Filtering of kinematic signals using the Hodrick-Prescott filter

The use of the Hodrick-Prescott (HP) filter is presented as an alternative to the traditional digital filtering and spline smoothing methods currently used in biomechanics. In econometrics, HP filtering is a standard tool used to decompose a macroeconomic time series into a nonstationary trend component and a stationary residual component. The use of the HP filter in the present work is based on reasonable assumptions about the jerk and noise components of the raw displacement signal. Its applicability was tested on 4 kinematic signals with different characteristics. Two are well known signals taken from the literature on biomechanical signal filtering, and the other two were acquired with our own motion capture system. The criterion for the selection of cutoff frequency was based on the power spectral density of the raw displacement signals. The results showed the technique to be well suited to filtering biomechanical displacement signals in order to obtain accurate higher derivatives in a simple and systematic way. Namely, the HP filter and the generalized cross-validated quintic spline (GCVSPL) produce similar RMS errors on the first (0.1063 vs. 0.1024 m/s2) and second (23.76 vs. 23.24 rad/s2) signals. The HP filter performs slightly better than GCVSPL on the third (0.209 vs. 0.236 m/s2) and fourth (1.596 vs. 2.315 m/s2) signals.     

SENSORY DRIVE DOES NOT EXPLAIN REPRODUCTIVE CHARACTER DISPLACEMENT OF MALE ACOUSTIC SIGNALS IN THE UPLAND CHORUS FROG (PSEUDACRIS FERIARUM)

Biotic and abiotic factors have been proposed to explain patterns of reproductive character displacement, but which factor is most important to character displacement of acoustic signals is not clear. Male vocalizations of the frog Pseudacris feriarum are known to undergo reproductive character displacement in areas of sympatry with P. brimleyi and P. nigrita. Despite evidence for reinforcement as an important mechanism, local adaptation via sensory drive might explain this pattern because Pseudacris breed in different habitat types and mating signals are exposed to a variety of environments. We tested the sensory drive hypothesis by playing synthesized vocalizations representing the spectrum of variation in P. feriarum at 12 different study sites. If sensory drive has occurred, then vocalizations should transmit better in the site of origin or at ecologically similar sites. We found that variation in acoustic signals did not produce better transmission in particular sites, the effect of site was uniform, and acoustic signals often transmitted better in habitats external to their origin. Ecological variation among habitats did not explain signal degradation. Our playback experiments, ecological analyses, and comparisons of different habitat types provide no support for sensory drive as a process promoting reproductive character displacement in this system. Reinforcement is the more likely primary mechanism.     

Character displacement from the receiver's perspective: species and mate recognition despite convergent signals in suboscine birds

Many social animals use long-distance signals to attract mates and defend territories. They face the twin challenges of discriminating between species to identify conspecific mates, and between individuals to recognize collaborators and competitors. It is therefore often assumed that long-distance signals are under strong selection for species-specificity and individual distinctiveness, and that this will drive character displacement when closely related species meet, particularly in noisy environments. However, the occurrence of signal stereotypy and convergence in rainforest species seems to contradict these ideas, and raises the question of whether receivers in these systems can recognize species or individuals by long-distance signals alone. Here, we test for acoustically mediated recognition in two sympatric antbird species that are known to have convergent songs. We show that male songs are stereotyped yet individually distinctive, and we use playback experiments to demonstrate that females can discriminate not only between conspecific and heterospecific males, but between mates and strangers. These findings provide clear evidence that stereotypy and convergence in male signals can be accommodated by fine tuning of perceptual abilities in female receivers, suggesting that the evolutionary forces driving divergent character displacement in animal signals are weaker than is typically assumed.     

Reproductive character displacement and signal ontogeny in a sympatric assemblage of electric fish

The reproductive signals of two or more taxa may diverge in areas of sympatry, due to selection against costly reproductive interference. This divergence, termed reproductive character displacement (RCD), is expected in species-rich assemblages, where interspecific signal partitioning among closely related species is common. However, RCD is usually documented from simple two-taxon cases, via geographical tests for greater divergence of reproductive traits in sympatry than in allopatry. We propose a novel approach to recognizing and understanding RCD in multi-species communities--one that traces the displacement of signals within multivariate signal space during the ontogeny of individual animals. We argue that a case for RCD can be made if the amount of signal displacement between a pair of species after maturation is negatively correlated to distance in signal space before maturation. Our application of this approach, using a dataset of communication signals from a sympatric Amazonian assemblage of the electric fish genus Gymnotus, provides strong evidence for RCD among multiple species. We argue that RCD arose from the costs of heterospecific mismating, but interacted with sexual selection--favoring the evolution of conspicuous male signals that not only serve for mate-choice, but which simultaneously facilitate species recognition.     

