A novel approach to determine the critical survival threshold of cellular oxygen within spheroids via integrating live/dead cell imaging with oxygen modeling.

Defining the oxygen level that induces cell death within 3-D tissues is vital for understanding tissue hypoxia; however, obtaining accurate measurements has been technically challenging. In this study, we introduce a noninvasive, high-throughput methodology to quantify critical survival partial oxygen pressure (pO2) with high spatial resolution within spheroids by using a combination of controlled hypoxic conditions, semiautomated live/dead cell imaging, and computational oxygen modeling. The oxygen-permeable, micropyramid patterned culture plates created a precisely controlled oxygen condition around the individual spheroid. Live/dead cell imaging provided the geometric information of the live/dead boundary within spheroids. Finally, computational oxygen modeling calculated the pO2 at the live/dead boundary within spheroids. As proof of concept, we determined the critical survival pO2 in two types of spheroids: isolated primary pancreatic islets and tumor-derived pseudoislets (2.43 ± 0.08 vs. 0.84 ± 0.04 mmHg), indicating higher hypoxia tolerance in pseudoislets due to their tumorigenic origin. We also applied this method for evaluating graft survival in cell transplantations for diabetes therapy, where hypoxia is a critical barrier to successful transplantation outcomes; thus, designing oxygenation strategies is required. Based on the elucidated critical survival pO2, 100% viability could be maintained in a typically sized primary islet under the tissue pO2 above 14.5 mmHg. This work presents a valuable tool that is potentially instrumental for fundamental hypoxia research. It offers insights into physiological responses to hypoxia among different cell types and may refine translational research in cell therapies.NEW & NOTEWORTHY Our study introduces an innovative combinatory approach for noninvasively determining the critical survival oxygen level of cells within small cell spheroids, which replicates a 3-D tissue environment, by seamlessly integrating three pivotal techniques: cell death induction under controlled oxygen conditions, semiautomated imaging that precisely identifies live/dead cells, and computational modeling of oxygen distribution. Notably, our method ensures high-throughput analysis applicable to various cell types, offering a versatile solution for researchers in diverse fields.

Hemodynamic simulation of complete transposition of the great arteries for optimal treatment strategies based on its circulatory physiology.

Our study aimed to elucidate the role of different shunts and provide novel insights into optimal treatment approaches for complete transposition of the great arteries (TGA), which is characterized by unique and complicated circulatory dynamics. We constructed a computational cardiovascular TGA model and manipulated cardiovascular parameters, such as atrial septal defect (ASD) and patent ductus arteriosus (PDA) sizes, to quantify their effects on oxygenation and hemodynamics. In addition, ASD flow patterns were investigated as innovative indications for balloon atrial septostomy (BAS). Our model of TGA with an intact ventricular septum (TGA-IVS) showed that a large ASD can achieve sufficient mixing for survival without PDA, and the presence of PDA is detrimental to oxygen delivery. A treatment strategy for TGA-IVS that enlarges the ASD as much as possible by BAS and PDA closure would be desirable. In TGA with a ventricular septal defect (TGA-VSD), the VSD allows for higher oxygenation and reduces the detrimental effects of PDA on systemic circulation. In TGA-VSD, both strategies of enlarging the ASD by BAS with a closed PDA and adjusting the PDA in response to pulmonary vascular resistance (PVR) reduction without BAS may be effective. The simulated ASD flow patterns showed that the sharp peak left-to-right flow pattern in systole (σ-wave) reflected the hemodynamically significant ASD size, independent of PDA, VSD, and PVR. The ASD flow pattern visualized by Doppler echocardiography provides clinical insights into the significance of an ASD and indications for BAS, which are not readily apparent through morphological assessment.NEW & NOTEWORTHY Complete transposition of the great arteries (TGA) represents complex and unique circulation that is dependent on blood mixing through multiple interacting shunts. Consequently, the role of each shunt and the treatment strategy remain unclear. We developed a mathematical model of TGA circulation, revealing the significant influence of atrial septal defect (ASD) on oxygenation and hemodynamics. The blood flow pattern through the ASD reflects its hemodynamic impact and helps determine treatment strategies.

