nils-herrmann/clean_scirepeval huggingface dataset:
Computational analysis of a flapping uvula on aerodynamics and pharyngeal wall collapsibility in sleep apnea.
Venue: Journal of biomechanics

Studying the airflows and the resultant aerodynamic pressure/force in the pharyngeal airway is critical for understanding the pathophysiology of snoring and sleep apnea. In this work, an experiment-driven computational study was conducted to examine the aerodynamics in human pharyngeal airway. An anatomically accurate pharynx model associated with different uvula kinematics was reconstructed from human magnetic resonance image (MRI) and high-speed photography. An immersed-boundary-method (IBM)-based direct numerical simulation (DNS) flow solver was adopted to simulate the corresponding unsteady flows in all their complexity. Analyses were performed on vortex dynamics and pressure fluctuations in the pharyngeal airway and force oscillations on the pharyngeal wall under the influence of varying airway obstructions, uvula flapping mode, and uvula flapping frequencies. It was found the vortex formation, aerodynamic pressure, and pharyngeal wall force were significantly affected by the width of the pharyngeal airway. By contrast, the influences from the uvula flapping mode were insignificant when other parameters were similar. Fast Fourier transformation (FFT) and continuous wavelet transform (CWT) analysis of the pressure time history revealed the existence of higher order harmonics of base frequency with significant pressure amplitudes and energy intensities. It was also found the airway pressure and pharyngeal wall force oscillate more dramatically at higher uvula flapping frequencies, which tends to promote the collapse of pharyngeal wall and initiates sleep apnea.
Representative 3D shape of the distal femur, modes of variation and relationship with abnormality of the trochlear region.
Venue: Journal of biomechanics

The anatomy of the distal femur has a predominant influence on the mechanics of both patello- and tibio-femoral joints. Especially, the morphological degeneration of the trochlear region dramatically affects the overall knee biomechanics and, from a clinical point of view, the staging of such a degeneration is fundamental to tailor the optimal therapeutic solution. The description of morphological variability and pathological inter-subject differences of the trochlea can be achieved by means of statistical shape modeling of a set of three-dimensional surfaces. This representation encodes information, spread into the dataset, in terms of modes of variations that model global, regional and even local morphological features. In view of that, the aim of this study was to develop a statistical shape model of the distal femur to capture the variability of the trochlear region into specific modes of variation and to study the interplay between the variation of the trochlea and the condylar regions. Using CT scans of patients affected by different levels of abnormality of the trochlear region, the distal femur geometries were co-registered to a reference shape using the pair-wise correspondence approach and principal component analysis provided the key modes of variation (MoVs). Apart from the first two MoVs, which described the global magnitude of the femur and the shaft length, the main following ones showed high correlation with sulcus depth (r2=0.70), sulcus angle (r2=0.70), lateral trochlear inclination (r2=0.66), and height of the two condylar facets in the anterior direction (r2=0.66), whose abnormal variations are typical signs of trochlear degeneration. High interplay between trochlear abnormalities and notch width (r2=0.71), lateral condylar size (r2=0.67), and medial condylar size (r2=0.99) was found. Interestingly, the model predicted morphological associations not included in the training dataset, nonetheless difficult to demonstrate physiologically. Interestingly from a biomechanical point of view, the distribution of some MoVs was found statistically different across the patients featuring physiological and pathological ranges of hip-knee-ankle alignment, femoral internal-external rotation and tibial slope. However, no linear correlation was found between the angular indexes and such MoVs. As a result, we can assert that statistical modeling of the distal femur are to date an effective way to visualize and quantify abnormalities of the trochlear regions supporting the introduction of advanced analysis, diagnostic and treatment support tools to elucidate physiologic and pathological variability in the morphology, to drive the staging and assist the selection of the optimal treatment option tailored to the patient.
Modeling methodology for defining a priori the hydrodynamics of a dynamic suspension bioreactor. Application to human induced pluripotent stem cell culture.
Venue: Journal of biomechanics

Three-dimensional dynamic suspension is becoming an effective cell culture method for a wide range of bioprocesses, with an increasing number of bioreactors proposed for this purpose. The complex hydrodynamics establishing within these devices affects bioprocess outcomes and efficiency, and usually expensive in vitro trial-and-error experiments are needed to properly set the working parameters. Here we propose a methodology to define a priori the hydrodynamic working parameters of a dynamic suspension bioreactor, selected as a test case because of the complex hydrodynamics characterizing its operating condition. A combination of computational and analytical approaches was applied to generate operational guideline graphs for defining a priori specific working parameters. In detail, 43 simulations were performed under pulsed flow regime to characterize advective transport within the device depending on different operative conditions, i.e., culture medium flow rate and its duty cycle, cultured particle diameter, and initial particle suspension volume. The operational guideline graphs were then used to set specific hydrodynamic working parameters for an in vitro proof-of-principle test, where human induced pluripotent stem cell (hiPSC) aggregates were cultured for 24 h within the bioreactor. The in vitro findings showed that, under the selected pulsed flow regime, sedimentation was avoided, hiPSC aggregate circularity and viability were preserved, and culture heterogeneity was reduced, thus confirming the appropriateness of the a priori method. This methodology has the potential to be adaptable to other dynamic suspension devices to support experimental studies by providing in silico-based a priori knowledge, useful to limit costs and to optimize culture bioprocesses.
Changes in shear wave propagation within skeletal muscle during active and passive force generation.
Venue: Journal of biomechanics

Muscle force can be generated actively through changes in neural excitation, and passively through externally imposed changes in muscle length. Disease and injury can disrupt force generation, but it can be challenging to separate passive from active contributions to these changes. Ultrasound elastography is a promising tool for characterizing the mechanical properties of muscles and the forces that they generate. Most prior work using ultrasound elastography in muscle has focused on the group velocity of shear waves, which increases with increasing muscle force. Few studies have quantified the phase velocity, which depends on the viscoelastic properties of muscle. Since passive and active forces within muscle involve different structures for force transmission, we hypothesized that measures of phase velocity could detect changes in shear wave propagation during active and passive conditions that cannot be detected when considering only group velocity. We measured phase and group velocity in the human biceps brachii during active and passive force generation and quantified the differences in estimates of shear elasticity obtained from each of these measurements. We found that measures of group velocity consistently overestimate the shear elasticity of muscle. We used a Voigt model to characterize the phase velocity and found that the estimated time constant for the Voigt model provided a way to distinguish between passive and active force generation. Our results demonstrate that shear wave elastography can be used to distinguish between passive and active force generation when it is used to characterize the phase velocity of shear waves propagating in muscle.
A simple method for computing sprint acceleration kinetics from running velocity data: Replication study with improved design.
Venue: Journal of biomechanics

Measuring the ground reaction forces (GRF) underlying sprint acceleration is important to understanding the performance of such a common task. Until recently direct measurements of GRF during sprinting were limited to a few steps per trial, but a simple method (SM) was developed to estimate GRF across an entire acceleration. The SM utilizes displacement- or velocity-time data and basic computations applied to the runner's center of mass and was validated against compiled force plate (FP) measurements; however, this validation used multiple-trials to generate a single acceleration profile, and consequently fatigue and error may have introduced noise into the analyses. In this study, we replicated the original validation by comparing the main sprint kinetics and force-velocity-power variables (e.g. GRF and its horizontal and vertical components, mechanical power output, ratio of horizontal component to resultant GRF) between synchronized FP data from a single sprinting acceleration and SM data derived from running velocity measured with a 100 Hz laser. These analyses were made possible thanks to a newly developed 50-m FP system providing seamless GRF data during a single sprint acceleration. Sixteen trained male sprinters performed two all-out 60-m sprints. We observed good agreement between the two methods for kinetic variables (e.g. grand average bias of 4.71%, range 0.696 ± 0.540-8.26 ± 5.51%), and high inter-trial reliability (grand average standard error of measurement of 2.50% for FP and 2.36% for the SM). This replication study clearly shows that when implemented correctly, this method accurately estimates sprint acceleration kinetics.
Effects of age and obesity on trunk kinetics and kinematics during dominant side one-handed carrying.
Venue: Journal of biomechanics

The proportions of older and obese people are increasing in both the general and working populations worldwide. Older and obese individuals are more susceptible to work-related musculoskeletal disorders (MSDs) in comparison with healthy, younger individuals. Manual material handling (MMH) is associated with the development of work-related MSDs. Although previous research has suggested that one-handed carrying is a particularly undesirable method of MMH, the effects of one-handed carrying on trunk kinetics and kinematics among older and/or obese people have not been adequately studied. The objective of this study was to examine the effects of age and obesity on trunk angles and moments during dominant side one-handed carrying of various load magnitudes. Twenty (20) participants divided into four groups with respect to age (young and older) and obesity (obese and non-obese) carried different loads (No-load [0 kg], Light [5.67 kg], and Heavy [10.21 kg]) in their dominant hand for approximately 6 m. Three-dimensional (3D) trunk angles and moments approximately about the L4/L5 vertebral segment were calculated using Visual3D. The findings indicated that while carrying a load in the dominant hand plays an important role in changing trunk kinematics and kinetics, the results were not dependent on age and/or obesity category. Absolute moments were greatest among participants in the obese groups; however, these moments were mitigated when normalized to body weight and height (%BW * Ht). Age did not exacerbate the effects of load magnitude on trunk kinetics and kinematics.
Significance of preoperative planning for prophylactic augmentation of osteoporotic hip: A computational modeling study.
Venue: Journal of biomechanics