A Novel Bio-Sensor Based on DNA Strand Displacement

DNA strand displacement technology performs well in sensing and programming DNA segments. In this work, we construct DNA molecular systems based on DNA strand displacement performing computation of logic gates. Specifically, a class of so-called “DNA neurons” are achieved, in which a “smart” way inspired by biological neurons encoding information is developed to encode and deliver information using DNA molecules. The “DNA neuron” is bistable, that is, it can sense DNA molecules as input signals, and release “negative” or “positive” signals DNA molecules. We design intelligent DNA molecular systems that are constructed by cascading some particularly organized “DNA neurons”, which could perform logic computation, including AND, OR, XOR logic gates, automatically. Both simulation results using visual DSD (DNA strand displacement) software and experimental results are obtained, which shows that the proposed systems can detect DNA signals with high sensitivity and accretion; moreover, the systems can process input signals automatically with complex nonlinear logic. The method proposed in this work may provide a new way to construct a sensitive molecular signal detection system with neurons spiking behavior in vitro, and can be used to develop intelligent molecular processing systems in vivo.     

Electric response of a back photoreaction in the bacteriorhodopsin photocycle.

The electric response of a back photoreaction in the bacteriorhodopsin photocycle was investigated. The proton pumping activity of green flash excited bacteriorhodopsin stops if the M412 form is illuminated by blue light (Karvaly and Dancsházy, 1977). In the present work a fast negative displacement current signal was measured in an oriented membrane suspension system, indicative of back movement of protons from M412 to BR570. Quantitative evaluation of the data shows that there are at least two steps in the back reaction, with different rate constants. The temperature dependence of the rate constants show simple linear Arrhenius behavior between 5 degree and 40 degree C. The rate constants were slower by a factor of 1.8 in D2O suspension. The relevance of the protein electric response signals (PERS) observed in this paper to the early receptor potential is discussed.     

Application of singular spectrum analysis to the smoothing of raw kinematic signals

Motion capture systems currently used in biomechanical analysis introduce systematic measurement errors that appear in the form of noise in recorded displacement signals. The noise is unacceptably amplified when differentiating displacements to obtain velocities and accelerations. To avoid this phenomenon, it is necessary to smooth the displacement signal prior to differentiation in order to eliminate the noise introduced by the experimental system. The use of singular spectrum analysis (SSA) is presented in this paper as an alternative to traditional digital filtering methods. SSA is a novel non-parametric technique based on principles of multivariate statistics. The original time series is decomposed into a number of additive time series, each of which can be easily identified as being part of the modulated signal, or as being part of the random noise. Several examples that demonstrate the superiority of this technique over other methods used in biomechanical analysis are presented in this paper.     

FTIR spectroscopic evidence for the involvement of an acidic residue in quinone binding in cytochrome bd from Escherichia coli

In this work, FTIR difference spectroscopy is used to search for possible binding partners and protonable groups involved in the binding of the quinol to cytochrome bd from Escherichia coli. In addition, the electrochemically induced FTIR difference spectra are compared for preparations of the enzyme isolated from cells grown at different oxygen levels in which the quinone content of the membrane is altered. On this basis, difference signals can be tentatively attributed to the vibrational modes of the different quinones types that are associated with the enzyme depending on growth conditions. Furthermore, vibrational modes due to the redox-dependent reorganization of the protein vary depending on the quinone associated with the isolated enzyme. Of particular interest are the observations that a mode at 1738 cm(-1) is decreased and a mode at 1595 cm(-1) is increased as observed in direct comparison to the data obtained from samples grown anaerobically. These signals indicate a change in the protonation state of an aspartic or glutamic acid. Since these changes are observed when the ubiquinone ratio in the preparation increases, the data provide evidence for the modulation of the binding site by the interacting quinone and the involvement of an acidic group in the binding site. The tentative assignments of the vibrational modes are supported by electrochemically induced FTIR difference spectra of cytochrome bd in the presence of the specific quinone binding site inhibitors heptylhydroxyquinoline-N-oxide (HQNO) or 2-methyl-3-undecylquinolone-4. Whereas HQNO leads to strong shifts in the FTIR redox difference spectrum, 2-methyl-3-undecylquinolone-4 induces a specific shift of a mode at 1635 cm(-1), which likely originates from the displacement of the C=O group of the bound quinone.     

