Search Results (895)

Zebrafish (Danio rerio) is an important animal model for a wide range of neurodegenerative diseases. However, obtaining the cellular resolution that is essential for studying the zebrafish brain remains challenging as it requires high spatial resolution and signal-to-noise ratios (SNR). In the current study, we present the first MRI results of the zebrafish brain at the state-of-the-art magnetic field strength of 28.2 T. The performance of MRI at 28.2 T was compared to 17.6 T. A 20% improvement in SNR was observed at 28.2 T as compared to 17.6 T. Excellent contrast, resolution, and SNR allowed the identification of several brain structures. The normative T₁ and T₂ relaxation values were established over different zebrafish brain structures at 28.2 T. To zoom into the white matter structures, we applied diffusion tensor imaging (DTI) and obtained axial, radial, and mean diffusivity, as well as fractional anisotropy, at a very high spatial resolution. Visualisation of white matter structures was achieved by short-track track-density imaging by applying the constrained spherical deconvolution method (stTDI CSD). For the first time, an algorithm for stTDI with multi-shell multi-tissue (msmt) CSD was tested on zebrafish brain data. A significant reduction in false-positive tracks from grey matter signals was observed compared to stTDI with single-shell single-tissue (ssst) CSD. This allowed the non-invasive identification of white matter structures at high resolution and contrast. Our results show that ultra-high field DTI and tractography provide reproducible and quantitative maps of fibre organisation from tiny zebrafish brains, which can be implemented in the future for a mechanistic understanding of disease-related microstructural changes in zebrafish models of various brain diseases. Full article

Improper thermal cycles on duplex stainless steels can lead to the formation of detrimental phases or alter the proportion of ferrite and austenite phases, thus influencing the material’s mechanical properties and corrosion resistance. Therefore, this study aimed to evaluate the effect of aging (at 850 and 950 °C) and solubilization (at 1000 and 1150 °C) thermal treatments on microstructure, indentation hardness, elasticity modulus, and susceptibility to intergranular corrosion of UNS S32205 duplex stainless steel. The sigma phase (σ) formation in the aged samples, with hardness values between 8 and 10 GPa, was confirmed. Furthermore, the pieces treated from 1000 °C upwards showed that increased temperature favored the formation of more equiaxial grains and the ferrite fraction growth. The thermal treatments barely affected the elasticity modulus of austenite and ferrite grains, increasing the hardness of ferrite. The effect of sulfuric acid concentration in the intergranular corrosion was evaluated. Also, the deconvolution of the corrosion curves permits the determination of the influence of the different phases in the corrosion performance. These tests revealed sensitization only at the σ phase grain boundaries in the samples treated at 850 °C in electrolytes containing H₂SO₄ 2.5 mol/L and HCl 1 mol/L. Although the treatment at 950 °C led to the σ phase formation, its higher corrosion resistance was ascribed to the lower volumetric fraction of this phase, its morphology, and its increased Cr mobility compared to the 850 °C treatment. Therefore, it was shown that the σ characteristics and the sulfuric acid concentrations are determining factors in the UNS S32205 intergranular corrosion resistance. Full article

Although much information can be gained about thermally induced microstructural changes in metals through the measurement of their thermophysical properties using a differential scanning calorimeter (DSC), due to competing influences on the signal, not all microstructural changes can be fully characterised this way. For example, accurate characterisation of recrystallisation, tempering, and changes in retained delta ferrite in alloyed steels becomes complex due to additional signal changes due to the Curie point, oxidation, and the rate (and therefore the magnitude) of transformation. However, these types of microstructural changes have been shown to invoke strong magnetic and electromagnetic (EM) responses; therefore, simultaneous EM measurements can provide additional complementary data which can help to emphasise or deconvolute these complex signals and develop a more complete understanding of certain metallurgical phenomena. This paper discusses how a DSC machine has been modified to incorporate an EM sensor consisting of two copper coils printed onto either side of a ceramic substrate, with one coil acting as a transmitter and the other as a receiver. The coil is interfaced with a custom-built data acquisition system, which provides current to the transmit coil, records signals from the receive coil, and is controlled by a graphical user interface which allows the user to select multiple excitation frequencies. The equipment has a useable frequency range of approximately 1–100 kHz and outputs phase and magnitude readings at a rate of approximately 50 samples per second. Simultaneous DSC-EM measurements were performed on a nickel sample up to a temperature of 600 °C, with the reversable ferromagnetic to paramagnetic transition in the nickel sample invoking a clear EM response. The results show that the combined DSC-EM apparatus has the potential to provide a powerful tool for the analysis of thermally induced microstructural changes in metals, feeding into research on steel production, development of magnetic and conductive materials, and many more areas. Full article

