science after the student has witnessed the clinical manifestation,” Kaushansky said. These approaches are part of translational pillars in areas such as cancer, physiology and infectious diseases.
As for what he’ll miss after he leaves, Kaushansky particularly appreciated the opportunity to speak with students. He used to hold a monthly breakfast with four or five students, where he learned about each student, their career goals and their medical journey.
A former colleague at the University of California at San Diego, John Carethers, who is the Chair in the Department of Internal Medicine at the University of Michigan, visited Kaushansky as a speaker twice at Stony Brook.
Carethers saw “first hand the wonderful impact he had on students — knowing their names, and providing wonderful advice,” he wrote in an email.
The Next Steps
For a decade, Kaushansky said he wanted to create a course about the future of medicine.
“There are a lot of great innovations in medicine that are fascinating from a scientific and clinical perspective,” Kaushansky said.
He will work on a course for use at Stony Brook in the main campus, the medical campus and for whichever program is interested in sharing these innovative medical and scientific steps in medicine.
He also plans to continue to be the lead editor of the primary textbook in hematology, called Williams Hematology. The textbook has gone through 10 editions.
Kaushansky and his wife Lauren, who is an author and education professor at Stony Brook, aren’t likely to remain on Long Island in the longer term. The couple has a getaway home in Santa Fe and may go there.
Kaushansky’s hobbies include wood working and running. He made a sofa when he was an undergraduate at UCLA, while his second significant work was a 16-foot sailboat he made as a second-year resident. He estimates he has made 40 pieces of furniture.
Kaushansky runs four miles a day four to six times a week. In 1990, he ran the Seattle Marathon which was the Goodwill Games Marathon, finishing in a time of around three hours and twenty-five minutes.
Culturally, Kaushansky hopes the school continues to embrace his focus on generosity.
“You’ve got to be generous with your time,” he said.
“No more can you say that you are too busy to talk. You have to be of a personality that takes pride and that gets the endorphins going from seeing the people you have brought, the people you have entrusted in leadership roles, succeed.”
People around the world are lining up, and in some cases traveling great distances, to get vaccinations to COVID-19 that will provide them with immune protection from the virus.
An important step in the vaccinations from Pfizer-BioNTech and Moderna, the two messenger RNA vaccinations, originated with basic research at Brookhaven National Laboratory in the 1980’s, close to 40 years before the pandemic infected millions and killed close to three million people.
At the national laboratory, scientists including F. William Studier, Alan Rosenberg, and the late John Dunn, among others, worked on another virus, called the T7 bacteriophage, which infects bacteria. T7 effectively corrupts a bacteria’s genetic machinery, turning it into a machine that makes copies of itself.
From top graphic, the T7 virus uses RNA polymerase and a promoter to start a process inside a bacteria that makes copies of itself; researchers use copies of the promoter and the polymerase to insert genes that code for a specific protein; the mRNAs are injected into our arms where human ribosomes make COVID-19 spike proteins. Those spike proteins train the attack dog cells of our immune system to recognize the virus if it attempts to invade.
Back in the 1980’s, Studier and Dunn in BNL’s Biology Department were trying to do something no one else had accomplished: they wanted to clone the T7 RNA polymerase. The use of this genetic region, along with a promoter that starts the process of transcription, enabled scientists to mimic the effect of the virus, directing a cell to make copies of genetic sequences or proteins.
The BNL researchers perfected that process amid a time when numerous labs were trying to accomplish the same molecular biological feat.
“Although there were several labs that were trying to clone the T7 RNA polymerase, we understood what made its cloning difficult,” said Alan Rosenberg, who retired as a senior scientist at BNL in 1996. The patented technology “became the general tool that molecular biologists use to produce the RNA and proteins they want to study.”
The scientists who worked on the process, as well as researchers who currently work at BNL, are pleased that this type of effort, which involves a desire for general knowledge and understanding before policy makers and funders are aware of all the implications and benefits, led to such life-saving vaccinations.
“This is an excellent example of the value of basic science in that the practical applications were quite unanticipated,” John Shanklin, Chair of BNL’s Biology Department, wrote in an email.
“The goal of the work Studier and his team did was to understand fundamental biological principles using a virus that infects bacteria. Once discovered, those principles led to a transformation of how biochemists and biomedical researchers around the world produce and analyze proteins in addition to providing a foundational technology that allowed the rapid development of mRNA vaccines,” he wrote.
Shanklin described Studier, who recruited him to join BNL 30 years ago from Michigan, as a mentor to numerous researchers, including himself. Shanklin credits Studier for helping him develop his career and is pleased that Studier is getting credit for this seminal work.
