Bipartite network analysis reveals metabolic gene expression profiles that are highly associated with the clinical outcomes of acute myeloid leukemia

Dysregulated and reprogrammed metabolism are one of the most important characteristics of cancer, and exploiting cancer cell metabolism can aid in understanding the diverse clinical outcomes for patients. To investigate the differences in metabolic pathways among patients with acute myeloid leukemia (AML) and differential survival outcomes, we systematically conducted microarray data analysis of the metabolic gene expression profiles from 384 patients available from the Gene Expression Omnibus and Cancer Genome Atlas databases. Pathway enrichment analysis of differentially expressed genes (DEGs) showed that the metabolic differences between low-risk and high-risk patients mainly existed in two pathways: biosynthesis of unsaturated fatty acids and oxidative phosphorylation. Using the gene-pathway bipartite network, 62 metabolic genes were identified from 272 DEGs involved in 88 metabolic pathways. Based on the expression patterns of the 62 genes, patients with shorter overall survival (OS) durations in the training set (hazard ratio (HR) = 1.58, p = 0.038) and in two test sets (HR = 1.69 and 1.56 and p = 0.089 and 0.029, respectively) were well discriminated by hierarchical clustering analysis. Notably, the expression profiles of ALAS2, BCAT1, BLVRB, and HK3 showed distinct differences between the low-risk and high-risk patients. In addition, models for predicting the OS outcome of AML from the 62 gene signatures achieved improved performance compared with previous studies. In conclusion, our findings reveal significant differences in metabolic processes of patients with AML with diverse survival durations and provide valuable information for clinical translation.     

Lead-free solder alloys: Thermodynamic properties of the (Au + Sb + Sn) and the (Au + Sb) system

The thermodynamic properties of liquid (Au–Sb–Sn) alloys were studied with an electromotive force (EMF) method using the eutectic mixture of KCl/LiCl with addition of SnCl₂ as a liquid electrolyte. Activities of Sn in the liquid alloys were measured at three cross-sections with constant molar ratios of Au:Sb = 2:1, 1:1, and 1:2 with tin in the concentration range between 5 at.% and 90 at.% from the liquidus of the samples up to 1073 K. The integral Gibbs excess energies and the integral enthalpies at 873 K were calculated by Gibbs–Duhem integration. Additionally liquid Au–Sb alloys have been measured at 913 K with the EMF method as no reliable data for the Gibbs excess energies have been found in literature. The eutectic mixture of KCl/LiCl with addition of SbCl₃ has been used as an electrolyte for the measurements. The Gibbs excess energies from the (Au + Sb) system were necessary for the integration of the thermodynamic properties of the ternary (Au + Sb + Sn) system.     

Monte Carlo bicanonical ensemble simulation for sodium cation hydration free energy in liquid water

A series of bicanonical ensemble Monte Carlo (BC MC) simulations has been performed to calculate Na⁺ hydration Gibbs energy in aqueous solution. The hydration Gibbs energy of Na⁺ ion in aqueous solution is the difference between formation free energies of Na⁺ (H₂O)_n and (H₂O)_n clusters at n → α. The convergence of the hydration free energy to bulk water value is fast, and the results at n = 60 turned out to be in good agreement with experimental ones and those calculated using free energy perturbation method [1]. The ion–water interaction has been described by Aqvist's pair potential [1] and SPC model [2] has been used for water–water interactions. The behaviour of the absolute Gibbs energy, the entropy, the internal energy of the clusters and the development of hydration shells’ structure with the increase of the number of water molecules are discussed.     

Determination of the activities in the (Ni + Al) alloys in the temperature range 870 K to 920 K by a solid-state galvanic cell using a CaF2 electrolyte

The activities of aluminium and nickel are constituents in the (Ni + Al) superalloys in the concentration range 50 mol% to 70 mol% of Al at the temperatures (870, 900, and 920) K were determined with the help of solid-state galvanic cells involving calcium fluoride as an electrolyte. The partial molar Gibbs free energies of aluminium and nickel in the alloys, and the Gibbs free energy of mixing were calculated from the e.m.f. data. The values of the standard Gibbs free energies of formation of the intermetallic compounds NiAl, Ni₂Al₃, and NiAl₃ are also given.     

Electrochemical oxidation behavior of nitrite on a chitosan-carboxylated multiwall carbon nanotube modified electrode

A novel chitosan-carboxylated multiwall carbon nanotube modified glassy carbon electrode (MC/GCE) was developed to investigate the oxidation behavior of nitrite using cyclic voltammetry and differential pulse voltammetry modes. The electrochemical mechanism of the MC/GCE towards nitrite was discussed. The MC/GCE exhibited fast response towards nitrite with a detection limit of 1 × 10⁻⁷ mol l⁻¹ and a linear range of 5 × 10⁻⁷–1 × 10⁻⁴ mol l⁻¹. The possible interference from several common ions was tested. The proposed method was successfully applied in the detection of nitrite in real samples.     

