Disordered enthalpy-entropy descriptor for high-entropy ceramics discovery.

The need for improved functionalities in extreme environments is fuelling interest in high-entropy ceramics1-3. Except for the computational discovery of high-entropy carbides, performed with the entropy-forming-ability descriptor4, most innovation has been slowly driven by experimental means1-3. Hence, advancement in the field needs more theoretical contributions. Here we introduce disordered enthalpy-entropy descriptor (DEED), a descriptor that captures the balance between entropy gains and enthalpy costs, allowing the correct classification of functional synthesizability of multicomponent ceramics, regardless of chemistry and structure. To make our calculations possible, we have developed a convolutional algorithm that drastically reduces computational resources. Moreover, DEED guides the experimental discovery of new single-phase high-entropy carbonitrides and borides. This work, integrated into the AFLOW computational ecosystem, provides an array of potential new candidates, ripe for experimental discoveries.

proMAD: semiquantitative densitometric measurement of protein microarrays.

BACKGROUND: Protein microarrays are a versatile and widely used tool for analyzing complex protein mixtures. Membrane arrays utilize antibodies which are captured on a membrane to specifically immobilize several proteins of interest at once. Using detection antibodies, the bound protein-antibody-complex is converted into visual signals, which can be quantified using densitometry. The reliability of such densitometric assessments depends on a variety of factors, not only sample preparation and the choice of acquisition device but also the selected analysis software and the algorithms used for readout and processing data. Currently available software packages use a single image of a membrane at an optimal exposure time selected for that specific experimental framework. This selection is based on a user's best guess and is subject to inter-user variability or the acquisition device algorithm. With modern image acquisition systems proving the capacity to collect signal development over time, this information can be used to improve densitometric measurements. Here we introduce proMAD, a toolkit for protein microarray analysis providing a novel systemic approach for the quantification of membrane arrays based on the kinetics of the analytical reaction. RESULTS: Briefly, our toolkit ensures an exact membrane alignment, utilizing basic computer vision techniques. It also provides a stable method to estimate the background light level. Finally, we model the light production over time, utilizing the knowledge about the reaction kinetics of the underlying horseradish peroxidase-based signal detection method. CONCLUSION: proMAD incorporates the reaction kinetics of the enzyme to model the signal development over time for each membrane creating an individual, self-referencing concept. Variations of membranes within a given experimental set up can be accounted for, allowing for a better comparison of such. While the open-source library can be implemented in existing workflows and used for highly user-tailored analytic setups, the web application, on the other hand, provides easy platform-independent access to the core algorithm to a wide range of researchers. proMAD's inherent flexibility has the potential to cover a wide range of use-cases and enables the automation of data analytic tasks.

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the API format, accompanying software tools, and provide an update on the implementation of OPTIMADE in contributing materials databases. We end by providing several use cases that demonstrate the utility of the OPTIMADE API in materials research that continue to drive its ongoing development.

Qiber3D-an open-source software package for the quantitative analysis of networks from 3D image stacks.

BACKGROUND: Optical slice microscopy is commonly used to observe cellular morphology in 3D tissue culture, e.g., the formation of cell-derived networks. The morphometric quantification of these networks is essential to study the cellular phenotype. Commonly, the quantitative measurements are performed on 2D projections of the image stack, resulting in the loss of information in the third dimension. Currently available 3D image analysis tools rely on manual interactions with the software and are therefore not feasible for large datasets. FINDINGS: Here we present Qiber3D, an open-source image processing toolkit. The software package includes the essential image analysis procedures required for image processing, from the raw image to the quantified data. Optional pre-processing steps can be switched on/off depending on the input data to allow for analyzing networks from a variety of sources. Two reconstruction algorithms are offered to meet the requirements for a wide range of network types. Furthermore, Qiber3D's rendering capabilities enable the user to inspect each step of the image analysis process interactively to ensure the creation of an optimal workflow for each application. CONCLUSIONS: Qiber3D is implemented as a Python package, and its source code is freely available at https://github.com/theia-dev/Qiber3D. The toolkit was designed using a building block principle to enable the analysis of a variety of structures, such as vascular networks, neuronal structures, or scaffolds from numerous input formats. While Qiber3D can be used interactively in the Python console, it is aimed at unsupervised automation to process large image datasets efficiently.

Recapitulating bone development events in a customised bioreactor through interplay of oxygen tension, medium pH, and systematic differentiation approaches.

Bone development and homeostasis are intricate processes that require co-existence and dynamic interactions among multiple cell types. However, controlled dynamic niches that derive and support stable propagation of these cells from single stem cell source is not sustainable in conventional culturing vessels. In bioreactor cultures that support dynamic niches, the limited source and stability of growth factors are often a major limiting factor for long-term in vitro cultures. Hence, alternative growth factor-free differentiation approaches are designed and their efficacy to achieve different osteochondral cell types is investigated. Briefly, a dynamic niche is achieved by varying medium pH, oxygen tension (pO2 ) distribution in bioreactor, initiating chondrogenic differentiation with chondroitin sulphate A (CSA), and implementing systematic differentiation regimes. In this study, we demonstrated that CSA is a potent chondrogenic inducer, specifically in combination with acidic medium and low pO2 . Further, endochondral ossification is recapitulated through a systematic chondrogenic-osteogenic (ch-os) differentiation regime, and multiple osteochondral cell types are derived. Chondrogenic hypertrophy was also enhanced specifically in high pO2 regions. Consequently, mineralised constructs with higher structural integrity, volume, and tailored dimensions are achieved. In contrast, a continuous osteogenic differentiation regime (os-os) has derived compact and dense constructs, whereas a continuous chondrogenic differentiation regime (ch-ch) has attenuated construct mineralisation and impaired development. In conclusion, a growth factor-free differentiation approach is achieved through interplay of pO2 , medium pH, and systematic differentiation regimes. The controlled dynamic niches have recapitulated endochondral ossification and can potentially be exploited to derive larger bone constructs with near physiological properties.

Developing a Customized Perfusion Bioreactor Prototype with Controlled Positional Variability in Oxygen Partial Pressure for Bone and Cartilage Tissue Engineering.

Skeletal development is a multistep process that involves the complex interplay of multiple cell types at different stages of development. Besides biochemical and physical cues, oxygen tension also plays a pivotal role in influencing cell fate during skeletal development. At physiological conditions, bone cells generally reside in a relatively oxygenated environment whereas chondrocytes reside in a hypoxic environment. However, it is technically challenging to achieve such defined, yet diverse oxygen distribution on traditional in vitro cultivation platforms. Instead, engineered osteochondral constructs are commonly cultivated in a homogeneous, stable environment. In this study, we describe a customized perfusion bioreactor having stable positional variability in oxygen tension at defined regions. Further, engineered collagen constructs were coaxed into adopting the shape and dimensions of defined cultivation platforms that were precasted in 1.5% agarose bedding. After cultivating murine embryonic stem cells that were embedded in collagen constructs for 50 days, mineralized constructs of specific dimensions and a stable structural integrity were achieved. The end-products, specifically constructs cultivated without chondroitin sulfate A (CSA), showed a significant increase in mechanical stiffness compared with their initial gel-like constructs. More importantly, the localization of osteochondral cell types was specific and corresponded to the oxygen tension gradient generated in the bioreactor. In addition, CSA in complementary with low oxygen tension was also found to be a potent inducer of chondrogenesis in this system. In summary, we have demonstrated a customized perfusion bioreactor prototype that is capable of generating a more dynamic, yet specific cultivation environment that could support propagation of multiple osteochondral lineages within a single engineered construct in vitro. Our system opens up new possibilities for in vitro research on human skeletal development.