A Comparison of Three Methods for Measure of Time to Contact

International audienceTime to Contact (TTC) is a biologically inspired method for obstacle detection and reactive control of motion that does not require scene reconstruction or 3D depth estimation. Estimating TTC is difficult because it requires a stable and reliable estimate of the rate of change of distance between image features. In this paper we propose a new method to measure time to contact, Active Contour Affine Scale (ACAS). We experimentally and analytically compare ACAS with two other recently proposed methods: Scale Invariant Ridge Segments (SIRS), and Image Brightness Derivatives (IBD). Our results show that ACAS provides a more accurate estimation of TTC when the image flow may be approximated by an affine transformation, while SIRS provides an estimate that is generally valid, but may not always be as accurate as ACAS, and IBD systematically over-estimate time to contact

Using stiffness to assess injury risk:comparison of methods for quantifying stiffness and their reliability in triathletes

Background: A review of the literature has indicated that lower body stiffness, defined as the extent to which the lower extremity joints resists deformation upon contact with the ground, may be a useful measure for assessing Achilles injury risk in triathletes. The nature of overuse injuries suggests that a variety of different movement patterns could conceivably contribute to the final injury outcome, any number and combination of which might be observed in a single individual. Measurements which incorporate both kinetics and kinematics (such as stiffness) of a movement may be better able to shed light on individuals at risk of injury, with further analysis then providing the exact mechanism of injury for the individual. Stiffness can be measured as vertical, leg or joint stiffness to model how the individual interacts with the environment upon landing. However, several issues with stiffness assessments limit the effectiveness of these measures to monitor athletes’ performance and/or injury risk. This may reflect the variety of common biomechanical stiffness calculations (dynamic, time, true leg and joint) that have been used to examine these three stiffness levels (vertical, leg and joint) across a variety of human movements (i.e. running or hopping) as well as potential issues with the reliability of these measures, especially joint stiffness. Therefore, the aims of this study were to provide a comparison of the various methods for measuring stiffness during two forms of human bouncing locomotion (running and hopping) along with the measurement reliability to determine the best methods to assess links with injury risk in triathletes. Methods: Vertical, leg and joint stiffness were estimated in 12 healthy male competitive triathletes on two occasions, 7 days apart, using both running at 5.0 ms−1 and hopping (2.2 Hz) tasks. Results: Inter-day reliability was good for vertical (ICC = 0.85) and leg (ICC = 0.98) stiffness using the time method. Joint stiffness reliability was poor when assessed individually. Reliability was improved when taken as the sum of the hip, knee and ankle (ICC = 0.86). The knee and ankle combination provided the best correlation with leg stiffness during running (Pearson’s Correlation = 0.82). Discussion: The dynamic and time methods of calculating leg stiffness had better reliability than the “true” method. The time and dynamic methods had the best correlation with the different combinations of joint stiffness, which suggests that they should be considered for biomechanical screening of triathletes. The knee and ankle combination had the best correlation with leg stiffness and is therefore proposed to provide the most information regarding lower limb mechanics during gait in triathletes

The validity and reliability of the my jump 2 app for measuring the reactive strength index and drop jump performance.

BACKGROUND: This is the first study to independently assess the concurrent validity and reliability of the My Jump 2 app for measuring drop jump performance. It is also the first to evaluate the app's ability to measure the reactive strength index (RSI). METHODS: Fourteen male sport science students (age: 29.5±9.9 years) performed three drop jumps from 20 cm and 40 cm (totaling 84 jumps), assessed via a force platform and the My Jump 2 app. Reported metrics included reactive strength index, jump height, ground contact time, and mean power. Measurements from both devices were compared using the intraclass correlation coefficient (ICC), Pearson product moment correlation coefficient (r), Cronbach's alpha (α), coefficient of variation (CV) and Bland-Altman plots. RESULTS: Near perfect agreement was seen between devices at 20 cm for RSI (ICC=0.95) and contact time (ICC=0.99) and at 40 cm for RSI (ICC=0.98), jump height (ICC=0.96) and contact time (ICC=0.92); with very strong agreement seen at 20 cm for jump height (ICC=0.80). In comparison with the force plate the app showed good validity for RSI (20 cm: r=0.94; 40 cm; r=0.97), jump height (20 cm: r=0.80; 40 cm; r=0.96) and contact time (20 cm=0.96; 40 cm; r=0.98). CONCLUSIONS: The results of the present study show that the My Jump 2 app is a valid and reliable tool for assessing drop jump performance

