Monday, August 13, 2012

Biology Games for Biomedical Research

Games have become important part of  the cultures, bringing lots of entertainment and creativity to the societies. Beyond the traditional understanding of games, recently researchers have started to explore new sets of "serious games" that could provide effective means, including  public understanding of science, crowd-source based diagnostics, physical therapy and as well as prediction of the protein folding.

In this post, we will summarize these recent efforts addressing the biology games for biomedical research and related applications:

1) Biotic Games [ at Riedel-Kruse Lab, Stanford ]

Games are a significant and defining part of human culture, and their utility beyond pure entertainment has been demonstrated with so-called ‘serious games’. Biotechnology – despite its recent advancements – has had no impact on gaming yet. Here we propose the concept of ‘biotic games’, i.e., games that operate on biological processes. Utilizing a variety of biological processes we designed and tested a collection of games: ‘Enlightenment’, ‘Ciliaball’, ‘PAC-mecium’, ‘Microbash’, ‘Biotic Pinball’, ‘POND PONG’, ‘PolymerRace’, and ‘The Prisoner's Smellemma’. We found that biotic games exhibit unique features compared to existing game modalities, such as utilizing biological noise, providing a real-life experience rather than virtual reality, and integrating the chemical senses into play. Analogous to video games, biotic games could have significant conceptual and cost-reducing effects on biotechnology and eventually healthcare; enable volunteers to participate in crowd-sourcing to support medical research; and educate society at large to support personal medical decisions and the public discourse on bio-related issues.

Ref: Design, engineering and utility of biotic games, Lab Chip, 2010.

2) Crowd-sources BioGames [ at Ozcan Lab, UCLA ]

We describe a crowd-sourcing based solution for handling large quantities of data that are created by e.g., emerging digital imaging and sensing devices, including next generation lab-on-a-chip platforms. We show that in cases where the diagnosis is a binary decision (e.g., positive vs. negative, or infected vs. uninfected), it is possible to make accurate diagnosis by crowd-sourcing the raw data (e.g., microscopic images of specimens/cells) using entertaining digital games (i.e., BioGames) that are played through PCs, tablets or mobile phones. We report the results and the analysis of a large-scale public BioGames experiment toward diagnosis of malaria infected human red blood cells (RBCs), where binary responses from approximately 1,000 untrained individuals from more than 50 different countries are combined together (corresponding to more than 1 million cell diagnoses), resulting in an accuracy level that is comparable to those of expert medical professionals. This BioGames platform holds promise toward cost-effective and accurate tele-pathology, improved training of medical personnel, and can also be used to manage the “Big Data” problem that is emerging through next generation digital lab-on-a-chip devices.

Ref: Crowd-sourced BioGames: Managing The Big Data Problem for Next-Generation Lab-on-a-Chip Platforms, Lab Chip, 2012

3) Game-based telerehabilitation [ at USC ]

This article summarizes the recent accomplishments and current challenges facing game-based virtual reality (VR) telerehabilitation. Specifically this article addresses accomplishments relative to realistic practice scenarios, part to whole practice, objective measurement of performance and progress, motivation, low cost, interaction devices and game design. Furthermore, a description of the current challenges facing game based telerehabilitation including the packaging, internet capabilities and access, data management, technical support, privacy protection, seizures, distance trials, scientific scrutiny and support from insurance companies.

Ref: Game-based telerehabilitation, Eur J Phys Rehabil Med., 2009. 

4) Foldit [ at University of Washington ]

Foldit is a multiplayer online game in which players collaborate and compete to create accurate protein structure models. For specific hard problems, Foldit player solutions can in some cases outperform state-of-the-art computational methods. However, very little is known about how collaborative gameplay produces these results and whether Foldit player strategies can be formalized and structured so that they can be used by computers. To determine whether high performing player strategies could be collectively codified, we augmented the Foldit gameplay mechanics with tools for players to encode their folding strategies as “recipes” and to share their recipes with other players, who are able to further modify and redistribute them. Here we describe the rapid social evolution of player-developed folding algorithms that took place in the year following the introduction of these tools. Players developed over 5,400 different recipes, both by creating new algorithms and by modifying and recombining successful recipes developed by other players. The most successful recipes rapidly spread through the Foldit player population, and two of the recipes became particularly dominant. Examination of the algorithms encoded in these two recipes revealed a striking similarity to an unpublished algorithm developed by scientists over the same period. Benchmark calculations show that the new algorithm independently discovered by scientists and by Foldit players outperforms previously published methods. Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms.

