Free energy approximations in simple lattice proteins

This work addresses the question of whether it is possible to define simple pairwise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how reliable it could possibly be. In a two-dimensional, infinite lattice model system one can calculate exact free energies by exhaustive enumeration. A series of approximations were fitted to exact results to assess the feasibility and utility of pairwise free energy terms. Approximating the true free energy with pairwise interactions gives a poor fit with little transferability between systems of different size. Adding extra artificial terms to the approximation yields better fits, but does not improve the ability to generalize from one system size to another. Furthermore, one cannot distinguish folding from nonfolding sequences via the approximated free energies. Most usefully, the methodology shows how one can assess the utility of various terms in lattice protein/polymer models. (C) 2001 American Institute of Physics.

Energy and averages in the mechanics of granular materials

We derive a general thermo-mechanical theory for particulate materials consisting of granules of arbitrary whose material points possess three translational and three independent rotational degrees of freedom. Additional field variables are the translational and rotational granular temperatures, the kinetic energies shape and size. The kinematics of granulate is described within the framework of a polar continuum theory of the velocity and spin fluctuations respectively and the usual thermodynamic temperature. We distinguish between averages over particle categories (averages in mass/velocity and moment of inertia/spin space, respectively) and particle phases where the average extends over distinct subsets of particle categories (multi phase flows). The relationship between the thermal energy in the granular system and phonon energy in a molecular system is briefly discussed in the main body of the paper and discussed in detail in the Appendix A. (C) 2001 Elsevier Science B.V. All rights reserved.

Predicting energy requirements in the clinical setting: Are current methods evidence based?

Estimating energy requirements is necessary in clinical practice when indirect calorimetry is impractical. This paper systematically reviews current methods for estimating energy requirements. Conclusions include: there is discrepancy between the characteristics of populations upon which predictive equations are based and current populations; tools are not well understood, and patient care can be compromised by inappropriate application of the tools. Data comparing tools and methods are presented and issues for practitioners are discussed. (C) 2003 International Life Sciences Institute.

Shell utilization by the land hermit crab Coenobita scaevola (Anomura, Coenobitidae) from Wadi El-Gemal, Red Sea

We conducted a study in order to determine the shell utilization pattern of the land hermit crab Coenobita scaevola (Forskal, 1775), the only species representing the family Coenobitidae in the Red Sea. Hermit crabs were collected during July 2003 and January 2004 along the sandy shores of protected area of Wadi-Elgemal, south Red Sea. Animals were fixed in 10% formalin and transported to the laboratory where they were weighed and measured for cephalothoracic shield length (CSL) and width, left propodus length and height. Gastropod shells species were identified, weighed and measured for shell aperture width and length and shell internal volume. A total of 391 individuals were collected (219 females, 172 males) and were found occupying ten shell species, with clear significant occupation of Nerita undata. A positive relationship was obtained between the size of the shells occupied and the hermit crabs. Analysis of shell internal volume and crab dimensions demonstrated that this shell dimension constitutes mainly the determinant for C. scaevola shell utilization. With respect to the size of the animals and the occupied shell type, Nerita undata was occupied by a wide range of CSL (2.5-8.5mm). Small sized crabs (2.5-3.5mm CSL) occupied Planaxis sulcatus and Nassarius arcularius plicatus while larger specimens (8.5-9.5mm CSL) occupied Turbo radiatits, Polinices milanostomus and Monodonta canilifera. Variations in the shell occupation were also recognized among male and females. Comparisons among populational and shell use features led us to suggest the use of this land hermit crab as key-species in the preserving program of shores and protected areas, since this species is the first organism to disappear from any shore when a new tourist establishment is implemented.

