By applying statistical techniques to previously collected data and computer simulations, scientists have tripled the fusion yields of experiments conducted on the OMEGA laser facility at the Laboratory for Laser Energetics.

The facility has taken the lead in the laser direct-drive approach to fusion energy by blasting spherical deuterium-tritium fuel pellets with 60 laser beams, converging directly on the pellet surface from all directions at once. This causes the pellet to heat and implode, forming a plasma. If sufficiently high temperatures and pressures could be confined at the center of the implosion, a thermonuclear burn wave would propagate radially through the entire fuel mass, producing fusion energy yields many times greater than the energy input.

The latest increase in yields, reported in Nature, brings scientists closer to an important milestone in their quest to achieve controlled thermonuclear fusion – getting the plasma to self-ignite, enabling an output of fusion energy that equals the laser energy coming in.

“That would be a major achievement,” says Michael Campbell, LLE’s director.

Controlled nuclear fusion would improve the ability to evaluate the safety and reliability of the nation’s stockpile of nuclear weapons — in labs in lieu of actual test detonations. Ultimately, if the fusion output greatly exceeded laser input, controlled fusion could produce an inexhaustible supply of clean energy.

However, designing optimal fusion experiments is a challenging task, due in large part to the difficulty of accurately modeling all of the complex physical processes that occur during an implosion. One of the biggest handicaps has been the lack of accurate predictive models to show in advance how target specifications and laser pulse shapes might be altered to increase fusion energy yields.

To create a predictive model, Varchas Gopalaswamy and Dhrumir Patel, PhD students in mechanical engineering, and their supervisor Riccardo Betti, chief scientist and Robert L . McCrory Professor at LLE, applied data science techniques to results from about 100 previous fusion experiments at OMEGA.

“This approach bridges the gap between experiments and simulations to improve the predictive capability of the computer programs used in the design of experiments.” Betti says. “We borrowed from advances in machine learning and data science over the last decade,” Gopalaswamy says.

The statistical analysis guided LLE scientists in altering the target specifications and temporal shape of the laser pulse used in the fusion experiments. This required a concerted effort by LLE experimental physicists who set up the experiments, and theorists who develop the simulation codes. James Knauer, LLE senior scientist, led the experimental campaign. “These experiments required exquisite control of the laser pulse shape”, Knauer says.  Patel applied the statistical technique to design the laser pulse shape leading to the best performing implosion.

“This was a very, very unusual pulse shape for us,” Campbell says. And yet, within three or four subsequent experiments, an experiment was designed that produced 160 trillion fusion reactions, tripling the previous record at OMEGA. “Only thanks to the dedication and expertise of the facility crew, target fabrication, cryogenic layering and system scientists, were we able to control the target quality and the laser pulse to the precision required for these experiments,” Betti says.

Read more here.

When researchers say they have sequenced the human genome, there is a caveat to this statement: a lot of the human genome is sequenced and assembled, but there are regions that are full of repetitive elements, making them difficult to map. One piece that is notoriously difficult to sequence is the Y chromosome.

Now, University researchers have found a way to sequence a large portion of the Y chromosome in the fruit fly Drosophila melanogaster—the most that the Y chromosome has been assembled in fruit flies. The research, published in the journal GENETICS, provides new insights into the processes that shape the Y chromosome, “and adds to the evidence that, far from a genetic wasteland, Y chromosomes are highly dynamic and have mechanisms to acquire and maintain genes,” says Amanda Larracuente, an assistant professor of biology.

Y chromosomes are sex chromosomes in males that are transmitted from father to son; they can be important for male fertility and sex determination in many species. Even though fruit fly and mammalian Y chromosomes have different evolutionary origins, they have parallel genome structures, says Larracuente, who co-authored the paper with her PhD student Ching-Ho Chang.

Typically, genes from the mother and father are shuffled—or, “cross over”—to produce a genetic combination unique to each offspring. But the Y chromosome does not undergo crossing over, and, as a result, its genes tend to degenerate, while repetitive DNA sequences accumulate.

When mapping a genome, traditional sequencing methods chop up strands of DNA and read—or sequence—them, then try to infer the order of those sequences and assemble them back together.

But, “there is a difference between sequencing a genome and assembling a genome,” Larracuente says. There are so many repetitive strands on the Y chromosome that the pieces tend to look the same. It is difficult, therefore, to figure out where they come from and how to reassemble the strands—like trying to put together a puzzle when all of the pieces are exactly the same color. “When we try to take those bits of DNA and assemble them to see what the chromosome looks like, we can’t fill in some of those gaps. We might have the sequence, but we don’t know where it goes.”

