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Figure 7 from: Okechukwu P, Sharma M, Tan WH, Chan HK, Chirara K, Gaurav A, Al-Nema M (2020) In-vitro antidiabetic activity and in-silico studies of the binding energies of palmatine and the standard compounds with the three receptors of alpha amylase, alpha glucosidase, and DPP-IV enzyme. Pharmacia 67(4): 363-371. https://doi.org/10.3897/pharmacia.67.e58392

Figure 7 Docking interaction and binding mode of palmatine and alpha-glucosidase enzyme. The hydrogen bonds are presented in green dotted lines and the π-alkyl interactions are presented in pink dotted lines.

Figure 2 from: Okechukwu P, Sharma M, Tan WH, Chan HK, Chirara K, Gaurav A, Al-Nema M (2020) In-vitro antidiabetic activity and in-silico studies of the binding energies of palmatine and the standard compounds with the three receptors of alpha amylase, alpha glucosidase, and DPP-IV enzyme. Pharmacia 67(4): 363-371. https://doi.org/10.3897/pharmacia.67.e58392

Figure 2 Alpha-glucosidase enzyme inhibting activity ((IC50(µM) of palmatine, glimepiride, metformin and standard drug(acarbose). The result are shown as Mean ± standard deviation in triplicates (n = 3). The data were statistically analyzed by One-way ANOVA followed by Dunnet's post hoc test. Graph showed that acarbose(a) vs. glimepiride = p < 0.0001 = d; acarbose vs. metformin = p < 0.0001 = d; acarbose vs. palmatine = p < 0.0001 = d. Glimepiride vs. metformin = No significant = d, glimepiride vs. palmatine = No significant = d and metformin vs. palmatine = No significant = d.

Figure 1 from: Okechukwu P, Sharma M, Tan WH, Chan HK, Chirara K, Gaurav A, Al-Nema M (2020) In-vitro antidiabetic activity and in-silico studies of the binding energies of palmatine and the standard compounds with the three receptors of alpha amylase, alpha glucosidase, and DPP-IV enzyme. Pharmacia 67(4): 363-371. https://doi.org/10.3897/pharmacia.67.e58392

Figure 1 Alpha-amylase enzyme inhibting activity (IC50(µM) of palmatine, glimepiride, metformin and standard drug(acarbose). The result are shown as Mean ± standard deviation in triplicates (n = 3). The data were statistically analyzed by One-way ANOVA followed by Dunnet's post hoc test. Graph showed that acarbose(a) vs. glimepiride = p < 0.001 = c; acarbose vs. metformin = p < 0.01 = b; acarbose vs. palmatine = p < 0.0001 = d. Glimepiride vs. Metformin = p < 0.001 = c, glimepiride vs. palmatine = p < 0.0001 = d, metformin vs. palmatine = p < 0.0001 = d.

Figure 9 from: Okechukwu P, Sharma M, Tan WH, Chan HK, Chirara K, Gaurav A, Al-Nema M (2020) In-vitro antidiabetic activity and in-silico studies of the binding energies of palmatine and the standard compounds with the three receptors of alpha amylase, alpha glucosidase, and DPP-IV enzyme. Pharmacia 67(4): 363-371. https://doi.org/10.3897/pharmacia.67.e58392

Figure 9 Docking interaction and binding mode of palmatine and DPP-IV enzyme. The hydrogen bonds are presented in green dotted lines, the π-π staked interactions are presented in magenta dotted lines and the π-alkyl interactions are presented in pink dotted lines.

Figure 3 from: Okechukwu P, Sharma M, Tan WH, Chan HK, Chirara K, Gaurav A, Al-Nema M (2020) In-vitro antidiabetic activity and in-silico studies of the binding energies of palmatine and the standard compounds with the three receptors of alpha amylase, alpha glucosidase, and DPP-IV enzyme. Pharmacia 67(4): 363-371. https://doi.org/10.3897/pharmacia.67.e58392

Figure 3 DPP-IV enzyme inhibting activity ((IC50(µM) of glimepiride, metformin, palmatine and standard drug(sitagliptin). The result are shown as Mean ± standard deviation in triplicates (n = 3). The data were statistically analyzed by One-way ANOVA followed by Dunnet's post hoc test. Graph showed that sitagliptin (a) vs. palmatine = p < 0.0001 = d. Glimepiride and metformin = NA = No activity.

