Complex Media Research Articles

A facile synthesis of a novel polymer-based nanocomposite as colorimetric response sensor for fluoride ion detection in real-life complex mediums

The surface modification of Poly (acrylamide-co-methylenbisacrylamide-co-N-(4-(2-(phenylcarbamothioyl)hydrazineyl)phenyl)methacrylamide) as a sensor (AR) via titanium dioxide as a novel colorimetric nanocomposite sensor with high sensitivity and selectivity for determination of fluoride anion was described. The colorimetric response of the AR has been screened in dimethyl sulfoxide /Water with a volumetric ratio of 7:3 and acetonitrile in separate media with equal amounts of various anions. In the presence of the mentioned anionic solutions, only the solutions containing fluoride ions, made a significant change in color from pale yellow to orange-red via the –NH deprotonation mechanism, which could be detected with the naked eye. The Box-Behnken design, response surface methodology through UV-Vis spectroscopy techniques in various pH and temperatures and reaction times were tested to optimize the AR conditions. Also, a lateral flow assay test of the synthesized AR detected fluoride ions in real-life samples, including water, contrary to different sources such as toothpaste and mouthwash. Furthermore, according to the World Health Organization report on fluoride ion toxicity in water, the detection limit of the AR was lower than of the declared level.

Mycobolome of Phialomyces macrosporus across OSMAC-based assorted culture media.

The fungus Phialomyces macrosporus was cultured using the One Strain Many Compounds (OSMAC) strategies to evaluate its metabolome. Variations in the nutrient culture media, culture regime, and cultivation parameters can significantly influence fungal extract quantity and chemical diversity. This study aimed to explore the mycobolome of P. macrosporus in five different culture media and two different cultivation conditions using NMR-based metabolomics. Principal component analysis (PCA) of 1H NMR spectra revealed clear differentiation between these samples, highlighting the rice dextrose agar medium (RDA) and potato dextrose broth (PDB) as standard complex media for conducting a fungal metabolite screening program.

A Comparison of DNA-DNA Hybridization Kinetics in Complex Media on Planar and Nanostructured Electrodes.

A comprehensive investigation into how nanostructures alter real-time DNA hybridization kinetics in both buffer and complex media and under a wide range of probe and target concentrations is currently lacking. In response, we use a real-time, wash-free, and in situ assay to study DNA hybridization kinetics by performing continuous electrochemical measurements in different media. We investigated the differences in hybridization kinetics under three regimes of probe density (low, medium, and high) and over three orders of magnitude of target concentrations (0.01-1 μM). Additionally, we compared the performance of planar and nanostructured electrodes in buffer, blood, urine, and saliva. Our experiments indicate that adding nanostructures to the transducer surface is only effective under a specific probe/target concentration regime. Additionally, we found that direct electrochemical readout is possible in the examined physiological media, with measurements in blood showing the highest and saliva showing the lowest signal magnitudes compared to buffer.

Sustainable Production of Lactic Acid Using a Perennial Ryegrass as Feedstock—A Comparative Study of Fermentation at the Bench- and Reactor-Scale, and Ensiling

Perennial ryegrass (Lolium perenne) is an underutilized lignocellulosic biomass that has several benefits such as high availability, renewability, and biomass yield. The grass press-juice obtained from the mechanical pretreatment can be used for the bio-based production of chemicals. Lactic acid is a platform chemical that has attracted consideration due to its broad area of applications. For this reason, the more sustainable production of lactic acid is expected to increase. In this work, lactic acid was produced using complex medium at the bench- and reactor scale, and the results were compared to those obtained using an optimized press-juice medium. Bench-scale fermentations were carried out in a pH-control system and lactic acid production reached approximately 21.84 ± 0.95 g/L in complex medium, and 26.61 ± 1.2 g/L in press-juice medium. In the bioreactor, the production yield was 0.91 ± 0.07 g/g, corresponding to a 1.4-fold increase with respect to the complex medium with fructose. As a comparison to the traditional ensiling process, the ensiling of whole grass fractions of different varieties harvested in summer and autumn was performed. Ensiling showed variations in lactic acid yields, with a yield up to 15.2% dry mass for the late-harvested samples, surpassing typical silage yields of 6–10% dry mass.

