First FSSHH of this year at Homewood!!

Come enjoy the friendly welcome from Homewood at this upcoming FSSHH!

Jake is presenting with food volunteered by Sravanti.

Who: Jake Simson

When: September 17th

Where: Clark 110 Homewood

See you all there!

Title: The application of a chondroitin sulfate-bone marrow adhesive towards

meniscal repair

Abstract: Meniscal injuries may lead to joint degeneration and the development of post-traumatic osteoarthritis. There are few technologies beyond sutures available for surgeons to repair the meniscus, and sutures inherently cause additional damage to the tissue. Adhesives that work to repair meniscus while fixing the tissue in place offer an appealing alternative solution. Here, we demonstrate the use of a NHS-functionalized chondroitin sulfate (CS-NHS) bioadhesive for use in meniscal repair. 10% CS-NHS was mixed with 10% Polyethylene Glycol (PEG) in a 1:1 ratio, and with BM in ratios of 3:7 (70% BM), 1:1 (50% BM), and 7:3 (30% BM). Meniscus cells were encapsulated in gels to quantify in vitro tissue generation, and bovine meniscus explants were glued to observe meniscus cell migration into the adhesive. Constructs were analyzed at one and three weeks using live/dead, H&E staining, and Hoescht dye DNA assays. Glued tissue explants were sectioned and stained with H&E at two and four weeks. Live/dead and Hoescht DNA assays showed statistically significantly higher viability at both time points in CS-BM gels in comparison to CS-PEG. At one week normalized DNA levels increased with BM concentration, but this effect diminished by week three. However, extensive clustering of cells was observed at three weeks in CS-BM gels, indicating cell proliferation. In the explant study cells were observed proliferating on the surface of 70% BM at week two, and at week four cells were seen within the gel proliferating and depositing matrix. These findings indicate that meniscal cell viability in the CS-BM gel remains high after several weeks in culture, they proliferate within the gel, and that meniscal cells are capable of migrating from meniscal tissue first onto the hydrogel surface, and later into BM gels. These are promising preliminary results for the use of CS-BM adhesive in regenerating meniscus tissue.

FSSHH this Friday!

Come to the first FSSHH (Friday Student Seminar and Happy Hour) of the year!

Food and drink and fun; plus learn about the cool work of one of your fellow grad students.

WHO: Matt Fifer, a second year student from Dr. Thakor's lab is giving the talk

WHAT: Decoding grasp kinematics from human electrocorticography (ECoG)

WHERE: Traylor 709

WHEN: 5pm Friday August 27th.

Title:

Decoding grasp kinematics from human electrocorticography (ECoG)

Abstract:

Human electrocorticography (ECoG) is a neural recording modality used for seizure localization in epileptic patients prior to resection surgery. We measured ECoG amplitude in 4 subjects and attempted to predict the degree of grasp aperture during a slow grasping motion of the hand. Decoding accuracy was found to be high (mean r > 0.6), to be relatively invariant to wrist rotation angle, and to require relatively few electrodes to achieve maximal performance. This work is promising for the potential future development of a reliable, low-footprint ECoG-driven neuroprosthetic. Future work is targeting the application of similar methods to more natural reach-to-grasp motions.

FSSHH: Friday April 2 5pm Traylor 709 Med Campus

Presenter: Susan Thompson

Title: Human Embryonic Stem Cell Derived Cardiomyocytes Ameliorate Vulnerability for Arrhythmias in an In Vitro Model of Cardiac Fibrosis

Abstract: Human embryonic stem cells (hESCs) are an attractive candidate for cardiac regeneration because of their potential to supply a large number of differentiated cardiomyocytes that can integrate into the host tissue, thereby replacing the myocytes lost during myocardial aging, disease or damage. Numerous studies have already demonstrated improved myocardial function with grafts of human embryonic stem cell-derived cardiomyocytes (hESC-CMs), alluding to possible roles of paracrine effects and direct myocardial regeneration. However, little attention has been given to the electrophysiological benefit that these cells may have on diseased myocardium, and specifically, on cardiac fibrosis, a pathological condition found in aging, heart failure, and myocardial infarction. We therefore set out to characterize the electrophysiological benefits of adding hESC-CMs to our previously reported, in vitro model of cardiac fibrosis. Following engraftment of hESC-CMs from beating hESC-CMs, LCV and TCV of fibrotic monolayers increased to 39.3±2.7 and 12.5±1.3 cm/s, respectively (n=6). In contrast, addition of hESCs from non-beating EBs suppressed LCV and TCV to 6.5±1.3 and 2.1±1 cm/s, respectively (n=4). We show for the first time that hESC-CMs reverse the loss of conduction velocity and reduce the incidence of spiral waves in an in vitro fibrosis model. This finding is significant in that it suggests that specifically hESC-CMs can directly participate in electrical propagation, perhaps through gap junction coupling, and can ameliorate abnormal conduction in fibrotic myocardium.