The potential of RNA-based liquid biopsy is increasingly being recognized in diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin’s lymphoma. This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n = 171) derived from a DLBCL PDTX model, including 27 humanized (HIS) PDTX, 8 HIS non-PDTX, and 21 non-HIS PDTX non-obese diabetic (NOD)-scid IL2Rgnull (NSG) mice were collected during humanization, xenografting, treatment, and sacrifice. The mice were treated with either rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP), CD20-targeted human IFNα2-based AcTaferon combined with CHOP (huCD20-Fc-AFN-CHOP), or phosphate-buffered saline (PBS). RNA was extracted using the miRNeasy serum/plasma kit and sequenced on the NovaSeq 6000 platform. RNA sequencing data of the formalin-fixed paraffin-embedded (FFPE) tissue and blood plasma samples of the original patient were included. Flow cytometry was performed on immune cells isolated from whole blood, spleen, and bone marrow. Bulk deconvolution was performed using the Tabula Sapiens v1 basis matrix. Both R-CHOP and huCD20-Fc-AFN-CHOP were able to control tumor growth in most mice. Xenograft tumor volume was strongly associated with circulating tumor RNA (ctRNA) concentration (p < 0.001, R = 0.89), as well as with the number of detected human genes (p < 0.001, R = 0.79). Abundance analysis identified tumor-specific biomarkers that were dynamically tracked during tumor growth or treatment. An 8-gene signature demonstrated high accuracy for assessing therapy response (AUC 0.92). The tumoral gene detectability in the ctRNA of the PDTX-derived plasma was associated with RNA abundance levels in the patient’s tumor tissue and blood plasma (p < 0.001), confirming that tumoral gene abundance contributes to the cell-free RNA (cfRNA) profile. Decomposing the transcriptome, however, revealed high inter- and intra-mouse variability, which was lower in the HIS PDTX mice, indicating an impact of human engraftment on the stability and profile of cfRNA. Immunochemotherapy resulted in B cell depletion, and tumor clearance was reflected by a decrease in the fraction of human CD45+ cells. Lastly, bulk deconvolution provided complementary biological insights into the composition of the tumor and circulating immune system. In conclusion, the blood plasma-derived transcriptome serves as a biomarker source in a preclinical PDTX model, enables the assessment of biological pathways, and enhances the understanding of cfRNA dynamics. Full article

Analysis of wave propagation within buildings in response to earthquakes enables the tracking of changes in dynamic characteristics using impulse response functions. The velocity of traveling shear waves and the intrinsic attenuation of buildings can be retrieved, providing valuable input for system identification. The Factor Building at the University of California, Los Angeles campus (henceforth referred to as the UCLA Factor Building), an instrumented 15-story steel moment frame structure, is selected for dynamic response characterization. Shear wave travel time and attenuation are computed from wave propagation using seismic interferometry applied to recorded motions, with deconvolved waves used to compute these parameters. In this study, the natural logarithm of the envelopes of waveforms deconvolved with the basement signal provided the measure of attenuation. Additionally, the waveforms deconvolved with the basement motion, indicating the building’s fundamental mode. The frequency and time decay further constrained the shear velocity and attenuation. Shear velocity was determined using arrival times measured from deconvolved waves, resulting in an average velocity of 147.1 m/s. The observed quality factor was 10.8, with a corresponding damping ratio of 5%. The shear wave velocity and damping ratio estimates derived from deconvolved waves showed consistency with those obtained from basement deconvolved waveforms. This consistency validates wave deconvolution as an effective method for isolating building response from excitation and ground coupling. By incorporating the resonant frequencies and damping ratios derived from previous analyses into a refined element model, this study underscores the potential of wave deconvolution for extracting building dynamic characteristics, thereby enhancing our understanding of their responses to earthquakes. Full article

