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RNA in situ hybridization (RNA-ISH) is a powerful spatial transcriptomics technology to characterize target RNA abundance and localization in individual cells. This allows analysis of tumor heterogeneity and expression localization, which are not readily obtainable through transcriptomic data analysis. RNA-ISH experiments produce large amounts of data and there is a need for automated analysis methods. Here we present QuantISH, a comprehensive open-source RNA-ISH image analysis pipeline that quantifies marker expressions in individual carcinoma, immune, and stromal cells on chromogenic or fluorescent in situ hybridization images. QuantISH is designed to be modular and can be adapted to various image and sample types and staining protocols. We show that in chromogenic RNA in situ hybridization images of high-grade serous carcinoma (HGSC) QuantISH cancer cell classification has high precision, and signal expression quantification is in line with visual assessment. We further demonstrate the power of QuantISH by showing that CCNE1average expression and DDIT3expression variability, as captured by the variability factor developed herein, act as candidate biomarkers in HGSC. Altogether, our results demonstrate that QuantISH can quantify RNA expression levels and their variability in carcinoma cells, and thus paves the way to utilize RNA-ISH technology.

RNA in situ hybridization (RNA-ISH) is a powerful spatial transcriptomics technology to characterize target RNA abundance and localization in individual cells. This allows analysis of tumor heterogeneity and expression localization, which are not readily obtainable through transcriptomic data analysis. RNA-ISH experiments produce large amounts of data and there is a need for automated analysis methods. Here we present QuantISH, a comprehensive open-source RNA-ISH image analysis pipeline that quantifies marker expressions in individual carcinoma, immune, and stromal cells on chromogenic or fluorescent in situ hybridization images. QuantISH is designed to be modular and can be adapted to various image and sample types and staining protocols. We show that in chromogenic RNA in situ hybridization images of high-grade serous carcinoma (HGSC) QuantISH cancer cell classification has high precision, and signal expression quantification is in line with visual assessment. We further demonstrate the power of QuantISH by showing that CCNE1average expression and DDIT3expression variability, as captured by the variability factor developed herein, act as candidate biomarkers in HGSC. Altogether, our results demonstrate that QuantISH can quantify RNA expression levels and their variability in carcinoma cells, and thus paves the way to utilize RNA-ISH technology.

Understanding the reactions taking place in the hematite-oxalic acid system is important in order to clean iron oxides from filters and to remove iron from mineral concentrates. Previous studies reported the formation of an unwanted solid phase during this process. The objective of the current work, therefore, was to visualize and rationalize the iron dissolution steps taking place in the hematite–oxalic acid reaction by combining density functional theory (DFT) calculations and experimental data. The results of DFT calculations indicated that a precipitate was formed in this reaction; XRD analysis of the solid phase after the dissolution experiment revealed the formation of humboldtine as the precipitate. The attachment of oxalate on the hematite surface and the reduction of Fe(III) to Fe(II) were key steps for humboldtine formation. Both simulations and the experimental results showed that greater oxalic acid concentrations yielded more precipitate, suggesting a simple and novel route to synthesize humboldtine, a material which is relevant to the demand for clean energy.

A new designed sonicated, continuous modular crystallizer was investigated and developed. The concept and design criteria for the designed crystallizer were examined and studied in a cooling crystallization process with three model compounds which were K2SO4, CuSO4, and phthalic acid. Results showed that ultrasound had significant effects, which can enhance the nucleation and avoid clogging in the tubular crystallizer. The present work shows the obtained results when different cooling strategies were studied. Equal supersaturation throughout the crystallization process was the best solution for designing temperature profiles for the modules. In addition to the cooling strategy, the residence time is one of the key factors to get feasible operating conditions in the designed crystallizer. Higher yields were obtained using ultrasound with phthalic acid crystallization, as a model compound, compared to a classical tubular flow reactor.