An efficient electrochemical biosensor based on double-conductive hydrogel as antifouling interface for ultrasensitive analysis of biomarkers in complex serum medium

Electrochemical biosensors are suitable for trace detection of biomarkers in serum due to their high sensitivity and fast response time. However, the extensive adsorption of non-specific biomolecules may affect detection results and reduce the operating life of sensors. Herein, an efficient electrochemical biosensor based on double-conductive antifouling hydrogel was developed for ultrasensitive detection of carcinoembryonic antigen (CEA) in serum. Specifically, the antifouling hydrogel was designed with MXene as the conductive framework, and its inherent surface hydrophilicity made it have good antifouling ability. Meanwhile, the introduction of conductive poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) further improved the conductivity and stability and of antifouling hydrogel. Furthermore, the prepared MXene nanosheets exhibited large surface area, which could load a large amount of [Ru(NH3)6]3+ as internal standards. Importantly, the encapsulation of [Ru(NH3)6]3+ in hydrogel can not only eliminate the environmental and instrument errors, but also realize the integration of antifouling and internal standards, thus simplifying the construction process and improving the detection accuracy of the biosensor. Based on this, the proposed signal “on-off” electrochemical antifouling biosensor realized trace detection of CEA in a wide linear range (1 pg/mL ∼ 1 μg/mL), with a detection limit as low as 0.41 pg/mL (3δ/k). This study broadens the application of hydrogels in electrochemical antifouling systems, providing a positive reference for sensitive and accurate determination of biomarkers in serum samples.

Compensating Acquisition Footprint for Amplitude-Preserving Angle Domain Common Image Gathers Based on 3D Reverse Time Migration

Angle domain common image gathers (ADCIGs) play a crucial role in seismic exploration, offering prestack underground illumination information that aids in validating migration velocity and conducting prestack amplitude versus angle (AVA) analysis for reservoir characterization. This paper introduces an innovative approach for compensating amplitude errors caused by irregular seismic acquisition geometries in ADCIGs. By incorporating an angle domain illumination compensation factor, the proposed method effectively modifies these errors, preserving the amplitude of seismic reflectivity in the prestack angle domain. The effectiveness of the proposed approach is validated through comprehensive tests conducted on synthetic and field data examples. The results demonstrate the capability of the method to enhance the quality of ADCIGs derived from 3D reverse time migration (RTM), yielding accurate and reliable amplitude preservation. While the illumination compensation factor assumes a vertically linear velocity model, the method holds promise for extension to more complex media and diverse migration techniques. This suggests its applicability and adaptability beyond the specific assumptions considered in this study. In conclusion, this paper presents an innovative angle domain illumination compensation factor that significantly improves the quality of ADCIGs by addressing amplitude errors arising from irregular seismic acquisition geometries. The experimental validation using synthetic and field data confirms the effectiveness of the proposed method within the context of 3D RTM. Furthermore, the technique holds potential for broader application in more complex subsurface scenarios and various migration methodologies.

Correlating light fields through disordered media across multiple degrees of freedom

Speckle patterns are inherent features of coherent light propagation through complex media. As a result of interference, they are sensitive to multiple experimental parameters such as the configuration of disorder or the propagating wavelength. Recent developments in wavefront shaping have made it possible to control speckle pattern statistics and correlations, for example using the concept of the transmission matrix. In this article, we address the problem of correlating scattered fields across multiple degrees of freedom. We highlight the common points between the specific techniques already demonstrated, and we propose a general framework based on the singular value decomposition of a linear combination of multiple transmission matrices. Following analytical predictions, we experimentally illustrate the technique on spectral and temporal correlations, and we show that both the amplitude and the phase of the field correlations can be tuned. Our work opens up new perspectives in speckle correlation manipulation, with potential applications in coherent control. Published by the American Physical Society 2024

Deep‐Learning‐Assisted Affinity Classification for Humoral Immunoprotein Complexes

