An algorithm to correct for camera vibrations in optical motion tracking systems

Recording and reconstruction of 3D motion capturing data relies on fixed, static camera positions with given inter-camera distances in a laboratory frame. To overcome this limitation, we present a correction algorithm that allows us to address camera movements in moving camera setups. Camera vibrations are identified by comparison of specialized target positions in dynamic measurements with their respective positions in static trials. This results in a 2D shift vector Δw with which the individual camera streams are corrected. The capabilities of this vibration reduction procedure are demonstrated in a test setup of four cameras that are (i) separately and (ii) simultaneously perturbed while capturing a static test object. In the former case, the correction algorithm is capable of reducing the reconstruction residuals to the order of the calibrations residual and enables reconstruction in the latter case, which is impossible without any correction. This approach extends the application of marker-based infrared motion tracking to moving and even accelerated camera setups.     

Versatile robotic interface to evaluate, enable and train locomotion and balance after neuromotor disorders

Central nervous system (CNS) disorders distinctly impair locomotor pattern generation and balance, but technical limitations prevent independent assessment and rehabilitation of these subfunctions. Here we introduce a versatile robotic interface to evaluate, enable and train pattern generation and balance independently during natural walking behaviors in rats. In evaluation mode, the robotic interface affords detailed assessments of pattern generation and dynamic equilibrium after spinal cord injury (SCI) and stroke. In enabling mode,the robot acts as a propulsive or postural neuroprosthesis that instantly promotes unexpected locomotor capacities including overground walking after complete SCI, stair climbing following partial SCI and precise paw placement shortly after stroke. In training mode, robot-enabled rehabilitation, epidural electrical stimulation and monoamine agonists reestablish weight-supported locomotion, coordinated steering and balance in rats with a paralyzing SCI. This new robotic technology and associated concepts have broad implications for both assessing and restoring motor functions after CNS disorders, both in animals and in humans.     

The use of sequential MR image sets for determining tibiofemoral motion: reliability of coordinate systems and accuracy of motion tracking algorithm

The use of magnetic resonance imaging has been proposed by many investigators for establishment of joint reference systems and kinematic tracking of musculoskeletal joints. In this study, the intraobserver and interobserver reliability of a strategy to establish anatomic reference systems using manually selected fiducial points were quantified for seven sets of MR images of the human knee joint. The standard error of the measurement of the intraobserver and interobserver errors were less than 2.6 degrees, and 1.2 mm for relative tibiofemoral orientation and displacement, respectively. An automated motion tracking algorithm was also validated with a controlled motion experiment in a cadaveric knee joint. The controlled displacements and rotations prescribed in our motion tracking validation were highly correlated to those predicted (Pearson's correlation = 0.99, RMS errors = 0.39 mm, 0.38 degree). Finally, the system for anatomic reference system definition and motion tracking was demonstrated with a set of MR images of in vivo passive flexion in the human knee.     

Feature point tracking and trajectory analysis for video imaging in cell biology

This paper presents a computationally efficient, two-dimensional, feature point tracking algorithm for the automated detection and quantitative analysis of particle trajectories as recorded by video imaging in cell biology. The tracking process requires no a priori mathematical modeling of the motion, it is self-initializing, it discriminates spurious detections, and it can handle temporary occlusion as well as particle appearance and disappearance from the image region. The efficiency of the algorithm is validated on synthetic video data where it is compared to existing methods and its accuracy and precision are assessed for a wide range of signal-to-noise ratios. The algorithm is well suited for video imaging in cell biology relying on low-intensity fluorescence microscopy. Its applicability is demonstrated in three case studies involving transport of low-density lipoproteins in endosomes, motion of fluorescently labeled Adenovirus-2 particles along microtubules, and tracking of quantum dots on the plasma membrane of live cells. The present automated tracking process enables the quantification of dispersive processes in cell biology using techniques such as moment scaling spectra.     

Blood pressure tracking systems and their application to biofeedback

Two automatic electronic systems for tracking diastolic or systolic blood pressure (BP) and their use in biofeedback experiments are described. Both systems are based on the use of an arm cuff and the recording of Korotkoff sounds with a microphone. An electronic control system receives input from the microphone and provides output to several solenoid valves that control compressed airflow to the cuff. For one of the tracking systems we devised, the cuff is alternately inflated for 45 sec and deflated for 45 sec. During inflation, small increments and decrements in cuff pressure, based on the occurrence of Korotkoff sounds, are used to track BP. The other tracking system is slower but provides more continuous measurements: The cuff is alternately inflated to approximately the BP level for 5 sec and then deflated for 5 sec. During each inflation, the number of Korotkoff sounds is recorded by the system and according to this number, the amount of inflation on the next trial is automatically adjusted so that the cuff pressure follows BP. Both systems have been used successfully in biofeedback applications.The authors thank Mark Goldman for helpful discussions of the techniques, and Maureen Delphia and Dianne Auty for their assistance in the preparation of this paper. This work was partially supported by a grant-in-aid from the Michigan Heart Association.     