Genome optimization via virtual simulation to accelerate maize hybrid breeding.

The employment of doubled-haploid (DH) technology in maize has vastly accelerated the efficiency of developing inbred lines. The selection of superior lines has to rely on genotypes with genomic selection (GS) model, rather than phenotypes due to the high expense of field phenotyping. In this work, we implemented 'genome optimization via virtual simulation (GOVS)' using the genotype and phenotype data of 1404 maize lines and their F1 progeny. GOVS simulates a virtual genome encompassing the most abundant 'optimal genotypes' or 'advantageous alleles' in a genetic pool. Such a virtually optimized genome, although can never be developed in reality, may help plot the optimal route to direct breeding decisions. GOVS assists in the selection of superior lines based on the genomic fragments that a line contributes to the simulated genome. The assumption is that the more fragments of optimal genotypes a line contributes to the assembly, the higher the likelihood of the line favored in the F1 phenotype, e.g. grain yield. Compared to traditional GS method, GOVS-assisted selection may avoid using an arbitrary threshold for the predicted F1 yield to assist selection. Additionally, the selected lines contributed complementary sets of advantageous alleles to the virtual genome. This feature facilitates plotting the optimal route for DH production, whereby the fewest lines and F1 combinations are needed to pyramid a maximum number of advantageous alleles in the new DH lines. In summary, incorporation of DH production, GS and genome optimization will ultimately improve genomically designed breeding in maize. Short abstract: Doubled-haploid (DH) technology has been widely applied in maize breeding industry, as it greatly shortens the period of developing homozygous inbred lines via bypassing several rounds of self-crossing. The current challenge is how to efficiently screen the large volume of inbred lines based on genotypes. We present the toolbox of genome optimization via virtual simulation (GOVS), which complements the traditional genomic selection model. GOVS simulates a virtual genome encompassing the most abundant 'optimal genotypes' in a breeding population, and then assists in selection of superior lines based on the genomic fragments that a line contributes to the simulated genome. Availability of GOVS (https://govs-pack.github.io/) to the public may ultimately facilitate genomically designed breeding in maize.

Deep eutectic solvent self-assembled reverse nanomicelles for transdermal delivery of sparingly soluble drugs.

BACKGROUND: Transdermal delivery of sparingly soluble drugs is challenging due to their low solubility and poor permeability. Deep eutectic solvent (DES)/or ionic liquid (IL)-mediated nanocarriers are attracting increasing attention. However, most of them require the addition of auxiliary materials (such as surfactants or organic solvents) to maintain the stability of formulations, which may cause skin irritation and potential toxicity. RESULTS: We fabricated an amphiphilic DES using natural oxymatrine and lauric acid and constructed a novel self-assembled reverse nanomicelle system (DES-RM) based on the features of this DES. Synthesized DESs showed the broad liquid window and significantly solubilized a series of sparingly soluble drugs, and quantitative structure-activity relationship (QSAR) models with good prediction ability were further built. The experimental and molecular dynamics simulation elucidated that the self-assembly of DES-RM was adjusted by noncovalent intermolecular forces. Choosing triamcinolone acetonide (TA) as a model drug, the skin penetration studies revealed that DES-RM significantly enhanced TA penetration and retention in comparison with their corresponding DES and oil. Furthermore, in vivo animal experiments demonstrated that TA@DES-RM exhibited good anti-psoriasis therapeutic efficacy as well as biocompatibility. CONCLUSIONS: The present study offers innovative insights into the optimal design of micellar nanodelivery system based on DES combining experiments and computational simulations and provides a promising strategy for developing efficient transdermal delivery systems for sparingly soluble drugs.

Integration of Febio as an Instructional Tool in the Undergraduate Biomechanics Curriculum.