Figure 6 from: Okechukwu P, Sharma M, Tan WH, Chan HK, Chirara K, Gaurav A, Al-Nema M (2020) In-vitro antidiabetic activity and in-silico studies of the binding energies of palmatine and the standard compounds with the three receptors of alpha amylase, alpha glucosidase, and DPP-IV enzyme. Pharmacia 67(4): 363-371. https://doi.org/10.3897/pharmacia.67.e58392

Figure 6 Docking interaction and binding mode of acarbose and alpha-glucosidase enzyme. The hydrogen bonds are presented in green dotted lines and the π-alkyl interactions are presented in pink dotted lines.

opencc-by-4.0Aug 2020View details →

Energy-dependent protein folding: modeling how a protein folding machine may work

MD trajectories of all-atom MD simulations for peptides P1-P5.

opencc-zeroDec 2020View details →

Raw data on computational analysis the relationships of energy and mechanical properties with sensitivity for 1, 1-diamino-2, 2-dinitroethene based polymer bonded explosives

The dataset provides raw data on key properties in the text as well as raw data on the temperature and energy balances of the P, P1, P2, P3 and P4 systems at room temperature. These data allow the results obtained in the article to be reproduced, while the reader can obtain the raw data for the plots not labeled with data in the article and thus quantify the exact magnitude of the changes shown in the plots. The main work of the article is: Molecular dynamics (MD) simulations have been applied to investigate 1, 1-diamino-2, 2-dinitroethene (FOX-7) crystal and FOX-7(011)-based polymer-bonded explosives (PBXs) with four typical polymers, polyethylene glycol (PEG), fluorine-polymer (F2603), ethylene-vinyl acetate copolymer (EVA) and ester urethane (ESTANE5703) under COMPASS force field. Binding energy (Ebind), cohesive energy density (CED), initiation bond length distribution, radial distribution function, and isotropic mechanical properties of FOX-7 and its PBXs at different temperatures were reported for the first time, and the relationship between them and sensitivity. Using quantum chemistry, FOX-7 was optimized with the four polymers at the B3LYP/6-311++G(d,p) level, and the structure and RDG of the optimized composite system were analyzed.

Data from: PCB126 inhibits the activation of AMPK-CREB signal transduction required for energy sensing in liver

3,3',4,4',5-pentachlorobiphenyl (PCB126), a dioxin-like PCB, elicits toxicity through a wide array of non-carcinogenic effects, including metabolic syndrome, wasting, and non-alcoholic fatty-liver disease (NAFLD). Previously, we reported decreases in the transcription of several enzymes involved in gluconeogenesis, before the early onset of lipid accumulation. Hence, this study was aimed at understanding the impact of resultant decreases gluconeogenic enzymes on growth, weight and metabolism in the liver, upon extended exposure. Male Sprague-Dawley rats (75-100 g), fed a defined AIN-93G diet, were injected (ip) with single dose of soy oil (5 ml/kg body weight; n=14) or PCB126 (5 µmol/kg; n=15), 28 d, prior euthanasia. A subset of rats from each group were fasted for 12h (vehicle (n=6) and PCB126 (n=4)). Rats only showed significant weight loss between days 14 and 28 (P<0.05) and some mortality (P=0.0413). As in our previous studies, the expression levels of enzymes involved in gluconeogenesis (Pepck-c, G6Pase, Sds, Pc and Ldh-A) and glycogenolysis (Pygl) were strongly downregulated. The decreased expression of these enzymes in PCB126 treated rats after a 12 h fast decreased hepatic glucose production from glycogen and gluconeogenic substrates, exacerbating the hypoglycemia. Additionally, PCB126 caused hepatic steatosis and decreased the expression of the transcription factor Pparα and its targets, necessary for fatty-acid oxidation. The observed metabolic disruption across multiple branches of fasting metabolism resulted from inhibition in the activation of enzyme AMPK and transcription factor CREB signaling, necessary for "sensing" energy-deprivation and the induction of enzymes that respond to the PCB126 triggered fuel crisis in liver.

