stanford bio-x interdisciplinary initiatives symposium … of medicine1 and departments of...

POSTER # TITLE AUTHORS

1 Folding and Catalysis of the glmS Ribozyme Riboswitch Studied at the

Single-Molecule Level

Andrew Savinov1, Steven M. Block2,3

Biophysics Program1 and Departments of Applied

Physics2 and Biology3, Stanford University

2 Topological Control of DNA Organization: Interfaces Between Physics,

Biology, and Materials Science

Brad A. Krajina1, Abbygail Foster2, Sarah C.

Heilshorn2, Andrew J. Spakowitz1

Departments of Chemical Engineering1 and

Materials Science & Engineering2, Stanford

University

3 Towards Engineered Plant-Microbe Symbioses

Mathias J. Voges1,2, Yang Bai3, Ruben G. Oter3,

Masayoshi Hashimoto3, Paul Schulze-Lefert3,

Elizabeth S. Sattely2

Departments of Bioengineering1 and Chemical

Engineering1, Stanford University; Department of

Plant Microbe Interactions, Max Planck Institute

for Plant Breeding Research, Germany3

4 Not Just a Black Box: Interpretable Deep Learning for Genomics

Avanti Shrikumar1*, Peyton Greenside2*, Anshul

Kundaje1,3

(*co-first authors) Departments of Computer

Science1, Biological Data Science2, and Genetics3,

Stanford University

5 Orientation Estimation of a Continuum Manipulator in a Phantom Lung

Jake Sganga1, David Camarillo1

Department of Bioengineering1, Stanford

University

6 Synergistic Direct Interactions Contribute to Cenp-A Histone Variant

Nucleosome Stability in Cells

Shengya Cao1, Keda Zhou2,3,4, Karolin Luger2,3,4,

Aaron F. Straight1

Department of Biochemistry1, Stanford

University; Departments of Chemistry2 and

Biochemistry3 and Howard Hughes Medical

Institute4, University of Colorado at Boulder

7 Imaging the Cardiac Field Potential with Graphene Optoelectronics

Allister F. McGuire1, Jason Horng2, Halleh B.

Balch2, Hsin-Zon Tsai2, Patrick R. Forrester2,

Michael F. Crommie2, Feng Wang2, Bianxiao

Cui1

Department of Chemistry, Stanford University1;

Department of Physics2, University of California-

Berkeley

8 Dynamic Genetic Control of Gene Expression and DNA Methylation in

Human Aging

Trevor Martin1, Hunter Fraser1

Department of Biology1, Stanford University

9 Multimodal Measurements of Single-Molecule Dynamics using FluoRBT

Ivan E. Ivanov1,2, Paul Lebel2,3,5, Florian C.

Oberstrass2,5, Zev Bryant2,4

Departments of Chemical Engineering1,

Bioengineering2, Applied Physics3, and Structural

Biology4, Stanford University; Berkeley Lights

Inc. and Ultima Genomics, Inc.5

10 Semiautomated Classification of Motion Modes in Complex Single-

Molecule Trajectories

Lucien E. Weiss1, Ljiljana Milenkovic2, Joshua Y.

Yoon1, Tim Stearns2, W. E. Moerner1

Departments of Chemistry1 and Biology2,

Stanford University

Stanford Bio-X Interdisciplinary Initiatives Seed Grants Symposium

Poster Session March 1, 2017

11 A Parameterized Family of Anatomically Accurate Human Upper-Body

Musculoskeletal Models

Samir Menon1, Toki Migimatsu1, Oussama

Khatib1

Department of Computer Science1, Stanford

University

12 Design of Self-Assembling Bio-Inks for Cell-Based 3D Printing

Karen Dubbin1, Yuki Hori1, Anthony Tabet1,

Kazuomori Lewis2, Sarah Heilshorn1

Departments of Materials Science & Engineering1

and Chemical Engineering2, Stanford University

13 Automatic Identification of Cellular Niches Using Deep Neural Networks

and Multi-Parameter Imaging

Salil S. Bhate1,2, Yury Goltsev1, Nikolay

Samusik1, Garry P. Nolan1

Baxter Lab1 and Department of Bioengineering2,

Stanford University

14

TREM2 Haplodeficiency Impairs the Protective Microglia Barrier

Function in Mice and Humans, Leading to Reduced Amyloid Plaque

Compactness and Insulation

Peng Yuan1, Carlo Condello2, Jaime Grutzendler3

Department of Biology1, Stanford University;

Department of Neurology2, University of

California-San Francisco; Department of

Neurology3, Yale University

15 Elastin-like Protein-Hyaluronic Acid (ELP-HA) Hydrogels with

Decoupled Mechanical and Biochemical Cues for Cartilage Regeneration

Danqing Zhu1, Huiyuan Wang2, Pavin Trinh3,

Sarah C. Heilshorn2, Fan Yang1,4

Departments of Bioengineering1,

Materials Science & Engineering2,

Biology3, and Orthopaedic Surgery4, Stanford

University

16 Engineering Patterned Biofilms for Microbial Consortia

Xiaofan Jin1, Ingmar Riedel-Kruse1


University

17 Identifying the Biomechanical Features of Football Head Impacts Using a

Support Vector Machine Classifier

Lyndia C. Wu1, Calvin Kuo2, Jesus Loza2,

Mehmet Kurt1, Kaveh Laksari1, Livia Zarnescu1,

Daniel Senif3, Scott C. Anderson3, Logan Miller4,

Jill Urban4, Joel Stitzel4, David Camarillo1,2

Departments of Bioengineering1, Mechanical

Engineering2, and Sports Medicine3, Stanford

University; Department of Biomedical

Engineering4, Wake Forest University

18 Speckle-Free Coherence Tomography of Turbid Media

Orly Liba1,2, Matthew D. Lew1, Elliott D.

