Multi-omics integration with weighted affinity and self-diffusion applied for cancer subtypes identification.

BACKGROUND: Characterizing cancer molecular subtypes is crucial for improving prognosis and individualized treatment. Integrative analysis of multi-omics data has become an important approach for disease subtyping, yielding better understanding of the complex biology. Current multi-omics integration tools and methods for cancer subtyping often suffer challenges of high computational efficiency as well as the problem of weight assignment on data types. RESULTS: Here, we present an efficient multi-omics integration via weighted affinity and self-diffusion (MOSD) to dissect cancer heterogeneity. MOSD first construct local scaling affinity on each data type and then integrate all affinities by weighted linear combination, followed by the self-diffusion to further improve the patients' similarities for the downstream clustering analysis. To demonstrate the effectiveness and usefulness for cancer subtyping, we apply MOSD across ten cancer types with three measurements (Gene expression, DNA methylation, miRNA). CONCLUSIONS: Our approach exhibits more significant differences in patient survival and computationally efficient benchmarking against several state-of-art integration methods and the identified molecular subtypes reveal strongly biological interpretability. The code as well as its implementation are available in GitHub: https://github.com/DXCODEE/MOSD .

Determination of self-diffusion coefficients in mixtures with benchtop 13C NMR spectroscopy via polarization transfer.

Nuclear magnetic resonance (NMR) is an established method to determine self-diffusion coefficients in liquids with high precision. The development of benchtop NMR spectrometers makes the method accessible to a wider community. In most cases, 1H NMR spectroscopy is used to determine self-diffusion coefficients due to its high sensitivity. However, especially when using benchtop NMR spectrometers for the investigation of complex mixtures, the signals in 1H NMR spectra can overlap, hindering the precise determination of self-diffusion coefficients. In 13C NMR spectroscopy, the signals of different compounds are generally well resolved. However, the sensitivity of 13C NMR is significantly lower than that of 1H NMR spectroscopy leading to very long measurement times, which makes diffusion coefficient measurements based on 13C NMR practically infeasible with benchtop NMR spectrometers. To circumvent this problem, we have combined two known pulse sequences, one for polarization transfer from 1H to the 13C nuclei (PENDANT) and one for the measurement of diffusion coefficients (PFG). The new method (PENPFG) was used to measure the self-diffusion coefficients of three pure solvents (acetonitrile, ethanol and 1-propanol) as well as in all their binary mixtures and the ternary mixture at various compositions. For comparison, also measurements of the same systems were carried out with a standard PFG-NMR routine on a high-field NMR instrument. The results are in good agreement and show that PENPFG is a useful tool for the measurement of the absolute value of the self-diffusion coefficients in complex liquid mixtures with benchtop NMR spectrometers.

Molecular Dynamics Study of the Green Solvent Polyethylene Glycol with Water Impurities.

Polyethylene glycol (PEG) is one of the environmentally benign solvent options for green chemistry. It readily absorbs water when exposed to the atmosphere. The Molecular Dynamics (MD) simulations of PEG200, a commercial mixture of low molecular weight polyethyelene glycol oligomers, as well as di-, tetra-, and hexaethylene glycol are presented to study the effect of added water impurities up to a weight fraction of 0.020, which covers the typical range of water impurities due to water absorption from the atmosphere. Each system was simulated a total of four times using different combinations of two force fields for the water (SPC/E and TIP4P/2005) and two force fields for the PEG and oligomer (OPLS-AA and modified OPLS-AA). The observed trends in the effects of water addition were qualitatively quite robust with respect to these force field combinations and showed that the water does not aggregate but forms hydrogen bonds at most between two water molecules. In general, the added water causes overall either no or very small and nuanced effects in the simulation results. Specifically, the obtained water RDFs are mostly identical regardless of the water content. The added water reduces oligomer hydrogen bonding interactions overall as it competes and forms hydrogen bonds with the oligomers. The loss of intramolecular oligomer hydrogen bonding is in part compensated by oligomers switching from inter- to intramolecular hydrogen bonding. The interplay of the competing hydrogen bonding interactions leads to the presence of shallow extrema with respect to the water weight fraction dependencies for densities, viscosities, and self-diffusion coefficients, in contrast to experimental measurements, which show monotonous dependencies. However, these trends are very small in magnitude and thus confirm the experimentally observed insensitivity of these physical properties to the presence of water impurities.