Fibroblast contractile force is independent of the stiffness which resists the contraction.

Using a device named the cell force monitor, the contractile force developed by fibroblasts has been studied by measuring the macroscopic contraction of porous collagen-glycosaminoglycan (GAG) matrices over the first 24 h following cell attachment. In this paper, the effect of a variation in the stiffness that resists matrix contraction by cells on the contractile force generated by the cells was determined. Data from these experiments revealed that the contractile force generated by the fibroblasts was independent of the stiffness of the resistance within the range tested (0.7-10.7 N/m). These results suggest that during the time when fibroblasts are attaching to and spreading on collagen-GAG matrices the contractile forces they generate are force limited, not displacement limited. Therefore, the cytoskeletal mechanism of force generation, corresponding with cell elongation, is capable of increasing the displacement of adhesion sites in order to develop the same level of force. Although a detailed understanding of how the passive mechanical signals provided by substrate materials affect cell processes is still unavailable, in vitro modeling of cell-mediated contraction continues to provide useful information.     

A telemetry-based device to determine the force-displacement behaviour of materials in high impact loading situations

Meaningful testing of stab resistant body armour requires the use of realistic body tissue simulants. A device for the determination of the force-displacement behaviour of materials in high impact loading situations has been developed for the testing of such simulants. Force measurement is achieved with the use of electrical foil strain gauges applied to a cylindrical load cell. A piezo-resistive accelerometer (+/- 500 g) is used to calculate the displacement of the device through double integration of its signal, with the impact velocity used as a boundary condition. The signals from the strain gauge circuit and the accelerometer are sampled at 2500 Hz. The data are transmitted to a receiver via telemetry using a 418 MHz FM transmitter and from the receiver to a laptop PC via the serial port. Calibration of the device is described and sample results showing forces up to 2500 N and displacements up to 0.04 m are presented.     

Hearing in honeybees: the mechanical response of the bee's antenna to near field sound

In the dance language, honeybees use airborne near field sound signals to inform their nestmates of the location of food sources. In behavioral experiments it has recently been shown that Johnston's organ, a chordotonal organ located in the pedicel of the antenna, is used to perceive these sound signals. In the present study the mechanical response of the antennal flagellum to stimulation with near field sound signals was investigated using laser vibrometry. The absolute amplitudes of antennal deflection with acoustical stimulation, the response to sounds of different displacement and velocity amplitudes, the shape of movement of the flagellum, the mechanical frequency response and the mechanical directional sensitivity of the auditory sense organ of the honeybee are described. Using pulsed stimuli simulating the dance sounds it is shown that the temporal pattern of the dance sound is resolved on the level of antennal vibrations.     

Transient removal of proflavine inhibition of bovine beta-trypsin by the bovine basic pancreatic trypsin inhibitor (Kunitz). A case for "chronosteric effects"

The formation of the bovine beta-trypsin-bovine basic pancreatic trypsin inhibitor (Kunitz) (BPTI) complex was monitored, making use of three different signals: proflavine displacement, optical density changes in the ultraviolet region, and the loss of the catalytic activity. The rates of the reactions indicated by the three different signals were similar at neutral pH, but diverged at low pH. At pH 3.50, proflavine displacement precedes the optical density changes in the ultraviolet and the loss of enzyme activity by several orders of magnitude in time (Antonini, E., Ascenzi, P., Menegatti, E., and Guarneri, M. (1983) Biopolymers 22, 363-375). These data indicated that the bovine beta-trypsin-BPTI complex formation is a multistage process and led to the prediction that, at pH 3.50, BPTI addition to the bovine beta-trypsin-proflavine complex would remove proflavine inhibition and the enzyme would recover transiently its catalytic activity before being irreversibly inhibited by completion of BPTI binding. The kinetic evidences, by completion of BPTI binding. The kinetic evidences, here shown, verified this prediction, indicating that during the bovine beta-trypsin-BPTI complex formation one transient intermediate occurs, which is not able to bind proflavine but may bind and hydrolyze the substrate. Thus, the observed peculiar catalytic behavior is in line with the proposed reaction mechanism for the bovine beta-trypsin-BPTI complex formation, which postulates a sequence of distinct polar and apolar interactions at the contact area.     