SoRelle1,3, Rebecca Dutta1, Derek Yecies1,4,

Debasish Sen1, Darius M. Moshfeghi5, Steven

Chu6,7, Adam de la Zerda1,2,3

Departments of Structural Biology1, Electrical

Engineering2, Neurosurgery4, Physics6, and

Molecular & Cellular Physiology7, Biophysics

Program3, and Byers Eye Institute5, Stanford

University

19 Males and Females Differ In Biochemical Composition of Platelet-Rich

Plasma

Grace Xiong1, Nithya Lingampalli2,4, Smritee

Dadhwal1, Lawrence Leung3,4, William

Robinson2,4, Constance R. Chu1,4

Departments of Orthopaedic Surgery1 and

Medicine (Divisions of Immunology and

Rheumatology2 and Hematology3), Stanford

University; VA Palo Alto Health Care System4

20 Connecting the Retina to the Brain: Specificity of Subcortical Targeting

Tania A. Seabrook1, Nao Ishiko1, Onkar S.

Dhande1, Victoria P. Wooley1, Phong L. Nguyen1,

Andrew D. Huberman1,2

Departments of Neurobiology1 and

Ophthalmology2, Stanford University

21 Segmentation of the Human Nucleus Accumbens Using High Resolution

Diffusion Tractography

Sam Cartmell1, Qiyuan Tian2, Christophe Leuze2,

Grant Yang2, Jennifer McNab2, Casey Halpern3

School of Medicine1 and Departments of

Radiology2 and Neurosurgery3, Stanford

University

22

Integrative, Multi-Cohort Analysis of Epstein-Barr Virus (EBV)-Positive

and Negative Tumor Samples to Identify Gene-Signatures Associated

with EBV Oncogenesis

Eden Maloney1, Erika Bongen1, Francesco

Vallania2, Purvesh Khatri3,5, Olivia M. Martinez4

Stanford Immunology Graduate Program1,

Departments of Immunity Transplant Infection2,

Medicine5, Biomedical Data Science3, and

Surgery4, Stanford University

23 Timing Performance Characterization of Two TOF-DOI PET Detector

Designs: Phoswich and Offset Crystal Layers

Chen-Ming Chang1,2 and Craig S. Levin2,3,4,5

Departments of Applied Physics1, Radiology2,

Physics3, Electrical Engineering4, and

Bioengineering5, Stanford University

24 A Spinal Cord Circuit for Thermosensation and Thermal Nociception

Chen Ran1, Gabriella Kamalani1, Mark Hoon2,

Xiaoke Chen1


Molecular Genetics Unit2, Laboratory of Sensory

Biology, National Institute of Dental &

Craniofacial Research–National Institutes of

Health

25 Variable Density Single-Shot Fast Spin Echo with Auto-Calibrated Wave

Encoding

Feiyu Chen1, Valentina Taviani2, Joseph Y.

Cheng3, Tao Zhang4, Brian A. Hargreaves3, John

M. Pauly1, Shreyas S. Vasanawala3

Departments of Electrical Engineering1 and

Radiology3, Stanford University; Global MR

Applications and Workflow2, GE Healthcare,

Menlo Park, CA; Global MR Applications and

Workflow4, GE Healthcare, Houston, TX

26 Stability of Monoclonal Antibodies in Solution Affected by Interfacial

Viscoelasticity

Aadithya Kannan1, Ian C. Shieh2, Danielle L.

Leiske2, Chunzi Liu1, Camila Kofman1, Gerald G.

Fuller1

Department of Chemical Engineering1, Stanford

University; Genentech, Inc.2

27 Mechanical Confinement Regulates Cartilage Matrix Formation by

Chondrocytes

Hong-pyo Lee1, Luo Gu2,3, David J. Mooney2,3,

Marc E. Levenston1, Ovijit Chaudhuri1

Department of Mechanical Engineering1, Stanford

University; School of Engineering & Applied

Sciences2 and Wyss Institute for Biologically

Inspired Engineering3, Harvard University

28 Comparison of CdTe and BSO Crystals for Optical Property Modulation-

Based Radiation Detection Method for PET

Li Tao1, Craig S. Levin1,2,3,4

Departments of Electrical Engineering1,

Radiology2, Physics3, and Bioengineering4,

Stanford University

29 A Scalable Active Framework for Region Annotation in 3D Shape

Collections

Li Yi1, Vladimir G. Kim2,3, Duygu Ceylan3, I-

Chao Shen4, Mengyan Yan1, Hao Su2, Cewu Lu2,

Qixing Huang5,6, Alla Sheffer4, Leonidas

Guibas1,2


Computer Science2, Stanford University; Adobe

Research3; University of British Columbia4; TTI

Chicago5; University of Texas-Austin6

30 Nanometer-Scale Lipid Clusters in Model Membranes Revealed by

Atomic Recombination in NanoSIMS

Frank R. Moss III1, Steven G. Boxer1

Department of Chemistry1, Stanford University

31

Detecting and Enumerating Soil-Transmitted Helminth Eggs in Soil:

New Method Development and Results from Field Testing in Kenya and

Bangladesh

Lauren Steinbaum1, Laura H. Kwong1, Ayse

Ercumen2, Makeda S. Negash3, Amira J. Lovely2,

Sammy M. Njenga4, Alexandria B. Boehm1, Amy

J. Pickering1, Kara L. Nelson5

Department of Civil & Environmental

Engineering1, Stanford University; School of

Public Health2, Departments of Integrative

Biology3 and Civil & Environmental

Engineering5, University of California-Berkeley;