When a wheel passes over a rail surface irregularity, the resulting vehicle excitations lead to the application of additional system forces to both the track and the vehicle. These forces contribute to an accelerated track geometry deterioration, which in turn results in increased costs. In a recent paper, a clear correlation between the presence of rail irregularities and poor track geometry quality was demonstrated. Rail surface irregularities thereby were quantified by raw data of a chord-based optical measurement system mounted on the regular track recording vehicle in Austria. This paper deals with deconvolution of the recorded data in order to guarantee irregularity quantification without any distortion. Two different deconvolution approaches are developed and validated by additional measurements. Using the deconvoluted data, previously published evaluations were repeated, and the impact of using deconvoluted data instead of chord values was analysed. The correlation between short-wave effects and track geometry quality can not only be confirmed; it is even stronger than predicted by the chord data. The results of the analysis demonstrate that irregularities with amplitudes exceeding 0.08 mm contribute to an accelerated deterioration in track geometry. Amplitudes of a greater severity result in track geometry levels that are up to 120% inferior to the average. Full article

The growth interruption technology is introduced to the growth of GaAsP/InAlGaAs quantum well (QW) structure using metal–organic chemical vapor deposition (MOCVD). The effect of growth interruption time (GIT) on the crystalline quality and optical properties are investigated. The two distinctive emission peaks are the transition recombination between the electron level of conduction band and the light and heavy hole level of valence band in the photoluminescence (PL) at room temperature. The PL peaks present a redshift and merge together with the increasing GIT, which is attributed to the QW energy level shift caused by the increase in arsenic concentrations in GaAsP QW, the diversified thickness of QW and the variations of indium components in the InAlGaAs barrier layer. The Gaussian deconvolution parameters in temperature-dependent PL (TDPL) show that the GaAsP/InAlGaAs QW with a GIT of 6 s has a 565.74 meV activation energy, enhancing the carrier confinement in QW and the PL intensity, while the 6 s-GIT GaAsP QW has the increasing interface roughness and the non-radiative centers at the InGaAsP intermediate layer, leading to a spectral broadening. The QW with 10 s-GIT exhibits a small full width at half maximum (FWHM) with the various temperature, indicating reduced interface roughness and excellent crystal quality. An increase in GIT may be suitable for optimizing the optical properties of GaAsP/InAlGaAs QW. Full article

A high-resolution seismic survey (HRSS) is often used in coal exploration to bridge the data gap between two consecutive boreholes and avoid ambiguity in geological interpretation. The application of high-resolution seismic surveys in the Indian context is challenging as the delineation of thin non-coal layers within the coal layer requires a very high seismic data resolution. However, conventional seismic processing techniques fail to resolve thin coal/non-coal layers and faults, which is crucial for the precise estimation of coal resources and mine economics. To address these issues, we applied the inverse continuous wavelet transform deconvolution (ICWT-Decon) technique to post-stack depth-migrated seismic sections. We examined the feasibility of the ICWT-Decon technique in both a synthetic post-stack depth-migrated model and 2D/3D seismic data from the North Karanpura and Talcher Coalfields in Eastern India. The results offered enhanced seismic sections, attributes (similarity and sweetness), and acoustic inversion that aided in the precise positioning of faults and the delineation of a thin non-coal layer of 4.68 m within a 16.7 m coal seam at an approximate depth of 450 m to 550 m. This helped in the refinement of the resource estimation from 74.96 MT before applying ICWT-Decon to 55.92 MT afterward. Overall, the results of the study showed enhancements in the seismic data resolution, the better output of seismic attributes, and acoustic inversion, which could enable more precise lithological and structural interpretation. Full article

