Impact of relative lower-limb length on heat loss and body temperature during running.

Objectives: Long lower limbs relative to body size are thought to be an adaptation to prevent excessive increases in body temperature during running in hot climate. The advantage of long lower limbs relative to body size is usually explained by an increase in body surface area relative to mass; however, the influence of limb length on relative body surface area was shown to be minor. We aimed to experimentally test the effect of relative lower-limb length (LLL) on body temperature changes during running.

Effect of Direct and Water-Mediated Interactions on the Identification of Hotspots in Biomolecular Complexes with Multiple Subsystems.

Identification of important residues in biochemical complexes is often a crucial step for many problems in molecular biology and biochemistry. A method is proposed to identify hotspots in biomolecular complexes based on a new metric, derived from networks representing molecular subunits (residues, bridging solvent molecules, ligands etc.) connected by interactions.

How E-, L-, and P-Selectins Bind to sLe and PSGL-1: A Quantification of Critical Residue Interactions.

Selectins and their ability to interact with specific ligands are a cornerstone in cell communication. Over the last three decades, a considerable wealth of experimental and molecular modeling insights into their structure and were gathered. Nonetheless, explaining the role of individual selectin residues on a quantitative level remained elusive, despite its importance in understanding the structure-function relationship in these molecules and designing their inhibitors.

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides.

Quantum mechanical (QM) calculations at the level of density-functional tight-binding are applied to a protein-DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 snapshots from molecular dynamics simulations. A detailed comparison of QM and force field (Amber) results is presented. It is shown that, when solvent screening is taken into account, the contributions of the backbones are small, and the binding of nucleotides in the double helix is governed by the base-base interactions.

Comparing walking and running in persistence hunting.

It has been proposed that humans' exceptional locomotor endurance evolved partly with foraging in hot open habitats and subsequently about 2 million years ago with persistence hunting, for which endurance running was instrumental. However, persistence hunting by walking, if successful, could select for locomotor endurance even before the emergence of any running-related traits in human evolution. Using a heat exchange model validated here in 73 humans and 55 ungulates, we simulated persistence hunts for prey of three sizes (100, 250, and 400 kg) and three sweating capacities (nonsweating, low, high) at 6237 combinations of hunter's velocity (1-5 m s, intermittent), air temperature (25-45 °C), relative humidity (30-90%), and start time (8:00-16:00).

Semi-Infinite Structure Analysis with Bimodular Materials with Infinite Element.

The modulus of elasticity of some materials changes under tensile and compressive states is simulated by constructing a typical material nonlinearity in a numerical analysis in this paper. The meshless Finite Block Method (FBM) has been developed to deal with 3D semi-infinite structures in the bimodular materials in this paper. The Lagrange polynomial interpolation is utilized to construct the meshless shape function with the mapping technique to transform the irregular finite domain or semi-infinite physical solids into a normalized domain.

Residue Folding Degree-Relationship to Secondary Structure Categories and Use as Collective Variable.

Recently, we have shown that the residue folding degree, a network-based measure of folded content in proteins, is able to capture backbone conformational transitions related to the formation of secondary structures in molecular dynamics (MD) simulations. In this work, we focus primarily on developing a collective variable (CV) for MD based on this residue-bound parameter to be able to trace the evolution of secondary structure in segments of the protein. We show that this CV can do just that and that the related energy profiles (potentials of mean force, PMF) and transition barriers are comparable to those found by others for particular events in the folding process of the model mini protein Trp-cage.

Geometrical Nonlinearity for a Timoshenko Beam with Flexoelectricity.

The Timoshenko beam model is applied to the analysis of the flexoelectric effect for a cantilever beam under large deformations. The geometric nonlinearity with von Kármán strains is considered. The nonlinear system of ordinary differential equations (ODE) for beam deflection and rotation are derived.

The Effect of Micro-Inertia and Flexoelectricity on Love Wave Propagation in Layered Piezoelectric Structures.

The non-classical linear governing equations of strain gradient piezoelectricity with micro-inertia effect are used to investigate Love wave propagation in a layered piezoelectric structure. The influence of flexoelectricity and micro-inertia effect on the phase wave velocity in a thin homogeneous flexoelectric layer deposited on a piezoelectric substrate is investigated. The dispersion relation for Love waves is obtained.

pyProGA-A PyMOL plugin for protein residue network analysis.

The field of protein residue network (PRN) research has brought several useful methods and techniques for structural analysis of proteins and protein complexes. Many of these are ripe and ready to be used by the proteomics community outside of the PRN specialists. In this paper we present software which collects an ensemble of (network) methods tailored towards the analysis of protein-protein interactions (PPI) and/or interactions of proteins with ligands of other type, e.

Challenging definitions and diagnostic approaches for ancient rare diseases: The case of poliomyelitis.

