3D Structure Research Articles

3D-Printed Sr-Doped TiO2 / Biowaste / Polymeric Structures for Mitigating Dye Contamination in Water

Wastewater laden with synthetic dyes from the textile industry poses a threat to natural water sources, the environment, and human health, contravening Sustainable Development Goals (SDGs). Addressing this challenge requires innovative solutions focusing on contaminant removal in wastewater treatment. This study explored the application of 3D-printed polymeric structure incorporating Sr-doped TiO2 and biowastes as photocatalysts and adsorbents to eliminate Methylene Blue (MB) from water. X-ray diffraction (XRD) analysis verified that the Sr-doped TiO2 powder synthesized by solution combustion technique predominantly exhibited the anatase phase. Transmission Electron Microscopy (TEM) showed that the average particle sizes for TiO2 doped with 1 mol% and 5 mol% Sr were 19.45±2.6 nm and 10.32±1.9 nm, respectively. The Brunauer–Emmett–Teller (BET) analysis determined the specific surface area as follows: 1 mol% Sr-doped TiO2 at 39.7 m²/g, 5 mol% Sr-doped TiO2 at 86.8 m²/g, SiO2 from sugarcane leaves at 168.2 m²/g, and bagasse ash at 8.5 m²/g. Over 24 hours in the dark, the 3D polymeric structure and the one incorporating Sr-doped TiO2/bagasse ash absorbed approximately 48% of the MB dye. For the structure containing Sr-doped TiO2/silica from sugarcane leaves, a 66% dye adsorption was observed. Exposure to UV light for 8 hours further enhanced dye removal in the Sr-doped TiO2/silica/polymeric structure, surpassing 84%. Reusability experiments over 10 cycles demonstrated the structures' stable performance, with dye degradation efficiency consistently exceeding 70%, and statistical analysis confirming no significant decline in efficiency across cycles. This study underscores the efficacy of 3D-printed Sr-Doped TiO2/biowaste/polymeric structures as a promising technology for mitigating water pollution, providing a viable solution to the environmental and health challenges arising from dye-contaminated wastewater in the textile industry.

Dictyophora indusiata polysaccharide improved 3D network structure and flavor benefits of set yoghurt

Dictyophora indusiata polysaccharide improved 3D network structure and flavor benefits of set yoghurt

A novel LVPA-UNet network for target volume automatic delineation: An MRI case study of nasopharyngeal carcinoma

Accurate delineation of Gross Tumor Volume (GTV) is crucial for radiotherapy. Deep learning-driven GTV segmentation technologies excel in rapidly and accurately delineating GTV, providing a basis for radiologists in formulating radiation plans. The existing 2D and 3D segmentation models of GTV based on deep learning are limited by the loss of spatial features and anisotropy respectively, and are both affected by the variability of tumor characteristics, blurred boundaries, and background interference. All these factors seriously affect the segmentation performance. To address the above issues, a Layer-Volume Parallel Attention (LVPA)-UNet model based on 2D-3D architecture has been proposed in this study, in which three strategies are introduced. Firstly, 2D and 3D workflows are introduced in the LVPA-UNet. They work in parallel and can guide each other. Both the fine features of each slice of 2D MRI and the 3D anatomical structure and spatial features of the tumor can be extracted by them. Secondly, parallel multi-branch depth-wise strip convolutions adapt the model to tumors of varying shapes and sizes within slices and volumetric spaces, and achieve refined processing of blurred boundaries. Lastly, a Layer-Channel Attention mechanism is proposed to adaptively adjust the weights of slices and channels according to their different tumor information, and then to highlight slices and channels with tumor. The experiments by LVPA-UNet on 1010 nasopharyngeal carcinoma (NPC) MRI datasets from three centers show a DSC of 0.7907, precision of 0.7929, recall of 0.8025, and HD95 of 1.8702 mm, outperforming eight typical models. Compared to the baseline model, it improves DSC by 2.14 %, precision by 2.96 %, and recall by 1.01 %, while reducing HD95 by 0.5434 mm. Consequently, while ensuring the efficiency of segmentation through deep learning, LVPA-UNet is able to provide superior GTV delineation results for radiotherapy and offer technical support for precision medicine.