Photophysical properties of 5-hydroxyflavone

To investigate the role of the excited triplet state in the deactivation process of 5-hydroxyflavone (5HF), the photophysical process of 5HF was studied by transient absorption, phosphorescence spectroscopies, and semiempirical calculations. The triplet–triplet absorption (T–T) spectra of 5HF and 5-methoxyflavone (5MF) were observed upon direct and triplet-sensitized excitation. The T–T spectrum of 5HF (λ_max=350 nm, τ_T=2.8 μs) was different from that of 5MF (λ_max=360 nm, τ_T=6.8 μs). Estimations of the triplet energies of 5HF and 5MF by quenching experiments, phosphorescence, and semiempirical (PM3/CI4) calculation revealed that 5HF underwent an intramolecular hydrogen atom transfer and formed the tautomer in the excited triplet state. The triplet energy of the normal form of 5HF was 260 kJ mol⁻¹, while that of the tautomer form (5HF′) was 197 kJ mol⁻¹. The triplet energy of 5MF, the model compound of the normal form of 5HF, was 261 kJ mol⁻¹. The PM3/CI4 calculation supported the experimental observations and suggested that the most stable conformer in the triplet state of 5HF is the tautomer form.     

A density model based on the Modified Quasichemical Model and applied to the (NaCl + KCl + ZnCl2) liquid

A theoretical model for the density of multicomponent inorganic liquids based on the Modified Quasichemical Model has been presented previously. By introducing in the Gibbs free energy of the liquid phase temperature-dependent molar volume expressions for the pure components and pressure-dependent excess parameters for the binary (and sometimes higher-order) interactions, it is possible to reproduce, and eventually predict, the molar volume and the density of the multicomponent liquid phase using standard interpolation methods. In the present article, this density model is applied to the (NaCl + KCl + ZnCl₂) ternary liquid and a Kohler–Toop-like asymmetric interpolation method is used. All available density data for the (NaCl + KCl + ZnCl₂) liquid were collected and critically evaluated, and optimized pressure-dependent model parameters have been found. This new volumetric model can be used with Gibbs free energy minimization software, to calculate the molar volume and the density of (NaCl + KCl + ZnCl₂) ternary melts.     

Gibbs free energy of transfer of a methylene group on {UCON + (sodium or potassium) phosphate salts} aqueous two-phase systems: Hydrophobicity effects

The Gibbs free energy of transfer of a suitable hydrophobic probe can be regarded as a measure of the relative hydrophobicity of the different phases. The methylene group (CH₂) can be considered hydrophobic, and thus be a suitable probe for hydrophobicity. In this work, the partition coefficients of a series of five dinitrophenylated-amino acids were experimentally determined, at 23 °C, in three different tie-lines of the biphasic systems: (UCON + K₂HPO₄), (UCON + potassium phosphate buffer, pH 7), (UCON + KH₂PO₄), (UCON + Na₂HPO₄), (UCON + sodium phosphate buffer, pH 7), and (UCON + NaH₂PO₄). The Gibbs free energy of transfer of CH₂ units were calculated from the partition coefficients and used to compare the relative hydrophobicity of the equilibrium phases. The largest relative hydrophobicity was found for the ATPS formed by dihydrogen phosphate salts.     

(Vapor + liquid) equilibria for the {water + poly(ethylene glycol diacetyl ether) (PEGDAE) and methanol + PEGDAE} systems

We measured binary (vapor + liquid) equilibrium data for the {water + poly(ethylene glycol diacetyl ether) (PEGDAE) and methanol + PEGDAE} systems at pressures up to 400 kPa and temperatures from 333 K to 393 K. A static apparatus was used in this study. The measured data were correlated by the Peng–Robinson equation of state using the Wong–Sandler mixing rules with NRTL as the excess Gibbs free energy model.     

Thermodynamic properties of sublimation of the ortho and meta isomers of acetoxy and acetamido benzoic acids

This paper reports vapour pressures measured at several different temperatures using the Knudsen effusion method of ortho-acetoxybenzoic acid (aspirin) (341.1 to 361.1) K, meta-acetoxybenzoic acid (344.2 to 362.2) K, ortho-acetamidobenzoic acid (367.2 to 389.2) K, and meta-acetamidobenzoic acid (423.2 to 441.1) K. The experimental results enabled the determination of the standard molar enthalpies, entropies and Gibbs energies of sublimation, at T = 298.15 K, of the four compounds studied. DSC experiments yield results of the temperature and enthalpy of fusion. The experimental results were compared with literature ones for the para isomers of the acids acetoxybenzoic and acetamidobenzoic. Correlations involving temperature of fusion, and standard molar enthalpy and Gibbs energy of sublimation of several substituted benzoic acids were proposed. Those correlation equations allow a good estimative of volatility of benzoic acid derivatives from their enthalpies of sublimation and temperatures of fusion.     