Green liquor dregs represent the most important inorganic residue of chemical pulp mills. The dregs are usually settled in thickeners, washed and deliquored with lime mud precoat filters, and transported to the landfill. The utilization of dregs is challenging, due to the high concentration of hazardous trace elements (HTE) in their solid phase. There are basically two potential strategies for the reduction of the HTE content of dregs: mechanical classification according to differences in the size and density of particles, and removal of HTE by various chemical treatments. The objective of this study was to evaluate the applicability of straightforward mechanical separation methods for the purification of dregs from HTE. The evaluated separation methods included particle size–based classification by sieving, and classification on the basis of differences in the settling properties of particles in gravitational and centrifugal separation. It can be concluded that all the evaluated separation methods could be used to reduce the HTE content of dregs, although the separation efficiency was not very high in most cases. Centrifugation had clearly the best performance of the investigated techniques. The fractions consisting of large particles contained consistently lower concentrations of HTE, compared to fractions containing a lot of fines.

•Ozonation of p-nitrophenol was carried out at constant pH values of 2, 7 and 10.•Radical scavenger t-butanol was used for different t-butanol concentrations.•pH determines the relative production rates of the first intermediates.•Radicals play an important role in ozonation at low pH.•There exists t-butanol concentration for the slowest 4-nitrocathecol production.

Magnetite (Fe3O4) is a key economically valuable component in iron ore and is extracted by dissolution processes, but among the Fe (oxyhydr)oxides its solubility behavior is one of the least understood. The objective of this study was to improve understanding of magnetite dissolution mechanisms leading to thermodynamic equilibrium by comparing the dissolution of two solid samples, one synthetic and one industrial, using oxalic, sulfuric, and nitric acids at varying concentrations and temperatures. Of the three solid-liquid systems investigated, only the system consisting of magnetite and oxalic acid reached an equilibrium state within the duration of an individual experiment (6 h). In this system, increasing the acid concentration resulted in a significant increase in the equilibrium concentration of dissolved Fe. When dissolving synthetic and industrial magnetite, increasing the temperature not only increased the rate of reaction but also affected the concentration of dissolved Fe. Significant effects were observed when increasing the temperature from 15 to 35°C, but only slight differences were seen on further increases in temperature. Observations regarding the equilibrium state of the sulfuric and nitric acid systems could not be made because equilibrium was not reached. The most important individual observation regarding the equilibrium state of the nitric- and sulfuric-acid systems seems to be that in future studies a much longer reaction time is necessary, due to slow kinetics of the dissolution mechanism. A proton-based mechanism has been hypothesized as the one governing the dissolution of magnetite by these two acids, but only the dissolution of the industrial sample yielded results that were similar for these two acids and consistent with that hypothesis.

The object of the research was to compare the corrosion resistance of three types of multioxide technical ceramics in hydrofluoric acid containing aqueous media according to a full factorial experimental plan with pH and fluoride ion concentration as variables. The samples were a silicon carbide doped aluminum silicate material, and two membrane coated aluminum silicates with one containing a membrane on both sides of the ceramic plate. The substrates contained more additives on alumina, while the membrane coats were of higher grade aluminum oxide. The samples were shaken in containers for up to two weeks, and their remaining hardness and weight losses were measured. Daily samples drawn from the liquid phase were analyzed for dissolved components. With respect to all measured properties, fluoride concentration affected the materials more detrimentally than alterations in pH.

The object of the research was to compare the corrosion resistance of three types of multioxide technical ceramics in hydrofluoric acid containing aqueous media according to a full factorial experimental plan with pH and fluoride ion concentration as variables. The samples were a silicon carbide doped aluminum silicate material, and two membrane coated aluminum silicates with one containing a membrane on both sides of the ceramic plate. The substrates contained more additives on alumina, while the membrane coats were of higher grade aluminum oxide. The samples were shaken in containers for up to two weeks, and their remaining hardness and weight losses were measured. Daily samples drawn from the liquid phase were analyzed for dissolved components. With respect to all measured properties, fluoride concentration affected the materials more detrimentally than alterations in pH.