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UCSF CCMBM Core Services - December 2019
CCMBM Cores:
Featured Services
The Core Center for Musculoskeletal Biology & Medicine (CCMBM) defines itself by emphasizing musculoskeletal-specific events, grants, and services that are critical to its members but not available elsewhere in the university system.

I was recently granted a Junior Investigator Travel Grant Award that provided partial support that enabled me to attend the Medical Image Computing and Computer Assisted Intervention (MICCAI) International Conference that was held in Shenzhen, China this past October. I would like to thank the CCMBM for this unique opportunity that exposed me to the latest advances in Deep Learning in Medical Imaging and provided opportunities to speak with well-known world experts in the field.

My group and I presented a new method to perform data augmentation using reinforcement learning (https://link.springer.com/chapter/10.1007/978-3-030-32226-7_50) at the conference. Furthermore, there was a plethora of workshops and tutorials covering topics that spanned Magnetic Resonance Imaging Reconstruction to Deep Learning methods in non-Euclidean space; from segmentation with weak and limited labels to new ideas based on generative adversarial networks; from Image Registration to automatic Physician prescriptions. I am eager to apply what I’ve learned and prepare next year’s paper submission!

-- Francesco Caliva, PhD, Postdoctoral Scholar, Department of Radiology and Biomedical Imaging
ACKNOWLEDGING THE CCMBM
If you have received a CCMBM grant, formed a collaboration at one of our events, or used one of our cores, please acknowledge the CCMBM in related publications and presentations. We suggest stating:

Research reported in this publication was supported by the UCSF Core Center for Musculoskeletal Biology and Medicine (CCMBM) of the National Institute of Health's National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) under the award number P30AR066262 .
UCSF Parnassus Campus
UPCOMING CCMBM EVENTS

January 28, 3:30-4:30pm; Parnassus, N-217
CCMBM Seminar Series - Neural contributions to skeletal health and pathophysiology
Erica L. Scheller, DDS, PhD, Assistant Professor, Division of Bone and Mineral Diseases, Washington University School of Medicine.
RSVP: bit.ly/CCMBMseminar
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March 10-11; Mission Bay Campus
Orthopaedic Surgery/CCMBM Scientific Retreat – Annual two-day retreat for musculoskeletal researchers, clinicians, and trainees. Featuring interactive exhibits; slam-style talks and posters by trainees; and special guest speakers. Invitations coming soon.


Specific Aims Review - Increase your chances of being funded for the next cycle of NIH R01 and K grants! This review is also helpful with intramural RAP applications. Have CCMBM established investigators give you personalized feedback on your specific aims page that can help focus your aims and improve your overall application for funding opportunities. 

Review appointments are limited and only available for CCMBM members (check if you are a member) at the following locations:

1. General sign up (Mission Bay, 1700 Owens)

2. Ortho-related sign up (Parnassus, Medical Sciences)

3. Radiology-related sign up (Mission Bay, Mission Hall)
CCMBM SBB CORE
 
Looking for a novel way to rapidly and quantitatively evaluate gene expression? The Nanostring nCounter fills the gap between qPCR and RNAseq by analyzing up to hundreds of transcripts at a time with small amounts of RNA.  Nanostring uses fluorescent color-coded barcode probes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction at high sensitivity (< 1 copy per cell). Starting with 50 - 100ng total RNA, no enzymatic processing steps are required for gene expression analysis. The probes hybridize to approximately 100 bases, and can be multiplexed to detect up to 800 different targets in a single reaction. Pre-built CodeSets are commercially available, as well as custom UCSF Skeletal Biology custom CodeSets that survey 94 or 627 mouse genes implicated in musculoskeletal biology, including bone, cartilage, tendon and muscle. For more info on the custom UCSF codesets, please see our core services page. For inquiries, please contact Katherine Popovich at katherine.popovich@ncire.org.




CCMBM EBSD CORE
 
The Epidemiology, Biostatistics, and Study Design (EBSD) Core seeks to strengthen patient-oriented clinical research in musculoskeletal health at UCSF by providing "study implementation coaching", targeting junior investigators and others new to the field. UCSF is internationally recognized for its basic/translational, radiologic, and epidemiologic musculoskeletal research. However, UCSF musculoskeletal investigators have traditionally conducted fewer patient-oriented mechanistic studies and small clinical trials enrolling UCSF patients. This represents a substantial untapped potential. The EBSD Core, through its consultative services, is developing a path to assist CCMBM members with the implementation of studies they have designed. Assistance may take the form of a navigation guide, as a CCMBM member completes requirements of the UCSF Office of Clinical Research and the CTSI Clinical Research Services. Or, it may focus on connecting CCMBM members who can share musculoskeletal clinical research protocol elements, ranging from eligibility criteria to case report forms to the selection of biochemical markers of bone turnover to measure.  
  To develop this program, the EBSD Core is eager to hear from CCMBM members about their "study implementation coaching" needs. Please email Dr. Anne Schafer at anne.schafer@ucsf.edu if you might be a future user of this service.

CCMBM IMAGING CORE

The CCMBM Imaging Core supports trabecular bone as well as bone marrow fat quantification of the hip and spine. We provide high-resolution MR image acquisition as well as image analysis for trabecular bone including trabecular bone fraction, density, thickness, and spacing. In addition, we can acquire MRI proton density fat fraction (PDFF) maps which accurately display the marrow fat content in a voxel. The figure below shows example images of healthy, osteopenic, and osteoporotic subjects. A decrease in trabecular bone structure can be appreciated with increasing osteoporotic status. The PDFF maps show a trend to higher bone marrow fat fractions with osteoporotic status. Also of note, the greater trochanter and the femoral head show high PDFF values in all three subjects whereas the femoral neck PDFF varies from lower values (healthy subject) to very high values in the patient with osteoporosis. The Imaging Core can help to acquire and analyze high-resolution MR images of the extremities and the hip as well as PDFF maps of the hip and spine. Contact: Roland Krug, Imaging Core Co-Director at roland.krug@ucsf.edu, for more information.


 
ACKNOWLEDGING THE CCMBM
If you have received a CCMBM grant, formed a collaboration at one of our events, or used one of our cores, please acknowledge the CCMBM in related publications and presentations. We suggest stating:

Research reported in this publication was supported by the UCSF Core Center for Musculoskeletal Biology and Medicine (CCMBM) of the National Institute of Health's National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) under the award number P30AR066262 .
Copyright © 2019 CCMBM, All rights reserved.


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