Using sequence data generated by new technology that reads long strands of individual DNA molecules, Chang and Larracuente developed a strategy to assemble a large part of the Y chromosome and other repeat-dense regions. By assembling a large portion of the Y chromosome, they discovered that the Y chromosome has a lot of duplicated sequences, where genes are present in multiple copies. They also discovered that although the Y chromosome does not experience crossing over, it undergoes a different type of recombination called gene conversion. While crossing over involves the shuffle and exchange of genes between two different chromosomes, gene conversion is not reciprocal, Larracuente says. “You don’t have two chromosomes that exchange material, you have one chromosome that donates its sequence to the other part of the chromosome” and the sequences become identical.

The Y chromosome has therefore found a way to maintain its genes via a process different from crossing over, Larracuente says. “We usually think of the Y chromosome as a really harsh environment for a gene to survive in, yet these genes manage to get expressed and carry out their functions that are important for male fertility. This rampant gene conversion that we’re seeing is one way that we think genes might be able to survive on Y chromosomes.”

Scientists can now print realistic organs to practice surgeries, bio-matrices to support damaged tissues, or even new ears to replace those that are injured or affected by congenital birth defects. As the utility of 3D printing continues to grow, so does the need for appropriate regulation of these products by the Food and Drug Administration (FDA).

Experts from academia, government, industry, and foundations discussed the emerging science and regulatory considerations of 3D printing at a forum in the fall of 2017. A sub-group of participants led by Joan Adamo, director of Regulatory Support Services at the University’s Clinical and Translational Science Institute (UR CTSI), and Scott Steele, director of UR CTSI Regulatory Science Programs, recently published their findings and recommendations in the Journal of Clinical and Translational Science.

The biggest challenge to assess the safety and efficacy of 3D printing medical technology is that uses for this technology are continuing to evolve, and will likely be developed as fast or faster than appropriate regulation can be analyzed and established. Therefore, it is important to consider exactly which steps in the process are being regulated and who is responsible for each step.

For a single 3D printing process, there may be several articles to regulate, each offering a separate regulatory path to licensing, clearance or FDA-approval. The “ink” used in 3D bio-printing, which is often composed of cell-based or cell-derived material; the hardware and software to design the printed product; and the printed product itself are all logical points of regulation. The authors recommend regulating these emerging technologies where it will have the broadest impact on future technologies.

To help regulatory science keep pace with rapidly advancing 3D printing technologies, the authors recommend developing educational opportunities. By training individuals in the process, development and regulatory science of 3D printing, the group believes regulation will develop at a similar speed as the technology.

The field of 3D printing represents an exciting avenue for medical advance. Ensuring that the technology makes it to patients in a safe and consistent manner will take work. Fortunately, stakeholders from government, industry, academia, and non-profit sectors are already working together to ensure the future workforce is well educated, and these new technologies can reach patients as quickly as possible.

Raven Osborn thought long and hard about continuing a PhD at the University of Rochester. Other minority students she knew at the Medical Center had also felt the isolation, the constant “being on edge” and “code-switching”—shifting the way they express themselves—that comes with being an underrepresented minority in a STEM field.

“Can I do this for another five and half years?” she wondered.

Antonio Tinoco, a DREAMer who was born in Mexico and raised in Los Angeles, is a fourth year PhD student in the Department of Chemistry on the River Campus. He can remember only one or two occasions when a visiting faculty member of underrepresented minority background was invited to give a seminar in his department.

“My goal is to go into academia to be a professor, do research, and teach. But there are so few examples to follow,” he says. “I don’t even know of anyone who, as a DACA recipient or DREAMer, is a professor in chemistry. So, I could easily tell myself nobody has done it; it’s impossible; maybe I should look for something else.”

Instead, Tinoco, Osborn, and five other graduate students have banded together to form the University of Rochester chapter of the Alliance for Diversity in Science and Engineering (ADSE). The mission of the national ADSE, which was founded in 2014, is to increase the participation of underrepresented groups in academia, industry, and government through graduate student organizations that reach out to students and scientists of all ages and backgrounds.

Other ADSE chapters are at the University of California campuses at Berkeley and Davis, the University of Central Florida, the University of Colorado, Columbia University, Drexel University, Georgia Institute of Technology, University of Maryland, New York University, Northeastern University, and Texas A&M.

Tinoco, the president and founding member of the new chapter, says its immediate goals are twofold:

• Establish a diversity lecture series to bring underrepresented faculty from other universities to Rochester. “It would be an opportunity for underrepresented minority students here to say ‘Wow, there’s someone out there like me who is making it, so maybe there’s hope for me.’” Underrepresented minority postdoctoral fellows would also be invited, especially ones who might be interested in eventually teaching here, Tinoco says.
• Provide a space where underrepresented graduate students in STEM fields from across the University can meet, network, and hold workshops and panels to openly discuss the issues they face. “If we can openly discuss these things, we won’t feel as isolated,” Tinoco says.