Eastern and Southern Africa Center of

International Parasite Control4, Kenya Medical

Research Institute (KEMRI), Nairobi, Kenya

32 Human Neck Musculature Cannot Significantly Reduce Brain Injury

During Concussive Sagittal Head Impacts

Michael Fanton1, Calvin Kuo1, Fidel Hernandez1,

David Camarillo1,2

Departments of Mechanical Engineering1 and


33 A New Spectral Contrast High-Resolution Optical Molecular Imaging

Platform for Medical and Biological Applications

Elliott D. SoRelle1,3,4,5, Orly Liba1,2,3,4, Debasish

Sen1, Adam de la Zerda1,2,3,4,5

Departments of Structural Biology1 and Electrical

Engineering2, Bio-X Program3, Molecular

Imaging Program at Stanford4, and Biophysics

Program5, Stanford University

34 Antibody Selection in Response to Influenza Vaccine

Lily Blair1, Steve Quake2,3,4, Daniel Fisher1,2,4

Departments of Biology1, Bioengineering2,

Physics3, and Applied Physics4, Stanford

University

35 Robust Self-Gated Free-Breathing Cardiac MRI Using Virtual Coils

Xinwei Shi1,2, Joseph Y. Cheng1,2, Michael

Lustig3,4, John M. Pauly2, Shreyas S. Vasanawala1

Departments of Radiology1 and Electrical

Engineering2, Stanford University; Departments

of Electrical Engineering3 and Computer

Science4, University of California-Berkeley

36 Accelerating MRI Scans Using Neural Networks

Xinwei Shi1,2, and Feiyu Chen1,2

Departments of Radiology1 and Electrical

Engineering2, Stanford University

37 Developing a Modular Virus-like Particle Vaccine Platform for Viral

Diseases

Julie A. Fogarty1, James R. Swartz1,2

Departments of Chemical Engineering1 and


38 Adaptable Elastin-like Protein - Hyaluronic Acid (ELP-HA) Hydrogels as

Customizable and Reproducible Matrices for Organotypic Cultures

Huiyuan Wang1, Xingnan Li2, Junzhe Lou1,

Chuck Zhang2, Yan Xia3, Calvin J. Kuo2, Sarah

C. Heilshorn1

Departments of Materials Science &

Engineering1, Medicine (Division of

Hematology)2, and Chemistry3, Stanford

University

39 Influenza Binding Avidity Governed by Sterol-Dependent Ganglioside

Dynamics

Isabel Goronzy1, Robert Rawle2, Peter Kasson2,

Steven Boxer1

Department of Chemistry1, Stanford University;

Department of Molecular Physiology &

Biological Physics2, University of Virginia

40 Investigating Novel Super Enhancer of Cardiac Development

Gunes Ates Akgun1, Jaecheol Lee2, Ningyi Shao2,

Joseph Wu2,3, Zhen Cheng3

Departments of Biology1, Cardiology2, and

Radiology3, Stanford University

41 Hunting for New Therapeutic Approaches: Using CRISPR Systems to

Treat Huntington’s Chorea

Aris John Kare1, Dehua Zhao1, Lei Stanley Qi1,2,3

Departments of Bioengineering1 and Chemical &

Systems Biology2 and ChEM-H3, Stanford

University

42 Effects of Posture on Resting-State Brain Networks

Grace Tam1, Hadi Hosseini2, Allan Reiss2,3

Departments of Biology1, Psychiatry &

Behavioral Sciences (Center for Interdisciplinary

Brain Sciences Research)2, and Radiology3,

Stanford University

43 Circumferential and Radial Variations in T2, T2* and T1rho in the

Osteoarthritic Meniscus

Marianne S. Black1, Garry E. Gold2,3, Marc E.

Levenston1,2,3, Brian A. Hargreaves2,3

Departments of Mechanical Engineering1,

Radiology2, and Bioengineering3, Stanford

University

44 Block Bootstrap Method for Analyzing Human Microbiota During

Pregnancy

Pratheepa Jeganathan1, Susan Holmes1

Department of Statistics1, Stanford University

45 Utilizing the Glutaminase Pathway for Treatment and Monitoring of

Cancer

Sonya Park1, Hongjuan Zhao2, Fred Chin3,

Andrei Iagaru1, Melinda Telli4, Donna Peehl2,

Erik Mittra1, Alice Fan4

Departments of Radiology (Nuclear Medicine)1,

Urology2, Radiochemistry2, and Medicine

(Division of Oncology)4, Stanford University

46 A Clinical Study to Utilize Captured CTCs for Early Cancer Therapy

Monitoring

Viola Chen1, Jared Nesvet2, Chin Chun Ooi2,

Sangeeta Kowli1, Christian Hoerner1, Shan

Wang2, Alice Fan1

Departments of Medicine (Division of Oncology)1

and Materials Science & Engineering2, Stanford

University

47 Spring-Mediated Intestinal Lengthening

Nhan Huynh1,2,3, Anne-Laure Thomas1,2,3, Genia

Dubrovsky1,2, Joshua D. Rouch1,2, Andrew

Scott1,2, Shant Shekherdimian1,2, James C.Y.

