The sensitivity of muscle force predictions to changes in physiologic cross-sectional area

The mechanical effects of a muscle are related in part to the size of the muscle and to its location relative to the joint it crosses. For more than a century, researchers have expressed muscle size by its 'physiological cross-sectional area' (PCSA). Researchers mathematically calculating muscle and joint forces typically use some expression of a muscle's PCSA to constrain the solution to one which is reasonable (i.e. a solution in which small muscles may not have large forces, and large muscles have large forces when expected or when there is significant electromyographic activity). It is obvious that muscle mass (and therefore any expression of PCSA) varies significantly from person to person, even in individuals of similar weight and height. Since it is not practical to predict the PCSA of each muscle in a living subject's limb or trunk, it is important to generally understand the sensitivity of muscle force solutions to possible variations in PCSA. We used nonlinear optimization techniques to predict 47 muscle forces and hip contact forces in a living subject. The PCSA (volume/muscle fiber length) of each of 47 lower limb muscle elements from two cadaver specimens and the 47 PCSA's reported by pierrynowski were input into an optimization algorithm to create three solution sets. The three solutions were qualitatively similar but at times a predicted muscle force could vary as much as two to eight times. In contrast, the joint force solutions were within 11% of each other and, therefore, much less variable.(ABSTRACT TRUNCATED AT 250 WORDS)     

Dry versus wet and gross: Comparisons between the dry skull method and gross dissection in estimations of jaw muscle cross-sectional area and bite forces in sea otters

Bite force is a measure of feeding performance used to elucidate links between animal morphology, ecology, and fitness. Obtaining live individuals for in vivo bite-force measurements or freshly deceased specimens for bite force modeling is challenging for many species. Thomason's dry skull method for mammals relies solely on osteological specimens and, therefore, presents an advantageous approach that enables researchers to estimate and compare bite forces across extant and even extinct species. However, how accurately the dry skull method estimates physiological cross-sectional area (PCSA) of the jaw adductor muscles and theoretical bite force has rarely been tested. Here, we use an ontogenetic series of southern sea otters (Enhydra lutris nereis) to test the hypothesis that skeletomuscular traits estimated from the dry skull method accurately predicts test traits derived from dissection-based biomechanical modeling. Although variables from these two methods exhibited strong positive relationships across ontogeny, we found that the dry skull method overestimates PCSA of the masseter and underestimates PCSA of the temporalis. Jaw adductor in-levers for both jaw muscles and overall bite force are overestimated. Surprisingly, we reveal that sexual dimorphism in craniomandibular shape affects temporalis PCSA estimations; the dry skull method predicted female temporalis PCSA well but underestimates male temporalis PCSA across ontogeny. These results highlight the importance of accounting for sexual dimorphism and other intraspecific variation when using the dry skull method. Together, we found the dry skull method provides an underestimation of bite force over ontogeny and that the underlying anatomical components driving bite force may be misrepresented.     

Fibre bundle element method of determining physiological cross-sectional area from three-dimensional computer muscle models created from digitised fibre bundle data

Physiological cross-sectional area (PCSA) is used to compare force-producing capabilities of muscles. A limitation of PCSA is that it cannot be measured directly from a specimen, as there is usually no area within the muscle traversed by all fibres. Traditionally, a formula requiring averaged architectural parameters has been used. The purpose of this paper is to describe the development of a fibre bundle element (FBE) method to calculate PCSA from digitised fibre bundle data of five architecturally distinct muscles and compare the FBE and PCSA formula. An FBE method was developed that used a serially arranged set of cylinders as the volumetric representation of each fibre bundle, and PCSA was computed as the summation of the cross-sectional area of each FBE. Four of five muscles had significantly different PCSA between FBE and formula methods. The FBE method provides an approach that considers architectural variances while minimising the need for averaged architectural parameters.     