Research on Modal Behavior of Large Francis Turbine Runner

The water-added-mass can affect the modal behavior of the Francis turbine runner largely. The sealing rings in the band-chamber and the crown-chamber outside of the runner are utilized to prevent leakage of water around the Francis turbine. The sealing rings and the chambers filled with water can also affect the modal behavior of the turbine. When the turbine runner operates in the power plant at various operating conditions, the seal clearances of the band-chamber and the crown-chamber filled with water may change the modal behavior of the large Francis turbine runner. Firstly, the 3D geometrical structure of the studied large-scale Francis turbine runner was constructed, and then the CAD model was meshed to establish the finite-element model for numerical analysis. Next, the modal shapes and the natural-frequencies of runners in the air were calculated, which is the traditional method used for the structural modal behavior analysis of the turbine runners. Finally, this paper investigates the modal behavior of a large-scale Francis runner prototype with the combined effects of sealing rings and water added-mass by direct water-structure coupled analysis via the finite element method (FEM) to obtain more realistic results. The results reveal that the effects of water-added-mass and sealing rings cause a significant decrease in the natural-frequency of the large Francis turbine runner, which may lead to an increase in the amplitude of vibrations and even cracks. Technical suggestions are proposed to improve the monitoring and maintenance in the power stations to maintain the safe and efficient operation of the large Francis turbine units.

Three-dimensional chromatin landscapes in somatotroph tumour.

The three-dimensional (3D) genome architecture plays a critical role inregulating gene expression. However, the specific alterations in thisarchitecture within somatotroph tumors and their implications for gene expression remain largely unexplored. We employed Hi-C and RNA-seq analyses to compare the 3D genomic structures of somatotroph tumors with normal pituitary tissue. This comprehensive approachenabled the characterization of A/B compartments, topologically associateddomains (TADs), and chromatin loops, integrating these with gene expression patterns. We observed a decrease in both the frequency of chromosomal interactions andthe size of TADs in tumor tissue compared to normal tissue. Conversely, the number of TADs and chromatin loops was found to be increased in tumors. Integrated analysis of Hi-C and RNA-seq data demonstrated that changes inhigher-order chromat in structure were associated with alterations in gene expression. Specifically, genes in A compartments showed higher density and increased expression relative to those in B compartments. Moreover, the weakand enhanced insulation boundaries were identified, and the associated genes were enriched in the Wnt/β-Catenin signaling pathway. We identified the gainedand lost loops in tumor and integrated these differences with transcriptional changes to examine the functional relevance of the identified loops. Notably, we observed an enhanced insulation boundary and a greater number of loops in the TCF7L2 gene region within tumors, which was accompanied by an upregulation of TCF7L2 expression. Subsequently, TCF7L2 expression was confirmed through qRT-PCR, and upregulated TCF7L2 prompted cell proliferation and growth hormone (GH) secretion in vitro. Our results provide comprehensive 3D chromatin architecture maps of somatotroph tumors and offer a valuable resource for furthering the understanding of the underlying biology and mechanisms of gene expression regulation.

Laser-induced nitrogen and phosphorus-doped spongy carbon with graphene wings derived from lignin for significantly enhanced capacitance deionization performance

Efficient capacitive deionization (CDI) technology puts forward higher requirements for electrode materials. However, the traditional process of preparing porous carbon (PC) electrodes by alkaline chemical activation is polluting and energy-consuming. In this work, the N/P co-doped biocarbon material (H-AL/APP) was prepared by using alkali lignin (AL) and ammonium polyphosphate (APP) as carbon precursors based on laser-induced carbonization and hydrothermal activation technology. The as-prepared carbon material shows a three-dimensional (3D) structure with a hierarchical porous structure, large specific surface area of 405.98 m2/g (SSA), excellent pore volume, and outstanding mesoporosity. Compared with commercial YP80 activated carbon, The H-AL/APP electrode exhibits a higher specific capacitance of 210F/g with excellent rate performance and cycle stability. When assembled for desalination, H-AL/APP shows the highest removal rate of 23 mg/g/min with an outstanding desalination capacity of 34.6 mg/g than those of YP80 activated carbon. Furthermore, reasonable cycle stability and reproducibility highlight their promising application prospects. In summary, this work provides a green, efficient, and economical method for preparing high-performance heteroatom-doped PCs for efficient CDI desalination.