Dunn1,2,3

Departments of Surgery (Pediatric Surgery)1 and

Bioengineering2, University of California-Los

Angeles; Department of Surgery (Pediatric

Surgery)3, Stanford University

48 A Large Animal Model of Gastrointestinal Aganglionosis

Nhan Huynh1,2,3, Anne-Laure Thomas1,2,3, Genia

Dubrovsky1,2, Joshua D. Rouch1,2, Andrew

Scott1,2, Elvin Chiang1,2, James C.Y. Dunn1,2,3

Departments of Surgery (Pediatric Surgery)1 and

Bioengineering2, University of California-Los

Angeles; Department of Surgery (Pediatric

Surgery)3, Stanford University

49 Elastic Polymer Sensor Arrays for High Spatiotemporal Resolution Mapping of Cardiac Arrhythmogenic Activity

Bartlomiej Imielski1, Jia Liu2, Yuxin Liu2,

Mahmood Alhusseini3, Joy Aparicio Valenzuela1,

Christopher Kowalewski3, Cholawat

Pacharinsak4, Sam Baker4, Sanjiv Narayan3,

Zhenan Bao2, Anson Lee1

Departments of Cardiothoracic Surgery1,

Chemical Engineering2, Medicine (Division of

Cardiovascular Medicine)3, and Comparative

Medicine (Veterinary Service Center)4, Stanford

University

50 Rivas Lab: Translating Biomedical Data into Meaningful Discoveries

Christopher DeBoever1,2, Mamie Wang3, Antonio

Edward Lindsey3, Oliver Bear Don’t Walk IV3,

Adam Lavertu3, Yosuke Tanigawa3, Greg

McInnes3, Manuel Rivas1

Departments of Biomedical Data Science1 and

Genetics2 and Biomedical Informatics Training

Program3, Stanford University

51 UK Biobank Browser: A Website for the Statistical Exploration of a

Large Genomic Datasets

Gregory McInnes1*, Adam Lavertu1*, Manuel

Rivas2*

(*equal contribution) Biomedical Informatics

Training Program1 and Department of Biomedical

Data Science2, Stanford University

52 Emerging Technologies for Efficient Clinical, Genetic, and Omics

Inference

Oliver Bear Don’t Walk IV1*, Yosuke

Tanigawa1*, Alice Yu1, Adam Lavertu1, Sandeep

Ayyar1, Manuel Rivas2

(*equal contribution) Biomedical Informatics

Training Program1 and Department of Biomedical

Data Science2, Stanford University

53 Pathway and Mechanism of Antagonist Binding to Opioid Receptors

Robin M. Betz1, Ron O. Dror2

Biophysics Program1 and Department of

Computer Science2, Stanford University

54 Loss and Recovery of Consciousness and the Chaotic EEG

M. Bruce MacIver1, Caitlin Drover1, David R.

Drover1

Department of Anesthesiology, Perioperative &

Pain Medicine1, Stanford University

55 High Dose Gamma Radiation Selectively Reduces GABAA-slow

Inhibition

Beza A. Dagne1, Melis K. Sunay1, Noëlie S.J.

Cayla1, Yi-Bing Ouyang1, Shoucheng Ning2,

Susan J. Knox2, Rona G. Giffard1, John R. Adler2,

M. Bruce MacIver1

Departments of Anesthesiology, Perioperative &

Pain Medicine1 and Radiation Oncology2,

Stanford University

56 New Anesthetic Drug Discovery: Towards a More Selective ‘Propofol’

Noëlie S.J. Cayla1, Beza A. Dagne1, Yun Wu1,

James R. Trudell1, M. Frances Davies1, M. Bruce

MacIver1, Edward J. Bertaccini1,2


Pain Medicine1, Stanford University; Department

of Anesthesia2, VA Palo Alto Health Care System

57 Single Molecule Imaging of Gene Expression and 3D Genome Structure

Alistair Boettiger1

Department of Developmental Biology1, Stanford

University

58 An Intravascular Magnetic Wire for High-Throughput in vivo Enrichment

of Rare Circulating Biomarkers

Ophir Vermesh1,2*, Amin Aalipour1,2,3*, Tianjia J.

Ge1,4*, Yamil Saenz2, Yue Guo5, Seung-min

Park1,2, Yoshiaki Mitsutake6, Michael

Bachmann2,7, Chin Chun Ooi8, Jennifer Lyons6,

Kerstin Mueller2, Hamed Arami1,2, Alfredo

Green6, Shan X. Wang5,9, Sanjiv S. Gambhir1,2,3

(*co-first authors) Molecular Imaging Program at

Stanford1, Departments of Radiology2,

Bioengineering3, Electrical Engineering5,

Medicine (Division of Cardiovascular Medicine)6,

Pediatrics7, Chemical Engineering8, and Materials

Science & Engineering9, and Howard Hughes

Medical Institute4, Stanford University

59 Directed Evolution of a Faster Promiscuous Biotin Ligase (BioID) for

Spatiotemporally Resolved Proteomic Mapping in Living Cells

Tess Branon1, Justin Bosch2, Norbert Perrimon2,

Alice Ting3

Department of Chemistry1, Massachusetts

Institute of Technology; Department of Genetics2,

Harvard University; Department of Genetics3,

Stanford University

60

Significance of the Double-Layer Capacitor Effect in Solution-

Processable Polymeric Dielectrics and Exceptionally Stable Low-Voltage

Organic Transistors

Raphael Pfattner1, Amir Foudeh1, Celine Liong1,

Chao Wang1, Wen-Ya Lee1, Desheng Kong1,

Zhenan Bao1

Department of Chemical Engineering1, Stanford

University

61 Orchestrating the Acquisition and Maintenance of Drug Seeking in a

Thalamic Circuit

Piper Keyes1, Eliza Adams1, Yingjie Zhu2, Greg

Nachtrab2, Xiaoke Chen2

Neurosciences Graduate Program1 and

Department of Biology2, Stanford University

62 Sub-Topographic Maps for Regionally-Enhanced Analysis of Visual

Space in the Mouse Retina

Rana N. El-Danaf1, Andrew D. Huberman1,2,3,4

Departments of Neurobiology1 and

Ophthalmology2, Stanford Neurosciences

Institute3, and Stanford Bio-X Program4, Stanford

University

63 A Mixed-Reality System for Breast Surgical Planning

Stephanie L. Perkins1,2, Subashini Srinivasan2,

Michael A. Lin3, Jung Hwa Bae3, Christoph W.

Leuze2, Johannes Weickenmeier3, Ellen Kuhl3,

Mark R. Cutkosky3, Amanda J. Wheeler4, Brian

A. Hargreaves2, Bruce L. Daniel2

Departments of Bioengineering1, Radiology2,

Mechanical Engineering3, and Surgery4, Stanford

University

64 Technical Developments for Medical Mixed-Reality

Michael A. Lin1, Jung Hwa Bae1, Subashini

Srinivasan2, Christoph W. Leuze2, Stephanie L.

Perkins2,3, Johannes Weickermeier1, Ellen Kuhl1,

Amanda J. Wheeler4, Mark R. Cutkosky1, Brian

A. Hargreaves2, Bruce L. Daniel2


Radiology2, Bioengineering3, and Surgery4,

Stanford University

65 Darwin: A Hardware-Accelerated Framework For Genomic Sequence

Alignment

Yatish Turakhia1, Gill Bejerano2,3,4, William

Dally1,2

Departments of Electrical Engineering1,

Computer Science2, Developmental Biology3,

and Pediatrics4, Stanford University

66 Micro RNA 200b Modulates ROS-Induced Injury in Neuronal Cells

Josh Bell1, Xiaoyun Sun2, Creed M. Stary2, Rona

G. Giffard2

Department of Anesthesia1, University of

Toronto; Department of Anesthesiology,

Perioperative & Pain Medicine2, Stanford

University

67 Novel Stem Cell-Based Bioconstruct Regenerates Functional Muscle

Tissue and Vascularization in a Volumetric Muscle Loss Model

Marco Quarta1,2, Melinda Cromie1,2, Robert

Chacon1,2; Jennifer Go2; Victor Garcia2; Justin

Blonigan1,2, Mark Hamer1,2, Michael Gibbons1,2,

Merel Stok3, Patrick Paine1,2, Thomas Rando1,2

Department of Neurology1, Stanford University;

Center for Tissue Regeneration, Restoration &

Repair (CTR3)2, VA Palo Alto Health Care

System; Department of Clinical Genetics3,

Erasmus Medical Center, The Netherlands

68 Investigating Metastasis-Specific Alteration of Serine Metabolism in

Breast Cancer

Jiangbin Ye1, Gregory Ducker3,4, Jiajun Zhu2,

Ling Liu3,4, Joshua D. Rabinowitz3,4, Craig B.

Thompson2

Department of Radiation Oncology1, Stanford

University; Cancer Biology and Genetics

Program2, Memorial Sloan Kettering Cancer

Center; Lewis-Sigler Institute for Integrative

Genomics3 and Department of Chemistry4,

Princeton University

69 Engineered Conductive Scaffolds to Improve Stroke Recovery

Byeongtaek Oh1, Alexa Levinson1, Paul George1

Department of Neurology & Neurological

Sciences1, Stanford University

70 Transport of Brownian Spheroidal Nanoparticles in Near-Wall Vascular

Flows for Cancer Therapy

Tiras Y. Lin1, Preyas N. Shah1, Bryan R. Smith2,

Eric S.G. Shaqfeh1,3


Radiology2, and Chemical Engineering3, Stanford

University

71 Mapping the Spatial Organization of Endogenous RNAs in Living Cells

via Peroxidase-Mediated Proximity Biotinylation

Pornchai Kaewsapsak1, David Shechner2, Furqan

Fazal3, John Rinn2, Howard Chang3, Alice Ting4

Department of Chemistry1, Massachusetts

Institute of Technology; Department of Stem Cell

& Regenerative Biology2, Harvard University;

Departments of Dermatology3 and Genetics4,

Stanford University

72 Temperature Simulation of W and W25Re Targets to Deliver High Dose

Rate 10 MV Photons

Jinghui Wang1, Stefania Trovati2, Philipp M.

Borchard3, Billy W. Loo Jr.2, Peter G. Maxim2,

Rebecca Fahrig4

Departments of Radiology1 and Radiation

Oncology2, Stanford University; TibaRay Inc.3,

San Francisco; Siemens Healthcare GmbH4,

Germany

73 Fine-Tuned Protein Production in Methanosarcina acetivorans C2A

Ann A. Karim1, Daniel R. Gestaut2, Alfred M.

Spormann1,3

Departments of Civil & Environmental

Engineering1, Biology2, and Chemical

Engineering3, Stanford University

74 Directed Evolution of Split APEX2 for the Proteomic Mapping of

Mitochondria-Endoplasmic Reticulum Contact Sites

Yisu Han1,2, Jeff D. Martell3, Alice Y. Ting1

Department of Genetics1, Stanford University;

Department of Chemistry2, MIT; Department of

Chemistry3, University of California-Berkeley

75 Development of Mini-Gut with Periodically Contracting Smooth Muscle

Organoids

Qianqian Wang1,2, Ke Wang3, R. Sergio

Solorzano-Vargas4, Po-Yu Lin1,2, Christopher M.

Walthers2, Anne-Laure Thomas1, Martín G.

Martín4, James C. Y. Dunn1,2

Department of Surgery (Division of Pediatric

Surgery)1, Stanford University; Department of

Bioengineering2 and Eli & Edythe Broad Center

of Regenerative Medicine & Stem Cell Research4,

University of California-Los Angeles;

Department of Computer Science3, University of

North Carolina at Chapel Hill

76 Automated Detection of Dendritic Spines in Microscopic Volumetric

Images

Xuerong Xiao1, Assaf Hoogi2, Daniel Rubin2



77 Miniaturized Optical BioSensor for Point-of-Care Total Protein

Measurement

Fariah Mahzabeen1, Ophir Vermesh2, Sanjiv S.

Gambhir2,3, James S. Harris1


Radiology2 and Canary Center for Cancer Early

Detection3, Stanford University

78 Biodegradation of Petroleum Based Plastics by Yellow Mealwosrms

(Larvae of Tenebrio molitor)

Wei-Min Wu1, Shanshan Yang1, Anja M.