Thermodynamic properties of soddyite from solubility and calorimetry measurements

The release of uranium from geologic nuclear waste repositories under oxidizing conditions can only be modeled if the thermodynamic properties of the secondary uranyl minerals that form in the repository setting are known. Toward this end, we synthesized soddyite ((UO₂)₂(SiO₄)(H₂O)₂), and performed solubility measurements from both undersaturation and supersaturation. The solubility measurements rigorously constrain the value of the solubility product of synthetic soddyite, and consequently its standard-state Gibbs free energy of formation. The log solubility product (lg K_sp) with its error (1σ) is (6.43 + 0.20/−0.37), and the standard-state Gibbs free energy of formation is (−3652.2 ± 4.2 (2σ)) kJ mol⁻¹. High-temperature drop solution calorimetry was conducted, yielding a calculated standard-state enthalpy of formation of soddyite of (−4045.4 ± 4.9 (2σ)) kJ · mol⁻¹. The standard-state Gibbs free energy and enthalpy of formation yield a calculated standard-state entropy of formation of soddyite of (−1318.7 ± 21.7 (2σ)) J · mol⁻¹ · K⁻¹. The measurements and associated thermodynamic calculations not only describe the T = 298 K stability and solubility of soddyite, but they also can be used in predictions of repository performance through extrapolation of these properties to repository temperatures.     

Meta-analysis of microarray data: The case of imatinib resistance in chronic myelogenous leukemia

With the proliferation of related microarray studies by independent groups, a natural approach to analysis would be to combine the results across studies. In this article, we address a meta-analysis of the gene expression data on imatinib resistance in chronic myelogenous leukemia. First, an analysis of the overlapping among 6 published studies revealed that only 3 genes were coincident between 2 studies. A later reprocessing using different methods on 4 publicly available datasets revealed that 2 extra genes were overlapped between two sets. Both poor overlappings may be due to large differences in the sample source, the microarray platforms used, and a small difference in gene expression between the imatinib non-responder and responder patients. A search of common genes inside 4 public datasets afforded 404 well defined genes. Nevertheless, this necessary condition for meta-analysis caused the loss of many genes of possible interest. The expression signals of the common genes in the four datasets were reanalyzed using three summary statistical methods for combining quantitative information: Fisher, Stouffer and effect-size. Taking the three methods together and using an FDR < 0.10 threshold, a gene-list with 33 differentially expressed genes was found. Considering all the reanalysis approaches used in this work, a final gene-list with 38 differentially expressed genes is reported. Despite the important limitations to this microarray meta-analysis, the presented procedures and integrated gene-list may have some potential value as regards imatinib resistance in CML patients since it is the first attempt to integrate evidence about gene-lists in this area.     

Isothermal (vapour + liquid) equilibrium at several temperatures of (1-chlorobutane + 1-butanol,or 2-methyl-2-propanol)

Vapour pressures of (1-chlorobutane  +  1-butanol, or 2-methyl-2-propanol) at several temperatures between T =  278.15 and T =  323.15 K were measured by a static method. Reduction of the vapour pressures to obtain activity coefficients and excess molar Gibbs energies was carried out by fitting the vapour pressure data to the Redlich–Kister equation according to Barker’s method. For (1-chlorobutane  +  2-methyl-2-propanol) azeotropic mixtures with a minimum boiling temperature were observed over the whole temperature range.     

High-surface-area microporous carbon as the efficient photocathode of dye-sensitized solar cells

This paper reports on the application of cornstalks-derived high-surface-area microporous carbon (MC) as the efficient photocathode of dye-sensitized solar cells (DSCs). The photocathode, which contains MC active material, Vulcan XC–72 carbon black conductive agent, and TiO₂ binder, was obtained by a doctor blade method. Electronic impedance spectroscopy (EIS) of the MC film uniformly coated on fluorine doped SnO₂ (FTO) glass displayed a low charge-transfer resistance of 1.32 Ω cm². Cyclic voltammetry (CV) analysis of the as-prepared MC film exhibited excellent catalytic activity for I₃^?/I^? redox reactions. The DSCs assembled with the MC film photocathode presented a short-circuit photocurrent density (J_sc) of 14.8 mA cm^?2, an open-circuit photovoltage (V_oc) of 798 mV, and a fill factor (FF) of 62.3%, corresponding to an overall conversion efficiency of 7.36% under AM 1.5 irradiation (100 mW cm^?2), which is comparable to that of DSCs with Pt photocathode obtained by conventional thermal decomposition.     