Quantitative analysis of deformation performance for skew slab based on deformation energy decomposition method of triangular prism element

In order to propose a simpler and more effective method to quantitatively analyze the macroscopic basic deformation properties such as tension, bending and shear of the skew slabs, and provide theoretical basis and technical support for targeted design and reinforcement. Based on mathematical orthogonality, mechanical equilibrium and physical parameters, this paper proposes a deformation energy decomposition method suitable for 3D 6-node arbitrary triangular prism elements. By applying this method to the finite element model discretized by triangular prism element, the quantitative information of 6 kinds of rigid body displacement and 12 kinds of deformation energy of skew slab can be obtained. The quantitative and visual analysis of the basic deformation performance of the skew slab is carried out by using the method in this paper. Then the targeted structural design and reinforcement design of the skew slab can be guided according to the principle of matching design with deformation. Compared with the existing deformation decomposition methods based on square elements, which are only applicable to 2D or quasi-3D regular structures, the deformation energy decomposition method based on arbitrary triangular prism elements in this paper can be used to analyze the deformation performance of 3D irregular structures. The influence of skew angle and span-width ratio on the deformation performance of skew slab is analyzed by deformation energy decomposition method. The results show that when the skew angle is greater than 25°, the proportion of ductile deformation energy such as tension and bending of skew slab decreases rapidly. In this case, the shear design of the skew slab should be focused on. When the angle is greater than 45°, the span-width ratio should be appropriately reduced to improve the ductility of the skew slab, and the torsion design needs to be focused on.

Asymptotic analysis of particle cluster formation in the presence of anchoring sites

The aggregation or clustering of proteins and other macromolecules plays an important role in the formation of large-scale molecular assemblies within cell membranes. Examples of such assemblies include lipid rafts, and postsynaptic domains (PSDs) at excitatory and inhibitory synapses in neurons. PSDs are rich in scaffolding proteins that can transiently trap transmembrane neurotransmitter receptors, thus localizing them at specific spatial positions. Hence, PSDs play a key role in determining the strength of synaptic connections and their regulation during learning and memory. Recently, a two-dimensional (2D) diffusion-mediated aggregation model of PSD formation has been developed in which the spatial locations of the clusters are determined by a set of fixed anchoring sites. The system is kept out of equilibrium by the recycling of particles between the cell membrane and interior. This results in a stationary distribution consisting of multiple clusters, whose average size can be determined using an effective mean-field description of the particle concentration around each anchored cluster. In this paper, we derive corrections to the mean-field approximation by applying the theory of diffusion in singularly perturbed domains. The latter is a powerful analytical method for solving two-dimensional (2D) and three-dimensional (3D) diffusion problems in domains where small holes or perforations have been removed from the interior. Applications range from modeling intracellular diffusion, where interior holes could represent subcellular structures such as organelles or biological condensates, to tracking the spread of chemical pollutants or heat from localized sources. In this paper, we take the bounded domain to be the cell membrane and the holes to represent anchored clusters. The analysis proceeds by partitioning the membrane into a set of inner regions around each cluster, and an outer region where mean-field interactions occur. Asymptotically matching the inner and outer stationary solutions generates an asymptotic expansion of the particle concentration, which includes higher-order corrections to mean-field theory that depend on the positions of the clusters and the boundary of the domain. Motivated by a recent study of light-activated protein oligomerization in cells, we also develop the analogous theory for cluster formation in a three-dimensional (3D) domain. The details of the asymptotic analysis differ from the 2D case due to the contrasting singularity structure of 2D and 3D Green’s functions.Graphical abstract2D model of diffusion-based protein cluster formation in the presence of anchoring cites and particle recycling. a A set of N anchoring sites at positions xj\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\ extbf{x}}_j$$\\end{document}, j=1,…,N\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$j=1,\\ldots ,N$$\\end{document}, in a bounded domain Ω\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\Omega $$\\end{document}. b Diffusing particles accumulate at the anchoring sites resulting in the formation of particle aggregates or clusters Uj\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{\\mathcal {U}}}_j$$\\end{document}. c The clusters are dynamically maintained by a combination of lateral diffusion outside the clusters and particle recycling

Fabrication of gelatin-based antibacterial bilayer wound dressing using direct writing and electrospinning methods