Brandon1, Zhiyue Wang1, Hanqing Fan1, James

Christopher Andrew Flanagan2, Daliang

Ning3, Shuhong Gao3, Robert Waymouth2,

Jizhong Zhou3, Craig S. Criddle1

Departments of Civil & Environmental

Engineering1, and Chemistry2, Stanford

University; Department of Botany &

Microbiology3, University of Oklahoma

79 Nondestructive Nanostraw Intracellular Sampling for Longitudinal Cell

Monitoring

Yuhong Cao1, Martin Hjort1, Nicholas Melosh1

Department of Materials Science & Engineering1,

Stanford University

80 Effectiveness of Screen-Based Approaches to Managing Preoperative

Anxiety in Children: Preliminary Data

Olivia Jang1, Samuel Rodriguez1, Thomas J.

Caruso1, Alex Joseph1, Maya Hernandez1, Laura

E. Simons1


Pain Medicine1, Stanford University

81 Detection of Spontaneous Action Potentials of HEK 293 Cells by

Prussian Blue Thin Films

Felix Alfonso1, Allister McGuire1, Thomas Li1,

Francesca Santoro1, Luke Kaplan1, Bianxiao Cui1

Department of Chemistry1, Stanford University

82 Charge-Altering Releasable Transporters (CARTs) for the Delivery and

Release of Messenger RNA in Living Animals

Colin J. McKinlay1, Jessica R. Vargas1, Timothy

R. Blake1, Jonathan W. Hardy2,7, Masamitsu

Kanada2,7, Christopher H. Contag2,3,4,5,7, Paul A.

Wender1,6, Robert M. Waymouth1

Departments of Chemistry1, Pediatrics2,

Microbiology & Immunology3, Bioengineering4,

Radiology5, and Chemical & Systems Biology6

and Molecular Imaging Program at Stanford

(MIPS)7, Stanford University

83 Enhancer Evolution and the Origins of Vertebrate Brain Development

Paul Minor1, Yao Yao2, Nat Clarke1, Doug

Epstein2, Christopher Lowe1


Department of Genetics2, University of

Pennsylvania

84 Pro-Inflammatory M1 Macrophages Promote Osteogenesis by

Mesenchymal Stem Cells via the COX-2-Prostaglandin E2 Pathway

Laura Y. Lu1, Florence Loi1, Karthik Nathan1,

Tzu-hua Lin1, Jukka Pajarinen1, Emmanuel

Gibon1,3, Akira Nabeshima1, Luis Cordova1,4,

Eemeli Jämsen5, Zhenyu Yao1, Stuart B.

Goodman1,2

Departments of Orthopaedic Surgery1 and

Bioengineering2, Stanford University; Laboratoire

de Biomécanique et Biomatériaux Ostéo-

Articulaires3, Faculté de Médecine - Université

Paris, France; Department of Oral and

Maxillofacial Surgery4, University of Chile,

Santiago, Chile; Department of Medicine5,

Clinicum, University of Helsinki, and Helsinki

University Hospital, Finland

85 A Novel Proliferating Cell Population in Human Brain Arteriovenous

Malformations and its Potential Contribution to Disease Pathology

Lorelei D. Shoemaker1,2, Steven D. Chang1,2

Department of Neurosurgery1 and the Stanford

Neuromolecular Innovation Program2, Stanford

University

86 Minimally Invasive Ultrasonically Powered Implantable Devices for

Next-Generation Therapies and Neuromodulation

Jayant Charthad1, Marcus J. Weber1, Jerry

Chang1, Syridon Baltsavias1, Max Wang1, Amin

Arbabian1

Department of Electrical Engineering1, Stanford

University

87 Impact of Homonymous Visual Field Defect on Reading

Jeehey Song1,2, Ali Shariati1,2, Joyce Y. Liao1,2

Department of Ophthalmology1 and Byers Eye

Institute2, Stanford University

88 Mechanisms for Persistent Atrial Fibrillation Revealed by 2 Independent

Algorithms at Sites of Termination by Localized Ablation

Mahmood Alhusseini1, Dave Vidmar2, Gabriela

Meckler1, Christopher Kowalewski1, Fatemah

Shenasa1, Albert J. Rogers1 , Tina Baykaner1,

Junaid Zaman1, Mallika Tamboli1, David E.

Krummen1, Paul Zei1, Mohan Viswanathan1, Paul

J. Wang1, Johannes Brachmann3, John M. Miller4,

Wouter-Jan Rappel2, Sanjiv M. Narayan1

Department of Medicine1, Stanford University;

Department of Physics2, University of California-

San Diego; Clinic of Cardiology3, Klinikum

Coburg, Germany; Department of Medicine4,

Indiana University

89 Behavioral Time-Scale Synaptic Plasticity Underlies Spatial Coding in

the Hippocampus

Aaron Milstein1, Katie C. Bittner2, Sandro

Romani2, Jeffrey C. Magee2, Ivan Soltesz1

Department of Neurosurgery1, Stanford

University; HHMI Janelia Research Campus2

90 Slow-Release Lipid Nanoparticles for Targeted Cardiac Delivery of

Allele-Specific siRNA to Treat Dilated Cardiomyopathy

Alexa Wnorowski1, Elena Matsa2,3,4,5, Alsu

Zamaleeva6, Mohammed Ahmed6, Arita

Dubnika6, John H. Ahrens2, Wenchao Sun6,

Vittavat Termglinchan2,3,4,5, Ioannis

Karakikes2,3,4,5, Oscar Abilez2,3,4,5, Jayakumar

Rajadas6, Joseph C. Wu2,3,4,5

Department of Bioengineering1, Medicine3, and

Radiology4, Stanford Cardiovascular Institute2,

Institute of Stem Cell Biology & Regenerative

Medicine5, and Biomaterials & Advanced Drug

Delivery Laboratory6, Stanford University

91 Fear Learning in Adolescents with Chronic Pain and Pain-Related Fear

Vaibhav Murali1, Corey Kronman2,3,4, Lauren

Heathcote1, Maya Hernandez1, Clas Linnman2,3,4,

David Borsook2,3,4, Laura Simons1


Pain Medicine1, Stanford University; Department

of Anesthesiology, Perioperative & Pain

Medicine2 and P.A.I.N. (Pain & Analgesia

Imaging Neuroscience) Group3, Boston

Children’s Hospital; Center for Pain in the Brain4,

Harvard Medical School

92 Charged Archaeal S-Layer Modulates Enzyme Kinetics in Pseudo-

Periplasmic Space

Po-Nan Li1,3, Frederic Poitevin2, Jonathan

Herrmann2, Henry van den Bedem3, Soichi

Wakatsuki2,3


Structural Biology2, Stanford University;