Robust estimation of physiological cross-sectional area and geometric reconstruction for human skeletal muscle

Understanding muscle architecture is crucial to determining the mechanical function of muscle during body movements, because architectural parameters directly correspond to muscle performance. Accurate parameters are thus essential for reliable simulation. Human cadaveric muscle specimen data provides the anatomical detail needed for in-depth understanding of muscle and accurate parameter estimation. However, as muscle generally has non-uniform architecture, parameter estimation, specifically, physiological cross-sectional area (PCSA), is rarely straightforward. To deal effectively with this non-uniformity, we propose a geometric approach in which a polygon is sought to best approximate the cross-sectional area of each fascicle by accounting for its three-dimensional trajectory and arrangement in the muscle. Those polygons are then aggregated to determine PCSA and volume of muscle. Experiments are run using both synthetic data and muscle specimen data. From comparison of PCSA using synthetic data, we conclude that the proposed method enhances the robustness of PCSA estimation against variation in muscle architecture. Furthermore, we suggest reconstruction methods to extract 3D muscle geometry directly from fascicle data and estimated parameters using the level set method.     

DNA sequence-dependent deformability--insights from computer simulations

The article reviews some recent developments in studying DNA sequence-dependent deformability, with emphasis on computer modeling. After a brief outline of available experimental techniques, we proceed to computational methods and focus on atomic-resolution molecular dynamics (MD) simulations. A sequence-dependent local (base-pair step) force field inferred from MD is compared with force fields obtained by other techniques. Various methods for establishing global (flexible-rod) DNA elastic constants are reviewed, including an approach based on atomic resolution MD. The problem of defining the global deformation variables, as well as the question of anisotropy and nonlocal effects, are discussed. As an example, both local and global deformability calculations from atomic-resolution MD of EcoRI dodecamer are presented.     

How to asses, visualize and compare the anisotropy of linear structures reconstructed from optical sections--a study based on histopathological quantification of human brain microvessels

Three-dimensional analyses of the spatial arrangement, spatial orientation and preferential directions of systems of fibers are frequent tasks in many scientific fields, including the textile industry, plant biology and tissue modeling. In biology, systems of oriented and branching lines are often used to represent the three-dimensional directionality and topology of microscopic blood vessels supplying various organs. In our study, we present a novel p(χ2) (chi-square) method for evaluating the anisotropy of line systems that involves comparing the observed length densities of lines with the discrete uniform distribution of an isotropic line system with the χ2-test. Using this method in our open source software, we determined the rose of directions, preferential directions and level of anisotropy of linear systems representing the microscopic blood vessels in samples of various regions from human brains (cortex, subcortical gray matter and white matter). The novel method was compared with two other methods used for anisotropy quantification (ellipsoidal and fractional anisotropy). All three methods detected different levels of anisotropy of blood microvessels in human brain. The microvascular bed in the cortex was closer to an isotropic network, while the microvessels supplying the white matter appeared to be an anisotropic and direction-sensitive system. All three methods were able to determine the differences between various brain regions. The advantage of our p(χ2) method is its high correlation with the number of preferential directions of the line system. However, the software, named esofspy, is able to calculate all three of the measures of anisotropy compared and documented in this paper, thus making the methods freely available to the scientific community.     

Highly sensitive quantitative analysis of nicotianamine using LC/ESI-TOF-MS with an internal standard

A highly sensitive quantitative method for analyzing nicotianamine (NA) by liquid chromatography/electrospray ionization time-of-flight mass spectrometry (LC/ESI-TOF-MS) is reported. Fluorenylmethoxycarbonylation of nicotianamine reduced its polarity and enabled its retention in a reversed-phase column. The adoption of N(epsilon)-nicotyllysine (NL) as an internal standard ensured reliable quantification by giving a linear calibration curve drawn between the NA/NL molar ratios of standard solutions injected and the NA/NL area ratios in mass chromatograms. The high sensitivity of this analytical method allowed us to measure the amount of NA. This analytical method has applications to all research concerning NA.     

Morphometry of Macaca mulatta forelimb. I. Shoulder and elbow muscles and segment inertial parameters

The present study examined the morphometric properties of the forelimb, including the inertial properties of the body segments and the morphometric parameters of 21 muscles spanning the shoulder and/or elbow joints of six Macaca mulatta and three M. fascicularis. Five muscle parameters are presented: optimal fascicle length (L(0)(M)), tendon slack length (L(S)(T)), physiological cross-sectional area (PCSA), pennation angle (alpha(0)), and muscle mass (m). Linear regressions indicate that muscle mass, and to a lesser extent PCSA, correlated with total body weight. Segment mass, center-of-mass, and the moment of inertia of the upper arm, forearm, and hand are also presented. Our data indicate that for some segments, radius of gyration (rho) predicts segment moment of inertia better than linear regressions based on total body weight. Key differences between the monkey and human forelimb are highlighted.     

