Synapse (4.2.2015)

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FEATURES

COLUMNS

An easy way for busy women in science to get a style fix in the New Year. » PAGE 3

A roundup of recently published research reviewed by the Science Editor of Synapse. » PAGE 4

Stitch Fix: Personal Styling by Mail

Journal Club

IN THIS ISSUE

Events » PAGE 2 Features » PAGE 3 Columns » PAGE 4 Puzzles » PAGE 5

SynapseNewspaper

The UCSF Student

synapse.ucsf.edu | Thursday, April 2, 2015 | Volume 59, Number 12

May I have a peek? Preparing to Make Reuse of publicly available biomedical data is increasing and Evidence-Based producing some great successes Career Decisions By Megan Laurance Contributing Writer

E volving scientific culture and policy are directing more and more biomedical

data into public data repositories. A number of the recent data sharing policy changes from funders and publishers were designed to improve data management and data sharing practices with the end goal of making it easy for researchers to discover and reuse biomedical datasets. However, not all researchers greet these policy changes with open arms, often questioning the proposed value and likelihood of their research data being reused. This issue came to a head in early 2014 when the non-profit publisher PLOS (Public Library of Science) updated their data sharing policy to require that authors provide a statement describing where the data would be deposited. The policy essentially went from “tell us how you plan to share your data” to “show us where the data is.” Many researchers objected to this new data policy. One frequently cited concern was that researchers would bear a tremendous cost – in time to describe and deposit their data and risk of getting scooped by other researchers publishing on their data – while receiving little benefit. In addition, they expressed doubt about the

By Bill Lindstaedt Contributing Writer

likelihood of their data being productively reused: for an excellent summary of the controversy that arose from PLOS’s data sharing policy and level-headed response, please take a look at this blog post from the California Digital Library’s blog DataPub. Widespread and productive use of public datasets So, what’s the deal? Are most research datasets so unique and complex that no one would bother trying to find them, let alone mine them for new insights? Who is reusing biomedical data? Well, it turns out, lots of people, both inside and outside of biomedical research institutions. You don’t need to look any further than Atul Butte, , MD, PhD who will lead UCSF’s Institute for Computational Biology, starting in April. Dr. Butte and his research lab provide us with great examples of the benefits of open data, and the value and novel discovery that can come from reanalysis of open, biomedical big data. At last year’s International Digital Curation Center Conference, Dr. Butte gave a fantastic presentation outlining some of his lab’s data reuse strategies and results. The

BIOMEDICAL DATA » PAGE 6

“M y friend told me that I should think about a career in medical writing because there are lots of jobs, and they need PhD’s, and I like to write. But—my friend also said writers tend to be freelancers, and I need a regular paycheck since I have a family. I haven’t been able to find much information about medical writing but I’m pretty sure it’s not right for me.”

about a potentially viable career path based on incorrect or incomplete information.

This all-too-typical statement demonstrates two huge mistakes made by many graduate students and postdoctoral fellows as they try to gather information about their career options. 1. Graduate students and postdocs rely too heavily on uninformed advice from labmates or other friends when making career decisions. That leads to misinformation and overgeneralization. When trainees make career decisions based on generalized statements such as: “Medical writers are freelancers,” or “Management consulting is a bad fit for me because it requires 100% travel,” it’s an indication that they have not learned enough about that career path. They are in danger of making an important decision

Are there medical-writing careers that do not require freelancing? Yes, most of them, probably. Is it possible to find consulting firms or subfields or niches that allow

CAREER DECISIONS » PAGE 6

Precision Medicine Student Alliance Elective By Priya Jayachandran and Chris Foo Contributing Writers

T he field of precision medicine has been garnering tremendous attention

lately. From President Barack Obama’s Precision Medicine Initiative (https:// w w w. w h i t e h o u s e . g o v / t h e - p r e s s office/2015/01/30/fact-sheet-presidentobama-s-precision-medicine-initiative) to the recent appointment of medical informatics expert Atul Butte, MD, PhD as leader of UCSF’s new Institute for Computational Health Sciences, the trend of genomics-guided medicine is taking center stage nationwide and on

campus. Second and third-year School of Pharmacy students Dalga Surofchy, Chris Foo, Priya Jayachandran, Lilian Kibathi, and Dor Keyvani founded the Precision Medicine Student Alliance (PMSA) last year. Today, the organization’s aim is to educate students about precision medicine by bringing together innovative minds actively working in the field from across the Bay Area. This Spring, PMSA is staying true to their mission by offering a 1-day elective

course on precision medicine. The elective, entitled Precision & Personalized Medicine: Healthcare Frontiers, will take place on Saturday, April 11, 2015. This 1-day conference will pull together leaders from industry and academia to highlight innovation in precision medicine. Invited speakers from 23andMe, the Gladstone Institutes, Genomic Health, and several UCSF Institutes and Centers of Excellence will share their insight on recent advances and challenges in the field.

PRECISION MEDICINE » PAGE 6


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Events » STUDENT LOAN MANAGEMENT SEMINAR

Friday, April 3, noon-1 p.m., Nursing, 517, Parnassus Wondering how you will manage student loan repayment? The Financial Aid Office of UCSF is offering workshops open to any student interested in learning more about repayment options, forgiveness programs, and strategies to best manage your loan portfolio. Bring a printout of your student loans.

MUSLIM FRIDAY PRAYER SERVICES

Friday, April 3, 1-1:30 p.m., Medical Sciences, 157, Parnassus Friday, April 3, 1:30-2 p.m., Helen Diller, 160, Mission Bay The Muslim Community at UCSF holds regular Friday prayer services (Jum’a) every week. Come join your fellow brothers and sisters for prayer and socializing. All are welcome!

MISSION BAY RIPS

Friday, April 3, 4-5 p.m., Genentech Hall Auditorium, Mission Bay RIPS is a seminar series wherein one student and one postdoc present their current research. Talks are 15 minutes in length and are preceded by a 20-minute social. Snacks and beverages are provided.

CAMPUS EVANGELISTIC FELLOWSHIP

Friday, April 3, 7-10:30 p.m., Nursing, 517, Parnassus Join the Campus Evangelistic Fellowship for their weekly meeting with Bible study, hymn singing, and fellowship.