A simple and fast heuristic for protein structure comparison

Background Protein structure comparison is a key problem in bioinformatics. There exist several methods for doing protein comparison, being the solution of the Maximum Contact Map Overlap problem (MAX-CMO) one of the alternatives available. Although this problem may be solved using exact algorithms, researchers require approximate algorithms that obtain good quality solutions using less computational resources than the formers. Results We propose a variable neighborhood search metaheuristic for solving MAX-CMO. We analyze this strategy in two aspects: 1) from an optimization point of view the strategy is tested on two different datasets, obtaining an error of 3.5%(over 2702 pairs) and 1.7% (over 161 pairs) with respect to optimal values; thus leading to high accurate solutions in a simpler and less expensive way than exact algorithms; 2) in terms of protein structure classification, we conduct experiments on three datasets and show that is feasible to detect structural similarities at SCOP's family and CATH's architecture levels using normalized overlap values. Some limitations and the role of normalization are outlined for doing classification at SCOP's fold level. Conclusion We designed, implemented and tested.a new tool for solving MAX-CMO, based on a well-known metaheuristic technique. The good balance between solution's quality and computational effort makes it a valuable tool. Moreover, to the best of our knowledge, this is the first time the MAX-CMO measure is tested at SCOP's fold and CATH's architecture levels with encouraging results. Software is available for download at http://modo.ugr.es/jrgonzalez/msvns4maxcmo webcite.This work is supported by Projects HeuriCosc TIN2005-08404-C04-01, HeuriCode TIN2005-08404-C04-03, both from the Spanish Ministry of Education and Science. JRG acknowledges financial support from Project TIC2002-04242-C03-02. Authors thank N. Krasnogor and ProCKSi project (BB/C511764/1) for their support

Nondestructive Multivariate Classification of Codling Moth Infested Apples Using Machine Learning and Sensor Fusion

Apple is the number one on the list of the most consumed fruits in the United States. The increasing market demand for high quality apples and the need for fast, and effective quality evaluation techniques have prompted research into the development of nondestructive evaluation methods. Codling moth (CM), Cydia pomonella L. (Lepidoptera: Tortricidae), is the most devastating pest of apples. Therefore, this dissertation is focused on the development of nondestructive methods for the detection and classification of CM-infested apples. The objective one in this study was aimed to identify and characterize the source of detectable vibro-acoustic signals coming from CM-infested apples. A novel approach was developed to correlate the larval activities to low-frequency vibro-acoustic signals, by capturing the larval activities using a digital camera while simultaneously registering the signal patterns observed in the contact piezoelectric sensors on apple surface. While the larva crawling was characterized by the low amplitude and higher frequency (around 4 Hz) signals, the chewing signals had greater amplitude and lower frequency (around 1 Hz). In objective two and three, vibro-acoustic and acoustic impulse methods were developed to classify CM-infested and healthy apples. In the first approach, the identified vibro-acoustic patterns from the infested apples were used for the classification of the CM-infested and healthy signal data. The classification accuracy was as high as 95.94% for 5 s signaling time. For the acoustic impulse method, a knocking test was performed to measure the vibration/acoustic response of the infested apple fruit to a pre-defined impulse in comparison to that of a healthy sample. The classification rate obtained was 99% for a short signaling time of 60-80 ms. In objective four, shortwave near infrared hyperspectral imaging (SWNIR HSI) in the wavelength range of 900-1700 nm was applied to detect CM infestation at the pixel level for the three apple cultivars reaching an accuracy of up to 97.4%. In objective five, the physicochemical characteristics of apples were predicted using HSI method. The results showed the correlation coefficients of prediction (Rp) up to 0.90, 0.93, 0.97, and 0.91 for SSC, firmness, pH and moisture content, respectively. Furthermore, the effect of long-term storage (20 weeks) at three different storage conditions (0 °C, 4 °C, and 10 °C) on CM infestation and the detectability of the infested apples was studied. At a constant storage temperature the detectability of infested samples remained the same for the first three months then improved in the fourth month followed by a decrease until the end of the storage. Finally, a sensor data fusion method was developed which showed an improvement in the classification performance compared to the individual methods. These findings indicated there is a high potential of acoustic and NIR HSI methods for detecting and classifying CM infestation in different apple cultivars

Gas injection in fractured reservoirs : emphasis on mass transfer

Mass transfer occurs in a number of Enhanced Oil Recovery (EOR) processes such as gas injection, solvent injection, Water Alternative Gas injection (WAG) processes and gas cycling. The role of mass transfer in gas injection into an oil phase at fractured media is significant. In naturally fractured reservoirs, fluid exists in two interconnected systems; the rock matrix, which contains the bulk of the volume of the oil reservoir, and the high permeability fractures medium.Laboratory measurements of the diffusion coefficient of methane into crude oil under both unsteady-state and steady-state conditions were carried out to obtain the dissolution rates of methane during gas injection and/or flooding in the short term, and for enhanced oil recovery at thermodynamic equilibrium in the long term. The pressure drop in the core flooding cell during the contact of the methane and oil phases was used to measure the diffusion coefficient of the system under the reservoir conditions. A new empirical correlation for the diffusion coefficient was achieved using the measured experimental data at reservoir conditions. A comparison of this new correlation and previous methods shows that the current method is more accurate than other methods at high pressure and temperature conditions.Experimental tests on fluid flow in tight carbonate porous media were carried out with single and composite core plugs. It was demonstrated that the swelling of oil strongly depended on the contact time of the oil and gas phases and heterogeneity of the system.The two and three-phase relative permeability in tight carbonate reservoirs was a major part of this research. It was carried out on single and composite core plugs at reservoir conditions. Modelling of the displacement of fluids in tight carbonate rocks was carried out with experimental data. Solving of the partial differential equation of displacement phenomena in porous media was carried out with the finite element method software (FLEXPDE). All of the experimental data with the new diffusion coefficient correlation were used to model the system.In the fracture medium, an artificial fracture in synthetic rock was made and all the parameters used for carbonate rock were considered without fracture. Modelling of the system was carried out between the matrix and fracture medium. The effect of mass transfer between gas in the fracture and oil in the matrix was evaluated and the variation of saturation in the matrix by applying the boundary condition method was evaluated. As a result, it was shown that the mass transfer significantly increased the recovery from the matrix by following the condensation and evaporation mechanisms

Residual Stress in Wheels: Comparison of Neutron Diffraction and Ultrasonic Methods, with Trends in RCF

The critical damage mechanism on many GB passenger train wheels is Rolling Contact Fatigue (RCF) cracking in the rim. Evidence from field observations suggests that RCF damage occurs much more quickly as the wheelsets near the end of their life. Wheel manufacturing processes induce a compressive hoop stress in the wheel rim; variations in residual stress through the life of a wheel may influence the observed RCF damage rates. This paper describes experiments to measure residual stresses in new and used wheel rims to identify whether this could be a significant factor, and compares the findings from neutron diffraction and ultrasonic birefringence methods. The scope goes beyond previous applications of neutron diffraction to railway wheels and identifies key considerations for future testing. Assuming that the as-manufactured stress distribution was similar for all three wheels tested, it is found that the stresses are redistributed within the wheel rim during its life as material is removed and plastic flow occurs. However, the hoop stress near the running surface remains compressive and may not have a large influence on the RCF damage rates

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/.Comment: Accepted by both RECOMB 2014 and PLOS Computational Biolog

Four-point probe measurements using current probes with voltage feedback to measure electric potentials

We present a four-point probe resistance measurement technique which uses four equivalent current measuring units, resulting in minimal hardware requirements and corresponding sources of noise. Local sample potentials are measured by a software feedback loop which adjusts the corresponding tip voltage such that no current flows to the sample. The resulting tip voltage is then equivalent to the sample potential at the tip position. We implement this measurement method into a multi-tip scanning tunneling microscope setup such that potentials can also be measured in tunneling contact, allowing in principle truly non-invasive four-probe measurements. The resulting measurement capabilities are demonstrated for BiSbTe$_3$ and Si$(111)-(7\times7)$ samples

Compensating for population sampling in simulations of epidemic spread on temporal contact networks

Data describing human interactions often suffer from incomplete sampling of the underlying population. As a consequence, the study of contagion processes using data-driven models can lead to a severe underestimation of the epidemic risk. Here we present a systematic method to alleviate this issue and obtain a better estimation of the risk in the context of epidemic models informed by high-resolution time-resolved contact data. We consider several such data sets collected in various contexts and perform controlled resampling experiments. We show how the statistical information contained in the resampled data can be used to build a series of surrogate versions of the unknown contacts. We simulate epidemic processes on the resulting reconstructed data sets and show that it is possible to obtain good estimates of the outcome of simulations performed using the complete data set. We discuss limitations and potential improvements of our method