Energy turnover in the normoxic and anoxic turtle heart

We examined the possibility that the heart of the turtle Chrysemys scripta is an exceptional anaerobic performer, by measuring myocardial power output, lactate output, and estimated ATP turnover in perfused heart preparations. Over a range of myocardial power outputs at 5 and 15 degrees C we find that turtle hearts perfused with anoxic saline do not show a particularly outstanding ability to produce ATP anaerobically. Furthermore, at 15 degrees C anoxia reduced the ATP turnover rate to 50% of the normoxic rate. At 5 degrees C the anoxia-induced depression of ATP turnover was even more pronounced, being 4-fold lower than the normoxic rate. In addition, anoxia at 5 degrees C reduced the basal metabolic rate of the turtle heart. We conclude that long-term cardiac tolerance of hypoxia in this species is more likely related to metabolic depression rather than to an exceptional anaerobic performance. (C) 1997 Elsevier Science Inc.

The influence of collision energy and strain accumulation on the kinetics of mechanical alloying

The kinetics of mechanical alloying have been investigated by examining the effect that ball mass has on the rate at which titanium carbide forms from the elements. By varying the ball density while keeping the ball diameter and the charge ratio constant, the collision energy was independently controlled. Grinding media with a density from 3.8 g cm(-3) (agate) to 16.4 g cm(-3) (tungsten carbide) were used. The reaction rate increases exponentially with ball mass until a critical level is reached, which is determined by the induced temperature rise. Above this level, collisions of higher energy have no advantage. It is also shown that the reaction rate increases exponentially with the rate at which strain accumulates in the reactants. It is suggested that the strain accumulation rate in mechanically induced reactions is analogous to temperature in thermally induced chemical reactions.

Characterization of Adherent Umbilical Cord Blood Stromal Cells Regarding Passage, Cell Number, and Nano-biomarking Utilization

Adherent umbilical cord blood stromal cells (AUCBSCs) are multipotent cells with differentiation capacities. Therefore, these cells have been investigated for their potential in cell-based therapies. Quantum Dots (QDs) are an alternative to organic dyes and fluorescent proteins because of their long-term photostability. In this study we determined the effects of the cell passage on AUCBSCs morphology, phenotype, and differentiation potential. QDs labeled AUCBSCs in the fourth cell passage were differentiated in the three mesodermal lineages and were evaluated using cytochemical methods and transmission electron microscopy (TEM). Gene and protein expression of the AUCBSCs immunophenotypic markers were also evaluated in the labeled cells by real-time quantitative PCR and flow cytometry. In this study we were able to define the best cellular passage to work with AUCBSCs and we also demonstrated that the use of fluorescent QDs can be an efficient nano-biotechnological tool in differentiation studies because labeled cells do not have their characteristics compromised.

Non-equilibrium energy and momentum accommodation coefficients of Ar atoms scattered from Ni(001) in the thermal regime: A molecular dynamics study

Molecular dynamics simulations are used to study energy and momentum transfer of low-energy Ar atoms scattered from the Ni(001) surface. The investigation concentrates on the dependence of these processes on incident energy, angles of incidence and surface temperature. Energy transfer exhibits a strong dependence on the surface temperature, at incident energies below 500 meV, and incident angles close to specular incidence. Above 500 meV, the surface temperature dependence vanishes, and a limiting value in the amount of energy transferred to the surface is attained. Momentum exchange is investigated in terms of tangential and normal components. Both components exhibit a weak surface temperature dependence, but they have opposite behaviours at all incidence angles. In each component, momentum can be lost or gained following the interaction with the surface. (C) 1997 Elsevier Science B.V.

Waterlogging and fire impacts on nitrogen availability and utilization in a subtropical wet heathland (wallum)

Protein, amino acids and ammonium were the main forms of soluble soil nitrogen in the soil solution of a subtropical heathland (wallum). After fire, soil ammonium and nitrate increased 90- and 60-fold, respectively. Despite this increase in nitrate availability after fire, wallum species exhibited uniformly low nitrate reductase activities and low leaf and xylem nitrate, During waterlogging soil amino acids increased, particularly gamma-aminobutyric acid (GABA) which accounted for over 50% of amino nitrogen. Non-mycorrhizal wallum species were significantly (P < 0.05) N-15-enriched (0.3-4.3 parts per thousand) compared to species with mycorrhizal associations (ericoid-type, ecto-, va-mycorrhizal) which were strongly depleted in N-15 (-6.3 to -1.8 parts per thousand). Lignotubers and roots had delta(15)N signatures similar to that of the leaves of respective species. The exceptions were fine roots of ecto-, ecto/va-, and ericoid type mycorrhizal species which were enriched in N-15 (0.1-2 4 parts per thousand). The delta(15)N signatures of delta(15)N(total soil N) and delta(15)N(soil NH4+) were in the range 3.7-4.5 parts per thousand, whereas delta(15)N(soil NO3-) was significantly (P < 0.05) more enriched in N-15 (9.2-9.8 parts per thousand). It is proposed that there is discrimination against N-15 during transfer of nitrogen from fungal to plant partner. Roots of selected species incorporated nitrogen sources in the order of preference: ammonium > glycine > nitrate. The exception were proteoid roots of Hakea (Proteaceae) which incorporated equal amounts of glycine and ammonium.