Covariation between forelimb muscle anatomy and bone shape in an Australian scratch-digging marsupial: Comparison of morphometric methods

The close association between muscle and bone is broadly intuitive; however, details of the covariation between the two has not been comprehensively studied. Without quantitative understanding of how muscle anatomy influences bone shape, it is difficult to draw conclusions of the significance of many morphological traits of the skeleton. In this study, we investigated these relationships in the Quenda (Isoodon fusciventer), a scratch-digging marsupial. We quantified the relationships between forelimb muscle anatomy and bone shape for animals representing a range of body masses (124–1,952 g) using two-block partial least square analyses. Muscle anatomy was quantified as muscle mass and physiological cross-sectional area (PCSA), and we used two morphometric methods to characterize bone shape: seven indices of linear bone proportions, and landmarks analysis. Bone shape was significantly correlated with body mass, reflecting allometric bone growth. Of the seven bone indices, only shoulder moment index (SMI) and ulna robustness index (URI) showed a significant covariation with muscle anatomy. Stronger relationships between muscle anatomy and forelimb bone shape were found using the landmark coordinates: muscle mass and PCSA were correlated with the geometric shape of the scapula, humerus, and third metacarpal, but to a lesser extent with shape of the ulna. Overall, our data show that landmark coordinates are more sensitive than bone indices to capturing shape changes evident throughout ontogeny, and is therefore a more appropriate method to investigate covariation with forelimb muscle anatomy. Single-species studies investigating ontogeny require refined methods to accurately develop understanding of the important relationships between muscle force generation and bone shape remodeling. Landmark analyses provide such a method.     

Enzyme activity in organic solvent as a function of water activity determined by membrane inlet mass spectrometry

Summary Membrane inlet mass spectrometry (MIMS) is introduced as a method for measuring water activity in nonpolar solvents, aqueous solutions and gas phase. The determination of the rate of hydrolysis of diphenyl carbonate by porcine liver esterase as a function of water activity in diisopropyl ether is presented as an example. A linear relationship is found between the enzyme activity and the water activity.     

Interaction of the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene with biomembranes

The relationship between the conditions of membrane labelling by the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene (DPH) and its fluorescence parameters was investigated. In the labelling solutions prepared by the usual method, the presence of DPH microcrystals was revealed which led to the lower resultant fluorescence anisotropy values. Lower labelling efficiency was observed with DPH solutions in tetrahydrofuran when compared with solutions in acetone. Modifications of the labelling procedure are proposed which give better reproducibility of the results. There modified method involves the preparation of a 2 X 10(-4) mol. 1(-1) DPH stock solution in acetone, a 100-fold dilution in an appropriate buffer, subsequent bubbling through with nitrogen for 30 min and mixing the resulting solution with cell/membrane suspension in a 1:1 (v/v) ratio. Changes in intensity, anisotropy and spectra of DPH fluorescence in the course of membrane labelling were studied. A two-stage model of the incorporation of DPH into membranes was proposed, according to which DPH molecules first quickly adhere to the membrane surface and then are slowly translocated to the apolar regions of the membrane.     

Mixed Convection Flow of Viscoelastic Fluid by a Stretching Cylinder with Heat Transfer

Flow of viscoelastic fluid due to an impermeable stretching cylinder is discussed. Effects of mixed convection and variable thermal conductivity are present. Thermal conductivity is taken temperature dependent. Nonlinear partial differential system is reduced into the nonlinear ordinary differential system. Resulting nonlinear system is computed for the convergent series solutions. Numerical values of skin friction coefficient and Nusselt number are computed and discussed. The results obtained with the current method are in agreement with previous studies using other methods as well as theoretical ideas. Physical interpretation reflecting the contribution of influential parameters in the present flow is presented. It is hoped that present study serves as a stimulus for modeling further stretching flows especially in polymeric and paper production processes.     

Muscle dimensions in the Japanese macaque hand

Macaques have been used as an important paradigm for understanding the neural control mechanisms of human precision grip capabilities. Therefore, we dissected the forearms and hands of two male Japanese macaques to systematically record the muscle mass, fascicle length and physiological cross-sectional area (PCSA). Comparisons of the mass fractions and PCSA fractions of the hand musculature among the Japanese macaque, chimpanzee, and human demonstrated that the sizes of the thenar and hypothenar eminence muscle groups are more balanced in the macaque and chimpanzee, but those of the thenar eminence group are much larger in the human, indicating that the capacity to generate force at the tip of the thumb is more restricted in macaques, despite their high manual dexterity. In the macaque, however, the extrinsic flexor muscles are much larger, possibly to facilitate weight bearing by the forelimbs in pronograde quadrupedal locomotion and forceful grasping of arboreal supports in gap-crossing movements such as leaping. Taking such anatomical differences imposed on the hand musculoskeletal system into consideration seems to be an important method of clarifying the mechanisms of precision grip in macaques.     

Improving Tikhonov regularization with linearly constrained optimization: application to the inverse epicardial potential solution.

Two methods to improve on the accuracy of the Tikhonov regularization technique commonly used for the stable recovery of solutions to ill-posed problems are presented. These methods do not require a priori knowledge of the properties of the solution or of the error. Rather they exploit the observed properties of overregularized and underregularized Tikhonov solutions so as to impose linear constraints on the sought-after solution. The two methods were applied to the inverse problem of electrocardiography using a spherical heart-torso model and simulated inner-sphere (epicardial) and outer-sphere (body) potential distributions. It is shown that if the overregularized and underregularized Tikhonov solutions are chosen properly, the two methods yield epicardial solutions that are not only more accurate than the optimal Tikhonov solution but also provide other qualitative information, such as correct position of the extrema, not obtainable using ordinary Tikhonov regularization. A heuristic method to select the overregularized and underregularized solutions is discussed.     

Mechanical similarity across ontogeny of digging muscles in an Australian marsupial (Isoodon fusciventer)

Many mammals dig, either during foraging to access subsurface food resources, or in creating burrows for shelter. Digging requires large forces produced by muscles and transmitted to the soil via the skeletal system; thus fossorial mammals tend to have characteristic modifications of the musculoskeletal system that reflect their digging ability. Bandicoots (Marsupialia: Peramelidae) scratch-dig mainly to source food, searching for subterranean food items including invertebrates, seeds, and fungi. They have musculoskeletal features for digging, including shortened, robust forelimb bones, large muscles, and enlarged muscle attachment areas. Here, we compared changes in the ontogenetic development of muscles associated with digging in the Quenda (Isoodon fusciventer). We measured muscle mass (m _m), pennation angle, and fiber length (FL) to calculate physiological cross-sectional area (PCSA; a proxy of maximum isometric force) as well as estimate the maximum isometric force (Fmax) for 34 individuals ranging in body size from 124 to 2,390 g. Males grow larger than females in this bandicoot species, however, we found negligible sex differences in mass-specific m _m, PCSA or FL for our sample. Majority of the forelimb muscles PCSA showed a positive allometric relationship with total body mass, while m _m and FL in the majority of forelimb muscles showed isometry. Mechanical similarity was tested, and two thirds of forelimb muscles maximum isometric forces (Fmax) scaled with isometry; therefore the forelimb is primarily mechanical similar throughout ontogeny. PCSA showed a significant difference between scaling slopes between main movers in the power stroke, and main movers of the recovery stroke of scratch-digging. This suggests that some forelimb muscles grow with positive allometry, specially these associated with the power stroke of digging. Intraspecific variation in PCSA is rarely considered in the literature, and thus this is an important study quantifying changes in muscle architectural properties with growth in a mammalian model of scratch-digging.     

