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Two biopolyol-based foams derived from banana leaves (BL) or stems (BS) were produced, and their compression mechanical behavior and 3D microstructure were characterized. Traditional compression and in situ tests were performed during 3D image acquisition using X-ray microtomography. A methodology of image acquisition, processing, and analysis was developed to discriminate the foam cells and measure their numbers, volumes, and shapes along with the compression steps.
The two foams had similar compression behaviors, but the average cell volume was five times larger for the BS foam than the BL foam. It was also shown that the number of cells increased with increasing compression while the average cell volume decreased. Cell shapes were elongated and did not change with compression. A possible explanation for these characteristics was proposed based on the possibility of cell collapse. The developed methodology will facilitate a broader study of biopolyol-based foams intending to verify the possibility of using these foams as green alternatives to the typical petrol-based foams.
To gain insight into the possible origin of the gold used in the production of tesserae containing gold leaf less than 0.5 μm thick placed between two layers of glass, we propose a non-destructive synchrotron radiation (SR) XRF protocol based on sequential analysis under optimised analytical conditions. Using this protocol, trace element analysis is achieved with detection limits of 1–6 mg/kg. As Pt and Au have adjacent fluorescence energies, we tested the most challenging situation, when Pt is present in very low concentrations in gold. Data obtained by double-dispersive XRF (D2XRF) and μXRF for fourth–ninth-century mosaics decorating nine Eastern and Western religious buildings show that the Eastern and Western tesserae are made from different alloys.
However, these alloys are identical to those used to make gold leaf for gilding, because plastic deformation requires the use of gold alloys with high ductility and malleability. Although trace element composition of gold used in the concerned period is only available for coins, by comparing the amounts of Pt contained in the tesserae and in the coins we show that Roman tesserae are made from Roman gold, as described in the documentary sources. We observe for the Byzantine period the use of a Byzantine gold and of gold supposedly from different stages of recycling, and we suggest the use of Umayyad and Abbasid gold for the production of Islamic tesserae.
The greatest challenge when using deep convolutional neural networks (DCNNs) for automatic segmentation of microstructural X-ray computed tomography (XCT) data is the acquisition of sufficient and relevant data to train the working network. Traditionally, these have been attained by manually annotating a few slices for 2D DCNNs. However, complex multiphase microstructures would presumably be better segmented with 3D networks. However, manual segmentation labeling for 3D problems is prohibitive. In this work, we introduce a method for generating synthetic XCT data for a challenging six-phase Al–Si alloy composite reinforced with ceramic fibers and particles. Moreover, we propose certain data augmentations (brightness, contrast, noise, and blur), a special in-house designed deep convolutional neural network (Triple UNet), and a multi-view forwarding strategy to promote generalized learning from synthetic data and therefore achieve successful segmentations. We obtain an overall Dice score of 0.77. Lastly, we prove the detrimental effects of artifacts in the XCT data on achieving accurate segmentations when synthetic data are employed for training the DCNNs. The methods presented in this work are applicable to other materials and imaging techniques as well. Successful segmentation coupled with neural networks trained with synthetic data will accelerate scientific output.
Optical Thermometry is popular among researchers because of its non-contact, high sensitivity, and fast measurement properties. In the present experiment, Er3+/Yb3+/K+ co-doped NaYF4 nanoparticles with different K+ concentrations were synthesized by solvothermal method, and the samples showed bright upconversion green emission under the excitation of a 980 nm laser. The powder X-ray diffractometer and transmission electron microscope were used to characterize the crystal structure and its surface morphology, respectively. The spectral characteristics of nanoparticles with K+ doping concentration from 10% to 30% (Molar ratio) were investigated by fluorescence spectroscopy, and it was observed that the fluorescence intensity reached the maximum at the K+ concentration of 20%, after which the intensity weakened when the K+ content continued to increase. According to the dependence between the luminescence intensity of the sample and the laser power density and fluorescence lifetime, the intrinsic mechanism was carefully investigated. Temperature-dependent spectra of the samples were recorded in the temperature range of 315–495 K, and the maximum values of absolute sensitivity (Sa) and relative sensitivity (Sr) were measured at 0.0041 K−1 (455 K) and 0.9220%K−1 (315 K). The experimental results show that K+/Er3+/Yb3+ triple-doped NaYF4 green fluorescent nanoparticles (GFNs) have good prospects for applications in display devices, temperature sensing, and other fields.