Understanding the characteristics of underwater sound channels is essential for various remote sensing applications. Typically, the time-domain Green’s function or channel impulse response (CIR) is obtained using computationally intensive acoustic propagation models that rely on accurate environmental data, such as sound speed profiles and bathymetry. Ray-based blind deconvolution (RBD) offers a less computationally demanding alternative using plane-wave beamforming to estimate the Green’s function. However, the presence of noise can obscure low coherence ray arrivals, making accurate estimation challenging. This paper introduces a method using the waveguide invariant to improve the signal-to-noise ratio (SNR) of broadband Green’s functions for a moving source without prior knowledge of range. By utilizing RBD and the frequency shifts from the striation slope, we coherently combine individual Green’s functions at adjacent ranges, significantly improving the SNR. In this study, we demonstrated the proposed method via simulation and broadband noise data (200–900 Hz) collected from a moving ship in 100 m deep shallow water. Full article

Coenurosis is a parasitic disease caused by the larval stage of Taenia multiceps, Coenurus cerebralis, typically found in the central nervous system of different livestock such as sheep and goats. The blood plasma from fifteen clinically healthy sheep and six sheep with neurological symptoms was studied by fluorescence spectroscopy in order to establish the contribution of kynurenic acid (KYNA), the neuroprotective metabolite of the kynurenine pathway, to the total fluorescence of the plasma. CT scans were used to confirm the presence of cysts in the central nervous system of sheep with neurological symptoms. The fluorescence spectroscopy analysis and further spectra deconvolution process revealed some significantly lower KYNA contributions to the total plasma fluorescence in sheep with coenurosis compared to healthy controls. Our results indicate that KYNA emission parameters could serve as valuable diagnostic markers, particularly for detecting preclinical cases of coenurosis, thus allowing for improved farm management practices. Full article

Ultrasound B-scan images are traditionally formed from the envelope of the received radiofrequency echoes, but the image texture is dominated by granular speckle patterns. Longstanding efforts at speckle reduction and deconvolution have been developed to lessen the detrimental aspects of speckle. However, we now propose an alternative approach to estimation (and image rendering) of the underlying fine grain scattering density of tissues based on power law constraints. The key steps are a whitening of the spectrum of the received signal while conforming to the original envelope shape and statistics, followed by a power law filtering in accordance with the known scattering behavior of tissues. This multiple step approach results in a high-spatial-resolution map of scattering density that is constrained by the most important properties of scattering from tissues. Examples from in vivo liver scans are shown to illustrate the change in image properties from this framework. Full article

The integrity of the reconstructed human epidermis generated in vitro can be assessed using histological analyses combined with immunohistochemical staining of keratinocyte differentiation markers. Technical differences during the preparation and capture of stained images may influence the outcome of computational methods. Due to the specific nature of the analyzed material, no annotated datasets or dedicated methods are publicly available. Using a dataset with 598 unannotated images showing cross-sections of in vitro reconstructed human epidermis stained with DAB-based immunohistochemistry reaction to visualize four different keratinocyte differentiation marker proteins (filaggrin, keratin 10, Ki67, HSPA2) and counterstained with hematoxylin, we developed an unsupervised method for the detection and quantification of immunohistochemical staining. The pipeline consists of the following steps: (i) color normalization; (ii) color deconvolution; (iii) morphological operations; (iv) automatic image rotation; and (v) clustering. The most effective combination of methods includes (i) Reinhard’s normalization; (ii) Ruifrok and Johnston color-deconvolution method; (iii) proposed image-rotation method based on boundary distribution of image intensity; and (iv) k-means clustering. The results of the work should enhance the performance of quantitative analyses of protein markers in reconstructed human epidermis samples and enable the comparison of their spatial distribution between different experimental conditions. Full article