“I am tremendously proud that the basic research done in the Biology Department has been instrumental in accelerating the production of a vaccine with the potential to save millions of lives worldwide,” Shanklin wrote. “I couldn’t be happier for [Studier] and his team being recognized for their tremendous basic science efforts.”
Steve Binkley, Acting Director of the Department of Energy’s Office of Science, acknowledged the importance of the earlier work.
“The fact that scientific knowledge and tools developed decades ago are now being used to produce today’s lifesaving mRNA vaccines for COVID-19 is a great example of how the Department of Energy’s long-term investments in fundamental research at our National Laboratories can improve American lives today and into the future,” Binkley said in a statement.
Studier explained that his interests were more modest when he started studying this particular virus, which infects the bacteria E. coli.
“T7 was not a well-studied bacteriophage when I came to Brookhaven in 1964,” Studier, who is a senior biophysicist Emeritus, said in a statement. “I was using it to study properties of DNA and decided also to study its molecular genetics and physiology. My goal, of course, was to understand as much as possible about T7 and how it works.”
In an email, Studier said he did not realize the connection between his work and the vaccinations until Venki Ramakrishnan, a Nobel-Prize winning structural biologists from the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, told him.
“I am pleased that our work with T7 is relevant for fighting this world-wide pandemic,” Studier wrote. “History shows that some of the most useful discoveries come from basic research that could not have been predicted.”
While BNL is one of 17 Department of Energy facilities, it has conducted scientific research in numerous fields.
Several translational achievements originated at BNL, Shanklin wrote, including the thalium stress test for evaluating heart function, the development of Fluoro Deoxy Glucose for Positron Emission Tomography and the first chemical synthesis for human insulin, which allowed human insulin to replace animal insulin.
As for the effort that led to the T7 discoveries, Studier worked with Parichehre Davanloo, who was a postdoctoral fellow, Rosenberg, Dunn and Barbara Moffatt, who was a graduate student.
Rosenberg appreciated the multi-national background of the researchers who came together to conduct this research, as Moffatt is Canadian and Davanloo is Iranian.
Rosenberg added that while the group had “an inkling” of the potential usefulness of the processes they were perfecting, they couldn’t anticipate its value over the next 40 years and, in particular, its current contribution.
“Nobody really understood or thought just how widely spread its use would be,” Rosenberg said. “We certainly had no idea it would be an important element in the technology” that would lead to the Pfizer and Moderna vaccinations.
After a year filled with various kinds of losses in 2020, many residents are coping with emotional burdens, including a calendar filled with anniversaries of painful memories.
Called the anniversary effect, people who have been grieving losses are approaching and, in some cases have passed, the one year anniversary of the death of a family member, the last time they saw a family member in person, or the day they dropped a friend who couldn’t breathe off at a hospital.
“It’s good to acknowledge an anniversary is coming up,” said Mandi Zucker, a licensed social worker with a certificate in grief recovery and in thanatology, which is the study of death and dying. Those who feel comfortable offering their support might want to ask someone who is grieving what they are doing, if they have any plans and how they might spend the day.
Zucker, who is the founder of Inner-Harbor, a center that helps young adults who are grieving, cautioned that reaching out to someone only as an anniversary approaches might backfire.
If the anniversary is the only time someone reaches out, “that might feel disingenuous,” Zucker cautioned. People who are grieving might wonder “where you’ve been for the past year, if you are reaching out as if the other 364 days have not been difficult.”
People eager to provide support to the many residents who are dealing with the symptoms and after effects of grief should first make sure they are comfortable enough with their own lives to respond to their family and friends.
“Don’t ask if you’re not ready to hear it,” Zucker suggested. “If you’re going through something yourself and you’re in a hurry and don’t have the time, don’t ask.”
Support often takes the form of listening, rather than interrupting or talking. Zucker suggests people encourage those who are grieving to speak, without interrupting them, sharing their own anecdotes or judging them.
While it might not sound like long, two minutes is considerably longer than most people can offer their thoughts and feelings, as others typically interrupt well before then.
“There is nothing we can say that’ll fix” grief, Zucker said. “Our goal to be supportive is to let them say more. When you’re talking with them, think about why you are talking.”
Commenting on someone’s experience, by acknowledging that their description sounds sad, scary or painful, gives them an opening to continue to share.
When someone says, “It’s been rough with COVID,” almost everyone can offer their own experiences with the virus, the losses of freedom, and opportunity that they’ve felt, she said. Even though a supporter might want to share their experience to relate, the person who is grieving is likely better off having an opening to continue to share and experience their feelings, Zucker suggested.
