nils-herrmann/clean_scirepeval huggingface dataset:
Competing tumor cell migration mechanisms caused by interstitial fluid flow.
Venue: Journal of biomechanics

In the seminal work by Swartz and collaborators (Shields et al., 2007) it was discovered that autologously secreted or activated (ECM-bound) chemokine forms local pericellular diffusion gradients skewed by fluid convection, and the cells subsequently chemotact up the flow-directed gradient. However, in (Polacheck et al., 2011) Kamm and collaborators found that there is a competing downstream and upstream migration transport mechanism. Their study showed that both mechanisms are present at the same time and the relative strength of these two stimuli governs the directional bias in migration for a cell population and is a function of cell density, interstitial flow rate, and CCR7 receptor availability. The main objective of this work is to give a possible explanation of these two different concurrent cell migration mechanisms by means of a theoretical model. Relying on multiphase modelling, separate momentum balance equations are formulated, respectively, for the cell phase and the interstitial fluid (IF) phase. In order to represent proteolytic activity and autologous chemotaxis a non-moving ECM component is included, as well as proteases secreted by the cancer cells and chemokine that can be released from ECM. The cell and IF momentum balance equations include cell-ECM and fluid-ECM resistance force terms (i.e., classical Darcy's equation terms), but also a cell-fluid interaction term that can account for a more indirect effect that fluid-generated stress may have on cancer cells. We illustrate how the cancer cells can work through this term and effectively avoid being pushed in the flow direction, and even create upstream migration by controlling its magnitude and sign. We think of this as the mathematical interpretation of the experimental observation by Kamm and collaborators that the fluid generated matrix adhesion tension on the upstream side of cells activates integrin adhesion complexes, resulting in activation of focal adhesion (FA) proteins. The model predicts that generally the strength of the upstream migration mechanism is sensitive to the cell volume fraction: a lower density of cells is subject to a weaker upstream migration effect; a higher density of cancer cells can more effectively generate upstream migration. This behavior is a result of the nonlinear coupling between cell-ECM, fluid-ECM, and cell-fluid interaction terms that naturally are involved in the mathematical expression for the net cell velocity.
Novel method for emboli analog formation towards improved stroke retrieval devices.
Venue: Journal of biomechanics

Unsuccessful recanalization attempts in stroke patients have been associated with fibrin-rich thromboemboli linking retrieval mechanism performance and clot composition. To continue development of stroke retrieval mechanisms, the material properties of cerebral thromboemboli must be replicated; however, current methods for emboli analog formation lack quantitative measurements for both material stiffness and composition of cerebral thromboemboli. This study investigates emboli analog (EA) formation to mimic the material stiffness and composition of cerebral thromboemboli to develop new retrieval mechanisms.



To induce static and dynamic environments for clot replication, a 9:1 ratio of porcine whole blood and 2.45% calcium chloride remained stationary or rotated at 34, 50 and 80 RPM. Histology and a custom MATLAB code provided composition analysis results. Likewise, quantitative results from biomechanical testing were obtained for direct comparison of the material stiffness of cerebral thromboemboli.



Fibrin/platelet content as well as material stiffness increased due to increasing rotational speed. Approximately 11% of the biomechanical testing results exhibited nonlinearity after an initial yield point, of which 60% were from statically formed EAs. Those formed at 50 RPM were most similar in material stiffness to thromboemboli extracted from carotid endarterectomy (CEA) procedures (p = 0.97).



The dynamically formed EAs may be altered to obtain a range of fibrin/platelet to erythrocyte ratios. The proposed methodology for EA formation offers a platform for continued development of retrieval mechanism prototypes.
Automatic registration of MRI-based joint models to high-speed biplanar radiographs for precise quantification of in vivo anterior cruciate ligament deformation during gait.
Venue: Journal of biomechanics

Understanding in vivo joint mechanics during dynamic activity is crucial for revealing mechanisms of injury and disease development. To this end, laboratories have utilized computed tomography (CT) to create 3-dimensional (3D) models of bone, which are then registered to high-speed biplanar radiographic data captured during movement in order to measure in vivo joint kinematics. In the present study, we describe a system for measuring dynamic joint mechanics using 3D surface models of the joint created from magnetic resonance imaging (MRI) registered to high-speed biplanar radiographs using a novel automatic registration algorithm. The use of MRI allows for modeling of both bony and soft tissue structures. Specifically, the attachment site footprints of the anterior cruciate ligament (ACL) on the femur and tibia can be modeled, allowing for measurement of dynamic ACL deformation. In the present study, we demonstrate the precision of this system by tracking the motion of a cadaveric porcine knee joint. We then utilize this system to quantify in vivo ACL deformation during gait in four healthy volunteers.
Minimum time required for assessing step variability during running at submaximal velocities.
Venue: Journal of biomechanics

This study aimed to determine the minimum time required for assessing spatiotemporal variability during continuous running at different submaximal velocities and, thereby, the number of steps required. Nineteen trained endurance runners performed an incremental running protocol, with a 3-min recording period at 10, 12, 14 and 16 km/h. Spatiotemporal parameters (contact and flight times, step length and step frequency) were measured using the OptoGait system and step variability was considered for each parameter, in terms of within-participants standard deviation (SD) and coefficient of variation (CV%). Step variability was considered over six different durations at every velocity tested: 0-10 s, 0-20 s, 0-30 s, 0-60 s, 0-120 s and 0-180 s. The repeated measures ANOVA revealed no significant differences in the magnitude of the four spatiotemporal parameters between the recording intervals at each running velocity tested (p ≥ 0.05, ICC > 0.90). The post-hoc analysis confirmed no significant differences in step variability (SD and CV% of each spatiotemporal parameter at any velocity tested) between measurements. The Bland-Altman limits of agreement method showed that longer recording intervals yield smaller systematic bias, random errors, and narrower limits of agreement, regardless of running velocity. The results suggest that the duration of the recording period required to estimate spatiotemporal variability plays an important role in the accuracy of the measurement, regardless of running velocity (10-16 km/h).
Errors in power-law estimations of inflow rates for intracranial aneurysm CFD.
Venue: Journal of biomechanics

Patient-specific inflow rates are rarely available for computational fluid dynamics (CFD) studies of intracranial aneurysms. Instead, inflow rates are often estimated from parent artery diameters via power laws, i.e. Q ∝ Dn, reflecting adaptation of conduit arteries to demanded flow. The present study aimed to validate the accuracy of these power laws. Internal carotid artery (ICA) flow rates were measured from 25 ICA aneurysm patients via 2D phase contrast MRI. ICA diameters, derived from 3D segmentation of rotational angiograms, were used to estimate inflow rates via power laws from the aneurysm CFD literature assuming the same inlet wall shear stress (WSS) (n = 3), velocity (n = 2) or flow rate (n = 0) for all cases. To illustrate the potential impact of errors in flow rate estimates, pulsatile CFD was carried out for four cases having large errors for at least one power law. Flow rates estimated by n = 3 and n = 0 power laws had significant (p < 0.01) mean biases of -22% to +32%, respectively, but with individual errors ranging from -78% to +120%. The n = 2 power law had no significant bias, but had non-negligible individual errors of -58% to +71%. CFD showed similarly large errors for time-averaged sac WSS; however, these were reduced after normalizing by parent artery WSS. High frequency WSS fluctuations, evident in 2/4 aneurysms, were also sensitive to inflow rate errors. Care should therefore be exercised in the interpretation of aneurysm CFD studies that rely on power law estimates of inflow rates, especially if absolute (vs. normalized) WSS, or WSS instabilities, are of interest.
Worm-like chain model extensions for highly stretched tropocollagen molecules.
Venue: Journal of biomechanics

Tropocollagen plays a very important role in the load bearing functionality of soft tissues. In the context of multi-scale modeling the response of tropocollagen molecules to stretch should be very carefully predicted in order to describe the mechanical behavior of soft tissues. To this end, the worm-like chain (WLC) model is often applied, although it is restricted to the entropic force regime which is essential at moderate deformations. To describe molecular forces under larger stretches several extensions of the WLC have been proposed for deoxyribonucleic acid (DNA). This contribution aims to investigate the applicability of these models in the context of tropocollagen and discusses the feasibility of their application. Finally, the models are validated in comparison to experimental data available in the literature.
Using a cost function based on kinematics and electromyographic data to quantify muscle forces.
Venue: Journal of biomechanics

A reliable evaluation of muscle forces in the human body is highly desirable for several applications in both clinical and research contexts. Several models of muscle force distribution based on non-invasive measurements have been proposed since 1836 (Weber and Weber, 1836), amongst which Crowninshield's model (Crowninshield and Brand, 1981), which maximizes a cost-function representing the muscle fiber endurance, is the most popular. It is worth noting that Crowninshield's model is the most widely adopted notwithstanding its major limitations of physiological coherence. Forster et al. (2004) pointed out that "these (conventional) criteria however do not predict co-contraction adequately". Besides, electromyographic (EMG)-driven models have been proposed to assess individual muscle forces, which have not been broadly adopted due to their complexity and the need for a calibration before each test. In this context, a cost function based on kinematic and electromyographic data could provide the advantage of being physiologically more coherent with muscle activations compared to conventional cost-functions based on kinematics solely, and easier to use than the EMG-driven models. The objective of this study is to propose the first cost-function based on kinematics and electromyographic data to quantify muscle forces. When applying this new cost-function on a database of upper limb motions data of 17 subjects, healthy or with cerebral palsy, the muscle force prediction of the proposed model was 17.74% more coherent with the EMG pattern than the prediction of Crowninshield's model. And on average, these results were more consistent whether the subjects were healthy or with cerebral palsy. In conclusion, we propose this cost-function for the quantification of muscle forces.
Shear wave elastography can assess the in-vivo nonlinear mechanical behavior of heel-pad.
Venue: Journal of biomechanics

This study combines non-invasive mechanical testing with finite element (FE) modelling to assess for the first time the reliability of shear wave (SW) elastography for the quantitative assessment of the in-vivo nonlinear mechanical behavior of heel-pad. The heel-pads of five volunteers were compressed using a custom-made ultrasound indentation device. Tissue deformation was assessed from B-mode ultrasound and force was measured using a load cell to calculate the force - deformation graph of the indentation test. These results were used to design subject specific FE models and to inverse engineer the tissue's hyperelastic material coefficients and its stress - strain behavior. SW speed was measured for different levels of compression (from 0% to 50% compression). SW speed for 0% compression was used to assess the initial stiffness of heel-pad (i.e. initial shear modulus, initial Young's modulus). Changes in SW speed with increasing compressive loading were used to quantify the tissue's nonlinear mechanical behavior based on the theory of acoustoelasticity. Statistical analysis of results showed significant correlation between SW-based and FE-based estimations of initial stiffness, but SW underestimated initial shear modulus by 64%(±16). A linear relationship was found between the SW-based and FE-based estimations of nonlinear behavior. The results of this study indicate that SW elastography is capable of reliably assessing differences in stiffness, but the absolute values of stiffness should be used with caution. Measuring changes in SW speed for different magnitudes of compression enables the quantification of the tissue's nonlinear behavior which can significantly enhance the diagnostic value of SW elastography.
Long-term hip loading in unilateral total hip replacement patients is no different between limbs or compared to healthy controls at similar walking speeds.
Venue: Journal of biomechanics

Variation in hip joint contact forces directly influences the performance of total hip replacements (THRs). Measurement and calculation of contact forces in THR patients has been limited by small sample sizes, wide variation in patient and surgical factors, and short-term follow-up. This study hypothesised that, at long-term follow-up, unilateral THR patients have similar calculated hip contact forces compared to controls walking at similar (self-selected) speeds and, in contrast, THR patients walking at slower (self-selected) speeds have reduced hip contact forces. It was further hypothesised that there is no difference in calculated hip contact forces between operated and non-operated limbs at long-term follow-up for both faster and slower patients. Gait analysis data for THR patients walking at faster (walking speed: 1.29 ± 0.12 m/s; n = 11) and slower (walking speed: 0.72 ± 0.09 m/s; n = 11) speeds were used. Healthy subjects constituted the control group (walking speed: 1.36 ± 0.12 m/s; n = 10). Hip contact forces were calculated using static optimisation. There was no significant difference (p > 0.31) in hip contact forces between faster and control groups. Conversely, force was reduced at heel strike by 19% (p = 0.002), toe-off by 31% (p < 0.001) and increased at mid-stance by 15% (p = 0.02) for the slower group compared to controls. There were no differences between operated and non-operated limbs for the slower group or the faster group, suggesting good biomechanical recovery at long-term follow-up. Loading, at different walking speeds, presented here can improve the relevance of preclinical testing methods.
Non-uniformity in the healthy patellar tendon is greater in males and similar in different age groups.
Venue: Journal of biomechanics

There is increasing evidence that tendons are heterogeneous and take advantage of structural mechanisms to enhance performance and reduce injury. Fascicle-sliding, for example, is used by energy-storing tendons to enable them to undergo large extensions while protecting the fascicles from damage. Reductions in fascicle-sliding capacity may thus predispose certain populations to tendinopathy. Evidence from the Achilles tendon of significant superficial-to-deep non-uniformity that is reduced with age supports this theory. Similar patellar tendon non-uniformity has been observed, but the effects of age and sex have yet to be assessed. Healthy adults (n = 50, 25M/25F) from a broad range of ages (23-80) were recruited and non-uniformity was quantified using ultrasound speckle-tracking during passive knee extension. Significant superficial-to-deep non-uniformity and proximal/distal variations were observed. No effect of age was found, but males exhibited significantly greater non-uniformity than females (p < 0.05). The results contrast with previous findings in the Achilles tendon; in this study, tendons and tendon regions at high risk for tendinopathy (i.e. males and proximal regions, respectively) exhibited greater non-uniformity, whereas high-risk Achilles tendons (i.e. older adults) previously showed reduced non-uniformity. This suggests that non-uniformity may be dominated by factors other than fascicle-sliding. Anatomically, the varied proximal attachment of the patellar tendon may influence non-uniformity, with quadriceps passive resistance limiting superficial tendon movement, thus linking flexibility, non-uniformity and injury risk. This study also provides evidence of a differential effect of aging on the patellar tendon compared with evidence from prior studies on other tendons necessitating further study to elucidate links between non-uniformity and injury.
Doxycycline improves cage activity, but not exercised, supraspinatus tendon and muscle in a rat model.
Venue: Journal of biomechanics

The objective of this study was to investigate the effects of doxycycline, a broad-spectrum MMP inhibitor, on cage activity and exercised supraspinatus tendon and muscle using a Sprague-Dawley rat model of non-injurious exercise. Because exercise may alter muscle and tendon MMP activity and matrix turnover, we hypothesized that doxycycline would abolish the beneficial adaptations found with exercise but have no effect on cage activity muscle and tendon properties. Rats were divided into acute or chronic exercise (EX) or cage activity (CA) groups, and half of the rats received doxycycline orally. Animals in acute EX groups were euthanized 24 h after a single bout of exercise (10 m/min, 1 h) on a flat treadmill. Animals in chronic EX groups walked on a flat treadmill and were euthanized at 2 or 8 week time points. Assays included supraspinatus tendon mechanics and histology and muscle fiber morphologic and type analysis. Doxycycline improved tendon mechanical properties and collagen organization in chronic cage activity groups, which was not consistently evident in exercised groups. Combined with exercise, doxycycline decreased average muscle fiber cross-sectional area. Results of this study suggest that administration of doxycycline at pharmaceutical doses induces beneficial supraspinatus tendon adaptations without negatively affecting the muscle in cage activity animals, supporting the use of doxycycline to combat degenerative processes associated with underuse; however, when combined with exercise, doxycycline does not consistently produce the same beneficial adaptations in rat supraspinatus tendons and reduces muscle fiber cross-sectional area, suggesting that doxycycline is not advantageous when combined with activity.
Automated, accurate, and three-dimensional method for calculating sagittal slope of the tibial plateau.
Venue: Journal of biomechanics

Increased posterior-inferior directed slope of the subchondral bone of the lateral tibial plateau is a risk factor for noncontact rupture of the anterior cruciate ligament (ACL). Previous measures of lateral tibial slope, however, vary from study to study and often lack documentation of their accuracy. These factors impede identifying the magnitude of lateral tibial slope that increases risk of noncontact ACL rupture. Therefore, we developed and evaluated a new method that (1) requires minimal user input; (2) employs 3D renderings of the tibia that are referenced to a 3D anatomic coordinate system; and (3) is precise, reliable, and accurate. The user first isolated the proximal tibia from computed tomography (CT) scans. Then, the algorithm placed the proximal tibia in an automatically generated tibial coordinate system. Next, it identified points along the rim of subchondral bone around the lateral tibial plateau, iteratively fit a plane to this rim of points, and, finally, referenced the plane to the tibial coordinate system. Precision and reliability of the lateral slope measurements were respectively assessed via standard deviation and intra- and inter-class correlation coefficients using CT scans of three cadaveric tibia. Accuracy was quantified by comparing changes in lateral tibial slope calculated by our algorithm to predefined in silico changes in slope. Precision, reliability, and accuracy were ≤0.18°, ≥0.998, and ≤0.13°, respectively. We will use our novel method to better understand the relationship between lateral tibial slope and knee biomechanics towards preventing ACL rupture and improving its treatment.
Articular-surface-based automatic anatomical coordinate systems for the knee bones.
Venue: Journal of biomechanics

Increasing use of patient-specific surgical procedures in orthopaedics means that patient-specific anatomical coordinate systems (ACSs) need to be determined. For knee bones, automatic algorithms constructing ACSs exist and are assumed to be more reliable than manual methods, although both approaches are based on non-unique numerical reconstructions of true bone geometries. Furthermore, determining the best algorithms is difficult, as algorithms are evaluated on different datasets. Thus, in this study, we developed 3 algorithms, each with 3 variants, and compared them with 5 from the literature on a dataset comprising 24 lower-limb CT-scans. To evaluate algorithms' sensitivity to the operator-dependent reconstruction procedure, the tibia, patella and femur of each CT-scan were each reconstructed once by three different operators. Our algorithms use principal inertia axis (PIA), cross-sectional area, surface normal orientations and curvature data to identify the bone region underneath articular surfaces (ASs). Then geometric primitives are fitted to ASs, and the ACSs are constructed from the geometric primitive points and/or axes. For each bone type, the algorithm displaying the least inter-operator variability is identified. The best femur algorithm fits a cylinder to posterior condyle ASs and a sphere to the femoral head, average axis deviations: 0.12°, position differences: 0.20 mm. The best patella algorithm identifies the AS PIAs, average axis deviations: 0.91°, position differences: 0.19 mm. The best tibia algorithm finds the ankle AS center and the 1st PIA of a layer around a plane fitted to condyle ASs, average axis deviations: 0.38°, position differences: 0.27 mm.