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Glioblastoma multiforme is a highly aggressive form of brain cancer, with a median survival time for diagnosed patients of 15 months. Treatment of this cancer is typically a combination of radiation, chemotherapy and surgical removal of the tumour. However, the highly invasive and diffuse nature of glioblastoma makes surgical intrusions difficult, and the diffusive properties of glioblastoma is poorly understood. In this paper, we introduce a stochastic interacting particle system as a model of in vitro glioblastoma migration, along with a maximum likelihood-algorithm designed for inference using microscopy imaging data. The inference method is evaluated on in silico simulation of cancer cell migration, and then applied to a real data set. We find that the inference method performs with a high degree of accuracy on the in silico data, and achieve promising results given the in vitro data set., (© The Author(s) 2024. Published by Oxford University Press.)

The development of a sample environment for in situ x-ray characterization during metal Electron Beam Powder Bed Fusion (PBF-EB), called MiniMelt, is presented. The design considerations, the features of the equipment, and its implementation at the synchrotron facility PETRA III at Deutsches Elektronen-Synchrotron, Hamburg, Germany, are described. The equipment is based on the commercially available Freemelt ONE PBF-EB system but has been customized with a unique process chamber to enable real-time synchrotron measurements during the additive manufacturing process. Furthermore, a new unconfined powder bed design to replicate the conditions of the full-scale PBF-EB process is introduced. The first radiography (15 kHz) and diffraction (1 kHz) measurements of PBF-EB with a hot-work tool steel and a Ni-base superalloy, as well as bulk metal melting with the CMSX-4 alloy, using the sample environment are presented. MiniMelt enables time-resolved investigations of the dynamic phenomena taking place during multi-layer PBF-EB, facilitating process understanding and development of advanced process strategies and materials for PBF-EB., (© 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

The Allee effect describes the phenomenon that the per capita reproduction rate increases along with the population density at low densities. Allee effects have been observed at all scales, including in microscopic environments where individual cells are taken into account. This is great interest to cancer research, as understanding critical tumour density thresholds can inform treatment plans for patients. In this paper, we introduce a simple model for cell division in the case where the cancer cell population is modelled as an interacting particle system. The rate of the cell division is dependent on the local cell density, introducing an Allee effect. We perform parameter inference of the key model parameters through Markov Chain Monte Carlo, and apply our procedure to two image sequences from a cervical cancer cell line. The inference method is verified on in silico data to accurately identify the key parameters, and results on the in vitro data strongly suggest an Allee effect., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Philip Gerlee reports financial support was provided by Swedish Foundation for Strategic Research., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Particle systems made up of interacting agents is a popular model used in a vast array of applications, not the least in biology where the agents can represent everything from single cells to animals in a herd. Usually, the particles are assumed to undergo some type of random movements, and a popular way to model this is by using Brownian motion. The magnitude of random motion is often quantified using mean squared displacement, which provides a simple estimate of the diffusion coefficient. However, this method often fails when data is sparse or interactions between agents frequent. In order to address this, we derive a conjugate relationship in the diffusion term for large interacting particle systems undergoing isotropic diffusion, giving us an efficient inference method. The method accurately accounts for emerging effects such as anomalous diffusion stemming from mechanical interactions. We apply our method to an agent-based model with a large number of interacting particles, and the results are contrasted with a naive mean square displacement-based approach. We find a significant improvement in performance when using the higher-order method over the naive approach. This method can be applied to any system where agents undergo Brownian motion and will lead to improved estimates of diffusion coefficients compared to existing methods., (© 2023. The Author(s).)