Thermodynamic evaluation and optimization of the (LiF + NaF + KF + MgF2 + CaF2 + SrF2) system

A complete critical evaluation of all available phase diagram and thermodynamic data has been performed for all condensed phases of the (LiF + NaF + KF + MgF₂ + CaF₂ + SrF₂) system, and optimized model parameters have been found. The (LiF + NaF + KF + MgF₂ + CaF₂) subsystem has been critically evaluated in a previous article. The model parameters obtained for the binary and ternary subsystems can be used to predict thermodynamic properties and phase equilibria for the multicomponent system. The Modified Quasichemical Model for short-range ordering was used for the molten salt phase, and the low-temperature and high-temperature (CaF₂ + SrF₂) solid solutions were modelled using a cationic substitutional model with an ideal entropy and an excess Gibbs free energy expressed as a polynomial in the component mole fractions. Finally, the (Li, Na, K)(Mg, Ca, Sr)F₃ perovskite phase was modelled using the Compound Energy Formalism.     

(Vapour + liquid) equilibrium and excess Gibbs functions of ternary mixtures containing 1-butanol or 2-butanol,n-hexane,and 1-chlorobutane at T = 298.15 K

Isothermal (vapour + liquid) equilibrium data for the ternary mixtures 1-butanol + n-hexane + 1-chlorobutane and 2-butanol + n-hexane + 1-chlorobutane have been studied with a recirculating still at T = 298.15 K. The experimental data were satisfactorily checked for thermodynamic consistency using the method of van Ness. Activity coefficients and excess Gibbs function have been correlated with the Wilson equation. The G^E values obtained for the two ternary systems are very similar.     

Thermodynamic and transport properties of (1,2-ethanediol + 1-nonanol) at temperatures from (298.15 to 313.15) K

Densities and kinematic viscosities have been measured for (1,2-ethanediol + 1-nonanol) over the temperature range from (298.15 to 313.15) K. The speeds of sound in those mixtures within the temperature range from (293.15 to 313.15) K have been measured as well. Using the measurement results, the molar volumes, isentropic compressibility coefficients, molar isentropic compressibilities, and the corresponding excess and deviation values (excess molar volumes, excess isentropic compressibility coefficients, excess molar isentropic compressibilities, differently defined deviations of the speed of sound, and dynamic viscosity deviations) were calculated. The excess Gibbs free energies estimated by the use of the UNIQUAC model are also reported. The excess molar volumes and Gibbs free energies are positive, whereas the compressibility excesses are s-shaped. The excess and deviation values are expressed by Redlich–Kister polynomials and discussed in terms of variations of the structure of the system caused by the participation of two different alcohol molecules in the dynamic intermolecular association process through hydrogen bonding. The effect of temperature is discussed. The predictive abilities of the McAllister equation for viscosities of the mixtures under test have also been examined.     

Thermodynamic features associated with intercalation of some n-alkylmonoamines into barium phosphate

Elemental analysis for the synthesized crystalline lamellar compound conforms to the formula Ba(H₂PO₄)₂ and the X-ray diffraction patterns is in agreement with the lamellar structure for this compound. The precursor host was intercalated with a series of n-alkylmonoamines of the general formula H₃C(CH₂)_n-NH₂ (n = 1 to 4) in aqueous solution. The lamellar host was calorimetrically titrated with an aqueous amine solution at T = (298.15 ± 0.02) K and the enthalpy, Gibbs free energy and entropy were calculated. The enthalpic values increased, although not uniformly, with the number of carbon atoms is the amine chain, to give (−13.96 ± 0.12, −14.00 ± 0.48, −15.75 ± 0.23, −16.05 ± 0.11) kJ · mol⁻¹, from n = 1 to 4. The exothermic enthalpy, the negative Gibbs free energy and positive entropic values are in agreement with the favourable energetic process of intercalation for this system.     

Experimental measurement and modelling of solubility of inosine-5′-monophosphate disodium in pure and mixed solvents

The solubility of biological chemicals in solvents provide important fundamental data and is generally considered as an essential factor in the design of crystallization processes. The equilibrium solubility data of inosine-5′-monophosphate disodium (5′-IMPNa₂) in water, methanol, ethanol, acetone, as well as in the solvent mixtures (methanol + water, ethanol + water, acetone + water), were measured by an isothermal method at temperatures ranging from (293.15 to 313.15) K. The measured data in pure and mixed solvents were then modelled using the modified Apelblat equation, van’t Hoff equation, λh equation, ideal model and the Wilson model. The modified Apelblat equation showed the best modelling results, and it was therefore used to predict the mixing Gibbs free energies, enthalpies, and entropies of 5′-IMPNa₂in pure and binary solvents. The positive values of the calculated partial molar Gibbs free energies indicated the variations in the solubility trends of 5′-IMPNa₂. Water and ethanol (in the binary mixture with water) were found to be the most effective solvent and anti-solvent, respectively.     

Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 10⁵ · M⁻¹ at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation.