A soft tissue artefact model driven by proximal and distal joint kinematics

When analysing human movement through stereophotogrammetry, skin-markers are used. Their movement relative to the underlying bone is known as a soft tissue artefact (STA). A mathematical model to estimate subject- and marker-specific STAs generated during a given motor task, is required for both skeletal kinematic estimators and comparative assessment using simulation. This study devises and assesses such a mathematical model using the paradigmatic case of thigh STAs. The model was based on two hypotheses: (1) that the artefact mostly depends on skin sliding, and thus on the angles of hip and knee; (2) that the relevant relationship is linear. These hypotheses were tested using data obtained from passive hip and knee movements in non-obese specimens and from running volunteers endowed with both skin- and pin-markers.     

Auditory evoked potentials for the assessment of depth of anaesthesia: different configurations of artefact detection algorithms.

Monitoring the depth of anaesthesia has become an important research topic in the field of biosignal processing. Auditory evoked potentials (AEPs) have been shown to be a promising tool for this purpose. Signals recorded in the noisy environment of an operating theatre are often contaminated by artefacts. Thus, artefact detection and elimination in the underlying electroencephalogram (EEG) are mandatory before AEP extraction. Determination of a suitable artefact detection configuration based on EEG data from a clinical study is described. Artefact detection algorithms and an AEP extraction procedure encompassing the artefact detection results are presented. Different configurations of artefact detection algorithms are evaluated using an AEP verification procedure and support vector machines to determine a suitable configuration for the assessment of depth of anaesthesia using AEPs.     

Proximal placement of lateral thigh skin markers reduces soft tissue artefact during normal gait using the Conventional Gait Model

A primary source of measurement error in gait analysis is soft-tissue artefact. Hip and knee angle measurements, regularly used in clinical decision-making, are particularly prone to pervasive soft tissue on the femur. However, despite several studies of thigh marker artefact it remains unclear how lateral thigh marker height affects results using variants of the Conventional Gait Model. We compared Vicon Plug-in Gait hip and knee angle estimates during gait using a proximal and distal thigh marker placement for ten healthy subjects. Knee axes were estimated by optimizing thigh rotation offsets to minimize knee varus-valgus range during gait. Relative to the distal marker, the proximal marker produced 37% less varus-valgus range and 50% less hip rotation range (p < 0.001), suggesting that it produced less soft-tissue artefact in knee axis estimates. The thigh markers also produced different secondary effects on the knee centre estimate. Using whole gait cycle optimization, the distal marker showed greater minimum and maximum knee flexion (by 6° and 2° respectively) resulting in a 4° reduction in range. Mid-stance optimization reduced distal marker knee flexion by 5° throughout, but proximal marker results were negligibly affected. Based on an analysis of the Plug-in Gait knee axis definition, we show that the proximal marker reduced sensitivity to soft-tissue artefact by decreasing collinearity between the points defining the femoral frontal plane and reducing anteroposterior movement between the knee and thigh markers. This study suggests that a proximal thigh marker may be preferable when performing gait analysis using the Plug-in Gait model.     

CAT & MAUS: A novel system for true dynamic motion measurement of underlying bony structures with compensation for soft tissue movement

Optoelectronic motion capture systems are widely employed to measure the movement of human joints. However, there can be a significant discrepancy between the data obtained by a motion capture system (MCS) and the actual movement of underlying bony structures, which is attributed to soft tissue artefact. In this paper, a computer-aided tracking and motion analysis with ultrasound (CAT & MAUS) system with an augmented globally optimal registration algorithm is presented to dynamically track the underlying bony structure during movement. The augmented registration part of CAT & MAUS was validated with a high system accuracy of 80%. The Euclidean distance between the marker-based bony landmark and the bony landmark tracked by CAT & MAUS was calculated to quantify the measurement error of an MCS caused by soft tissue artefact during movement. The average Euclidean distance between the target bony landmark measured by each of the CAT & MAUS system and the MCS alone varied from 8.32 mm to 16.87 mm in gait. This indicates the discrepancy between the MCS measured bony landmark and the actual underlying bony landmark. Moreover, Procrustes analysis was applied to demonstrate that CAT & MAUS reduces the deformation of the body segment shape modeled by markers during motion. The augmented CAT & MAUS system shows its potential to dynamically detect and locate actual underlying bony landmarks, which reduces the MCS measurement error caused by soft tissue artefact during movement.     