Data from: Flexibility, variability and constraint in energy management strategies across vertebrate taxa revealed by long-term heart rate measurements

1) Animals are expected to be judicious in the use of the energy they gain due to the costs and limits associated with its intake. The management of energy expenditure (EE) exhibited by animals has previously been considered in terms of three patterns: the constrained, independent and performance patterns of energy management. These patterns can be interpreted by regressing daily EE against maintenance EE measured over extended periods. From the multiple studies on this topic, there is equivocal evidence about the existence of universal patterns in certain aspects of energy management. 2) The implicit assumption that animals exhibit specifically one of three discrete energy management patterns, and without variation, seems simplistic. We suggest that animals can exhibit gradations of different energy management patterns and that the exact pattern will fluctuate as their environmental context changes. 3) To investigate these ideas, and for possible large-scale patterns in energy management pattern, we analysed long-term heart rate data – a strong proxy for EE – across and within individuals in 16 species of birds, mammals, and fish. 4) Our analyses of 292 individuals representing 46 539 observation-days suggest that vertebrates typically exhibit predominantly the independent or performance energy patterns at the across-individual level, and that the pattern does not associate with taxonomic group. Within individuals, however, animals generally exhibit some degree of energy constraint. Together, these findings indicate that across diverse species, some individuals supply more energy to all aspects of their life than do others, however all individuals must trade-off deployment of their available energy between competing functions. This demonstrates that within-individual analyses are essential for interpretation of energy management patterns. 5) We also found that species do not necessarily exhibit a fixed energy management pattern but rather temporal variation in their energy management over the year. Animals' energy management exhibited stronger energy constraint during periods of higher EE, which typically coincided with clear and key life cycle events such as reproduction, suggesting an adaptive plasticity to respond to fluctuating energy demands.

opencc-zeroDec 2016View details →

Data from: Travelling Wave Pulse Coupled Oscillator (TWPCO) Using a Self-Organizing Scheme for Energy-efficient Wireless Sensor Networks

Recently, Pulse Coupled Oscillator (PCO)-based travelling waves have attracted substantial attention by researchers in wireless sensor network (WSN) synchronization. Because WSNs are generally artificial occurrences that mimic natural phenomena, the PCO utilizes firefly synchronization of attracting mating partners for modelling the WSN. However, given that sensor nodes are unable to receive messages while transmitting data packets (due to deafness), the PCO model may not be efficient for sensor network modelling. To overcome this limitation, the current study proposed a new scheme called the Travelling Wave Pulse Coupled Oscillator (TWPCO). For this, the study used a self-organizing scheme for energy-efficient WSNs that adopted travelling wave biologically inspired network systems based on phase locking of the PCO model to counteract deafness. From the simulation, it was found that the proposed TWPCO scheme attained a steady state after a number of cycles. It also showed superior performance compared to other mechanisms, with a reduction in the total energy consumption of 25 %. The results showed that the performance improved by 13 % in terms of data gathering. Based on the results, the proposed scheme avoids the deafness that occurs in the transmit state in WSNs and increases the data collection throughout the transmission states in WSNs.

opencc-zeroDec 2011View details →

Data from: Density-dependent energy use contributes to the self-thinning relationship of cohorts

In resource-limited populations, an increase in average body size can occur only with a decline in abundance. This is known as self-thinning, and the decline in abundance in food-limited populations is considered proportional to the scaling of metabolism with body mass. This popular hypothesis may be inaccurate, because self-thinning populations can also experience density-dependent competition, which could alter their energy use beyond the predictions of metabolic scaling. This study tested whether density-dependent competition has an energetic role in self-thinning, by manipulating the abundance of the fish Macquaria novemaculeata and tank size to partition the effects of competition from metabolic scaling. We found that self-thinning can be density dependent and that changes in intraspecific competition may be more influential than metabolic scaling on self-thinning relationships. The energetic mechanism we propose is that density-dependent competition causes variation in the allocation of energy to growth, which alters the energetic efficiency of self-thinning cohorts. The implication is that food-limited cohorts and populations with competitive strategies that encourage fast-growing individuals will have less body mass at equilibrium and higher mortality rates. This finding sheds light on the processes structuring populations and can be used to explain inconsistencies in the mass-abundance scaling of assemblages and communities (the energetic-equivalence rule).

