We would like to thank Kun Lu and Ronald Kurz for technical assistance. This work was supported by ONR MURI Award No.:N00014-10-1-0072, NSF grant #SBE-0542013 to the Temporal Dynamics of Learning Center, an NSF Science of Learning Center, and NIH grant #2 R01 NS036449-11.

1. Outside the scanner room
<ol>
<li>Place the rolling table with the free end supported and the exterior end of the long handle detached.</li>
<li>Check that the robot is switched off.</li>
<li>Place the robot in the table socket and secure the aluminum safety plate over the robot with 2 screws.</li>
<li>Attach the end effecter to the robot handle with the aluminum adapter and check that it moves freely.</li>
<li>Attach the 10' parallel cable with aluminum shielding to the robot and check that the shielding is intact. Add extra foil if needed.</li>
<li>Place the aluminum shielding box over the robot being careful to place the parallel and power cables into the groove on the back.</li>
<li>Carefully screw on the shielding box.</li>
<li>Pack aluminum foil into the cable groove on the shielding box and be sure the foil makes contact with the shielding on the parallel cable.</li>
</ol>
2. Moving into the scanner room with two people, A and B
<ol>
<li>Prepare to enter a high magnetic field environment by removing any and all metallic objects including non-ferrous ones, e.g., cell phones, keys, coins, etc...</li>
<li>With person A holding the free end of the robot table and person B stabilizing the box end, roll it free end first until the robot just enters the door of the room.</li>
<li>Person B clips the security rope tethered to an anchor hole on the back of the shielding case and checks that the other end is firmly attached to a wall anchor.</li>
<li>Working together, roll the table into the room and attach it with Velcro straps to the foot of the fMRI table. The robot end of the table must stay as far from the scanner as possible.</li>
<li>Attach the robot's parallel cable to the custom filter on the pass through to the control room, and plug in the robot. The shielding foil on the parallel cable should make contact with the filter.</li>
<li>Attach the exterior part of the long handle (end effecter) and verify that it will enter the bore of the fMRI cleanly.</li>
</ol>
3. In the control room
<ol>
<li>Start the control computer and attach the 6' parallel cable to the robot. Be sure to remove any extra filters that may be on the interior part of the pass through.</li>
<li>Verify that the robot motors are turned off, start up the Phantom calibration routine and verify that the position readouts of the motors from the robot's calibration routine are stable.</li>
<li>Double check the parallel cable connection and that only the large custom filter is attached if the calibration routine cannot see the robot or there are large variations in the motor readout.</li>
<li>Turn on the robot by opening the port on the back of the shielding box and press the switches with a stick.</li>
<li>Restart the calibration routine with the end effecter approximately centered at the end of the conical waveguide. Step through the calibration and check that the box calibration box has the appropriate
haptic interaction.</li>
<li>Attach the TTL output from the fMRI (BNC connector) to the Labjack ADC on the control computer.</li>
</ol>
4. The subject
<ol>
<li>Prepare the subject for a high magnetic field environment with the standard fMRI protocols.</li>
<li>Set up any extra equipment for the experiment, e.g., visual display system. We use the NordicNeuro Lab, Inc. Vision System which provides stereo viewing of visual displays, a feature that is particularly helpful when presenting virtual environments.</li>
<li>After the subject lies down on the table and the head coil is situated, adjust the distance of the robot by loosening the hand screws and sliding the top of the table until the subject can move comfortably.</li>
<li>Guide the table manually by holding onto the robot end while the fMRI table is moving in and out of the bore to prevent the casters from wobbling. Make sure the end effecter goes into the bore and does not catch on the outside.</li>
<li>Run the experiment.</li>
</ol>
5. Break down the setup with two people A and B
<ol>
<li>After the patient exits, remove the exterior end of the long handle and detach the robot table from the fMRI table by undoing the Velcro strap.</li>
<li>From the robot, undo the shielded parallel cable and unplug the power cable.</li>
<li>With person A holding the free end of the robot table and person B guiding the robot end, move the table to the door. At the door, undo the tether, and roll the robot table out to the hall.</li>
<li>Undo all the screws from the shielding box and the two screws from the safety plate and remove the robot.</li>
</ol>
6. Representative results: 
Ideally, the haptic robot and fMRI should not affect each other. We can tell online if the robot is being affected by the fMRI. Generally, if the robot's parallel cable is not properly shielded and filtered, then the readout of the motors will oscillate rapidly. This can be fixed by double checking the aluminum shielding on the cable, that the ferrous core is properly placed on the parallel cable near the robot, and that the only filter to the robot is the custom filter on the scanner room side of the pass through. Detecting errors in the fMRI is really only possible after the data have been reduced and analyzed, but an anatomical scan should be taken early in the study and checked for zipper effects or other artifacts indicative of correlated noise (e.g. spike noise) 7. Frequently, such noise comes from metal on metal contact and can be cleaned up by tightening all the screws on the robot table, especially the hand adjustment screws on the side of the table. From our tests the baseline fMRI signal to noise ratio (SNR) is &tilde;380 and with the robot fully shielded in the room that drops to a still reasonable &tilde;330. If the shield is not in place on the robot, then the SNR drop further to &tilde;250, and noise effects become very significant.
As shown in 4, the 3 degree of freedom joint in the center of the handle has little effect on the dynamics of the robot/hand interaction except to shift it away from the robot. The joint in the center of the handle acts like a fulcrum and reverses the apparent motion in two of the directions (left-right and up-down) but not the third (forward-back). Since the Phantom and the hand are at opposite ends of the lever like handle with its fulcrum in the middle, gains are applied in software in each of the three Euclidean directions: negative gains in the two directions controlled by the swivel joint and a positive gain in the direction of the slider joint. The net effect of the handle and swivel reproduces the full 3 degrees of freedom of the Phantom robot, just 9' away.
<img src="/files/ftp_upload/3364/3364fig1.jpg" alt="Figure 1"/> Figure 1&nbsp;The apparatus used to mount the haptic robot for use in the fMRI environment. Top shows the haptic robot mounted in the case prior to enclosure (top, left) and the gimbal/slider joint at the midpoint of the handle (top, right). Bottom, left shows a subject in the scanner manipulating the handle. Bottom, right is a cartoon of the shielding and end effecter.
<img src="/files/ftp_upload/3364/3364fig2.jpg" alt="Figure 2"/> Figure 2&nbsp;Results of the BIRN test for the fully shielded robot with movement. The three images with crosses show sections of the spherical head model, and the bottom right shows a three dimensional view. The small dots are bubbles in the static head model and are always present. The lack of large stripes or zippers indicates that the noise from the robot is uncorrelated.