To join the University of Rochester chapter of ADSE or learn more, email adserochester@gmail.com

Warner School faculty member Tricia Shalka, who has been selected as a 2019-21 Emerging Scholar Designee by the American College Personnel Association (ACPA). With her research agenda broadly grounded in student affairs and higher education practice, Shalka will receive a $3,000 research grant from ACPA as part of the honor to help fund her upcoming research on the impacts of trauma experiences on college students. More specifically, she will engage in a phenomenological study of how individuals navigate their lives as college students while recovering from trauma. Read more here.

The Ernest J. Del Monte Institute for Neuroscience announces the availability of up to 17 pilot project awards (maximum budget of $50,000 per award) to support novel basic, clinical and translational projects in the neurosciences. These awards will be supported under 5 programs for 2019 and are open to all faculty members across both the Medical School and the River Campus.  Funds available for this year’s program are $660,000. 

The Schmitt Program in Integrative Neuroscience (SPIN) supports pilot and feasibility awards (up to $50,000 per award) for basic science and translational projects that advance our understanding of both normal and abnormal brain functioning (4-5 awards available).

The Harry T. Mangurian Jr. Foundation (MF) offers pilot and feasibility awards (up to $50,000 per award) for basic, clinical and translational projects that specifically support research on Autism Spectrum Disorder (ASD) (2 awards available).

The Rochester Center for Alzheimer’s Disease Research (RCADR), supports pilot and feasibility awards (up to $50,000 per award) for basic science and translational projects that advance our understanding of Alzheimer’s disease and related dementias (2 awards available).

Center for Health + Technology Clinical Neuroscience Pilot Program (CHET) offers pilot and feasibility awards (up to $50,000 per award) for clinical research projects that advance our understanding of areas of unmet need in clinical neuroscience (2 awards available).

University of Rochester Center for Advanced Brain Imaging and Neurophysiology (UR CABIN) offers pilot and feasibility funds (up to $10,000 per award) to support innovative, investigator-initiated basic and clinical neuroscience research using the PRISMA 3T magnet (up to 6 awards available).

For more information and to download the RFA, click here.  Application submissions are due on Monday, March 18.

The Furth Fund, established in 1986 by Valerie and Frank Furth, provides early career scientists with $12,500 in research funds to help foster the development of promising scientists.

Nominees should be junior, tenure track faculty appointed in natural or biological science departments within ASE, SMD or SON who have been hired within the past three academic years.  Preference will be given to nominees who wish to use the award to support the active engagement of graduate students or postdocs in their research.

All nominations must include the nominee’s curriculum vitae and a short (1-2 page) letter from the departmental chair describing the nominee’s research activities and proposed use of the funds, and an endorsement from the dean of the school.  Completed nominations should be directed to Adele Coelho at adele.coelho@rochester.edu

Additional information about the Furth Fund may be found here.

The 2020–21 Fulbright Scholar Program competition offers nearly 500 teaching, research, or combination teaching and research awards in over 125 countries.

Opportunities are available for college and university faculty and administrators as well as for professionals, artists, journalists, scientists, lawyers, and independent scholars.

Visit www.cies.org to learn more and explore the catalog of awards.

The NIH recently revamped its Rigor and Reproducibility webpage, updating terms and offering simple, easy-to-read resources to help grant writers meet the requirements implemented in 2016.

Among the language changes, “scientific premise” is now “rigor of the prior research” in response to confusion expressed by applicants, investigators, and reviewers. Other helpful new material addresses calculating sample sizes, developing an authentication plan, study design for pre-clinical animal model experiments, and including both sexes in research plans.

The site also offers video tutorials and a podcast series in which NIH extramural research integrity officer Patricia Valdez discusses key policy elements in an application, the peer review process, and post-award annual progress reporting.

Jared Mereness, genetics, “Collagen 6 is critical component of lung structure and pulmonary epithelial cell function.” 9 a.m., March 7, 2019. Medical Center 3-6408 (K-307 Auditorium). Advisor: Patricia Sime.

Tiffany Lee, health services research & policy, “Effect of Medicare Dialysis Payment Reform on Care Practices and Health Outcomes for ESRD Patients Receiving Dialysis.” Noon, March 11, 2019. Helen Wood Hall 1W 501 (Medical Center). Advisor: Pattie Kolomic.

Leslie Laam, health services research & policy, “Patient Safety in United States Hospitals: A Culture-based Explanation of Variation in Outcomes.” 9:30 a.m. March 15, 2019. Helen Wood Hall 1W 502 (Medical Center). Advisor: Pattie Kolomic.

