Name: haptic/graphic rehabilitation: integrating a robot into a virtual environment library and applying it to stroke therapy
Uploaded: 2011-08-08T13:00:00
Duration: 13 min 44 s
Description: Watch this Scientific Journal Video about Haptic/Graphic Rehabilitation: Integrating a Robot into a Virtual Environment Library and Applying it to Stroke Therapy at JoVE.com

I would like to acknowledge the technical help of Brian Zenowich, Daniel Evestedt and Winsean Lin.

Introduction
There is a growing need in all of human-machine interaction (HMI) for intuitive and efficient interactive environments. Numerous industries continue to depend more heavily on HMI, such as: rehabilitation robotics, the automotive industry, metals manufacturing, packaging machinery, pharmaceuticals, food, beverage, and utilities. Technologies employed in these industries include: display terminals, personal computers, and HMI software. These technologies may be combined together to perform unlimited functions.
Robots may be used to facilitate direct interaction with users, such as serving as a music instructor. For example, researchers at Waseda University have created a robot that plays the saxophone to teach people how to play and to understand the interaction between student and teacher 1. Other robotics researchers have made a vision-based flying robot in order to determine how artificial intelligence may evolve into intelligent interactions with the environment 2. The particular concentration of this paper resides within rehabilitation robotics.
Within the realm of research and industry, the quick pace of change for new products and user requirements continues to grow. These demands impose greater challenges in scalability. Therefore code design has become integral in meeting the needs of these entities in a timely manner. Hence, the quality of a strong architectural candidate would include easily interchangeable graphic-robot systems that include driver support. The H3DAPI architecture meets these needs and thus a wrapper class has been created. Furthermore, H3D is designed for virtual reality environments, such as those needed in rehabilitation robotics.
Neural rehabilitation robotics seeks to utilize robots for the purpose of assisting rehabilitation professionals. The assistance that these robots provide comes in the form of a force-field. Passed motor command researchers such as Shadmehr and Mussa-Ivaldi, used force-fields to foster motor adaptation, and have found 1) adaptation to an externally applied force field occurs with different classes of movements including but not limited to reaching movements, and 2) adaptation generalizes across different movements that visit the same regions of the external field3. Research from biomechanical engineers in Performance-Based Progressive Robot-Assisted therapy shows that repetitive, task-specific, goal-directed, robot-assisted therapy is effective in reducing motor impairments in the affected arm after stroke4, but the exact therapeutic effects and parameters continue to be a field of research.
Sensory feedback affects learning and adaptation. Therefore the next logical question would be to ask whether or not artificially increasing the magnitude of such feedback would promote faster or more complete learning/adaptation. Some researchers have found that applying greater sensory feedback forces or visual cues to enhance mistakes can provide an adequate neurological stimulus to promote higher levels of adaptation/learning5,6. This is known as "error augmentation". This phenomenon may be due to the fact that once outcomes of a motor control action deviate from the ideal, our internal model self-adjusts according to the magnitude of error. Consequently, as our internal model approaches the external environment, error in the execution of a task decreases.
Research continues to support prolonged practice of functionally relevant activities for restoration of function, although many current health care policies limit the amount of time patients can spend time with therapists. The compelling question is whether these new applications of technology can go further than simply giving a higher dosage of the current state of care. Human-machine interaction studies have revealed new prospects in the areas of motor learning, and can in some cases offer added value to the therapeutic process. Specialized robotic devices combined with computer-displays can augment feedback of error in order to speed up, enhance, or trigger motor relearning. This paper will present a methodology of using a developed system for a clinical intervention as one such example of the application of this technology.
1. Establishing HAPI wrapper class for a robot
<ol>
<li>Create a wrapper for HAPI the haptics library by creating your own .cpp and header
file. For example we will use the name HAPIWAM.cpp and HAPIWAM.h.
</li>
<li>Place HAPIWAM.cpp into the source directory: HAPI/src</li>
<li>Place HAPIWAM.h into the header file directory: HAPI/include/HAPI</li>
<li>At the top of HAPIWAM.h, include the main header file(s) of your robot, in the case of the Barrett WAM, that would be:</li>
</ol>

extern "C" { 
#include &lt;include/btwam.h&gt; 
} 
#include &lt;HAPI/HAPIHapticsDevice.h&gt; 


Note: extern "C" is required to resolve compiler mangling, because the included library is written in 'C' and the H3DAPI is written in C++.