GPSA MONTHLY MEETING

Monday, April 6, 5:30-7:30 p.m., Genentech Hall, N-114, Mission Bay Meet your assembly members at the monthly GPSA meeting and be a part of the discussion on topics relating to student priorities. Dinner provided with RSVP: gpsa@ucsf.edu.

GRADUATE DIVISION ALUMNI SEMINAR SERIES: VEENA SINGLA, PHD

Monday, April 6, 7-8:30 p.m., Helen Diller, 160, Mission Bay Join the Graduate Division for a new seminar series and learn about the diverse careers of PhD alumni! This month features Veena Singla, Staff Scientist at the National Resources Defense Council, a non-profit environmental advocacy group. http://biophysics.ucsf.edu/seminarsevents/ipqb-alumni-speaker-series

8TH ANNUAL CHANCELLOR’S LEADERSHIP FORUM ON DIVERSITY AND INCLUSION

Tuesday, April 7, noon -1:30 p.m., Cole Hall, Parnassus Hear from senior leadership on diversity initiatives at UCSF. The event will be livestreamed and ASL interpreters will be provided.

STUDENT LOAN MANAGEMENT SEMINAR

Tuesday, April 7, noon-1 p.m., Nursing, 729, Parnassus Wondering how you will manage student loan repayment? The Financial Aid Office of UCSF is offering workshops open to any student interested in learning more about repayment options, forgiveness programs, and strategies to best manage your loan portfolio. Bring a printout of your student loans.

CARRY THE ONE RADIO WORKSHOP

Tuesday, April 7, 5 -7 p.m., Mission Hall, 1107, Mission Bay Carry the One Radio is a UCSF-based science podcast. The show is run completely by a dedicated group of young scientists who want to share their enthusiasm for research with a wider audience. The group meets weekly to workshop various pieces. All are welcome, no radio experience needed.

PRIMARY CARE PROGRESS MONTHLY MEETING

Tuesday, April 7, 5-6:30 p.m., Library, CL220, Parnassus Dr. Margot Kuschel, a leading primary care researcher in the topics of pain management in safety net settings, and homeless healthcare will present. Social Histories and other spring events will also be discussed. Dinner provided.

SYNAPSE MEETING

Wednesday, April 8, noon-1 p.m., Millberry Union, 111W, Parnassus Synapse is looking for Mission Bay and Parnassus writers, bloggers, photographers, and designers. Come to the lunch meeting and share your story ideas.

CHOOSING A THESIS LAB

Wednesday, April 8, noon-1:30 p.m., Mission Hall, 1401, Mission Bay Choosing a thesis lab is an important decision that will affect the direction of your graduate research and your academic success and even your ultimate career choices. A panel of senior students will share their insights and provide advice for selecting a rotation and thesis (dissertation) lab. Learn about factors that are often overlooked. Gain strategies for using your rotation experiences to their fullest. RSVP: choosingathesislab2015.eventbrite.com

DISCOVERY FELLOWS RESEARCH SYMPOSIUM

Wednesday, April 8, 4-6:30 p.m., Genentech Hall Auditorium, Mission Bay UCSF Chancellor Sam Hawgood and Dean of the Graduate Division and Vice Chancellor of Student Academic Affairs, Elizabeth Watkins,will host the first annual Discovery Fellows Research Symposium. Five of the Graduate Division’s fifthyear Discovery Fellows will give short talks about their research, followed by a reception and poster session. Open to the campus community. RSVP: mary. hoffman@ucsf.edu.

IMN MIDWEEK MEDITATION HOUR

Wednesday, April 8, 5:30-6:30 p.m., Library, CL215, Parnassus The Integrative Medicine Network (IMN) 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.

UCSF RUN CLUB

Wednesday, April 8, 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 (3-6 miles) at a 9-11 minute per mile.

ENGLISH CORNER

Wednesday, April 8, 6-8:30 p.m., Nursing, 527, 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 US.

CHANCELLOR’S CONCERT SERIES

Thursday, April 9, noon-1 p.m., Cole Hall, Parnassus Looking for a place to study or relax between classes? CLS Arts & Events has got just what you need. The Chancellor’s Concert Series on Thursdays is a great place to set up your laptop and study or just take a break from classes while listening to classical music. Seating begins at noon. Lunch will be served while supplies last.

IMN ANNUAL CONFERENCE

Saturday, April 11, 8 a.m.-6 p.m., Cole Hall, Parnassus The 17th Annual Integrative Medicine Network (IMN) will explore how integrative modalities such as yoga, acupuncture, and good nutrition can improve the quality of life for patients and oneself. Invited speakers will teach methods of self-care while also doing demonstrations so that everyone can see how accessible and easy caring for oneself really is! Workshops include yoga, meditation, nutrition, energy-work, qigong, acupuncture, as well as dancing.

OUT IN SCIENCE

Wednesday, April 15, 4-6 p.m., Gladstone, Mahley Auditorium, Mission Bay Join the Graduate Queer Alliance, the LGBT Resource Center, and the Gladstone Institutes for a panel discussion with Bay Area academic and industry scientists. Reception to follow.

150TH ANNIVERSARY CAMPUS CELEBRATION

Tuesday, April 21, 11:30 a.m.-1:30 p.m., Millberry Union Gym, Parnassus Come celebrate the 150th UCSF Anniversary. Lunch will be served to the first 4,000 attendees. Enjoy carnival-style games, such as ring toss, skee ball, baseball toss, prize wheel and musical entertainment by DJ.

NAHA ANNUAL CULTURAL EVENT

Wednesday, April 22, noon-1 p.m., Millberry Union Conference Center The Native American Health Alliance (NAHA) Annual Cultural Event brings together Native American drummers and dancers of various tribal origins to perform on the UCSF Parnassus Campus. Visitors are welcome. Traditional Native foods are served for all attendees.

LAST LECTURE 2015

Wednesday, April 22, 5:30-6:30 p.m., Cole Hall, Parnassus The students have spoken and hundreds voted for Dr. Kimberly Topp to deliver the Last Lecture. Dr. Topp will deliver a lecture on the prompt, “If you had but one lecture to give, what would you say?” This interprofessional event will bring out stories intertwining various dimensions of Dr. Topp’s professional, personal, spiritual, and cultural experiences that have brought her to UCSF today. Immediately following the lecture enjoy a reception and network with UCSF alums at the Zero Year Reunion in Millberry Union. Sponsors: GPSA, Student Life, and AAUCSF.