Powder Bed Fusion-Laser Beam (PBF-LB) processing of magnesium (Mg) alloys is gaining increasing attention due to the possibility of producing complex biodegradable implants for improved healing of large bone defects. However, the understanding of the correlation between the PBF-LB process parameters and the microstructure formed in Mg alloys remains limited. Thus, the purpose of this study was to enhance the understanding of the effect of the PBF-LB process parameters on the microstructure of Mg alloys by investigating the applicability of computational thermodynamic modelling and verifying the results experimentally. Thus, PBF-LB process parameters were optimized for a Mg WE43 alloy (Mg-Y 3. 9wt% -Nd 3wt% -Zr 0.5wt% ) on a commercially available machine. Two sets of process parameters successfully produced sample densities >99.4%. Thermodynamic computations based on the Calphad method were employed to predict the phases present in the processed material. Phases experimentally established for both processing parameters included α-Mg, Y 2 O 3 , Mg 3 Nd, Mg 24 Y 5 and hcp-Zr. Phases α-Mg, Mg 24 Y 5 and hcp-Zr were also predicted by the calculations. In conclusion, the extent of the applicability of thermodynamic modeling was shown, and the understanding of the correlation between the PBF-LB process parameters and the formed microstructure was enhanced, thus increasing the viability of the PBF-LB process for Mg alloys.

The microstructure of a hot-work tool steel additively manufactured using laser powder-bed fusion (L-PBF), and its response to post heat treatment, is studied in detail by microstructure characterization and computational thermodynamics and kinetics. The high solidification and cooling rates during the L-PBF process lead to suppression of δ -ferrite and instead solidification of an austenite phase directly containing a cellular substructure where the alloying elements have segregated to the inter-cellular regions and where solidification carbides have formed in the cell junctions. The austenite is then partly decomposed into martensite at lower temperatures. The micro-segregation can be predicted by reducing the complex solidification behavior to a diffusion problem in one dimension enabling detailed comparisons with the measured segregation profiles quantified at a nanometer scale. Martensite start temperature (M s ) calculations along the spatially varying composition show that the M s temperature decreases in the inter-cellular regions where austenite is observed. The network of austenite in the as-built microstructure can be understood from the combined influence of the composition dependence of the M s temperature in relation to the build plate temperature and the mechanical stabilization of the small-sized austenite regions. This work demonstrates the power of computational tools based on computational thermodynamics and kinetics for designing tool steels for additive manufacturing by predictions of the steel's response to the L-PBF process and post heat treatments., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Inconel 625, a nickel-based superalloy, has drawn much attention in the emerging field of additive manufacturing (AM) because of its excellent weldability and resistance to hot cracking. The extreme processing condition of AM often introduces enormous residual stress (hundreds of MPa to GPa) in the as-fabricated parts, which requires stress-relief heat treatment to remove or reduce the internal stresses. Typical residual stress heat treatment for AM Inconel 625, conducted at 800 °C or 870 °C, introduces a substantial precipitation of the δ phase, a deleterious intermetallic phase. In this work, we used synchrotron-based in situ scattering and diffraction methods and ex situ electron microscopy to investigate the solid-state transformation of an AM Inconel 625 at 700 °C. Our results show that while the δ phase still precipitates from the matrix at this temperature, its precipitation rate and size at a given time are both smaller when compared with their counterparts during typical heat treatment temperatures of 800 °C and 870 °C. A comparison with thermodynamic modeling predictions elucidates these experimental findings. Our work provides the rigorous microstructural kinetics data required to explore the feasibility of a promising lower-temperature stress-relief heat treatment for AM Inconel 625. The combined methodology is readily extendable to investigate the solid-state transformation of other AM alloys., Competing Interests: Conflicts of Interest: The authors declare no conflict of interest.

The multicomponent alloy HfNbTiVZr has been described as a single-phase high-entropy alloy (HEA) in the literature, although some authors have reported that additional phases can form during annealing. The thermal stability of this alloy has therefore been investigated with a combination of experimental annealing studies and thermodynamic calculations using the CALPHAD approach. The thermodynamic calculations show that a single-phase HEA is stable above about 830 °C. At lower temperatures, the most stable state is a phase mixture of bcc, hcp, and a cubic C15 Laves phase. Annealing experiments followed by quenching confirm the results from thermodynamic calculations with the exception of the Laves phase structure, which was identified as a hexagonal C14 type instead of the cubic C15 type. Limitations of the applied CALPHAD thermodynamic description of the system could be an explanation for this discrepancy. As-synthesized HfNbTiVZr alloys prepared by arc-melting form a single-phase bcc HEA at room temperature. In situ annealing studies of this alloy show that additional phases start to form above 600 °C. This indicates that the observed HEA is metastable at room temperature and stabilized by a slow kinetics during cooling. X-ray diffraction analyses using different cooling rates and annealing times show that the phase transformations in this HEA are slow and that completely different phase compositions can be obtained depending on the annealing procedure. In addition, it has been shown that the sample preparation method (mortar grinding, heat treatment, etc.) has a significant influence on the collected diffraction patterns and therefore on the phase identification and analysis.

Elemental segregation is a ubiquitous phenomenon in additive-manufactured (AM) parts due to solute rejection and redistribution during the solidification process. Using electron microscopy, in situ synchrotron X-ray scattering and diffraction, and thermodynamic modeling, we reveal that in an AM nickel-based superalloy, Inconel 625, stress-relief heat treatment leads to the growth of unwanted δ-phase precipitates on a time scale much faster than that in wrought alloys (minutes versus tens to hundreds of hours). The root cause for this behavior is the elemental segregation that results in local compositions of AM alloys outside the bounds of the allowable range set for wrought alloys. In situ small angle scattering experiments reveal that platelet-shaped δ phase precipitates grow continuously and preferentially along their lateral dimensions during stress-relief heat treatment, while the thickness dimension reaches a plateau very quickly. In situ XRD experiments reveal that nucleation and growth of δ-phase precipitates occur within 5 min during stress-relief heat treatment, indicating a low nucleation barrier and a short incubation time. An activation energy for the growth of δ phase was found to be (131.04 ± 0.69) kJ mol -1 . We further demonstrate that a subsequent homogenization heat treatment can effectively homogenize the AM alloy and remove the deleterious δ phase. The combined experimental and modeling methodology in this work can be extended to elucidate the phase evolution during heat treatments in a broad range of AM materials.

Oxygen is always a constituent in "real" titanium alloys including titanium alloy powders used for powder-based additive manufacturing (AM). In addition, oxygen uptake during powder handling and printing is hard to control and, hence, it is important to understand and predict how oxygen is affecting the microstructure. Therefore, oxygen is included in the evaluation of the thermodynamic properties of the titanium-vanadium system employing the CALculation of PHAse Diagrams method and a complete model of the O-Ti-V system is presented. The β -transus temperature is calculated to increase with increasing oxygen content whereas the extension of the α -Ti phase field into the binary is calculated to decrease, which explains the low vanadium solubilities measured in some experimental works. In addition, the critical temperature of the metastable miscibility gap of the β -phase is calculated to increase to above room temperature when oxygen is added. The effects of oxygen additions on phase fractions, martensite and ω formation temperatures are discussed, along with the impacts these changes may have on AM of titanium alloys.

Numerical simulations are used in this work to investigate aspects of microstructure and microseg-regation during rapid solidification of a Ni-based superalloy in a laser powder bed fusion additive manufacturing process. Thermal modeling by finite element analysis simulates the laser melt pool, with surface temperatures in agreement with in situ thermographic measurements on Inconel 625. Geometric and thermal features of the simulated melt pools are extracted and used in subsequent mesoscale simulations. Solidification in the melt pool is simulated on two length scales. For the multicomponent alloy Inconel 625, microsegregation between dendrite arms is calculated using the Scheil-Gulliver solidification model and DICTRA software. Phase-field simulations, using Ni-Nb as a binary analogue to Inconel 625, produced microstructures with primary cellular/dendritic arm spacings in agreement with measured spacings in experimentally observed microstructures and a lesser extent of microsegregation than predicted by DICTRA simulations. The composition profiles are used to compare thermodynamic driving forces for nucleation against experimentally observed precipitates identified by electron and X-ray diffraction analyses. Our analysis lists the precipitates that may form from FCC phase of enriched interdendritic compositions and compares these against experimentally observed phases from 1 h heat treatments at two temperatures: stress relief at 1143 K (870 °C) or homogenization at 1423 K (1150 °C).

