Glioblastoma biomarkers in urinary extracellular vesicles reveal the potential for a 'liquid gold' biopsy.

BACKGROUND: Biomarkers that reflect glioblastoma tumour activity and treatment response are urgently needed to help guide clinical management, particularly for recurrent disease. As the urinary system is a major clearance route of circulating extracellular vesicles (EVs; 30-1000 nm nanoparticles) we explored whether sampling urinary-EVs could serve as a simple and non-invasive liquid biopsy approach for measuring glioblastoma-associated biomarkers. METHODS: Fifty urine specimens (15-60 ml) were collected from 24 catheterised glioblastoma patients immediately prior to primary (n = 17) and recurrence (n = 7) surgeries, following gross total resection (n = 9), and from age/gender-matched healthy participants (n = 14). EVs isolated by differential ultracentrifugation were characterised and extracted proteomes were analysed by high-resolution data-independent acquisition liquid chromatography tandem mass spectrometry (DIA-LC-MS/MS). RESULTS: Overall, 6857 proteins were confidently identified in urinary-EVs (q-value ≤ 0.01), including 94 EV marker proteins. Glioblastoma-specific proteomic signatures were determined, and putative urinary-EV biomarkers corresponding to tumour burden and recurrence were identified (FC ≥ | 2 | , adjust p-val≤0.05, AUC > 0.9). CONCLUSION: In-depth DIA-LC-MS/MS characterisation of urinary-EVs substantiates urine as a viable source of glioblastoma biomarkers. The promising 'liquid gold' biomarker panels described here warrant further investigation.

Limb Salvage Surgery in a Rare Case of Recurrent Parosteal Osteosarcoma with Vascular Graft Thrombosis.

Recurrent parosteal sarcomas with vascular involvement are rare and present unique challenges in their diagnosis and management. We report the case of a 21-year-old woman with parosteal osteosarcoma of the left distal femur, encasing the popliteal vessels. En bloc transarticular resection of the distal femur and popliteal vessels was performed, followed by reconstruction using a modular prosthesis and a saphenous vein autograft for both the artery and vein. On the 1st postoperative day, the patient developed an arterial thrombus requiring reintervention with a jump polytetrafluoroethylene (PTFE) graft. Histopathology confirmed parosteal osteosarcoma. After a disease-free survival of 41 months, the patient experienced local recurrence involving the PTFE graft, leading to graft compression, erosion, and subsequent thrombosis. Despite these complications, limb salvage was possible due to adequate collateral blood supply. This case highlights the feasibility of limb salvage surgery in select cases of parosteal osteosarcoma with vascular involvement.

Influence of Halides on the Interactions of Ammonium Acids with Metal Halide Perovskites.

Additive engineering is a common strategy to improve the performance and stability of metal halide perovskite through the modulation of crystallization kinetics and passivation of surface defects. However, much of this work has lacked a systematic approach necessary to understand how the functionality and molecular structure of the additives influence perovskite performance and stability. This paper describes the inclusion of low concentrations of 5-aminovaleric acid (5-AVA) and its ammonium acid derivatives, 5-ammoniumvaleric acid iodide (5-AVAI) and 5-ammoniumvaleric acid chloride (5-AVACl), into the precursor inks for methylammonium lead triiodide (MAPbI3) perovskite and highlights the important role of halides in affecting the interactions of additives with perovskite and film properties. The film quality, as determined by X-ray diffraction (XRD) and photoluminescence (PL) spectrophotometry, is shown to improve with the inclusion of all additives, but an increase in annealing time from 5 to 30 min is necessary. We observe an increase in grain size and a decrease in film roughness with the incorporation of 5-AVAI and 5-AVACl with scanning electron microscopy (SEM) and atomic force microscopy (AFM). Critically, X-ray photoelectron spectroscopy (XPS) measurements and density functional theory (DFT) calculations show that 5-AVAI and 5-AVACl preferentially interact with MAPbI3 surfaces via the ammonium functional group, while 5-AVA will interact with either amino or carboxylic acid functional groups. Charge localization analysis shows the surprising result that HCl dissociates from 5-AVACl in vacuum, resulting in the decomposition of the ammonium acid to 5-AVA. We show that device repeatability is improved with the inclusion of all additives and that 5-AVACl increases the power conversion efficiency of devices from 17.61 ± 1.07 to 18.07 ± 0.42%. Finally, we show stability improvements for unencapsulated devices exposed to 50% relative humidity, with devices incorporating 5-AVAI and 5-AVACl exhibiting the greatest improvements.

