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"Becker, Aaron"
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Journey
A lonely girl draws a magic door on her bedroom wall and through it escapes into a world where wonder, adventure, and danger abound.
Book
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
Sources of error and bias in PCR amplification of microbial samples for 16S rRNA gene sequencing are systematically evaluated, and best-practice recommendations for reliable amplification are made.
Amplicon-based marker gene surveys form the basis of most microbiome and other microbial community studies. Such PCR-based methods have multiple steps, each of which is susceptible to error and bias. Variance in results has also arisen through the use of multiple methods of next-generation sequencing (NGS) amplicon library preparation. Here we formally characterized errors and biases by comparing different methods of amplicon-based NGS library preparation. Using mock community standards, we analyzed the amplification process to reveal insights into sources of experimental error and bias in amplicon-based microbial community and microbiome experiments. We present a method that improves on the current best practices and enables the detection of taxonomic groups that often go undetected with existing methods.
Journal Article
Quest
In this story without words, \"a king emerges from a hidden door in a city park, startling two children sheltering from the rain. No sooner does he push a map and some strange objects into their hands than he is captured by hostile forces that whisk him back through the enchanted door. Just like that, the children are caught up in a quest to rescue the king and his kingdom from darkness, while illuminating the farthest reaches of their imagination\"--Amazon.com.
Book
User interfaces for actuated scope maneuvering in surgical systems: a scoping review
BackgroundA variety of human computer interfaces are used by robotic surgical systems to control and actuate camera scopes during minimally invasive surgery. The purpose of this review is to examine the different user interfaces used in both commercial systems and research prototypes.MethodsA comprehensive scoping review of scientific literature was conducted using PubMed and IEEE Xplore databases to identify user interfaces used in commercial products and research prototypes of robotic surgical systems and robotic scope holders. Papers related to actuated scopes with human–computer interfaces were included. Several aspects of user interfaces for scope manipulation in commercial and research systems were reviewed.ResultsScope assistance was classified into robotic surgical systems (for multiple port, single port, and natural orifice) and robotic scope holders (for rigid, articulated, and flexible endoscopes). Benefits and drawbacks of control by different user interfaces such as foot, hand, voice, head, eye, and tool tracking were outlined. In the review, it was observed that hand control, with its familiarity and intuitiveness, is the most used interface in commercially available systems. Control by foot, head tracking, and tool tracking are increasingly used to address limitations, such as interruptions to surgical workflow, caused by using a hand interface.ConclusionIntegrating a combination of different user interfaces for scope manipulation may provide maximum benefit for the surgeons. However, smooth transition between interfaces might pose a challenge while combining controls.
Journal Article
A stone for Sascha
A young girl, still reeling from her dog's death, finds solace while picking up stones on the beach during her family's vacation.
Book
Simultaneous steering and imaging of magnetic particles using MRI toward delivery of therapeutics
Magnetic resonance navigation (MRN) offers the potential for real-time steering of drug particles and cells to targets throughout the body. In this technique, the magnetic gradients of an MRI scanner perform image-based steering of magnetically-labelled therapeutics through the vasculature and into tumours. A major challenge of current techniques for MRN is that they alternate between pulse sequences for particle imaging and propulsion. Since no propulsion occurs while imaging the particles, this results in a significant reduction in imaging frequency and propulsive force. We report a new approach in which an imaging sequence is designed to simultaneously image and propel particles. This sequence provides a tradeoff between maximum propulsive force and imaging frequency. In our reported example, the sequence can image at 27 Hz while still generating 95% of the force produced by a purely propulsive pulse sequence. We implemented our pulse sequence on a standard clinical scanner using millimetre-scale particles and demonstrated high-speed (74 mm/s) navigation of a multi-branched vascular network phantom. Our study suggests that the magnetic gradient magnitudes previously demonstrated to be sufficient for pure propulsion of micron-scale therapeutics in magnetic resonance targeting (MRT) could also be sufficient for real-time steering of these particles.
Journal Article
Return
\"Failing to get the attention of her busy father, a lonely girl turns back to a fantastic world for friendship and adventure. It's her third journey into the enticing realm of kings and emperors, castles and canals, exotic creatures and enchanting landscapes. This time, it will take something truly powerful to persuade her to return home\"--Dust jacket flap.
Book
A generic scope actuation system for flexible endoscopes
BackgroundA scope actuation system assists a surgeon in steering a scope for navigating an operative field during an interventional or diagnostic procedure. Each system is tailored for a specific surgical procedure. The development of a generic scope actuation system could assist various laparoscopic and endoscopic procedures. This has the potential to reduce the deployment and maintenance costs for a hospital, making it more accessible for clinical usage.MethodsA modular actuation system (for maneuvering rigid laparoscopes) was adapted to enable incorporation of flexible endoscopes. The design simplifies the installation and disassembly processes. User studies were conducted to assess the ability of the system to focus onto a diagnostic area, and to navigate during a simulated esophagogastroduodenoscopy procedure. During the studies, the endoscope was maneuvered with (robotic mode) and without (manual mode) the actuation system to navigate the endoscope’s focus on a predefined track.ResultsResults show that the robotic mode performed better than the manual mode on all the measured performance parameters including (a) the total duration to traverse a track, (b) the percentage of time spent outside a track while traversing, and (c) the number of times the scope focus shifts outside the track. Additionally, robotic mode also reduced the perceived workload based on the NASA-TLX scale.ConclusionsThe proposed scope actuation system enhances the maneuverability of flexible endoscopes. It also lays the groundwork for future development of modular and generic scope assistant systems that can be used in both laparoscopic and endoscopic procedures.
Journal Article
Scope actuation system for articulated laparoscopes
BackgroundAn articulated laparoscope comprises a rigid shaft with an articulated distal end to change the viewing direction. The articulation provides improved navigation of the operating field in confined spaces. Furthermore, incorporation of an actuation system tends to enhance the control of an articulated laparoscope.MethodsA preliminary prototype of a scope actuation system to maneuver an off-the-shelf articulated laparoscope (EndoCAMaleon by Karl Storz, Germany) was developed. A user study was conducted to evaluate this prototype for the surgical paradigm of video-assisted thoracic surgery. In the study, the subjects maneuvered an articulated scope under two modes of operation: (a) actuated mode where an operating surgeon maneuvers the scope using the developed prototype and (b) manual mode where a surgical assistant directly maneuvers the scope. The actuated mode was further assessed for multiple configurations based on the orientation of the articulated scope at the incision.ResultsThe data show the actuated mode scored better than the manual mode on all the measured performance parameters including (a) total duration to visualize a marked region, (a) duration for which scope focus shifts outside a predefined visualization region, and (c) number of times for which scope focus shifts outside a predefined visualization region. Among the different configurations tested using the actuated mode, no significant difference was observed.ConclusionsThe proposed articulated scope actuation system facilitates better navigation of an operative field as compared to a human assistant. Secondly, irrespective of the orientation in which an articulated scope’s shaft is inserted through an incision, the proposed actuation system can navigate and visualize the operative field.
Journal Article
Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification
Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next-generation sequencing. However, PCR amplification can introduce significant quantitative error. We describe REcount, a novel PCR-free direct counting method. Comparing measurements of defined plasmid pools to droplet digital PCR data demonstrates that REcount is highly accurate and reproducible. We use REcount to provide new insights into clustering biases due to molecule length across different Illumina sequencers and illustrate the impacts on interpretation of next-generation sequencing data and the economics of data generation.
Journal Article