Sometimes, just allowing the person to tell you to go away gives people control over a life that seems out of control.
“You can give them space, [but] you can also send an email or text saying that you are still thinking about them,” Zucker said. “You don’t have to imply that they must respond.”
Zucker is a fan of handwritten notes, which provide a material connection when someone doesn’t feel like talking, but can see a physical reminder of their connection to others.
If people notice that someone who is grieving isn’t getting dressed or showering, they can comment on it, letting them “know you see them.”
Zucker has a contrary view to the comment people often receive about being strong. For her, people show strength by being vulnerable, not by masking their feelings.
People who might be experiencing grief might also need to diversify their sources of support and strength. That could include meditating or going for walks.
From left, Dr. Sunil Kumar Sharma, Dr. Priyanka Sharma, Ritika Joshi, and Dr. Ben Hsiao. Photo by Lynn Spinnato
By Daniel Dunaief
“Water, water everywhere, nor any drop to drink,” according to Samuel Taylor Coleridge in his poem “The Rime of the Ancient Mariner.”
That won’t be the case, particularly in areas with fresh water that needs decontamination, if Stony Brook’s Ben Hsiao and Priyanka Sharma have anything to say about it.
The duo recently won first place for creativity in the prestigious Prince Sultan Bin Abdulaziz International Prize for Water that drew research applicants, and runners up, from all over the world who are addressing water-related challenges. Hsiao, Distinguished Professor in the Department of Chemistry at Stony Brook University and Sharma, Research Assistant Professor, will receive $133,000 for winning first place for the award which is given every other year.
Hsiao and Sharma are continuing to develop a plant biomass-based filtration system that is designed to make drinking water, a scarce necessity in developing nations around the world, more accessible to people who sometimes have to walk hours each day for their allotment.
Hsiao said he was “really honored [just] to be nominated” by the Department Chair Peter Tonge. “There are so many people in the whole world working on water purification.”
Winning the award was “truly a surprise,” with Hsiao adding that he is “humbled” by the honor.
Sharma said it was an “amazing feeling to receive an international prize.” The work, which has received two other awards including from the New York Academy of Science, has “truly gained its importance,” she wrote in an email.
Sharma said her parents and her husband Sunil Kumar Sharma’s parents, who live in her native India, have been “spreading the news” in India and are excited for the recognition and for the potential benefit to society from the research.
Hsiao, who started working on filtration systems in 2009 after Richard Leakey invited him to visit the Turkana Basin Institute in Kenya, has made several discoveries in connection with a process he hopes becomes widely available to people in communities that don’t have electricity.
He and Sharma have developed adsorbents, coagulants and membrane materials from biomass-sourced nanocellulose fibers.
The standard commercial water purification system involves using artificial polymers, in which electricity pumps water through the filter that can remove bacteria, viruses, heavy metals and other potential contaminants.
Hsiao and Sharma, however, have turned to the plant world for a more readily available and cost effective solution to the challenge of filtering water. Plants of all kinds, from shrubs to bushes to feedstock, have overlapping cellulose fibers. By deploying these overlapping needles in filters, the Stony Brook scientists can remove the kind of impurities that cause sickness and disease, while producing cleaner water.
The needles, which are carboxy-cellulose nanofibers, act as a purifying agent that has negative surface charge which causes the removal of oppositely charged impurities. By using these fibers for water purification, Sharma said the team has improved the efficiency and cost related to impurity removal.
Hsiao and Sharma have not tested this material for filters yet. A few years ago, Hsiao used a similar material for filtration. When Sharma joined Hsiao’s lab, she helped develop a cost effective and simpler method, which is how she started working on the nitro-oxidation process. The substrate from nitro-oxidation acts as a purifying agent like charcoal.
The substrates they created can benefit the developed as well as the developing world. In the future, if they receive sufficient funds, they would like to address the ammonium impurities initially on Long Island. The area regularly experiences algal blooms as a result of a build up of nitrogen, often from fertilizers.
The negatively charged substrate attracts the positively charged ammonium impurities. They have tested this material in the lab for the removal of ammonium from contaminated water. Not only does that cleanse the water, but it also collects the ammonium trapped on the carboxycellulose fibers that can be recycled as fertilizer.
Hsiao is working with two countries on trying to make this approach available: Kenya and Botswana. The Kenya connection came through the work he has been doing with Richard Leakey at Stony Brook’s Turkana Basin Institute, while Botswana is a “small but stable country [in which he can] work together to have some field applications.”