Fabricating a fibrous well-ordered wound dressing for accelerating full-thickness wounds is a desirable treatment vector. Here, through modifications in the material extrusion device and adding a pneumatic-based injection, a material extrusion method for gelatin was introduced with the ability to fabricate 3D structure with repeat layers to support cell activity for the under layer. Furthermore, in the upper layer, the co-electrospinning of PU with gelatin was designed to simultaneously exploit the oxygen permeability and mechanical stability of PU with regenerative properties and collagen-like structure of gelatin. Moreover, zinc oxide nanoparticles (ZnO) was added into the 3D-printed under layer to synergistically benefit from the antibacterial properties of ZnO and the excellent biocompatibility of gelatin. The controllable porosity of the under layer, enabled through the additive manufacturing method, was adjusted to mimic the extracellular matrix of natural tissue with around (127.28 ± 20.70) μm pore size after swelling with smooth fibers. S. aureus, E. coli, Bacillus subtilis, and Pseudomonas with inhibition zone diameters at ∼ 2.14 cm and ∼ 1.96 cm, ∼ 4.01 cm, and ∼ 2.24 cm, respectively. Moreover, the scaffold showed great biocompatibility toward fibroblast cells after 7 days of cell culture with ∼ 89 % cell viability.

Preparation of a class of cucurbit[6]uril-light rare-earth-based supramolecular assemblies and its efficient detection of chloramphenicol

By introducing 4,4′-naphthalenedisulfonic acid (4,4′-H2BPs) as a structure-induced agent, four novel cucurbit[6]uril-based supramolecular assemblies have been successfully prepared in the cucurbit[6]uril (Q[6]) system with light rare-earth elements (La3+, Ce3+, Pr3+, Nd3+) under hydrothermal conditions. Crystal structure analysis shows that the assemblies 1 (La3+), 2 (Ce3+), 3 (Pr3+) are isomorphism 3D frameworks, where Q[6] can directly coordinate with light rare-earth metal ions to form 1D −Ln(III)- Q[6]-Ln(III)- chains, while the 4 (Nd3+) presents 3D structures stacking by the unit of Q[6]@Nd3+@ Q[6]@Nd3+@ Q[6], respectively. In these structures, 4,4′-H2BPs ligands all can act as an organic counter anion and bridging via the outer-surface interaction of cucurbit[n]uril (OSIQ) in the system, which is the main driving force from low-dimensional to high-dimensional. Meanwhile, the fluorescence sensing performance of the two assemblies for antibiotics was investigated, and the results showed that assembly 1 could be used as a promising fluorescent sensor material to detect chloramphenicol (CAP).

Prediction of Solar Coronal Structures Using Fourier Neural Operators Based on the Solar Photospheric Magnetic Field Observation

AbstractThis paper constructs the structures of the solar corona (SC) using Fourier neural operators (FNO) based on solar photospheric magnetic field observation. The purpose is to learn the mapping between two infinite‐dimensional function spaces, which takes the photospheric magnetic field as input and the magnetohydrodynamic (MHD) solar wind plasma parameters as output, from a finite collection of input‐output pairs. The FNO‐SC model is established using MHD simulated results of 36 Carrington rotations (CRs) from 2008, 2009, and 2020. The performance of the FNO‐SC model is tested for 6 CRs during various phases of the solar activity such as descending, minimum, and ascending phases to generate the 3D structures of the SC. With the MHD simulations as references, the average structure similarity index measure (SSIM) value for the magnetic field topology from 1 to 3Rs is around 0.88. From 1 to 20Rs, the SSIM values for the number density and radial speed surpass 0.9. Relative to OMNI observations, the mean absolute percentage error for the radial speed generated from the FNO‐SC model does not exceed 0.25. These results indicate that the FNO‐SC model effectively captures the solar coronal structures typical of the periods investigated, by recovering the MHD simulations as well as the observations. The FNO‐SC model is further trained with enriched data from the maximum phase to assess the capability of modeling such a situation. The FNO‐SC model costs 48.7 s for a single CR prediction, and thus facilitates real‐time space weather forecasting.

