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A guide to climbing spots in San Francisco » PAGE 4

Therapy for knock kneed pain » PAGE 6

Go Climb a Rock

Let's Get Physical...


News Briefs » PAGE 3 Journal Club » PAGE 5 Puzzles » PAGE 7

Synapse The UCSF Student Newspaper

Thursday, March 27, 2014

Volume 58, Number 24


Scientific Publishing: An Industry in Flux For scientists around the world, the open access movement has changed how journal articles are read and distributed by offering an alternative to the dominant subscription-based access model. Today, many scientific journal articles are available for free on the web. In this three-part series, we examine the impact of open access journals on the scientific publishing industry.

By Alexandra Greer Science Editor


s scientists and medical researchers at UCSF, we are accustomed to having ready access to the current body of scientific knowledge at our fingertips. It’s simply a matter of hopping on the Internet or heading over to the library. We give little thought to how this scientific data made its way to us. We may be somewhat familiar with the publication process: scientists write up their laboratory findings and submit it to a scientific journal for consideration and pay the necessary fees. If all goes well, it gets published. End of story. In fact, the business of scientific publishing is a complex, multi-layered infrastructure, not unlike the television industry where producers create programs, networks buy the programs, and large cable and satellite distributors bundle the networks into packages which are then sold to end users on a subscription basis. The annual revenues generated from English-language scientific journal publishing are estimated at $9.4 billion in 2011, with 52 percent coming from the United States, according to Outsell, Inc., a marketing agency focused on the publishing industry. The total size of the global science, technology and medicine (STM) market in 2011 (including journals, books, technical information and standards, databases and tools and medical communications) was estimated by Outsell at $23.5 billion. For decades, the large publishers have served as a middleman between the individual journals and the universities, operating on a subscription business model. Publishers, such as Reed Elsevier, John Wiley & Sons, Springer, and Ovid, bundle an array of scien-

Illustration by Jillian Varonin/BMS4

tific journals and then charge university libraries a subscription fee to access the journals. However, like other publishing industries today, disruptive technologies and new business models are forcing rapid and massive changes. And these changes are already affecting how and where scientists publish their research. “I think the subscription model’s days are very numbered now,” said Dr. Peter Binfield, cofounder of the open access journal PeerJ, in describing the changing publishing landscape. “It’s been driven by all sorts of things, like legislation, peoples’ education about the issues, the fact that library can’t pay for their subscriptions. All of that comes into play.” Most notably, open access journals—peer-reviewed scientific journals where accepted manuscripts are publicly available through a Creative Commons license and do not require a subscription for access—have become increasingly popular with scientists around the world and are challenging the traditional business model based on journal subscription fees.



DentStay Helps Minority Dental School Candidates Feel Welcome By Angela Broad Staff Writer


Photo courtesy of DentStay Dinner with pre-dents: (left to right) Ramon Gutierrez (D3), Ngan Tran (D2), Yamrot Alemu (D2), Maximillion Jensen (D3), Eric Brown (D2), Jennifer Villalta (pre-dent), Hannah Garcia (pre-dent), Whitney Bryant (pre-dent)

hen Eric Brown and Yamrot Alemu were applying to dental schools, they would stay with students from campus minority organizations whenever possible, as a way to save money on housing before their interviews and gain valuable insight into campus life. Now in their second year at UCSF School of Dentistry, they wondered why such a program didn’t exist here. So Brown, Alemu and classmate Ivy Fua, along with the Student National Dental Association (SNDA), formed DentStay this academic year. The organization offers underrepresented minority (URM) students interviewees the opportunity to stay with a dental student of a similar background, relieving the candidates of the expense of staying in a hotel in San Francisco, which can cost several hundred dollars a night. “Ivy Fua and I learned more about the program at SNDA's National Convention in the summer of 2013,” said Brown. “We both

knew this could be a great opportunity for us to get involved with and help increase minority student matriculation here on campus.” In addition to offering overnight lodging, a group of student hosts provide the prospective students with dinner the evening before their big day. In an informal atmosphere, SNDA members answer applicants’ questions about UCSF and try to ease the natural stresses of interviewing. In this way, DentStay helps to better prepare URM students for their interviews, gives them an opportunity to spend time with dental students of similar backgrounds and ultimately, encourages them to matriculate at UCSF. “Meeting members of the SNDA community help interviewees see that we are here to encourage and support them throughout their time in dental school,” said Alemu. “Students see that they will always receive help from the SNDA community. In addition, our members are able to answer last minute questions from the interviewees about the curriculum, out-


2 | March 27, 2014 |


Thursday, March 27, 11 a.m.-2 p.m., 4th Street & Nelson Rising Lane, Mission Bay
 Join the food truck lunch party every Thursday at Mission Bay and explore the tasty culinary options to break up your routine. Each week will feature two different vendors, so there will always be something new. Grab some friends, get some food, and take your lunch experience up a notch.