A potential effective treatment for prevention of osteoporotic hip fractures is augmentation of the mechanical properties of the femur by injecting it with bone cement. This therapy, however, is only in research stage and can benefit substantially from computational simulations to optimize the pattern of cement injection. Some studies have considered a patient-specific planning paradigm for Osteoporotic Hip Augmentation (OHA). Despite their biomechanical advantages, customized plans require advanced surgical systems for implementation. Other studies, therefore, have suggested a more generalized injection strategy. The goal of this study is to investigate as to whether the additional computational overhead of the patient-specific planning can significantly improve the bone strength as compared to the generalized injection strategies attempted in the literature. For this purpose, numerical models were developed from high resolution CT images (n = 4). Through finite element analysis and hydrodynamic simulations, we compared the biomechanical efficiency of the customized cement-based augmentation along with three generalized injection strategies developed previously. Two series of simulations were studied, one with homogeneous and one with inhomogeneous material properties for the osteoporotic bone. The customized cement-based augmentation inhomogeneous models showed that injection of only 10 ml of bone cement can significantly increase the yield load (79.6%, P < 0.01) and yield energy (199%, P < 0.01) of an osteoporotic femur. This increase is significantly higher than those of the generalized injections proposed previously (23.8% on average). Our findings suggest that OHA can significantly benefit from a patient-specific plan that determines the pattern and volume of the injected cement.
Estimation of valvular resistance of segmented aortic valves using computational fluid dynamics.
Venue: Journal of biomechanics

Aortic valve stenosis is associated with an elevated left ventricular pressure and transaortic pressure drop. Clinicians routinely use Doppler ultrasound to quantify aortic valve stenosis severity by estimating this pressure drop from blood velocity. However, this method approximates the peak pressure drop, and is unable to quantify the partial pressure recovery distal to the valve. As pressure drops are flow dependent, it remains difficult to assess the true significance of a stenosis for low-flow low-gradient patients. Recent advances in segmentation techniques enable patient-specific Computational Fluid Dynamics (CFD) simulations of flow through the aortic valve. In this work a simulation framework is presented and used to analyze data of 18 patients. The ventricle and valve are reconstructed from 4D Computed Tomography imaging data. Ventricular motion is extracted from the medical images and used to model ventricular contraction and corresponding blood flow through the valve. Simplifications of the framework are assessed by introducing two simplified CFD models: a truncated time-dependent and a steady-state model. Model simplifications are justified for cases where the simulated pressure drop is above 10 mmHg. Furthermore, we propose a valve resistance index to quantify stenosis severity from simulation results. This index is compared to established metrics for clinical decision making, i.e. blood velocity and valve area. It is found that velocity measurements alone do not adequately reflect stenosis severity. This work demonstrates that combining 4D imaging data and CFD has the potential to provide a physiologically relevant diagnostic metric to quantify aortic valve stenosis severity.
Neural coding of sound envelope structure in songbirds
Venue: Journal of Comparative Physiology A

Songbirds are a well-established animal model to study the neural basis of learning, perception and production of complex vocalizations. In this system, telencephalic neurons in HVC present a state-dependent, highly selective response to auditory presentations of the bird’s own song (BOS). This property provides an opportunity to study the neural code behind a complex motor behavior. In this work, we explore whether changes in the temporal structure of the sound envelope can drive changes in the neural responses of highly selective HVC units. We generated an envelope-modified BOS (MOD) by reversing each syllable’s envelope but leaving the overall temporal structure of syllable spectra unchanged, which resulted in a subtle modification for each song syllable. We conducted in vivo electrophysiological recordings of HVC neurons in anaesthetized zebra finches (Taeniopygia guttata). Units analyzed presented a high BOS selectivity and lower response to MOD, but preserved the profile response shape. These results show that the temporal evolution of the sound envelope is being sensed by the avian song system and suggest that the biomechanical properties of the vocal apparatus could play a role in enhancing subtle sound differences.
Size discrimination in barn owls as compared to humans
Venue: Journal of Comparative Physiology A