Dynamics of the DNA duplex formation studied by single molecule force measurements

DNA is partly denatured in vitro by applying a force that mechanically separates the two strands of the double helix. Sudden reduction of the imposed displacement triggers spontaneous reannealing of the molecule. The corresponding force signals are measured by optical trapping interferometry for backward steps of various amplitudes and base sequence intervals. The measured signals frequently show plateaus of varying duration at discrete values that are dependent on the base sequence. Additional measurements are performed with proteins bound to the double helix. When the opening fork encounters such a protein during mechanical unzipping, force increases until the protein is ejected. This ejection induces fast release of tension and fast unzipping. Comparing our different measurements, we find that both DNA unzipping and the relaxation of tension in DNA are faster than the formation of the double helix.     

Kinetics of the fast electric signal from oriented purple membrane

The photoinduced electric response of oriented purple membranes associated with processes before the K-intermediate decay of bacteriorhodopsin was measured in the 180-300 K temperature range. These response signals consist of two kinetically distinct components (both temperature dependent). The experimental data show a correlation between the time constants of the rise of the signal and solution resistance. A model is proposed to assign these components to two diffusion-limited processes of charge displacement in the solution. The displacement is caused by the electric field of the photoinduced transient dipole which is formed in the primary act of the bacteriorhodopsin photocycle. The two processes are assigned as: (a) the conduction of electrical current through H-bonds (time resolved only in the temperature range 180-200 K) and (b) the diffusion of charges through the interfacial layer.     

A novel interpretation for the collicular role in saccade generation

Recently, we found evidence that the activity of neurons in the deep layers of the monkey superior colliculus (SC) is modulated by initial eye position (gain fields). In this paper, we propose a quantitative model of the motor SC which incorporates these new findings. Inputs to the motor map represent the desired eye displacement vector (motor error), as well as initial eye position. A unit's activity in the motor map is described by multiplying a weak linear eye position sensitivity with a gaussian tuning to motor error. The motor map projects to several sets of output neurons, representing the coordinates of the desired eye displacement vector, the desired eye position in the head, and the three-dimensional ocular rotation axis for saccades in Listing's plane, respectively. All these signals have been hypothesized in the literature to drive the saccade burst generator. We show that these signals can be extracted from the motor map by a linear weighting of the population activity. The saccadic system may employ all coding strategies in parallel to ensure high spatial accuracy in many complex sensorimotor tasks, such as orienting to multimodal stimuli.     

Investigation of the transduction mechanism of infrared detection in Melanophila acuminata: photo-thermal-mechanical hypothesis

Differential phase optical low coherence reflectometry (OLCR) was used to detect sub-wavelength displacements in the infrared-sensitive thoracic pit organ of Melanophila acuminata (Coleoptera: Buprestidae) upon absorption of infrared radiation at 3.39 microm. The displacement had more complex morphology but similar amplitude ( approximately 100 nm at 1 W cm(-2)) when compared to the displacement measured from the exocuticle in an alternate region on the beetle's body. In addition, a simplified finite difference model was developed to predict the temperature distribution and resultant thermal expansion in the pit organ tissue. The experimental and model results were interpreted to help clarify the mechanism by which the sensilla in the pit organ convert infrared radiation to neural signals. The results of this paper are discussed in relation to the photo-thermal-mechanical transduction hypothesis. This is the first experimental examination of the transduction mechanism in Melanophila acuminata.     