Hsiao said Sharma, whom he convinced to join his lab in 2015, has a complementary skill set that enables their shared vision to move closer to a reality.
Sharma’s “cellulose chemistry is a lot better than mine,” Hsiao said. “I have these crazy visions that this is going to happen. She allows me to indulge my vision. Plus, we have a team of dedicated students and post docs working on this.”
Hsiao encouraged Sharma to join his research effort when he offered his idea for the potential benefits of the work.
Hsiao said he “ wanted to do something for societal benefit,” Sharma said. “That one sentence excited me.” Additionally, she said his lab was well known for using the synchrotron to characterize cellulose nanofibers and for developing cellulose based filtration membranes.
Coming from India to the United States “wasn’t easy,” as no one in her extended family had been to the states, but she felt a strong desire to achieve her academic and professional mission.
Hsiao described Sharma as a “promising, talented scientist,” and said he hopes they can land large research grants so they can continue to develop and advance this approach.
Back in 2016, Hsiao set an ambitious goal of creating a process that could have application throughout the world within five years, which would be around now.
“I was naive” about the challenges and the timing, Hsiao said. “I still have another five to 10 years to go, but we’re getting closer.”
Broadly, the effort to provide drinkable water that is accessible to people throughout the world is a professional challenge Hsiao embraces.
The effort “consumes me day and night,” he said. “I’m dedicating the rest of my life to finding solutions. I’m doing this because I feel like it’s really needed and can have a true impact to help people.”
Bringing together researchers and clinicians from six countries, including scientists scattered throughout the United States, a team of scientists co-led by Stony Brook University’s Michael Frohman linked mutations in a gene to congenital heart disease.
Frohman, Chair of the Department of Pharmacological Sciences in the Renaissance School of Medicine at SBU, has worked with the gene Phospholipidase D1 (or PLD1), for over 25 years. Researchers including Najim Lahrouchi and Connie Bezzina at the University of Amsterdam Heart Center linked this gene to congenital heart disease.
“The current study represents a seminal finding in that we provide a robust link between recessive genetic variants of PLD1 and a rather specific severe congenital heart defect comprising right-side valvular abnormalities,” Bezzina wrote in an email.
Michael Frohman at Glymur Falls in Iceland.
The international group collected information from 30 patients in 21 unrelated families and recently published their research in the Journal of Clinical Investigation.
A number of other genes are also involved in congenital heart disease, which is the most common type of birth defect. People with congenital heart disease have a range of symptoms, from those who can be treated with medication and/or surgery for pre-term infants to those who can’t survive.
The discovery of this genetic link and congenital heart disease suggests that PLD1 “needs to be screened in cases with this specific presentation as it has implications for reproductive counseling in affected families,” Bezzina explained.
Bezzina wrote that she had identified the first family with this genetic defect about five years ago.
“We had a strong suspicion that we had found the causal gene, but we needed confirmation and for that, we needed to identify additional families,” she said. “That took some time.
Bezzina described the collaboration with Frohman as “critical,” as she and Lahrouchi had been struggling to set up the PLD1 enzymatic assay in their lab, without any success. Lahrouchi identified Frohman as a leading expert in the study of PLD1 and the team reached out to him.
His work was instrumental in determining the effect of the mutations on the enzymatic activity of PLD1, Bezzina explained.
The timing in connecting with Frohman proved fortuitous, as Frohman had been collaborating with Michael Airola, Assistant Professor in the Department of Biochemistry & Cell Biology at Stony Brook University, on the structure of the PLD1 catalytic domain.
“Together, they immediately saw that the mutations found in the patients were located primarily in regions of the protein that are important for catalysis and this provided detailed insight into why the mutations caused the PLD1 enzyme to become non-functional,” Bezzina wrote.
These findings have implications for reproductive counseling, the scientists suggested.
A couple with an affected child who has a recessive variation of PLD1 could alert parents to the potential risk of having another child with a similar defect.
One of the variants the scientific team identified occurs in about two percent of Ashkenazi Jews, which means that 1 in 2,500 couples will have two carriers and a quarter of their conceptions will be homozygous recessive, which virtually guarantees congenital heart disease. This, however, is about three times less frequent than Tay-Sachs. “This has, in our view, clinical implications for assessing the risk of congenital heart defects among individuals of this ancestry,” said Bezzina.
The mutation probably arose among Ashkenazi Jews around 600 to 800 years ago. There are about 20 known disease mutations like Tay-Sachs in this population that are found only rarely in other groups.