We tested how well barn owls can discriminate objects of different sizes. This ability may be important for the owls when catching prey. We performed a quantitative experiment in the laboratory and trained owls in a task in which the owls had to discriminate whether two rhombi presented simultaneously on a computer monitor were of the same or of different sizes. We obtained full data sets with two experienced owls and one data point with a third owl. For objects being sufficiently larger than the spatial resolution of the barn owl, the angular threshold was related to object size, implying that the discrimination followed Weber’s law. The range of Weber fractions we determined was between 0.026 and 0.09. For object sizes close to the spatial resolution, performance degraded. We conducted similar experiments with human subjects. Human thresholds showed the same dependence on object size, albeit down to smaller object sizes. Human performance resulted in a range of Weber fractions extending from 0.025 to 0.036. The differences between owls and humans could be explained by the much higher spatial acuity of humans compared with owls.
Non-auditory, electrophysiological potentials preceding dolphin biosonar click production
Venue: Journal of Comparative Physiology A

The auditory brainstem response to a dolphin’s own emitted biosonar click can be measured by averaging epochs of the instantaneous electroencephalogram (EEG) that are time-locked to the emitted click. In this study, averaged EEGs were measured using surface electrodes placed on the head in six different configurations while dolphins performed an echolocation task. Simultaneously, biosonar click emissions were measured using contact hydrophones on the melon and a hydrophone in the farfield. The averaged EEGs revealed an electrophysiological potential (the pre-auditory wave, PAW) that preceded the production of each biosonar click. The largest PAW amplitudes occurred with the non-inverting electrode just right of the midline—the apparent side of biosonar click generation—and posterior of the blowhole. Although the source of the PAW is unknown, the temporal and spatial properties rule out an auditory source. The PAW may be a neural or myogenic potential associated with click production; however, it is not known if muscles within the dolphin nasal system can be actuated at the high rates reported for dolphin click production, or if sufficiently coordinated and fast motor endplates of nasal muscles exist to produce a PAW detectable with surface electrodes.
Do free-ranging rattlesnakes use thermal cues to evaluate prey?
Venue: Journal of Comparative Physiology A

Rattlesnakes use infrared radiation to detect prey animals such as small mammals and lizards. Because ectotherm locomotor performance depends on temperature, rattlesnakes could use prey temperature to evaluate the potential of lizards to evade attacks. Here, we tested whether hunting rattlesnakes use infrared information to (1) detect and (2) evaluate prey before attack. We expected thermal contrast between prey and background to be the best predictor of predatory behaviour under the prey detection hypothesis, and absolute prey temperature under the prey evaluation hypothesis. We presented lizard carcasses of varying temperatures to free-ranging sidewinder rattlesnakes (Crotalus cerastes) and scored behavioural responses as a function of thermal contrast, absolute lizard temperature, and light level. Thermal contrast and light level were the most salient predictors of snake behaviour. Snakes were more likely to respond to lizards and/or respond at greater distances at night and when thermal contrast was high, supporting the known prey detection function of infrared sensing. Absolute lizard temperature was not an important predictor of snake behaviour; thus, we found no evidence for temperature-based prey evaluation. Infrared sensing is still poorly understood in ecologically relevant contexts; future research will test whether rattlesnakes learn to evaluate prey based on temperature with experience.
Enhanced hemoglobin–oxygen unloading in migratory salmonids
Venue: Journal of Comparative Physiology B

Recent findings indicate that some teleost fishes may be able to greatly enhance hemoglobin–oxygen (Hb–O2) unloading at the tissues under conditions that result in catecholamine release. The putative mechanism relies on the high pH sensitivity of teleost hemoglobin (Hb), intracellular red blood cell (RBC) pH regulation via β-adrenergic Na+/H+ exchanger (β-NHE) activity, and plasma-accessible carbonic anhydrase at the tissues that short-circuits RBC pH regulation. Previous studies have shown that in rainbow trout, this system may double Hb–O2 unloading to red muscle compared to a situation without short-circuiting. The present study determined that: (1) in rainbow trout this system may be functional even at low concentrations of circulating catecholamines, as shown by conducting a dose–response analysis; (2) Atlantic and coho salmon also possess β-NHE activity, as shown by changes in hematocrit in adrenergically stimulated cells; and (3) with β-NHE short-circuiting, Atlantic and coho salmon may be able to increase Hb–O2 unloading by up to 74 and 159%, respectively, as determined by modeling based on O2 equilibrium curves. Together, these results indicate that a system to enhance Hb–O2 unloading may be common among salmonids and may be operational even under routine conditions. In view of the life histories of Atlantic and coho salmon, a system to enhance Hb–O2 unloading during exercise may help determine a successful spawning migration and thus reproductive success.