Computer simulations play an important role in a range of biomedical engineering applications. Thus, it is important that biomedical engineering students engage with modeling in their undergraduate education and establish an understanding of its practice. In addition, computational tools enhance active learning and complement standard pedagogical approaches to promote student understanding of course content. Herein, we describe the development and implementation of learning modules for computational modeling and simulation (CM&S) within an undergraduate biomechanics course. We developed four CM&S learning modules that targeted predefined course goals and learning outcomes within the febio studio software. For each module, students were guided through CM&S tutorials and tasked to construct and analyze more advanced models to assess learning and competency and evaluate module effectiveness. Results showed that students demonstrated an increased interest in CM&S through module progression and that modules promoted the understanding of course content. In addition, students exhibited increased understanding and competency in finite element model development and simulation software use. Lastly, it was evident that students recognized the importance of coupling theory, experiments, and modeling and understood the importance of CM&S in biomedical engineering and its broad application. Our findings suggest that integrating well-designed CM&S modules into undergraduate biomedical engineering education holds much promise in supporting student learning experiences and introducing students to modern engineering tools relevant to professional development.

Anti-Melanogenic Effects of Takifugu flavidus Muscle Hydrolysate in B16F10 Melanoma Cells and Zebrafish.

Abnormal melanogenesis can lead to hyperpigmentation. Tyrosinase (TYR), a key rate-limiting enzyme in melanin production, is an important therapeutic target for these disorders. We investigated the TYR inhibitory activity of hydrolysates extracted from the muscle tissue of Takifugu flavidus (TFMH). We used computer-aided virtual screening to identify a novel peptide that potently inhibited melanin synthesis, simulated its binding mode to TYR, and evaluated functional efficacy in vitro and in vivo. TFMH inhibited the diphenolase activities of mTYR, reducing TYR substrate binding activity and effectively inhibiting melanin synthesis. TFMH indirectly reduced cAMP response element-binding protein phosphorylation in vitro by downregulating melanocortin 1 receptor expression, thereby inhibiting expression of the microphthalmia-associated transcription factor, further decreasing TYR, tyrosinase related protein 1, and dopachrome tautomerase expression and ultimately impeding melanin synthesis. In zebrafish, TFMH significantly reduced black spot formation. TFMH (200 µg/mL) decreased zebrafish TYR activity by 43% and melanin content by 52%. Molecular dynamics simulations over 100 ns revealed that the FGFRSP (T-6) peptide stably binds mushroom TYR via hydrogen bonds and ionic interactions. T-6 (400 µmol/L) reduced melanin content in B16F10 melanoma cells by 71% and TYR activity by 79%. In zebrafish, T-6 (200 µmol/L) inhibited melanin production by 64%. TFMH and T-6 exhibit good potential for the development of natural skin-whitening cosmetic products.

Emergent inequality and business cycles in a simple behavioral macroeconomic model.

Standard macroeconomic models assume that households are rational in the sense that they are perfect utility maximizers and explain economic dynamics in terms of shocks that drive the economy away from the steady state. Here we build on a standard macroeconomic model in which a single rational representative household makes a savings decision of how much to consume or invest. In our model, households are myopic boundedly rational heterogeneous agents embedded in a social network. From time to time each household updates its savings rate by copying the savings rate of its neighbor with the highest consumption. If the updating time is short, the economy is stuck in a poverty trap, but for longer updating times economic output approaches its optimal value, and we observe a critical transition to an economy with irregular endogenous oscillations in economic output, resembling a business cycle. In this regime households divide into two groups: poor households with low savings rates and rich households with high savings rates. Thus, inequality and economic dynamics both occur spontaneously as a consequence of imperfect household decision-making. Adding a few "rational" agents with a fixed savings rate equal to the long-term optimum allows us to match business cycle timescales. Our work here supports an alternative program of research that substitutes utility maximization for behaviorally grounded decision-making.

6'-O-Caffeoylarbutin from Quezui Tea: A Highly Effective and Safe Tyrosinase Inhibitor.