The NaYF4: Yb3+/Tm3+@NaYF4@β-CD upconversion nanoparticles were successfully prepared by the solvothermal method, and the samples were pure hexagonal phase with good crystallinity and homogeneous size, asevidenced by XRD and TEM analysis. The FT-IR analysis shows that β-CD is successfully encapsulated on the surface of NaYF4: Yb3+/Tm3+@NaYF4 nanoparticles. The fluorescence intensity 3and lifetime were significantly increased after coating the inert layer on the surface of core nanoparticles. After further surface modification of β-CD, the fluorescence intensity and fluorescence lifetime were reduced, but the overall fluorescence was stronger. Temperature measurements using the fluorescence intensity ratio technique were found to have relatively low reliability and absolute sensitivity for temperature measurements using thermally coupled energy levels. However, the reliability of temperature measurements using non-thermally coupled energy levels is significantly higher and the absolute sensitivity is much higher than for measurements at thermally coupled levels. Since the maximum absolute sensitivity, maximum relative sensitivity and minimum temperature resolution are determined to be 0.1179 K-1, 2.19 %K 1 and 0.00019 K, respectively, NaYF4: Yb3+/Tm3+@NaYF4@β-CD upconversion nanoparticles are expected to be widely used in the biomedical field due to their feasibility, reliability, non-toxicity and harmlessness.
Concrete structures experience severe damage during service, for example due to pitting corrosion of rebars caused by the ingress of chlorine (Cl) into the porous concrete structure. The ingress can be monitored using laser-induced breakdown spectroscopy (LIBS), a recently introduced civil engineering technique used to detect Cl in concrete structures in addition to conventional wet chemistry methods. The key advantages of LIBS are high spatial resolution, which is important when analyzing heterogeneous concrete samples, as well as the almost complete absence of sample preparation. To assess LIBS as a reliable analytical method, its accuracy and robustness must be carefully tested. This paper presents the results of an interlaboratory comparison on the analysis of Cl in cement paste samples conducted by 12 laboratories in 10 countries. Two sets of samples were prepared with Cl content ranging from 0.06 to 1.95 wt% in the training set and 0.23–1.51 wt% in the test set, with additional variations in the type of cement and Cl source (salt type). The overall result shows that LIBS is suitable for the quantification of the studied samples: the average relative error was generally below 15%. The results demonstrate the true status quo of the LIBS method for this type of analysis, given that the laboratories were not instructed on how to perform the analysis or how to process the data.
Quantitative 1H nuclear magnetic resonance (qNMR) of aromatic amino acids for protein quantification
(2023)
Hydrolysis of protein samples into amino acids facilitates the use of NMR spectroscopy for protein and peptide quantification. Different conditions have been tested for quantifying aromatic amino acids and proteins. The pH-dependent signal shifts in the aromatic region of amino acid samples were examined. A pH of 12 was found to minimize signal overlap of the four aromatic amino acids. Several aromatic compounds, such as terephthalic acid, sulfoisophthalic acid, and benzene tricarboxylic acid, were applied as internal standards. The quantification of amino acids from an amino acid standard was performed. Using the first two suggested internal standards, recovery was ~97% for histidine, phenylalanine, and tyrosine at a concentration of approximately 1 mM in solution. Acidic hydrolysis of a certified reference material (CRM) of bovine serum albumin (BSA) and subsequent quantification of Phe and Tyr yielded recoveries of 98% ± 2% and 88% ± 4%, respectively, at a protein concentration of 16 g/L or 250 µM.