<ol>
	<li>Ogawa, S., Lee, T. M., Kay, A. R., Tank, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Brain+magnetic+resonance+imaging+with+contrast+dependent+on+blood+oxygenation.">Brain magnetic resonance imaging with contrast dependent on blood oxygenation.</a> Proc. Natl. Acad. Sci. U.S.A. 87, 9868-9872 (1990).</li><li>Heeger, D. J., Ress, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=What+does+fMRI+tell+us+about+neuronal+activity.">What does fMRI tell us about neuronal activity.</a> Nat. Rev. Neurosci. 3, 142-151 (2002).</li><li>deCharms, R. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Applications+of+real-time+fMRI.">Applications of real-time fMRI.</a> Nat. Rev. Neurosci. 9, 720-729 (2008).</li><li>Hribar, A., Koritnik, B., Munih, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phantom+haptic+device+upgrade+for+use+in+fMRI.">Phantom haptic device upgrade for use in fMRI.</a> Medical and Biological Engineering and Computing. 47, 677-684 (2009).</li><li>Trommershauser, J., Gepshtein, S., Maloney, L. T., Landy, M. S., Banks, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimal+compensation+for+changes+in+task-relevant+movement+variability.">Optimal compensation for changes in task-relevant movement variability.</a> J. Neurosci. 25, 7169-7178 (2005).</li><li>Konczak, J., Li, K. Y., Tuite, P. J., Poizner, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Haptic+perception+of+object+curvature+in+Parkinson's+disease.">Haptic perception of object curvature in Parkinson's disease.</a> PLoS ONE. 3, e2625-e2625 (2008).</li><li>Lipton, M. L., Lipton, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Artifacts:+When+things+go+wrong,+it's+not+necessarily+all+bad.">Artifacts: When things go wrong, it's not necessarily all bad.</a> Totally Accessible MRI. , 139-153 (2008).</li><li>Rajh, M., Glodez, S., Flasker, J., Gotlih, K., Kostanjevec, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+analysis+of+an+fMRI+compatible+haptic+robot.">Design and analysis of an fMRI compatible haptic robot.</a> Robotics and Computer-Integrated Manufacturing. 27, 267-275 (2011).</li><li>Burdet, E., Gassert, R., Gowrishankar, G., Chapuis, D., Bleuler, H., Ang, M., Khatib, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=fMRI+compatible+haptic+interfaces+to+investigate+human+motor+control.">fMRI compatible haptic interfaces to investigate human motor control.</a> Experimental Robotics IX, of Springer Tracts in Advanced Robotics. 21, 25-34 (2006).</li><li>Nakamura, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+networks+in+motor+sequence+learning:+abnormal+topographies+in+Parkinson's+disease.">Functional networks in motor sequence learning: abnormal topographies in Parkinson's disease.</a> Hum Brain Mapp. 12, 42-60 (2001).</li></ol>

No conflicts of interest declared.