Last FSSHH of this year: Jacob Koskimaki

Last FSSHH of this year!!!!

Come enjoy Jacob's presentation, free food + drinks and awesome company of fellow BMEers!

Dec 11th (Friday) 5pm at Clark 110.

Title & abstract: Peptide optimization strategies: merging experimental data with bioinformatics tools to develop potent inhibitors of angiogenesis in breast cancer

The emergence of genomics, proteomics and new peptidomics has provided several advances in the data available to develop endogenous regulators of angiogenesis. Angiogeneis, or neovascularization, is the process where new vessels form from a preexisting microvasculature, and involves interactions among several cell types. Tumors require a blood supply to grow; similarly, abrogating this blood supply is an emerging paradigm to treat diseases such as breast cancer. Our laboratory recently developed a systematic bioinformatics-based methodology to identify several endogenous regulators of angiogenesis, and experimentally verified their activity in vitro and in vivo breast xenograft models. We now have begun to optimize these sequences to enhance activity, and show different experimental techniques combined with bioinformatics tools to increase activity of endogenous therapeutics.

FSSHH Friday Nov 6

This Friday Nov 6, 5pm - 6pm, Med school (Traylor 709)

Mohsen Mollazadeh is presenting! Title and abstract coming soon

title: Monitoring of neuronal activity during dexterous hand movements.
abstract: In the first part of the talk, I will present the VLSI circuit we have developed for monitoring neuronal activity in awake behaving studies. In the second part, I will present the study of population neuronal activity in primate's motor cortex during dexterous hand movements. I will present how LFP signals are modulated with various grasp patterns and their relationship to single unit activity.

FSSHH this Friday!!!

This Friday Sept 25th 5pm - 6pm, Med school (Traylor 709)

Kartik is presenting on 'optical techniques and VLSI systems for structural and functional brain imaging'.

See you all there!

Abstract: optical techniques for investigating the brain offer several key strengths - non-contact, minimally invasive, multi-scale (single cells to populations), functional/structural observation. currently, most small animal imaging is restricted to restrained &/or anesthetized animals. electrophysiology in awake, behaving rodents has led to many interesting behavioral results, but imaging in a similar scenario has not been explored well. i've been working on designing miniaturized optical imaging systems that incorporate illumination, optics and image sensing electronics in a small volume device that can be mounted on a rodent for chronic imaging in awake and behaving animals. i'll talk about the design and characterization of the imaging system and the image sensor and some preliminary experiments in rats.

Next FSSHH Friday Sept 11 2009: Sabyasachi Roy

FSSHH Returns this fall on Friday Setp 11, 2009. Sabyasachi Roy will be presenting at Talbot Library (Traylor 709)

Abstract:
Application of multi-channel telemetry in auditory neurophysiology & behavior

The neural basis of vocal control and auditory feedback has long interested neuroscientist and biomedical engineers alike. Our lab has focused on studying the cortical neural activity in the common marmoset in understanding this basic sensory-motor system. The marmoset monkeys (Callithrix Jacchus) is an ideal animal model given the fact that they remain highly vocal in captivity. This essential vocal behavior is primarily elicited when the subject is in a natural behavior state i.e. free roaming condition. Typically, neurophysiological experiments on vocal production and feedback have involved either restrained subjects or tethered setups that severely restrict the behavior of the subject. This is where multi-channel neural telemetry can play a vital role of enabling the vocal behavior of primates during auditory experiments and providing the same quality of neural data as tethered setups. We are developing the essential wireless radio link as well as the backend processing capability to make this technology practical and effective. These small, lightweight wireless devices can continuously transmit multiple channels of neural data from the relevant cortical area of the marmoset while it is engaged in an experimental task. I will briefly highlight our progress in developing custom telemetry system and integrating existing devices as well as the experimental opportunities that this technology opens up.

Need volunteers for Fall 2009!

please email luke ( lukejohnson07 AT gmail.com) and/or Yoonju (cho.yoonju AT jhmi.edu) to volunteer!