Immunoglobulins are important building blocks in biology and biotechnology. With the emergence of comprehensive deep‐learning approaches, there are enormous opportunities for fast and accurate methods of classification of protein–protein interactions to arise. Herein, widely accessible image classification algorithms for species‐specific typification of a range of different immunoglobulin G (IgG) complexes are repurposed. Droplets of various immunoglobulins mixed with a B‐cell superantigen (SAg) (recombinant staphylococcal Protein A) are deposited onto hydrophobic polymer substrates and the resulting protein stains are imaged using polarized light microscopy. A comprehensive study based on 23 745 images finds that the pretrained convolutional neural network (CNN) InceptionV3 not only successfully categorizes IgGs from four different species but also predicts their binding affinity to Protein A: averaged over 36 binding pairs, the following are observed: 1) an overall accuracy of 81.4%, 2) the highest prediction accuracy for human IgG, the antibody with the highest binding affinity for Protein A, and 3) that the classification accuracy regarding the various IgG/Protein A ratios generally correlates with the binding strength of the protein–protein–complex as determined via circular dichroism spectroscopy. In addition, the CNN pretrained with IgG/Protein A stain images has been challenged with a new set of images using a different superantigen (SAg, Protein G). Despite the use of the unknown SAg, the CNN correctly classifies the images of human IgG and Protein G as indicated by a 94% accuracy over the various molar binding ratios. These findings are noteworthy because they demonstrate that appropriately pretrained CNNs can be used for the prediction of protein–protein interactions beyond the scope of the original training set. Aided by deep‐learning methods, simple stains of mixed protein solutions may serve as accurate predictors of the strength of protein–protein interactions with relevance to protein engineering, self‐aggregation, or protein stability in complex media.

Identifying Quinones in Complex Aqueous Environmental Media (Biochar Extracts) through Tagging with Cysteine and Cysteine-Contained Peptides and High Resolution Mass Spectrometry Analysis.

Quinones are among the most important components in natural organic matter (NOM) for redox reactions; however, no quinones in complex environmental media have been identified. To aid the identification of quinone-containing molecules in ultracomplex environmental samples, we developed a chemical tagging method that makes use of a Michael addition reaction between quinones and thiols (-SH) in cysteine (Cys) and cysteine-contained peptides (CCP). After the tagging, candidates of quinones in representative aqueous environmental samples (water extractions of biochar) were identified through high-resolution mass spectrometry (HRMS) analysis. The MS and UV spectra analysis showed rapid reactions between Cys/CCP and model quinones with β-carbon from the same benzene ring available for Michael addition. The tagging efficiency was not influenced by other co-occurring nonquinone representative compounds, including caffeic acid, cinnamic acid, and coumaric acid. Cys and CCP were used to tag quinones in water extractions of biochars, and possible candidates of quinones (20 and 53 based on tagging with Cys and CCP, respectively) were identified based on the HRMS features for products of reactions with Cys/CCP. This study has successfully demonstrated that such a Michael addition reaction can be used to tag quinones in complex environmental media and potentially determine their identities. The method will enable an in-depth understanding of the redox chemistry of NOM and its critical chemical compositions and structures.

Quantitative analysis of microplastics in beach sand via low-temperature solvent extraction and thermal degradation: Effects of particle size and sample depth