Ref: Algorithm discovery by protein folding game players, PNAS, 2011.

4) ERIAInteractive [ at University of Wisconsin ]

The Educational Research Integration Area (ERIA) studies how interactive digital tools -- like video games -- might transform learning. Our goal is to improve public understanding of science through games. These games are designed to be used in homes, schools, and after school settings, because we think the future of learning lies in connected learning across these contexts. Tomorrow's learners will access learning resources on their digital tablets, phones, and computers, and our learner profiles will cross these contexts. Learners, parents, teachers, and administrators have unprecedented opportunities for using data to improve learning.

To reach tomorrow's learners, educational materials have to be deeply engaging. We build games that can capture intrinsically interesting aspects of science and present it authentically to learners of all ages. We firmly believe that education should be energizing and life enhancing. Our games seek to put players in roles where they use science to do interesting things, setting up opportunities for learners to develop new identities -- and potentially even careers -- as people who affiliate with science.

Ref: ERIA Interactive Web.

5) reCAPTCHA [ at Carnegie Mellon University ]

CAPTCHAs (Completely Automated Public Turing test to tell Computers and Humans Apart) are widespread security measures on the World Wide Web that prevent automated programs from abusing online services. They do so by asking humans to perform a task that computers cannot yet perform, such as deciphering distorted characters. Our research explored whether such human effort can be channeled into a useful purpose: helping to digitize old printed material by asking users to decipher scanned words from books that computerized optical character recognition failed to recognize. We showed that this method can transcribe text with a word accuracy exceeding 99%, matching the guarantee of professional human transcribers. Our apparatus is deployed in more than 40,000 Web sites and has transcribed over 440 million words.

Ref: reCAPTCHA: Human-Based Character Recognition via Web Security Measures, Science, 2008.

Sunday, July 15, 2012

Optofluidics: Fusion of Optics and Microfluidics

Optofluidics is a research and technology area that combines the advantages of microfluidics and optics. Applications of the technology include displays, biosensors, lab-on-chip devices, lenses, and molecular imaging tools and energy.
Since the term “optofluidics” was coined in 2003 to describe systems that combine optics and fluidics, its usage has grown exponentially. Therefore, we will summarize the recent efforts on optofluidics in this post: 
Review Papers on Optofluidics:

Special Issues on Optofluidics:
1) Nature Photonics, October 2011 Issue, "Although the term 'optofluidics' is less than 10 years old, the combination of light and non-solids is being exploited by researchers who are finding applications in fields ranging from imaging, detection of chemical or biological agents and particle control, through to enhancing photonic circuits and energy generation. The October 2011 issue of Nature Photonics has a special focus on optofluidics dedicated to some of the latest advances in field." Link to the issue

2) Biomicrofluidics, December 2010 Issue, "This Special Topic section of Biomicrofluidics is on optofluidics or micro-optofluidic systems (MOFS), a burgeoning technology that aims to manipulate light and fluid at microscale and exploits their interaction to create highly versatile devices and integrated systems. This special issue puts together various contributed articles focusing on optofluidics or MOFS, which help inspire new research ideas and innovation in the microfluidics and nanofluidics community." Link to the issue
3) Microfluidics and Nanofluidics, September 2007 Issue, "Optical devices which incorporate liquids as a fundamental part of the structure can be traced at least as far back as the eighteenth century when rotating pools of mercury were proposed as a simple technique to create smooth mirrors for use in reflecting telescopes. Modern microfluidic and nanofluidics have enabled the development of a present day equivalent of such devices centered on the marriage of fluidics and optics which has come to be known over thelast few years as ‘‘Optofluidics.’’ Recent review articles by two of the pioneering groups in the field, namely the Psaltis (Psaltis et al. 2006) and Eggleton (Monat et al. 2007) groups, as well as a number of conferences and conference sessions have helped to distinguish Optofluidics as a separate research field rather than a simple subdiscipline of either microfluidics or optics. Building on these earlier efforts, this special issue represents the first attempt to bring together a collection of journal papers spanning the areas of interest of prestigious investigators in the field." Link to the issue