TRANSITIONING TO INDUSTRY: A TALK BY TOBY FREEDMAN, AUTHOR OF CAREERS IN BIOTECHNOLOGY CHANCELLOR’S CONCERT SERIES Thursday, April 16, noon-1 p.m., Cole AND DRUG DEVELOPMENT Hall, Parnassus Looking for a place to study or relax between classes? CLS Arts & Events has got just what you need. The Chancellor’s Concert Series on Thursdays is a great place to set up your laptop and study or just take a break from classes while listening to classical music. Lunch will be served while supplies last.

CASINO NIGHT 2015

Thursday, April 16, 5-8 p.m., Millberry Union, Parnassus Join the GPSA for an evening filled with games, entertainment, food, drinks and a chance to win some prizes! Come ready to play black jack, poker, craps and roulette. Gambling not up your alley? Then experience a live performance from Bay Area’s Premier Top 40 Band. Event is FREE and open to all UCSF students. RSVP by April 9: ucsfcasinonight2015. eventbrite.com

Thursday, April 23, 5:30-9 p.m., Genentech Hall, N114, Mission Bay Do you want to know more about what career paths exist in industry? How to build a good resume? How to use your LinkedIn network? How to make yourself an attractive applicant to biochtechnology companies? Come hear from Toby Freedman, author of Career Opportunities in Biotechnology and Drug Development. She will cover these topics and more! Networking will follow her talk.

Write for Synapse

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Announcements »

UCSF GREEN CHALLENGE: $5,000 PRIZE

The Office of Sustainability is pleased to announce the UCSF Green Challenge, a competition open to faculty, students, staff, and trainees. Submit your ideas on how to make UCSF a leader in innovation for sustainability in health care, research and education. A panel will review all submissions and select one to receive $5,000. In addition, up to $25,000 will be made available for its implementation, demonstration, or proof of concept. Applications due April 6.

JOIN THE UCSF CONTINGENT AT THE SAN FRANCISCO PRIDE PARADE Sunday, June 28, 10:30 a.m.-noon, Market Street between Beale and 8th Street Come join friends and family of UCSF and be a part of the San Francisco Pride Parade. This year’s theme is, “Equality Without Exception.” Register: http://ucsfpride2015.eventbrite.com

ARE YOU A FIRST GENERATION TO COLLEGE STUDENT (FG2C)?

Register with the First Generation Support Services Office to give you access to all of the First Generation Support Services and helps the office advocate for you!


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Features »

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Opinion »

Stitch Fix: an easy way for New UCSF Alcohol Policy is busy women in science to get Indicative of Deeper Problems By Akshay Govind a style fix in the New Year Staff Writer By Alex Greer Contributing Writer

S cientists often view fashion as a frivolous concern, but studies indicate that a person’s attire can significantly influence self-confidence. In a popular 2012 study from the Journal of Experimental Social Psychology, Adam and Galinsky found that doctors performed a memorization task significantly better when wearing their white coats. Dress to impress, indeed! Self-confidence increases when you feel attractive and professional, and clothing is an easy way to get you one step closer. Stitch Fix—a by-mail, personal styling service for women based in South San Francisco—can help. When you first sign up for Stitch Fix on their website (stitchfix.com), you are asked to fill out an extensive survey about the types of styles you typically like to wear. Romantic? Bohemian? Preppy? For those who want a more detailed picture of their style, Stitch Fix also encourages users to link to a specific Pinterest page that will give a more comprehensive idea

of what they like. The survey also includes important questions like: what type of clothes you are looking for (Work? Date night? Casual?) and what price range you are most comfortable with. The cheapest option is “the cheaper the better,” but pieces often range around $40 to $70 for tops and about $70 for bottoms. They carry a variety of sizes (currently sizes 0-14) and styles, many from small designers that can only be found in boutiques. Once you fill out the forms, you pick a date for delivery, which is about two to four weeks in the future. After your order is complete, you are assigned a stylist who will look at your style profile. The stylist then requests and picks out five pieces for you. (In my experience, that generally entails one bottom, three tops and an accessory— perhaps jewelry or a scarf.) The pieces are carefully packed and sent to you. Once you receive them, you have three business days to try

STITCH FIX » PAGE 6

T here has been a fair amount of attention paid to UCSF’s new policy that a staff or

faculty member must be present at campus events that will be serving alcohol. On one hand, administrators have put the policy forth to help ensure student safety, but on the other hand, many students who are able to make their own legal decisions about alcohol in any other setting feel infantilized or insulted by the need for a chaperone. In a recent Synapse article, Nicolas Strauli expresses his dismay over the policy, stating that if UCSF allows its students to perform medical procedures on patients, surely it should trust them to consume alcohol responsibly. Having had some training in both medicine and dentistry at two different institutions prior to starting my time at UCSF, I would actually argue that this new policy is quite in line with the meager limits typically placed on students’ clinical experiences during pre-doctoral training here. As an example, as a medical student on my OB-GYN rotation, I participated in a total of one vaginal delivery from start to finish and performed a total of zero digital vaginal exams on laboring women. There was always a reason why a particular case might not be a good one for a student – this patient has had some emotional distress or this resident (who was higher on the totem pole) needs some more experience. When my own wife was pregnant and unsure if the sensations she was having at 34 weeks were early labor, she asked if I would check her cervix. I did, and frankly, I had no idea what to tell her. In my own field of oral surgery, when

dental students rotate through our clinic at San Francisco General Hospital, there is a sign over the drawer holding Cowhorn forceps (an instrument designed beautifully for removing lower molars) that reads “No Students.” Granted, there are precautions that need to be taken to use the instrument safely, but shouldn’t that be exactly what we teach during professional school? This is not isolated to the oral surgery department, as dental students are almost never given the chance to perform root canals on molars (which can have challenging root systems) and are not allowed to do simple gum surgeries, even under direct supervision. These procedures are well within the scope of pre-doctoral education at many other institutions. I believe these patterns hold relatively constant across lower level training at UCSF. After all, there are so many specialists in any given field that there is inherent tension in letting someone still training as a generalist to do much of anything. I believe it is that culture that has contributed to the acceptance of the new alcohol policy, and it is my hope that UCSF grows to appreciate that students need to be given a certain amount of freedom to grow. While legal counsel will usually advise taking an approach that avoids risk of liability or mistakes, it is up to clinical instructors and policymakers to take appropriate precautions to minimize risks and maximize learning while giving students the opportunities they need to become the best they can be. Akshay Govind is a fourth-year resident in the department of Oral and Maxillofacial Surgery.

