July 2016

New “All About Grants” Podcast on How to Use the New Assignment Request Form

In a recent NIH All About Grants podcast, we talk to Dr. Cathie Cooper, Director of the Division of Receipt and Referral at NIH’s Center of Scientific Review, about how you can influence the assignment of your application to a particular study section for peer review, or to a particular NIH Institute or Center for funding consideration. Check out “Using the PHS Assignment Request Form” (mp3) (transcript), as well as other podcast episodes on our All About Grants page, http://grants.nih.gov/news/virtual-learning/podcasts.htm under the Preparing a Successful Grant Application heading. When there you can also check out the latest pod cast on Choosing a Submission Method which goes through the benefits of the current four methods of submitting a NIH Grants.gov package.
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Just announced changes that effect F30/31 NIH Fellowships due 8/8

On 7/28/2016 NIH released additional changes that will effect F30/31 Fellowship submissions that are due on 8/8/2016. This deadline will be the first that uses the “D Forms” which had a quite a few changes to begin with.

Among the changes are the addition of several new attachments:
• Applicant’s Background and Goals for Fellowship Training (6 page limit)
• Letters of Support from Collaborators, Contributors, and Consultants (6 page limit)
• Description of Institutional Environment and Commitment to Training (2 page limit; includes Additional Education Information section required for F30 and F31 applications which was previously included as an “Other Attachment” in FORMS-C applications)
• Data Safety Monitoring Plan (used with applications involving Clinical Trials)
• Authentication of Key Biological and/or Chemical Resources (use of this attachment has been delayed - NOT-OD-16-034; don’t use it yet)

Earlier changes have been announced regarding the Fellows bio. Applicants for predoctoral and postdoctoral fellowships should use section D (Additional Information, Research Support. Scholastic Performance) to provide information on their scholastic performance (instead of Research Support).

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New process for resetting FastLane/Research.gov passwords

On Monday, July 25, NSF will implement a more convenient and secure process for resetting passwords. NSF awardees and applicants will no longer be able to reach out to you to reset their passwords; instead, they can reset their own password. To do this, awardees and applicants can go to www.research.gov and click “Log In,” then “Forgot Password.” After entering their NSF ID and clicking, “Send Temporary Password,” they will be able to reset their passwords using the temporary password sent to their email address on file.

Passwords must be between 8 and 20 characters and use three of the four categories below:
· Upper-case letter

· Lower-case letter

· Number

· One of these special characters # & % ! @ ( )

In addition, the last six passwords cannot be reused, and accounts will be locked for five minutes after the tenth unsuccessful password attempt.
Need Help?

To learn more about Research.gov/FastLane password modernization, including accessing a getting started guide and FAQs, please click here.

You can also find helpful Research.gov information by clicking Help in the top right-hand corner of Research.gov or on FastLane, by clicking the FastLane Help in the top right-hand corner of the homepage. We encourage you to review this information to learn how to efficiently use the site.
For additional assistance, please contact the NSF Help Desk at 1-800-381-1532 or Rgov@nsf.gov 

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High-Speed Protein Modeling Could Accelerate Drug Development

A team of international scientists led by Stony Brook University researchers have created an ultra-fast, computerized way to model protein interactions, potentially helping to speed needed drugs to market.

Dima Kozakov, PhD, lead author and Assistant Professor in the Department of Applied Mathematics and Statistics

Protein-protein interactions (PPIs) are the basis of cellular functions, and when these processes are compromised diseases such as cancer emerge. For years scientists have tried with mixed success to map out PPIs to understand cellular processes. Now researchers led by Stony Brook’s Dima Kozakov have outlined a method that could pave the way to designing new drugs that prevent problematic protein interactions that lead to disease. The findings are published in the early online edition of PNAS.

Proteins are the major building blocks of the cell. Many proteins perform their function by interacting with other proteins. In a typical cell, hundreds of thousands of different protein interactions take place. Characterizing the structure of these interactions helps elucidate how organisms function normally and during disease development.

“The problem considered is given three dimensional structures of two individual proteins to predict how these protein interact with each other,” said  Kozakov, lead author and Assistant Professor in the Department of Applied Mathematics and Statistics in the College of Engineering and Applied Sciences, and a faculty member of the  Laufer Center for Physical and Quantitative Biology and Institute for Advanced Computational Science (IACS) at Stony Brook University. He likened the method to characterizing all the possible structures that pairs of “lego blocks” form out of a huge set of different individual starting blocks.

