Functional-structural Model Research Articles

Optimisation design of water-fertiliser infiltration device based on TRIZ theory

Abstract This paper is based on functional flow and modular design to optimize the design of water-fertilizer integrated percolation irrigation device. Functional decomposition and the construction of functional structure model are completed, and the detection module and the delivery and irrigation module are identified as the modules to be optimized. Apply TRIZ theory to solve the power supply problem of the detection module in harsh environment and design the energy conversion structure. For the clogging problem of the irrigator, an anti-clogging design, labyrinth flow channel and unclogging pipe are proposed. For the labyrinth flow channel built-in elastic small pieces, can be compensated for the pressure of the irrigator outlet, labyrinth flow channel to form turbulence is not easy to form a blockage. When the pipe is clogged, through the inflatable unclogging pipe, to realize the clogging position of the air pressure impact, to complete the clogging unclogging.

Structural basis of S-adenosylmethionine-dependent allosteric transition from active to inactive states in methylenetetrahydrofolate reductase

Methylenetetrahydrofolate reductase (MTHFR) is a pivotal flavoprotein connecting the folate and methionine methyl cycles, catalyzing the conversion of methylenetetrahydrofolate to methyltetrahydrofolate. Human MTHFR (hMTHFR) undergoes elaborate allosteric regulation involving protein phosphorylation and S-adenosylmethionine (AdoMet)-dependent inhibition, though other factors such as subunit orientation and FAD status remain understudied due to the lack of a functional structural model. Here, we report crystal structures of Chaetomium thermophilum MTHFR (cMTHFR) in both active (R) and inhibited (T) states. We reveal FAD occlusion by Tyr361 in the T-state, which prevents substrate interaction. Remarkably, the inhibited form of cMTHFR accommodates two AdoMet molecules per subunit. In addition, we conducted a detailed investigation of the phosphorylation sites in hMTHFR, three of which were previously unidentified. Based on the structural framework provided by our cMTHFR model, we propose a possible mechanism to explain the allosteric structural transition of MTHFR, including the impact of phosphorylation on AdoMet-dependent inhibition.

Identification of User Requirements and their Influencing Factors Based on Online Reviews and Operational Data

It is crucial for enterprises to clearly identify user needs during the process of formulating product design improvement plans. Therefore, it is essential to comprehensively and accurately identify user needs, explore the reasons behind the emergence of these needs, and incorporate user opinions into the process of product design improvement. A method is proposed to comprehensively and accurately capture user requirements and address the challenge of identifying the underlying causes of user requirements. This method utilizes online comments and operational data to identify user requirements and their influencing factors. First, text sentiment analysis techniques are employed to quantify the importance and performance values of product feature topics. Second, we construct a quadrant model to identify product features requiring improvement, and the original negative comments related to these features are traced. However, the quadrant model alone is insufficient to reflect specific product issues that users are concerned about. Therefore, a functional structure model based on product issues is designed to filter and identify factors that influence user requirements using operational data. Finally, a Bayesian network inference approach is utilized to identify the key influencing factors on user requirements, enabling analysis of the causes behind user requirements and the proposal of product design improvement strategies. The feasibility and effectiveness of the proposed method are validated through experiments conducted on heavy-duty truck data. By analyzing the original negative comments related to the power characteristics, specific user demands regarding the insufficient power of the product were identified, such as “obviously insufficient power when climbing slopes” and other issues. Based on the vehicle power system functional structure model, combined with expert knowledge and operational data, factors related to the state of parts and user behavior that may affect “insufficient vehicle power” were identified. Based on the analysis results, suggestions were made to improve the engine intake air temperature control strategy and to enhance vehicle performance by promoting correct user behavior through informational campaigns.

Cortical parenchyma wall width regulates root metabolic cost and maize performance under suboptimal water availability.

We describe how increased root cortical parenchyma wall width (CPW) can improve tolerance to drought stress in maize by reducing the metabolic costs of soil exploration. Significant variation (1.0-5.0 µm) for CPW was observed in maize germplasm. The functional-structural model RootSlice predicts that increasing CPW from 2 µm to 4 µm is associated with a ~15% reduction in root cortical cytoplasmic volume, respiration rate, and nitrogen content. Analysis of genotypes with contrasting CPW grown with and without water stress in the field confirms that increased CPW is correlated with an ~32-42% decrease in root respiration. Under water stress in the field, increased CPW is correlated with 125% increased stomatal conductance, 325% increased leaf CO2 assimilation rate, 73-78% increased shoot biomass, and 92-108% increased yield. CPW was correlated with leaf mesophyll midrib parenchyma wall width, indicating pleiotropy. Genome-wide association study analysis identified candidate genes underlying CPW. OpenSimRoot modeling predicts that a reduction in root respiration due to increased CPW would also benefit maize growth under suboptimal nitrogen, which requires empirical testing. We propose CPW as a new phene that has utility under edaphic stress meriting further investigation.

Innovative design of multi-contradiction systems based on the function-structure model

Innovative design of complex systems faces multi-contradiction (MC). The existing methods to solve MC are mainly based on the General Theory of Powerful Thinking (OTSM) which is independent of the classical Engineering Design Method (ED) to form the process model, they cannot inherit the accumulated knowledge and advantages of ED. This paper proposes a product innovation design process model for MC based on the function-structure model. It starts with an initial scenario of the system to build the function-structure model and MC network based on the root contradiction analysis. The network structure entropy and function importance decision methods are introduced for the trimming target confirming. The key contradiction-node is identified and solved by strategies of trimming based on internal and external resources of the system. The function-structure model in ED and trimming in TRIZ are combined to form an innovative design process for MC systems. The proposed method is evaluated in a case study of an innovative design of the girder bridge erector.

Cortical cell size regulates root metabolic cost.

It has been hypothesized that vacuolar occupancy in mature root cortical parenchyma cells regulates root metabolic cost and thereby plant fitness under conditions of drought, suboptimal nutrient availability, and increased soil mechanical impedance. However, the mechanistic role of vacuoles in reducing root metabolic cost was unproven. Here we provide evidence to support this hypothesis. We first show that root cortical cell size is determined by both cortical cell diameter and cell length. Significant genotypic variation for both cortical cell diameter (~1.1- to 1.5-fold) and cortical cell length (~ 1.3- to 7-fold) was observed in maize and wheat. GWAS and QTL analyses indicate cortical cell diameter and length are heritable and under independent genetic control. We identify candidate genes for both phenes. Empirical results from isophenic lines contrasting for cortical cell diameter and length show that increased cell size, due to either diameter or length, is associated with reduced root respiration, nitrogen content, and phosphorus content. RootSlice, a functional-structural model of root anatomy, predicts that an increased vacuolar: cytoplasmic ratio per unit cortical volume causes reduced root respiration and nutrient content. Ultrastructural imaging of cortical parenchyma cells with varying cortical diameter and cortical cell length confirms the in silico predictions and shows that an increase in cell size is correlated with increased vacuolar volume and reduced cytoplasmic volume. Vacuolar occupancy and its relationship with cell size merits further investigation as a phene for improving crop adaptation to edaphic stress.

ISG15 blocks cardiac glycolysis and ensures sufficient mitochondrial energy production during Coxsackievirus B3 infection.

Virus infection triggers inflammation and, may impose nutrient shortage to the heart. Supported by type I interferon (IFN) signalling, cardiomyocytes counteract infection by various effector processes, with the IFN-stimulated gene of 15 kDa (ISG15) system being intensively regulated and protein modification with ISG15 protecting mice Coxsackievirus B3 (CVB3) infection. The underlying molecular aspects how the ISG15 system affects the functional properties of respective protein substrates in the heart are unknown. Based on the protective properties due to protein ISGylation, we set out a study investigating CVB3-infected mice in depth and found cardiac atrophy with lower cardiac output in ISG15-/- mice. By mass spectrometry, we identified the protein targets of the ISG15 conjugation machinery in heart tissue and explored how ISGylation affects their function. The cardiac ISGylome showed a strong enrichment of ISGylation substrates within glycolytic metabolic processes. Two control enzymes of the glycolytic pathway, hexokinase 2 (HK2) and phosphofructokinase muscle form (PFK1), were identified as bona fide ISGylation targets during infection. In an integrative approach complemented with enzymatic functional testing and structural modelling, we demonstrate that protein ISGylation obstructs the activity of HK2 and PFK1. Seahorse-based investigation of glycolysis in cardiomyocytes revealed that, by conjugating proteins, the ISG15 system prevents the infection-/IFN-induced up-regulation of glycolysis. We complemented our analysis with proteomics-based advanced computational modelling of cardiac energy metabolism. Our calculations revealed an ISG15-dependent preservation of the metabolic capacity in cardiac tissue during CVB3 infection. Functional profiling of mitochondrial respiration in cardiomyocytes and mouse heart tissue by Seahorse technology showed an enhanced oxidative activity in cells with a competent ISG15 system. Our study demonstrates that ISG15 controls critical nodes in cardiac metabolism. ISG15 reduces the glucose demand, supports higher ATP production capacity in the heart, despite nutrient shortage in infection, and counteracts cardiac atrophy and dysfunction.

Coordinated restoration of inverter‐based power sources and synchronous generators for the high renewable penetrated power system considering the dynamic frequency regulation capability

AbstractExtensive inverter‐based power sources (IPS) impose significant challenges on the restoration of high renewable penetrated power systems (HRPPS). To enhance HRPPS resilience, the proper utilization of IPSs must be implemented. Combining frequency dynamics of IPSs and synchronous generators, this paper proposes a coordinated restoration method for multi‐type power sources after a major blackout. First, interactions between synchronous generators and IPSs are systematically analyzed. Based on this, output characteristics and constraints of IPSs in the power sources restoration process are quantified. Second, the dynamic frequency regulation capability (DFRC) of restored systems is quantified based on a unified transfer function structure model. Then the maximum power disturbance that restored systems can bear is derived based on DFRC indices including the maximum frequency deviation and the rate of change of frequency. Third, considering interactions between power sources and the DFRC of restored systems, a coordinated restoration optimization model of multi‐type power sources is proposed. Finally, case studies based on a modified IEEE 39‐bus system are simulated to verify the applicability and superiority of the proposed method. Meanwhile, results show that the proposed method for quantifying DFRC is more suitable for HRPPSs than traditional inertia‐based methods.

MODEL FUNKCJONALNO-PRZESTRZENNY (W STRATEGII ROZWOJU) JAKO INSTRUMENT PLANOWANIA I STEROWANIA PRZEKSZTAŁCENIAMI STRUKTURY MIASTA I AGLOMERACJI

The article, based on the example of Krakow and the Krakow metropolis, discusses the method of managing space through the Development Strategy document, and in particular the recently launched Functional and Spatial Structure Model. After analyzing three documents of the Strategy, conclusions are drawn regarding the shortcomings resulting from these documents and good practices related to them. The guidelines may be helpful for other metropolises and for improving the current economic and spatial planning system in Poland. The article also draws attention to the authors of individual documents, which is particularly important in times of depreciation of the urban planning profession.

Novice engineer vs. machine: comparing artificial neural network predictions with student estimates of market price using function structure models

This paper investigates the use of Artificial Neural Networks (ANN) to model human behaviour in early-stage engineering design; specifically, by comparing the predictive capability of ANNs and engineering novices. The comparison is between ‘crowds' of ANNs and humans. Function structure models of fifteen products are used as input for prediction. Additionally, the type of information provided is varied between topology information and vocabulary information. Prediction accuracy is compared, with the results showing that ANN crowd performs comparably to the novice estimates. However, students are more precise with their predictions. Moreover, student confidence in predictions is analyzed, and results suggest that students have low to moderate confidence in their predictions. Confidence increased with the addition of vocabulary information. Finally, limitations and future work are discussed, with research questions presented for subsequent research. This work motivates future studies on crowds, both human and virtual and the cost-benefits associated with collective intelligence.

A role for fermentation in aerobic conditions as revealed by computational analysis of maize root metabolism during growth by cell elongation.

The root is a well-studied example of cell specialisation, yet little is known about the metabolism that supports the transport functions and growth of different root cell types. To address this, we used computational modelling to study metabolism in the elongation zone of a maize lateral root. A functional-structural model captured the cell-anatomical features of the root and modelled how they changed as the root elongated. From these data, we derived constraints for a flux balance analysis model that predicted metabolic fluxes of the 11 concentric rings of cells in the root. We discovered a distinct metabolic flux pattern in the cortical cell rings, endodermis and pericycle (but absent in the epidermis) that involved a high rate of glycolysis and production of the fermentation end-products lactate and ethanol. This aerobic fermentation was confirmed experimentally by metabolite analysis. The use of fermentation in the model was not obligatory but was the most efficient way to meet the specific demands for energy, reducing power and carbon skeletons of expanding cells. Cytosolic acidification was avoided in the fermentative mode due to the substantial consumption of protons by lipid synthesis. These results expand our understanding of fermentative metabolism beyond that of hypoxic niches and suggest that fermentation could play an important role in the metabolism of aerobic tissues.