opencc-zeroFeb 2020View details →

Spatio-temporal variability of tidal-stream energy in north-western Europe

Initial selection of tidal stream energy sites is primarily based on identifying areas with the maximum current speeds. However, optimal design and deployment of turbines requires detailed investigations of the temporal variability of the available resource, focusing on areas with reduced variability, and hence the potential for more continuous energy conversion. These aspects were investigated in some of the most promising sites for tidal array development across the north-western European shelf seas: the Alderney Race, the Fromveur Strait, the Pentland Firth, and the Orkney channels. Particular attention was dedicated to asymmetry between the flood and ebb phases of the tidal cycle (due to the phase relationship between M2 and M4 constituents), and spring-neap variability of the available resource (due to M2 and S2 compound tides). A series of high resolution models were exploited to (i) produce a detailed harmonic database of these three components, and (ii) characterize, using energy resource metrics, temporal variability of the available power density. There was a clear contrast between the Alderney Race, with reduced temporal variability over semi-diurnal and fortnightly time scales, and sites in western Brittany and North Scotland which, due to increased variability, appeared less attractive for optimal energy conversion.

opencc-zeroDec 2018View details →

Data from: Nocturnal torpor by superb fairy-wrens: a key mechanism for reducing winter daily energy expenditure

Many passerine birds are small and require a high mass-specific rate of resting energy expenditure, especially in the cold. The energetics of thermoregulation is therefore an important aspect of their ecology, yet few studies have quantified thermoregulatory patterns in wild passerines. We used miniature telemetry to record the skin temperature (Tskin) of free-living superb fairy-wrens (Malurus cyaneus, 8.6 g; n = 6 birds over N = 7 to 22 days) and determine the importance of controlled reductions in body temperature during resting to their winter energy budgets. Fairy-wrens routinely exhibited large daily fluctuations in Tskin between maxima of 41.9 ± 0.6°C and minima of 30.4 ± 0.7°C, with overall individual minima of 27.4 ± 1.1°C (maximum daily range: 14.7 ± 0.9 °C). These results provide strong evidence of nocturnal torpor in this small passerine, which we calculated to provide a 42% reduction in resting metabolic rate at a Ta of 5 °C compared to active-phase Tskin. A capacity for energy-saving torpor has important consequences for understanding the behaviour and life-history ecology of superb fairy-wrens. Moreover, our novel field data suggest that torpor could be more widespread and important than previously thought within passerines, the most diverse order of birds.

Data from: Electron correlation in Li+, He, H− and the critical nuclear charge system ZC: energies, densities and Coulomb holes

This paper presents high accuracy correlation energies, intracule densities and Coulomb hole(s) for the lithium cation, helium, hydride ion and the system with the critical nuclear charge, Z_C, for binding two electrons. The fully-correlated (FC) wavefunction and the Hartree-Fock (HF) wavefunction are both determined using a Laguerre-based wavefunction. It is found that for the lithium cation and the helium atom a secondary Coulomb hole is present, in agreement with a previous literature finding, confirming a counter-intuitive conclusion that electron correlation can act to bring distant electrons closer together. However, no evidence for a tertiary Coulomb hole is found. For the hydride anion and the system just prior to electron detachment only a single Coulomb hole is present and electron correlation decreases the probability of finding the electrons closer together at all radial distances. The emergence of a secondary Coulomb hole is investigated and found to occur between Z = Z = 1.15 and Z = 1.20. The FC and HF energies and intracule densities (in atomic units) used to calculate the correlation energy and Coulomb hole respectively, are accurate to at least the nano-scale for helium and the cation and at least the micro-scale for the anions.

opencc-zeroDec 2018View details →

Data from: Destabilitation and energy characteristics of coal pillar in roadway driving along gob based on rockburst risk assessment

