Applying structure-from-motion habitat reconstruction and GIS terrain analysis to test hypotheses about nest-site selection by shorebirds

Habitat variables related to vegetation type and structure are routinely identified as important components of nest-site selection for birds. For ground-nesting birds, small-scale (< 0.5 m) microtopography may also play a role in nest-site selection through its effects on nest concealment and microclimate. Manual measurements of microtopography are challenging, time-consuming, and subject to user error. Ultrahigh-density point clouds generated using structure-from-motion (SfM) algorithms and photomosaics captured during Unmanned Aerial Vehicle (UAV) surveys can potentially provide detailed topographical measurements with less error. We used multiple indices of surface roughness to examine the effect of microtopography on nest site selection by White-rumped Sandpipers (Calidris fuscicollis) at East Bay Migratory Bird Sanctuary, Nunavut, Canada. We measured microtopography manually using the relative height index within a 1-m radius of used and unused sites. We generated three digital indices of surface roughness for 1-m and 5-m scales around nests and unused sites, including standard deviation of slope, slope variability, and 2D:3D area ratio. We compared the digital indices of used and unused sites at both spatial scales. Relative height of nearby hummocks was significantly lower at nests than at unused sites, indicating selection for flatter sites. Similarly, two of three digitally calculated terrain roughness indices were significantly lower at nests than unused sites at both the 1-m and 5-m scales. The 2D:3D ratio did not differ between nests and unused sites. Manual and UAV-derived measures were significantly correlated, but with substantial unexplained variation (Pearson’s r = 0.35–0.46). Our results suggest that White-rumped Sandpipers select nest sites in areas with low terrain roughness, potentially to increase their field of view to monitor approaching predators. We also demonstrate the applicability of SfM habitat reconstruction for testing hypotheses of small-scale habitat variables that may be impossible to study using traditional methods.     

Real-time measurement of repetitive micro bulk motion vector and motion noise removal in optical coherence tomography angiography

In this work, we developed a motion estimation and correction method which real-time obtained the direction and displacement of repetitive micro bulk motion (such as cardiac and respiratory motion) on an SS-OCT system without additional tracking hardware, and reduced the motion noise in optical coherence tomography angiography (OCTA). In the approach, the direction of repetitive micro bulk motion was considered fixed, and proportional relationships between the motion components in three directions were determined; Then we performed one-dimension cross-correlation to obtain depth displacement which was further used to obtain other two motion components, and greatly reduced the computation; The processing speed on a graphic processing unit was 478 pairs of B-Scans per second, and the measurement range was larger than the range of the angiogram-based methods. Lastly, corrupt angiograms were recovered by adaptive scan protocol, and reduced acquisition time in comparison with the previous work.     

Influence of thermal motion on 1H chemical shifts in proteins: the case of bovine pancreatic trypsin inhibitor.

The possible influence of thermal motion on 1H chemical shifts is discussed for a small stable protein, the bovine pancreatic Kunitz trypsin inhibitor (BPTI). The thermal effects on the aromatic side chains and on the backbone are treated separately. The thermal motion of the aromatic side chains is accounted for in terms of their rotation around the C(alpha)-C(beta) bond and the motion of each individual proton is interpreted as a ratio between the amount of ordered and quite disordered states. The influence of hydrogen bonds is introduced as an extra contribution to the chemical shifts of the bonded proton. Their contribution to the chemical shifts resulting from the polarization of the peptide bond is investigated, as is their influence on local flexibility. Finally, the relative importance of each contribution to the chemical shift information is compared.     

Anthropomorphic Design of the Human-Like Walking Robot

In this paper, we present a new concept of the mechanical design of a humanoid robot. The goal is to build a humanoid robot utilizing a new structure which is more suitable for human-like walking with the characteristics of the knee stretch, heel-contact, and toe-off. Inspired by human skeleton, we made an anthropomorphic pelvis for the humanoid robot. In comparison with conventional humanoid robots, with such the anthropomorphic pelvis, our robot is capable of adjusting the center of gravity of the upper body by the motion of pelvic tilt, thus reducing the required torque at the ankle joint and the velocity variations in human-like walking. With more precise analysis of the foot mechanism, the fixed-length inverted pendulum can be used to describe the dynamics of biped walking, thus preventing redundant works and power consumption in length variable inverted pendulum system. As the result of the new structure we propose, a humanoid robot is able to walk with human-like gait.     

Fundamental Differences in Visual Perceptual Learning between Children and Adults

1. Download : Download high-res image (157KB)
2. Download : Download full-size image

     