NMR Self-Diffusion and Transverse Relaxation Time in Bitumen: The Effect of Aging.

In this investigation the dynamics of two types of bitumens with different penetration grade were tested by using dynamic shear rheometry (DSR) and Nuclear Magnetic Resonance (NMR) at unaged conditions, and upon both short- and long-term artificial aging. The gel-sol transition temperature T g e l → s o l * ${{T}_{gel\to sol}^{^{\ast}}}$ was found to increase with increasing the time of aging treatment. Arrhenius parameters of the viscosity were found, unexpectedly, to be correlated with those of simple liquids, suggesting that the two kinds of systems, although chemically and physically quite different, share the same basic process at the molecular level. The molecular dynamics has been then investigated by NMR Pulsed Field Gradient Stimulated-Echo (PFGSE) and relaxometry (Carr-Purcell-Meiboom-Gill, CPMG, spin-echo pulse sequence) to capture the effect of aging upon dynamics variables such as self-diffusion coefficients D and transverse relaxation times T2 . The translational diffusion at T> T g e l → s o l * ${{T}_{gel\to sol}^{^{\ast}}}$ of the light molecular components of both types of bitumens was characterized by broad distributions of D which were found independent of the experimental time scale up to 0.2 s. Similarly, T2 data could be described as a continuous unimodal distributions of relaxation times determined both at T< T g e l → s o l * ${{T}_{gel\to sol}^{^{\ast}}}$ and T> T g e l → s o l * ${{T}_{gel\to sol}^{^{\ast}}}$ .

Biophysical Determinants for the Viscosity of Concentrated Monoclonal Antibody Solutions.

Monoclonal antibodies (mAbs) are particularly relevant for therapeutics due to their high specificity and versatility, and mAb-based drugs are hence used to treat numerous diseases. The increased patient compliance of self-administration motivates the formulation of products for subcutaneous (SC) administration. The associated challenge is to formulate highly concentrated antibody solutions to achieve a significant therapeutic effect, while limiting their viscosity and preserving their physicochemical stability. Protein-protein interactions (PPIs) are in fact the root cause of several potential problems concerning the stability, manufacturability, and delivery of a drug product. The understanding of macroscopic viscosity requires an in-depth knowledge on protein diffusion, PPIs, and self-association/aggregation. Here, we study the self-diffusion of different mAbs of the IgG1 subtype in aqueous solution as a function of the concentration and temperature by quasi-elastic neutron scattering (QENS). QENS allows us to probe the short-time self-diffusion of the molecules and therefore to determine the hydrodynamic mAb cluster size and to gain information on the internal mAb dynamics. Small-angle neutron scattering (SANS) is jointly employed to probe structural details and to understand the nature and intensity of PPIs. Complementary information is provided by molecular dynamics (MD) simulations and viscometry, thus obtaining a comprehensive picture of mAb diffusion.

Ion Transport in Glyme- and Sulfolane-Based Highly Concentrated Electrolytes.

Highly concentrated electrolytes (HCEs) have a similarity to ionic liquids (ILs) in high ionic nature, and indeed some of HECs are found to behave like an IL. HCEs have attracted considerable attention as prospective candidates for electrolyte materials in future lithium secondary batteries owing to their favorable properties both in the bulk and at the electrochemical interface. In this study, we highlight the effects of the solvent, counter anion, and diluent of HCEs on the Li+ ion coordination structure and transport properties (e. g., ionic conductivity and apparent Li+ ion transference number measured under anion-blocking conditions, t L i a b c ${{t}_{{\rm L}{\rm i}}^{{\rm a}{\rm b}{\rm c}}}$ ). Our studies on dynamic ion correlations unveiled the difference in the ion conduction mechanisms in HCEs and their intimate relevance to t L i a b c ${{t}_{{\rm L}{\rm i}}^{{\rm a}{\rm b}{\rm c}}}$ values. Our systematic analysis of the transport properties of HCEs also suggests the need for a compromise to simultaneously achieve high ionic conductivity and high t L i a b c ${{t}_{{\rm L}{\rm i}}^{{\rm a}{\rm b}{\rm c}}}$ values.

