nils-herrmann/clean_scirepeval huggingface dataset:
Influence of position and angulation of a voice prosthesis on the aerodynamics of the pseudo-glottis.
Venue: Journal of biomechanics

The use of a tracheoesophageal valve, also known as voice prosthesis, is currently the most appealing solution for recovering the ability to speak in subjects who have undergone a total laryngectomy. The prosthesis allows the passage of air from the trachea to the esophagus, thereby promoting the flow-induced vibration of the subject's pharyngoesophageal segment. In turn, the pharyngoesophageal segment modulates the air flow from the lungs into the subject's vocal tract, acting as an alternative source of acoustic energy to generate voice. The vibration of the pharyngoesophageal segment will likely depend on the aerodynamic forces acting on its wall, which will be defined by the flow characteristics downstream from the valve's outlet. Previous works have investigated the pressure drop across different prosthesis designs with both in-vitro and in-vivo experiments. Nevertheless, the aerodynamic aspects of the flow in the tracheoesophageal region have only been investigated experimentally in an idealized geometry. This work investigates the influence of the prosthesis position on the aerodynamic behavior of the pharyngoesophageal segment in terms of wall pressure distribution and characteristics of the velocity field. The investigations were carried out with a static model of the tracheoesophageal region based on the finite volume method and a Reynolds-averaged Navier-Stokes solver. The geometry of the system was based on computed tomography images obtained from laryngectomized subjects during phonation at different voice registers and included the geometry of a commercially available voice prosthesis. The results suggest that the position and angulation of the voice prosthesis have a minor influence on the pressure loss along the tracheoesophageal segment and on the pressure distribution on the pharyngoesophageal segment's wall.
Functional assistance for stress distribution in cell culture membrane under periodically stretching.
Venue: Journal of biomechanics

Dynamic cell cultures simulate the in vivo cell environment for a regular loading system with curtain strains. However, it is difficult to obtain strains that are suitable for cells without conducting multiple trials. This study develops a device that increases the strain gradient by changing the tensile section, in order to determine the effect of various cyclic strains on cultured human keratinocytes (HK) cells. This device is used to determine the effect of 3% and 5% cyclic strain and shear strain on cell proliferation and arrangement at 1 Hz. The results show that compared with static and 3% strain, a 5% cyclic strain better inhibits the proliferation of HK cells. Compared to the initial cell attachment when there is no specific directionality, the cells are aligned in the vertical stretching direction after cyclic stretching. This equipment increases the efficiency of the experiment and more intuitively maps the cell behavior and shape to the strain field and the response to the shear strain.
A heuristic model-based approach for compensating wind effects in ski jumping.
Venue: Journal of biomechanics

Wind influences the jump length in ski jumping, which raises questions about the fairness. To counteract the wind problem, the International Ski Federation has introduced a wind compensation system in 2009: time-averaged wind velocity components tangential to the landing slope are obtained from several sites along the landing slope, and these data are used in a linear statistical model for estimating the jump length effect of wind. This is considered in the total score of the ski jump. However, it has been shown that the jump length effect estimates can be inaccurate and misleading. The present article introduces an alternative mathematical wind compensation approach that is based on an accurate mechanistic model of the flight phase. This estimates the jump length effect as difference between the jump length of the real ski jump at the given wind condition and the computed jump length of the simulated ski jump at calm wind. Inputs for the computer simulation are the initial flight velocity and aerodynamic coefficients of the real ski jump that can be obtained from kinematic and wind velocity data collected during the flight. The initial flight velocity is readily available from the kinematic data and inverse dynamics can be used to compute the aerodynamic coefficients. The accuracy of the estimated jump length effect of the mechanistic model-based approach depends only on the measurement errors in the kinematic and wind velocity data, but not on inaccuracies of an approach that is based on a linear statistical model.
Comparison of two coupling methods regarding coupling patterns, sensitivity to footwear and potential future injury applications.
Venue: Journal of biomechanics