Volatile organic compounds (VOCs) are of interest in many different fields. Among them are food and fragrance analysis, environmental and atmospheric research, industrial applications, security or medical and life science. In the past, the characterization of these compounds was mostly performed via sample collection and off-site analysis with gas chromatography coupled to mass spectrometry (GC-MS) as the gold standard. While powerful, this method also has several drawbacks such as being slow, expensive, and demanding on the user. For decades, intense research has been dedicated to find methods for fast VOC analysis on-site with time and spatial resolution. We present the working principles of the most important, utilized, and researched technologies for this purpose and highlight important publications from the last five years. In this overview, non-selective gas sensors, electronic noses, spectroscopic methods, miniaturized gas chromatography, ion mobility spectrometry and direct injection mass spectrometry are covered. The advantages and limitations of the different methods are compared. Finally, we give our outlook into the future progression of this field of research.
The core−shell NaYF4:Yb3+/Tm3+@NaYF4:Yb3+ upconversion nanoparticles were successfully prepared by a solvothermal method, and a layer of mesoporous silica (mSiO2) was successfully coated on the periphery of the core−shell nanoparticles to transform their surface from lipophilic to hydrophilic, further expanding their applications in biological tissues. The physical phase, morphology, structure, and fluorescence properties were characterized by X-ray diffraction (XRD), field emission transmission electron microscopy (TEM), Fourier infrared spectroscopy (FT-IR), ζ potential analysis, and fluorescence spectroscopy. It was found that the material has a hexagonal structure with good hydrophilicity and emits intense fluorescence under 980 nm pump laser excitation. The non-contact temperature sensing performance of nanoparticles was evaluated by analyzing the upconversion fluorescence of Tm3+ (1G4 → 3F4 and 3F3 → 3H6) in the temperature range of 284−344 K. The absolute and relative sensitivities were found to be 0.0067 K−1 and 1.08 % K−1, respectively, with high-temperature measurement reliability and good temperature cycling performance. More importantly, its temperature measurement in phosphate-buffered saline (PBS) solution is accurate. In addition, the temperature of the cells can be increased by adjusting the laser power density and laser irradiation time. Therefore, an optical temperature sensing platform was built to realize the application of real-time monitoring of cancer cell temperature and the dual function of photothermal therapy.
Chromium(III) complexes can show phosphorescence from the spin-flip excited doublet states 2E/2T1 in the near-infrared with high photoluminescence quantum yields and extremely long lifetimes in the absence of dioxygen. The prototype molecular ruby, [Cr(ddpd)2]3+ (ddpd = N,N’-dimethyl-N,N’-dipyridine-2-ylpyridine-2,6-diamine), has a photoluminescence quantum yield and a luminescence lifetime of 13.7% and 1.1 ms in deaerated acetonitrile, respectively. However, its luminescence is strongly quenched by 3O2 via an efficient Dexter-type energy transfer process. To enable luminescence applications of molecular rubies in solution under aerobic conditions, we explored the potential of sterically demanding ddpd ligands to shield the chromium(III) center from O2 using steady state and time-resolved photoluminescence spectroscopy. The structures of the novel complexes with sterically demanding ligands were investigated by single crystal X-ray diffraction and quantum chemically by density functional theory calculations. The O2 sensitivity of the photoluminescence was derived from absolutely measured photoluminescence quantum yields and excited state lifetimes under inert and aerobic conditions and by Stern–Volmer analyses of these data. Optimal sterically shielded chromium(III) complexes revealed photoluminescence quantum yields of up to 5.1% and excited state lifetimes of 518 μs in air-saturated acetonitrile, underlining the large potential of this ligand design approach to broaden the applicability of highly emissive chromium(III) complexes.
Microscopic knowledge of the structural, energetic, and electronic properties of scandium fluoride is still incomplete despite the relevance of this material as an intermediate for the manufacturing of Al−Sc alloys. In a work based on first-principles calculations and X-ray spectroscopy, we assess the stability and electronic structure of six computationally predicted ScF3 polymorphs, two of which correspond to experimentally resolved single-crystal phases. In the theoretical analysis based on density functional theory (DFT), we identify similarities among the polymorphs based on their formation energies, chargedensity distribution, and electronic properties (band gaps and density of states). We find striking analogies between the results obtained for the ow- and high-temperature phases of the material, indirectly confirming that the transition occurring between them mainly consists of a rigid rotation of the lattice. With this knowledge, we examine the X-ray absorption spectra from the Sc and F K-edge contrasting firstprinciples results obtained from the solution of the Bethe−Salpeter equation on top of all-electron DFT with high-energy-resolution fluorescence detection measurements. Analysis of the computational results sheds light on the electronic origin of the absorption maxima and provides information on the prominent excitonic effects that characterize all spectra. A comparison with measurements confirms that the sample is mainly composed of the high- and low-temperature polymorphs of ScF3. However, some fine details in the experimental results suggest that the probed powder sample may contain defects and/or residual traces of metastable polymorphs.