What is the Friday Student Seminar and Happy Hour?

FSSHH is a regularly scheduled seminar series for Johns Hopkins BME grad students and other interested students that includes a seminar talk, happy hour refreshments (beer, soda appetizers), and fun social interactions.

Why have it?

It has gives students opportunities to present their work and learn about their peers research in a relaxed environment. It also is a great opportunity for students to socialize and meet students from other labs and years.

When is it?

One or two Fridays a month @ 5pm

Where is it?

Either Homewood Clark 110, or 7th floor Library in Traylor (Talbot) at the Med Campus

What will go on?

Generally, the first 15 - 30 minutes will be spent drinking, eating snacks, etc, and the last 20-30 minutes there will be a talk by a fellow grad student. The nature of the talk is completely up to the presenter, but the hope is that they wont be overly technical, so that anybody from our very diverse department could listen and be interested and at least somewhat understand.

Questions/Comments? email lukejohnson07 AT gmail.com or cho.yoonju AT jhmi.edu

June 19th, Homewood Clark 110

-- Yi Zhang

We performed on-chip DNA methylation analysis using methylation-specific PCR (MSP) within an arrayed micro droplet-in-oil platform that is designed for more practical application of microfluidic droplet technologies in clinical applications. Unique features of this ready-to-use device include arrayed primers that are pre-deposited into micro-reaction chambers and use of the oil phase as a companion fluid for both sample actuation and compartmentalization. These technical advantages allow for infusion of minute amounts of sample for arrayed MSP analysis, without the added complexities inherent in microfluidic droplet-based studies. Ease of use of this micro device is exemplified by analysis of two tumor suppressor promoters, p15 and TMS1 using an on-chip methylation assay. These results were consistent with standard MSP protocols, yet the simplicity of the droplet-in-oil microfluidic PCR platform provides and easy and efficient tool for DNA methylation analysis in a large-scale arrayed manner.

May 15, 2009; Homewood, Clark 110
-- Chris Puleo

Title: "Accessible Single Molecule Detection Technologies: Microfluidic Interfaces
for Diagnostic and Single Cell Applications"

Abstract: The long term goal of this proposal is to develop microfluidic technologies that enable the widespread use of confocal fluorescence spectroscopy (CFS) for single molecule detection (SMD) in vital applications including, single molecule diagnostics and single cell analysis. Currently amplification techniques have been used to determine the presence of rare biomolecules in such applications; however, the cost, complexity, and time requirements associated with these tests limit clinical value and general utility. Direct molecule-by-molecule assessment using SMD remains an intriguing replacement for amplification technologies due to high sensitivity, assay simplicity, and low costs; however, technical challenges continue to limit the utility of these single molecule techniques. We use microfluidic interfaces for SMD platforms to expand applicability in the analysis of rare molecules from complex biological fluids. The overall goal of this work is apply microfluidics to SMD assays in order to obtain the lowest possible detection limits from the smallest possible sample volume. Direct implications are clear, high-throughput biomolecular analysis from the most precious and rare biological samples. In theory, single molecule sensitivity confers infinite detection limits in CFS platforms; however, in practice SMD platforms rely on continuous flow formats and bulk probe-target reactions. These design flaws yield significant fundamental pitfalls and result in practical limitations: 1) Analyte delivery to the microscale sensing elements is wasteful, leading to extremely low measurement efficiencies and the need for excessive sample volumes. 2) Passive probe-target interactions result in slow reaction kinetics and prohibitive assay run times. 3) Unoptimized and manual processing of target molecules results in low molecular throughput and incompatibility with arrayed formats. Experiments will be performed using two microfluidic platforms, multilayer soft lithography and water-in-oil droplets. Coupling these discrete volume control technologies with SMD provides direct control over probe hybridization, efficient transfer of target molecules to optical detection volumes, and automated processing of large numbers of sample in relatively short assay times. These improvements serve to open the door to practical use of single molecule assays in areas of vital need, such as, non-invasive diagnostic screening and investigation of cell-to-cell heterogeneity. Our lab stands in a unique position to take advantage of this potential due to practical experience in all three aspects of this challenge, including single molecule probe design, microfluidic device design and fabrication, and optical CFS platform engineering.

FSSHH still in water!

Need a pregame(?) before the cruise?