Unprecedented interest has been spurred recently in two-dimensional (2D) layered transition metal dichalcogenides (TMDs) that possess tunable electronic and optical properties. However, synthesis of a wafer-scale TMD thin film with controlled layers and homogeneity remains highly challenging due mainly to the lack of thermodynamic and diffusion knowledge, which can be used to understand and design process conditions, but falls far behind the rapidly growing TMD field. Here, an integrated density functional theory (DFT) and calculation of phase diagram (CALPHAD) modeling approach is employed to provide thermodynamic insight into lateral versus vertical growth of the prototypical 2D material MoS2. Various DFT energies are predicted from the layer-dependent MoS2, 2D flake-size related mono- and bilayer MoS2, to Mo and S migrations with and without graphene and sapphire substrates, thus shedding light on the factors that control lateral versus vertical growth of 2D islands. For example, the monolayer MoS2 flake in a small 2D lateral size is thermodynamically favorable with respect to the bilayer counterpart, indicating the monolayer preference during the initial stage of nucleation; while the bilayer MoS2 flake becomes stable with increasing 2D lateral size. The critical 2D flake-size of phase stability between mono- and bilayer MoS2 is adjustable via the choice of substrate. In terms of DFT energies and CALPHAD modeling, the size dependent pressure-temperature-composition (P-T-x) growth windows are predicted for MoS2, indicating that the formation of MoS2 flake with reduced size appears in the middle but close to the lower T and higher P "Gas + MoS2" phase region. It further suggests that Mo diffusion is a controlling factor for MoS2 growth owing to its extremely low diffusivity compared to that of sulfur. Calculated MoS2 energies, Mo and S diffusivities, and size-dependent P-T-x growth windows are in good accord with available experiments, and the present data provide quantitative insight into the controlled growth of 2D layered MoS2.

A thermodynamic database for the Al-Co-Cr-Ni system is built via the Calphad method by extrapolating re-assessed ternary subsystems. A minimum number of quaternary parameters are included, which are optimized using experimental phase equilibrium data obtained by electron probe micro-analysis and x-ray diffraction analysis of NiCoCrAlY alloys spanning a wide compositional range, after annealing at 900 °C, 1100 °C and 1200 °C, and water quenching. These temperatures are relevant to oxidation and corrosion resistant MCrAlY coatings, where M corresponds to some combination of nickel and cobalt. Comparisons of calculated and measured phase compositions show excellent agreement for the β - γ equilibrium, and good agreement for three-phase β - γ - σ and β - γ - α equilibria. An extensive comparison with existing Ni-base databases (TCNI6, TTNI8, NIST) is presented in terms of phase compositions.

The phase relations and thermodynamic properties of the condensed Al-Co-Cr ternary alloy system are investigated using first-principles calculations based on density functional theory (DFT) and phase-equilibria experiments that led to X-ray diffraction (XRD) and electron probe micro-analysis (EPMA) measurements. A thermodynamic description is developed by means of the calculations of phase diagrams (CALPHAD) method using experimental and computational data from the present work and the literature. Emphasis is placed on modeling the bcc-A2, B2, fcc-γ, and tetragonal-σ phases in the temperature range of 1173 to 1623 K. Liquid, bcc-A2 and fcc-γ phases are modeled using substitutional solution descriptions. First-principles special quasirandom structures (SQS) calculations predict a large bcc-A2 (disordered)/B2 (ordered) miscibility gap, in agreement with experiments. A partitioning model is then used for the A2/B2 phase to effectively describe the order-disorder transitions. The critically assessed thermodynamic description describes all phase equilibria data well. A2/B2 transitions are also shown to agree well with previous experimental findings.