Effect of stress on the dissolution/crystallization of apatite in aqueous solution: a thermochemical equilibrium study.

Bone mineralization is critical to maintaining tissue mechanical function. The application of mechanical stress via exercise promotes bone mineralization via cellular mechanotransduction and increased fluid transport through the collagen matrix. However, due to its complex composition and ability to exchange ions with the surrounding body fluids, bone mineral composition and crystallization is also expected to respond to stress. Here, a combination of data from materials simulations, namely density functional theory and molecular dynamics, and experimental studies were input into an equilibrium thermodynamic model of bone apatite under stress in an aqueous solution based on the theory of thermochemical equilibrium of stressed solids. The model indicated that increasing uniaxial stress induced mineral crystallization. This was accompanied by a decrease in calcium and carbonate integration into the apatite solid. These results suggest that weight-bearing exercises can increase tissue mineralization via interactions between bone mineral and body fluid independent of cell and matrix behaviours, thus providing another mechanism by which exercise can improve bone health. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

A nanometric window on fullerene formation in the interstellar medium: Insights from molecular dynamics studies.

Understanding the fundamental mechanisms that underlie the synthesis of fullerene molecules in the interstellar medium (ISM) and in the environments of astrophysical objects is an open question. In this regard, using classical molecular dynamics, we demonstrate the possibility of in situ formation of fullerene molecules, such as C60 from graphite, which is known to occur in the ISM, in particular, circumstellar environments. Specifically, when graphite is subjected to thermal and mechanical stimuli that are typical of circumstellar shells, we find that the graphite sheet edges undergo significant restructuring and curling, leading to edge-induced interlayer-interactions and formation of mechanically strained five-membered-ring structural units. These units serve as precursors for the formation of fullerene structures, such as pristine and metastable C60 molecules. The pathways leading to molecular C60 formation consist of a series of steps that involve bond-breakage and subsequent local rearrangement of atoms, with the activation energy barriers of the rate-limiting step(s) being comparable to the energetics of Stone-Wales rearrangement reactions. The identified chemical pathways provide fundamental insights into the mechanisms that underlie C60 formation. Moreover, they clearly demonstrate that top-down synthesis of C60 from graphitic sources is a viable synthesis route at conditions pertaining to circumstellar matter.

Comparison of the Filtration Efficiency of Different Face Masks Against Aerosols.

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic can spread through virus-containing aerosols ( ≤ 5 µm) and larger airborne droplets. Quantifying filtration efficiency of different kinds of masks and linings for aerosols that fall within the most penetrating particle size (80-400 nm) is critical to limiting viral transmission. The objective of our experiment was to compare the "real-world" filtering efficiency of different face masks for fine aerosols (350 nm) in laboratory simulations. Methods: We performed a simulated bench test that measured the filtering efficiency of N95 vs. N99 masks with elastomeric lining in relation to baseline ("background") aerosol generation. A mannequin head was placed within a chamber and was attached to an artificial lung simulator. Particles of known size (350 ± 6 nm aerodynamic diameter) were aerosolized into the chamber while simulating breathing at physiological settings of tidal volume, respiratory rate, and airflow. Particle counts were measured between the mannequin head and the lung simulator at the tracheal airway location. Results: Baseline particle counts without a filter (background) were 2,935 ± 555 (SD) cm-3, while the N95 (1348 ± 92 cm-3) and N99 mask with elastomeric lining (279 ± 164 cm-3; p <0.0001) exhibit lower counts due to filtration. Conclusion: The filtration efficiency of the N95 (54.1%) and N99 (90.5%) masks were lower than the filtration efficiency rating. N99 masks with elastomeric lining exhibit greater filtration efficiency than N95 masks without elastomeric lining and may be preferred to contain the spread of SARS-CoV-2 infection.