Protein targeting by tyrosine- and di-leucine-based signals: evidence for distinct saturable components

Targeting of transmembrane proteins to lysosomes, endosomal compartments, or the trans-Golgi network is largely dependent upon cytoplasmically exposed sorting signals. Among the most widely used signals are those that conform to the tyrosine-based motif, YXXO (where Y is tyrosine, X is any amino acid, and O is an amino acid with a bulky hydrophobic group), and to the di-leucine (or LL) motif. Signals conforming to both motifs have been implicated in protein localization to similar post-Golgi compartments. We have exploited the saturability of sorting to ask whether different YXXO or LL signals use shared components of the targeting machinery. Chimeric proteins containing various cytoplasmic domains and/or targeting signals were overexpressed in HeLa cells by transient transfection. Endogenous transferrin receptor and lysosomal proteins accumulated at the cell surface upon overexpression of chimeric proteins containing functional YXXO targeting signals, regardless of the compartmental destination imparted by the signal. Furthermore, overexpression of these chimeric proteins compromised YXXO-mediated endocytosis and lysosomal delivery. These activities were ablated by mutating the signals or by appending sequences that conformed to the YXXO motif but lacked targeting activity. Interestingly, overexpression of chimeric proteins containing cytoplasmic LL signals failed to induce surface displacement of endogenous YXXO-containing proteins, but did displace other proteins containing LL motifs. Our data demonstrate that: (a) Protein targeting and internalization mediated by either YXXO or LL motifs are saturable processes; (b) common saturable components are used in YXXO-mediated protein internalization and targeting to different post-Golgi compartments; and (c) YXXO- and LL-mediated targeting mechanisms use distinct saturable components.     

A strand exchange FRET assay for DNA

A new displacement hybridisation method is reported using a single strand DNA probe, labelled with an acceptor fluorophore (oregon green 488). Detection of double stranded sample target is shown, with discrimination between the probe, duplexed during the assay, and free single stranded probe DNA achieved through the FRET from a donor grove fluorophore (Hoechst 33258). A model for the kinetics of the displacement assay is presented and the course of the assay predicted according to probe/target ratios and sequence. The modelled predictions are consistent with the experimental data showing single base pair mismatch discrimination. The pattern of response according to the mismatch/perfect complement ratio in a mixed sample is also considered with an allele-discrimination ratio lying between the homozygous gene and total mismatch case, according to ratio. The assay is shown to be tolerant of different probe concentrations and ratios and through the dual wavelength recorded signals from donor and FRET acceptor, internal baseline correction is achieved with excellent noise reduction through ratiometric measurement.     

Dendritic cells distinguish individual chemokine signals through CCR7 and CXCR4

Dendritic cells (DCs) respond to chemotactic signals to migrate from sites of infection to secondary lymphoid organs where they initiate the adaptive immune response. The key chemokines directing their migration are CCL19, CCL21, and CXCL12, but how signals from these chemokines are integrated by migrating cells is poorly understood. Using a microfluidic device, we presented single and competing chemokine gradients to murine bone-marrow derived DCs in a controlled, time-invariant microenvironment. Experiments performed with counter-gradients revealed that CCL19 is 10-100-fold more potent than CCL21 or CXCL12. Interestingly, when the chemoattractive potencies of opposing gradients are matched, cells home to a central region in which the signals from multiple chemokines are balanced; in this region, cells are motile but display no net displacement. Actin and myosin inhibitors affected the speed of crawling but not directed motion, whereas pertussis toxin inhibited directed motion but not speed. These results provide fundamental insight into the processes that DCs use to migrate toward and position themselves within secondary lymphoid organs.     

Emphasizing Difficulties in the Detection of Rhythms with Lomb-Scargle Periodograms

The Lomb-Scargle periodogram was introduced in astrophysics to detect sinusoidal signals in noisy unevenly sampled time series. It proved to be a powerful tool in time series analysis and has recently been adapted in biomedical sciences. Its use is motivated by handling non-uniform data which is a common characteristic due to the restricted and irregular observations of, for instance, free-living animals. However, the observational data often contain fractions of non-Gaussian noise or may consist of periodic signals with non-sinusoidal shapes. These properties can make more difficult the interpretation of Lomb-Scargle periodograms and can lead to misleading estimates. In this letter we illustrate these difficulties for noise-free bimodal rhythms and sinusoidal signals with outliers. The examples are aimed to emphasize limitations and to complement the recent discussion on Lomb-Scargle periodograms.