This Friday 4/17 Hannah will be presenting at Homewood Clark 110 from 5:00 though 6:00pm (5:00 for food and 5:30 for the talk). We still need a volunteer for food and drinks, so if you are interested in it, please contact me (cho.yoonju@jhmi.edu) or Luke (luke.johnson@jhu.edu).

This is going to be AWESOME so just come and enjoy some 1st light dinner for the day before your 2nd light dinner at the cruise :)

See you all there!

April 17, 2009; Homewood, Clark 110
-- Hannah Carter

In cancer, normal cells are transformed through accumulated genetic alterations that confer a selective advantage. Somatic missense mutations are one form of genetic aberration that contribute to tumor initiation and progression. Each tumor harbors a set of these mutations, but it is unclear which are drivers, causally associated with the tumor's progression, and which are passengers, neutral in the context of selective advantage for the cancer cell. We have applied modern machine learning techniques to develop a high-throughput method for discriminating between driver and passenger somatic missense mutations identified in large scale tumor sequencing studies.

April 3, 2009; Homewood, Clark 110
-- Raymond Cheong

Title: "How to use bioinformatics and other methods to win sports pools without knowing anything (much) about sports"

Abstract: In sports pools, such as those related to the ongoing men's college basketball tournament, it is often observed that those who know the least about sports end up making more accurate predictions than those who are more "knowledgeable" about sports. As a hobby project over the past ~10 years, I have been putting this idea to the test by investigating the performance of unsupervised algorithms to predict the winner of team sports. In this informal talk, I will highlight a variety of creative algorithms and discuss associated methodology and strategy. These algorithms include simple coin-flipping and Google-based methods, as well as bioinformatics-inspired linear models, network-oriented ratings, and clustering.

First FSSHH of 2009!!!!

FSSHH is back for 2009!!

The honorable speaker of this year's first FSSHH is Deok-Ho and it will be held on Jan 23rd Friday - of course ;) - at Homewood Clark 110 from 5:00pm through 6:00pm. As usual, the food and drinks at 5pm and the talk will begin at 5:30.

Hope to see you all there!

Jan 23, 2009; Homewood Clark 110
-- Deok-Ho Kim

Title: Analysis and Engineering of Cell Function with Nanoscale Cues

Abstract: In this talk, I will present multidisciplinary efforts directed towards better understanding of how diverse cell functions are controlled by the nano-scale features of cell micro-environment through active mechanosensing. I will particularly focus on three different settings in normal and pathophysiological contexts, in which cellular sensing of local force and geometry can have dramatic consequences: guided cell migration by well organized extracellular matrix, controlled stem cell differentiation via matrix topology, and development of tissue-engineered cardiac grafts. As novel tools to address these questions, I will introduce a series of biomimetic micro-devices combining the advantages of precise definition of both nano-topographic features and chemical ligands on chips, and then discuss how these tools help to gain better understanding of the fundamental aspects of establishment of cell polarity and guidance, and allow us to establish general principles for development of more precise and defined scaffolds for tissues engineering.

FSSHH will return after the holidays. (January sometime)

Yoonju Cho will now be in charge of organizing FSSHH on the Homewood Campus!!!

Please talk to Yoonju or Luke Johnson if you want to volunteer to present or get food/drink for one of the happy hours.

NEXT FSSHH: Holiday Extravaganza!

As the final FSSHH of this semester, and given the season, I think it makes sense to make it a holiday extravaganza. If you have ideas for food/drink fitting for such an event, please let me know: luke.johnson AT jhu.edu

Dec 5, 2008
-- Jacob Koskimaki

Location: Med School Talbot Library (Traylor 709)

Title: A Peptidomic approach to curing breast cancer

Abstract: Breast cancer is the most commonly diagnosed female malignancy in the United States, proving fatal to nearly 40,000 people in 2007 with 180,000 additional diagnoses. Angiogenesis or neovascularization, the process of new blood vessel formation from pre-existing microvasculature, involves interactions between several types of cells including endothelial cells (ECs), and stromal cells. We previously introduced a novel systematic methodology to identify putative endogenous antiangiogenic peptides and validated these predictions in vitro in human umbilical vein endothelial cell (HUVEC) proliferation and migration assays [1]. These peptides are derived from several protein families including type IV collagen, thrombospondin domain-containing proteins, and CXC chemokines. Based on the results from the in vitro screening, we have evaluated the ability of several peptides selected from the different families to suppress angiogenesis in breast cancer orthotopic xenograft models in severe combined immunodeficient (SCID) mice using MDA-MB-231 human breast cancer cells. We have demonstrated significant suppression of tumor growth in vivo, indicating the potential of these peptides as novel breast cancer therapeutics.