Food for all: designing sustainable and secure future seafood systems

Reviews in Fish Biology and Fisheries - Food from the sea can make a larger contribution to healthy and sustainable diets, and to addressing hunger and malnutrition, through improvements in...     

How the carotid body works: different strategies and preparations to solve different problems

This is a review of the different experimental approaches developed to solve the problems in our progress towards a comprehensive understanding of how arterial chemoreceptors operate. An analysis is performed oi the bases, advantages and limits of the following preparations: studies of ventilatory reflexes originated from carotid bodies (CBs) in the entire animal; recordings of CB chemosensory discharges in situ; CB preparations perfused in situ; CB explants in oculo; CB explants in ovo; CB preparations incubated in vitro; CB preparations superfused in vitro; CB preparations perfused and superfused in vitro: CB tissue slices in vitro; cells acutely dissociated from CBs; CB cells in tissue culture; petrosal ganglia superfused in vitro; petrosal ganglion cells in tissue culture; and co-cultures of CB and sensory ganglion cells. A brief historical account is given of the passage from one preparation to the next one. Emphasis is placed on personal experience with the different preparations whenever possible. Examples are given of the importance of selecting the appropriate experimental preparation for solving each particular theoretical problem. In fact, brilliant ideas on how the CB works have been unproductive until finding the adequate experimental approach to explore the validity of such ideas.     

Agnostic particle tracking for three-dimensional motion of cellular granules and membrane-tethered bead dynamics

The ability to detect biological events at the single-molecule level provides unique biophysical insights. Back-focal-plane laser interferometry is a promising technique for nanoscale three-dimensional position measurements at rates far beyond the capability of standard video. We report an in situ calibration technique for back-focal-plane, low-power (nontrapping) laser interferometry. The technique does not rely on any a priori model or calibration knowledge, hence the name “agnostic”. We apply the technique to track long-range (up to 100 μm) motion of a variety of particles, including magnetic beads, in three-dimensions with high spatiotemporal resolution (∼2 nm, 100 μs). Our tracking of individual unlabeled vesicles revealed a previously unreported grouping of mean-squared displacement curves at short timescales (<10 ms). Also, tracking functionalized magnetic beads attached to a live cell membrane revealed an anchorage-dependent nonlinear response of the membrane. The software-based technique involves injecting small perturbations into the probe position by driving a precalibrated specimen-mounting stage while recording the quadrant photodetector signals. The perturbations and corresponding quadrant photodetector signals are analyzed to extract the calibration parameters. The technique is sufficiently fast and noninvasive that the calibration can be performed on-the-fly without interrupting or compromising high-bandwidth, long-range tracking of a particle.     

Model-based identification of motion sensor placement for tracking retraction and elongation of the tongue

Electromagnetic articulography (EMA) is designed to track facial and tongue movements. In practice, the EMA sensors for tracking the movement of the tongue’s surface are placed heuristically. No recommendation exists. Within this paper, a model-based approach providing a mathematical analysis and a computational-based recommendation for the placement of sensors, which is based on the tongue’s envelope of movement, is proposed. For this purpose, an anatomically detailed Finite Element (FE) model of the tongue has been employed to determine the envelope of motion for retraction and elongation using a forward simulation. Two optimality criteria have been proposed to identify a set of optimal sensor locations based on the pre-computed envelope of motion. The first one is based on the assumption that locations exhibiting large displacements contain the most information regarding the tongue’s movement and are less susceptible to measurement errors. The second one selects sensors exhibiting each the largest displacements in the anterior-posterior, superior-inferior, medial-lateral and overall direction. The quality of the two optimality criteria is analysed based on their ability to deduce from the respective sensor locations the corresponding muscle activation parameters of the relevant muscle fibre groups during retraction and elongation by solving the corresponding inverse problem. For this purpose, a statistical analysis has been carried out, in which sensor locations for two different modes of deformation have been subjected to typical measurement errors. Then, for tongue retraction and elongation, the expectation value, the standard deviation, the averaged bias and the averaged coefficient of variation have been computed based on 41 different error-afflicted sensor locations. The results show that the first optimality criteria is superior to the second one and that the averaged bias and averaged coefficient of variation decrease when the number of sensors is increased from 2, 4 to 6 deployable sensors.     