Biosciences Division3, SLAC National

Accelerator Laboratory

93 ApoE2, ApoE3 and ApoE4 Differentially Activate a Non-Canonical

MAP-Kinase Cascade Stimulating Abeta-Secretion

Yu-Wen Alvin Huang1, Marius Wernig2, Thomas

C. Südhof1

Department of Molecular & Cellular Physiology1

and Institute for Stem Cell Biology &

Regenerative Medicine2, Stanford University

94 Living Galapagos Islands

Alexander Tarashansky1, Bo Wang1


University

95 Ecosystem Regeneration in Single Animals

Youngbin Lim1, Margarita Khariton1, Yuan Xue1,

Bo Wang1


University

96 Environmental Calcium Controls Alternate Physical States of the

Caulobacter Surface Layer

Jonathan Herrmann1,2, Paul Bargar3, Po-Nan Li4,

Thomas Lane2, Thomas Weiss2, Lucy Shapiro5,

Soichi Wakatsuki1,2

Departments of Structural Biology1, Electrical

Engineering4, and Developmental Biology5,

Stanford University; SLAC National Accelerator

Laboratory2; Menlo-Atherton High School3

97 Probing the Binding Specificity in Protein Interaction Networks Using

Spectrally Encoded Peptide-Bead Libraries

Huy Q. Nguyen1, Nikhil P. Damle2, Jagoree Roy2,

Bjorn Harink3, Kara Brower1, Scott Longwell1,

Brian Baxter3, Kurt Thorn3, Martha Cyert2, Polly

Fordyce1

Departments of Bioengineering1 and Biology2,

Stanford University; Department of Biophysics &

Biochemistry3, University of California-San

Francisco

98 Programmed Cell Fate Changes in Embryonic Stem Cells Using CRISPR

Technology

Marie La Russa1,2, Yanxia Liu2, Marcos Torres2,

Yuchen Gao3, Barbara Panning4, Stanley Lei Qi2,5

Biomedical Sciences Program1 and Department of

Biochemistry & Biophysics4, University of

California-San Francisco; Departments of

Bioengineering2 and Chemical & Systems

Biology5 and Cancer Biology Program3, Stanford

University

99 Adhesion Prevention Using Polymer Nanoparticle (PNP) Hydrogels

Lyndsay Stapleton1, Amanda Steele1, Joseph

Woo2, Eric Appel3

Departments of Bioengineering1, Cardiothoracic

Surgery2, and Materials Science & Engineering3,

Stanford University

100 Multimodal Oscillatory Coupling and Spectral Features in Epileptic

Focus Localization from Sleep Electroencephalography Recordings

Tibor Nánási1, Balint File2, Zoltan Karasz2,

Emilia Toth3,4, Daniel Fabo3,4, Laszlo Entz5,

Lorand Eross5, Istvan Ulbert1

Institute of Cognitive Neuroscience &

Psychology, Research Centre for Natural

Sciences1, Hungarian Academy of Sciences;

Faculty of Information Technology & Bionics2,

Pázmány Péter Catholic University; Epilepsy

Centrum3 and Departments of Neurology4 and

Functional Neurosurgery5, National Institute for

Clinical Neurosciences, Budapest, Hungary

101 2nd Generation “Trigger and Release” Smart Probes for Imaging Tumor

Hypoxia in vivo

Bin Shen1, Samuel Banister1, Walid Fawzi

Alrashed Alsharif1, Zheng Miao1, Marjan Rafat2,

Marta Vilalta2, Edward E. Graves2, Ananth

Srinivasan1, Frederick T. Chin1

Departments of Radiology1 and Radiation

Oncology2, Stanford University

102 Gradient Control and Microporosity Guidance in 3D Structures for

Regenerative Medicine

Raphaël F. Canadas1,2,3, Alessandro Tocchio1,

Alexandra P. Marques2,3, Joaquim M. Oliveira2,3,

Rui L. Reis2,3, Utkan Demirci1

Bio-Acoustic MEMS in Medicine (BAMM)

Laboratory, Canary Center for Cancer Early

Detection1, Stanford University; 3B’s Research

Group – Biomaterials, Biodegradables &

Biomimetics2, Headquarters of the European

Institute of Excellence on Tissue Engineering &

Regenerative Medicine, Barco, Portugal;

ICVS/3B’sPT Government Associate

Laboratory3, University of Minho, Braga,

Portugal

103 A Next Generation-Differential Extraction Device for Sperm Isolation

and DNA Processing On-Chip

Fatih Inci1, Mehmet O. Ozen1, Yeseren Saylan1,

Morteza Miansari1, Duygu Cimen1, George

Duncan2, Leonard Klevan3*, and Utkan

Demirci1*

(*corresponding authors) Bio-Acoustic MEMS in

Medicine (BAMM) Laboratory, Canary Center

for Cancer Early Detection1, Stanford University;

Broward County Sheriff’s Office, Crime

Laboratory2, Fort Lauderdale, Florida; DxNow

Inc.3, Natick, Massachusetts

104 Mechanosensing of Neurons in 3D Brain Surrogate

Tanchen Ren1, Esra Karaca1, Raphaël

Canadas1,2,3, Utkan Demirci1*



Detection1, Stanford University; 3B’s Research

Group – Biomaterials, Biodegradables &

Biomimetics2, Headquarters of the European



ICVS/3B’sPT Government Associate

Laboratory3, University of Minho, Braga,

Portugal

105 Evolutionary-Like Selection On-a-Chip: Using Microfluidics to Isolate

the Fittest Sperm

Thiruppathiraja Chinnasamy1, James Kingsley2,

Naside Gozde Durmus3,7, Paul J. Turek4,

Mitchell P. Rosen5, Barry Behr6, Lars M.

Steinmetz7, Erkan Tüzel2, Utkan Demirci1.



Detection1, Stanford Genome Technology

Center7, Departments of Biochemistry3,

Obstetrics & Gynecology5, and Genetics6,

Stanford University; Department of Physics2,

Worcester Polytechnic Institute; The Turek

Clinic4, San Francisco

106 Monitoring Neutropenia in Cancer Patients at Point-of-Care (POC)

Hakan Inan1, Mehmet O. Ozen1, Utkan Demirci1


Laboratory1, Canary Center for Cancer Early

Detection, Stanford University

107 Exosome-Total-Isolation-Chip (ExoTIC) Device for Identification of

New Lung Cancer Biomarkers

Fei Liu1,2, Ophir Vermesh2,3, Tianjia J. Ge2,3,

Steven Madsen4, Andrew Sabour2,3, Gayatri

Gowrishankar2,3, Masamitsu Kanada3,5,

Jessie V. Jokerst2,3, Raymond G. Sierra6, Edwin

Chang1,2,3, Robert Sinclair4, Sanjiv Sam

Gambhir1,2,3, Viswam S. Nair2,7, Utkan Demirci1,2



Detection1, Departments of Radiology2, Materials

Science & Engineering4, Pediatrics5, and

Medicine7, Molecular Imaging Program at

Stanford (MIPS)3, and Stanford PULSE Institute6,

Stanford University

108 LEVITAS: Levitating Cells for Chemistry-Free Sorting of Rare

Circulating Cancer Cells and Cell Clusters from Whole Blood

N. Gozde Durmus1,5, Kaushik Sridhar2, Hojae

Lee2, Shreya Sanjay Deshmoukh2,3, Christian

Hoerner6, Fatih Inci2, Ozlem Ercal2, Neeraja

Ravi3, Yoriko Imae7, Jordan Preiss7, Heather A.

Wakelee6, Alice C. Fan6, Ronald W. Davis1,4,5,

Lars M. Steinmetz4,5*, Utkan Demirci2*

(*corresponding authors) Departments of

Biochemistry1, Bioengineering3, Genetics4, and

Medicine (Division of Oncology)6, Bio-Acoustic

MEMS in Medicine (BAMM) Laboratory, Canary

Center for Cancer Early Detection2, Stanford

Genome Technology Center5, and Cancer

Clinical Trials Office7, Stanford University

109 Flow Induces Epithelial-Mesenchymal Transition (EMT) in Dynamic

Bioengineered Lung Cancer Microenvironment

Vigneshwaran Mani1, Zhonglin Lyu1, Baris

Dercal1, Ramasamy Paulmurugan2,3,4, Utkan

Demirci1



Detection1, Stanford University; Molecular

Imaging Program at Stanford2, Cellular Pathway

Imaging Laboratory (CPIL)3, and Department of


110 Multiplexed µ-fluidic-ELISA for Cardiovascular Disorders

Mehmet O. Ozen1*, Vigneshwaran Mani1*, Utkan

Demirci1

(*equal contribution) Bio-Acoustic MEMS in

Medicine (BAMM) Laboratory, Canary Center

for Cancer Early Detection1, Stanford University

111 Guided Self-Assembly of Functional Cellular Architectures Based on

Magnetic Levitation

Alessandro Tocchio1, Naside Gozde Durmus2,3,

Bukre Coskun4, Vigneshwaran Mani1, Kaushik

Sridhar1, Raphael Faustino Canadas1,5,6, Rami El

Assal1, Utkan Demirci1



Detection1, Department of Biochemistry2, and

Stanford Genome Technology Center3, Stanford

University; Department of Molecular & Cellular

Biology, University of California-Davis; 3B’s

Research Group – Biomaterials, Biodegradables

& Biomimetics5, Headquarters of the European



ICVS/3B’sPT Government Associate Laboratory,

University of Minho6, Braga, Portugal

112

Identifying Regions Where Targeted Ablation Terminated Persistent

Atrial Fibrillation: Interobserver Variability in Multiple Mapping

Systems

Gabriela L. Meckler1, Mallika Tamboli1,

Bartolomiej Imielski1, Christopher A.B.

Kowalewski1, Mahmood Alhusseini1, David

Vidmar2, Fatemah Shenasa1, Tina Baykaner1,

Junaid Zaman1, David E. Krummen3, Paul J.

Wang1, Johannes Brachmann4, John M. Miller5,

Wouter‐Jan Rappel2, Sanjiv M. Narayan1

Department of Medicine1, Stanford University;

Departments of Physics2 and Medicine3,

University of California-San Diego; Clinic of

Cardiology4, Klinikum Coburg, Germany;

Department of Medicine5, Indiana University

113 Global Representations of Goal-Directed Behavior in Distinct Cell Types

of Mouse Neocortex

William E. Allen1,3,4*, Isaac V. Kauvar2,4*,

Michael Z. Chen4, Ethan B. Richman1,3,4, Samuel

J. Yang2, Ken Chan7, Viviana Gradinaru7,

Benjamin E. Deverman7, Liqun Luo3,5, Karl

Deisseroth4,5,6

(*equal contribution) Neurosciences Graduate

Program1, Electrical Engineering Graduate

Program2, Departments of Biology3,

Bioengineering4, and Psychiatry & Behavioral

Sciences6, and Howard Hughes Medical Institute5,

Stanford University; Division of Biology &

Bioengineering7, California Institute of

Technology

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