Resting energy expenditure in white and non-white severely obese women

This study aimed to compare the resting energy expenditure (REE) of white and non-white severely obese Brazilian women. REE was examined in 83 severely obese Brazilian women (n = 58 white and 25 non-white) with mean (+/- SD) age 42.99 +/- 11.35 and body mass index 46.88 +/- 6.22 kg/m(2) who were candidates for gastric bypass surgery. Body composition was assessed by air displacement plethysmography (ADP) BOD PODO body composition system (Life Measurement Instruments, Concord, CA) and REE was measured, under established protocol, with an open-circuit calorimeter (Deltatrac II MBM-200, Datex-Ohmeda, Madison, WI, USA). There was no significant difference between the REE of white and non-white severely obese women (1,953 +/- 273 and 1,906 +/- 271 kcal/d, respectively; p = 0.48). However, when adjusted for fat free mass (MLG), REE was significantly higher in non-white severely obese women (difference between groups of 158.4 kcal, p < 0.01). REE in white women was positively and significantly correlated to C-reactive protein (PCR) (r = 0.41.8; P < 0.001) and MLG (r = 0.771; P < 0.001). In the non-white women, REE was only significantly correlated to MLG (r = 0.753; P < 0.001). The multiple linear regression analysis showed that skin color, MLG and PCR were the significant determinants of REE (R(2) = 0.55). This study showed that, after adjustment for MLG, non-white severely obese women have a higher REE than the white ones. The association of body composition inflammation factors and REE in severely obese Brazilian women remains to be further investigated.

New Specific Equation to Estimate Resting Energy Expenditure in Severely Obese Patients

Calculating the estimated resting energy expenditure (REE) in severely obese patients is useful, but there is controversy concerning the effectiveness of available prediction equations (PE) using body weight (BW). We evaluated the efficacy of REE equations against indirect calorimetry (IC) in severely obese subjects and aimed to develop a new equation based on body composition compartments. One hundred and twenty severely obese patients had their REE measured (MREE) by IC and compared to the most commonly used PE (Harris-Benedict (HB), Ireton-Jones, Owen, and Mifflin St. Jeor). In a random sample (n = 60), a new REE equation based on fat-free mass (FFM) was developed and validated. All PE studied failed to estimate REE in severe obesity (low concordance correlation coefficient (CCC) and limits of agreement of nearly 50% of the sample +/- 10% of MREE). The HB equation using actual BW exhibited good results for all samples when compared to IC (2,117 +/- 518 kcal/day by HB vs. 2,139 +/- 423 kcal/day by MREE, P > 0.01); these results were blunted when patients were separated by gender (2,771 vs. 2,586 kcal/day, P < 0.001 in males and 1,825 vs. 1,939 kcal/day, P < 0.001 in females). A new resting energy expenditure equation prediction was developed using FFM, Horie-Waitzberg, & Gonzalez, expressed as 560.43 + (5.39 x BW) + (14.14 x FFM). The new resting energy expenditure equation prediction, which uses FFM and BW, demonstrates higher accuracy, precision, CCC, and limits of agreement than the standard PE in patients when compared to MREE (2,129 +/- 45 kcal/day vs. 2,139 +/- 423 kcal/day, respectively, P = 0.1). The new equation developed to estimate REE, which takes into account both FFM and BW, provides better results than currently available equations.