Companies and Centers on Optofludics:
1) Optofluidics Corp:
2) DARPA Center for Optofluidics:
3) W. M. Keck Center For Nanoscale Optofluidics:
4) Liquilume Diagnostic Inc:

Research Groups working on Optofluidics:
The list of the research group worldwide can be viewed at wikipedia of optofluidics:

Conferences on Optofluidics:
EOS Conference on Optofluidics
International Conference on Optofluidics

Final Remarks:
Optofluidic devices continue to be developed and will benefit from these and other techniques, including liquid crystals in microfluidic channels. In the future, optofluidics may have far-reaching consequences. For example, an on-chip nanofabrication factory could take advantage of the various control techniques such as optical tweezers to build molecular constructions in a fluid environment. Also, some authors look forward to a photonic integrated circuit, where one can reconfigure optical components with on-chip fluidics. Such a multitasking device might become possible though a combination of optical devices that use fluidics for reconfigurability. However, the current work with single-task devices should be developed first before we can correctly design devices that can be reconfigured to perform multiple tasks. For example, the optofluidic microscope shows promise as a single-task device, but combining it with other devices may also eventually prove to be fruitful. Of course, optics and fluidics can be combined with other lab on chip techniques: electric, mechanical, thermal, magnetic, etc. The integration of optics and fluidics on-chip will certainly become more prominent as the methods are developed. As a technique, optofluidics will create new possibilities for tunable microscale devices across fields. (Reference: Optofluidics: field or technique?, Lab Chip, 2008. )

Sunday, June 3, 2012

Speckle-free laser imaging using random laser illumination

Many imaging applications require increasingly bright illumination sources, motivating the replacement of conventional thermal light sources with bright light-emitting diodes, superluminescent diodes and lasers. Despite their brightness, lasers and superluminescent diodes are poorly suited for full-field imaging applications because their high spatial coherence leads to coherent artefacts such as speckle that corrupt image formation. We recently demonstrated that random lasers can be engineered to provide low spatial coherence. Here, we exploit the low spatial coherence of specifically designed random lasers to demonstrate speckle-free full-field imaging in the setting of intense optical scattering. We quantitatively show that images generated with random laser illumination exhibit superior quality than images generated with spatially coherent illumination. By providing intense laser illumination without the drawback of coherent artefacts, random lasers are well suited for a host of full-field imaging applications from full-field microscopy to digital light projector systems.
To read the paper:

Compressive sensing resources: An emerging method for all

The dogma of signal processing maintains that a signal must be sampled at a rate at least twice its highest frequency in order to be represented without error. However, in practice, we often compress the data soon after sensing, trading off signal representation complexity (bits) for some error (consider JPEG image compression in digital cameras, for example). Clearly, this is wasteful of valuable sensing resources. Over the past few years, a new theory of "compressive sensing" has begun to emerge, in which the signal is sampled (and simultaneously compressed) at a greatly reduced rate.
As the compressive sensing research community continues to expand rapidly, it behooves us to heed Shannon's advice.
Compressive sensing is also referred to in the literature by the terms: compressed sensing, compressive sampling, and sketching/heavy-hitters.
The Compressive Sensing Resources: 
Rice University Resources:
Compressive Sensing Research Groups:
The Rice group led by Richard Baraniuk has been the leader in spearheading information diffusion on the subject of compressive sensing through theirRice Compressive Sensing Resource page.  They also have a nice presentation of the now famous Rice Single pixel camera.

Terry Tao has made a list of the different matrices and their properties wrt compressive sensing in this page: Preprints in sparse recovery / Summary of properties of random matrices.

Compressive Optical Systems, NISLab led by Rebecca Willett at Duke. 

Faster STORM using compressed sensing

In super-resolution microscopy methods based on single-molecule switching, the rate of accumulating single-molecule activation events often limits the time resolution. Here we developed a sparse-signal recovery technique using compressed sensing to analyze images with highly overlapping fluorescent spots. This method allows an activated fluorophore density an order of magnitude higher than what conventional single-molecule fitting methods can handle. Using this method, we demonstrated imaging microtubule dynamics in living cells with a time resolution of 3 s. 
This work was published in Nature Methods.

Friday, February 10, 2012

Cellphone-based Diagnostic Technologies

In many third world and developing countries, the distance between people in need of health care and the facilities capable of providing it constitutes a major obstacle to improving health. One solution involves creating medical diagnostic applications small enough to fit into objects already in common use, such as cell phones — in effect, bringing the hospital to the patient. Here we list some of the emerging cell-phone based diagnostics technologies:

  1) Cell-phone lensfree microscope: UCLA researchers have advanced a novel lens-free, high-throughput imaging technique for potential use in such medical diagnostics, which promise to improve global disease monitoring, especially in resource-limited settings such as in Africa.

  2) Cell-phone imaging with microchip ELISA: Ovarian cancer is asymptomatic in the early stages and most patients present with advanced levels of disease. The lack of cost-effective methods that can achieve frequent, simple and non-invasive testing hinders early detection and causes high mortality in ovarian cancer patients. Here, we report a simple and inexpensive microchip ELISA-based detection module that employs a portable detection system, i.e., a cell phone/charge-coupled device (CCD) to quantify an ovarian cancer biomarker, HE4, in urine. Integration of a mobile application with a cell phone enabled immediate processing of microchip ELISA results, which eliminated the need for a bulky, expensive spectrophotometer.

3) Mobile phone based clinical microscopy: Light microscopy provides a simple, cost-effective, and vital method for the diagnosis and screening of hematologic and infectious diseases. In many regions of the world, however, the required equipment is either unavailable or insufficiently portable, and operators may not possess adequate training to make full use of the images obtained. Counterintuitively, these same regions are often well served by mobile phone networks, suggesting the possibility of leveraging portable, camera-enabled mobile phones for diagnostic imaging and telemedicine. Toward this end 1we have built a mobile phone-mounted light microscope and demonstrated its potential for clinical use by imaging P. falciparum-infected and sickle red blood cells in brightfield and M. tuberculosis-infected sputum samples in fluorescence with LED excitation.

 4) Cell-phone based platform as a biomedical device: In this paper we report the development of two attachments to a commercial cell phone that transform the phone's integrated lens and image sensor into a 350× microscope and visible-light spectrometer. The microscope is capable of transmission and polarized microscopy modes and is shown to have 1.5 micron resolution and a usable field-of-view of 150×150 with no image processing, and approximately 350×350 when post-processing is applied. The spectrometer has a 300 nm bandwidth with a limiting spectral resolution of close to 5 nm. We show applications of the devices to medically relevant problems.

5) Telemedicine tools with cell-phone cameras and paper microfluidics: This article describes a prototype system for quantifying bioassays and for exchanging the results of the assays digitally with physicians located off-site. The system uses paper-based microfluidic devices for running multiple assays simultaneously, camera phones or portable scanners for digitizing the intensity of color associated with each colorimetric assay, and established communications infrastructure for transferring the digital information from the assay site to an off-site laboratory for analysis by a trained medical professional; the diagnosis then can be returned directly to the healthcare provider in the field.

 And also other technologies are coming up soon by various researchers...

Bleaching/blinking assisted localization microscopy

Superresolution imaging techniques based on the precise localization of single molecules, such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), achieve high resolution by fitting images of single fluorescent molecules with a theoretical Gaussian to localize them with a precision on the order of tens of nanometers. PALM/STORM rely on photoactivated proteins or photoswitching dyes, respectively, which makes them technically challenging. We present a simple and practical way of producing point localization-based superresolution images that does not require photoactivatable or photoswitching probes. Called bleaching/blinking assisted localization microscopy (BaLM), the technique relies on the intrinsic bleaching and blinking behaviors characteristic of all commonly used fluorescent probes. To detect single fluorophores, we simply acquire a stream of fluorescence images. Fluorophore bleach or blink-off events are detected by subtracting from each image of the series the subsequent image. Similarly, blink-on events are detected by subtracting from each frame the previous one. After image subtractions, fluorescence emission signals from single fluorophores are identified and the localizations are determined by fitting the fluorescence intensity distribution with a theoretical Gaussian. We also show that BaLM works with a spectrum of fluorescent molecules in the same sample. Thus, BaLM extends single molecule-based superresolution localization to samples labeled with multiple conventional fluorescent probes. For more: Biological Sciences - Cell Biology: Dylan T. Burnette, Prabuddha Sengupta, Yuhai Dai, Jennifer Lippincott-Schwartz, and Bechara Kachar Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules PNAS 2011 108 (52) 21081-21086; published ahead of print December 13, 2011, doi:10.1073/pnas.1117430109