Quantifying trace levels of microplastics in complex environmental media remains a challenge. In this study, an approach combining field collection of samples from different depths, sample size fractionation, and plastic quantification via pyrolysis-gas chromatography–mass spectrometry (Py-GC–MS) was employed to identify and quantify microplastics at two public beaches along the northeast coast of the U.S. (Salisbury beach, MA and Hampton beach, NH). A simple sampling tool was used to collect beach sand from depth intervals of 0–5 cm and 5–10 cm, respectively. The samples were sieved to give three size fractions: coarse (>1.2 mm), intermediate (100 μm–1.2 mm), and fine (1.2 μm–100 μm) particles. Following density separation and wet peroxide oxidation, a low-temperature solvent extraction protocol involving 2-chlorophenol was used to extract polyester (PET), polystyrene (PS), polyamide (PA), and polyvinyl chloride (PVC). The extract was analyzed using Py-GC–MS for the respective polymers, while the solid residue was pyrolyzed separately for polyethylene (PE) and polypropylene (PP). The one-step solvent extraction method significantly simplified the sample matrix and improved the sensitivity of analysis. Among the samples, PET was detected in greater quantities in the fine fraction than in the intermediate size fraction, and PET fine particles were located predominantly in the surface sand. Similar to PET, PS was detected at higher mass concentrations in the fine particles in most samples. These results underscore the importance of beach environment for plastic fragmentation, where a combination of factors including UV irradiation, mechanical abrasion, and water exposure promote plastic breakdown. Surface accumulation of fine plastic particles may also be attributed to transport of microplastics through wind and tides. The proposed sample treatment and analysis methods may allow sensitive and quantitative measurements of size or depth-related distribution patterns of microplastics in complex environmental media.

Reflection Artifacts Removal of Photoacoustic Imaging in Complex Medium

Abstract Photoacoustic (PA) imaging owns a great prospect in medical diagnosis because of its high contrast and capability in functional imaging. While, the detected PA signals are always a mix of direct-arrived signals (DAS) and reflected (scattered) signals (RS) in inhomogeneous and bounded samples such as human tissues. The RS can lead to many artifacts and severely affect the final image, which confuses the artifacts with the real PA sources. This paper employed a spatial singular value decomposition (SVD) filter to abstract the DAS and thus remove the reflection artifacts. We conducted experiments on an agar phantom and an in vitro tissue to verify the method. The results show that the proposed method can effectively remove RS, resulting in fewer reflection artifacts in PA images.

Evolution recovers the fitness of Acinetobacter baylyi strains with large deletions through mutations in deletion-specific targets and global post-transcriptional regulators.

Organelles and endosymbionts have naturally evolved dramatically reduced genome sizes compared to their free-living ancestors. Synthetic biologists have purposefully engineered streamlined microbial genomes to create more efficient cellular chassis and define the minimal components of cellular life. During natural or engineered genome streamlining, deletion of many non-essential genes in combination often reduces bacterial fitness for idiosyncratic or unknown reasons. We investigated how and to what extent laboratory evolution could overcome these defects in six variants of the transposon-free Acinetobacter baylyi strain ADP1-ISx that each had a deletion of a different 22- to 42-kilobase region and two strains with larger deletions of 70 and 293 kilobases. We evolved replicate populations of ADP1-ISx and each deletion strain for ~300 generations in a chemically defined minimal medium or a complex medium and sequenced the genomes of endpoint clonal isolates. Fitness increased in all cases that were examined except for two ancestors that each failed to improve in one of the two environments. Mutations affecting nine protein-coding genes and two small RNAs were significantly associated with one of the two environments or with certain deletion ancestors. The global post-transcriptional regulators rnd (ribonuclease D), csrA (RNA-binding carbon storage regulator), and hfq (RNA-binding protein and chaperone) were frequently mutated across all strains, though the incidence and effects of these mutations on gene function and bacterial fitness varied with the ancestral deletion and evolution environment. Mutations in this regulatory network likely compensate for how an earlier deletion of a transposon in the ADP1-ISx ancestor of all the deletion strains restored csrA function. More generally, our results demonstrate that fitness lost during genome streamlining can usually be regained rapidly through laboratory evolution and that recovery tends to occur through a combination of deletion-specific compensation and global regulatory adjustments.

High-resolution ultrasound imaging based on spatio-temporal MUSIC

Abstract Time-reversal MUltiple SIgnal Classification (TR-MUSIC) is known for its super-resolution capability in locating point scatterers. However, a prerequisite for the application of the TR-MUSIC method is a thorough understanding of the properties of the medium and its background Green’s function. In general, it is difficult to obtain an accurate model of the Green’s function in advance for non-uniform or complex media, necessitating the use of approximate Green’s functions. When TR-MUSIC relies on these approximations, the impact on lateral resolution may be minimal, but the axial resolution is significantly reduced. In addition, we have proposed the Range-MUSIC (R-MUSIC) method, which exploits the linear relationship between the rotation of the echo phases and the positions of the scatterers. This approach uses subbands of different frequencies, differentiating multiple point scatterers by the speed of phase rotation associated with each frequency. By analyzing the profile in the time domain of echoes within the noise subspace, R-MUSIC achieves super-resolution in the axial direction without improving lateral resolution. Therefore, our study combines R-MUSIC with TR-MUSIC to improve axial resolution while maintaining lateral resolution. Through simulation and experimental evidence, we have shown that this combined approach yields better imaging performance than either method used independently.

