Stride lengths and stride frequencies of primates

Stride lengths and stride frequencies of primates have been observed or collected from the literature. Data for Galago , various monkeys and apes, and man have been collected. The quadrupedal primates take longer strides, at any particular speed, than would be predicted for non-primates. When they gallop they use lower stride frequencies than non-primates of equal mass.     

Laterality in the gallop gait of horses

Bilateral asymmetry in gallop stride limb contact patterns of four Quarter Horse fillies was documented by high-speed cinematography. Horses were filmed with rider by two cameras simultaneously while galloping along a straightaway. Even though signaled for each gallop lead an equivalent number of times, horses frequently switched leads, selecting the left lead nearly twice as often as the right. Velocities and stride lengths were greater for the left lead than the right, but stride frequencies did not differ between leads. Velocity effects were partitioned out in limb contact data analysis to enable the determination of persistent gallop stride asymmetries. The contact duration for the trailing (right) fore limb on the left lead exceeded the contact duration for the trailing (left) fore limb on the right lead. Selecting the right fore limb as the trailing fore limb may have allowed horses to use it to withstand the greater stresses and caused them to preferentially gallop with the left fore limb leading. Laterality may have an important influence on equine gallop motion patterns and thereby influence athletic performance.     

Phenotype prediction using regularized regression on genetic data in the DREAM5 Systems Genetics B Challenge

A major goal of large-scale genomics projects is to enable the use of data from high-throughput experimental methods to predict complex phenotypes such as disease susceptibility. The DREAM5 Systems Genetics B Challenge solicited algorithms to predict soybean plant resistance to the pathogen Phytophthora sojae from training sets including phenotype, genotype, and gene expression data. The challenge test set was divided into three subcategories, one requiring prediction based on only genotype data, another on only gene expression data, and the third on both genotype and gene expression data. Here we present our approach, primarily using regularized regression, which received the best-performer award for subchallenge B2 (gene expression only). We found that despite the availability of 941 genotype markers and 28,395 gene expression features, optimal models determined by cross-validation experiments typically used fewer than ten predictors, underscoring the importance of strong regularization in noisy datasets with far more features than samples. We also present substantial analysis of the training and test setup of the challenge, identifying high variance in performance on the gold standard test sets.     

Pattern recognition software and techniques for biological image analysis

The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays.     

Ambulatory estimation of foot placement during walking using inertial sensors

This study proposes a method to assess foot placement during walking using an ambulatory measurement system consisting of orthopaedic sandals equipped with force/moment sensors and inertial sensors (accelerometers and gyroscopes). Two parameters, lateral foot placement (LFP) and stride length (SL), were estimated for each foot separately during walking with eyes open (EO), and with eyes closed (EC) to analyze if the ambulatory system was able to discriminate between different walking conditions. For validation, the ambulatory measurement system was compared to a reference optical position measurement system (Optotrak). LFP and SL were obtained by integration of inertial sensor signals. To reduce the drift caused by integration, LFP and SL were defined with respect to an average walking path using a predefined number of strides. By varying this number of strides, it was shown that LFP and SL could be best estimated using three consecutive strides. LFP and SL estimated from the instrumented shoe signals and with the reference system showed good correspondence as indicated by the RMS difference between both measurement systems being 6.5±1.0 mm (mean ±standard deviation) for LFP, and 34.1±2.7 mm for SL. Additionally, a statistical analysis revealed that the ambulatory system was able to discriminate between the EO and EC condition, like the reference system. It is concluded that the ambulatory measurement system was able to reliably estimate foot placement during walking.     

Strategy quantification using body worn inertial sensors in a reactive agility task

Agility performance is often evaluated using time-based metrics, which provide little information about which factors aid or limit success. The objective of this study was to better understand agility strategy by identifying biomechanical metrics that were sensitive to performance speed, which were calculated with data from an array of body-worn inertial sensors. Five metrics were defined (normalized number of foot contacts, stride length variance, arm swing variance, mean normalized stride frequency, and number of body rotations) that corresponded to agility terms defined by experts working in athletic, clinical, and military environments. Eighteen participants donned 13 sensors to complete a reactive agility task, which involved navigating a set of cones in response to a vocal cue. Participants were grouped into fast, medium, and slow performance based on their completion time. Participants in the fast group had the smallest number of foot contacts (normalizing by height), highest stride length variance (normalizing by height), highest forearm angular velocity variance, and highest stride frequency (normalizing by height). The number of body rotations was not sensitive to speed and may have been determined by hand and foot dominance while completing the agility task. The results of this study have the potential to inform the development of a composite agility score constructed from the list of significant metrics. By quantifying the agility terms previously defined by expert evaluators through an agility score, this study can assist in strategy development for training and rehabilitation across athletic, clinical, and military domains.     

High-recall protein entity recognition using a dictionary

SUMMARY: Protein name extraction is an important step in mining biological literature. We describe two new methods for this task: semiCRFs and dictionary HMMs. SemiCRFs are a recently-proposed extension to conditional random fields (CRFs) that enables more effective use of dictionary information as features. Dictionary HMMs are a technique in which a dictionary is converted to a large HMM that recognizes phrases from the dictionary, as well as variations of these phrases. Standard training methods for HMMs can be used to learn which variants should be recognized. We compared the performance of our new approaches with that of Maximum Entropy (MaxEnt) and normal CRFs on three datasets, and improvement was obtained for all four methods over the best published results for two of the datasets. CRFs and semiCRFs achieved the highest overall performance according to the widely-used F-measure, while the dictionary HMMs performed the best at finding entities that actually appear in the dictionary-the measure of most interest in our intended application. AVAILABILITY: Dictionary HMMs were implemented in Java. Algorithms are available through an information extraction package MINORTHIRD on http://minorthird.sourceforge.net     

Stride length determination during overground running using a single foot-mounted inertial measurement unit

From a research perspective, detailed knowledge about stride length (SL) is important for coaches, clinicians and researchers because together with stride rate it determines the speed of locomotion. Moreover, individual SL vectors represent the integrated output of different biomechanical determinants and as such provide valuable insight into the control of running gait. In recent years, several studies have tried to estimate SL using body-mounted inertial measurement units (IMUs) and have reported promising results. However, many studies have used systems based on multiple sensors or have only focused on estimating SL for walking. Here we test the concurrent validity of a single foot-mounted, 9-degree of freedom IMU to estimate SL for running. We employed a running-specific, Kalman filter based zero-velocity update (ZUPT) algorithm to calculate individual SL vectors with the IMU and compared the results to SLs that were simultaneously recorded by a 6-camera 3D motion capture system. The results showed that the analytical procedures were able to successfully identify all strides that were recorded by the camera system and that excellent levels of absolute agreement (ICC(3,1) = 0.955) existed between the two methods. The findings demonstrate that individual SL vectors can be accurately estimated with a single foot-mounted IMU when running in a controlled laboratory setting.     

Predicting Classifier Performance with Limited Training Data: Applications to Computer-Aided Diagnosis in Breast and Prostate Cancer

Clinical trials increasingly employ medical imaging data in conjunction with supervised classifiers, where the latter require large amounts of training data to accurately model the system. Yet, a classifier selected at the start of the trial based on smaller and more accessible datasets may yield inaccurate and unstable classification performance. In this paper, we aim to address two common concerns in classifier selection for clinical trials: (1) predicting expected classifier performance for large datasets based on error rates calculated from smaller datasets and (2) the selection of appropriate classifiers based on expected performance for larger datasets. We present a framework for comparative evaluation of classifiers using only limited amounts of training data by using random repeated sampling (RRS) in conjunction with a cross-validation sampling strategy. Extrapolated error rates are subsequently validated via comparison with leave-one-out cross-validation performed on a larger dataset. The ability to predict error rates as dataset size increases is demonstrated on both synthetic data as well as three different computational imaging tasks: detecting cancerous image regions in prostate histopathology, differentiating high and low grade cancer in breast histopathology, and detecting cancerous metavoxels in prostate magnetic resonance spectroscopy. For each task, the relationships between 3 distinct classifiers (k-nearest neighbor, naive Bayes, Support Vector Machine) are explored. Further quantitative evaluation in terms of interquartile range (IQR) suggests that our approach consistently yields error rates with lower variability (mean IQRs of 0.0070, 0.0127, and 0.0140) than a traditional RRS approach (mean IQRs of 0.0297, 0.0779, and 0.305) that does not employ cross-validation sampling for all three datasets.     

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions

Background

It is important to accurately determine the performance of peptide:MHC binding predictions, as this enables users to compare and choose between different prediction methods and provides estimates of the expected error rate. Two common approaches to determine prediction performance are cross-validation, in which all available data are iteratively split into training and testing data, and the use of blind sets generated separately from the data used to construct the predictive method. In the present study, we have compared cross-validated prediction performances generated on our last benchmark dataset from 2009 with prediction performances generated on data subsequently added to the Immune Epitope Database (IEDB) which served as a blind set.

Results

We found that cross-validated performances systematically overestimated performance on the blind set. This was found not to be due to the presence of similar peptides in the cross-validation dataset. Rather, we found that small size and low sequence/affinity diversity of either training or blind datasets were associated with large differences in cross-validated vs. blind prediction performances. We use these findings to derive quantitative rules of how large and diverse datasets need to be to provide generalizable performance estimates.