Micellar and solubilizing properties of rhamnolipids.

We studied the micellar and solubilizing properties of aqueous solutions of unfractionated rhamnolipids produced by Pseudomonas aeruginosa. We used nuclear magnetic resonance (NMR) diffusometry, dynamic light scattering, and conductometry to measure the critical micelle concentration (CMC) of rhamnolipid solutions and determined the effective hydrodynamic radii of rhamnolipid monomers and micelles. Based on selective measurements of the self-diffusion coefficients of molecules, performed by NMR diffusometry, the solubilizing properties of rhamnolipids were studied depending on their concentration in solution; aromatic hydrocarbons, benzene, toluene, ethylbenzene, and para-xylene were taken as solubilizates. On the basis of the measurement results, we estimated the distribution coefficient of the solubilizate between the micellar (solubilized) and free (in the aqueous phase) states and the solubilizing capacity of rhamnolipid micelles.

Semi-Autonomic AI LF-NMR Sensor for Industrial Prediction of Edible Oil Oxidation Status.

The evaluation of an oil's oxidation status during industrial production is highly important for monitoring the oil's purity and nutritional value during production, transportation, storage, and cooking. The oil and food industry is seeking a real-time, non-destructive, rapid, robust, and low-cost sensor for nutritional oil's material characterization. Towards this goal, a 1H LF-NMR relaxation sensor application based on the chemical and structural profiling of non-oxidized and oxidized oils was developed. This study dealt with a relatively large-scale oil oxidation database, which included crude data of a 1H LF-NMR relaxation curve, and its reconstruction into T1 and T2 spectral fingerprints, self-diffusion coefficient D, and conventional standard chemical test results. This study used a convolutional neural network (CNN) that was trained to classify T2 relaxation curves into three ordinal classes representing three different oil oxidation levels (non-oxidized, partial oxidation, and high level of oxidation). Supervised learning was used on the T2 signals paired with the ground-truth labels of oxidation values as per conventional chemical lab oxidation tests. The test data results (not used for training) show a high classification accuracy (95%). The proposed AI method integrates a large training set, an LF-NMR sensor, and a machine learning program that meets the requirements of the oil and food industry and can be further developed for other applications.

The Hydrophobic Effect Studied by Using Interacting Colloidal Suspensions.

Interactions between nanoparticles (NPs) determine their self-organization and dynamic processes. In these systems, a quantitative description of the interparticle forces is complicated by the presence of the hydrophobic effect (HE), treatable only qualitatively, and due to the competition between the hydrophobic and hydrophilic forces. Recently, instead, a sort of crossover of HE from hydrophilic to hydrophobic has been experimentally observed on a local scale, by increasing the temperature, in pure confined water and studying the occurrence of this crossover in different water-methanol solutions. Starting from these results, we then considered the idea of studying this process in different nanoparticle solutions. By using photon correlation spectroscopy (PCS) experiments on dendrimer with OH terminal groups (dissolved in water and methanol, respectively), we show the existence of this hydrophobic-hydrophilic crossover with a well defined temperature and nanoparticle volume fraction dependence. In this frame, we have used the mode coupling theory extended model to evaluate the measured time-dependent density correlation functions (ISFs). In this context we will, therefore, show how the measured spectra are strongly dependent on the specificity of the interactions between the particles in solution. The observed transition demonstrates that just the HE, depending sensitively on the system thermodynamics, determines the hydrophobic and hydrophilic interaction properties of the studied nanostructures surface.