Background: Previous studies of epidermal kinetics in psoriasis have relied on invasive biopsy procedures or the use of radioactive labels. We previously developed a non-invasive method for measuring keratin synthesis in human skin using deuterated water labeling, serial collection of tape strips and measurement of deuterium enrichment in protein by mass spectrometry. This powerful method can be applied to measure other skin proteins and lipids collected by tape stripping. Here, for the first time, we apply this technique to investigate the epidermal kinetics of psoriasis, the first step in defining a kinetic profile for normal skin versus activated or quiescent psoriatic skin., Methods: Psoriatic subjects were given (2)H2O orally as twice-daily doses for 16-38 days. Affected and unaffected skin was sampled by tape stripping and washing (modified Pachtman method). Proteins were isolated from the tape strips by a method that enriches for keratin. Turnover times were determined by gas chromatography/mass spectrometry. Kinetic data were compared to transepidermal water loss (TEWL)., Results: Deuterium-labeled protein from lesional psoriatic skin appeared at the skin surface within 3-8 days of label administration, whereas labeled protein from non-lesional skin requires 10-20 days to appear. Psoriatic skin had similar rate of growth despite varying anatomic location. Proteins recovered from tape strips were identified by nanoscale liquid chromatography/tandem mass spectrometry. Isolated peptides were >98% from keratin in uninvolved skin and >72% keratin in psoriatic skin. Revealing that one-quarter of all newly synthesized proteins in psoriatic skin are antimicrobial defense and other immune-related proteins. TEWL values were greater in lesional than non-lesional skin, suggesting barrier compromise in psoriatic skin despite increased clinical thickness., Conclusions: This simple, elegant, and non-invasive method for measuring epidermal protein synthesis, which can also be adapted to measure epidermal lipids, provides a metric that may reveal new insights into the mechanisms and dynamic processes underlying psoriasis and may also provide an objective scale for determining response to therapeutic agents in pre-clinical and clinical trials. This opens a pathway to the non-invasive study of kinetics of protein formation in psoriasis or other skin diseases.

Glucocorticoids are widely prescribed to treat autoimmune and inflammatory diseases. Although they are extremely potent, their utility in clinical practice is limited by a variety of adverse side effects. Development of compounds that retain the potent immunomodulating and anti-inflammatory properties of classic glucocorticoids while exhibiting reduced adverse actions is therefore a priority. Using heavy water labeling and mass spectrometry to measure fluxes through multiple glucocorticoid-responsive, disease-relevant target pathways in vivo in mice, we compared the effects of a classic glucocorticoid receptor (GR) ligand, prednisolone, with those of a novel arylpyrazole-based compound, L5 {[1-(4-fluorophenyl)-4a-methyl-5,6,7,8-tetrahydro-4H-benzo[f]indazol-5-yl]-[4-(trifluoromethyl)phenyl]methanol}. We show for the first time that L5 exhibits clearly selective actions on disease-relevant pathways compared with prednisolone. Prednisolone reduced bone collagen synthesis, skin collagen synthesis, muscle protein synthesis, and splenic lymphocyte counts, proliferation, and cell death, whereas L5 had none of those actions. In contrast, L5 was a more rapid and potent inhibitor of hippocampal neurogenesis than prednisolone, and L5 and prednisolone induced insulin resistance equally. Administration of prednisolone or L5 increased expression comparably for one GR-regulated gene involved in protein degradation in skeletal muscle (Murf1) and one GR-regulated gluconeogenic gene in liver (PEPCK). In summary, L5 dissociates the pleiotropic effects of the GR ligand prednisolone in intact animals in ways that neither gene expression nor cell-based models were able to fully capture or predict. Because multiple actions can be measured concurrently in a single animal, this method is a powerful systems approach for characterizing and differentiating the effects of ligands that bind nuclear receptors.

The optical properties of quantum dots embedded in a catalytically grown semiconductor nanowire are studied theoretically. In comparison to dots in a bulk environment, the excitonic absorption is strongly modified by the one-dimensional character of the nanowire phonon spectrum. In addition to pronounced satellite peaks due to phonon-assisted absorption, we find a finite width of the zero-phonon line already in the lowest-order calculation.