Outcomes of Vascular Resection and Reconstruction in Extremity Soft Tissue Sarcoma and Bone Tumors.

PURPOSE: This study aimed to evaluate and analyze the feasibility and the oncological and functional outcomes of limb salvage surgery in extremity soft tissue sarcomas (ESTS) and bone tumors invading vessels. MATERIALS AND METHODS: This single-center retrospective analysis included patients with ESTS encasing or invading major blood vessels that were treated by limb salvage surgery with vascular resection and reconstruction between January 1995 and December 2019. Patients with contiguous involvement of major blood vessels and nerves and patients requiring amputation were excluded from the study. RESULTS: A total of 24 vessels (14 arteries and 10 veins) in 14 patients were reconstructed. Ten (71.4%) patients underwent both arterial and venous reconstruction, and four (28.6%) underwent only arterial reconstruction. Reconstruction was performed with a reversed saphenous vein (RSV) graft in 12 patients and with a synthetic graft (SG) in the other 12 patients. At a median follow-up of 27 months, RSV grafts were patent in 10 of 12 (83.3%) vessels and SGs were patent in 6 of 12 (50.0%) vessels (log-rank test, P=0.083). Out of 14 arteries and 10 veins, 11 arteries and 5 veins were patent, respectively. No patient developed local recurrence, and 2 (14.3%) patients developed distant metastases. Limb salvage rate was 13/14 (92.9%). The mean Musculoskeletal Tumor Society score was 83.3%. The 5- and 10-year overall survival rates were 80% and 50%, respectively. CONCLUSION: Limb salvage surgery in ESTS with vascular resection and reconstruction is feasible and provides favorable oncological and functional outcomes.

Effect of Ligand Adsorption on the Electronic Properties of the PbS(100) Surface.

A first-principles density functional theory calculation was carried out to study the adsorption of acetic acid, methyl amine, methanethiol, and hydrogen iodide on the (100) surface of PbS. All four ligands are common capping agents used in colloidal PbS quantum dot-based photovoltaics. Interestingly, among the considered adsorbates, dissociative adsorption was energetically preferred for hydrogen iodide, while associative adsorption was favorable for the rest. Associative adsorption was driven by strong interactions between the electronegative elements (Y) in the respective ligands and the Pb surface atoms via Pb 6p-Y np bond hybridization (n represents the valence quantum number of the respective electronegative elements). Importantly, the adsorption of ligands altered the work function of PbS, with contrasting trends for associative (decrease in the work function) versus dissociative (increase in the work function) adsorption. The changes in the work function correlates well with a corresponding shift in the 5d level of surface Pb atoms. Other important observations include variations in the work function that linearly change with increasing the surface coverage of adsorbed ligands as well as with the strength of the adsorption of ligands.

Structure of ZnCl2 Melt. Part II: Fragile-to-Strong Transition in a Tetrahedral Liquid.

The fraction of edge- and corner-sharing tetrahedra in liquid ZnCl2 is quantified as a function of temperature using Raman spectroscopy and ab initio molecular dynamic simulations. Two distinct regimes are found in the temperature dependence of the change in these structural units. This behavior is consistent with the existence of a fragile-to-strong transition in liquid ZnCl2 as suggested by calorimetric and viscosity measurements. The structural origin of this transition is rationalized in terms of a constraint counting formalism. It is suggested that the ratio of edge- to corner-sharing tetrahedra controls the configurational entropy and in turn the viscosity of the melt. The temperature dependence of this ratio above the melting point is also found to be qualitatively consistent with neutron diffraction data. The observation of a similar fragile-to-strong transition in the isostructural GeSe2 melt indicates that it may be a common feature of tetrahedral liquids.