<ol start="5"><li>In HAPIWAM.h, create your class and include the following 4 functions</li></ol>

bool initHapticsDevice(int); 
bool releaseHapticsDevice(); 
void updateDeviceValues(DeviceValues &amp;dv, HAPITime dt); 
void sendOutput(HAPIHapticsDevice::DeviceOutput &amp;d, HAPITime t); 


<ol start="6">
<li>Make sure your class inherits publicly from the HAPIhapticsdevice class.</li>

<li>Create a header guard for your class.</li>
<li>Create static DeviceOutput and static HapticsDeviceRegistration attributes under the HAPIWAM class.</li>
<li>Create your static member functions for callbacks.</li>
<li>Define your constructor and destructor in HAPIWAM.cpp.</li>
<li>Register your device in HAPIWAM.cpp.</li>
<li>Define your 4 inherited functions and callbacks in HAPIWAM.cpp.</li>
</ol>

2. HAPI library creation
<ol>
 <li>Now that we have created the HAPI wrapper class, we need to build your wrapper into the
HAPI library. The WAM depends on some libraries that H3DAPI does not depend on in its raw form, therefore these libraries will need to be added to HAPI. Go to HAPI/HAPI/build, and edit CMakeLists.txt. Add the dependent libraries after the line that says 'SET(OptionalLibs)'.
</li>
 
 <li>Open a command console and navigate to: HAPI/HAPI/build and type the following 3 commands in this order:</li>
</ol>
cmake . 
sudo make 
sudo make install 

3. H3D wrapper class
<ol>
 <li>To create the wrapper class for the H3D library with your HAPIWAM, first create WAMDevice.cpp in the source directory: H3DAPI/src</li>
 <li>Place WAMDevice.h into the header file directory: H3DAPI/include/H3D</li>
 <li>WAMDevice.h should contain the standard header file for all H3DAPI devices, with the name replaced to whatever you want.</li>
 <li>WAMDevice.cpp should contain the standard source for all H3DAPI devices, with the name replaced to whatever you want.</li>
 <li>Now that the wrapper class has been created, rebuild the H3DAPI library. Do this by editing CMakeLists.txt in the same way that was performed in step 2.1, only under the directory: H3DAPI/build. </li>
 <li>Rebuild the H3DAPI library under the directory H3DAPI/build</li>
</ol>
cmake . 
sudo make 
sudo make install 