UCSF School of Nursing Welcomes Soka University Nursing Student Delegation By Nhat Bui Contributing Writer

R ecently, the UCSF School of Nursing(SON) welcomed Nursing Students

from Soka University of Japan (SUJ). An opening ceremony featured Dean David Vlahov, RN PhD and Department Chair, Carmen Portillo RN, PhD, FAAN. Dr. Daisaku Ikeda, who fostered peace, culture and international exchanges, founded

the Soka University School of Nursing. Naturally the University’s program is based in humanistic education with a global perspective. UCSF volunteer faculty, Gene Marie O’Connell, RN, MS, went to Japan to be the first Guest lecturer from UCSF to SUJ

Synapse

Jenny Qi | EDITOR-IN-CHIEF Taylor LaFlam | SCIENCE EDITOR Bryne Ulmschneider | CAREER EDITOR Hanna Starobinets | STAFF WRITER Akshay Govind | STAFF WRITER Ilka Fensen | STAFF WRITER Yarrow Madrona | STAFF WRITER Yi Lu | STAFF WRITER Anna Nokana | STAFF WRITER Lauren Shields | STAFF WRITER Mayya Shveygert | STAFF WRITER Charllotte Anderson | STAFF WRITER Andrea Villaroman | STAFF WRITER

SON educational programs and research while observing varied nursing methods of healthcare delivery. The group visited San Francisco General Hospital, Laguna Honda Hospital, Department of Public Health, Progress

SOKA UNIVERSITY » PAGE 7

500 Parnassus Avenue, Millberry Union 108W, San Francisco, CA 94143 tel: 476-2211 | fax: 502-4537 synapse@ucsf.edu | synapse.ucsf.edu

The UCSF Student Newspaper Staff

last May. As a follow-up to this agreement seven of the students and two professors arrived from Japan to begin a weeklong training program. Through the guidance of Dr. Karen Duderstadt, both Drs. Beth Phoenix and Gene O’Connell organized a program so that the students and faculty could gain an understanding of UCSF

About

Synapse is the UCSF student-run biweekly newspaper which runs on Thursdays during the academic year and publishes online in between print issues. 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.

Advertising

Paid advertisements do not necessarily reflect the views of Synapse. Synapse and its editorial board reserve the right to decline advertisements promoting false or misleading claims, known health risks, or content deemed by the editors to be antithetical to the interests of UCSF students or the UCSF community. Synapse does not accept advertisements from tobacco or alcohol manufacturers, or sexually oriented personal ads. Synapse reserves the right to run any ad Submissions Announcements and letters should be submitted with a disclaimer. seven days before publication. All submissions must be emailed to synapse@ucsf.edu. All material is Visit synapse.ucsf.edu to view the publication schedule and to submit an ad. subjected to editing.


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Columns »

This Date in UCSF History

Also from 50 years ago:

By Taylor LaFlam Science Editor

F rom 50 Years Ago: Vol. 9, No. 10, April 5, 1965:

A half century ago, UCSF played host to a several cultural events and exhibits, including an art exhibit featuring a Bay Area native and a collection of controversial films. In April 1965, the campus hosted the art exhibit “Looking at Pictures with Gertrude Stein.” An unattributed author opened Synapse’s article on it, “Gertrude Stein is the subject, object and predicate of an art exhibit opening April 6, at Millberry Union. Viewers will be looking at pictures with Gertrude Stein, looking at pictures, looking at pictures of Gertrude Stein looking at Gertrude Stein. . .” More concretely, the exhibit featured “more than a hundred rare photographs of her in the milieu she made famous -- Paris fin de siecle, Paris of the expatriates, Paris--her “home town”-through two world wars.” After premiering at UCSF, the collection was to travel to a number of other universities across the country. An article by Carol Mosotovy covered the March 1965 visit of “well known and

highly controversial film maker” Kenneth Anger--still alive today and now 88 years old--at which he provided commentary at a program at which four of his short films were shown. Mostovoy focused her article on the film “Scorpio Rising.” That film centers on a “group of motorcycle cultists and their practice of homosexual activities.” Some in the audience were displeased with the film: “it was commented that “’Scorpio Rising’ had no socially redeeming value, and that Mr. Anger is merely playing on the sexual ‘weakness’ of man..” “To such an evaluation, what can be said?. . . as far as the content and subject are concerned, it is reality,” countered Mostovoy in her piece. “There is no question that the film is of human value, if merely in its statement of a reality of human behavior, which is not necessarily weakness or perversion, but part of the human condition that should be recognized and accepted as part of a world which we cannot refuse to see.” Although only a qualified defense of the film and homosexuality, I think that Mostovoy deserves some credit given the prevailing attitudes of the time.

Let’s Get Physical...Therapy!

Osteoarthritis and Running By Ilka Felsen Staff Writer

O steoarthritis (OA) occurs when the cartilage lining the bone surface

wears away. At its worst, OA leads to bone on bone contact, with debilitating pain that may eventually result in a joint replacement. While symptoms do not always correlate with disease progression, over 27 million individuals in the US are affected, with more than 7 million having received a joint replacement. OA is multifactorial, and sports participation, frequent squatting, previous injury, obesity, muscle weakness, genetics and old age are associated with an increased risk of knee OA in particular. Running and Osteoarthritis Mechanical forces exerted on weight bearing joints are a known risk factor for OA, leading many to wonder: does running cause OA? While the evidence is conflicting, most studies indicate that running is not associated with an increased

prevalence of OA. In fact, in a retrospective analysis by Williams, recreational runners were found to have a decreased risk of hip OA and hip replacement, which the researchers associate with the runners’ lower BMIs. Indeed, running may be protective against OA. Many studies have examined the effect of moderate running on OA progression, so what about high level athletics participation? In a systematic review, Driban et al. examined the risk of developing knee OA as a result of sport participation. They found an increase in knee OA prevalence in soccer, elite-level long-distance running, competitive weight lifting, and wrestling athletes.

GET PHYSICAL » PAGE 5

UCSF Journal Club By Taylor LaFlam Science Editor

C ARDIOLOGY & CELL BIOLOGY: Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency. Theodoris, C.V., et al. (Srivastava, D.). Cell. 2015. 160(6):10721086

Sometimes both copies of a given gene can be severely mutated, and the body can compensate just fine. At other times,

however, even having one perfectly good copy isn’t enough. Severe mutations in just one allele of NOTCH1 cause abnormal aortic valve development, leading to valve calcification and damage. Here, Theodoris and colleagues report mechanisms by which decreased NOTCH1 dosage leads to disrupted cell biology.

Taylor LaFlam is a fourth-year BMS/sixth-year MSTP student.

[Exit, Pursued by Science]

Expanding Biomedical Degree Options By Hanna Starobinets Staff Writer

E very week we see exciting science and technology news pop up in our social media news feeds. From the outside it may seem that the science industry is blazing forward in an unstoppable surge of discovery and innovation. On the inside, though, those exciting publications are relatively rare examples of success that result from some talent, a lot of hard work, and a boatload of luck. The luck part wouldn’t be such a problem if an impactful publication record weren’t a prerequisite for “making it” in the science industry.

There are many ongoing discussions of the science pyramid: where one principal investigator trains several postdoctoral fellows and graduate students, most of whom have traditionally had their eyes set on a research career. This system is not sustainable. This isn’t news, given that the system has always been set up this way, but the issue has gotten a lot more attention since cuts in the government’s science budgets and the financial struggles of the pharmaceutical industry have put additional pressure on Ph.D. scientists’ job searches and job security. The modern world we live in requires a lot of innovation in science and engineering. This has made STEM fields particularly They studied endothelial cells derived from induced pluripotent stem cells. They found that when only one normal copy of NOTCH1 was present, there were widespread changes in gene expression and chromatin state, including activation of genes involved in bone formation and inflammation. Shear stress--like that experienced by endothelial cells on valves as blood flows by them--could cause repression of such genes only in endothelial cells in which both copies of NOTCH were functional. CANCER BIOLOGY: Brg1 promotes both tumor-suppressive and oncogenic activities at distinct stages of pancreatic

lucrative and prestigious, evidenced by the wave of young tech billionaires and the number one world university ranking of MIT. Many, including President Obama, are urging more young people to get into STEM fields to keep making discoveries, solving problems, and improving lives. The problem is, we have too many biology Ph.D. scientists and not enough jobs for them. Every year a new batch of bright young scientists enter Ph.D. programs, expecting that their passion and talent for science will make them the next wildly successful researcher. Passion and talent work out well for engineering majors, most of whom go into tech companies either fresh out of college or after a master’s degree. You don’t need an advanced degree or an established reputation to make it big at a company like Apple, Google or SpaceX; if you’re good at what you do and work hard, you can quickly rise into management positions. For biology major fresh out of college, on the other hand, has the most prominent options ar entering a life sciences PhD program, going to medical medical school, or heading straight into biotech, where

EXIT SCIENCE » PAGE 7 cancer formation. Roy, N., et al. (Hebrok, M.). Genes Dev. 2015. 29(6):658-71. Understanding biology and treating disease would be much simpler if each protein did one, and only one thing, in every situation. Alas, context is often crucial, as members of the Hebrok lab found in this paper. A common type of pancreatic cancer first passes through precursor lesions in which what were once acinar cells become more like ductal cells. In this paper, the authors show that development of this cancer from ductal cells involves a similar “retrogression”.

JOURNAL CLUB » PAGE 7


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Puzzles »

Humans of UCSF »

The Crossword

ACROSS 1 Street sign 5 Way to pay 9 Sandwich alternative 13 Seer's deck 15 Clickable image 16 Visibility hindrance 17 Milky, in a way 19 Border on 20 Educated 21 All-inclusive 23 False friend 24 Ramble on 25 Kerrigan or Kwan, e.g. 28 Falling-out 29 Capitol or Columbia 30 Ocean motion 31 Come clean 35 CBS logo 36 Rigging support 39 Routing word 40 Lavish attention (on) 42 Pickling herb 43 Not quite right 45 Struck, old-style 47 Emulate Rodin 48 Place to graze 51 Fall on ____ ears 52 Bronchial woe 53 Lottery jackpot, perhaps 57 Brake part 58 Unproductive path 60 Police, slangily 61 Turner of film

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Coin collector? Feed the kitty Water pitcher Kate's "Titanic" role

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This and that Overly eager Blue as the sky Brady boy Without wasted words 18 Palmist, e.g. DOWN 22 Enthusiast 1 1 TuckApril away 2015 -24Issue Olympian's 2 Sticky stuff quest 3 Like some 25 Winter ride 26 Fight stopper exams 4 Contaminate, as 27 Aid in crime 28 Move like a crab air 5 Parish priest 30 Old hat 6 Knocked off 32 Sinister 7 Mama's boy 33 Talk like Daffy 8 Termite targeter 34 Go on and on

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37 Cuter than cute 38 Road material 41 Lover of beauty (var.) 44 Sound stifler 46 It's the word 47 Email option 48 Old Turkish title 49 Washed-out 50 Weasel's kin 51 Mideast money 53 Chianti, e.g. 54 Palo ____, CA 55 Bruce and Peggy, et. al. 56 Bard's instrument 59 Barrister's field

Edited by Margie E. Burke

Difficulty : Easy

Humans of UCSF is a student-run project aimed at putting a name to the faces we see on campus. View the project on our Facebook page (facebook.com/UCSFsynapse) or on our website (synapse.ucsf.edu/humans-of-ucsf).

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Get Physical » FROM PAGE 4 The Bottom Line In other words, there appears to be a dosedependent relationship between OA and Solution to Sudoku activity level. This parallels conclusions  from research      models,  made in animal namely  of loading  is   that  some  amount crucial for bone and cartilage health, but      much  can  be  detrimental. too

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Why is running ok?          Contact forces in running are certainly   but Miller  et al.  than inwalking, higher argue that runners   do  nothave  anespecially   

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HOW TO SOLVE:        

Photo by Jenny Qi

“My mom is a biologist, so when I was growing up, all my bath toys were lab plastics. Eppendorf tubes, conical tubes, foam floaties, you name it. During school vacations she’d bring me to lab and let me draw cells on culture dishes with a sharpie and feed them with real media. Now that I’m working on a PhD in biomedical science, my mom and I go to conferences together.” —Hanna Starobinets UCSF Graduate Division fourth-year BMS student

Comics »

Piled Higher and Deeper

By Jorge Cham

(Answer appears elsewhere in this issue)

SOLUTIONS » PAGE 7

high risk for OA due to the relatively short duration of contact with the ground and relatively long length of strides. The peak load is higher in runners, but the short amount of time spent in a loaded position seems to blunt this effect. Running has additional benefits of increased bone density and weight control, but also a long and tumultuous history of overuse injuries. Up to 70% of runners get injured in a given year, and a history of injury—acute or overuse—can accelerate OA. Ilka Felsen is a third-year physical therapy student.

Read Synapse Online synapse.ucsf.edu

xkcd

Correction »

In the article, “Synapse Speaks to Startups: KNOX Medical Diagnostics Wants to Let Patients Test Their Lungs at Home” published on March 19, 2015, a few of the names of the individuals and company

By Randall Monroe

identified were misspelled: Dr. Kensho Iwanaga, Dr. David Van Sickle, Allan May, and Bayer. To view the complete article, please visit: http://synapse.ucsf. edu/synapse-speaks-to-startups


6 | Arpil 2, 2015

| synapse.ucsf.edu

Articles continued » Biomedical Data » FROM FRONT PAGE title of his talk “Big Data in Biomedicine: Discovering new drugs and diagnostics from a trillion points of data” – could be amended to “a trillion points of public data.” Butte and colleagues used reanalysis of publicly available data to identify novel disease biomarkers and facilitated drug repositioning. They also launched two start-up biotech companies and the public immunology data resource ImmPort. But you don’t have to be an academic researcher to gain value out of public biomedical data. Amateur scientists and high school science fair participants are also jumping on the data reuse bandwagon, using publicly available datasets to make novel discoveries, such developing algorithms for cancer diagnosis: http:// mashable.com/2013/05/21/computerleukemia-diagnosis/ Giving and getting credit where it’s due So we’ve established that concerns that publicly available data won’t be widely or successfully reused are overblown. What about the oft-voiced concern that the original data provider won’t get any credit for that data reuse? Well, we do still have some work to do to ensure that data citation is easy to do and becomes a cultural norm (and therefore provide researchers with more incentives for releasing their data to public repositories), but some things are falling into place. Many public data repositories utilize the Creative Commons CC-BY Attribution license to ensure that data depositors get proper credit when their dataset is reused. Other repositories rely on Data Use Agreements to establish a contract between a data depositor and data consumer with stipulations on proper citation if data reuse results in a new publication. In fact, citation of datasets is increasing, and has become the norm in some fields,

Stitch Fix

everything on and return any items you don’t like in the included pre-paid USPS bag. If you like all five items, you get a 25 percent discount on the entire order! There are many reasons why Stitch Fix is perfect for busy women in the lab and in the clinic. The most obvious advantage is that it allows you to get a fresh batch of clothes without having to spend time trying on pieces in the store. Instead of schlepping over to a local boutique, you get to avoid the stress and receive a box of pieces prepicked and sized for your personal style. Stitch Fix also helps you if you’re in a style rut. There were years in grad school when I bought only T-shirts and ratty jeans on sale, convinced that finding and buying nicer clothes took too much time and that the expense wasn’t worth the inevitable bleach stain. With Stitch Fix, you can request only tops if you’re afraid of bleach stains, or keep your requests as low-cost as possible. But by getting a Fix, you let someone else

a panel discussin for graduate students

For example, searching on “asthma” in the Data Citation Index reveals >3,600 publicly available data records that have been indexed by the Data Citation Index. These datasets encompassed many different types of data, including gene expression, imaging, protein sequence and structure, and survey data. Sorting these datasets by the number of times they have been cited in other publications revealed that the most highly cited asthma datasets were public health datasets from national health surveys and social science datasets. The next most frequently cited data types were molecular in nature, such as gene expression and protein structure. Data Citation Index does not yet index all public data repositories, but it is a good start for tracking the impact of public datasets. As standards for citing datasets are adopted and more tools like the Data Citation Index emerge, many hope that data citations will become included in the metrics used to measure the impact of a researcher’s output. Giving shared data publicly the same respect and impact trackings more traditional measures of academic output, such as publications, would provide greater incentive for researchers to publicly available research datasets. Currently, policy changes and mandates from funders and publishers are predominantly driving the shift toward depositing data publicly; but as data reuse cases that demonstrate these datasets grow more abundant, benefits to the depositing researchers could become an even stronger driver. Megan Laurance is a UCSF Library research informationist .

help you find new, fun and professional looks.

» FROM PAGE 3

Choosing a Thesis Lab

such as genomic datasets from the Gene Expression Omnibus. One way to track data citation activity is through the Data Citation Index, a great resource provided by the UCSF Library, which enables you to search for datasets by subject area, institution and data type, as well as identify the datasets that have been cited the most in original research articles.

The only drawback may be that after you establish that sense of style, Stitch Fix can lose its edge. After using the service a couple of times, I developed a better idea of the styles and pieces that I wanted to find and began to feel disappointed by the familiar styles I got in my Fix. I’ve seen people get the same pair of pants multiple times, each time in a different shade. For some, that feels uninspired, but others may still appreciate their increased options. Another thing for lab workers to keep in mind is that many tops may be made of synthetic material (based on cost— synthetics are much cheaper than silk), which is a potential hazard in the lab if you work with open flames. If this is the case and you still want a Fix, you can request only natural fibers, like silk (which can be expensive), cotton or wool. Alex Greer is a postdoctoral scholar at Genentech and a UCSF BMS alumna.

Wednesday, April 8 12-1:30 p.m.

Mission Hall Room 1401/02 Mission Bay RSVP: choosingathesislab2015.eventbrite.com

Career Decisions » FROM FRONT PAGE employees a chance to spend most of their time at home? Absolutely! 2. After a quick, unsuccessful search, graduate students and postdocs often assume that no information is available about career options. Actually, there is PLENTY of information to be found about medical writing careers, and other career paths. One of the most comprehensive resources on careers for PhD scientists is myIDP, a career development tool hosted by Science Magazine’s careers site and co-authored by UCSF’s OCPD staff. For each of the 20 scientific career path categories represented on myIDP, we’ve provided links to several articles, books, and professional societies. (After you’re registered on the myIDP site, you’ll need to navigate to the “Read About Careers” section.) But myIDP is just a starting point: don’t limit yourself to the information provide on that site; much more can be found at Science Careers and other web-based publications. Many career paths have an organization that promotes and represents the interests of the field—such as RAPS (Regulatory Affairs Professionals Society) whose members include many PhD’s who have moved from their bench research roles into careers where they assist with the development of drugs. Such organizations often provide inexpensive membership rates for trainees. Even without membership access, their Web sites often provide excellent information about what it’s like to work in the field. And speaking of medical writers, another professional organization with a useful web site is the American Medical Writers Association, which offers extensive information about the field, training programs for entering the field, and current job descriptions that

might help those considering a medicalwriting career gain a better understanding of the various job options available. Additionally, there are some excellent books about career options for scientists. Many are out there, but here are two examples: •• At the Helm, by Kathy Barker (about academic careers) •• Career Opportunities in Biotechnology and Drug Development, by Toby Freedman (features information about many career options for scientists in the industry sector)

Scientists interested in exploring career options should begin by reading about a variety of career options using the resources listed above. But don’t forget about personal interactions: This may be the most important method for gathering information on career options. Attend career panels on your campus or at conferences for your scientific society and talk to the presenters. Most importantly, set up a one-on-one informational interview with a scientist who has transitioned into a career you find interesting and who will meet with you to provide advice and a description of their career path. You’ll end up better informed and you’ll benefit from the advice of a new member of your network. Conferences are a great place to do this—just don’t be a wallflower! It takes a lot of work to gather enough reliable information for you to make informed decisions about your future career options. This is not something you should expect to accomplish in a day or a week, so start early, make use of the many resources available to you through OCPD and beyond. Adapted from an article by Bill Lindstaedt, Cynthia N. Fuhrmann, Jennifer A. Hobin, and Phillip S. Clifford, published in Science Magazine’s careers site, Sciencecareers.org.

drug development platforms that Precision Medicine future can test gene variants associated with drug

» FROM FRONT PAGE

Atul Butte, MD, PhD will highlight the motivation behind creating UCSF’s Institute for Computational Health Sciences, its future plans, and how health professional students can become involved with the Institute. Kristen McCaleb, PhD, will speak about UCSF’s Genomic Medicine Initiative and its collaboration with Sypase, a Bay Area precision medicine biotechnology company, to develop a cloud-computing software program that integrates cancer genetics data with patient electronic medical records. The program will inform physicians and researchers to develop better treatments. Barbara Koenig, PhD and Lisa Denney, MPH will address ethical considerations surrounding precision medicine technologies and how the issue of informed consent is being overcome. Audrey Goddard, PhD of Genomic Health will speak about OncoType Dx, one of the most successful precision medicine products currently on the market. She will explain how the product impacts treatments of breast, prostate, and colon cancers. The Chief Medical Officer of 23andMe, Jill Hagenkord, MD, will address how the personal genetics company optimizes genomic data to guide patient care. Bruce Conklin, MD, from the Gladstone Institutes will speak about the use of inducedpluripotent stem cells disease models as

responses like cardiomyopathies. Finally, Kathryn Phillips, PhD, from UCSF’s Institute for Health Policy Studies will provide insight into the economics of precision medicine and how it is affecting future growth in the field. Students who enroll in the one day-elective course will be awarded one unit of credit. In addition to listening to talks, students will also get a chance to eat lunch with the speakers and network. “It is our hopes that this elective course will introduce students to Precision Medicine for the first time, or give people who are already familiar with the field more knowledge,” says Dor Keyvani, co-founder of PMSA. “I really want our audience to walk away thinking they learned a lot and established strong contacts with our speakers - perhaps even one day consider somehow working within the field of Precision Medicine.” The elective is open to students and faculty from UCSF and surrounding universities and to the general public. To sign up for the elective go to the Eventbrite link (PMSA. eventbrite.com) to purchase a ticket! UCSF students can register under BPS 171 to receive 1-unit elective credit. Join us in making history by attending the very first Precision and Personalized Medicine course at UCSF! Priya Jayachandran and Chris Foo are second-year pharmacy students.


synapse.ucsf.edu

Articles continued » Soka University » FROM PAGE 3 Foundation’s Schrader house, and the new UCSF Benioff Children’s Hospital. A special visit to San Francisco City Hall occurred when Supervisor Malia Cohen of the District 10, presented a Certificate of Honor that acknowledged the meaningful visit of the Soka Students to UCSF SON. Touring the program sites demonstrated how knowledge, skills and expertise gained at UCSF SON could translate into excellence in nursing and health care delivery. The SUJ students were able to meet for lunch meetings with UCSF SON students. Also, the Alpha Eta Chapter (AEC) of Sigma Theta Tau International (STTI) hosted a reception at the home of AEC board member Elizabeth Halifax RN, PhD so they could meet with current and future nursing leaders. These small groups allowed for true international exchange of thoughts and concerns. The SUJ students each had a topic ranging from child abuse to palliative care. At the end of reception, Alpha Eta’s President, Therese Doan RN, PhD, welcomed the students and professors to join our chapter as international members. At the conclusion of the training program each student presented a ten-minute presentation of their topic of interest