A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders.

In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

Structure of ZnCl2 Melt. Part I: Raman Spectroscopy Analysis Driven by Ab Initio Methods.

The structure of molten ZnCl2 is investigated using a combination of computer simulation and experimental methods. Ab initio molecular dynamics (AIMD) is used to model the structure of ZnCl2 at 600 K. The structure factors and pair distribution functions derived from AIMD show a good match with those previously measured by neutron diffraction (ND). In addition, Raman spectroscopy is used to investigate the structure of liquid ZnCl2 and identify the relative fractions of constituent structural units. To ascertain the assignment of each Raman mode, a series of ZnCl2 crystalline prototypes are modeled and the corresponding Raman modes are derived by first-principles calculations. Curve fitting of experimental Raman spectra using these mode assignments shows excellent agreement with both AIMD and ND. These results confirm the presence of significant fractions of edge-sharing tetrahedra in liquid ZnCl2. The presence of these structural motifs has significant impact on the fragility of this tetrahedral glass-forming liquid. The assignment of Raman bands present in molten ZnCl2 is revised and discussed in view of these results.

Interplay between structure and transport properties of molten salt mixtures of ZnCl2-NaCl-KCl: A molecular dynamics study.

Molten mixtures of network-forming covalently bonded ZnCl2 and network-modifying ionically bonded NaCl and KCl salts are investigated as high-temperature heat transfer fluids for concentrating solar power plants. Specifically, using molecular dynamics simulations, the interplay between the extent of the network structure, composition, and the transport properties (viscosity, thermal conductivity, and diffusion) of ZnCl2-NaCl-KCl molten salts is characterized. The Stokes-Einstein/Eyring relationship is found to break down in these network-forming liquids at high concentrations of ZnCl2 (>63 mol. %), while the Eyring relationship is seen with increasing KCl concentration. Further, the network modification due to the addition of K ions leads to formation of non-bridging terminal Cl ions, which in turn lead to a positive temperature dependence of thermal conductivity in these melts. This new understanding of transport in these ternary liquids enables the identification of appropriate concentrations of the network formers and network modifiers to design heat transfer fluids with desired transport properties for concentrating solar power plants.

Graphene mediated self-assembly of fullerene nanorods.

A simple procedure for solution-based self-assembly of C60 fullerene nanorods on graphene substrates is presented. Using a combination of electron microscopy, X-ray diffraction and Raman spectroscopy, it is shown that the size, shape and morphology of the nanorods can be suitably modified by controlling the kinetics of self-assembly.

Multi-phonon scattering processes in one-dimensional anharmonic biological superlattices: understanding the dissipation of mechanical waves in mineralized tissues.

The scattering of elastic waves in a one dimensional phononic (PnC) crystal composed of alternate collagen and hydroxy-apatite constituent layers is studied. These superlattices are metaphors for mineralized tissues present in bones and teeth. The collagen is treated as an open system elastic medium with water content which can vary depending on the level of stress applied. The open system nature of the collagen-water system leads to a non-linear stress-strain response. The finite difference time domain method is employed to investigate the propagation of non-linear mechanical waves through the superlattice. The spectral energy density method enables the calculation of the non-linear vibrational wave band structure. The non-linearity in the mechanical response of the collagen-water system enables a variety of multi-phonon scattering processes resulting in an increase in the number of channels for the dissipation of elastic waves and therefore for the dissipation of mechanical energy. These results provide an explanation for the relationship between bone fragility and decreased hydration.

Size-dependent permittivity and intrinsic optical anisotropy of nanometric gold thin films: a density functional theory study.

Physical properties of materials are known to be different from the bulk at the nanometer scale. In this context, the dependence of optical properties of nanometric gold thin films with respect to film thickness is studied using density functional theory (DFT). We find that the in-plane plasma frequency of the gold thin film decreases with decreasing thickness and that the optical permittivity tensor is highly anisotropic as well as thickness dependent. Quantitative knowledge of planar metal film permittivity's thickness dependence can improve the accuracy and reliability of the designs of plasmonic devices and electromagnetic metamaterials. The strong anisotropy observed may become an alternative method of realizing indefinite media.