Characterizing the 3D Structure of Molecular Cloud Envelopes in the Cloud Factory Simulations

We leverage recent numerical simulations of highly resolved star-forming regions in a Milky Way–like galaxy to explore the nature of extended gaseous envelopes around molecular clouds. We extract a sample of two dozen star-forming clouds from the feedback-dominated suite of Cloud Factory simulations. With the goal of exploring the 3D thermal and chemical structure of the gas, we measure and fit the clouds’ radial profiles with multiple tracers, including nHI , nH2 , nHtot , n CO, and gas temperature. We find that while solar neighborhood clouds recently detected via 3D dust mapping have radially symmetric, low-density envelopes that extend ∼10–15 pc, the simulated cloud envelopes are primarily radially asymmetric with low-density envelopes that extend only ∼2–3 pc. One potential explanation for the absence of extended envelopes in the simulated clouds may be the lack of magnetic fields, while a stronger local feedback prescription compared to solar neighborhood conditions may drive the radially asymmetric cloud morphologies. We make the pipeline used to extract and characterize the radial profiles of the clouds publicly available, which can be used in complementary and future simulations to shed additional light on the key physics shaping the formation and evolution of star-forming structures in the Milky Way.

A Three-Dimensional Open-Framework Tin(II) Sulfate with Near-Unity Photoluminescence Quantum Yield.

A new open-framework tin(II) sulfate, formulated as C4H12N2·Sn(SO4)2·H2O, was prepared under the structure-directing effect of piperazine. This compound features a 3D structure with 16-ring channels. Under ultraviolet light irradiation, it emits bright yellow luminescence with a near-unity photoluminescence quantum yield. Theoretical calculations were carried out to understand the luminescence mechanism.

A bionic mimosa soft robot based on a multi-responsive PNIPAM-PEGDA hydrogel composition.

Deformation plays a vital role in the survival of natural organisms. One example is that plants deform themselves to face the sun for sufficient sunlight exposure, which allows them to produce nutrients through photosynthesis. Drawing inspiration from nature, researchers have been exploring the development of 3D deformable materials. However, the traditional approach to manufacturing deformable hydrogels relies on complex technology, which limits their potential applications. In this study, we simulate the stress variations observed in the plant tissue to create a 3D structure from a 2D material. Using UV curing technology, we create a single-layer poly(N-isopropylacrylamide) hydrogel sheet with microchannels that exhibit distinct swelling rates when subjected to stimulation. After a two-step curing process, we produce a poly(N-isopropylacrylamide)-polyethylene glycol diacrylatedouble-layer structure that can be manipulated to change its shape by controlling the light and solvent content. Based on the double-layer structure, we fabricate a dual-response driven bionic mimosa robot that can perform a variety of functions. This soft robot can not only reversibly change its shape but also maintain a specific shape without continuous stimulation. Its capacity for reversible deformation, resulting from internal stress, presents promising application prospects in the biomedical and soft robotics domain. This study delivers an insightful framework for the development of programmable soft materials.

Regional and Sex Differences in the Mouse Colonic Innervation Assessed Using a Computerized Quantitative Approach in Three-dimension of the Enteric Nervous System (ENS)

The ENS consists of the submucosal and myenteric plexus (SMP, MP) and controls a variety of gut functions. The quantitative analysis of innervation in the ENS is still a challenge because the ENS forms a mesh-like three-dimensional (3D) network embedded in the gut wall. We developed a computerized approach to perform direct, objective and automatic measurements of innervation in 3D structures of the mouse colonic ENS. The whole mounts of SMP and MP were prepared along the proximal, transverse and distal colon (pC, tC, dC) collected from 8 naïve mice (C57BL/6J, 6 weeks, 4 of each sex). Each 3D image of SMP or MP was reconstructed from Z-stack confocal images with 50-100 or 30-50 optical sections in the frame 1415×1415 or 708×708 μm and 1 μm apart. The Hu C/D, peripheral form of choline acetyltransferase (pChAT), nitric oxide synthase (nNOS), vasoactive intestinal peptide (VIP), tyrosine hydroxylase (TH) and calcitonin gene-related protein (CGRP) immunoreactive (ir) enteric neurons or fibers were digitally traced and automatically measured with Imaris 9.7 for neuroscientists. The co-localization of pChAT and nNOS was determined with ImarisColoc tool. The densities of neurons and nerve fibers, co-localization of pChAT and nNOS were calculated from 6-8 of 3D images/marker/plexus/segment/mouse (total 2304 3D images) and expressed as the percentage of each type of neurons in total neurons, the volume of each type of nerve fibers in the volume of SMP and MP and co-labeled neurons in each type of neurons. The results demonstrate significant differences in the numbers of two major neuronal populations, their co-localization and densities of three representative nerve fibers among three colonic segments, between two plexuses and sexes. 1. pChAT- and nNOS-ir neurons in the MP: the density of pChAT-ir neurons was 1.4- and 2.1-fold lower in the pC than in the tC and dC (p<0.05, p<0.001), and 1.6- and 4.0-fold higher than that of nNOS-ir neurons in the tC and dC (p<0.001, p<0.001), respectively. In contrast, the density of nNOS-ir neurons was 1.4- or 2.3-fold higher in the pC or tC than dC (p<0.001, p<0.01). 2. Co-localization of pChAT and nNOS in the MP: Co-labeled neurons in the nNOS-ir neurons were 1.4- or 1.5-fold lower in the pC or tC than dC (p<0.05, p<0.05). 3. Nerve fibers: The density of VIP-ir fibers in the SMP was 2.4- and 1.8-fold higher in the pC than tC and dC (p<0.001, p<0.001) while 3.0- and 2.4-fold lower than in the MP in both tC and dC (p<0.001, 0.001). TH-ir fibers in the SMP were 1.6-fold lower in both tC or dC than pC (p<0.01, p<0.01), 1.6-, 2.2- and 1.4-fold lower than MP in the pC, tC and dC (p<0.001, p<0.001, p<0.05). In the MP, they were 1.8- and 1.6-fold lower in the dC than in pC and tC (p<0.001, p<0.001). CGRP-ir fibers did not show significant difference between two plexuses among three segments. 4. Sex differences: The co-labeled neurons in the pChAT-ir neurons were 2.2-, 2.7- and 2.2-fold more in the males than females in three segments (p<0.001, p<001, p<0.001) while those in the nNOS-ir neurons were 1.9-fold more in the males than females only in the dC (p<0.05). VIP-ir fibers in the dC-MP were 1.2-fold higher in the males than females (p<0.05). These data and the novel approach developed in this study will contribute to further assessments of the structure-function relationships and pathological alterations in the colon with mouse models. Supported by NIH/SPARC 1OT2OD024899-01. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Aptamer Biosensor Design for the Detection of Endocrine-disrupting chemicals Small Organic Molecules Using Novel Bioinformatics Methods

Endocrine-disrupting chemicals (EDCs) are a class of substances, either synthetic or naturally occurring, that can disrupt the normal functioning of hormones. Using aptamers, which are biological recognition elements, biosensors can quickly and accurately detect EDCs in environmental samples. However, the elucidation of aptamer structures by conventional methods is highly challenging due to their complexity.This has led to the development of three-dimensional aptamer structures based on different models and techniques. To do this, we developed a way to predict the 3D structures of the SS DNA needed for this sequence by starting with an aptamer sequence that has biosensor properties specific to bisphenol-A (BPA), one of the chemicals found in water samples that can interfere with hormones. In addition, we will elucidate the intermolecular mechanisms and binding affinity between aptamers and endocrine disruptors using bioinformatics techniques such as molecular docking, molecular dynamics simulation, and binding energies. The outcomes of our study are to compare modeling programs and force fields to see how reliable they are and how well they agree with results found in the existing literature, to understand the intermolecular mechanisms and affinity of aptamer-based biosensors, and to find a new way to make aptamers that takes less time and costs less.

Sulfonamide-induced DNA hypomethylation disturbed sugar metabolism in rice (Oryza sativa L.)

DNA methylation is well-accepted as a bridge to unravel the complex interplay between genome and environmental exposures, and its alteration regulated the cellular metabolic responses towards pollutants. However, the mechanism underlying site-specific aberrant DNA methylation and metabolic disorders under pollutant stresses remained elusive. Herein, the multilevel omics interferences of sulfonamides (i.e., sulfadiazine and sulfamerazine), a group of antibiotics pervasive in farmland soils, towards rice in 14 days of 1 mg/L hydroponic exposure were systematically evaluated. Metabolome and transcriptome analyses showed that 57.1–71.4 % of mono- and disaccharides were accumulated, and the differentially expressed genes were involved in the promotion of sugar hydrolysis, as well as the detoxification of sulfonamides. Most differentially methylated regions (DMRs) were hypomethylated ones (accounting for 87–95 %), and 92 % of which were located in the CHH context (H = A, C, or T base). KEGG enrichment analysis revealed that CHH-DMRs in the promoter regions were enriched in sugar metabolism. To reveal the significant hypomethylation of CHH, multi-spectroscopic and thermodynamic approaches, combined with molecular simulation were conducted to investigate the molecular interaction between sulfonamides and DNA in different sequence contexts, and the result demonstrated that sulfonamides would insert into the minor grooves of DNA, and exhibited a stronger affinity with the CHH contexts of DNA compared to CG or CHG contexts. Computational modeling of DNA 3D structures further confirmed that the binding led to a pitch increase of 0.1 Å and a 3.8° decrease in the twist angle of DNA in the CHH context. This specific interaction and the downregulation of methyltransferase CMT2 (log2FC = –4.04) inhibited the DNA methylation. These results indicated that DNA methylation-based assessment was useful for metabolic toxicity prediction and health risk assessment.

A detailed 3D stoichiometric map of spinels and oxides in structurally critical passivation layers on Inconel 718 superalloy after heating up to 650 °C

This research presents a detailed structure and time evolution for forming the passivation layer during oxidation of Selective Laser Melted (SLM-IN718) and commercially cast (Comm-IN718) Inconel 718 at 650 °C. It reveals that this layer has a complex 3D structure, with a top layer of Fe-Ni Chromite spinels (NiFexCr(2−x)O4) and a sublayer of Cr2O3. Raman maps and statistical analysis estimate x in NiFexCr(2−x)O4 for different heating times. The heating process initially forms iron-rich NiFexCr(2−x)O4 with x≈2, decreasing to ≈1 after 72 h of heating for both Comm- and SLM-IN718. Interestingly, a slightly different result was observed for the heat-treated SLM sample (HTSLM-IN718), where x increased again to 1.2 and 1.4 after 72 h. Secondary Ion Mass Spectrometry (SIMS) results reveal the depth hierarchy of the passivation layer profile, with the chromite layer covering a thicker Cr2O3 layer forming above the niobium-rich intermetallic layer above the alloy. Passivation layers are critical to the endurance of superalloys during extreme thermal cycling conditions. Therefore, by precisely determining the complex stoichiometry and hierarchy of the layer, this study can guide the development of durable superalloys with improved resistance to extreme thermal cycling conditions.

Aerodynamic and acoustic study of a small scale lightly loaded hovering rotor using large eddy simulation

The aerodynamics and acoustics of a small-scale lightly loaded hovering rotor operating at low Reynolds number is investigated using high-fidelity numerical simulation. A canonical geometry is considered, which allows for different flow topologies typical of transitional flows to develop along the span. Specifically, regions with laminar attached flow, trailing edge laminar separation with prominently 2D structures, and successive laminar separation, transition and reattachment with prominently 3D structures are identified. Furthermore, the lightly loaded configuration is conducive to significant blade-wake interaction, that in turn affects the dynamics of the boundary layer. The acoustic footprint of these phenomena are analyzed by correlating pressure fluctuations in the flow to those at the blade surface. It is found that the radiated noise is characterized by tonal peaks at the blade passing frequency and harmonics, and by a broadband hump at higher frequencies, consistent with experimental observations. The broadband hump exhibits distinct peaks that are found to originate from the separated shear layers on both pressure and suction sides. In particular, two noise generation mechanisms arising at two different frequencies in the broadband hump are identified. One is due to the interaction between an instability transported in the tip vortex of one blade and the leading edge of the following blade, and another one is found to rely on the interaction between an instability transported in the tip vortex and in the wake of one blade scattered by the trailing edge of the following blade.

Removing the uncertainty of chitin structure in chitons (Mollusca: Polyplacophora: Chitonida)

Chitons, also known as "living fossils", have been proposed as one of the earliest differentiated groups of molluscs. Although Polyplacophora is an ancient group of molluscs, very few studies have been conducted on the chitin of these organisms compared tobivalves, gastropods and cephalopods. The few available studies have provided contradictory results regarding the present chitin types, depending on the examined body parts. Herein, to solve this controversy, we studied the chitin from valve, girdle and radula of a chiton species by protecting the 3D structure of the body parts. Results obtained using infrared spectroscopy and Thermogravimetric analysis clearly showed chitons contain β-chitin in the girdle and valve; however, the signal detected for the type of chitin contained in the chiton radula appears to be α-chitin. In addition, chitin content of the whole chiton body on dry basis was recorded as 22.78%.