Exit Science » FROM PAGE 4

they’ll hold lower positions than PhD scientists and won’t necessarily be able to climb into management. A biology major with big dreams generally chooses between the all-too-binary MD or PhD options. If you don’t want to be a physician but want to move forward in science, you typically go to graduate school and get a PhD. I know PhD candidates who want to continue in academic research, transition into industry, or go into science policy, law, writing, communication, or outreach. Is a five-year research project on one focused topic the correct preparation for all of these careers? That brings me to my proposition. The biomedical industry in the United States is lacking a meaningful master’s degree – not just a terminal master’s given to those leaving their Ph.D. programs. It needs to take a leaf out of engineering’s book and create a solid degree program that focuses on breadth and prepares science students for the many career options outside of academic research. A two-year master’s program in biomedical science would have classwork covering basic biology subjects such as physiology, immunology, stem cells and development, and human diseases including cancer, diabetes and obesity, infection and allergy, neurodegeneration, etc. In addition to broad and extensive coursework, students would rotate through laboratories in different broad categories throughout the program. Working in labs for six weeks at a time over two years

Solutions » Solution to Crossword:

incorporating what they had learned from their training. One student commented on the effect of seeing diversity at UCSF, “I was most impressed by the acceptance of diversity. Japan is an island and difference is not embraced. Here I felt accepted—Americans accept diversity. Now I understand how important it is to adjust our care based on the culture of the patient.” Another student was very impressed by UCSF’s conscious effort to have interprofessional groups and for different disciplines to work together. The student said, “collaboration is so important. We witnessed a team approach to patients and how much nurses are given power to improve patient care.” Through this program, the UCSF SON engaged in global outreach and influenced future nursing leaders. Even during their short time here, the students were tremendously appreciative and felt supported in our community. One student commented, “people kept telling us, ‘You are the leaders of the future.’ I was surrounded by people who believe in my potential. This training course has motivated me to study and achieve.” Of course, after their visit all of the students want to return UCSF SON to attend graduate school. In June, Dr. Beth Phoenix will be a guest lecturer at SUJ. Nhat Bui, RN, is an Adult-Gerontology Nurse Practitioner student.

would expose students to the traditional and cutting edge laboratory approaches used in each field and give them a basic level of hands-on experience in a wide variety of biomedical fields. I believe that a focus on breadth, both in coursework and in the lab, would be more valuable training for the scientists who want to make contributions to science but not necessarily as independent academic principal investigators. If you’re going into a biotech company that develops new therapies for both cancer and Alzheimer’s disease, you’d want to have some knowledge and experience in both diseases – something your PhD thesis research is unlikely to give you. If you’re going to be a science writer or policy maker, breadth is also more important than depth. In fact, even academic research-bound scientists would benefit from going through a breadth-oriented master’s program that could show them firsthand what questions in biomedical science they’re passionate about answering before they narrow their interest and choose a PhD thesis lab. I know I would love that kind of education. It’s the 21st century, and our industry needs an updated education program. Our undergraduate programs need to be more open with their students about what they’re getting themselves into if they pursue a PhD, but our graduate programs also need to step up and create new ways for bright young students to succeed in this field. Hanna Starobinets is a fourth-year BMS student.

Save the Date

2015 Last Lecture with Anatomy professor Dr. Kimberly Topp Wednesday, April 22 5-8 p.m. in Cole Hall

| April 2, 2015 | 7

Zero Year Reunion Immediately Following

S T O W S L E D P A S H A

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P O L L U K A T A B E Y E O T E S A S T S T H H O E E A T N T E

V T I E S C R E A S E R E R L T Y A R D I M O T U R E M A B L L A E W

I S A C O N E N T D E N M A U S E T T I D E D A R M L L A E S C D E A W I N D I N D A N A M E R

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Journal Club » FROM PAGE 4 They find that Brg1, part of the SWI/SNF complex, normally acts in pancreatic ductal cells to prevent such dedifferentiation. Surprisingly, in pancreatic tumor cells, Brg1 actually supports their tumorigenic state. The authors also demonstrate that JQ1, a drug currently being tested as treatment for hematologic cancers, has mixed effects on Brg1 that together impair pancreatic tumorigenesis. IMMUNOLOGY: IgE-activated basophils regulate eosinophil tissue entry by modulating endothelial function. Cheng, L.E. et al (Locksley, R.M.). J Exp Med. 2015. Epub ahead of print. Allergies, in which the body’s immune system acts against non-threatening environmental targets, are a source of annoyance for millions of people and for some a potentially deadly threat A number of classic features of allergic responses have been identified, including an important role for IgE antibodies and entry of eosinophils into the tissue, but many important details in this process have remained unclear. In this paper, the authors identify an important role for basophils in allergy. They find that interaction between the allergen and IgE-displaying basophils leads to basophil activation and positioning

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Solution to Sudoku

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near blood vessels. There, the basophils induce changes in the endothelium that promote eosinophil exit and accumulation in the tissue. CELL BIOLOGY: Increased H+ efflux is sufficient to induce dysplasia and necessary for viability with oncogene expression. Grillo-Hill, B.K., et al. (Barber, D.L.). Elife. 2015. Epub ahead of print The pH of the blood and body fluids are carefully regulated, and even small changes--from say 7.4 to 7.2--are a cause for concern. Recent research has begun to explore the effects of changes in pH within a single tissue or even a single cell Previous research has found that increased intracellular pH is common in cancer and supports increased proliferation and decreased apoptosis. In this paper, GrilloHill and colleagues provide new insights into this process. Working with flies, they demonstrated that increased intracellular pH alone leads to tissue dysplasia. Moreover, such increases heighten the effects of tumor-promoting mutations in Ras. They further find that partly blocking efflux of H+, which prevents this increase in pH, is deleterious to tumors in flies and in human tumor cell lines, suggesting a possible new avenue for therapy. Taylor LaFlam is a fourth-year BMS/sixth-year MSTP student.

GPSA Presents

Casino Night 2015 Thursday, April 16 5-8 p.m. Millberry Union RSVP: ucsfcasinonight2015.eventbrite.com Join the Graduate & Professional Student Association for an evening filled with games, entertainment, food, drinks and a chance to win some prizes! Come ready to play black jack, poker, craps and roulette. Gambling not up your alley? Then experience a live performance from Bay Area’s Premier Top 40 Band, Ascension. Event is FREE and open to all UCSF students. Must RSVP via eventbrite.


8 | Arpil 2, 2015

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