Tyrosinase is vital in fruit and vegetable browning and melanin synthesis, crucial for food preservation and pharmaceuticals. We investigated 6'-O-caffeoylarbutin's inhibition, safety, and preservation on tyrosinase. Using HPLC, we analyzed its effect on mushroom tyrosinase and confirmed reversible competitive inhibition. UV_vis and fluorescence spectroscopy revealed a stable complex formation with specific binding, causing enzyme conformational changes. Molecular docking and simulations highlighted strong binding, enabled by hydrogen bonds and hydrophobic interactions. Cellular tests showed growth reduction of A375 cells with mild HaCaT cell toxicity, indicating favorable safety. Animal experiments demonstrated slight toxicity within safe doses. Preservation trials on apple juice showcased 6'-O-caffeoylarbutin's potential in reducing browning. In essence, this study reveals intricate mechanisms and applications of 6'-O-caffeoylarbutin as an effective tyrosinase inhibitor, emphasizing its importance in food preservation and pharmaceuticals. Our research enhances understanding in this field, laying a solid foundation for future exploration.

Three-Dimensional Bowing Measurement of Distal Femur at Actual Size and Clinical Implications of Total Knee Arthroplasty.

Background and Objectives: To assess femoral shaft bowing (FSB) in coronal and sagittal planes and introduce the clinical implications of total knee arthroplasty (TKA) by analyzing a three-dimensional (3D) model with virtual implantation of the femoral component. Materials and Methods: Sixty-eight patients (average age: 69.1 years) underwent 3D model reconstruction of medullary canals using computed tomography (CT) data imported into Mimics® software (version 21.0). A mechanical axis (MA) line was drawn from the midportion of the femoral head to the center of the intercondylar notch. Proximal/distal straight centerlines (length, 60 mm; diameter, 1 mm) were placed in the medullary canal's center. Acute angles between these centerlines were measured to assess lateral and anterior bowing. The acute angle between the distal centerline and MA line was measured for distal coronal and sagittal alignment in both anteroposterior (AP) and lateral views. The diameter of curve (DOC) along the posterior border of the medulla was measured. Results: The mean lateral bowing in the AP view was 3.71°, and the mean anterior bowing in the lateral view was 11.82°. The average DOC of the medullary canal was 1501.68 mm. The average distal coronal alignment of all femurs was 6.40°, while the distal sagittal alignment was 2.66°. Overall, 22 femurs had coronal bowing, 42 had sagittal bowing, and 15 had both. Conclusions: In Asian populations, FSB can occur in coronal, sagittal, or both planes. Increased anterolateral FSB may lead to cortical abutment in the sagittal plane, despite limited space in the coronal plane. During TKA, distal coronal alignment guides the distal femoral valgus cut angle, whereas distal sagittal alignment aids in predicting femoral component positioning to avoid anterior notching. However, osteotomies along the anterior cortical bone intended to prevent notching may result in outliers due to differences between the distal sagittal alignment and the distal anterior cortical axis.

Multiple breast cancer liver metastases response to macrophage-delivered nanotherapy evaluated via a 3D continuum model.

Breast cancer liver metastases (BCLM) are usually unresectable and difficult to treat with systemic chemotherapy. A major reason for chemotherapy failure is that BCLM are typically small, avascular nodules, with poor transport and fast washout of therapeutics from surrounding capillaries. We have previously shown that nanoalbumin-bound paclitaxel (nab-PTX) encapsulated in porous silicon multistage nanovectors (MSV) is preferentially taken up by tumour-associated macrophages (TAM) in the BCLM microenvironment. The TAM alter therapeutic transport characteristics and retain it in the tumour vicinity, increasing cytotoxicity. Computational modeling has shown that therapeutic regimens could be designed to eliminate single lesions. To evaluate clinically-relevant scenarios, this study develops a modeling framework to evaluate MSV-nab-PTX therapy targeting multiple BCLM. An experimental model of BCLM, splenic injection of breast cancer 4 T1 cells was established in BALB/C mice. Livers were analyzed histologically to determine size and density of BCLM. The data were used to calibrate a 3D continuum mixture model solved via distributed computing to enable simulation of multiple BCLM. Overall tumour burden was analyzed as a function of metastases number and potential therapeutic regimens. The computational model enables realistic 3D representation of metastatic tumour burden in the liver, with the capability to evaluate BCLM growth and therapy response for hundreds of lesions. With the given parameter set, the model projects that repeated MSV-nab-PTX treatment in intervals <7 days would control the tumour burden. We conclude that nanotherapy targeting TAM associated with BCLM may be evaluated and fine-tuned via 3D computational modeling that realistically simulates multiple metastases.