Researchers have quantified the effect of footwear conditions on movement patterns and injury risk for runners using discrete kinematic variables and/or relative coupling variables. Coupling is typically assessed using the transfer coefficient (TC) or the vector coding (VC) approach. However, a thorough comparison of both methods regarding their interpretation, sensitivity to testing conditions and information regarding coupling strength as one overall coupling score is missing. This study aimed to compare both methods regarding a) their coupling patterns, b) their sensitivity to footwear conditions and c) to discuss both coupling approaches regarding an overall coupling score. 3D motion capture data was collected of 10 males running on a treadmill with and without shoes. Rearfoot frontal and tibia transverse plane motion was analyzed. Discrete kinematic variables and relative coupling variables were calculated via the TC and VC approach for the landing and push-off phase. A novel variable, the coupling score, was developed and calculated using both coupling methods. Coupling variables calculated with both methods showed differences in coupling patterns, especially for the landing phase (TC ≈ 0.5/in-phase towards rearfoot-phase, VC ≈ 300°/anti-phase). VC offers further details, such as coupling frequencies, compared to the TC. Moreover, both methods were unable to distinguish between footwear conditions regarding their coupling patterns or coupling scores. Strong correlations (r ≤ 0.7, p < 0.0125) between coupling scores assessed with either method suggest that both methods contain similar information regarding coupling strength. The coupling score represents a first attempt to quantify a weighted coupling pattern quantitatively. Future studies have to validate whether the coupling score might be linked to injury risks.
Is age rating enough to investigate changes in breathing motion pattern associated with aging of physically active women?
Venue: Journal of biomechanics

The most common way to analyze the effect of aging on breathing is to divide subjects into age groups. However, in addition to the fact that there is no consensus in the literature regarding age group division, such design critically influences the interpretation of the effects attributed to aging. Thus, this study aimed to investigate the feasibility to distinguish different age groups from the 3D kinematic variables of breathing motion (i.e., markers' coordinate as a function of time allowing the calculation of compartmental volume variations) and to analyze whether the aging could influence these variables. Seventy-three physically active women aged 19-80 years performed quiet breathing and vital capacity maneuvers. To record the thoracoabdominal breathing motion, the 3D coordinates of 32 retroreflective markers positioned on the trunk were used to estimate the volume variation of the superior thorax, inferior thorax, and abdomen. The percentage of contribution and the correlation coefficient were calculated to analyze the breathing motion pattern from the estimated volumes. The k-means cluster analysis was performed to analyze the age group classification. Linear regression was performed to investigate whether age can predict changes in the breathing motion pattern. The results showed that physically active women could not be classified into age groups from breathing motion. Despite significant p values of the linear regression, the high variability of the data suggested that age itself is not enough to predict the changes in breathing motion pattern when non-sedentary women are considered.
Torsion Tool: An automated tool for personalising femoral and tibial geometries in OpenSim musculoskeletal models.
Venue: Journal of biomechanics

Common practice in musculoskeletal modelling is to use scaled musculoskeletal models based on a healthy adult, but this does not consider subject-specific geometry, such as tibial torsion and femoral neck-shaft and anteversion angles (NSA and AVA). The aims of this study were to (1) develop an automated tool for creating OpenSim models with subject-specific tibial torsion and femoral NSA and AVA, (2) evaluate the femoral component, and (3) release the tool open-source. The Torsion Tool (https://simtk.org/projects/torsiontool) is a MATLAB-based tool that requires an individual's tibial torsion, NSA and AVA estimates as input and rotates corresponding bones and associated muscle points of a generic musculoskeletal model. Performance of the Torsion Tool was evaluated comparing femur bones as personalised with the Torsion Tool and scaled generic femurs with manually segmented bones as golden standard for six typically developing children and thirteen children with cerebral palsy. The tool generated femur geometries closer to the segmentations, with lower maximum (-19%) and root mean square (-18%) errors and higher Jaccard indices (+9%) compared to generic femurs. Furthermore, the tool resulted in larger improvements for participants with higher NSA and AVA deviations. The Torsion Tool allows an automatic, fast, and user-friendly way of personalising femoral and tibial geometry in an OpenSim musculoskeletal model. Personalisation is expected to be particularly relevant in pathological populations, as will be further investigated by evaluating the effects on simulation outcomes.
Measuring and modeling in vivo human gracilis muscle-tendon unit length.
Venue: Journal of biomechanics

Musculoskeletal models rely heavily on the use of an anatomical dataset and clearly defined assumptions to accurately model the subject being studied. Therefore, it is important to understand the limitations of using musculoskeletal models to study individuals. This paper describes a method of measuring in vivo gracilis muscle-tendon unit length and presents a comparison of experimental data versus predictions from four musculoskeletal models in OpenSim. The largest errors occurred when the knee was fully extended. At this position, the absolute average muscle-tendon unit length error was 7% and the absolute average fiber length error was between 15% and 32%. However, the variability of these errors was significant. Manual linear scaling based on an anthropometric database did not capture the variability observed in subjects. The fiber length errors observed are predicted to have a significant impact on muscle force production that may not represent true subject specific force-length relationship of the gracilis.
On delayed transition to turbulence in an eccentric stenosis model for clean vs. noisy high-fidelity CFD.
Venue: Journal of biomechanics