Enhanced production of collagen is central to fibrotic disorders such as hepatic cirrhosis and pulmonary fibrosis. We describe a sensitive, quantitative, and high-throughput technique for measuring hepatic collagen synthesis in vivo through metabolic labeling with heavy water ((2)H(2)O). Rats and mice received (2)H(2)O in drinking water for up to 35 days. Deuterium incorporation into collagen-bound amino acids (AA) alanine and hydroxyproline (OHP) was measured by gas chromatography-mass spectrometry. A threefold stimulation of collagen fractional synthesis was observed under the maximum dosage of carbon tetrachloride (CCl(4); 1.67 ml/kg). Deuterium enrichment was systematically 20% higher in AA from monomeric collagen relative to dimeric collagen, consistent with slower turnover of the latter. Administration of 1% griseofulvin to mice resulted in a significant, threefold increase in liver collagen synthesis, observable within 12 days and consistent with predicted interstrain differences (C57/Bl6J > BALB/c). Deuterium enrichments of OHP from total liver proteins correlated well with alanine or OHP from isolated collagen. Fibrogenesis subsided after withdrawal of CCl(4) exposure and was reduced to various degrees by coadministration of interferon-gamma, rosiglitazone, atorvastatin, or enalapril. Changes in isotopically measured collagen synthesis correlated with, but were more sensitive and reproducible than, standard histological staining (trichrome) for fibrosis. In summary, liver collagen synthesis can be measured sensitively and with high precision over a short time period, without radioactivity, thereby providing a relatively high-throughput in vivo strategy for rapidly measuring profibrotic activities of suspected hepatotoxicants and antifibrotic activities of drug candidates.

Measurement of skin turnover has been problematic in humans. Heavy water (2H2O) labeling has recently been developed as a safe, simple method to study in vivo kinetics of many biosynthetic processes, including DNA and protein synthesis. Here, we apply this approach to the measurement of 2H incorporation into skin keratin and show close agreement between keratin and keratinocyte turnover data in the epidermis of rodents. Elevated turnover rates of both keratin and keratinocytes were observed in the epidermis of the flaky skin mouse, although topical treatments effective in human psoriasis had no effect on either turnover rate in these mice. In humans, keratin turnover was monitored non-invasively by serial tape stripping during and after 2H2O labeling. Kinetic data were consistent with previous estimates of epidermal turnover, with a lag time of 18 days before label appeared at the skin surface and a transit time of 4-5 weeks. Variability in skin keratin turnover rates was present among healthy individuals. In summary, 2H2O labeling of skin keratin represents a non-invasive approach for assessing skin turnover dynamics in pre-clinical models and in human subjects.

Ku is a heterodimer composed of p70 and p80, and is the regulatory subunit of DNA-dependent protein kinase. As a multifunctional DNA-binding protein complex, Ku plays important roles in DNA damage repair through non-homologous end joining and in V(D)J recombination. In addition, Ku has also been implicated in various biological functions including growth control, cell proliferation, cell cycle, chromosome maintenance, transcriptional regulation, apoptosis, and viral infection. In particular, using our Inverse Genomics (Immusol, Inc., San Diego, CA) platform technology, we recently identified Ku80 as an essential co-factor for human immunodeficiency virus replication. Although Ku has been studied extensively in the past years, its in-depth study as well as development as a drug target has been limited by conventional DNA-binding activity assay. Here we describe the development and applications of a nonradioactive DNA binding assay in the 96-well format. We show that this plate-formatted assay is more sensitive and allows for direct quantification when compared with an electrophoretic mobility shift assay. The establishment of this assay will not only facilitate structure and function studies on Ku, but also help the development of Ku protein or its DNA repair enzyme complex as a drug target.

We have used X-ray fiber diffraction to probe the structure of fibers of tau and tau fragments. Fibers of fragments from the microtubule binding domain had a cross beta-structure that closely resembles that reported both for neurofibrillary tangles found in Alzheimer's disease brain and for fibrous lesions from other protein folding diseases. In contrast, fibers of full-length tau had a different, more complex structure. Despite major differences at the molecular level, all fiber types exhibited very similar morphology by electron microscopy. These results have a number of implications for understanding the etiology of Alzheimer's and other tauopathic diseases. The morphology of the peptide fibers suggests that the region in tau corresponding to the peptides plays a critical role in the nucleation of fiber assembly. The dramatically different structure of the full length tau fibers suggests that some region in tau has enough inherent structure to interfere with the formation of cross beta-fibers. Additionally, the similar appearance by electron microscopy of fibrils with varying molecular structure suggests that different molecular arrangements may exist in other samples of fibers formed from tau.