Non-stationary aging dynamics in ant societies

In recent experiments by Richardson et al. (2010) [Richardson, T.O., Robinson, E.J.H., Christensen, K., Jensen, H.J., Franks, N.R., Sendova-Franks, A.B., 2010. PLoS ONE 5, e9621.] ant motion out of the nest is shown to be a non-stationary process intriguingly similar to the dynamics encountered in physical aging of glassy systems. Specifically, exit events can be described as a Poisson process in logarithmic time, or, for short, a log-Poisson process. Nouvellet et al. (2010) [Nouvellet, P., Bacon, J.P.,Waxman, D., 2010. J. Theor. Biol. 266, 573.] criticized these conclusions and performed new experiments where the exit process could more simply be described by standard Poisson statistics. In their reply Richardson et al. (2011b) [Richardson, T.O., Robinson, E.J.H., Christensen, K., Jensen, J.H., Christensen, K., Jensen, H.J., Franks, N.R., Sendova-Franks, A.B., 2011b. J. Theor. Biol. 269, 356-358.] stressed that the two sets of experiments were performed under very different conditions and claimed that this was the likely source of the discrepancy. Ignoring any technical issues which are part of the above discussion, the focal point of this work is to ascertain whether or not both log-Poisson and Poisson statistics are possible in an ant society under different external conditions. To this end, a model is introduced where interacting ants move in a stochastic fashion from one site to a neighboring site on a finite 2D lattice. The probability of each move is determined by the ensuing changes of a utility function which is a sum of pairwise interactions between ants, weighted by distance. Depending on how the interactions are defined and on a control parameter dubbed ‘degree of stochasticity’ (DS), the dynamics either quickly converges to a stationary state, where movements are a standard Poisson process, or may enter a non-stationary regime, where exits can be described as suggested by Richardson et al. Other aspects of the model behavior are also discussed, i.e. the time dependence of the average value of the utility function, and the statistics of spatial re-arrangements happening anywhere in the system. Finally, we discuss the role of record events and their statistics in the context of ant societies and suggest the possibility that a transition from non-stationary to stationary dynamics can be triggered experimentally.     

Protein structural dynamics revealed by site-directed spin labeling and multifrequency EPR

Multifrequency electron paramagnetic resonance (EPR), combined with site-directed spin labeling, is a powerful spectroscopic tool to characterize protein dynamics. The lineshape of an EPR spectrum reflects combined rotational dynamics of the spin probe's local motion within a protein, reorientations of protein domains, and overall protein tumbling. All these motions can be restricted and anisotropic, and separation of these motions is important for thorough characterization of protein dynamics. Multifrequency EPR distinguishes between different motions of a spin-labeled protein, due to the frequency dependence of EPR resolution to fast and slow motion of a spin probe. This gives multifrequency EPR its unique capability to characterize protein dynamics in great detail. In this review, we analyze what makes multifrequency EPR sensitive to different rates of spin probe motion and discuss several examples of its usage to separate spin probe dynamics and overall protein dynamics, to characterize protein backbone dynamics, and to resolve protein conformational states.     

Piecewise Whittle estimator for trabecular bone radiograph characterization

Osteoporosis is a disease in which low bone mass and microarchitectural deterioration of bone tissue lead to increased bone fragility and a consequent increase in fracture risk. The objective of this paper is to develop and validate a new method to assess bone microarchitecture on radiographs. Taking into account the piecewise fractal nature of bone radiograph images, an appropriate fractal model (piecewise fractional Brownian motion) is used to characterize the trabecular bone network. Based on the Whittle estimator, a new method for calculating the Hurst exponent H is developed to better consider the piecewise fractal nature of the data. Different estimators are used and compared to the proposed method to discriminate two populations composed of healthy controls and osteoporotic patients. Our findings demonstrate that the new estimator proposed here provides effective results in terms of discrimination of the subjects and is better adapted to bone radiograph image analysis.     

A software platform for statistical evaluation of patient respiratory patterns in radiation therapy

AimThe aim of this work was to design and evaluate a software tool for analysis of a patient’s respiration, with the goal of optimizing the effectiveness of motion management techniques during radiotherapy imaging and treatment.Materials and methodsA software tool which analyses patient respiratory data files (.vxp files) created by the Varian Real-Time Position Management System (RPM) was developed to analyse patient respiratory data. The software, called RespAnalysis, was created in MATLAB and provides four modules, one each for determining respiration characteristics, providing breathing coaching (biofeedback training), comparing pre and post-training characteristics and performing a fraction-by-fraction assessment. The modules analyse respiratory traces to determine signal characteristics and specifically use a Sample Entropy algorithm as the key means to quantify breathing irregularity. Simulated respiratory signals, as well as 91 patient RPM traces were analysed with RespAnalysis to test the viability of using the Sample Entropy for predicting breathing regularity.ResultsRetrospective assessment of patient data demonstrated that the Sample Entropy metric was a predictor of periodic irregularity in respiration data, however, it was found to be insensitive to amplitude variation. Additional waveform statistics assessing the distribution of signal amplitudes over time coupled with Sample Entropy method were found to be useful in assessing breathing regularity.ConclusionsThe RespAnalysis software tool presented in this work uses the Sample Entropy method to analyse patient respiratory data recorded for motion management purposes in radiation therapy. This is applicable during treatment simulation and during subsequent treatment fractions, providing a way to quantify breathing irregularity, as well as assess the need for breathing coaching. It was demonstrated that the Sample Entropy metric was correlated to the irregularity of the patient’s respiratory motion in terms of periodicity, whilst other metrics, such as percentage deviation of inhale/exhale peak positions provided insight into respiratory amplitude regularity.     

Artificial extracellular matrix scaffolds of mobile molecules enhance maturation of human stem cell-derived neurons

1. Download : Download high-res image (218KB)
2. Download : Download full-size image