A set of Eu³⁺-doped molybdates, Y₂₋xEuxMo₃O₁₂ (x = 0.04; 0.16; 0.2; 0.4; 0.8; 1; 1.6; 2), was synthesized using a solid-state technique and their properties studied as a function of Eu³⁺ concentration. X-ray diffraction showed that the replacement of Y³⁺ with larger Eu³⁺ resulted in a transformation from orthorhombic (low doping concentrations) through tetragonal (high doping concentrations), reaching monoclinic structure for full replacement in Eu₂Mo₃O₁₂. The intensity of typical Eu³⁺ red emission slightly increases in the orthorhombic structure then rises significantly with dopant concentration and has the highest value for the tetragonal Y₂Mo₃O₁₂:80mol% Eu³⁺. Further, the complete substitution of Y³⁺ with Eu³⁺ in the case of monoclinic Eu₂Mo₃O₁₂ leads to decreased emission intensity. Lifetime follows a similar trend; it is lower in the orthorhombic structure, reaching slightly higher values for the tetragonal structure and showing a strong decrease for monoclinic Eu₂Mo₃O₁₂. Temperature-sensing properties of the sample with the highest red Eu³⁺ emission, Y₂Mo₃O₁₂:80mol% Eu³⁺, were analyzed by the luminescence intensity ratio method. For the first time, the peak-sharpening algorithm was employed to separate overlapping peaks in luminescence thermometry, in contrast to the peak deconvolution method. The Sr (relative sensitivity) value of 2.8 % K⁻¹ was obtained at room temperature. Full article

Worldwide, it is estimated that there are 1.8 to 2.7 million cases of envenoming caused by snakebites. Snake venom is a complex mixture of protein toxins, lipids, small molecules, and salts, with the proteins typically responsible for causing pathology in snakebite victims. For their chemical characterization and identification, analytical methods are required. Reversed-phase liquid chromatography coupled with electrospray ionization mass spectrometry (RP-LC-ESI-MS) is a widely used technique due to its ease of use, sensitivity, and ability to be directly coupled after LC separation. This method allows for the efficient separation of complex mixtures and sensitive detection of analytes. On the other hand, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is also sometimes used, and though it typically requires additional sample preparation steps, it offers desirable suitability for the analysis of larger biomolecules. In this study, seven medically important viperid snake venoms were separated into their respective venom toxins and measured by ESI-MS. In parallel, using nanofractionation analytics, post-column high-resolution fractionation was used to collect the eluting toxins for further processing for MALDI-MS analysis. Our comparative results showed that the deconvoluted snake venom toxin masses were observed with good sensitivity from both ESI-MS and MALDI-MS approaches and presented overlap in the toxin masses recovered (between 25% and 57%, depending on the venom analyzed). The mass range of the toxins detected in high abundance was between 4 and 28 kDa. In total, 39 masses were found in both the ESI-MS and/or MALDI-MS analyses, with most being between 5 and 9 kDa (46%), 13 and 15 kDa (38%), and 24 and 28 kDa (13%) in size. Next to the post-column MS analyses, additional coagulation bioassaying was performed to demonstrate the parallel post-column assessment of venom activity in the workflow. Most nanofractionated venoms exhibited anticoagulant activity, with three venoms additionally exhibiting toxins with clear procoagulant activity (Bothrops asper, Crotalus atrox, and Daboia russelii) observed post-column. The results of this study highlight the complementarity of ESI-MS and MALDI-MS approaches for characterizing snake venom toxins and provide a complementary overview of defined toxin masses found in a diversity of viper snake venoms. Full article

Strawberry aroma, crucial for determining quality, involves complex volatile compounds which are challenging to identify. This study explores strawberry aroma analysis using Gas Chromatography-Mass Spectrometry (GC-MS) and the Automated Mass Spectral Deconvolution and Identification System (AMDIS). Central to our research is the creation of a bespoke strawberry Volatile Organic Compounds (VOCs) user library using AMDIS, specifically for analyzing strawberry aromas. The library contains VOCs from 61 strawberry cultivars, integrating information on 104 VOCs, including mass spectra, retention index, chemical class, CAS number, formula, odor threshold, and odor description. This custom library significantly outperformed a commercial library by reducing potential false hits by 200, decreasing the size of report files by over 96%, and, most importantly, shortening AMDIS analysis processing time from 31 s to 9 s, representing an approximate 71% reduction. Further, the study demonstrates the library’s practical application by contrasting the aroma profiles of strawberries harvested in winter and spring. This comparison revealed significant VOC variations depending on seasonal temperature changes, offering insights into environmental influences on strawberry aroma. In conclusion, this research marks a significant advance in strawberry aroma quality analysis. The strawberry VOC library developed in this study is expected to greatly aid targeted metabolomics and flavor research in strawberry breeding. Full article