October 24, 2008
-- Tao Yu

Location: Homewood Clark 110

Title: An introduction to Synthetic Biology and the iGEM competition

Abstract: Synthetic biology, a new discipline to "make biology easier to be engineered", is an emerging branch of biology in recent years. Though quite some researchers are participating the research in such a field, synthetic biology is still far from familiar to a broad range of investigators in biology, medicine and engineering scopes. iGEM, which is short for the international Genetically Engineered Machines competition, is an annual undergrad competition aiming to recruit more participants in the community of synthetic biology. Here, I would like to introduce you to some key concepts and typical research in synthetic biology, and share with you the great fun I had in the iGEM competition last year.

October 10, 2008
-- Suneil Hosmane

Location: Med Campus Talbot Library (Traylor 709)

Title: TBA

Abstract: Microfluidics has the potential to uncover mechanisms behind many neurodegenerative diseases by enabling engineers and scientists to recreate the diseased cellular microenvironment. By doing so, a repeatable, efficient, and quantitative approach can be taken to understand the neurobiology of disease in vitro. To this extent, we have developed a novel device platform that merges conventional macro-sized features with microfluidic technology to yield a hybrid device compatible with standard biological protocols. This device allows for numerous experimental modalities through the replication of a single master design using conventional polymethyldisiloxane (PDMS) soft lithography.


Laboratory: Biomedical Instrumentation and Neuroengineering Laboratory
http://www.jhu.edu/nthakor/

September 26 2008
-- Tri Ngo

A first year has stepped up and volunteered to present. How awesome is that?

Title: Stochastic White Matter Tractography

Abstract: Stochastic Tractography is a Bayesian approach for inferring nerve
fiber tract parameters from DTI (Diffusion Tensor Imaging) data. We
use this framework to calculate the posterior probability of the
existence of tracts given our observations. Additionally, the
Bayesian framework allows the algorithm to infer tracts which pass
through regions with uncertain fiber orientations, previously
unreachable by non-Bayesian methods, thereby revealing more details
about structural connectivity.

We have implemented the algorithm into the ITK medical image analysis
toolkit, an open source NIH supported medical image analysis toolkit.
Additionally we created a user interface which allows the program to
be integrated in the popular 3D Slicer medical image visualization
program. Finally we present some potential clinical studies for the
algorithm.
Location: Clark 110 Homewood

September 12 2008
-- Robert Jacques

Location: Med Campus Talbot Library (Traylor 709)

Title: Towards Real-Time Radiation Therapy:GPU Accelerated Superposition/Convolution

Abstract: We demonstrate the use of highly parallel graphics processing units (GPUs) to accelerate the Superposition/Convolution (S/C) algorithm to interactive rates while reducing the number of approximations. S/C first transports the incident fluence to compute the total energy released per unit mass (TERMA) grid. Dose is then calculated by superimposing the dose
deposition kernel at each point in the TERMA grid and summing the contributions to the surrounding voxels. The TERMA algorithm was enhanced with physically correct multi-spectral attenuation and a novel inverse formulation for increased performance, accuracy and simplicity. Dose deposition utilized a tilted poly-energetic inverse cumulative-cumulative kernel, with the novel option of using volumetric mip-maps to approximate solid angle ray-casting. Exact radiological path ray-casting decreased discretization errors. We achieved a speed-up of 34x-98x over a highly optimized CPU implementation.

Full Paper:
http://www.cse.buffalo.edu/hpmiccai/pdf/HPMICCAI2008-V1.pdf


Laboratory: The Computer Integrated Interventional Systems Laboratory
New page: http://ciis.lcsr.jhu.edu/Research
Old page: http://www.cisst.org/

Friday Sept 12 2008 at 5pm, Med Campus Talbot 709

Wow, that was a pretty fantastic FSSHH on Aug 13th. Great turnout -- I'd say 35 people or so, plus tons of first years. It was nice to have a happy hour after so many months off.

Next FSSHH is Friday Sept 12. Robert Jacques is giving the talk. Special thanks to him for volunteering, and thanks to John Issa for getting the refreshments.

STILL NEED VOLUNTEERS!

• We are looking for groups of 1-2 students to sign up to get the food
  and drinks for each week.
• NEED SPEAKERS! (20-30 minute informal talk) -- see schedule at right