Multipoint identity-by-descent prediction using dense markers to map quantitative trait loci and estimate effective population size

A novel multipoint method, based on an approximate coalescence approach, to analyze multiple linked markers is presented. Unlike other approximate coalescence methods, it considers all markers simultaneously but only two haplotypes at a time. We demonstrate the use of this method for linkage disequilibrium (LD) mapping of QTL and estimation of effective population size. The method estimates identity-by-descent (IBD) probabilities between pairs of marker haplotypes. Both LD and combined linkage and LD mapping rely on such IBD probabilities. The method is approximate in that it considers only the information on a pair of haplotypes, whereas a full modeling of the coalescence process would simultaneously consider all haplotypes. However, full coalescence modeling is computationally feasible only for few linked markers. Using simulations of the coalescence process, the method is shown to give almost unbiased estimates of the effective population size. Compared to direct marker and haplotype association analyses, IBD-based QTL mapping showed clearly a higher power to detect a QTL and a more realistic confidence interval for its position. The modeling of LD could be extended to estimate other LD-related parameters such as recombination rates.     

Muscle architectural properties in the common marmoset (<Emphasis Type="Italic">Callithrix jacchus</Emphasis>)

The common marmoset, Callithrix jacchus, is a small New World monkey that has recently gained attention as an important experimental animal model in the field of neuroscience as well in rehabilitative and regenerative medicine. This attention reflects the closer phylogenetic relationship between humans and common marmosets compared to that between humans and other experimental animals. When studying the neuronal mechanism behind various types of neurological motor disorders using the common marmoset, possible differences in muscle parameters (e.g., the force-generating capacity of each of the muscles) between the common marmoset and other animals must be taken into account to permit accurate interpretation of observed motor behavior. Differences in the muscle architectural properties are expected to affect biomechanics, and hence to affect neuronal control of body movements. Therefore, we dissected the forelimbs and hind limbs of two common marmosets, including systematic analysis of the muscle mass, fascicle length, and physiological cross-sectional area (PCSA). Comparisons of the mass fractions and PCSA fractions of the forelimb and hind limb musculature among the common marmoset, human, Japanese macaque, and domestic cat demonstrated that the overall muscle architectural properties of the forelimbs and hind limbs in the common marmoset are very similar to those of the Japanese macaque, a typical quadrupedal primate. However, muscle architectural properties of the common marmoset differ from those of the domestic cat, which has relatively larger hamstrings and pedal digital flexor muscles. Compared to humans, the common marmoset exhibits relatively smaller shoulder protractor, retractor, and abductor muscles and larger elbow extensor and rotator-cuff muscles in the forelimb, and smaller plantarflexor muscles in the hind limb. These differences in the muscle architectural properties must be taken into account when interpreting motor behaviors such as locomotion and arm-reaching movements in the common marmoset.     

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods.     

Density and hydration of fresh and fixed human skeletal muscle

The maximum tetanic tension of skeletal muscle (P(0)) is often estimated based on calculation of physiological cross-sectional area (PCSA). PCSA depends on muscle volume, pennation angle, and fiber length. Studies documenting PCSA in fixed human muscles usually compute muscle volume by dividing muscle mass by density. These studies use a density value of 1.0597 g/cm(3), which was originally based on unfixed rabbit and canine muscle tissue. Due to the dehydration effects of different fixation methods, the variable hydration that occurs when fixed tissue is stored in buffered saline, and the potential for species-specific muscle density, this value may be incorrect and an accurate value for fixed human muscle density is needed. To obtain an accurate density and water content values, 4% formaldehyde-fixed (n=54) and 37% formaldehyde-fixed (n=54) cadaveric human muscle samples were divided into 6 groups (0, 6, 12, 18, 24, or 30 h) for hydration in phosphate buffered saline (PBS). Measurements of volume, water content, and mass were made enabling calculation of muscle density. Additionally, water content was measured in living muscle (n=4) to determine the appropriate hydration time in PBS. Comparisons among groups demonstrated a significant increase in muscle water content and muscle volume over time, reaching living tissue levels after 24h, but, interestingly, the hydration process did not affect muscle density. These data yield a density value (mean+/-SE) of 1.112+/-0.006 g/cm(3) in 4% formaldehyde-fixed muscle and 1.055+/-0.006 g/cm(3) in 37% formaldehyde-fixed muscle. These results indicate that the use of inappropriate hydration times or density values can produce PCSA errors of 5-10%.