Objective: This paper aims to contribute to the definition of ancient rare diseases in skeletons displaying pathologies associated with paralysis. It uses a new suite of methods, which can be applied to challenging cases of possible paralysis in archaeologically-derived human skeletal material, specifically applied to the identification of poliomyelitis.

Materials: An adult male skeleton from Roman Halbturn, Austria.

Weak O binding and strong HO binding at the non-heme diiron center of trypanosome alternative oxidase.

Alternative oxidase (AOX) catalyzes the four-electron reduction of dioxygen to water as an additional terminal oxidase, and the catalytic reaction is critical for the parasite to survive in its bloodstream form. Recently, the X-ray crystal structure of trypanosome alternative oxidase (TAO) complexed with ferulenol was reported and the molecular structure of the non-heme diiron center was determined. The binding of O was a unique side-on type compared to other iron proteins.

Non-destructive lock-picking of a historical treasure chest by means of X-ray computed tomography.

An innovative approach to a non-destructive lock mechanism examination by means of X-ray computed tomography (CT) was involved in a careful opening of a locked 19th century chest missing the key, as an interdisciplinary cooperation with the restorers. In regard of the exploration and conservation of such locked objects, their opening is important to the restorers. However, the opening may be complicated, if not impossible, without damaging the object when the key is missing.

The Meshless Analysis of Scale-Dependent Problems for Coupled Fields.

The meshless local Petrov-Galerkin (MLPG) method was developed to analyze 2D problems for flexoelectricity and higher-grade thermoelectricity. Both problems were multiphysical and scale-dependent. The size effect was considered by the strain and electric field gradients in the flexoelectricity, and higher-grade heat flux in the thermoelectricity.

Ab initio relativistic potential energy surfaces of benzene-Xe complex with application to intermolecular vibrations.

The benzene-Xe (BXe) complex in its electronic ground state is studied using ab initio methods. Since this complex contains the heavy Xe atom, the relativistic effects cannot be neglected. We test two different approaches that describe the scalar relativistic effects in the framework of the coupled-cluster level of theory with single, double, and perturbative triple excitations, used for the interaction energy calculations.

Protein Dynamics and the Folding Degree.

The analysis of folding trajectories for proteins is an open challenge. One of the problems is how to describe the amount of folded secondary structure in a protein. We extend the use of Estradas' folding degree ( , , 697) for the analysis of the evolution of the folding stage during molecular dynamics (MD) simulation.

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method.

Proteins are vital components of living systems, serving as building blocks, molecular machines, enzymes, receptors, ion channels, sensors, and transporters. Protein-protein interactions (PPIs) are a key part of their function. There are more than 645,000 reported disease-relevant PPIs in the human interactome, but drugs have been developed for only 2% of these targets.

Dehydration and persistence hunting in Homo erectus.

Persistence hunting has been suggested to be a key strategy for meat acquisition in Homo erectus. However, prolonged locomotion in hot conditions is associated with considerable water losses due to sweating. Consequently, dehydration has been proposed to be a critical limiting factor, effectively curtailing the usefulness of persistence hunting prior to the invention of water containers.

Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins.

Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is a method for enhanced conformational sampling of proteins. To search a broad conformational subspace, nt-PaCS-MD repeats cycles of conformational resampling from relevant initial structures. Generally, the conformational sampling efficiency of nt-PaCS-MD depends on a selection rule for the initial structures.

Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein Dynamics.

Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is an enhanced conformational sampling method of proteins, which does not rely on knowledge of the target structure. It makes use of cyclic resampling from some relevant initial structures to expand the searched conformational subspace. The efficiency of nt-PaCS-MD depends on the selections of these initial structures.

Error in the estimation of periosteal and endosteal contours from micro-CT scans for nonadult tibiae and humeri.

Objectives: This article summarized errors obtained by diverse techniques used for the derivation of cross-sectional contours in nonadult humeri and tibiae.

Materials And Methods: We analyzed cross-sectional contours in a total sample of 62 humeral and 75 tibial diaphyses in the age between birth and 12 years divided into three age groups. Long bone 35% (humeri) and midshaft (tibiae) cross-sections were taken on micro-CT images and analyzed by EPJMacro in FIJI.

Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction.

Geometric and electronic structure changes in the copper (Cu) centers in bilirubin oxidase (BOD) upon a four-electron reduction were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. For the QM region, the unrestricted density functional theory (UDFT) method was adopted for the open-shell system. We found new candidates of the native intermediate (NI, intermediate II) and the resting oxidized (RO) states, i.

Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations.

In modern praxis, a knowledge-driven design of pharmaceutical compounds relies heavily on protein structure data. Nonetheless, quantification of the interaction between protein and ligand is of great importance in the theoretical evaluation of the ability of a pharmaceutical compound to comply with certain expectations. The FMO (fragment molecular orbital) method is handy in this regard.