In this work, we present a novel approach to photothermal super resolution based thermographic resolution of internal defects using two-dimensional pixel pattern-based active photothermal laser heating in conjunction with subsequent numerical reconstruction to achieve a high-resolution reconstruction of internal defect structures. With the proposed adoption of pixelated patterns generated using laser coupled high-power DLP projector technology the complexity for achieving true two-dimensional super resolution can be dramatically reduced taking a crucial step forward towards widespread practical viability. Furthermore, based on the latest developments in high-power DLP projectors, we present their first application for structured pulsed thermographic inspection of macroscopic metal samples. In addition, a forward solution to the underlying inverse problem is proposed along with an appropriate heuristic to find the regularization parameters necessary for the numerical inversion in a laboratory setting. This allows the generation of synthetic measurement data, opening the door for the application of machine learning based methods for future improvements towards full automation of the method. Finally, the proposed method is experimentally validated and shown to outperform several established conventional thermographic testing techniques while conservatively improving the required measurement times by a factor of 8 compared to currently available photothermal super resolution techniques.
Episodic failures of ice-dammed lakes have produced some of the largest floods in history, with disastrous consequences for communities in high mountains. Yet, estimating changes in the activity of ice-dam failures through time remains controversial because of inconsistent regional flood databases. Here, by collating 1,569 ice-dam failures in six major mountain regions, we systematically assess trends in peak discharge, volume, annual timing and source elevation between 1900 and 2021. We show that extreme peak flows and volumes (10 per cent highest) have declined by about an order of magnitude over this period in five of the six regions, whereas median flood discharges have fallen less or have remained unchanged.
Ice-dam floods worldwide today originate at higher elevations and happen about six weeks earlier in the year than in 1900. Individual ice-dammed lakes with repeated outbursts show similar negative trends in magnitude and earlier occurrence, although with only moderate correlation to glacier thinning8. We anticipate that ice dams will continue to fail in the near future, even as glaciers thin and recede. Yet widespread deglaciation, projected for nearly all regions by the end of the twenty-first century9, may bring most outburst activity to a halt.
The combination of acoustically levitated droplets, mid-IR laser evaporation, and subsequent post-ionization by secondary electrospray ionization was applied for monitoring the enzymatic digestion of various proteins. Acoustically levitated droplets are an ideal, wall-free model reactor, readily allowing compartmentalized microfluidic trypsin digestions. Time-resolved interrogation of the droplets yielded real-time information on the progress of the reaction and thus provided insights into reaction kinetics. After 30 min of digestion in the acoustic levitator, the obtained protein sequence coverages were identical to the reference overnight digestions. Importantly, our results clearly demonstrate that the applied experimental setup can be used for the real-time investigation of chemical reactions. Furthermore, the described methodology only uses a fraction of the typically applied amounts of solvent, analyte, and trypsin. Thus, the results exemplify the use of acoustic levitation as a green analytical chemistry alternative to the currently used batch reactions.
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly
(2023)
Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody–antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69–99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences.
Showcasing research from the Federal Institute for Material Research and Testing Berlin and Fraunhofer Institute for Celltherapy and Immunology Branch Bioanalytics and Bioprocesses Potsdam.
Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine.
We aimed to increase the possible undisturbed exposure time during bio-SAXS measurements of single-stranded DNA-binding proteins. Therefore small angle X-ray scattering was performed on Gene-V Protein (G5P/GVP), which is involved in DNA repair processes. To achieve this, irradiations were performed in presence and absence of the hydroxyl-radical scavenger and osmolyte Ectoine, which showed efficient radiation protection and prevented protein aggregation, thus allows for a non-disturbing way to improve structure-determination of biomolecules.