In the paper titled “Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds,” the authors explain a new algorithm used to create ultra-fast approach to modeling protein interactions. They discovered that the method runs 10 to 100 times faster than previous state-of-the-art methods, without compromising accuracy.

The researchers used something called fast Manifold Fourier transform (FMFT) that help speed the calculations, enabling them to sample a large number of putative protein-protein complex conformations.

Correct structure of a protein-protein complex together with an ensemble of alternative structures sampled by the new algorithm.

“The idea behind the approach is to present proteins as a combination of quantum shapes that enable fast simultaneous analysis of many pairs using a single calculation rather than assessing each pair independently,” summarized Dr. Kozakov. “The approach can be run in under 15 minutes on a personal laptop and can be used instead of costly experimental techniques to determine the structure of the protein-protein complex.”

The new algorithm will soon be available to the scientific community through the publicly available protein-protein docking server called ClusPro. This resource, with more than 15000 academic users worldwide, supported by the National Science Foundation and the Binational Science Foundation, is being developed by the same research team at the Laufer Center and IACS, in collaboration with scientists at Boston University.

ClusPro was judged to be the best automated docking server in the latest rounds of the international blind protein docking competition called CAPRI (Critical Assessment of Prediction Interaction).

Dr. Kozakov and colleagues believe the new method, implemented in the ClusPro server, will enable scientists to model protein interactions for the whole cell, a key step to designing drugs that prevent defective protein interactions that lead to disease.

NSF Updates as of July 25th 2016

NSF continues to focus on the automated compliance checks of proposals in order to decrease the burden on both the research community and NSF staff. Effective July 25, 2016, all proposals through Fastlane will be subject to a new series of automated compliance validation checks to ensure proposals comply with requirements outlined in Chapter II.C.2. of the Proposal and Award Policies and Procedures Guide(PAPPG).

The new set of automated compliance checks will trigger error messages for each of the following rules:
o Biographical Sketch(es) and Current and Pending Support files are required for each Senior Personnel associated with a proposal; and
o Biographical Sketch(es) can only be uploaded as a file, must not exceed two pages and can no longer be entered as text.

Note About Proposal File Update (PFU): Proposers should be aware should that if a proposal was received prior to July 25 and contained only one Biographical Sketch and/or Current & Pending Support file (rather than individual files for each senior personnel), a PFU addressing any section of the proposal will result in the proposal not being accepted if it does not comply with these new compliance checks. The checks will be run on all sections of the proposal regardless of which section was updated during the PFU.

Note About Grants.gov:
Proposers should also be aware that Grants.gov will allow a proposal to be submitted, even if it does not comply with these proposal preparation requirements. Should NSF receive a proposal from Grants.gov that is not compliant, it will be returned without review.

Please note that the new set of compliance checks are in addition to the compliance checks that currently exist in FastLane. You can view a complete list of FastLane auto-compliance checks,including these checks, by clicking here . The list specifies which checks are run depending on funding opportunity type (GPG, Program Description, Program Announcement, or Program Solicitation) and type of proposal (Research, RAPID, EAGER, Ideas Lab, Conference, Equipment, International Travel, Facility/Center, or Fellowship). It also specifies whether the check triggers a “warning” or error” message for non-compliant proposals.

We encourage you to share this information with your colleagues. For system-related questions, please contact the NSF Help Desk at 1-800-381-1532 or Rgov@nsf.gov. Policy-related questions should be directed to policy@nsf.gov.

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Meave Leakey Awarded Hubbard Medal, National Geographic Society’s Highest Honor

Millions of years from now, an aspiring anthropology student may brush the dust off a gleaming gold artifact we call the Hubbard Medal, and wonder to whom it belonged.

But today, we know the most recently minted Hubbard Medal belongs to world-renowned paleoanthropologist Meave Leakey, research professor in Stony Brook University’s Department of Anthropology.

Meave is also director of field research at the Turkana Basin Institute in Kenya, a unique nonprofit initiative co-founded by the Leakey family and Stony Brook to drive research at one of the best locations on Earth for studying the origins of humankind.

The National Geographic Society awards the Hubbard Medal, its highest honor, to the world’s most intrepid explorers, discoverers and researchers in recognition of a lifetime of achievement.

Robert E. Peary won the medal first in 1906 for his unprecedented Arctic explorations. Charles Lindbergh won for making the first non-stop transatlantic flight in 1927. Neil Armstrong, Buzz Aldrin and Michael Collins won for landing on the moon in 1969. Jane Goodall won in 1995 for her 35-year study of wild chimpanzees.

Meave Leakey joins this class of fewer than 100 distinguished honorees with good reason. Thanks to her groundbreaking anthropological finds and continued dedication and inspiration to her field of research, we humans know more about our prehistoric ancestors than once ever believed.

A Lifetime of Discovery

Meave Leakey accepts the Hubbard Medal, alongside fellow honoree Nainoa Thompson, at the 2016 National Geographic Explorer Awards in Washington, D.C. on June 16, 2016. Photo by Randall Scott/National Geographic Society.

Born in London in 1942, Meave was always interested in animals. After obtaining degrees in zoology and marine zoology from the University of North Wales, she traveled to Kenya to work for Louis Leakey at his primate research center while pursuing her PhD.

In 1969, Louis’ son (and Meave’s future husband) Richard Leakey invited her to join a field expedition investigating the newly discovered paleontological site of Koobi Fora on the eastern shores of Kenya’s Lake Turkana. That same year, she began working at the National Museums of Kenya (NMK), where she lead the paleontology division from 1982 to 2001.

Meave became coordinator of the NMK’s field research at the Turkana Basin in 1989. Among many major discoveries, her team uncovered remains of a new species and the oldest known hominin to date, Australopithecus anamensis. More than 4 million years old, those fossils revealed that bipedalism, the ability to walk upright, evolved half a million years earlier than researchers once thought.

Then in 1999, Meave’s team uncovered a 3.5-million-year-old skull and partial jaw belonging to an early hominin they named Kenyanthropus platyops. This discovery showed that a third species of Homo lived around the same time as Homo habilis and Homo erectus, significantly impacting how we view human ancestry today.

Familial Footsteps

Meave is the fourth Leakey to earn the prestigious Hubbard Medal, making her family the most-awarded in Hubbard history.

Louis and Mary Leakey, Meave’s parents-in-law, both received the Hubbard Medal in 1962 for their anthropological discoveries in East Africa, including the skull of a Miocene hominoid named Proconsul africanus that lived 23 million to 14 million years ago. Further finds led the Leakeys to announce the species Homo habilis or “handy man,” believed to be a direct human ancestor.

Following his parents’ lead, Richard Leakey was honored with the Hubbard Medal in 1994. As director of the NMK from 1968 to 1989, Richard coordinated field expeditions near Lake Turkana that unearthed stone age tools dating to around 1.9 million years old and evidence of early members of the genus Homo, including skulls of Homo habilis and Homo erectus and a nearly complete 1.6-million-year-old skeleton of a Homo erectus youth.

Partners in Exploration

Meave Leakey discusses fossil sieving with TBI Origins Field School students in Kenya. Photo credit Mike Hettwer.

The Leakeys share a distinguished history of partnership with Stony Brook.

In 2002, Richard joined the University as a visiting professor of anthropology, conducting lectures for undergraduate and graduate students while developing major international conferences on world issues such as global warming, biodiversity conservation and sustainable development. Meave also joined Stony Brook as an adjunct professor of anthropology in 2003.

Two years later, the Leakeys pitched a concept to Stony Brook administration — to develop an institute that could provide permanent infrastructure enabling year-round research in the Turkana Basin, a remote region of sub-Saharan Africa where explorers and scientists have made many major discoveries revealing human’s prehistoric past for more than 50 years.

The Turkana Basin is a hot spot for fossil discoveries thanks to its long history of concentrated tectonic activity in an area where a lake or large river has been present for 7 million years — perfect conditions for evidence of human evolution to be buried and fossilized, then exposed through erosion.

The University enthusiastically endorsed the Leakeys’ concept and together created what is now the Turkana Basin Institute (TBI). As fundraising began in 2006, Meave was appointed research professor in the Department of Anthropology and the TBI. Construction of basic facilities began in 2007, and the first full field center was completed in 2012.

The Leakey Legacy

Meave Leakey and her daughter Louise examine a find at the Turkana Basin Institute. Photo credit Mike Hettwer.

Alongside her daughter Louise, Meave continues to oversee research in the Turkana Basin, making annual expeditions there to recover and study important hominin and faunal remains.

While maintaining her positions as director of field research at the TBI and research professor for Stony Brook, Meave takes a leading role in the TBI’s Origins Field School, which offers both full-semester and summer abroad programs for undergraduates of all majors to study human evolution hands-on at Lake Turkana.

Anthropology undergraduate Evan Wilson wasn’t sure he chose the right major. That all changed when he studied at the TBI under Meave Leakey.

“After hearing Meave’s personal accounts of what are now legendary fossil finds, my whole mindset changed — the passion and drive she still has for a field that seems to answer all its important questions with even more questions is truly inspiring,” said Wilson, who graduates in 2018. “Should I be so lucky to spend my life in this field, I’d be even luckier if I could conduct myself with the poise, intellect and determination that Meave Leakey has for over four decades now.”

Meave also serves as National Geographic explorer-in-residence, research affiliate at the NMK, foreign associate of the U.S. National Academy of Sciences, and an African Academy of Sciences fellow.

To learn more about Meave Leakey, Stony Brook’s Department of Anthropology, and the Turkana Basin Institute’s study abroad opportunities, visit turkanabasin.org andkenyastudyabroad.org.

Diamond Beams Could Revolutionize Radiation Treatment for Cancer

Diamond beam monitors could form the basis of the next generation of radiation therapy for cancer, according to a national team of researchers led by Stony Brook’s Erik Muller, PhD.

Erik Muller holds one of the diamond monitor devices that could potentially be adapted to newer radiation beam systems that Dr. Samuel Ryu has incorporated into treatment protocols at Stony Brook University Cancer Center.

Muller, Senior Research Scientist and Adjunct Professor, Department of Materials Science and Chemical Engineering in theCollege of Engineering and Applied Sciences, is developing high-speed synthetic diamond beam monitors that detect proton and carbon ion beams used for cancer radiation therapy. The research team also includes scientists fromBrookhaven National Laboratory.

The technology, supported by a two-year $500,000 grant from the High Energy Physics Section of the Department of Energy, is designed to provide much higher precision of radiation therapy.

Proton/ion beam therapy remains an emerging area of cancer treatment, with the growing potential for specific targeting of tumors without significant damage to surrounding tissue. One of the most challenging areas for the development of this technology is with the beam delivery system, which ensures that the patient receives the required dose while minimizing the risk of exposure to healthy tissue.

“We believe that diamond is a remarkable material for the beam delivery system because it is radiation hard, tissue equivalent, and has a huge linear dynamic range for delivery,” said Dr. Muller. “By using this technology, our team is developing new beam monitors that will provide three orders of magnitude improvement in speed and precision, and has more durability over current technology.”

The team is focusing its research on the diamond beam detector technology in relation to the dose, timing and shape of the beams.

Dr. Muller is also working with Samuel Ryu, MD, Chair of the Department of Radiation Oncology and Deputy Director for Clinical Affairs at Stony Brook University Cancer Center, to adapt the diamond detectors for use in radiation monitoring for cancer therapy. Dr. Ryu is incorporating the latest high-energy photon radiation systems into the Department, and the diamond detectors could potentially be used to enhance these systems even more once commercialized.

Advancing Virtual Colonoscopy for Early Cancer Screening

Computed tomography colonography (CTC), also known as Virtual Colonoscopy, was invented at Stony Brook University and has been developed as a clinical option recommended by the U.S.Preventive Services Task Force, for screening of early colorectal cancer, http://www.uspreventiveservicestaskforce.org/Page/Document/RecommendationStatementFinal/colorectal-cancer-screening2#pod4 .
 
The development was a joined effort among Stony Brook University faculty of Radiology, Computer Science and Gastroenterology, and has been supported by multiple R01 research awards from the National Institutes of Health (NIH). Professor Jerome Z. Liang, PhD, Principal investigator, was recently awarded over $2 million to continue this NIH R01 research project for another five years under the title of “Advancing Virtual Colonoscopy for Early Cancer Screening”.  This research will not only advance the CTC’s current paradigm of detecting polyps but will also differentiate malignant polyps from non-malignant ones in a cost-effective fashion.
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