Feb. 13: Managing Your Scholarly Identity. Time-saving strategies and University tools that help you connect with colleagues, discover collaborators, manage research data, find funders, and expose your work to new audiences. Facilitated by librarians from both the River Campus and Medical Center. Please register. 11:30 a.m. to 2 p.m., Learning Lab 2-7544, School of Medicine and Dentistry. For more information, email adele.coelho@rochester.edu

Feb. 15: Applications due for Wilmot Cancer Research postdoctoral fellowship providing mentored research training for physicians with MD or MD/PhD degrees who have completed their residency training and intend to pursue an academic career in clinical, translational, or basic cancer research. View application details. For questions, email Pamela Iadarola or call 585-275-1537.

Feb. 21: Jesse L. Rosenberger Works-in-Progress seminar. Christopher Rovee, Humanities Center Fellow, presents “The New Critical Nostalgia” as part of the theme of expertise and evidence. Noon to 2 p.m. Humanities Center Conference Room D at Rush Rhees LIbrary. Lunch provided. RSVP by clicking here.

Feb. 27: Phelps Colloquium Series: Elizabeth West Marvin, professor of music theory and of brain and cognitive sciences, Experiencing Absolute Pitch: Insights from AP Possessors in the US and Asia, and Gilbert “Rip” Collins, professor of mechanical engineering and of physics and astronomy, Extreme Matters: A Laboratory Exploration of Planets, Stars, and Quantum Materials. 4-5:30 p.m. Max at Eastman. Register here. Questions? Contact Adele Coelho or call 273-2571.

March 6: Jesse L. Rosenberger Works-in-Progress seminar. Anna Rosensweig, assistant professor of French, presents “Affective Evidence: Rights of Resistance on the Early Modern French Stage” as part of the theme of expertise and evidence. Noon to 2 p.m. Humanities Center Conference Room D at Rush Rhees LIbrary. Lunch provided. RSVP by clicking here.

March 13: Translational genomics and proteomics un-meeting. Researchers from across UNYTE Translational Research Network member institutions will discuss and develop new, innovative, and effective ideas for genomics and proteomics translational research. 9 a.m. to 4 p.m. Helen Wood Hall 1-304. Click here for registration and agenda.

March 18: Applications due for up to 17 pilot project awards (maximum budget of $50,000 per award) to support novel basic, clinical and translational projects in the neurosciences. Ernest J. Del Monte Institute for Neuroscience. Open to all Medical Center and River Campus faculty. For more information and to download the RFA, click here.

March 19: Nominations due for the Furth Fund, which provides early career scientists with $12,500 in research funds to help foster the development of promising scientists. Nominees should be junior, tenure track faculty appointed in natural or biological science departments within ASE, SMD or SON who have been hired within the past three academic years. Completed nominations should be directed to Adele Coelho at adele.coelho@rochester.edu Additional information about the Furth Fund may be found here.

March 21: Jesse L. Rosenberger Works-in-Progress seminar. William Miller, assistant professor of English, presents “The Prophet Muhammad in the Early English Enlightenment” as part of the theme of expertise and evidence. Noon to 2 p.m. Humanities Center Conference Room D at Rush Rhees LIbrary. Lunch provided. RSVP by clicking here.

March 27: Phelps Colloquium Series: Huaxia Rui, associate professor, Simon Business School, Open Voice or Private Message? The Hidden Tug-of-War on Social Media Customer Service, and Maria Marconi, assistant professor of clinical nursing, and specialty director of Health Care Organization and Management Master’s Program and of the master’s program in nursing, Leveraging Generational Diversity in Our Classrooms. 4-5:30 p.m. Location TBD. Register here. Questions? Contact Adele Coelho or call 273-2571.

April 3: Jesse L. Rosenberger Works-in-Progress seminar. Jennifer Kyker, associate professor of music, presents “Sekuru’s Stories: Musical Sound and the Digital Humanities” as part of the theme of expertise and evidence. Noon to 2 p.m. Humanities Center Conference Room D at Rush Rhees LIbrary. Lunch provided. RSVP by clicking here.

April 17: Jesse L. Rosenberger Works-in-Progress seminar. Anaar Desai-Stephens, assistant professor of ethnomusicology, presents “‘You have to feel to sing!’: Affective Pedagogy, and the Commodification of  ‘Feel’ in (Neo)liberalizing India” as part of the theme of expertise and evidence. Noon to 2 p.m. Humanities Center Conference Room D at Rush Rhees LIbrary. Lunch provided. RSVP by clicking here.

May 2: Jesse L. Rosenberger Works-in-Progress seminar. Tracy Stuber and Anastasia Nikolis, Public Humanities graduate fellows, present a public humanities fellowship update. Noon to 2 p.m. Humanities Center Conference Room D at Rush Rhees LIbrary. Lunch provided. RSVP by clicking here.