4. Finite state machine
<ol>
 <li>Every targeted reaching program requires the creation of a finite state machine to control the experimental protocol or practice regime. Typical state machines include: Start of trial, Launch, Target Contact, and End of Trial. An example of the function of each state, and criteria to transfer between states is listed below.</li>
 <li>The Start of Trial requires the allocation of a target. Targets locations may be set randomly for each trial or may be set from a file. The start of the trial ends once the user has launched toward the target above velocity threshold, typically 0.06 meters per second.</li>
 <li>The Launch state occurs after the start of the trial. This state ends either once the user touches the target or stays inside of the target for a period of time. Once the target is touched, this enables the Target Contact state.</li>
 <li>Target Contact occurs during the Launch state. It may end as soon as the target is touched or after the subject resides within the target for a specific period of time. Once this time has elapsed, the End of Trial state is enabled.</li>
 <li>The End of Trial state should signal the data collection software to mark the data file, in whatever parsing the software developer has used, to delimit the end of the each trial. Unless the final trial has been completed, the end of the End of Trial state enables the Start of Trial state.</li>
</ol>
5. Application: rehabilitation of the stroke patient 
<ol>
 <li>The robotic interface was designed to involve therapist expertise while using the robot to enable something that could not otherwise be done. The technology enabled application (described in more detail below) of error augmentation, which magnified the errors perceived by the patient, which for several well-known reasons enhances the relearning process (fig 1).</li>
 <li>A three-dimensional haptics/graphics system called the Virtual Reality Robotic and Optical Operations Machine (VRROOM). This system, presented previously6, combined a projected stereo, head-tracked rendering on a semi-silvered mirror overlay display with a robotic system that recorded wrist position and generated a force vector (fig 2).</li>
 <li>A cinema-quality digital projector (Christie Mirage 3000 DLP) displayed the images that spanned a five-foot-wide 1280x1024 pixel display, resulting in a 110&deg; wide viewing angle. Infrared emitters synchronized separate left and right eye images through Liquid Crystal Display (LCD) shutter glasses (Stereographics, Inc). Ascension Flock of Birds magnetic elements tracked motion of the head so that the visual display was rendered with the appropriate head-centered perspective.</li>
 <li>Upon qualifying for the study, each participant's functional ability was evaluated by a blind rater at the start and finish of each treatment paradigm with a one-week follow-up after each and an overall 45-day follow-up evaluation. Each evaluation consisted of a range of motion (ROM) assessment performed in the VRROOM as well as clinical measures including: the Box and Blocks Assessment, Wolf Motor Function Test (WMFT), Arm Motor Section of the Fugl-Meyer (AMFM), and Assessment of Simple Functional Reach (ASFR). </li>
 <li>An exotendon glove with wrist splint was utilized to assist in neutral wrist and hand alignment. The center of the robot handle was attached to the forearm was placed posterior to the radiocarpal joint so that its forces acted at the wrist but allowed motion at the hand.</li>
 <li>The patient's arm weight was lessened using a spring-powered Wilmington Robotic Exoskeleton (WREX) gravity-balanced orthosis. The patient's instructed goal was to chase a cursor presented in front of them moved via a tracking device in the hand of the therapist (therapist teleoperation).</li>
 <li>Patients practice three days per week for approximately 40-60 minutes, with the patient, the therapist, and the robot working together in a trio. Subject and therapist sat side-by-side, and the subject was connected to the robot at the wrist. </li>
 <li>Each session began with five minutes of passive range of motion exercises (PROM) with the therapist, followed by approximately ten minutes for situating the patient in the machine. The subject then completed six blocks of movement training lasting five minutes each with two-minute rest periods between each block.</li>
 <li>During training, participants viewed two cursors on the stereo display. The treating therapist manipulated one cursor while the participant controlled the other. Patients were instructed to follow the exact path of the therapist&#x2019;s cursor as it moved throughout the workspace. </li>
 <li>Error augmentation was provided both visually and by forces generated by the robot. When participants deviated from therapist&#x2019;s cursor, an instantaneous error vector e was established as the difference in position between the therapist&#x2019;s cursor and the participant&#x2019;s hand. Error was visually magnified by a factor of 1.5e (m) as part of the error augmentation. Additionally, an error augmenting force of 100e (N/m) was also applied, which was programmed to saturate at a maximum of 4 N for safety reasons.</li>
 <li>Every other treatment block consisted of specific, standardized motions that were the same for each session. The other blocks allowed the therapist to customize training at specific areas of weakness based on therapist expertise and their observations. The treatment protocol included the practice of specific movements for all participants; including forward and side reaching, shoulder-elbow coupling, and diagonal reaching across the body.</li>
 <li>While practicing, day-to-day median error was measured as one outcome of the practice. Special attention was given to blocks of standardized motions that were the same for each session. These were compared to previous days to determine if any incremental improvement could be observed on a day-to-day basis, which can be reported to the patient, the therapist, and the caregivers (fig 3).</li>
 <li>Primary measures of outcome were measured weekly, 1 week after the end of treatment, and 45 days post to determine the retention of benefits. Key outcomes were the Fugl-Meyer motor ability score and our customized arm reach test that measured range of motion. </li>
</ol>
6. Representative Results: 
When the protocol is done correctly, then once the &lt;AnyDevice&gt; node is loaded into the H3DViewer or H3DLoad, the WAM device should be recognized and initiated. If the WAM were replaced with another robot, the code itself would not need to be changed.
<img src="/files/ftp_upload/3007/3007fig1.jpg" alt="Figure 1"/> 
Figure 1. Subject seated at the haptic/graphic apparatus.
<img src="/files/ftp_upload/3007/3007fig2.jpg" alt="Figure 2"/> 
Figure 2. Subject seated at the haptic/graphic apparatus with physical therapist.
<img src="/files/ftp_upload/3007/3007fig3.jpg" alt="Figure 3"/> 
Figure 3. Configuration for rehabilitation of the stroke patient. A) subject and therapist working together, seated and using the large-workspace haptic/graphic display to practice movement. The Therapist provides a cue for the subject, and can tailor conditioning to the needs of the patient. The robot provides forces that push the limb away from the target and the visual feedback system enhances the error of the cursor. B) Typical chronic stroke patient improvement from day to day. Each dot represents the median error measured for a 2-minute block of stereotypical functional movement. While the patient shows progress across the 2-week period and overall benefit, this person did not always improve each day.