Interactions between polycyclic musks and human lactoferrin: Multi-spectroscopic methods and docking simulation.

Galaxolide (1,3,4,6,7,8-hexahydro-4,6,6,7,8-hexamethylcyclopenta-γ-2-benzopyrane; HHCB) and Tonalide (7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene; AHTN) are "pseudo-persistent" pollutants that can cause DNA damage, endocrine disruption, organ toxicity, and reproductive toxicity in humans. HHCB and AHTN are readily enriched in breast milk, so exposure of infants to HHCB and AHTN is of concern. Here, the molecular mechanisms through which HHCB and AHTN interact with human lactoferrin (HLF) are investigated using computational simulations and spectroscopic methods to identify indirectly how HHCB and AHTN may harm infants. Molecular docking and kinetic simulation studies indicated that HHCB and AHTN can interact with and alter the secondary HLF structure. The fluorescence quenching of HLF by HHCB, AHTN was static with the forming of HLF-HHCB, HLF-AHTN complex, and accompanied by non-radiative energy transfer and that 1:1 complexes form through interaction forces. Time-resolved fluorescence spectroscopy indicated that binding to small molecules does not markedly change the HLF fluorescence lifetime. Three-dimensional fluorescence spectroscopy indicated that HHCB and AHTN alter the peptide chain backbone structure of HLF. Ultraviolet-visible absorption spectroscopy, simultaneous fluorescence spectroscopy, Fourier-transform infrared spectroscopy, and circular dichroism spectroscopy indicated that HHCB and AHTN change the secondary HLF conformation. Antimicrobial activity experiments indicated that polycyclic musks decrease lactoferrin activity and interact with HLF. These results improve our understanding of the mechanisms involved in the toxicities of polycyclic musks bound to HLF at the molecular level and provide theoretical support for mother-and-child health risk assessments.

Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae.

This work provides a systematic and comprehensive overview of available resources for the molecular-scale modelling of the translation process through agent-based modelling. The case study is the translation in Saccharomyces cerevisiae, one of the most studied yeasts. The data curation workflow encompassed structural information about the yeast (i.e. the simulation environment), and the proteins, ribonucleic acids and other types of molecules involved in the process (i.e. the agents). Moreover, it covers the main process events, such as diffusion (i.e. motion of molecules in the environment) and collision efficiency (i.e. interaction between molecules). Data previously determined by wet-lab techniques were preferred, resorting to computational predictions/extrapolations only when strictly necessary. The computational modelling of the translation processes is of added industrial interest, since it may bring forward knowledge on how to control such phenomena and enhance the production of proteins of interest in a faster and more efficient manner.

Anatomical Characteristics Contributing to Patellar Dislocations Following MPFL Reconstruction: A Dynamic Simulation Study.

Pathologic anatomy is a primary factor contributing to redislocation of the patella following reconstruction of the medial patellofemoral ligament (MPFL). A pivot landing was simulated following MPFL reconstruction, with the hypothesis that position of the tibial tuberosity, depth of the trochlear groove, and height of the patella are correlated with lateral patellar maltracking. Thirteen dynamic simulation models represented subjects being treated for recurrent patellar instability. Simplified Hertzian contact governed patellofemoral and tibiofemoral joint reaction forces. Pivot landing was represented with and without an MPFL graft in place. Measurements related to patellar height (Caton-Deschamps index), trochlear groove depth (lateral trochlear inclination), and position of the tibial tuberosity (lateral tibial tuberosity to posterior cruciate attachment distance, or lateral TT-PCL distance) were measured from the models and correlated with patellar lateral shift with the knee extended (5 deg of flexion) and flexed (40 deg). The patella dislocated for all models without an MPFL graft and for two models with a graft represented. With an MPFL graft represented, patellar lateral shift was correlated with Caton-Deschamps index (r2 > 0.35, p < 0.03) and lateral trochlear inclination (r2 ≥ 0.45, p < 0.02) at both 5 deg and 40 deg of flexion. For a simulated pivot landing with an MPFL graft in place, lateral patellar tracking was associated with a high patella (alta) and shallow trochlear groove. The study emphasizes the importance of simulating activities that place the patella at risk of dislocation when evaluating patellar stability.