Transport Properties of Protic Ionic Liquids Based on Triazolium and Imidazolium: Development of an Air-Free Conductivity Setup.

The dynamical properties of four protic ionic liquids, based on the ethyltriazolium ([C2HTr124]) and the ethylimidazolium ([C2HIm]) cation, were investigated. The associated anions were the triflate ([TfO]) and the bistriflimide ([TFSI]). Ionic conductivity values and self-diffusion coefficients were measured and discussed, extending the discussion to the concept of fragility. Furthermore, in order to allow the measurement of the ionic conductivity of very small volumes (<0.5 mL) of ionic liquid under an inert and dry atmosphere, a new setup was developed. It was found that the cation nature strongly affected the transport properties, the [C2HTr124] cation resulting in slower dynamics than the [C2HIm] one. This was concluded from both conductivity and diffusivity measurements while for both properties, the anion had a lesser effect. By fitting the conductivity data with the Vogel-Fulcher-Tammann (VFT) equation, we could also estimate the fragility of these ionic liquids, which all fell in the range of very fragile glass-forming materials. Finally, the slower dynamics observed in the triazolium-based ionic liquids can be rationalized by the stronger interactions that this cation establishes with both anions, as deduced from the frequency analysis of relevant Raman signatures and density functional theory (DFT) calculations.

Polymer Dynamics in Glycerol-Water Mixtures.

Velocity correlation spectra (VAS) in binary mixtures of water and glycerol (G/W), obtained by measurements using the modulated gradient spin echo (MGSE) NMR method, were explained by the interactions of water molecules with clusters formed around the hydrophilic glycerol molecule, which drastically change the molecular dynamics and rheology of the mixture. It indicates a thickening of the shear viscosity, which could affect the dynamics of submerged macromolecules. The calculation of the polymer dynamics with the Langevin equations according to the Rouse model, where the friction was replaced by the memory function of the retarded friction, gave the dependence of the dynamics of the polymer on the rate of shear viscous properties of the solvent. The obtained formula was used to calculate the segmental VAS of the polymer when immersed in pure water and in a G/W mixture with 33 vol% glycerol content, taking into account the inverse proportionality between the solvent VAS and friction. The spectrum shows that in the G/W mixture, the fast movements of the polymer segments are strongly inhibited, which creates the conditions for slow processes caused by the internal interaction between the polymer segments, such as interactions that cause disordered polypeptides to spontaneously fold into biologically active protein molecules when immersed in such a solvent.

Nuclear magnetic resonance footprint of Wharton Jelly mesenchymal stem cells death mechanisms and distinctive in-cell biophysical properties in vitro.

The importance of the biophysical characterization of mesenchymal stem cells (MSCs) was recently pointed out for supporting the development of MSC-based therapies. Among others, tracking MSCs in vivo and a quantitative characterization of their regenerative impact by nuclear magnetic resonance (NMR) demands a full description of MSCs' MR properties. In the work, Wharton Jelly MSCs are characterized in a low magnetic field (LF) in vitro by using different approaches. They encompass various settings: MSCs cultured in a Petri dish and cell suspensions; experiments- 1D-T 1 , 1D-T 2 , 1D diffusion, 2D T 1 -T 2 and D-T 2 ; devices- with a bore aperture and single-sided one. Complex NMR analysis with the aid of random walk simulations allows the determination of MSCs T 1 and T 2 relaxation times, cells and nuclei sizes, self-diffusion coefficients of the nucleus and cytoplasm. In addition, the influence of a single layer of cells on the effective diffusion coefficient of water is detected with the application of a single-sided NMR device. It also enables the identification of apoptotic and necrotic cell death and changed diffusional properties of cells suspension caused by compressing forces induced by the subsequent cell layers. The study delivers MSCs-specific MR parameters that may help tracking MSCs in vivo.

Prediction of self-diffusion coefficients of chemically diverse pure liquids by all-atom molecular dynamics simulations.