Friday, March 28, 1-2:30 p.m., Helen Diller, 160, Mission Bay
 The Muslim Community at UCSF holds regular Friday prayer services (Jum’a) for the UCSF Muslim community every week. Come join your fellow brothers and sisters for prayer, lunch and socializing. All are welcome.


Tuesday, April 1, 8:30 a.m., Student Lounge, Genentech Hall 2nd Floor, Mission Bay Come enjoy some free bagels, pastries and coffee. Learn about campus services and events and build a community at Mission Bay. Open to Students and Postdocs.


Friday, March 28, 1:30-2 p.m., Medical Sciences, 168, Parnassus The Muslim Community at UCSF holds regular Friday prayer services (Jum’a) for the UCSF Muslim community every week. Come join your fellow brothers and sisters for prayer, lunch and socializing.


Friday, March 28, 7-10:30 p.m., Nursing, 517, Parnassus Join the Campus Evangelistic Fellowship for its weekly meeting, with Bible study, hymn singing and fellowship.


Wednesday, April 2, 10 a.m.-3 p.m., ACC, 400 Parnassus Ave.
 Shop the Farmers’ Markets on Wednesdays to pick up locally grown produce and more. Sponsor: Pacific Coast Farmers’ Market Association.


Wednesday, April 2, 9:45 a.m., Nursing Mezzanine, Parnassus Come enjoy some free bagels, pastries and coffee. Learn about campus services and events and build a community at Parnassus.


Wednesday, April 2, noon-1 p.m., Millberry Union 123W, Parnassus Synapse is looking for Mission Bay and Parnassus writers, bloggers, photographers and designers. Come to the lunch meeting, share your story ideas and enjoy a free lunch. Email for more information and to RSVP:


Wednesday, April 2, 5:30-6:30 p.m., Library, CL 211, Parnassus

The Integrative Medicine Network invites everyone in the UCSF community to experience a weekly guided meditation. All are welcome, whether you are looking to combat day-to-day stress using meditation or you'd like to uncover subtle layers of your self by diving deep. No experience in meditation is necessary. Both regular meditators as well as amateurs are welcome.


Wednesday, April 2, 5:30-6:30 p.m., Millberry Union Central Desk, Parnassus Please drop by and join UCSF Fit & Rec for a run. Each Wednesday night, the Run Club runs various distances (from 3-6 miles) at 9 to 11 minutes per mile.


Wednesday, April 2, 6-8:30 p.m., Clinical Sciences, 130, Parnassus English Corner is an informal conversational English class given as a free community service and provided on a voluntary basis by both people born and raised in the United States as well as many people who have, at one time in their lives, experienced life as a new immigrant to the United States.


Thursday, March 27, 5- 6:30 p.m., Herbst Hall, 2nd floor, 1600 Divisadero St., SF Join us for Dr. Robert Lustig's bilingual (English/Cantonese) lecture to raise community’s awareness on how excess sugar consumption can compromise our health and cause many chronic health issues, with diabetes and heart disease in the lead. Light refreshments will be served. Sponsored by Asian Health Institute. Please RSVP to the registration hotline (415) 885-3678.


Thursday, March 27, 5-9 p.m., Stanyan and Waller Streets, SF Off the Grid is a roaming mobile food extravaganza that travels to different locations daily to serve delicious food, with a free side of amazing music, craft and soul.


Thursday, March 27, 6-10 p.m., Cal Academy, Golden Gate Park It’s a robot world—we’re just living in it. Meet your maker bot with Evil Mad Scientist, Type A Machines, and Other Machine Co. Watch a robot boxing match by Other Lab, have a conversation with Bot & Dolly's "Scout", and participate in a group tinkering session with community-minded Robot Garden. Plus, interact with robots from BeatBots, Barobo, Origami Robotics, Unbounded Robotics, CAS AVEE's Jon Britton & Tosh Chiang, amongst others. Want to learn more about the business of ‘bots? Chat with experts SRI International and Andra Keay, director of Silicon Valley Robotics. NightLifeTickets,


Saturday, March 29, 7-11 p.m., Castro Theatre, SF Producer and celebutante, Sasha Soprano, brings you 11 of the most outrageous and hilarious drag queens for this epic, not-to-bemissed, comedy extravaganza as these girls come together for the first time on the same stage! Hosted by Peaches Christ and Heklina, The Drag Queens of Comedy features live

performances by Coco Peru, Sasha Soprano, Lady Bunny, Shangela, Pandora Boxx, Bianca Del Rio, and DWV. UCSF friends and family receive 10% all ticket types with code UCSFFUN. Registration the-drag-queens-of-comedy-early-showtickets-9228349241?aff=eorg


Monday, March 31, 6:30 p.m., AT&T Park, SF Cheer on the San Francisco Giants even though they are on the road and join other fans at AT&T Park to watch the Giants vs. Arizona Diamondbacks for opening day 2014 live from Phoenix. Arrive early for the best seats and for free hot dogs, free pennants, and to take a photo with the World Series Trophies. Gates open at 5:30 p.m.


Run for office in the inaugural Graduate and Professional Student Association! It is a unique interprofessional experience and gives you the opportunity to experience leadership that makes a difference. Visit the GPSA website for details on how to submit a candidate application. Applications are due on March 31.


Monday, April 14, 5:30-7:30 p.m., Byers Hall, 212, Mission Bay Financing New Ventures is an eight-week survey of the financing landscape for life science/healthcare ventures that explores the range of options to get your venture funded ranging from SBIR grants to seed funding, angel funding, venture capital and alternative sources of capital. Co-taught by Adjunct Professors Stephanie Marrus, Director of the Entrepreneurship Center and Naeem Zafar, UC Berkeley/UCSF. This is a non-credit course and is open to Berkeley, Stanford and life science businesses. com/forms/d/1NhvYiHOv4DEkHk9Cpa5laf UoZ7aUYNGRhWyHnavwIoo/viewform


The Visual Arts Club, Campus Life Services Arts & Events and Living Green are excited to present The Recycled/Reclaimed Art Show on Thursday, May 8. UCSF students, staff and facility are invited to join the show. All submittals must be 99% made from recycled, reused or reclaimed material. Applications are due by April 15. campuslifeservices.ucsf. edu/upload/artsevents/files/Recycled_Art_ Show_Application_2014.


Saturday, April 5, 1:30-4 p.m., Student Resource Center, Mission Bay From placid waters fished by ancient peoples to the biggest construction project in San Francisco since 1906, the transformation of Mission Bay has been incredible. Gain a unique perspective on the area. (If it's a bay, where's the water?). eventbrite. com/e/city walks-s er ies-mission-baytickets-10161071037.


April 5-7, Sacramento, CA Join fellow UC students in speaking with state legislators at the State Capitol about legislation related to higher education issues. Never done it before? No problem! The weekend is full of workshops devoted to showing you how. All reasonable costs will be reimbursed by ASUC & GSA. Learn more: slc/. Registration is required, so please sign up in advance with Christoph Hanssmann. Register:


Register with the First Generation Support Services Office, for access to all of the First Generation Support Services and to help the office advocate for you. Register before April 15, 2014 to be entered to win one of three giveaways!


UCSF students and staff can now post online classified ads for free on the Synapse website. All you need is an email account. Try it out!


This Brown Bag Mentoring program is designed to help UCSF first generation college students connect with first gen faculty, postdocs, residents, fellows and alumni who have generously offered to meet with you over lunch. And we'll help you pay for lunch! Sign up today at

TABULA THE SYNAPSE LITERARY ISSUE IS COMING IN THREE WEEKS! Submit poems, short stories and photos with captions to Synapse by APRIL 12. | March 27, 2014 | 3

Scientific Publishing » FROM HOME PAGE


“In the next five years,” Binfield predicted, “open access will become the dominant business model in the industry.”

Scientists: University faculty and researchers who write articles and submit them to journals, may provide peer review services, also are the primary end users of the journals.

The Unbreakable Circle Scientific publishers have traditionally distributed their packages of journals for an annual subscription fee. While it’s possible to unbundle the package of journals to separate the so-called dud journals from the big-ticket journals, this can be time consuming and cumbersome. Still, universities do sometimes pick and choose which journals to subscribe to. More commonly, universities opt for the publishers’ “big deal,” which is a subscription to all the journals in a publisher’s offerings. The UC Libraries do not subscribe to the big deals for most publishers, according to Anneliese Taylor, assistant director of Scholarly Communications and Collections at the UCSF Library. UCSF, as part of the University of California system, benefits greatly when it comes to access to publications. It gets access to most of the journals the entire university system subscribes to, and pays a portion of the total UC cost. Each year, the California Digital Library (CDL), on behalf of the University of California, negotiates with the publishers that represent scientific journals. In the 2012-2013 academic year, UCSF contributed $1.5 million for its share of journal subscriptions. A majority of that money came from state funds, followed by gifts/endowments and a small contribution from the UCSF Medical Center. Traditional journals make money by signing contracts with the publishers, who often vie for representation of well-regarded journals. “Sometimes the publishers fight over them,” said Taylor. “Every year there’s a group of them [journals] that will switch. It’s often that these publishers are offering different incentives to those societies for hosting their journals. A lot of it is financial, because these publishers are doing really well.” The journals themselves charge authors to publish. There are “page fees” for accepted papers, and occasionally submission fees (even those that are ultimately rejected). These fees often even rise with “impact factor”—a mea-


Scientific Journals: Publications usually based on some form of peer review or editorial refereeing to qualify submissions for scientists. Publishers: Companies that act as “middle men” by vetting, publishing and distributing the scholarly content of the journals and charge universities subscription fees for access to their package of journals. Colleges and Universities: Academic institutions that purchase subscriptions to journals usually through their library systems so their scientists can access the latest research. sure of a scientific journal’s prestige based on the rate that articles published in that journal are in turn referenced by other articles from any journal. However, the majority of a journal’s revenues come from subscription fees, usually via the publisher, as opposed to page fees, according to Binfield, who prior to co-founding PeerJ was also an executive at several subscription-based publishers. Between 68-75 percent of the publishers’ revenues come from subscriptions, according to the 2012 STM Report by the International Association of Scientific, Technical and Medical Publishers. At an academic institution like UCSF, it not uncommon to pay for doing research at the front end, and then pay subscription fees so that the UCSF researchers and their colleagues may access the results of that research in a scientific journal. Until recently, this was the unbreakable circle of scientific publishing. Meanwhile, those outside the circle— meaning outside of academia—or without the means to pay the often exorbitant prices (as much as $31.50) for individual articles, had no way of accessing primary scientific data

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Synapse is the UCSF student-run weekly newspaper, which runs on Thursdays during the academic year and monthly during the summer. Synapse seeks to serve as a forum for the campus community. Articles and columns represent the views of the authors and not necessarily those of the Board of Publications or the University of California.


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that in many times cases was derived from public funding. Then, the open access movement came along. Opening the Circle Open access was an idea that emerged in the late 1990s with the goal of making scientific research available to all. An open letter was circulated amongst the scientific community, signed by Dr. Patrick Brown of Stanford University, Dr. Michael Eisen of UC Berkeley, and Dr. Harold Varmus of the National Institute of Health, urging scientific publishers to provide access to journal articles for free. Thousands of scientists from universities around the world pledged only to “publish in, edit and review for, and personally subscribe to” open access journals. However, the goal remained out of reach without the support of the journals and publishers, as researchers had no publication alternative that offered the promise of open access, but still maintained the rigorous peer review, impact and reach of current publications. Despite overwhelming public support for open access, researchers quickly found it was exceedingly difficult to build a new model of scientific publishing from the ground up. One of the leaders in this push was a nonprofit scientific publishing project called the Public Library of Science, or PLoS. The goal of PLoS was very different from many other journals: to provide an online-only, free-for access, peer-reviewed journal of scientific research. In 2003, PLoS realized that to attain its goal of open access, it would have to become a publisher itself and on October 13, 2003, it launched its operation with the publication of a peer-reviewed, online-only, scientific journal entitled PLOS Biology. Since then, PLoS One has gone from publishing roughly 1000 articles/year to an overwhelming 33,000/year in 2013. In addition, many new open access journals have also begun publishing. In just the last five years, the number of open access journals has increased 183 percent. As of 2013, more than 10 percent of published STM research was published in open access journals, and it’s projected to increase. “In four to five years that could easily reach around 50 percent,” said Binfield. Based on the initial response to PLoS and other open-access journals, it seemed like closed-access journals’ lucrative lock on the industry was in trouble. Scientists were increasingly publishing in open access journals, and it was becoming a stipulation of many scientific grants. In 2008, the NIH stated in its Public Access Policy that the results


of any research funded by the NIH must be made available for free to the public within 12 months of publication. In 2012, UCSF additionally required that all research published by UCSF authors be made available for free, regardless of which journal published the research. In July 2013, the entire UC system also adopted this open access policy. Despite significant investment by UCSF in the open access movement, there is still pressure for UCSF scientists to publish in closed-access journals because of the prestige associated with such closed-access journals as Science, Nature and Cell. “Closed-access subscription journals have been around longer,” said Taylor of the UCSF Library. “They’ve had time and an opportunity to build reputation and build prestige.” Open Access’ Increasing Influence Open access journals, by comparison, are relatively new to the playing field. PloS One, for example, only started receiving an impact factor in 2007. Impact factor is a measure of the frequency with which the average article in a journal has been cited during the two preceding years. The Web of Science, which calculates impact factor, typically only indexes journals that are three or more years old. Since 2007, PLoS One has significantly increased in prestige: its 2012 impact factor was calculated to 4.092, and PloS Biology was recently calculated at a strong 11.452—higher than many influential closed-access journals such as Journal of Cell Biology or Blood. In just the past 10 years, open access publishing went from a theoretical model to a substantial and respected part of scientific publishing. PLoS’s CEO Elizabeth Marincola has witnessed much of this growth first-hand. “The open access movement is growing and thriving, with an increasing number of open access journals and articles being published, more institutions and funders implementing open access policies, and more people accessing open access research,” she said. PART 2: What happens to a subscriptionbased industry when more and more journals start offering a free alternative? In the next installment of this series, we examine how the open access movement continues to disrupt the scientific publishing industry, and how journals and publishers are adapting to the changing landscape.

Alexandra Greer recently received her PhD and is a postdoc at Genetech.

UCSF School of Medicine Ranked Among Nation's Best

British Scientist Named Head of Helen Diller Cancer Center

UCSF’s School of Medicine ranked fourth nationwide in both research and primary care education this year, according to a new survey conducted by U.S. News & World Report. Results are published in the magazine’s 2015 issue of “Best Graduate Schools,” which appears online today and will be available in stores on April 8. UCSF has the only school of medicine in the nation that ranks in the top five in both research and primary care education, including a tie for fourth place in research education, alongside University of Pennsylvania. The school also ranked in the top 10 in every medical specialty in which it was assessed. Among those, UCSF ranked first for its medical program in HIV/AIDS; third in family medicine, internal medicine and women’s health; and tied for fourth in drug/alcohol abuse education.

One of the world’s preeminent cancer scientists, Alan Ashworth, PhD, FRS, has been appointed the new director of the UCSF Helen Diller Family Comprehensive Cancer Center. Ashworth is chief executive of The Institute of Cancer Research, London, one of the world’s most influential cancer research organizations. Together with its partner hospital, The Royal Marsden NHS Foundation Trust, the ICR is one of the top-rated cancer centers globally. He will formally assume his new position at UC San Francisco in January 2015. Ashworth, whose major contribution to cancer research has been his work on genes involved in cancer risk, was a central part of the team that in 1995 discovered the gene BRCA2, which is linked to a heightened risk of some types of cancer.

4 | March 27, 2014 |


It’s Springtime: Go Climb a Real Rock A guide to climbing spots in San Francisco By T. Booth Haley Staff Writer


alifornia is home to the most famous rock climbing spot in the world, Yosemite. Our fair city of San Francisco, however, is not so blessed. While Yosemite boasts the 3000-foot tall cliff of El Capitan—the highest cliffs anywhere outside of the Trango Towers in Pakistan and Mt. Thor on Baffin Island—San Francisco can barely claim a 30-foot cliff, the humble Beaver St. Wall on Corona Heights. While Yosemite is comprised of magnificent sparkling granite, the rock of San Francisco is a lowly type called chert, crumbly and dirt colored. The one advantage San Francisco climbing has over Yosemite: you don’t need a car and three-day weekend to make it happen. Climbing in San Francisco has been popular for many years. With the recent opening of a third rock gym, Dog Patch Boulders, in the Dog Patch neighborhood near the Mission Bay campus, that popularity seems to only be growing. For many climbers who start in the gym, it’s a big jump in terms of gear acquisition and mental toughness to start climbing outdoors. The biggest barrier may be distance, especially for those young urbanites, who choose to not own expensive, polluting personal automobiles. There is good news: Decent climbing, in fact, does exist right here in the city of San Francisco, accessible by bus or bike. The recent publication of Bay Area Rock – Climbing and Bouldering in the San Francisco Bay Area (Potlicker Press; 7th edition), by

Jim Thornburg, has introduced to the climbing public a new cliff, freshly cleaned of loose rock, bringing our total number of climbing areas to three. The classics are the Beaver St. Wall, with two top-rope routes, and the Glen Canyon Boulders, with many easy bouldering problems. (A boulder “problem” is the term for a short route around 10-feet tall that is climbed without ropes.) The new area, which is getting a lot more traffic since the Thornburg book came out, is the scenic Ocean Beach Boulders on a gray cliff right below the Cliff House. Beaver St. This old standard is an essential San Francisco climbing experience. The cliff looms above a pre-school at the end of Beaver St., right above the Castro on the western aspect of Corona Heights. A top-rope can be anchored to the cement posts of the chain-link fence above. The diagonal crack on the left is a 5.9 and if you climb the face directly up it is around 5.10. (For roped climbing the difficulty rating system starts at 5.5 and goes to 5.15.) The chert here is fantastically smooth and polished; it is sometimes said that climbers can see their reflection in the rock. Although friction for foot-holds is low, having a true full length climbing route in the middle of The City is very special treat. Glen Canyon This area offers a greater array of rocks to play on, with two large cliff bands in this un-

der-appreciated, natural and peaceful canyon park. The climbs here are all boulder problems from 10- to 15-feet tall, with many in the V0 realm. (For boulder problems the difficulty rating system ranges from V0 to V15.) The outstanding routes are the Glen Canyon traverse (V4), starting on the lowest leftmost edge of the lower cliff, and Unnatural Act, the famously intimidating and overhung V3 roof on the upper cliff. The former is never high enough to require a crash pad, but the latter will feel safe only with two or three pads and spotters. Glen Canyon is long enough to even go for a lovely hike of sorts which can make the trip an appealing full outdoors experience. If you bring a baby or small domesticated animal watch out for coyotes! Ocean Beach Boulders It is kind of amazing that after 50 years of climbers inhabiting the Bay Area, “new” climbing spots are still being discovered. It demonstrates how dependent most climbers are on guidebooks and how reluctant they are to venture onto unknown rocks. Well, this new spot is a gem, with a fantastic setting next to the crashing waves and jagged rocks at the north end of Ocean Beach. The climbs are tall, around 20 feet, which makes them a bit more psychologically challenging. At least the second half of all the routes get quite easy, so the chances of falling decrease as you go higher. The landings are sandy, which means you don’t need a crash pad unless the sand is wet. The sand, in fact, is the big wildcard be-

The author bouldering on a sunny day at the scenic Ocean

cause it can fluctuate drastically throughout the year, changing in height by as much as six feet! When the sand is low, the climbs are even taller and the landings wetter and harder. When the sand is high, the climbs are less imposing and the landings soft and dry. Going during low tide is also advantageous, but not essential if the sand is in. While most of the cliffs in the area are yellow, the one section with good bouldering can be identified by its dull gray hue. Two striking vertical cracks run up the face, both

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UCSF JOURNAL CLUB Recent research by UCSF scientists By Taylor LaFlam Staff Writer

MICROBIAL PATHOGENESIS: The microRNAs in an ancient protist repress the variant-specific surface protein expression by targeting the entire coding sequence. Saraiya, A.A., et al. (Wang). PLoS Pathog. 2014. 10(2):e1003791. Ingestion of the flagellated protozoan Giardia lamblia causes giardiasis, a disease with a rhyming sobriquet, "beaver fever," and the rather unpleasant major symptom of slow-to-resolve diarrhea. Giardia switches between numerous variants of its surface proteins (VSPs), effectively disguising itself from the immune system. Previous studies have found that all VSPs are being transcribed at once, with regulation hypothesized to occur largely through microRNAs (miRNAs) degrading all but a few of the variants. In this paper, Saraiya and colleagues identified 99 new probable miRNAs as well as sites in all 73 VSPs that are likely targeted by these miRNAs. They further showed that full repression of a given variant requires the combined action of several miRNAs specific for it. Notably, some of miRNA-targeted sites are within coding sequence of the targeted RNA. CANCER BIOLOGY: The chromatin regulator Brg1 suppresses formation of intraductal papillary mucinous neoplasm and pancreatic ductal adenocarcinoma. von Figura, G., et al. (Hebrok). Nat Cell Biol. 2014. 16(3):255-67.

Photo by Heather Dinh/D4

n Beach Boulders, just below the Cliff House.

of which are nice V1 routes. The column between them is a dramatic V2, which finishes with a scary but easy mantle over a small roof. Harder problems exist on the right side of the cliff towards the mysterious cave, from the depths of which a tunnel leads back towards the main beach. For details on this location or the other two San Francisco climbing spots I recommend the Thornburg book. Other guides exist but none of them include Ocean Beach. And if you’re an ambitious biker (or own a car), there are even more and better climbing

spots in the Berkeley Hills, high on Mt. Tamalpias and at Stinson Beach, which are also described in the guidebook. Climbing in the gym is great, but it truly gets exciting once you transition onto real rock. It’s like doing CPR on a mannequin versus actually saving the life of a hot-blooded human being—one is only practice for the other. Enjoy the rock and climb safe so you don’t end up needing CPR yourself!

T. Booth Haley is a fourth-year dental student.

Each year, a few hundred thousand people die from pancreatic cancer, which is notoriously difficult to treat. The most common form of pancreatic cancer, pancreatic ductal adenocarcinoma (PDA), originates from any of three distinct types of precursors, including intraductal papillary mucinous neoplasms (IPMNs). The genetic differences between these three subtypes of PDA have remained poorly understood, though previous research has found that Brg1, which is part of a chromatin-remodelling protein complex, is frequently mutated in IPMN-derived PDA. In this article, the authors reported that pancreatic deletion of Brg1 in mice, in the presence of mutant Kras, leads to the formation of cystic neoplasms reminiscent of IPMN. They further found that these lesions developed into PDA and that, as with IPMN-PDA in humans, this PDA had a better prognosis than another type of PDA. NEUROSCIENCE: Axonal Control of the Adult Neural Stem Cell Niche. Tong, C.K., et al. Cell Stem Cell. 2014 Feb. 19. Epub ahead of print. What was once dogma—that no new neurons were produced after birth—has been fully upended over the last two decades. It is now clear that neural stem cells can be found in a region of the adult brain called the ventricular-subventricular zone. Although much work has been done in characterizing these neural stem cells (NSCs), the role of fully developed neurons on these NSCs has not been characterized well. Here, Tong and colleagues reported a role for nerve impulses in regulating these NSCs. They found that a population of distant serotonin-producing neurons synapse with the NSCs, that the NSCs express receptors for serotonin, and used pharmacologic targeting of these receptors to show that receptor signaling correlates with proliferation. IMMUNOLOGY: Serum IgE clearance is facilitated by human FcεRI internalization. Greer, A.M., et al. (Shin). J Clin Invest. 2014. 124(3):1187-98.

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The watery eyes, itchy rash, or tight throat of an allergic reaction are due to binding of the allergen to IgE, a type of antibody, bound to the receptor FcεRI on the surface of basophils and mast cells. An alternative form of this receptor is also expressed on other white blood cells in humans, including dendritic cells and monocytes, but the role of the receptor on these cells has been wholly unknown. In this article, Greer (longtime former writer of this column) and colleagues reported that IgE that binds to dendritic cells is taken up rapidly and degraded; this is unlike basophils, in which the IgE remains on the surface for an extended period of time. They further found that mice with human FcεRI rapidly clear circulating IgE and that this clearance depends on dendritic cells and monocytes.

Taylor LaFlam is a fifth-year MSTP student.

6 | March 27, 2014 |


Let’s Get Physical...Therapy! Help! I'm Knock Kneed By Ilka Felsen Staff Writer


ear PT-roomie, my knees touch when I walk, and sometimes I have knee pain after a long hike or spinning class. What’s the deal? First of all, being knock kneed is not necessarily a bad thing. But it can predispose the body to knee pain with activities that require repeated knee flexion, such as running, cycling and stair climbing. What are knock knees? Knock knees is an informal term for genu valgum, when the knees nearly touch from angling inward. Genu valgum is the result of three factors: skeletal alignment, muscle strength and muscle activation. Skeletal alignment is not easily modifiable and is related to the intrinsic posturing of the femur, tibia and patella, with the femurs angling towards each other and tibias angling outwards. However, muscle strength and activation are modifiable! Often weak quads, weak gluteals (i.e. butt muscles) and weak abdominals are the culprits. Additionally, a tightened IT band (which runs along the side of the upper thighs) and collapsed arches can contribute to genu valgum. Why do I feel pain? The pain is related to loading forces on the tibiofemoral and patellofemoral joints. Individuals with genu valgum often have pain



on the outside of their knees, from increased compression at the lateral tibiofemoral compartment, or a tight IT band that courses laterally to insert onto the outside of the femur, patella and tibia. Anterior knee pain is due to poor alignment of the patella on top of the femur, usually from too much angling inward of the femur during weight bearing. What are three simple things I can do? 1. Strengthen your gluteals. This large muscle group is responsible for hip extension, external rotation and abduction, all of which are usually deficient in individuals with genu valgum. This means that squats, bridges, monster walks and clamshells should be your new best friends! 2. Clench your butt cheeks together when you walk, and point your knees and toes forward. Often individuals may have adequate muscle strength, but are not actively recruiting their muscles while walking—which basically counteracts the whole point of having strong muscles! 3. Wear supportive shoes with arches, and strengthen your arches by folding clothes with your feet (yes, really!), grabbing objects with your toes and scrunching a towel with your toes. Collapsed arches make it easier for the thigh bones to angle inwards and allow the feet to roll medially. Giving your arches some lift actually supports your entire leg.

Ilka Felsen is a second-year physical therapy student.

The officers and members of DentStay. (Photo courtesy of DentStay)

reach events and must-see places in San Francisco.” Since October 2013, SNDA members have hosted more than 20 applicants at pre-interview dinners, overnight housing or both. A number of applicants who participated in the DentStay program have been accepted to UCSF and many more are currently awaiting the status of their acceptance. SNDA has had an overwhelmingly positive response from applicants who participated in the DentStay program. SNDA hopes to

continue supporting underrepresented minority students at UCSF in the future by improving the program in the coming years. Looking toward the future, Brown said, “We are hoping to get more students involved in the dinners to show how diverse UCSF really is. The future is bright for this program. I would not be surprised to see it expand to other health professional schools here on campus.”

Angela Broad is a first-year medical student. | March 27, 2014 | 7


The Weekly Crossword

ACROSS 1 Cameroon export 6 Pound hound, often 10 Upper limit 13 Grape-shaped 14 Sun screen? 15 Hail, to Caesar 16 Doppelganger 18 Double-crosser 19 Brake part 20 One in a million 21 Firefox alternative 23 At the peak 25 Bulb rating 27 Lifeboat lowerer 28 Modern factory worker 30 Talk like Fudd 32 Defensive spray 33 Pencil topper 35 Semiautomatic rifle 37 Drawn tight 39 Winning streak 40 Attribute (to) 43 Minor failing 47 Stage in a bug's life 48 Church center 50 Brady Bunch mom 51 Spoilage signs 53 Tear to pieces 55 Vulgar 56 Hal of "Barney Miller" 58 Financial worry 60 Census statistic 61 Computer pros 62 Dealmaker in politics





by Margie E. Burke 5










21 25

24 29


26 30

34 37 40




43 49


52 57

32 36





















54 58

starts with our scholarship.