Efficient approach for generating vortex sources with arbitrary orbital angular momentum in acoustic experiments

Abstract In theoretical research framework of acoustics or optics, how to provide stable and efficient experimental vortex sources with arbitrary orbital angular momentum (OAM) (especially with larger OAM) is a highly challenging research topic. Here, we propose and demonstrate the general principle of two different methods to generate vortex sources with arbitrary OAM, based on the point-sources array and acoustic metamaterials, respectively. Specifically, the general synthetic law is summarized from the analytical perspective behind generating two-dimensional vortex waves using different point sources with different phases, and the design flexibility of acoustic metamaterials is also utilized to provide an ideal solution for generating vortex sources with larger OAM. Besides, we qualitatively and quantitatively determine the OAM of generated vortex waves through simple formulas, and briefly discuss the applicability and stability of two different methods with complementary advantages. The principles of vortex sources generation revealed in this work provide direct theoretical support for the experimental exploration of interactions between multiphysics fields and complex media, with potential applications in vortex fields manipulation and OAM detection.

Analysis of the competitive influence of gas adsorption and interface modification on the surface free energy of coal matrix

Coal is a complex porous medium characterized by numerous pores and fractures within its internal structure, which provide a natural space for the storage of coalbed methane. The high surface free energy of coal significantly inhibits the efficient extraction of coalbed methane, resulting in the escape of considerable amounts of greenhouse gas during the later stages of coal mining. This exacerbates the challenges and costs associated with environmental governance. According to the principle of minimum capacity, the surface of the coal matrix reduces its surface free energy through gas adsorption. To investigate the competitive influence of gas adsorption and interface modification on the surface free energy of the coal matrix, isothermal adsorption and contact angle determination experiments were conducted. The results indicate that as equilibrium pressure increases, the amount of gas adsorption on the surface of the coal matrix also increases, while the adsorption potential exhibits a contrasting trend. Under the influence of gas adsorption, there is a significant increase in Gibbs variation, indicating a substantial decrease in the surface free energy of the coal matrix. Under the influence of interface modification, an increase in surfactant concentration resulted in a trend of energy reduction characterized by an initial increase followed by a subsequent decrease. Moreover, interface modification effectively eliminated the water-blocking effect, leading to a significant enhancement in gas desorption. Consequently, interface modification offers important theoretical support for improving production in coalbed methane and mitigating the greenhouse effect.

Image-domain least-squares imaging in an elastic vertically transversely isotropic medium: Multiparameter point-spread function deconvolution

By solving a linear inverse problem, least-squares migration (LSM) can provide higher-precision images of complex subsurface structures than traditional adjoint-operator-based migration. LSM can be conducted in the data domain and the image domain (IDLSM). IDLSM in acoustic media has been extensively studied, commonly using single-parameter point-spread function (PSF) deconvolution. For high-accuracy imaging of complex media, we develop an image-domain elastic least-squares imaging method using multiparameter PSF deconvolution for vertically transversely isotropic (VTI) media. The multiparameter PSFs, including P-P, P-S, S-P, and S-S components, are calculated on a sparse grid using elastic VTI wave equation Born modeling and migration. The traditional migration result is then decomposed into individual local results, each corresponding to the size of a single PSF, through unit partitioning. Finally, a set of filters is derived from four elastic VTI PSF components to approximate the Hessian inverse, which are subsequently assembled to reconstruct an entire deconvolved image. The numerical experiments confirm that our method can significantly decrease multiparameter crosstalk artifacts and improve spatial resolution and amplitude fidelity.