Patient-reported impairment following TKA is reduced when a computationally simulated predicted ideal alignment is achieved.

PURPOSE: Joint dynamics following Total Knee Arthroplasty (TKA) may influence patient-reported outcome. Simulations allow many knee alignment approaches to a single patient to be considered prior to surgery. The simulated kinematics can be matched to patient-reported outcome to predict kinematic patterns most likely to give the best outcome. This study aims to validate one such previously developed algorithm based on a simulated deep knee bend (the Dynamic Knee Score, DKS). METHODS: 1074 TKA patients with pre- and post-operative Computerised Tomography (CT) scans and 12-month post-operative Knee Injury and Osteoarthritis Outcomes (KOOS) Scores were identified from the 360 Med Care Joint Registry. Landmarking and registration of implant position was performed on all CT scans, and each of the achieved TKAs was computationally simulated and received a predictive outcome score from the DKS. In addition, a set of potential alternative surgical plans which might have been followed were simulated. Comparison of patient-reported issues and DKS score was evaluated in a counter-factual study design. RESULTS: Patient-reported impairment with the knee catching and squatting was shown to be 30% lower (p = 0.005) and 22% lower (p = 0.026) in patients where the best possible DKS result was the one surgically achieved. Similar findings were found relating attainment of the best tibial slope and posterior femoral resection DKS plans to patient-reported difficulty straightening the knee (40% less likely, p < 0.001) and descending stairs (35% less likely, p = 0.006). CONCLUSION: The DKS has been shown to correlate with presence of patient-reported impairments post-TKA and the resultant algorithm can be applied in a pre-operative planning setting. Outcome optimization in the future may come from patient-specific selection of an alignment strategy and simulations may be a technological enabler of this trend. LEVEL OF EVIDENCE: III (Retrospective Cohort Study).

Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks under Drought Stress Reveal Major Transcriptional Regulators in Arabidopsis.

Drought is one of the most serious abiotic stressors in the environment, restricting agricultural production by reducing plant growth, development, and productivity. To investigate such a complex and multifaceted stressor and its effects on plants, a systems biology-based approach is necessitated, entailing the generation of co-expression networks, identification of high-priority transcription factors (TFs), dynamic mathematical modeling, and computational simulations. Here, we studied a high-resolution drought transcriptome of Arabidopsis. We identified distinct temporal transcriptional signatures and demonstrated the involvement of specific biological pathways. Generation of a large-scale co-expression network followed by network centrality analyses identified 117 TFs that possess critical properties of hubs, bottlenecks, and high clustering coefficient nodes. Dynamic transcriptional regulatory modeling of integrated TF targets and transcriptome datasets uncovered major transcriptional events during the course of drought stress. Mathematical transcriptional simulations allowed us to ascertain the activation status of major TFs, as well as the transcriptional intensity and amplitude of their target genes. Finally, we validated our predictions by providing experimental evidence of gene expression under drought stress for a set of four TFs and their major target genes using qRT-PCR. Taken together, we provided a systems-level perspective on the dynamic transcriptional regulation during drought stress in Arabidopsis and uncovered numerous novel TFs that could potentially be used in future genetic crop engineering programs.

Biogas production from malt bagasse from craft beer industry: kinetic modeling and process simulation.