Tendon conditioning: artefact or property?

Isolated tendons subjected to cyclic tensile loads higher than those experienced in the tendons' recent history exhibit 'conditioning', i.e. gradually increasing elongations upon loading and gradually increasing residual elongations after unloading in the first few loading-unloading cycles. The present study examines whether this behaviour is a measurement artefact or an actual time-dependent property. The gastrocnemius tendons of six men who refrained from rigorous physical activities prior to the experiment were loaded cyclically by 10 repeated isometric plantarflexion contractions at 80% of the moment generated during plantarflexion maximal voluntary contraction (MVC). In each contraction, the elongation of the gastrocnemius tendon at 80% of MVC and the residual tendon elongation after relaxation were obtained from the analysis of sonographs recorded during the test. The tendon elongation during activation and the residual tendon elongation after relaxation increased by ca. 5 mm from the first contraction to the tenth contraction, with no changes obtained after the fifth contraction. The behaviour of the tendon in the first five contractions indicates the presence of conditioning. It is therefore concluded that conditioning is a relevant property and not an artefact associated with in vitro testing. This has implications for joint kinematics and muscle excursion.     

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics

In the context of exponential growing molecular databases, it becomes increasingly easy to assemble large multigene data sets for phylogenomic studies. The expected increase of resolution due to the reduction of the sampling (stochastic) error is becoming a reality. However, the impact of systematic biases will also become more apparent or even dominant. We have chosen to study the case of the long-branch attraction artefact (LBA) using real instead of simulated sequences. Two fast-evolving eukaryotic lineages, whose evolutionary positions are well established, microsporidia and the nucleomorph of cryptophytes, were chosen as model species. A large data set was assembled (44 species, 133 genes, and 24,294 amino acid positions) and the resulting rooted eukaryotic phylogeny (using a distant archaeal outgroup) is positively misled by an LBA artefact despite the use of a maximum likelihood-based tree reconstruction method with a complex model of sequence evolution. When the fastest evolving proteins from the fast lineages are progressively removed (up to 90%), the bootstrap support for the apparently artefactual basal placement decreases to virtually 0%, and conversely only the expected placement, among all the possible locations of the fast-evolving species, receives increasing support that eventually converges to 100%. The percentage of removal of the fastest evolving proteins constitutes a reliable estimate of the sensitivity of phylogenetic inference to LBA. This protocol confirms that both a rich species sampling (especially the presence of a species that is closely related to the fast-evolving lineage) and a probabilistic method with a complex model are important to overcome the LBA artefact. Finally, we observed that phylogenetic inference methods perform strikingly better with simulated as opposed to real data, and suggest that testing the reliability of phylogenetic inference methods with simulated data leads to overconfidence in their performance. Although phylogenomic studies can be affected by systematic biases, the possibility of discarding a large amount of data containing most of the nonphylogenetic signal allows recovering a phylogeny that is less affected by systematic biases, while maintaining a high statistical support.     

Lateral bud development and shoot growth in low-pruned Morus alba as affected by stem orientation

Two phases of bud activity were identified in the new growth of one-year-old erect coppice shoots on 11-year-old low-pruned stumps of mulberry (Morus alba L. cv. Shin-ichinose) in spring, the sprouting phase in which the majority of the buds, including the basal ones, sprout and elongate, and the dominance phase (starting 4–5 weeks after sprouting) during which the upper laterals begin to assert dominance and suppress the growth of lower laterals, becoming new leading shoots. In contrast, arching before sprouting markedly inhibited buds on the under side, leading to poor shoots. By late April, the sprouts on the upper side grew readily into new erect shoots, resulting in considerable dominance over those from the lateral sides. Of these erect shoots, those located closer to the stem base grew more in May and June. The effects of arching made during the sprouting phase (late April) on bud activity and shoot lengths were generally similar to those of earlier archings before spring bud bursting. Separation of the shoots from the upper and under sides by longitudinal, horizontal splitting of the arched stems in late April did not affect the inhibited elongation of the shoots from the under side. These results suggest that in the response to arching before and in late April, the effects are related to spring bud bursting and gravimorphism. In contrast, arching during and after the dominance phase (May) had no gravimorphic effects on growth of the shoots on the upper side, although there was a stimulation of outbreak of the buds on the upper side, which remained dormant during spring bud bursting. Continuous basal applications of abscisic acid in aqueous solution inhibited bud break and shoot growth of the postdormant erect stem segments, and defoliation of the new shoots markedly. In contrast, similar applications of an ethylene-releasing compound, Ethephon, depressed shoot elongation slightly, but enhanced defoliation greatly. Gibberellic acid (GA₃) stimulated shoot elongation, but depressed leaf enlargement.     