This paper discusses the feasibility of a novel strategy based on the combination of bioprinting nano-doping technology and laser ablation-inductively coupled plasma time-of-flight mass spectrometry analysis for the preparation and characterization of gelatin- based multi-element calibration standards suitable for quantitative imaging. To achieve this, lanthanide up-conversion nanoparticles were added to a gelatin matrix to produce the bioprinted calibration standards. The features of this bioprinting approach were com- pared with manual cryosectioning standard preparation, in terms of throughput, between batch repeatability and elemental signal homogeneity at 5 μm spatial resolution. By using bioprinting, the between batch variability for three independent standards of the same concentration of 89 Y (range 0–600 mg/kg) was reduced to 5% compared to up to 27% for cryosectioning. On this basis, the relative standard deviation ( RSD ) obtained between three independent calibration slopes measured within 1 day also reduced from 16% (using cryosectioning ) to 5% (using bioprinting), supporting the use of a single standard preparation replicate for each of the concentrations to achieve good calibration performance using bioprinting. This helped reduce the analysis time by approximately 3-fold. With cryosectioning each standard was prepared and sectioned individually, whereas using bio-printing it was possible to have up to six different standards printed simultaneously, reducing the preparation time from approximately 2 h to under 20 min (by approxi- mately 6-fold). The bio-printed calibration standards were found stable for a period of 2 months when stored at ambient temperature and in the dark.
This study shows remarkably different features between the oxidation of secondary and primary C₃-C₅ alcohols. The oxidation of primary alcohols is controlled by the oxidative removal of blocking adsorbates, such as CO, formed after the dissociative adsorption of alcohol molecules. Conversely, secondary alcohols do not undergo dissociative adsorption and therefore their oxidation is purely controlled by the energetics of the elementary reaction steps. In this respect, a different role of ruthenium is revealed for the electrooxidation of primary and secondary alcohols on bimetallic platinum-ruthenium catalysts. Ruthenium enhances the oxidation of primary alcohols via the established bifunctional mechanism, in which the adsorption of (hydr)oxide species that are necessary to remove the blocking adsorbates is favored. In contrast, the oxidation of secondary alcohols is enhanced by the Ru-assisted stabilization of an O-bound intermediate that is involved in the potential-limiting step. This alternative pathway enables the oxidation of secondary alcohols close to the equilibrium potential.
This work aimed to evaluate high-resolution continuum source molecular absorption spectrometry (HR-CS MAS), traditionally used to determine non-metals, for the determination of a new element, metal, vanadium. VO was selected as a target molecule because it is relatively stable and was expected to be spontaneously generated in a flame or a graphite furnace (GF). The high-resolution overview spectra of the molecule were obtained in a wide range of 480–630 nm, and absorption due to the X4Σ−–C4Σ− electronic transition was registered. A unique instrumental setup, comprising a prototype Modular Simultaneous Echelle Spectrograph (MOSES) and a commercial HR-CS MAS apparatus, was applied in the research. Finally, the spectral area centered at 550.6230 nm was selected for analysis. A method was developed to determine V in solutions of catalysts of heavy petroleum oil hydroprocessing using a commercial HR-CS spectrometer in a flame version. Although sensitivity was relatively poor (characteristic concentration 380 mg L−1), an extremely low noise enabled reaching a satisfactory detection limit (20 mg L−1 in solution, i.e. 0.1% m:m in the catalyst). For the first time vanadium was determined using ordinary air-acetylene flame. The obtained results were consistent with the results of atomic absorption spectrometry with N2O-C2H2 flame. Unfortunately, only a small population of VO molecules could have been generated in GF measurements. Furthermore, the observed VO molecules appeared only at unfavorably high temperatures. The work shows the potential of HR-CS MAS as a scientific tool for investigating the mechanism of processes occurring in the GF. This work can inspire other research of new analytes for HR-CS MAS.