In this work, biogas was synthesized from malt enriched-craft beer bagasse with the objective to generate clean energy. Thus, a kinetic model based on thermodynamic parameters was proposed to represent the process with coefficient determination (R2) of 0.82. A bench-top biodigester of 2.0 × 10-3 m3 was built in glass, and equipped with sensors to measure pressure, temperature, and methane concentration. The inoculum selected for the anaerobic digestion was the granular sludge, and malt bagasse was used as substrate. Data were fitted to a pseudo-first-order model for the formation of methane gas using the Arrehnius equation as basis. For the simulations of biogas production, the Aspen Plus™ software was used. Results from 23 factorial design experiments evidenced that equipment was efficient, and the craft beer bagasse showed great biogas production, with nearly 95% of methane yield. The temperature was the variable that showed most influence in the process. Moreover, the system has a potential for the generation of 10.1 kWh of clean energy. Kinetic constant rate for methane production was 5.42 × 10-7 s-1 and activation energy 8.25 kJ mol-1. A statistical analysis using a math software was performed and evidenced that the temperature played a major role in the biomethane conversion. Supplementary Information: The online version contains supplementary material available at 10.1007/s10163-023-01715-7.

Growth orientations, rather than heterogeneous growth rates, dominate jaw joint morphogenesis in the larval zebrafish.

In early limb embryogenesis, synovial joints acquire specific shapes which determine joint motion and function. The process by which the opposing cartilaginous joint surfaces are moulded into reciprocal and interlocking shapes, called joint morphogenesis, is one of the least understood aspects of joint formation and the cell-level dynamics underlying it are yet to be unravelled. In this research, we quantified key cellular dynamics involved in growth and morphogenesis of the zebrafish jaw joint and synthesised them in a predictive computational simulation of joint development. Cells in larval zebrafish jaw joints labelled with cartilage markers were tracked over a 48-h time window using confocal imaging. Changes in distance and angle between adjacent cell centroids resulting from cell rearrangement, volume expansion and extracellular matrix (ECM) deposition were measured and used to calculate the rate and direction of local tissue deformations. We observed spatially and temporally heterogeneous growth patterns with marked anisotropy over the developmental period assessed. There was notably elevated growth at the level of the retroarticular process of the Meckel's cartilage, a feature known to undergo pronounced shape changes during zebrafish development. Analysis of cell dynamics indicated a dominant role for cell volume expansion in growth, with minor influences from ECM volume increases and cell intercalation. Cell proliferation in the joint was minimal over the timeframe of interest. Synthesising the dynamic cell data into a finite element model of jaw joint development resulted in accurate shape predictions. Our biofidelic computational simulation demonstrated that zebrafish jaw joint growth can be reasonably approximated based on cell positional information over time, where cell positional information derives mainly from cell orientation and cell volume expansion. By modifying the input parameters of the simulation, we were able to assess the relative contributions of heterogeneous growth rates and of growth orientation. The use of uniform rather than heterogeneous growth rates only minorly impacted the shape predictions, whereas isotropic growth fields resulted in altered shape predictions. The simulation results suggest that growth anisotropy is the dominant influence on joint growth and morphogenesis. This study addresses the gap of the cellular processes underlying joint morphogenesis, with implications for understanding the aetiology of developmental joint disorders such as developmental dysplasia of the hip and arthrogryposis.

Insight on the microscopic binding mechanism of bisphenol compounds (BPs) with transthyretin (TTR) based on multi-spectroscopic methods and computational simulations.