A novel specific edge effect correction method for RNA interference screenings

MOTIVATION: High-throughput screening (HTS) is an important method in drug discovery in which the activities of a large number of candidate chemicals or genetic materials are rapidly evaluated. Data are usually obtained by measurements on samples in microwell plates and are often subjected to artefacts that can bias the result selection. We report here a novel edge effect correction algorithm suitable for RNA interference (RNAi) screening, because its normalization does not rely on the entire dataset and takes into account the specificities of such a screening process. The proposed method is able to estimate the edge effects for each assay plate individually using the data from a single control column based on diffusion model, and thus targeting a specific but recurrent well-known HTS artefact. This method was first developed and validated using control plates and was then applied to the correction of experimental data generated during a genome-wide siRNA screen aimed at studying HIV-host interactions. The proposed algorithm was able to correct the edge effect biasing the control data and thus improve assay quality and, consequently, the hit-selection step.     

Cell Lysis Due to Ultrasound Gel In Fine Needle Aspirates; an Important New Artefact In Cytology

An important new artefact in cytopathology is described. the initial observation of the artefact followed contamination of a breast fine needle aspiration (FNA) sample by ultrasound gel which was used to localize the lesion. the changes proved reproducible ex vivo. the changes varied depending on the conditions and degree of contamination, and ranged from cell swelling to leakage of nuclear chromatin and cell lysis. This artefact is discussed in the context of other major sources of cytology artefact. Pathologists and radiologists should beware of the detrimental effects of ultrasound gel on cytology specimens.     

To what extent is joint and muscle mechanics predicted by musculoskeletal models sensitive to soft tissue artefacts?

Musculoskeletal models are widely used to estimate joint kinematics, intersegmental loads, and muscle and joint contact forces during movement. These estimates can be heavily affected by the soft tissue artefact (STA) when input positional data are obtained using stereophotogrammetry, but this aspect has not yet been fully characterised for muscle and joint forces. This study aims to assess the sensitivity to the STA of three open-source musculoskeletal models, implemented in OpenSim.A baseline dataset of marker trajectories was created for each model from experimental data of one healthy volunteer. Five hundred STA realizations were then statistically generated using a marker-dependent model of the pelvis and lower limb artefact and added to the baseline data. The STA׳s impact on the musculoskeletal model estimates was finally quantified using a Monte Carlo analysis.The modelled STA distributions were in line with the literature. Observed output variations were comparable across the three models, and sensitivity to the STA was evident for most investigated quantities. Shape, magnitude and timing of the joint angle and moment time histories were not significantly affected throughout the entire gait cycle, whereas magnitude variations were observed for muscle and joint forces. Ranges of contact force variations differed between joints, with hip variations up to 1.8 times body weight observed. Variations of more than 30% were observed for some of the muscle forces.In conclusion, musculoskeletal simulations using stereophotogrammetry may be safely run when only interested in overall output patterns. Caution should be paid when more accurate estimated values are needed.     

Relax and refill: xylem rehydration prior to hydraulic measurements favours embolism repair in stems and generates artificially low PLC values

Diurnal changes in percentage loss of hydraulic conductivity (PLC), with recorded values being higher at midday than on the following morning, have been interpreted as evidence for the occurrence of cycles of xylem conduits' embolism and repair. Recent reports have suggested that diurnal PLC changes might arise as a consequence of an experimental artefact, that is, air entry into xylem conduits upon cutting stems, even if under water, while under substantial tension generated by transpiration. Rehydration procedures prior to hydraulic measurements have been recommended to avoid this artefact. In the present study, we show that xylem rehydration prior to hydraulic measurements might favour xylem refilling and embolism repair, thus leading to PLC values erroneously lower than those actually experienced by transpiring plants. When xylem tension relaxation procedures were performed on stems where refilling mechanisms had been previously inhibited by mechanical (girdling) or chemical (orthovanadate) treatment, PLC values measured in stems cut under native tension were the same as those measured after sample rehydration/relaxation. Our data call for renewed attention to the procedures of sample collection in the field and transport to the laboratory, and suggest that girdling might be a recommendable treatment prior to sample collection for PLC measurements.     