Conclusion

It has long been known that cross-validated prediction performance estimates often overestimate performance on independently generated blind set data. We here identify and quantify the specific factors contributing to this effect for MHC-I binding predictions. An increasing number of peptides for which MHC binding affinities are measured experimentally have been selected based on binding predictions and thus are less diverse than historic datasets sampling the entire sequence and affinity space, making them more difficult benchmark data sets. This has to be taken into account when comparing performance metrics between different benchmarks, and when deriving error estimates for predictions based on benchmark performance.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-241) contains supplementary material, which is available to authorized users.     

An analysis of protein folding type prediction by seed-propagated sampling and jackknife test

In the development of methodology for statistical prediction of protein folding types, how to test the predicted results is a crucial problem. In addition to the resubstitution test in which the folding type of each protein from a training set is predicted based on the rules derived from the same set, cross-validation tests are needed. Among them, the single-testset method seems to be least reliable due to the arbitrariness in selecting the test set. Although the leaving-one-out (or jackknife) test is more objective and hence more reliable, it may cause a severe information loss by leaving a protein in turn out of the training set when its size is not large enough. In order to overcome the above drawback, a seed-propagated sampling approach is proposed that can be used to generate any number of simulated proteins with a desired type based on a given training set database. There is no need to make any predetermined assumption about the statistical distribution function of the amino acid frequencies. Combined with the existing cross-validation methods, the new technique may provide a more objective estimation for various protein-folding-type prediction methods.     

The influence of inertial sensor sampling frequency on the accuracy of measurement parameters in rearfoot running

Increasingly, inertial sensors are being used for running analyses. The aim of this study was to systematically investigate the influence of inertial sensor sampling frequencies (SF) on the accuracy of kinematic, spatio-temporal, and kinetic parameters. We hypothesized that running analyses at lower SF result in less signal information and therefore the inability to sufficiently interpret measurement data. Twenty-one subjects participated in this study. Rearfoot strikers ran on an indoor running track at a velocity of 3.5 ± 0.1 ms^?1. A uniaxial accelerometer was attached at the tibia and an inertial measurement unit was mounted at the heel of the right shoe. All sensors were synchronized at the start and data was measured with 1000 Hz (reference SF). Datasets were reduced to 500, 333, 250, 200, and 100 Hz in post-processing. The results of this study showed that a minimum SF of 500 Hz should be used to accurately measure kinetic parameters (e.g. peak heel acceleration). In contrast, stride length showed accurate results even at 333 Hz. 200 Hz were required to calculate parameters accurately for peak tibial acceleration, stride duration, and all kinematic measurements. The information from this study is necessary to correctly interpret measurement data of existing investigations and to plan future studies.     

Muscle activity in rat locomotion: movement analysis and electromyography of the flexors and extensors of the elbow.

Footfall patterns and time sequence of activity are described for white rats conditioned to run freely in an activity wheel (which they drive). Motion is described in terms of soft contact, hard contact, soft contact, and flip phases. Duration of stride decreases and length of stride increases from walk to trot to canter to gallop. Myographic analysis shows that the brachialis has a major tonic function after it fires strongly during the flip phase and during much of the hard contact phase. Animals running at canter or gallop show major asymmetries between forelimb muscles on the first paw and on the lead paw sides.     

Analysis of the spatio-temporal parameters of gaits in Dasypus novemcinctus (Xenarthra: Dasypodidae)

Armadillos comprise a particular group of armoured animals whose functional morphology of locomotion remains unclear. For the first time, the kinematic patterns of Dasypus novemcinctus are analysed. Eight specimens of nine-banded armadillos were studied at a research institute in São Paulo State, Brazil. The individuals were induced to cross a horizontal corridor and each gait performed during the time each of them was kept inside this structure was recorded to a detailed analysis posteriorly performed in a computer program. Four parameters regarding speed range were considered: stride frequency (Hz) (1/stride period), stride length (m), speed (ms⁻¹) and duty factor (%). A total of 89 strides have been analysed among symmetrical (60.6%) and asymmetrical gaits (39.4%), and six footfall patterns were here reported as follows: lateral sequences (symmetrical), transverse gallop, canter, bound, half-bound and crutch walk (asymmetrical). This kind of analysis implements our knowledge on the locomotory aspects of these animals, hence contributing to the improvement of our knowledge on this still poorly known group.     

Estimation of stride length in level walking using an inertial measurement unit attached to the foot: a validation of the zero velocity assumption during stance

In a variety of applications, inertial sensors are used to estimate spatial parameters by double integrating over time their coordinate acceleration components. In human movement applications, the drift inherent to the accelerometer signals is often reduced by exploiting the cyclical nature of gait and under the hypothesis that the velocity of the sensor is zero at some point in stance. In this study, the validity of the latter hypothesis was investigated by determining the minimum velocity of progression of selected points of the foot and shank during the stance phase of the gait cycle while walking at three different speeds on level ground. The errors affecting the accuracy of the stride length estimation resulting from assuming a zero velocity at the beginning of the integration interval were evaluated on twenty healthy subjects. Results showed that the minimum velocity of the selected points on the foot and shank increased as gait speed increased. Whereas the average minimum velocity of the foot locations was lower than 0.011 m/s, the velocity of the shank locations were up to 0.049 m/s corresponding to a percent error of the stride length equal to 3.3%. The preferable foot locations for an inertial sensor resulted to be the calcaneus and the lateral aspect of the rearfoot. In estimating the stride length, the hypothesis that the velocity of the sensor can be set to zero sometimes during stance is acceptable only if the sensor is attached to the foot.     

HMMConverter 1.0: a toolbox for hidden Markov models

Hidden Markov models (HMMs) and their variants are widely used in Bioinformatics applications that analyze and compare biological sequences. Designing a novel application requires the insight of a human expert to define the model''s architecture. The implementation of prediction algorithms and algorithms to train the model''s parameters, however, can be a time-consuming and error-prone task. We here present HMMConverter, a software package for setting up probabilistic HMMs, pair-HMMs as well as generalized HMMs and pair-HMMs. The user defines the model itself and the algorithms to be used via an XML file which is then directly translated into efficient C++ code. The software package provides linear-memory prediction algorithms, such as the Hirschberg algorithm, banding and the integration of prior probabilities and is the first to present computationally efficient linear-memory algorithms for automatic parameter training. Users of HMMConverter can thus set up complex applications with a minimum of effort and also perform parameter training and data analyses for large data sets.     

Stride length and its determinants in humans, early hominids, primates, and mammals

Primate stride lengths during quadrupedal locomotion are very long when compared to those of nonprimate quadrupedal mammals at the speed of trot/gallop transition. These exceptional lengths are a consequence of the relatively long limbs of primates and the large angular excursions of their limbs during quadrupedalism. When quadrupedal primates employ bipedal gaits they exhibit much lower angular excursions. Consequently their bipedal stride lengths do not appear to be exceptional in length when compared to other mammals. Angular excursions of the lower limbs of modern humans are not exceptionally large. However, when running, humans exhibit relatively long periods of flight (i.e., they have low duty factors) when compared to other mammals including primates. Because of these long periods of flight and their relative long lower limbs, humans have running stride lengths that are at the lower end of the range of stride lengths of quadrupedal primates. The stride length of the Laetoli hominid trails are evaluated in this context.     

Unsupervised segmentation of continuous genomic data

The advent of high-density, high-volume genomic data has created the need for tools to summarize large datasets at multiple scales. HMMSeg is a command-line utility for the scale-specific segmentation of continuous genomic data using hidden Markov models (HMMs). Scale specificity is achieved by an optional wavelet-based smoothing operation. HMMSeg is capable of handling multiple datasets simultaneously, rendering it ideal for integrative analysis of expression, phylogenetic and functional genomic data. AVAILABILITY: http://noble.gs.washington.edu/proj/hmmseg     

Walking at the preferred stride frequency maximizes local dynamic stability of knee motion

Healthy humans display a preference for walking at a stride frequency dependent on the inertial properties of their legs. Walking at preferred stride frequency (PSF) is predicted to maximize local dynamic stability, whereby sensitivity to intrinsic perturbations arising from natural variability inherent in biological motion is minimized. Previous studies testing this prediction have employed different variability measures, but none have directly quantified local dynamic stability by computing maximum finite-time Lyapunov exponent (λ^Max), which quantifies the rate of divergence of nearby trajectories in state space. Here, ten healthy adults walked 45 m overground while sagittal motion of both knees was recorded via electrogoniometers. An auditory metronome prescribed 7 different frequencies relative to each individual's PSF (PSF; ±5, ±10, ±15 strides/min). Stride frequencies were performed under both freely adopted speed (FS) and controlled speed (CS: set at the speed of PSF trials) conditions. Local dynamic stability was maximal (λ^Max was minimal) at the PSF, becoming less stable for higher and lower stride frequencies. This occurred under both FS and CS conditions, although controlling speed further reduced local dynamic stability at non-preferred stride frequencies. In contrast, measures of variability revealed effects of stride frequency and speed conditions that were distinct from λ^Max. In particular, movement regularity computed by approximate entropy (ApEn) increased for slower walking speeds, appearing to depend on speed rather than stride frequency. The cadence freely adopted by humans has the benefit of maximizing local dynamic stability, which can be interpreted as humans tuning to their resonant frequency of walking.