A study on the effective use of Tongyeong’s complex cultural space and media façade: Tongyeong’s historical, artistic and cultural resources

A study on the effective use of Tongyeong’s complex cultural space and media façade: Tongyeong’s historical, artistic and cultural resources

Capture of RNA G-quadruplex structures using an l-RNA aptamer.

G-quadruplexes (dG4 and rG4) are nucleic acid secondary structures formed by the self-assembly of certain G-rich sequences, and they have distinctive chemical properties and play crucial roles in fundamental biological processes. Small molecule G4 ligands were shown to be crucial in characterizing G4s and understanding their functions. Nevertheless, concerns regarding the specificity of these synthetic ligands for further investigation of G4s, especially for rG4 isolation purposes, have been raised. In comparison to G4 ligands, we propose a novel magnetic bead-based pulldown assay that enables the selective capture of general rG4s using functionalized l-Apt.4-1c from both simple buffer and complex media, including total RNA and the cell lysate. We found that our l-RNA aptamer can pulldown general rG4s with a higher efficiency and specificity than the G4 small molecule ligand BioTASQ v.1 in the presence of non-target competitors, including dG4 and non-G4 structures. Our findings reveal that biotinylated l-aptamers can serve as effective molecular tools for the affinity-based enrichment of rG4 of interest using this new assay, which was also verified by quantitative reverse transcription-polymerase chain reaction (RT-qPCR) on endogenous transcripts. This work provides new and important insights into rG4 isolation using a functionalized l-aptamer, which can potentially be applied in a transcript-specific or transcriptome-wide manner in the future.

Correlation between sporogenesis and lipopeptide production in Paenibacillus elgii.

Pelgipeptins, tridecaptins, and elgicins are among the antimicrobials produced by Paenibacillus elgii. Growth in complex media is commonly applied to obtain lipopeptides from culture's supernatant, but it requires further purification. This study aimed to improve the yield of pelgipeptins and tridecaptins using chemically defined media. The kinetics of antimicrobial lipopeptide yield in chemically defined media were evaluated in P. elgii AC13. Pelgipeptins were detected in the supernatant and the culture pellet, but tridecaptins were mainly associated with cell debris or endospores. We investigated whether removing Ca2+ would impair P. elgii sporogenesis, consequently improving the yield of tridecaptin. The kinetics of both lipopeptides in the presence and absence of Ca2+ were quantitatively and qualitatively evaluated and further correlated with the cell cycle. The impairment of P. elgii AC13 sporogenesis had no effect on tridecaptin production, which remained undetected in the supernatant of the culture. On the other hand, the yield of pelgipeptin in a Ca2+-free medium increased. We showed for the first time that the removal of Ca2+ interrupted the sporogenesis in P. elgii and improved the yield of pelgipeptins. However, Ca2+ absence had no effect on tridecaptin yield, which is possibly degraded or associated with other cell debris components.

Shaping entangled photons through arbitrary scattering media using an advanced wave beacon

Entangled photons provide transformative new paths in the fields of communication, sensing, and computing. However, when entangled photons propagate through a complex medium, their correlations are scrambled. Using wavefront shaping to compensate for the scattering and retrieve the two-photon correlations is challenging due to the low signal-to-noise ratio of the two-photon signal. While previous works partly addressed this challenge by using feedback from a strong classical laser beam that co-propagates with the entangled photons, such methods frequently depend on assumptions about the complex medium, limiting the applicability of quantum wavefront shaping. In this work, we propose and demonstrate a new feedback mechanism that is inspired by Klyshko’s advanced wave picture: the classical laser beam is emitted in one of the detection modes, counter-propagates with one of the entangled photons, reflects at the crystal plane, and co-propagates with the other. The new Klyshko feedback allows compensation of scattering in arbitrary samples and even in situations where each photon propagates through a different scattering medium. Since the advanced wave picture applies whenever optical reciprocity is valid, such Klyshko optimization can be used across a wide range of configurations, offering a robust and alignment-free setup. We therefore believe this protocol will open the door for real-world applications of quantum wavefront shaping.