Advances in CRISPR-Cas systems for RNA targeting,tracking and editing

Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely used in gene/genome targeting. Modifications of Cas9 enable these systems to become platforms for precise DNA manipulations. However, the utilization of CRISPR-Cas systems in RNA targeting remains preliminary. The discovery of type VI CRISPR-Cas systems (Cas13) shed light on RNA-guided RNA targeting. Cas13d, the smallest Cas13 protein, with a length of only ~930 amino acids, is a promising platform for RNA targeting compatible with viral delivery systems. Much effort has also been made to develop Cas9, Cas13a and Cas13b applications for RNA-guided RNA targeting. The discovery of new RNA-targeting CRISPR-Cas systems as well as the development of RNA-targeting platforms with Cas9 and Cas13 will promote RNA-targeting technology substantially. Here, we review new advances in RNA-targeting CRISPR-Cas systems as well as advances in applications of these systems in RNA targeting, tracking and editing. We also compare these Cas protein-based technologies with traditional technologies for RNA targeting, tracking and editing. Finally, we discuss remaining questions and prospects for the future.     

Fluorescent reporter systems for tracking probiotic lactic acid bacteria and bifidobacteria

In the last two decades, there has been increasing evidence supporting the role of the intestinal microbiota in health and disease, as well as the use of probiotics to modulate its activity and composition. Probiotic bacteria selected for commercial use in foods, mostly lactic acid bacteria and bifidobacteria, must survive in sufficient numbers during the manufacturing process, storage, and passage through the gastro-intestinal tract. They have several modes of action and it is crucial to unravel the mechanisms underlying their postulated beneficial effects. To track their survival and persistence, and to analyse their interaction with the gastro-intestinal epithelia it is essential to discriminate probiotic strains from endogenous microbiota. Fluorescent reporter proteins are relevant tools that can be exploited as a non-invasive marker system for in vivo real-time imaging in complex ecosystems as well as in vitro fluorescence labelling. Oxygen is required for many of these reporter proteins to fluoresce, which is a major drawback in anoxic environments. However, some new fluorescent proteins are able to overcome the potential problems caused by oxygen limitations. The current available approaches and the benefits/disadvantages of using reporter vectors containing fluorescent proteins for labelling of bacterial probiotic species commonly used in food are addressed.     

Contribution to the mechanics of worm-like motion systems and artificial muscles

In this paper the author presents a mathematical model of a device that can be seen as a segment of an artificial worm (following the paradigm earthworm) and as an artificial muscle as well. Confining considerations to statics, the model shows up as an ordinary parameter-dependent boundary value problem. It is tackled numerically in various particular forms by means of Maple and thus gives a good view of the segment's behavior during inflation and under longitudinal load. Segments of maximal volume present a useful preliminary stage of the investigations.Thanks are to Klaus Zimmermann and his Motion Systems Group at TU Ilmenau for discussions and experiments, to Katrin Knabe for typing, and to an unknown reviewer for directing the author's attention to physical nonlinearity.     

On geometric mean fitness: a reply to Takacs and Bourrat

Biology & Philosophy -     

Quantification of human motion: gait analysis-benefits and limitations to its application to clinical problems

The technology supporting the analysis of human motion has advanced dramatically. Past decades of locomotion research have provided us with significant knowledge about the accuracy of tests performed, the understanding of the process of human locomotion, and how clinical testing can be used to evaluate medical disorders and affect their treatment. Gait analysis is now recognized as clinically useful and financially reimbursable for some medical conditions. Yet, the routine clinical use of gait analysis has seen very limited growth. The issue of its clinical value is related to many factors, including the applicability of existing technology to addressing clinical problems; the limited use of such tests to address a wide variety of medical disorders; the manner in which gait laboratories are organized, tests are performed, and reports generated; and the clinical understanding and expectations of laboratory results. Clinical use is most hampered by the length of time and costs required for performing a study and interpreting it. A “gait” report is lengthy, its data are not well understood, and it includes a clinical interpretation, all of which do not occur with other clinical tests. Current biotechnology research is seeking to address these problems by creating techniques to capture data rapidly, accurately, and efficiently, and to interpret such data by an assortment of modeling, statistical, wave interpretation, and artificial intelligence methodologies. The success of such efforts rests on both our technical abilities and communication between engineers and clinicians.