Recent comparisons between experiments and computational fluid dynamics (CFD) simulations of flow in the Food and Drug Administration (FDA) standardized nozzle geometry have highlighted the potential sensitivity of axisymmetric CFD models to small perturbations induced by mesh and inlet velocity, particularly for Reynolds numbers (Re) in the transitional regime. This evokes the classic experiment of Reynolds on transition to turbulence in a straight pipe, which can be delayed, apparently indefinitely, if special care is taken to control for external influences. Such idealized experiments are, however, extremely difficult to perform and, in the context of cardiovascular modeling, belie the "noise" inherent in typical experimental and physiological systems. Previous high-fidelity CFD of a canonical eccentric (i.e., non-axisymmetric) stenosis model showed transition occurring for steady flow at Re ~ 700-800, with modest delay caused by the introduction of shear-thinning rheology. On the other hand, recent experimental measurements of steady flowing blood and blood-mimicking fluids in this same stenosis model report transition for Re ~ 400-500. Taking a cue from the FDA nozzle controversy, the present study demonstrates that the addition of small-magnitude random noise at the inlet brings the eccentric-stenosis CFD results more in-line with experiments, and reveals a more gradual transition towards turbulence. This highlights that, even in non-axisymmetric idealized geometries, unnaturally "clean" high-fidelity CFD may impede not only good agreement with experiments, but also understanding of the onset and character of blood flow instabilities as they may exist, naturally, in the vasculature.
ISB recommendations for skin-marker-based multi-segment foot kinematics.
Venue: Journal of biomechanics

The foot is anatomically and functionally complex, and thus an accurate description of intrinsic kinematics for clinical or sports applications requires multiple segments. This has led to the development of many multi-segment foot models for both kinematic and kinetic analyses. These models differ in the number of segments analyzed, bony landmarks identified, required marker set, defined anatomical axes and frames, the convention used to calculate joint rotations and the determination of neutral positions or other offsets from neutral. Many of these models lack validation. The terminology used is inconsistent and frequently confusing. Biomechanical and clinical studies using these models should use established references and describe how results are obtained and reported. The International Society of Biomechanics has previously published proposals for standards regarding kinematic and kinetic measurements in biomechanical research, and in this paper also addresses multi-segment foot kinematics modeling. The scope of this work is not to prescribe a particular set of standard definitions to be used in all applications, but rather to recommend a set of standards for collecting, calculating and reporting relevant data. The present paper includes recommendations for the overall modeling and grouping of the foot bones, for defining landmarks and other anatomical references, for addressing the many experimental issues in motion data collection, for analysing and reporting relevant results and finally for designing clinical and biomechanical studies in large populations by selecting the most suitable protocol for the specific application. These recommendations should also be applied when writing manuscripts and abstracts.
Stability recovery performance in adults over a wide age range: A multicentre reliability analysis using different lean-and-release test protocols.
Venue: Journal of biomechanics

The ability to effectively increase the base of support is crucial to prevent from falling due to stability disturbances and has been commonly assessed using the forward-directed lean-and-release test. With this multicentre study we examined whether the assessment of stability recovery performance using two different forward lean-and-release test protocols is reliable in adults over a wide age range. Ninety-seven healthy adults (age from 21 to 80 years) were randomly assigned to one out of two lean angle protocols: gradual increase to maximal forward-lean angle (maximal lean angle; n = 43; seven participants were excluded due to marker artefacts) or predefined lean angle (single lean angle; n = 26; 21 participants needed to be excluded due to multiple stepping after release or marker artefacts). Both protocols were repeated after 0.5 h and 48 h to investigate intra- and inter-session reliability. Stability recovery performance was examined using the margin of stability at release (MoSRL) and touchdown (MoSTD) and increase in base of support (BoSTD). Intraclass correlation coefficients (confidence intervals at 95%) for the maximal lean angle and for the single lean angle were respectively 0.93 (0.89-0.96) and 0.94 (0.89-0.97) in MoSRL, 0.85 (0.77-0.91) and 0.67 (0.48-0.82) in MoSTD and 0.88 (0.81-0.93) and 0.80 (0.66-0.90) in BoSTD, with equivalence being revealed for each parameter between all three measurements (p < 0.01). We concluded that the assessment of stability recovery performance parameters in adults over a wide age range with the means of the forward lean-and-release test is reliable, independent of the used lean angle protocol.
Method of creating 3D models of small caliber cerebral arteries basing on anatomical specimens.
Venue: Journal of biomechanics

The cerebral circulation is a common site of vascular lesions and concurrent hemodynamic accidents, which often lead to serious neurological disabilities. Recent advances in understanding pathogenesis, improving diagnostics and developing new treatment methods for these conditions result from an interdisciplinary approach to the problem - linking clinical sciences, basic medical sciences and hemodynamical analyses. Most common techniques used in such studies include computational fluid dynamics, which allows for development of 3D models of cerebral vasculature, basing on radiological studies. However, these methods remain flawed, mainly because of their spatial resolution, which is not high enough to visualize the smallest arterial branches (perforating branches) in the models. That leaves the perforators (<1.0 mm) out of most of the contemporary studies, whilst their clinical importance is widely recognized in clinical practice. Obstruction of these vessels by atherosclerotic plaques, thrombi or implantation of flow diverting stents may result in neurological complications such as paralysis or coma. Our research team has recently developed a new method of creating 3D models of the cerebral arterial system based on anatomical specimens and micro computed tomography (micro-CT). We have infused fresh brainstem vasculature specimens with contrast medium, subsequently scanned them using an industrial-grade micro-CT system and finally, created spatial models, which included branches of diameter less than 0.1 mm. None of the current methods have been able to produce models of detail as high as this, which allows us to presume, that our procedure may open up new opportunities for hemodynamical studies within cerebral circulation and beyond.
3D printed clamps for fixation of spinal segments in biomechanical testing.
Venue: Journal of biomechanics

3D printed clamps provide multiple advantages compared to potting for the fixation of spinal specimens and in a recent study, superior fixation stability was reported. The aim of this study was to evaluate the fixation efficacy of 3D printed vertebra clamps during routine application and to present and evaluate a novel clamp for sacrum fixation. Further, public access to the template files is provided. 98 human single-level cadaveric specimens were biomechanically tested in flexion-extension (FE), lateral bending (LB), axial rotation (AR), anteroposterior shear (AS), lateral shear (LS) and axial compression-decompression (AC). Loading amplitudes were +/-7.5 Nm for FE, LB and AR, +/- 150 N for AS and LS and + 400/-100 N for AC. The novel sacrum clamp was used in 8 specimens. The median relative motion between clamps and specimens was 0.6° in FE, 0.7° in LB, 0.3° in AR, 0.5 mm in AS, 0.5 mm in LS and 0.1 mm in AC. With sacrum clamps, the median relative motion was 0.3° in FE, 0.1° in LB, 0.08° in AR, 0.8 mm in AS, 0.7 mm in LS and 0.2 mm in AC. The vertebra clamps used during routine testing provided better stability compared to the values in the literature in all six loading directions (p < 0.05). The sacrum clamp showed superior anchoring stability in three loading directions compared to the caudal vertebra clamps (p < 0.05), while inferior stability was measured in AS (p < 0.001). We conclude that 3D printed vertebra clamps and 3D printed sacrum clamps represent reliable methods for specimen fixation during routine biomechanical testing.
Scapular and humeral elevation coordination patterns used before vs. after Reverse Total Shoulder Arthroplasty.
Venue: Journal of biomechanics

The purpose of this study was to compare scapulohumeral coordination used before and after Reverse Total Shoulder Arthroplasty (RTSA) during the ascent phase of scapular plane arm elevation tasks performed with varied shoulder rotations (neutral, external rotation, and internal rotation). We expected that after RTSA, participants would decrease scapulothoracic upward rotation angular displacement and increase the scapulohumeral rhythm (SHR) vs. before RTSA. 11 RTSA patients (12 shoulders) participated in this study before and after RTSA while optical motion capture measured kinematics of the humerus and scapula relative to the thorax. Angular kinematics were compared pre vs. post-RTSA within-participant using One Dimensional Statistical Parametric Mapping (SPM) t-tests (α = 0.05) and across-participants, using paired t-tests (α = 0.05) adjusted for multiple comparisons. As a group, during arm elevation with neutral rotation, the mean (SD) SHR pre-RTSA was 1.5 (0.5) and increased to 1.7 (0.3) post-RTSA, though, not significantly (p = 0.182). In contrast, during arm elevation with external rotation, the mean (SD) SHR pre-RTSA was 1.3 (0.4) and significantly increased (p = 0.018) post-RTSA to 1.7 (0.3). Likewise, during arm elevation with internal rotation, the mean (SD) SHR pre-RTSA was 1.2 (0.3) and significantly increased (p < 0.001) post-RTSA to 1.7 (0.2). In addition to these and other group trends, participant-specific patterns were uncovered through SPM analyses - with some participants significantly increasing and others significantly decreasing scapulothoracic angular displacements across humerothoracic elevation ranges. Both before and after RTSA, scapulohumeral rhythm ratios were within the range of those previously reported in post-RTSA patients and were smaller than those used by healthy populations.