Lahrouchi and Bezzina specialize in the genetics of congenital heart disease, which occurs worldwide in 7 out of every 1,000 live births.
With 56 coauthors, Frohman said this publication had the largest number of collaborators he’s ever had in a career that includes about 200 papers. While this is unusual for him, it’s not uncommon among papers in clinical research.
The lead researchers believed a comprehensive report with a uniform presentation of clinical data and biochemical analysis would provide a better resource for the field, so they brought together research from The Netherlands, the Czech Republic, Israel, France, Italy and the United States.
Previous research that involved Frohman revealed other patterns connected to the PLD1 gene.
About a dozen years ago, Frohman helped discover that mice lacking the PLD1 gene, or that were inhibited by a drug that blocked its function, had platelets that are less easily activated, which meant they were less able to form large blood clots.
These mice had better outcomes with strokes, heart attacks and pulmonary embolisms.
The small molecule inhibitor was protective for these conditions before strokes, but only provided a small amount of protection afterwards. Technical reasons made it difficult to use this inhibitor in clinical trials.
The primary work in Frohman’s lab explores the link between PLD1 and cancer. He has shown that loss of PLD1 decreases breast cancer tumor growth and metastasis.
As for what’s next, Frohman said he has a scientific focus and a translational direction. On the scientific front, he would like to know why the gene is required for heart development. He is launching into a set of experiments in which he can detect what might go wrong in animal models early in the development of the heart.
Clinically, he hopes to explore how one bad copy of the PLD1 gene combines with other genes that might contribute to cause enough difficulties to challenge the survival of a developing heart.
A resident of Old Field, Frohman lives with his wife Stella Tsirka, who is in the pharmacology department and is Vice Dean for Faculty Affairs in the Renaissance School of Medicine. The couple has two children, Dafni, who is a first-year medical student at Stony Brook and Evan, who is a lawyer clerking with a judge in Philadelphia.
Outside of work, Frohman, who earned MD and PhD degrees, enjoys hikes in parks, kayaking and biking.
Having a medical background helped him learn a “little bit about everything,” which gave him the opportunity to prepare for anything new, which included the medical implications of mutations in the PLD1 gene.
Bezzina hopes to continue to work with Frohman, on questions including how the mutation type affects disease severity. “An interplay with other predisposing genetic factors is very interesting to explore as that could also help us in dissecting the disease mechanism further,” she wrote.
When I was in college, I learned an important lesson in class that had nothing to do with the subject I was studying. Many years ago, I attended an early morning anthropology lecture.
Pacing at the front and bottom of a semicircular stage, the professor shared details about the hungry ghost festival. In various parts of Asia and India, people practice a ritual in which they relieve the suffering of their deceased relatives by providing food. During this time, the professor said, people prepare meals and leave empty seats for ghosts, who ritualistically consume the food.
Seated next to a friend from our dorm, I was busily taking notes, not only because I wanted to do well on a future test, but because I also found the description fascinating.
That’s when the professor became distracted. Someone from the audio visual department was quietly packing up equipment at the back of the room.
“Excuse me,” the professor yelled to the man. “What are you doing?”
“I’m sorry,” the man said.
“Well, you should be,” the professor barked back.
The man continued to try to pack up the materials quietly. The noise, which I barely heard from a seat that was much closer to the back of the room, was still too much for my professor.
“You’re sorry, but you’re still disrupting my class!” he shouted.
“I’m packing up the material. I work for the university. One of the other classes needs it now,” the man replied. “I’ll keep it down.”
“No, this is ridiculous,” the professor said through gritted teeth. “I won’t tolerate this. You will leave.”
The man stood still, unsure of what to do. In that moment, I felt like I had a choice: I could either say something to support the man in the back of the room or walk out of the class. By doing and saying nothing, which is what I did, I felt like I was accepting the professor’s behavior.
When the man spent one more minute doing his work, the professor demanded to know where he worked so he could show up and bother him while he was trying to concentrate.
All these years later, I still think of that small moment. These types of incidents require a readiness to think, speak or act, especially to something that disturbs or distresses us. It’s akin to what coaches say all the time in sports: know what you’re going to do with the ball before it comes to you. If you have to think too much about your next move, it’s going to be too late.
A recent anti-Asian incident in New York City, in which security guards watched as a man knocked down and kicked a 65-year-old woman on her way to church, reminded me of the need to be prepared to do the right thing, even when someone wrongs someone else.
We are more likely to act when we are prepared to help, even if the moment creates discomfort for us.
Nowadays, we all have an opportunity to support each other, particularly amid anti-American attacks on members of the Asian American community. These cowardly verbal and physical assaults will become less prevalent if perpetrators know we’re all prepared to stand up for our friends and neighbors who have become the target for random anger during the pandemic. Asian Americans are not an enemy of the rest of us any more than our heart is the enemy of our body. We should stand with, and for, each other.
The goal sounds like a dystopian version of a future in which computers make critical decisions that may or may not help humanity.
Peter Koo, Assistant Professor and Cancer Center Member at Cold Spring Harbor Laboratory, would like to learn how to design neural networks so they are more interpretable, which will help build trust in the networks.
The neural networks he’s describing are artificial intelligence programs designed to link a molecular function to DNA sequences, which can then inform how mutations to the DNA sequences alter the molecular function. This can help “propose a potential mechanism that plays a causal role” for a mutation in a given disease, he explained in an email.
Researchers have created numerous programs that learn a range of tasks. Indeed, scientists can and have developed neural networks in computer vision that can perform a range of tasks, including object recognition that might differentiate between a wolf and a dog.
Koo when he received a COVID vaccination.
With the pictures, people can double check the accuracy of these programs by comparing the program’s results to their own observations about different objects they see.
While the artificial intelligence might get most or even all of the head-to-head comparisons between dogs and wolves correct, the program might arrive at the right answer for the wrong reason. The pictures of wolves, for example, might have all been taken during the winter, with snow in the background The photos of dogs, on the other hand, might have cues that include green grass.
The neural network program can arrive at the right answer for the wrong reason if it is focused on snow and grass rather than on the features of the animal in a picture.
Extending this example to the world of disease, researchers would like computer programs to process information at a pace far quicker than the human brain as it looks for mutations or genetic variability that suggests a predisposition for a disease.
The problem is that the programs are learning in the same way as their programmers, developing an understanding of patterns based on so-called black box thinking. Even when people have designed the programs, they don’t necessarily know how the machine learned to emphasize one alteration over another, which might mean that the machine is focused on the snow instead of the wolf.
Koo, however, would like to understand the artificial intelligence processes that lead to these conclusions.
In research presented in the journal Nature Machine Intelligence, Koo provides a way to access one level of information learned by the network, particularly DNA patterns called motifs, which are sites associated with proteins. It also makes the current tools that look inside black boxes more reliable.
“My research shows that just because the model’s predictions are good doesn’t mean that you should trust the network,” Koo said. “When you start adding mutations, it can give you wildly different results, even though its predictions were good on some benchmark test set.”
Indeed, a performance benchmark is usually how scientists evaluate networks. Some of the data is held out so the network has never seen these during training. This allows researchers to evaluate how well the network can generalize to data it’s never seen before.
When Koo tests how well the predictions do with mutations, they can “vary significantly,” he said. They are “given arbitrary DNA positions important scores, but those aren’t [necessarily] important. They are just really noisy.”
Through something Koo calls an “exponential activation trick,” he reduces the network’s false positive predictions, cutting back the noise dramatically.
“What it’s showing you is that you can’t only use performance metrics like how accurate you are on examples that you’ve never seen before as a way to evaluate the model’s ability to predict the importance of mutations,” he explained.
Like using the snow to choose between a wolf and a dog, some models are using shortcuts to make predictions.
“While these shortcuts can help them make predictions that [seem more] accurate, like with the data you trained it on, it may not necessarily have learned the true essence of what the underlying biology is,” Koo said.
By learning the essence of the underlying biology, the predictions become more reliable, which means that the neural networks will be making predictions for the right reason.
The exponential activation is a noise suppressor, allowing the artificial intelligence program to focus on the biological signal.
The data Koo trains the program on come from ENCODE, which is the ENCyclopedia Of DNA Elements.
“In my lab, we want to use these deep neural networks on cancer,” Koo said. “This is one of the major goals of my lab’s research at the early stages: to develop methods to interpret these things to trust their predictions so we can apply them in a cancer setting.”
At this point, the work he’s doing is more theoretical than practical.
“We’re still looking at developing further tools to help us interpret these networks down the road so there are additional ways we can perform quality control checks,” he said.
Koo feels well-supported by others who want to understand what these networks are learning and why they are making a prediction.
From here, Koo would like to move to the next stage of looking into specific human diseases, such as breast cancer and autism spectrum disorder, using techniques his lab has developed.
He hopes to link disease-associated variance with a molecular function, which can help understand the disease and provide potential therapeutic targets.
While he’s not a doctor and doesn’t conduct clinical experiments, Koo hopes his impact will involve enabling more trustworthy and useful artificial intelligence programs.
Artificial intelligence is “becoming bigger and it’s undoubtedly impactful already,” he said. “Moving forward, we want to have transparent artificial intelligence we can trust. That’s what my research is working towards.”
He hopes the methods he develops in making the models for artificial intelligence more interpretable and trustworthy will help doctors learn more about diseases.
Koo has increased the size and scope of his lab amid the pandemic. He current has eight people in his lab who are postdoctoral students, graduate students, undergraduates and a master’s candidate.
Some people in his lab have never met in person, Koo said. “I am definitely looking forward to a normal life.”
No matter how much uncertainty and anxiety clouds our lives, the passion that inspires us canpenetrate the haze.
My retired neighbors, whom I see regularly on our walks, have shared their lives with us over the last year, offering news updates about their two grown children as well as their pursuit of vaccinations. Amid all the other news, they shared a development in their backyard that has completely captivated their attention.
Andrea and Bob said they were doing their usual gardening, trimming their bushes and reseeding their lawn, when they noticed something new next to their grill. Two mallards had decided to nest in a nearby bush.
The presence of this nest has captivated them to such a degree that it’s clear that the first place they look when they return from their walks is in the direction of the nest. They are eager to see whether their visitors, whom they assure us will take about the same 28 days to hatch that it takes between each of the two Moderna vaccinations for COVID, have pushed their way out of their eggs.
Each day, the parent mallards swim in their pool, taking short breaks from their early parenting duties to wade back and forth in a water body that Andrea and Bob assure us won’t have any chemicals or even salt until later in the summer.
They seem so thrilled to host their new guests that the bird droppings or other germs that might clog their filter or encourage bacterial growth don’t seem to concern them.
Indeed, they are so focused on these duck eggs that they have told anyone who ventures in their backyard, including insect control experts, not to spray or go near the nest.
Just to make sure the nest remains undisturbed from human activities, they have also put sawhorses — the kinds of temporary fencing police use to control crowds and building managers use to keep people away from exclusive entrances and exits to buildings — on either side of the nest.
Once the ducks hatch, they plan to take pictures from their window or around their yard, sharing them with friends and family.
The excitement this nest has created not only speaks to the Groundhog Day nature of our lives, but also to the core passion some people feel for nature.
When the right kind of animals appear, and I suspect a young raccoon or a nest of vultures wouldn’t make the cut, people will go well out of their way to support those creatures and to encourage the safety of their young.
Perhaps the arrival of spring and the renewal and hope it brings offers a fitting backdrop for the affection and appreciation of this collection of eggs.
After all, this spring in particular is unlike any other, as people hope to get vaccinated, emerge from their versions of hibernations and plan, tentatively, for the next steps over the next few months and year.
We will hopefully see friends and family we haven’t seen in months or even a year and, in some cases, will also visit with extended friends and family fortunate enough to have added new life to their ranks as well. Despite the baby bust, two sisters in my wife’s extended family gave birth to baby girls within weeks of each other. They will have their own stories to tell, passed down to them from their parents and extended family, about the unusual and challenging environment into which they were born.
In the meantime, however, Andrea and Bob can plan for something in the next few weeks that is unexpected, unplanned and wonderful: the hatching of new ducklings.
On that day, the Mars Perseverance rover descended through the atmosphere with considerable fanfare back on Earth. Using some of the 23 cameras on Perseverance, engineers took pictures and videos of the landing.
The National Aeronautics and Space Administration not only shared the video of the rover descending into the Jezero crater which held water and, perhaps, life three billion years ago, but also offered a view of the elated engineers who had spent years planning this mission.
In a calm, but excited voice, a female narrator counted down the height and speed of the rover, which weighs about a ton on Earth and closer to 800 pounds in the lower gravity of Mars. The NASA video showed staff jumping out of their seats, cheering for the achievement.
Launched from Cape Canaveral, the rover took 233 days to reach Mars, which is about the gestation period for a chimpanzee.
Some of the engineers “who got us there have reached the end of their marathon,” said Joel Hurowitz, Associate Professor in the Department of Geosciences at Stony Brook University and Deputy Principal Investigator for one of the seven scientific instruments aboard the Perseverance.
With ongoing support from other engineers who helped design and build the rover, the scientists “get the keys to the vehicle and we get to start using these things.”
Indeed, Hurowitz and Scott McLennan, Distinguished Professor in the Department of Geosciences at Stony Brook University are part of teams of scientists who will gather information to answer basic questions about Mars, from whether life existed, to searching for evidence of ancient habitable environments, to seeking evidence about the changing environment.
Both Stony Brook scientists were riveted by the recordings of the landing.
Scott McLennan
Hurowitz marveled at the cloud of dust that formed as the rover approached the surface.“You could see these chunks of rock flying back up at the sky crane cameras,” he said. “I was amazed at the amount of debris that was kicked up in the landing process.”
Hurowitz had seen pieces of rock on top of the Curiosity rover after it landed, but he felt he understood more about the process from the new video. “To see it happening, I realized how violent that final stage of the landing is,” he said.
McLennan said this has been his sixth Mars mission and he “never tires of it. It’s always exciting, especially when there is a landing involved.”
Like Hurowitz, who earned his PhD in McLennan’s lab at Stony Brook, McLennan was impressed by the dust cloud. “I understood that a lot of dust and surface debris was displaced, but it was quite remarkable to see the rover disappear into the dust for a short while,” he wrote in an email.
While previous missions and orbiting satellites have provided plenty of information about Mars, the Perseverance has the potential to beam pictures and detailed analysis of the elements inside rocks.
Hurowitz, who helped build the Planetary Instrument for X-ray Lithochemistry, or PIXL, said the team, led by Abigail Allwood at the Jet Propulsion Laboratory, has conducted its first successful instrument check, which involves turning everything on and making sure it works. Around April, the PIXL team will start collecting its first scientific data.
In addition to searching for evidence of previous life on Mars, Hurowitz will test a model for climate variation.
The SuperCam on the Perseverance Rover. Photo by Gregory M. Waigand
From measurements of the chemistry and mineralogy of sedimentary rock, the scientists can deduce whether the rocks formed in an environment that was oxygen-rich or oxygen-poor. Additionally, they can make inferences about temperature conditions based on their chemical compositions.
Looking at variations in each layer, they can see whether Mars cycled back and forth between cold and warm climates.
Warmer periods could have lasted for hundreds, thousands or even tens of thousands of years, depending on how much greenhouse gas was injected at any time, Hurowitz explained. “Whether this is long enough to enable biological development is probably one of the great questions in the field of pre-biotic chemistry,” he said.
The Martian atmosphere could have had dramatic swings between warm and oxygen-poor conditions and cold and oxygen-rich conditions. “This has not really been predicted before and provides a hypothesis we can test with the rover payload for how climate might have varied on Mars,” he added.
Tempering the expectation of confirming the existence of life, Hurowitz said he would be “shocked if we woke one morning and a picture in the rover image downlink [included] a fossil,” he said. “It’s going to take time for us to build up our understanding of the geology of the site well enough.” The process could take months or even years.
Using information from orbiters, scientists have seen minerals in the Jezero crater that are only found when water and rock interact.
With the 11-minute time lag between when a signal from Earth reaches Perseverance, Hurowitz said scientific teams send daily codes up to the rover and its instrument. Hurowitz will be involved in uploading the signals for PIXL.
A Martian day is 40 minutes longer than the Earth day, which is why the Matt Damon movie “The Martian” used the word “sol,” which represents the time between sunrises on Mars.
McLennan, who works on three teams, said PIXL and the SuperCam provide complementary skill sets. With its laser, the SuperCam can measure the chemical composition of rocks at under seven meters away. Up close, PIXL can measure sub millimeter spot sizes for chemistry.
SuperCam will then find areas of interest, enabling PIXL to focus on a postage-stamp sized area.
As a member of the Returned Sample Science Working Group, McLennan, who is a specialist in studying the chemical composition of sedimentary rocks, helps choose which rocks to collect and set aside to bring back to Earth. The rocks could return on a mission some time in the 2030s.
The scientists will collect up to 43 samples, including some that are completely empty. The empty tubes will monitor the history of contamination that the other rock samples experienced.
For McLennan, the involvement of his former student is especially rewarding. Hurowitz “didn’t just help build the instrument, he’s one of the leaders,” McLennan said. “That’s really fabulous.”
For Hurowitz, any data that supports or refutes the idea about the potential presence of life on Mars is encouraging.
He is “cautiously optimistic” about finding evidence of past life on Mars. “We’ve done everything we can as a scientific community to maximize the chance that we’ve landed some place that might preserve signs of life.”
Using information from orbiters, scientists have seen minerals in the Jezero crater that are only found when water and rock interact.
As a member of the Returned Sample Science Working Group, McLennan, who is a specialist in studying the chemical composition of sedimentary rocks, helps choose which rocks to collect and set aside to bring back to Earth. The rocks could return on a mission some time in the 2030s.
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