<ol>
	<li>Solis, J., Takeshi, N., Petersen, K., Takeuchi, M., Takanishi, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+the+anthropomorphic+saxophonist+robot+WAS-1:+Mechanical+design+of+the+simulated+organs+and+implementation+of+air+pressure.">Development of the anthropomorphic saxophonist robot WAS-1: Mechanical design of the simulated organs and implementation of air pressure.</a> Advanced Robotics Journal. 24, 629-650 (2010).</li><li>Zufferey, J. C., Floreano, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evolving+Won-Based+Flying+Robots.">Evolving Won-Based Flying Robots.</a> , 592-600 (2002).</li><li>Conditt, M. A., Gandolfo, F., Mussa-Ivaldi, F. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+motor+system+does+not+learn+the+dynamics+of+the+arm+by+rote+memorization+of+past+experience.">The motor system does not learn the dynamics of the arm by rote memorization of past experience.</a> Journal of Neurophysiology. 78, 554-554 (1997).</li><li>Krebs, H. I., Palazzolo, J. J., Dipietro, L., Ferraro, M., Krol, J., Rannekleiv, K., Volpe, B. T., Hogan, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rehabilitation+robotics:+Performance-based+progressive+robot-assisted+therapy.">Rehabilitation robotics: Performance-based progressive robot-assisted therapy.</a> Autonomous Robots. 15, 7-20 (2003).</li><li>Wei, K., Kording, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relevance+of+error:+what+drives+motor+adaptation.">Relevance of error: what drives motor adaptation.</a> Journal of neurophysiology. 101, 655-65 (2009).</li><li>Wei, Y., Bajaj, P., Scheidt, R., Patton, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visual+error+augmentation+for+enhancing+motor+learning+and+rehabilitative+relearning.">Visual error augmentation for enhancing motor learning and rehabilitative relearning.</a> IEEE International Conference on Rehabilitation Robotics. , 505-510 (2005).</li></ol>

The wrapper classes in this tutorial are under copyright by Ian Sharp.

This method of wrapper class implementation allows for different robots to be used, without changing the source code, when using the H3DAPI. Specifically, researchers who have written their haptic/graphic environment in H3D and tested their experiment with a phantom robot would be able to carry out the same or similar experiment using the Barrett WAM, and vice versa. This type of device independent cross-communication carries implications for international rehabilitation robotics research. Such implications facilitate rapid haptic/graphic development, international research collaboration, and inter-research lab communication.
Rehabilitation robotics has yet to uncover the numerous parameters involved in motor learning. One of the time consuming steps during haptic/graphics development includes compilation time. With numerous rehabilitation parameters, compounded with the compilation time for each program, the development life cycle to test all possible group permutations rises rapidly. H3D, with its absence of compilation requirements, allows for quick development of numerous virtual reality scenes. This comes as an advantage for those researchers aspiring to probe the effects of various training scenarios.
Limitations of this 'hard-coded' wrapper class integration approach include the fact that this procedure must be repeated each time there is a new distribution of the H3DAPI. Possible modifications to integrating the wrapper class into your latest distribution of the H3DAPI would be to create the wrapper class separately from the H3DAPI. You would then put your wrapper class into a *.so library file. This would isolate your class from the original H3DAPI distribution.

<ol>
	<li>The Display called paris (personal augmented reality immersion system), can be found at <a href="http://www.evl.uic.edu">www.evl.uic.edu</a></li>
	<li>The large gray robot is the Barrett WAM: <a href="http://www.barrett.com">www.barrett.com</a></li>
	<li>The smaller, skinnier black robot is the Phantom: <a href="http://www.sensable.com">www.sensable.com</a></li>
	<li>The arm mount is the T-WREX, developed at the RIC: <a href="http://www.ric.org/research/centers/mars2/Projects/development/d3.aspx">http://www.ric.org/research/centers/mars2/Projects/development/d3.aspx</a></li>
	<li>The shutter glasses for 3d vision: <a href="http://www.vrlogic.com">www.vrlogic.com</a></li>
	<li>Head tracking software. <a href="http://www.mechdyne.com">www.mechdyne.com</a></li>
	<li>The H3DAPI itself: <a href="http://www.h3dapi.org">www.h3dapi.org</a></li>
</ol>

haptic/graphic rehabilitation: integrating a robot into a virtual environment library and applying it to stroke therapy

Recent research that tests interactive devices for prolonged therapy practice has revealed new prospects for robotics combined with graphical and other forms of biofeedback. Previous human-robot interactive systems have required different software commands to be implemented for each robot leading to unnecessary developmental overhead time each time a new system becomes available. For example, when a haptic/graphic virtual reality environment has been coded for one specific robot to provide haptic feedback, that specific robot would not be able to be traded for another robot without recoding the program. However, recent efforts in the open source community have proposed a wrapper class approach that can elicit nearly identical responses regardless of the robot used. The result can lead researchers across the globe to perform similar experiments using shared code. Therefore modular "switching out"of one robot for another would not affect development time. In this paper, we outline the successful creation and implementation of a wrapper class for one robot into the open-source H3DAPI, which integrates the software commands most commonly used by all robots.

Watch this Scientific Journal Video about Haptic/Graphic Rehabilitation: Integrating a Robot into a Virtual Environment Library and Applying it to Stroke Therapy at JoVE.com

Haptic/Graphic Rehabilitation: Integrating a Robot into a Virtual Environment Library and Applying it to Stroke Therapy

Recently, a vast amount of prospects have come available for human-robot interactive systems. In this paper we outline the integration of a new robotic device with open source software that can rapidly make possible a library of interactive functionality. We then outline a clinical application for a neurorehabilitation application.