Roadway driving along adjacent goafs is an effective method to develop the recovery rate of coal resources. However, rock burst triggered by dynamic destabilization of coal pillars poses serious threats to safe and efficient mining, thereby significantly restricting the sustainable development of coal mines. In this study, from the perspectives of energy accumulation and dissipation, a mathematic model of coal pillar is established and the energy equilibrium relationship of the mechanical system is analyzed. The rock burst mechanism of coal pillars in gob-side entry is obtained based on a fold catastrophe mathematical model. Results indicate that the rock burst triggered by the instability is a destabilization phenomenon. If the stiffness factor of the mechanical system is less than 1 and the external force is enough to lead coal pillars to the peak stress point, then rock burst disaster occurs. The engineering analysis and numerical simulation are conducted to study the rock burst in the gob-side entry that occurred in Xin'an coal mine. Stress release caused by mining can reduce the risk of rock burst to a certain extent. The amount of elastic energy released is 6.4512×107 J, which is close to the observation data and verifies the correctness and rationality of the research method. The research result provides a theoretical basis and technical guidance for rock burst prevention and control in roadway driving along adjacent goafs.

opencc-zeroDec 2015View details →

Data from: Experimental measurements of water molecule binding energies for the second and third solvation shells of [Ca(H2O)n]2+ complexes

Further understanding of the biological role of the Ca2+ ion in an aqueous environment requires quantitative measurements of both the short- and long-range interactions experienced by the ion in an aqueous medium. Here, we present experimental measurements of binding energies for water molecules occupying the second and, quite possibly, the third solvation shell surrounding a central Ca2+ ion in [Ca(H2O)n]2+ complexes. Results for these large, previously inaccessible, complexes have come from the application of finite heat bath theory to kinetic energy measurements following unimolecular decay. Even at n = 20, the results show water molecules to be more strongly bound to Ca2+ than would be expected just from the presence of an extended network of hydrogen bonds. For n > 10, there is very good agreement between the experimental binding energies and recently published density functional theory calculations. Comparisons are made with similar data recorded for [Ca(NH3)n]2+ and [Ca(CH3OH)n]2+ complexes.

Data from: Maternal immunization increases nestling energy expenditure, immune function, and fledging success in a passerine bird

Female birds transfer maternally-derived antibodies (matAb) to their nestlings, via the egg yolk. These antibodies are thought to provide passive protection, and allow nestlings to avoid the costs associated with mounting an innate immune response. To test whether there is an energetic benefit to nestlings of receiving matAb, we challenged adult female tree swallows (Tachycineta bicolor) prior to clutch initiation with either lipopolysaccharide (LPS) or saline (Control). Following hatching, one half of each females nestlings were immunized on day 8 post-hatch with LPS or saline, and for 4-hrs post immunization nestling metabolic rate (MR) was measured. There was no difference in either LPS-reactive antibodies or total Ig levels between offspring of immunized and non-immunized mothers on day 6 or 14 post-hatch, possibly reflecting a relatively short half-life of matAbs in altricial birds. Additionally, we found no evidence that nestlings from LPS-immunized mothers could avoid the growth-suppression that may result from activation of an inflammatory response. Unexpectedly, we found that control-nestlings from LPS-mothers had higher resting MR than control-nestlings of control-mothers. We attribute the increased MR to the costs associated with a general nonspecific enhancement of immune function in nestlings from LPS-immunized mothers. Consistent with enhanced immune function, nestlings of immunized mothers had a more robust inflammatory response to phytohaemagglutinin, and higher fledging success. Our results suggest maternal antigen exposure pre-laying can result in increased fitness for both mothers and offspring, depending on food availability.

opencc-zeroDec 2013View details →

Data from: Eyeless Mexican cavefish save energy by eliminating the circadian rhythm in metabolism

The eyed surface form and eyeless cave form of the Mexican tetra Astyanax mexicanus experience stark differences in the daily periodicities of light, food and predation, factors which are likely to have a profound influence on metabolism. We measured the metabolic rate of Pachón cave and surface fish at a fixed swimming speed under light/dark and constant dark photoperiods. In constant darkness surface forms exhibited a circadian rhythm in metabolism with an increase in oxygen demand during the subjective daytime, whereas cave forms did not. The lack of circadian rhythm in metabolism leads to a 27% energy savings for Pachón cave fish compared to surface fish when comparing both forms in their natural photoperiods. When surface forms were tested under constant dark conditions they expended 38% more energy than cave forms under equivalent conditions. Elimination of the circadian rhythm in metabolism may be a general feature of animals that live in perpetually dark food-limited environments such as caves or the deep sea.