Modela-r as a Froude and Strouhal dimensionless numbers combination for dynamic similarity in running

The aim of this study was to test the hypothesis that running at fixed fractions of Froude (Nfr) and Strouhal (Str) dimensionless numbers combinations induce dynamic similarity between humans of different sizes. Nineteen subjects ran in three experimental conditions, (i) constant speed, (ii) similar speed (Nfr) and (iii) similar speed and similar step frequency (Nfr and Str combination). In addition to anthropometric data, temporal, kinematic and kinetic parameters were assessed at each stage to measure dynamic similarity informed by dimensional scale factors and by the decrease of dimensionless mechanical parameter variability. Over a total of 54 dynamic parameters, dynamic similarity from scale factors was met for 16 (mean r=0.51), 32 (mean r=0.49) and 52 (mean r=0.60) parameters in the first, the second and the third experimental conditions, respectively. The variability of the dimensionless preceding parameters was lower in the third condition than in the others. This study shows that the combination of Nfr and Str, computed from the dimensionless energy ratio at the center of gravity (Modela-r) ensures dynamic similarity between different-sized subjects. The relevance of using similar experimental conditions to compare mechanical dimensionless parameters is also proved and will highlight the study of running techniques, or equipment, and will allow the identification of abnormal and pathogenic running patterns. Modela-r may be adapted to study other abilities requiring bounces in human or animal locomotion or to conduct investigations in comparative biomechanics.     

Testing prediction accuracy in short-term ecological studies

Applied ecology is based on an assumption that a management action will result in a predicted outcome. Testing the prediction accuracy of ecological models is the most powerful way of evaluating the knowledge implicit in this cause-effect relationship, however, the prevalence of predictive modeling and prediction testing are spreading slowly in ecology. The challenge of prediction testing is particularly acute for small-scale studies, because withholding data for prediction testing (e.g., via k-fold cross validation) can reduce model precision. However, by necessity small-scale studies are common. We use one such study that explored small mammal abundance along an elevational gradient to test prediction accuracy of models with varying degrees of information content. For each of three small mammal species, we conducted 5000 iterations of the following process: (1) randomly selected 75 % of the data to develop generalized linear models of species abundance that used detailed site measurements as covariates, (2) used an information theoretic approach to compare the top model with detailed covariates to habitat type-only and null models constructed with the same data, (3) tested those models’ ability to predict the 25 % of the randomly withheld data, and (4) evaluated prediction accuracy with a quadratic loss function. Detailed models fit the model-evaluation data best but had greater expected prediction error when predicting out-of-sample data relative to the habitat type models. Relationships between species and detailed site variables may be evident only within the framework of explicitly hierarchical analyses. We show that even with a small but relatively typical dataset (n = 28 sampling locations across 125 km over two years), researchers can effectively compare models with different information content and measure models’ predictive power, thus evaluating their own ecological understanding and defining the limits of their inferences. Identifying the appropriate scope of inference through prediction testing is ecologically valuable and is attainable even with small datasets.     

Characterization of Competitive Inhibitors for the Transferase Activity of Pseudomonas aeruginosa Exotoxin A

A series of small, nonpolar compounds were tested for their ability to inhibit the ADP-ribosyl transferase activity of Pseudomonas aeruginosa exotoxin A. The IC 50 values for the compounds tested ranged from 87 nM to 484 μM for NAP and CMP12, respectively. It was demonstrated that NAP was a competitive inhibitor of the ADPRT reaction for the NAD + substrate with a K i of 45 ± 5 nM, which was in good agreement with the dissociation constant determined independently (K D =56 ± 6 nM). The IC 50 value for NAP was 87 ± 12 nM, which strongly correlated with the K i and K D values. Furthermore, NAP was shown to noncovalently associate with the exotoxin A active site using exhaustive dialysis, NMR, and electrospray mass spectrometry. Finally, a computer molecular model using the X-ray structure of the substrate-bound toxin was generated with NAP bound to the active site of exotoxin A at the nicotinamide-binding site. This model is consistent with the X-ray structure of the catalytic domain of poly-ADP-ribose polymerase complexed with 4-amino-naphthalimide (Compound 4) that was included in this study.     

Human sleep and circadian rhythms: a simple model based on two coupled oscillators

We propose a model of the human circadian system. The sleep-wake and body temperature rhythms are assumed to be driven by a pair of coupled nonlinear oscillators described by phase variables alone. The novel aspect of the model is that its equations may be solved analytically. Computer simulations are used to test the model against sleep-wake data pooled from 15 studies of subjects living for weeks in unscheduled, time-free environments. On these tests the model performs about as well as the existing models, although its mathematical structure is far simpler.Supported by NIGMS Grant No. 5-R01-GM-30719-03     

A bar model for the pump and channel function of the reconstituted Na+,K+-ATPase

Purified Na+,K+-ATPase is treated with trypsin. The altered enzyme is then reconstituted into liposomes and the change in active and passive Na+,K+-fluxes is recorded. Trypsin treatment transforms the slow passive Na+,K+-fluxes into leaks. The leak formation is correlated with the degree of proteolysis and the associated decrease in Na+,K+-ATPase activity. The active Na+,K+-transport capacity decreases in parallel with the passive transport. It is thus proposed that the Na+,K+-ATPase molecule primarily contains unspecific transmembrane tunnels that are rendered ion-selective by transverse bars of specific length (bar model).     

Temporal species richness‐biomass relationships along successional gradients

Abstract. Diversity‐biomass relationships are frequently reported to be hump‐shaped over space at a given time. However, it is not yet clear how diversity and biomass change simultaneously and how they are related to each other over time (e.g. in succession) at one locality. This study develops a temporal model based on the projected changes of various community variables in a generalized terrestrial environment after fire and uses post‐fire succession data on Santa Monica Mountains of southern California and other published succession data to examine the temporal diversity‐biomass relationships. The results indicate that in the early stages of succession, both diversity and biomass increase and a positive relationship appears, while in the late stages of succession, biomass continued to increase but diversity usually declines; thus a negative relationship may be observed. When the scales of measurement become sufficiently large so that the measured diversity and biomass cross various stages of succession, a ‘hump‐shaped’ relationship can emerge. The diversity‐biomass relationship appears to be concordant in space and time when appropriate scales are used. Formerly proposed explanations for spatial patterns may well apply to the temporal patterns (particularly colonization, facilitation and competitive exclusion).