A first-principles characterization of water adsorption on forsterite grains.

Numerical simulations examining chemical interactions of water molecules with forsterite grains have demonstrated the efficacy of nebular gas adsorption as a viable mechanism for water delivery to the terrestrial planets. Nevertheless, a comprehensive picture detailing the water-adsorption mechanisms on forsterite is not yet available. Towards this end, using accurate first-principles density functional theory, we examine the adsorption mechanisms of water on the (001), (100), (010) and (110) surfaces of forsterite. While dissociative adsorption is found to be the most energetically favourable process, two stable associative adsorption configurations are also identified. In dual-site adsorption, the water molecule interacts strongly with surface magnesium and oxygen atoms, whereas single-site adsorption occurs only through the interaction with a surface Mg atom. This results in dual-site adsorption being more stable than single-site adsorption.

Accretion disc origin of the Earth's water.

Earth's water is conventionally believed to be delivered by comets or wet asteroids after the Earth formed. However, their elemental and isotopic properties are inconsistent with those of the Earth. It was thus proposed that water was introduced by adsorption onto grains in the accretion disc prior to planetary growth, with bonding energies so high as to be stable under high-temperature conditions. Here, we show both by laboratory experiments and numerical simulations that water adsorbs dissociatively on the olivine {100} surface at the temperature (approx. 500-1500 K) and water pressure (approx. 10⁻8 bar) expected for the accretion disc, leaving an OH adlayer that is stable at least up to 900 K. This may result in the formation of many Earth oceans, provided that a viable mechanism to produce water from hydroxyl exists. This adsorption process must occur in all disc environments around young stars. The inevitable conclusion is that water should be prevalent on terrestrial planets in the habitable zone around other stars.

Where on Earth has our water come from?

The presence of water in the Earth has long been an enigma. However, computer modelling techniques have shown that the adsorption of water onto the fractal surfaces of interplanetary dust particles, which are present in the planetary accretion disk, is sufficiently strong to provide a viable origin of terrestrial water.

Modeling the coupling of reaction kinetics and hydrodynamics in a collapsing cavity.

We introduce a model of cavitation based on the multiphase Lattice Boltzmann method (LBM) that allows for coupling between the hydrodynamics of a collapsing cavity and supported solute chemical species. We demonstrate that this model can also be coupled to deterministic or stochastic chemical reactions. In a two-species model of chemical reactions (with a major and a minor species), the major difference observed between the deterministic and stochastic reactions takes the form of random fluctuations in concentration of the minor species. We demonstrate that advection associated with the hydrodynamics of a collapsing cavity leads to highly inhomogeneous concentration of solutes. In turn these inhomogeneities in concentration may lead to significant increase in concentration-dependent reaction rates and can result in a local enhancement in the production of minor species.

Dynamic compound wavelet matrix method for multiphysics and multiscale problems.

The paper presents the dynamic compound wavelet method (dCWM) for modeling the time evolution of multiscale and/or multiphysics systems via an "active" coupling of different simulation methods applied at their characteristic spatial and temporal scales. Key to this "predictive" approach is the dynamic updating of information from the different methods in order to adaptively and accurately capture the temporal behavior of the modeled system with higher efficiency than the (nondynamic) "corrective" compound wavelet matrix method (CWM), upon which the proposed method is based. The system is simulated by a sequence of temporal increments where the CWM solution on each increment is used as the initial conditions for the next. The numerous advantages of the dCWM method such as increased accuracy and computational efficiency in addition to a less-constrained and a significantly better exploration of phase space are demonstrated through an application to a multiscale and multiphysics reaction-diffusion process in a one-dimensional system modeled using stochastic and deterministic methods addressing microscopic and macroscopic scales, respectively.