The fMRI compatible robot opens up new possibilities for experiments in the neuroscience of motor control. The most critical step in the setup is the shielding of the robot to prevent artifacts in the fMRI, which we do in two steps. First, the robot itself is about 9' away from the bore with a long, lightweight, handle supported in its middle with a 3 degree of freedom joint . Second, the robot is encased in a 1/16&quot;-1/4&quot; aluminum box with a plastic conical (13&quot; base diameter, 6&quot; top diameter x 42&quo...

<table border="1">
<tbody>
<tr>
<td>Phantom premium 1.5/6dof, high force model</td>
<td>Sensable</td>
<td><a href="www.sensable.com">www.sensable.com</a></td>
</tr>
</tbody>
</table>

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.

Watch this Scientific Journal Video about Adaptation of a Haptic Robot in a 3T fMRI at JoVE.com

Adaptation of a Haptic Robot in a 3T fMRI

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 ...

adaptation-of-a-haptic-robot-in-a-3t-fmri

Research

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Bioengineering

9.6K Views.  University of California. הסתגלות ושימוש רובוט לתחושה ב fMRI 3T מתואר.

Video: Adaptation of a Haptic Robot in a 3T fMRI

Fabrication of Electrochemical-DNA Biosensors for the Reagentless Detection of Nucleic Acids, Proteins and Small Molecules

As medicine is currently practiced, doctors send specimens to a central laboratory for testing and thus must wait hours or days to 
receive the results. Many patients would be better served by rapid, bedside tests. To this end our laboratory and others have developed a versatile, reagentless 
biosensor platform that supports the quantitative, reagentless, electrochemical detection of nucleic acids (DNA, RNA), proteins (including antibodies) and small 
molecules analytes directly in unprocessed clinical and environmental samples. In this video, we demonstrate the preparation and use of several biosensors in this 
"E-DNA" class. In particular, we fabricate and demonstrate sensors for the detection of a target DNA sequence in a polymerase chain reaction mixture, an HIV-specific antibody and the drug cocaine. The preparation procedure requires only three hours of hands-on effort followed by an overnight incubation, and their use requires only minutes.

"E-DNA" sensors, reagentless, electrochemical biosensors that perform well even when challenged directly in blood and other complex matrices, have been adapted to the detection of a wide range of nucleic acid, protein and small molecule analytes. Here we present a general procedure for the fabrication and use of such sensors.

As medicine is currently practiced, doctors send specimens to a central laboratory for testing and thus must wait hours or days to 
receive the results. ...

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.

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 ...

Creating Two-Dimensional Patterned Substrates for Protein and Cell Confinement

Microcontact printing provides a rapid, highly reproducible method for the creation of well-defined patterned substrates.1 While microcontact printing can be employed to directly print a large number of molecules, including proteins,2 DNA,3 and silanes,4 the formation of self-assembled monolayers (SAMs) from long chain alkane thiols on gold provides a simple way to confine proteins and cells to specific patterns containing adhesive and resistant regions. This confinement can be used to control cell morphology and is useful for examining a variety of questions in protein and cell biology. Here, we describe a general method for the creation of well-defined protein patterns for cellular studies.5 This process involves three steps: the production of a patterned master using photolithography, the creation of a PDMS stamp, and microcontact printing of a gold-coated substrate. Once patterned, these cell culture substrates are capable of confining proteins and/or cells (primary cells or cell lines) to the pattern.
The use of self-assembled monolayer chemistry allows for precise control over the patterned protein/cell adhesive regions and non-adhesive regions; this cannot be achieved using direct protein stamping. Hexadecanethiol, the long chain alkane thiol used in the microcontact printing step, produces a hydrophobic surface that readily adsorbs protein from solution. The glycol-terminated thiol, used for backfilling the non-printed regions of the substrate, creates a monolayer that is resistant to protein adsorption and therefore cell growth.6 These thiol monomers produce highly structured monolayers that precisely define regions of the substrate that can support protein adsorption and cell growth. As a result, these substrates are useful for a wide variety of applications from the study of intercellular behavior7 to the creation of microelectronics.8
While other types of monolayer chemistry have been used for cell culture studies, including work from our group using trichlorosilanes to create patterns directly on glass substrates,9 patterned monolayers formed from alkane thiols on gold are straight-forward to prepare. Moreover, the monomers used for monolayer preparation are commercially available, stable, and do not require storage or handling under inert atmosphere. Patterned substrates prepared from alkane thiols can also be recycled and reused several times, maintaining cell confinement.10

Self-assembled monolayers (SAMs) formed from long chain alkane thiols on gold provide well-defined substrates for the formation of protein patterns and cell confinement. Microcontact printing of hexadecanethiol using a polydimethylsiloxane (PDMS) stamp followed by backfilling with a glycol-terminated alkane thiol monomer produces a pattern where protein and cells adsorb only to the stamped hexadecanethiol region.

Microcontact printing provides a rapid, highly reproducible method for the creation of well-defined patterned substrates.1  While microcontact printing ...

Cellular Lipid Extraction for Targeted Stable Isotope Dilution Liquid Chromatography-Mass Spectrometry Analysis

The metabolism of fatty acids, such as arachidonic acid (AA) and linoleic acid (LA), results in the formation of oxidized bioactive lipids, including numerous stereoisomers1,2. These metabolites can be formed from free or esterified fatty acids. Many of these oxidized metabolites have biological activity and have been implicated in various diseases including cardiovascular and neurodegenerative diseases, asthma, and cancer3-7. Oxidized bioactive lipids can be formed enzymatically or by reactive oxygen species (ROS). Enzymes that metabolize fatty acids include cyclooxygenase (COX), lipoxygenase (LO), and cytochromes P450 (CYPs)1,8. Enzymatic metabolism results in enantioselective formation whereas ROS oxidation results in the racemic formation of products.
While this protocol focuses primarily on the analysis of AA- and some LA-derived bioactive metabolites; it could be easily applied to metabolites of other fatty acids. Bioactive lipids are extracted from cell lysate or media using liquid-liquid (l-l) extraction. At the beginning of the l-l extraction process, stable isotope internal standards are added to account for errors during sample preparation. Stable isotope dilution (SID) also accounts for any differences, such as ion suppression, that metabolites may experience during the mass spectrometry (MS) analysis9. After the extraction, derivatization with an electron capture (EC) reagent, pentafluorylbenzyl bromide (PFB) is employed to increase detection sensitivity10,11. Multiple reaction monitoring (MRM) is used to increase the selectivity of the MS analysis. Before MS analysis, lipids are separated using chiral normal phase high performance liquid chromatography (HPLC). The HPLC conditions are optimized to separate the enantiomers and various stereoisomers of the monitored lipids12. This specific LC-MS method monitors prostaglandins (PGs), isoprostanes (isoPs), hydroxyeicosatetraenoic acids (HETEs), hydroxyoctadecadienoic acids (HODEs), oxoeicosatetraenoic acids (oxoETEs) and oxooctadecadienoic acids (oxoODEs); however, the HPLC and MS parameters can be optimized to include any fatty acid metabolites13.
Most of the currently available bioanalytical methods do not take into account the separate quantification of enantiomers. This is extremely important when trying to deduce whether or not the metabolites were formed enzymatically or by ROS. Additionally, the ratios of the enantiomers may provide evidence for a specific enzymatic pathway of formation. The use of SID allows for accurate quantification of metabolites and accounts for any sample loss during preparation as well as the differences experienced during ionization. Using the PFB electron capture reagent increases the sensitivity of detection by two orders of magnitude over conventional APCI methods. Overall, this method, SID-LC-EC-atmospheric pressure chemical ionization APCI-MRM/MS, is one of the most sensitive, selective, and accurate methods of quantification for bioactive lipids.

This protocol will demonstrate the extraction and analysis of free and esterified bioactive fatty acids from cells. Fatty acids are accurately quantified using stable isotope dilution, chiral liquid chromatography, electron capture atmospheric chemical ionization multiple reaction monitoring mass spectrometry (SID-LC-ECAPCI-MRM/MS).

The metabolism of fatty acids, such as arachidonic acid (AA) and linoleic acid (LA), results in the formation of oxidized bioactive lipids, including ...

Designing a Bio-responsive Robot from DNA Origami

Nucleic acids are astonishingly versatile. In addition to their natural role as storage medium for biological information1, they can be utilized in parallel computing2,3 , recognize and bind molecular or cellular targets4,5 , catalyze chemical reactions6,7 , and generate calculated responses in a biological system8,9. Importantly, nucleic acids can be programmed to self-assemble into 2D and 3D structures10-12, enabling the integration of all these remarkable features in a single robot linking the sensing of biological cues to a preset response in order to exert a desired effect.
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 ...

Medical-grade Sterilizable Target for Fluid-immersed Fetoscope Optical Distortion Calibration

We have developed a calibration target for use with fluid-immersed endoscopes within the context of the GIFT-Surg (Guided Instrumentation for Fetal Therapy and Surgery) project. One of the aims of this project is to engineer novel, real-time image processing methods for intra-operative use in the treatment of congenital birth defects, such as spina bifida and the twin-to-twin transfusion syndrome. The developed target allows for the sterility-preserving optical distortion calibration of endoscopes within a few minutes. Good optical distortion calibration and compensation are important for mitigating undesirable effects like radial distortions, which not only hamper accurate imaging using existing endoscopic technology during fetal surgery, but also make acquired images less suitable for potentially very useful image computing applications, like real-time mosaicing. In this paper proposes a novel fabrication method to create an affordable, sterilizable calibration target suitable for use in a clinical setup. This method involves etching a calibration pattern by laser cutting a sandblasted stainless steel sheet. This target was validated using the camera calibration module provided by OpenCV, a state-of-the-art software library popular in the computer vision community.

This article describes the design and development of a sterilizable custom camera optical distortion calibration target for the peri-operative, fluid-immersed calibration of endoscopes during endoscopic interventions.

We have developed a calibration target for use with fluid-immersed endoscopes within the context of the GIFT-Surg (Guided Instrumentation for Fetal ...

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 ...

Decellularization of Whole Human Heart Inside a Pressurized Pouch in an Inverted Orientation

The ultimate solution for patients with end-stage heart failure is organ transplant. But donor hearts are limited, immunosuppression is required, and ultimately rejection can occur. Creating a functional, autologous bio-artificial heart could solve these challenges. Biofabrication of a heart comprised of scaffold and cells is one option. A natural scaffold with tissue-specific composition as well as micro- and macro-architecture can be obtained by decellularizing hearts from humans or large animals such as pigs. Decellularization involves washing out cellular debris while preserving 3D extracellular matrix and vasculature and allowing &#34;cellularization&#34; at a later timepoint. Capitalizing on our novel finding that perfusion decellularization of complex organs is possible, we developed a more &#34;physiological&#34; method to decellularize non-transplantable human hearts by placing them inside a pressurized pouch, in an inverted orientation, under controlled pressure. The purpose of using a pressurized pouch is to create pressure gradients across the aortic valve to keep it closed and improve myocardial perfusion. Simultaneous assessment of flow dynamics and cellular debris removal during decellularization allowed us to monitor both fluid inflow and debris outflow, thereby generating a scaffold that can be used either for simple cardiac repair (e.g. as a patch or valve scaffold) or as a whole-organ scaffold.

This method enables decellularization of a complex solid organ using a simple protocol based on osmotic shock and perfusion of ionic detergent with minimal organ matrix disruption. It comprises a novel decellularization technique for human hearts inside a pressurized pouch with real-time monitoring of flow dynamics and cellular debris outflow.

The ultimate solution for patients with end-stage heart failure is organ transplant. But donor hearts are limited, immunosuppression is required, and ...

A Tripeptide-Stabilized Nanoemulsion of Oleic Acid

We describe a method to produce a nanoemulsion composed of an oleic acids-Pt(II) core and a lysine-tyrosine-phenylalanine (KYF) coating (KYF-Pt-NE). The KYF-Pt-NE encapsulates Pt(II) at 10 wt. %, has a diameter of 107 &#177; 27 nm and a negative surface charge. The KYF-Pt-NE is stable in water and in serum, and is biologically active. The conjugation of a fluorophore to KYF allows the synthesis of a fluorescent nanoemulsion that is suitable for biological imaging. The synthesis of the nanoemulsion is performed in an aqueous environment, and the KYF-Pt-NE forms via self-assembly of a short KYF peptide and an oleic acids-platinum(II) conjugate. The self-assembly process depends on the temperature of the solution, the molar ratio of the substrates, and the flow rate of the substrate addition. Crucial steps include maintaining the optimal stirring rate during the synthesis, permitting sufficient time for self-assembly, and pre-concentrating the nanoemulsion gradually in a centrifugal concentrator.

This protocol describes an efficient method to synthesize a nanoemulsion of an oleic acids-platinum(II) conjugate stabilized with a lysine-tyrosine-phenylalanine (KYF) tripeptide. The nanoemulsion forms under mild synthetic conditions via self-assembly of the KYF and the conjugate.

We describe a method to produce a nanoemulsion composed of an oleic acids-Pt(II) core and a lysine-tyrosine-phenylalanine (KYF) coating (KYF-Pt-NE). The ...

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 ...