Molecular self-diffusion coefficients underlie various kinetic properties of the liquids involved in chemistry, physics, and pharmaceutics. In this study, 547 self-diffusion coefficients are calculated based on all-atom molecular dynamics (MD) simulations of 152 diverse pure liquids at various temperatures employing the OPLS4 force field. The calculated coefficients are compared with experimental data (424 extracted from the literature and 123 newly measured by pulsed-field gradient nuclear magnetic resonance). The calculations well agree with the experimental values. The determination coefficient and root mean square error between the observed and calculated logarithmic self-diffusion coefficients of the 547 entries are 0.931 and 0.213, respectively, demonstrating that the MD calculation can be an excellent industrial tool for predicting, for example, molecular transportation in liquids such as the diffusion of active ingredients in biological and pharmaceutical liquids. The self-diffusion coefficients collected in this study are compiled into a database for broad researches including artificial intelligence calculations.

A Direct NMR Method To Measure Self-Diffusion Coefficients in Liquids by Monitoring Diffusing Molecules through One-Dimensional Imaging.

Diffusion processes can be followed directly by recording one-dimensional images of a selected slice at variable intervals after selective inversion of the magnetization. The resulting diffusion coefficients of H2 O and DMSO are consistent with earlier studies at different temperatures, obtained by monitoring the attenuation of NMR signals as a function of the gradient amplitude in gradient echo sequences.

NMR and dynamic light scattering give different diffusion information for short-living protein oligomers. Human serum albumin in water solutions of metal ions.

Diffusive behavior of human serum albumin (HSA) in the presence of Mg2+ and Cu2+ ions was studied by pulsed field gradient nuclear magnetic resonance (PFG NMR) and dynamic light scattering (DLS). According to NMR data yielding measurements of HSA self-diffusion coefficient, a weighted average of the protein monomers and oligomers diffusion mobility in the presence of metal ions was observed. While the short-time collective diffusion measured by DLS showed one type of diffusing species in ion-free HSA solution and two molecular forms of HSA in the presence of metal ions. The light intensity correlation function analysis showed that HSA oligomers have a limited lifetime (lower limit is about 0.4 ms) intermediate between characteristic time scales of PFG NMR and DLS experiments. For a theoretical description of concentration dependence of HSA self- and collective diffusion coefficients, the phenomenological approach based on the frictional formalism of non-equilibrium thermodynamics was used (Vink theory), allowing analysis of the solvent-solute and solute-solute interactions in protein solutions. In the presence of metal ions, a significant increase of HSA protein-protein friction coefficient was shown. Based on theoretical analysis of collective diffusion data, the positive values of second virial coefficients A2 for HSA monomers were obtained. The A2 values were found to be higher for the HSA with metal ions compared with the ion-free HSA solution. This is due to the more pronounced contribution of repulsion in protein-protein interactions of HSA monomers in the presence of Mg2+ and Cu2+ ions.

Dynamic and molecular association in premicellar aqueous solutions of dicarboxylate amino acid-based surfactant as studied by 1 H NMR.

We examined a series of amino acid-based surfactants with two carboxylic groups separated by a spacer of one, two, or three carbon atoms with sodium and calcium counterions in the premicellar concentration region near the CMC. 1 H nuclear magnetic resonance (NMR) spectroscopy and NMR diffusometry techniques were used to study the local environment, association, and translational dynamics of the surfactant's molecules. We measured the self-diffusion coefficients of the micelles, calculated the effective hydrodynamic radii, and determined the temperature region in which the premicelles exist. With an increase in temperature from 295 to 335 K, the premicellar state of the surfactant is replaced by the monomeric state.

Effect of Protein-Protein Interactions on Translational Diffusion of Spheroidal Proteins.