Ground reaction: intrinsic and extrinsic variability assessment and related method for artefact treatment

Ground reaction (GR) components measured by a dynamometric platform represent the dynamic interaction of the moving human body with the ground and depend on the subject-platform relative position and orientation. The observed variability among the GR measurements of the walking trials of an individual is either due to variability in the motor performance (intrinsic variability) or due to changes in the direction of walking and in the position and orientation of the striking foot relative to the platform (extrinsic variability). A method, based on the median operator, is presented here which lets us quantify the two components of variability. The application of the method to a large data set of normal subjects evidenced changes in progression direction/foot orientation (95th percentile value is 6.9 degrees ), which can dramatically change the patterns of GR components. This result warns about improper analysis of ground reaction measurement.An algorithm for restoring GR measurements affected by artefact was derived from the above method. This tool can be of valuable aid in clinical practice where patients' conditions suggest to not insist on repetition of trials even if the required number of correct foot placements has not been achieved. The artefact correction algorithm has been applied to a large data set artificially corrupted to evaluate its robustness.     

A fast bilateral filter with application to artefact reduction

Elastography in medical ultrasound is an imaging technique that displays information about tissue stiffness. However, elastography suffers from artefact noise that may come from two dominant sources: decorrelation error and amplitude modulation error. In order to reduce artefact and improve the quality of ultrasonic elastography, a fast bilateral filter is proposed in this study based on local histogram. The presented filter is derived from a conventional bilateral filter, and a local histogram is introduced to speed up the filter. The proposed algorithm can reduce artefact noise and, at the same time, maintain the tissue structure. Both simulation and phantom testing show that the proposed method can improve the quality of ultrasonic elastography in terms of tissue elastographic signal-to-noise ratio and elastographic contrast-to-noise ratio values.     

Excising stem samples underwater at native tension does not induce xylem cavitation

Xylem resistance to water stress‐induced cavitation is an important trait that is associated with drought tolerance of plants. The level of xylem cavitation experienced by a plant is often assessed as the percentage loss in conductivity (PLC) at different water potentials. Such measurements are constructed with samples that are excised underwater at native tensions. However, a recent study concluded that cutting conduits under significant tension induced cavitation, even when samples were held underwater during cutting. This resulted in artificially increased PLC because of what we have termed a ‘tension‐cutting artefact’. We tested the hypothesized tension‐cutting artefact on five species by measuring PLC at native tension compared with after xylem tensions had been relaxed. Our results did not support the tension‐cutting artefact hypothesis, as no differences were observed between native and relaxed samples in four of five species. In a fifth species (Laurus nobilis), differences between native and relaxed samples appear to be due to vessel refilling rather than a tension‐cutting effect. We avoided the tension‐cutting artefact by cutting samples to slightly longer than their measurement length and subsequent trimming of at least 0.5 cm of sample ends prior to measurement.     

Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California

Aim Several studies have found that more accurate predictive models of species’ occurrences can be developed for rarer species; however, one recent study found the relationship between range size and model performance to be an artefact of sample prevalence, that is, the proportion of presence versus absence observations in the data used to train the model. We examined the effect of model type, species rarity class, species’ survey frequency, detectability and manipulated sample prevalence on the accuracy of distribution models developed for 30 reptile and amphibian species. Location Coastal southern California, USA. Methods Classification trees, generalized additive models and generalized linear models were developed using species presence and absence data from 420 locations. Model performance was measured using sensitivity, specificity and the area under the curve (AUC) of the receiver‐operating characteristic (ROC) plot based on twofold cross‐validation, or on bootstrapping. Predictors included climate, terrain, soil and vegetation variables. Species were assigned to rarity classes by experts. The data were sampled to generate subsets with varying ratios of presences and absences to test for the effect of sample prevalence. Join count statistics were used to characterize spatial dependence in the prediction errors. Results Species in classes with higher rarity were more accurately predicted than common species, and this effect was independent of sample prevalence. Although positive spatial autocorrelation remained in the prediction errors, it was weaker than was observed in the species occurrence data. The differences in accuracy among model types were slight. Main conclusions Using a variety of modelling methods, more accurate species distribution models were developed for rarer than for more common species. This was presumably because it is difficult to discriminate suitable from unsuitable habitat for habitat generalists, and not as an artefact of the effect of sample prevalence on model estimation.     