Thyroid hormones are involved in numerous physiological processes as regulators of metabolism, regulating organ growth, and mental state. Bisphenol compounds (BPs) are recognized as chemicals that interfere with endocrine balance. Because BPs have a similar structure to thyroxine, they can compete for binding to thyroid protein and disrupt the normal physiological activity of the thyroid system. In this study, three typical bisphenol compounds were selected to explore the interaction between BPs and TTR by computer simulations and multi-spectroscopic methods. The results revealed that BPs quenched the endogenous fluorescence of TTR via the combination of static quenching and non-radiative energy transfer, and the van der Waals forces and hydrogen bonding played a synergistic role in the binding process of BPs and TTR. Furthermore, the three-dimensional fluorescence spectroscopy, UV-vis spectroscopy, and Fourier transform infrared (FT-IR) spectroscopy, which were employed to determine the conformation of protein, revealed that binding of BPs with TTR could induce conformational changes in TTR. In addition, the binding sites and the residues surrounding the BPs within the TTR were determined through molecular docking and molecular dynamics simulation. Therefore, this work provides new insights into the interaction between BPs and TTR to evaluate the potential toxicity of BPs.

Computational modelling of the crushing of carbon fibre-reinforced polymer composites.

The use of lightweight carbon fibre-reinforced polymer (CFRP) composites in transportation vehicles has necessitated the need to guarantee that these new materials and their structures are able to deliver a sufficient level of crashworthiness to ensure passenger safety. Unlike their metallic counterparts, which absorb energy primarily through plastic deformation, CFRPs absorb energy through a complex interaction of damage mechanisms involving matrix (polymer) cracking, fibre/matrix debonding, fibre pull-out/kinking/fracture, delamination and inter/intralaminar friction. CFRP is primarily deployed as a laminate and can potentially deliver a higher specific energy absorption than metals. Translating this capability to a structural scale requires careful design and is dependent on geometry, fibre architecture, laminate stacking sequence and damage initiation strategies for optimal uniform crushing. Consequently, the design of crashworthy CFRP structures currently entails extensive physical testing which is expensive and time consuming. This paper reports on progress and challenges in the development of a finite-element computational capability for simulating the crushing of composites for crashworthiness assessments, with the aim of reducing the burden of physical testing. It addresses the 'tyranny of scales' in modelling structures constructed of CFRP composites. Intrinsic to this capability is the acquisition of reliable material data for the damage model, in particular interlaminar and intralaminar fracture toughness values. While quasi-static values can be obtained with a reasonable level of confidence, results achieved through dynamic testing are still the subject of debate and the relationship between fracture toughness and strain rate has yet to be satisfactorily resolved. This article is part of the theme issue 'Nanocracks in nature and industry'.

A miniaturized analytical method based on molecularly imprinted absorbents for selective extraction of (S)-1,1'-binaphthyl-2,2'-diamine and combinatorial screening of polymer precursors by computational simulation.

Chiral resolution of binaphthylamine is often a toilful conundrum in the field of analytical chemistry and biomedicine. The work puts forward a selective, sensitive, and miniaturized analytical method based on molecularly imprinted polymers (MIPs) as adsorbent for miniaturized tip solid-phase extraction (MTSPE) in the separation of binaphthylamine enantiomer. This method combines the advantages of MIPs (high selectivity), MTSPE (low consumption), and high-performance liquid chromatography (HPLC, high sensitivity). A simple synthesis methodology of MIP (P2) was conducted through bulk polymerization with (S)-(-)-1,1'-binaphthyl-2,2'-diamine (S-DABN) as template together with methacrylic acid monomer, and ethylene glycol dimethacrylate as cross-linker in proper porogen, realizing a selective recognition and efficient enrichment for S-DABN. The method exhibited appreciable linearity (0.06-1.00 mg ml-1 ), low quantification limit (0.056 mg ml-1 ), good absolute recoveries (45.70%-69.29%), and high precision (relative standard deviations ≤ 3.54%), along with low consumption (0.50 ml sample solution and 25.0 mg adsorbent). Based on the density functional theory, computational simulation was used to make a preliminary prediction for rational design of MIPs and gave a reasonable elaboration involving the potential mechanism of templates interacting with functional monomers. The adsorption kinetics and thermodynamics were investigated to evaluate the recombination process of substrates. In addition, the selectivity of MIPs for S-DABN was obtained by MIP-MTSPE coupled with HPLC, which supports the feasibility of this convenient design process. The proposed method was employed for selective extraction of S-DABN and exhibited promising potential in the application of chiral analysis.