One of the commonly accepted approaches to estimate protein-protein interactions (PPI) in aqueous solutions is the analysis of their translational diffusion. The present review article observes a phenomenological approach to analyze PPI effects via concentration dependencies of self- and collective translational diffusion coefficient for several spheroidal proteins derived from the pulsed field gradient NMR (PFG NMR) and dynamic light scattering (DLS), respectively. These proteins are rigid globular α-chymotrypsin (ChTr) and human serum albumin (HSA), and partly disordered α-casein (α-CN) and ß-lactoglobulin (ß-Lg). The PPI analysis enabled us to reveal the dominance of intermolecular repulsion at low ionic strength of solution (0.003-0.01 M) for all studied proteins. The increase in the ionic strength to 0.1-1.0 M leads to the screening of protein charges, resulting in the decrease of the protein electrostatic potential. The increase of the van der Waals potential for ChTr and α-CN characterizes their propensity towards unstable weak attractive interactions. The decrease of van der Waals interactions for ß-Lg is probably associated with the formation of stable oligomers by this protein. The PPI, estimated with the help of interaction potential and idealized spherical molecular geometry, are in good agreement with experimental data.

Self-Organization of Fullerene Derivatives in Solutions and Biological Cells Studied by Pulsed Field Gradient NMR.

Fullerene derivatives are of great interest in various fields of science and technology. Fullerene derivatives are known to have pronounced anticancer and antiviral activity. They have antibacterial properties. Their properties are largely determined by association processes. Understanding the nature and properties of associates in solvents of various types will make it possible to make significant progress in understanding the mechanisms of aggregation of molecules of fullerene derivatives in solutions. Thus, this work, aimed at studying the size and stability of associates, is relevant and promising for further research. The NMR method in a pulsed field gradient was used, which makes it possible to directly study the translational mobility of molecules. The sizes of individual molecules and associates were calculated based on the Stokes-Einstein model. The lifetime of associates was also estimated. The interaction of water-soluble C60 fullerene derivatives with erythrocytes was also evaluated. The values of self-diffusion coefficients and the lifetime of molecules of their compounds in cell membranes are obtained. It is concluded that the molecules of fullerene derivatives are fixed on the cell surface, and their forward movement is controlled by lateral diffusion.

1H LF-NMR Self-Diffusion Measurements for Rapid Monitoring of an Edible Oil's Food Quality with Respect to Its Oxidation Status.

The food quality of edible oils is dependent on basic chemical and structural changes that can occur by oxidation during preparation and storage. A rapid and efficient analytical method of the different steps of oil oxidation is described using a time-domain nuclear magnetic resonance (TD-NMR) sensor for measuring signals related to the chemical and physical properties of the oil. The degree of thermal oxidation of edible oils at 80 °C was measured by the conventional methodologies of peroxide and aldehyde analysis. Intact non-modified samples of the same oils were more rapidly analyzed for oxidation using a TD-NMR sensor for 2D T1-T2 and self-diffusion (D) measurements. A good linear correlation between the D values and the conventional chemical analysis was achieved, with the highest correlation of R2 = 0.8536 for the D vs. the aldehyde concentrations during the thermal oxidation of poly-unsaturated linseed oils, the oil most susceptible to oxidation. A good correlation between the D and aldehyde levels was also achieved for all the other oils. The possibility to simplify and minimize the time of oxidative analysis using the TD NMR sensors D values is discussed as an indicator of the oil's oxidation quality, as a rapid and accurate methodology for the oil industry.

Study of the premicellar state in aqueous solutions of sodium dodecyl sulfate by nuclear magnetic resonance diffusion.

Self-diffusion coefficients of sodium dodecyl sulfate (SDS) were measured in aqueous solutions in the premicellar range of the SDS concentrations 7-34.7 mM and temperatures 30-90°C. Average effective hydrodynamic radii and aggregation numbers of SDS in the premicellar region were determined. At C < CMC at all temperatures, the SDS solution is the solution of monomers. At C > CMC, the increase of temperature leads to decrease in the effective hydrodynamic radii and the average aggregation numbers. At C > > CMC, it is impossible to reach the monomeric state by increasing the temperature.