The SCoRE residual: a quality index to assess the accuracy of joint estimations

The determination of an accurate centre of rotation (CoR) from skin markers is essential for the assessment of abnormal gait patterns in clinical gait analysis. Despite the many functional approaches to estimate CoRs, no non-invasive analytical determination of the error in the reconstructed joint location is currently available. The purpose of this study was therefore to verify the residual of the symmetrical centre of rotation estimation (SCoRE) as a reliable indirect measure of the error of the computed joint centre. To evaluate the SCoRE residual, numerical simulations were performed to evaluate CoR estimations at different ranges of joint motion. A statistical model was developed and used to determine the theoretical relationships among the SCoRE residual, the magnitude of the skin marker artefact, the corrections to the marker positions, and the error of the CoR estimations to the known centre of rotation. We found that the equation err=0.5r(s) provides a reliable relationship among the CoR error, err, and the scaled SCoRE residual, r(s), providing that any skin marker artefact is first minimised using the optimal common shape technique (OCST). Measurements on six healthy volunteers showed a reduction of SCoRE residual from 11 to below 6mm and therefore demonstrated consistency of the theoretical considerations and numerical simulations with the in vivo data. This study also demonstrates the significant benefit of the OCST for reducing skin marker artefact and thus for predicting the accuracy of determining joint centre positions in functional gait analysis. For the first time, this understanding of the SCoRE residual allows a measure of error in the non-invasive assessment of joint centres. This measure now enables a rapid assessment of the accuracy of the CoR as well as an estimation of the reproducibility and repeatability of skeletal motion patterns.     

On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations

Background  

Phylogenetic reconstruction methods based on gene content often place all the parasitic and endosymbiotic eubacteria (parasites for short) together in a clan. Many other lines of evidence point to this parasites clan being an artefact. This artefact could be a consequence of the methods used to construct ortholog databases (due to some unknown bias), the methods used to estimate the phylogeny, or both.     

旧石器时代早期石制品分析方案

本文提出一种应用于旧石器时代早期石制品研究的分析方案。本方案以宏观分析方法为主,不包括同样重要的微观分析方法,主要应用于旧石器时代早期石制品的技术-类型学分析,不涉及特定地区和特殊石制品的讨论。在旧大陆旧石器时代早期石器研究中,鉴于学者们使用的技术学与类型学分析方案总体相似,我们认为在研究中使用标准化的分析方案会提高地区间石器面貌的可比性,并有助于理解旧石器时代早期旧大陆古人类的技术行为模式。从这个角度出发,本文将回顾旧石器时代早期石器研究的主要理论和方法,并提出分析视角和术语建议,希望有助于研究中对描述剥片类、废片类、锤击工具、拼合工具和传统石制品的测量与绘图惯例。     

BASH: a tool for managing BeadArray spatial artefacts

SUMMARY: With their many replicates and their random layouts, Illumina BeadArrays provide greater scope fordetecting spatial artefacts than do other microarray technologies. They are also robust to artefact exclusion, yet there is a lack of tools that can perform these tasks for Illumina. We present BASH, a tool for this purpose. BASH adopts the concepts of Harshlight, but implements them in a manner that utilizes the unique characteristics of the Illumina technology. Using bead-level data, spatial artefacts of various kinds can thus be identified and excluded from further analyses. AVAILABILITY: The beadarray Bioconductor package (version 1.10 onwards), www.bioconductor.org     

Metabolic cold adaptation of polar fish based on measurements of aerobic oxygen consumption: fact or artefact? Artefact!

Whether metabolic cold adaptation in polar fish, based on measurements of aerobic standard metabolic rate, is a fact or an artefact has been a dispute since Holeton asked the question in 1974. So far polar fish had been considered to be metabolically cold adapted because they were reported to have a considerably elevated resting oxygen consumption, or standard metabolic rate, compared with oxygen consumption values of tropical or temperate fish extrapolated to similar low polar temperatures. Recent experiments on arctic and Antarctic fish, however, do not show elevated resting aerobic oxygen consumption values, or standard metabolic rate, and hence it is concluded that that metabolic cold adaptation in the traditional sense is an artefact.