55 59











65 66 67 68 69 70

8 Clothes, in old slang 9 Tire feature 10 Desert parade 11 Miserly desire 12 Daintily small 14 Like some online videos DOWN 17 One way to 1 Stack up against serve veggies 2 Earhart, for one 22 Hereditary 3 70's 24 Traveler's Chrysler Week of 3/24/14 - 3/30/14 model purchase 4 Bubble maker 26 Despot 5 Unpleasant 29 Eye drop? 31 Educator, briefly emanation 6 Imitative 34 Make a mess of 7 Beach Boys hit, 36 Political coalition 38 Ski lift "Surfin' ___" Before-long link Deep distress Shining example Go astray Rioter's take Like Robin Hood's men

40 Reviewer of books 41 TV advertiser 42 Obvious 44 Surfer's challenge 45 What trucks go uphill in 46 On in years 47 Genteel 49 Part of EGBDF 52 Petal neighbor 54 Type of tide 57 Scrapped, at NASA 59 Barbershop request 63 Pursue, in a way 64 Poetic homage

Edited by Margie E. Burke

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HOW TO SOLVE:         (Answer appears elsewhere in this issue)

Copyright 2014 by The Puzzle Syndicate

Piled Higher  and  Deeper  by  Jorge  Cham

Solution to Sudoku

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You can begin training for the career you’ve always dreamed of with financial assistance from the U.S. Army. Through the Health Professions Scholarship Program (HPSP)*, you could be eligible to receive a full tuition scholarship for an accredited medical program.

Copyright 2014 by The Puzzle Syndicate

Difficulty : Medium

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Capt. Ana Morgan, M.D., HPSP Medical Recipient Brooke Army Medical Center, Texas





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The HPSP provides reimbursement for books, laboratory equipment and academic fees. You’ll also receive a sign-on bonus of $20,000 and a monthly stipend of $2,157. During breaks, you’ll have the opportunity to train alongside other members of our health care organization. To learn more, call (650)347-3967 or visit San Mateo Medical Recruiting Center 400 S. El Camino Real, STE 450 San Mateo, CA 94402 Email:

*Certain requirements and eligibility criteria apply. ©2013. Paid for by the United States Army. All rights reserved. Information subject to change.


Student Loan Consolidation: Should You, or Shouldn’t You? `By Carrie Steere-Salazar Contributing Writer


tudent debt is in the headlines, and offers to help consolidate and manage that debt are beginning to appear in advertisements on TV, radio and on the sides of the local MUNI buses. But that special service comes at a price. “While students are enrolled and borrowing sensibly to meet their costs of attendance, there is little action that needs to take place,” said Carole Ann Simpson, UCSF’s new resource advisor in the Financial Aid Office. “Loan consolidation, in almost every case, should not be considered until after graduation. Students do not need to pay anyone in order to consolidate their student loans.” Companies advertise student loan solutions and charge a fee to help students navigate the loan process and take advantage of income-based repayment plans and loan con-

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title: "Amount  of  food  you  eat  out  of  a  bowl"  -­  originally  published  2/3/2014

solidation. Some charge as much as $1000 for the service, and Simpson reported that she already has a list of just over 20 companies— and the list gets longer every day. UCSF has resources to help you, and all of the options are available to you free of charge at This official (Department of Education) website has a great calculator, the Repayment Estimator, which Simpson recommends students use to think about their choices. “If students remember their PIN from the FAFSA, they can see all of the repayment choices for their Federal loans and the estimated monthly payments in about five seconds,” said Simpson. “There’s no need to pay someone to help you navigate repayment.” The time to consider loan repayment options and create an individual repayment plan is just before graduation from UCSF. “There are many available options to assist students as they transition from student through residencies and post graduate program experiences to full professional earning status. We will be here to help borrowers navigate the choices and come up with a plan that makes sense for their career,” said Simpson. Simpson also pointed out that students should feel confident in their future ability to manage student loan repayment. “Your colleagues who attended in just the past few years have done quite well—UCSF’s current student loan default rate is just 0.3%—one of the lowest rates around. Having serious difficulty during repayment is a very rare occurrence for our students,” she stated. If you would like to ask questions or make an appointment to review your student loans and learn more, contact Carole Ann Simpson at

Carrie Steere-Salazar is the director of Student Financial Aid.

8 | March 27, 2014 |


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Solution to Sudoku

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Write for Synapse

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Synapse (03.27.14)  
Synapse (03.27.14)  

Volume 58, Number 24