Recent research that tests interactive devices for prolonged therapy practice has revealed new prospects for robotics combined with graphical and other ...

hapticgraphic-rehabilitation-integrating-robot-into-virtual

Research

JoVE Journal

Bioengineering

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic valve leaflets are composed of interstitial cells suspended within an extracellular matrix (ECM) and are lined with an endothelial cell monolayer. The valve withstands a harsh, dynamic environment and is constantly exposed to shear, flexion, tension, and compression. Research has shown calcific lesions in diseased valves occur in areas of high mechanical stress as a result of endothelial disruption or interstitial matrix damage1-3. Hence, it is not surprising that epidemiological studies have shown high blood pressure to be a leading risk factor in the onset of aortic valve disease4. 
The only treatment option currently available for valve disease is surgical replacement of the diseased valve with a bioprosthetic or mechanical valve5. Improved understanding of valve biology in response to physical stresses would help elucidate the mechanisms of valve pathogenesis. In turn, this could help in the development of non-invasive therapies such as pharmaceutical intervention or prevention. Several bioreactors have been previously developed to study the mechanobiology of native or engineered heart valves6-9. Pulsatile bioreactors have also been developed to study a range of tissues including cartilage10, bone11 and bladder12. The aim of this work was to develop a cyclic pressure system that could be used to elucidate the biological response of aortic valve leaflets to increased pressure loads. 
The system consisted of an acrylic chamber in which to place samples and produce cyclic pressure, viton diaphragm solenoid valves to control the timing of the pressure cycle, and a computer to control electrical devices. The pressure was monitored using a pressure transducer, and the signal was conditioned using a load cell conditioner. A LabVIEW program regulated the pressure using an analog device to pump compressed air into the system at the appropriate rate. The system mimicked the dynamic transvalvular pressure levels associated with the aortic valve; a saw tooth wave produced a gradual increase in pressure, typical of the transvalvular pressure gradient that is present across the valve during diastole, followed by a sharp pressure drop depicting valve opening in systole. The LabVIEW program allowed users to control the magnitude and frequency of cyclic pressure. The system was able to subject tissue samples to physiological and pathological pressure conditions. This device can be used to increase our understanding of how heart valves respond to changes in the local mechanical environment.

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

A cyclic pressure bioreactor capable of subjecting heart valve tissue to physiological and pathological pressure conditions has been designed. A LabVIEW program allows users to control pressure magnitude, amplitude and frequency. This device can be used to study the mechanobiology of heart valve tissue or isolated cells.

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic ...

Adaptation of a Haptic Robot in a 3T fMRI

Functional magnetic resonance imaging (fMRI) provides excellent functional brain imaging via the BOLD signal 1 with advantages including non-ionizing radiation, millimeter spatial accuracy of anatomical and functional data 2, and nearly real-time analyses 3. Haptic robots provide precise measurement and control of position and force of a cursor in a reasonably confined space. Here we combine these two technologies to allow precision experiments involving motor control with haptic/tactile environment interaction such as reaching or grasping. The basic idea is to attach an 8 foot end effecter supported in the center to the robot 4 allowing the subject to use the robot, but shielding it and keeping it out of the most extreme part of the magnetic field from the fMRI machine (Figure 1).
The Phantom Premium 3.0, 6DoF, high-force robot (SensAble Technologies, Inc.) is an excellent choice for providing force-feedback in virtual reality experiments 5, 6, but it is inherently non-MR safe, introduces significant noise to the sensitive fMRI equipment, and its electric motors may be affected by the fMRI's strongly varying magnetic field. We have constructed a table and shielding system that allows the robot to be safely introduced into the fMRI environment and limits both the degradation of the fMRI signal by the electrically noisy motors and the degradation of the electric motor performance by the strongly varying magnetic field of the fMRI. With the shield, the signal to noise ratio (SNR: mean signal/noise standard deviation) of the fMRI goes from a baseline of &tilde;380 to &tilde;330, and &tilde;250 without the shielding. The remaining noise appears to be uncorrelated and does not add artifacts to the fMRI of a test sphere (Figure 2). The long, stiff handle allows placement of the robot out of range of the most strongly varying parts of the magnetic field so there is no significant effect of the fMRI on the robot. The effect of the handle on the robot's kinematics is minimal since it is lightweight (&tilde;2.6 lbs) but extremely stiff 3/4" graphite and well balanced on the 3DoF joint in the middle. The end result is an fMRI compatible, haptic system with about 1 cubic foot of working space, and, when combined with virtual reality, it allows for a new set of experiments to be performed in the fMRI environment including naturalistic reaching, passive displacement of the limb and haptic perception, adaptation learning in varying force fields, or texture identification 5, 6.

The adaptation and use of a haptic robot in a 3T fMRI is described.

Functional magnetic resonance imaging (fMRI) provides excellent functional brain imaging via the BOLD signal 1 with advantages including non-ionizing ...

Designing a Bio-responsive Robot from DNA Origami

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Creating shapes from nucleic acids was first proposed by Seeman13, and several variations on this theme have since been realized using various techniques11,12,14,15 . However, the most significant is perhaps the one proposed by Rothemund, termed scaffolded DNA origami16. In this technique, the folding of a long (&gt;7,000 bases) single-stranded DNA 'scaffold' is directed to a desired shape by hundreds of short complementary strands termed 'staples'. Folding is carried out by temperature annealing ramp. This technique was successfully demonstrated in the creation of a diverse array of 2D shapes with remarkable precision and robustness. DNA origami was later extended to 3D as well17,18 .
 
The current paper will focus on the caDNAno 2.0 software19 developed by Douglas and colleagues. caDNAno is a robust, user-friendly CAD tool enabling the design of 2D and 3D DNA origami shapes with versatile features. The design process relies on a systematic and accurate abstraction scheme for DNA structures, making it relatively straightforward and efficient.
In this paper we demonstrate the design of a DNA origami nanorobot that has been recently described20. This robot is 'robotic' in the sense that it links sensing to actuation, in order to perform a task. We explain how various sensing schemes can be integrated into the structure, and how this can be relayed to a desired effect. Finally we use Cando21 to simulate the mechanical properties of the designed shape. The concept we discuss can be adapted to multiple tasks and settings.

DNA origami is a powerful method for fabricating precise nanoscale objects by programming the self-assembly of DNA molecules. Here, we describe how DNA origami can be utilized to design a robotic robot capable of sensing biological cues and responding by shape shifting, subsequently relayed to a desired effect.

Nucleic acids are astonishingly versatile. In addition to their natural role as storage medium for biological information1, they can be utilized in ...

A Method for Evaluating Timeliness and Accuracy of Volitional Motor Responses to Vibrotactile Stimuli

Artificial sensory feedback (ASF) systems can be used to compensate for lost proprioception in individuals with lower-limb impairments. Effective design of these ASF systems requires an in-depth understanding of how the parameters of specific feedback mechanism affect user perception and reaction to stimuli. This article presents a method for applying vibrotactile stimuli to human participants and measuring their response. Rotating mass vibratory motors are placed at pre-defined locations on the participant's thigh, and controlled through custom hardware and software. The speed and accuracy of participants' volitional responses to vibrotactile stimuli are measured for researcher-specified combinations of motor placement and vibration frequency. While the protocol described here uses push-buttons to collect a simple binary response to the vibrotactile stimuli, the technique can be extended to other response mechanisms using inertial measurement units or pressure sensors to measure joint angle and weight bearing ratios, respectively. Similarly, the application of vibrotactile stimuli can be explored for body segments other than the thigh.

This article describes a technique for applying vibrotactile stimuli to the thigh of a human participant, and measuring the accuracy and reaction time of the participant&#39;s volitional response for various combinations of stimulation location and frequency.

Artificial sensory feedback (ASF) systems can be used to compensate for lost proprioception in individuals with lower-limb impairments.  Effective design ...

Using Extraordinary Optical Transmission to Quantify Cardiac Biomarkers in Human Serum

For a biosensing platform to have clinical relevance in point-of-care (POC) settings, assay sensitivity, reproducibility, and ability to reliably monitor analytes against the background of human serum are crucial.
Nanoimprinting lithography (NIL) was used to fabricate, at a low cost, sensing areas as large as 1.5 mm x 1.5 mm. The sensing surface was made of high-fidelity arrays of nanoholes, each with an area of about 140 nm2. The great reproducibility of NIL made it possible to employ a one-chip, one-measurement strategy on 12 individually manufactured surfaces, with minimal chip-to-chip variation. These nanoimprinted localized surface plasmon resonance (LSPR) chips were extensively tested on their ability to reliably measure a bioanalyte at concentrations varying from 2.5 to 75 ng/mL amidst the background of a complex biofluid-in this case, human serum. The high fidelity of NIL enables the generation of large sensing areas, which in turn eliminates the need for a microscope, as this biosensor can be easily interfaced with a commonly available laboratory light source. These biosensors can detect cardiac troponin in serum with a high sensitivity, at a limit of detection (LOD) of 0.55 ng/mL, which is clinically relevant. They also show low chip-to-chip variance (due to the high quality of the fabrication process). The results are commensurable with widely used enzyme-linked immunosorbent assay (ELISA)-based assays, but the technique retains the advantages of an LSPR-based sensing platform (i.e., amenability to miniaturization and multiplexing, making it more feasible for POC applications).

This work describes a nanoimprinting lithography method to fabricate high-quality sensing arrays that work on the principle of extraordinary optical transmission. The biosensor is low-cost, robust, easy to use, and can detect cardiac troponin I in serum at clinically relevant concentrations (99th percentile cutoff &#8764;10-400 pg/mL, depending on the assay).

For a biosensing platform to have clinical relevance in point-of-care (POC) settings, assay sensitivity, reproducibility, and ability to reliably monitor ...

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of flexible polymers nor of rigid rods. Underlying filaments remain outstretched due to their non-vanishing backbone stiffness, which is quantified via the persistence length (lp), but they are also subject to strong thermal fluctuations. Their finite bending stiffness leads to unique, non-trivial collective mechanics of bulk networks, enabling the formation of stable scaffolds at low volume fractions while providing large mesh sizes. This underlying principle is prevalent in nature (e.g., in cells or tissues), minimizing the high molecular content and thereby facilitating diffusive or active transport. Due to their biological implications and potential technological applications in biocompatible hydrogels, semiflexible polymers have been subject to considerable study. However, comprehensible investigations remained challenging since they relied on natural polymers, such as actin filaments, which are not freely tunable. Despite these limitations and due to the lack of synthetic, mechanically tunable, and semiflexible polymers, actin filaments were established as the common model system. A major limitation is that the central quantity lp cannot be freely tuned to study its impact on macroscopic bulk structures. This limitation was resolved by employing structurally programmable DNA nanotubes, enabling controlled alteration of the filament stiffness. They are formed through tile-based designs, where a discrete set of partially complementary strands hybridize in a ring structure with a discrete circumference. These rings feature sticky ends, enabling the effective polymerization into filaments several microns in length, and display similar polymerization kinetics as natural biopolymers. Due to their programmable mechanics, these tubes are versatile, novel tools to study the impact of lp on the single-molecule as well as the bulk scale. In contrast to actin filaments, they remain stable over weeks, without notable degeneration, and their handling is comparably straightforward.

Semiflexible polymers display unique mechanical properties that are extensively applied by living systems. However, systematic studies on biopolymers are limited since properties such as polymer rigidity are inaccessible. This manuscript describes how this limitation is circumvented by programmable DNA nanotubes, enabling experimental studies on the impact of filament rigidity.

Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of ...

Optimizing the Use of a Liquid Handling Robot to Conduct a High Throughput Forward Chemical Genetics Screen of Arabidopsis thaliana

Chemical genetics is increasingly being employed to decode traits in plants that may be recalcitrant to traditional genetics due to gene redundancy or lethality. However, the probability of a synthetic small molecule being bioactive is low; therefore, thousands of molecules must be tested in order to find those of interest. Liquid handling robotics systems are designed to handle large numbers of samples, increasing the speed with which a chemical library can be screened in addition to minimizing/standardizing error. To achieve a high-throughput forward chemical genetics screen of a library of 50,000 small molecules on Arabidopsis thaliana (Arabidopsis), protocols using a bench-top multichannel liquid handling robot were developed that require minimal technician involvement. With these protocols, 3,271 small molecules were discovered that caused visible phenotypic alterations. 1,563 compounds induced short roots, 1,148 compounds altered coloration, 383 compounds caused root hair and other, non-categorized, alterations, and 177 compounds inhibited germination.

Optimizing the Use of a Liquid Handling Robot to Conduct a High Throughput Forward Chemical Genetics Screen of Arabidopsis thaliana

A high throughput screen of synthetic small molecules was conducted on the model plant species, Arabidopsis thaliana. This protocol, developed for a liquid handling robot, increases the speed of forward chemical genetics screens, accelerating the discovery of novel small molecules affecting plant physiology.

Chemical genetics is increasingly being employed to decode traits in plants that may be recalcitrant to traditional genetics due to gene redundancy or ...

Three-dimensional Patterning of Engineered Biofilms with a Do-it-yourself Bioprinter

Biofilms are aggregates of bacteria embedded in a self-produced spatially-patterned extracellular matrix. Bacteria within a biofilm develop enhanced antibiotic resistance, which poses potential health dangers, but can also be beneficial for environmental applications such as purification of drinking water. The further development of anti-bacterial therapeutics and biofilm-inspired applications will require the development of reproducible, engineerable methods for biofilm creation. Recently, a novel method of biofilm preparation using a modified three-dimensional (3D) printer with a bacterial ink has been developed. This article describes the steps necessary to build this efficient, low-cost 3D bioprinter that offers multiple applications in bacterially-induced materials processing. The protocol begins with an adapted commercial 3D printer in which the extruder has been replaced with a bio-ink dispenser connected to a syringe pump system enabling a controllable, continuous flow of bio-ink. To develop a bio-ink suitable for biofilm printing, engineered Escherichia coli bacteria were suspended in a solution of alginate, so that they solidify in contact with a surface containing calcium. The inclusion of an inducer chemical within the printing substrate drives expression of biofilm proteins within the printed bio-ink. This method enables 3D printing of various spatial patterns composed of discrete layers of printed biofilms. Such spatially-controlled biofilms can serve as model systems and can find applications in multiple fields that have a wide-ranging impact on society, including antibiotic resistance prevention or drinking water purification, among others.

This article describes a method of transforming a low-cost commercial 3D printer into a bacterial 3D printer that can facilitate printing of patterned biofilms. All necessary aspects of preparing the bioprinter and bio-ink are described, as well as verification methods to assess the formation of biofilms.

Biofilms are aggregates of bacteria embedded in a self-produced spatially-patterned extracellular matrix. Bacteria within a biofilm develop enhanced ...

Isokinetic Robotic Device to Improve Test-Retest and Inter-Rater Reliability for Stretch Reflex Measurements in Stroke Patients with Spasticity

Measuring spasticity is important in treatment planning and determining efficacy after treatment. However, the current tool used in clinical settings has been shown to be limited in inter-rater reliability. One factor in this poor inter-rater reliability is the variability of passive motion while measuring the angle of catch (AoC) measurements. Therefore, an isokinetic device has been proposed to standardize the manual joint motion; however, the benefits of isokinetic motion for AoC measurements has not been tested in a standardized manner. This protocol investigates whether isokinetic motion itself can improve inter-rater reliability for AoC measurements. For this purpose, a robotic isokinetic device was developed that is combined with surface electromyography (EMG). Two conditions, manual and isokinetic motions, are compared with the standardized method to measure the angle and subjective feeling of catch. It is shown that in 17 stroke patients with mild elbow flexor spasticity, isokinetic motion improved the intraclass correlation coefficient (ICC) for inter-rater reliability of AoC measurements to 0.890 [95% confidence interval (CI): 0.685&#8211;0.961] by the EMG criteria, and 0.931 (95% CI: 0.791&#8211;0.978) by the torque criteria, from 0.788 (95% CI: 0.493&#8211;0.920) by manual motion. In conclusion, isokinetic motion itself can improve inter-rater reliability of AoC measurements in stroke patients with mild spasticity. Given that this system may provide greater standardized angle measurements and catch of feeling, it may be a good option for the evaluation of spasticity in a clinical setting.

Using a robotic isokinetic device with electromyography (EMG) measurements, this protocol illustrates that isokinetic motion itself can improve inter-rater reliability for the angle of catch measurements in stroke patients with mild elbow flexor spasticity.

Measuring spasticity is important in treatment planning and determining efficacy after treatment. However, the current tool used in clinical settings has ...

Setup of a Microfluidic Device for Combinatorial Plug  Production

Bilayer Microfluidic Device for Combinatorial Plug Production

Droplet microfluidics is a versatile tool that allows the execution of a large number of reactions in chemically distinct nanoliter compartments. Such systems have been used to encapsulate a variety of biochemical reactions - from incubation of single cells to implementation of PCR reactions, from genomics to chemical synthesis. Coupling the microfluidic channels with regulatory valves allows control over their opening and closing, thereby enabling the rapid production of large-scale combinatorial libraries consisting of a population of droplets with unique compositions. In this paper, protocols for the fabrication and operation of a pressure-driven, PDMS-based bilayer microfluidic device that can be utilized to generate combinatorial libraries of water-in-oil emulsions called plugs are presented. By incorporating software programs and microfluidic hardware, the flow of desired fluids in the device can be controlled and manipulated to generate combinatorial plug libraries and to control the composition and quantity of constituent plug populations. These protocols will expedite the process of generating combinatorial screens, particularly to study drug response in cells from cancer patient biopsies.

Author Spotlight: Integrating Computational and Experimental Approaches in Precision Oncology

The fabrication of a polydimethylsiloxane (PDMS)-based bilayer device for the production of combinatorial libraries in water-in-oil emulsions (plugs) is presented here. The necessary hardware and software required to automate plug production are detailed in the protocol, and the production of a quantitative library of fluorescent plugs is also demonstrated.

Droplet microfluidics is a versatile tool that allows the execution of a large number of reactions in chemically distinct nanoliter compartments. Such ...