Coupled maize model: A 4D maize growth model based on growing degree days

Crop canopy parameters are critical for environmental remote sensing, describing crop phenotypes, and ensuring food security. Evaluating the effect of temperature on crop growth is crucial for estimating crop canopy parameters. However, existing crop growth and plant functional-structural models cannot simultaneously model temperature responses, perform accurate dynamic simulations, and provide multi-scale computer visualizations. This limitation has hindered the application of structural models of maize plants for use in 3D radiative transfer models, crop structure evaluations, and crop phenotype descriptions. We improve the leaf/organ-level thermal-driven crop growth model (MAIZSIM) and the plant functional-structural algorithm. To address these limitations, we propose the coupled maize model, a four-dimensional (4D) growth model based on growing degree days. This model can simulate and visualize the structural parameters of the maize canopy at the organ, plant, seasonal, and population levels. The model outputs three-dimensional (3D) predictions of the maize structure (file format.obj), enabling editing and 3D visualizations. We use maize datasets from multiple phenological periods to test the proposed model’s accuracy and stability in simulating the canopy parameters at multiple levels. The results show that the normalized root mean square errors (NRMSEs) between the simulated and measured maize leaf size, area, leaf node height, and vein curve derived from the coupled maize model are below 0.1, demonstrating the model's high accuracy.

GrapevineXL reliably predicts multi-annual dynamics of vine water status, berry growth, and sugar accumulation in vineyards.

Climate and water availability greatly affect each season's grape yield and quality. Using models to accurately predict environment impacts on fruit productivity and quality is a huge challenge. We calibrated and validated the functional-structural model, GrapevineXL, with a data set including grapevine seasonal midday stem water potential (Ψxylem), berry dry weight (DW), fresh weight (FW), and sugar concentration per volume ([Sugar]) for a wine grape cultivar (Vitis vinifera cv. Cabernet Franc) in field conditions over 13years in Bordeaux, France. Our results showed that the model could make a fair prediction of seasonal Ψxylem and good-to-excellent predictions of berry DW, FW, [Sugar] and leaf gas exchange responses to predawn and midday leaf water potentials under diverse environmental conditions with 14 key parameters. By running virtual experiments to mimic climate change, an advanced veraison (i.e. the onset of ripening) of 14 and 28days led to significant decreases of berry FW by 2.70% and 3.22%, clear increases of berry [Sugar] by 2.90% and 4.29%, and shortened ripening duration in 8 out of 13 simulated years, respectively. Moreover, the impact of the advanced veraison varied with seasonal patterns of climate and soil water availability. Overall, the results showed that the GrapevineXL model can predict plant water use and berry growth in field conditions and could serve as a valuable tool for designing sustainable vineyard management strategies to cope with climate change.

Identification of prolactin receptor variants with diverse effects on receptor signalling.

The prolactin receptor (PRLR) signals predominantly through the JAK2-STAT5 pathway regulating multiple physiological functions relating to fertility, lactation, and metabolism. However, the molecular pathology and role of PRLR mutations and signalling are incompletely defined, with progress hampered by a lack of reported disease-associated PRLR variants. To date, two common germline PRLR variants are reported to demonstrate constitutive activity, with one, Ile146Leu, overrepresented in benign breast disease, while a rare activating variant, Asn492Ile, is reported to be associated with an increased incidence of prolactinoma. In contrast, an inactivating germline heterozygous PRLR variant (His188Arg) was reported in a kindred with hyperprolactinaemia, while an inactivating compound heterozygous PRLR variant (Pro269Leu/Arg171Stop) was identified in an individual with hyperprolactinaemia and agalactia. We hypothesised that additional rare germline PRLR variants, identified from large-scale sequencing projects (ExAC and GnomAD), may be associated with altered in vitro PRLR signalling activity. We therefore evaluated >300 previously uncharacterised non-synonymous, germline PRLR variants and selected 10 variants for in vitro analysis based on protein prediction algorithms, proximity to known functional domains and structural modelling. Five variants, including extracellular and intracellular domain variants, were associated with altered responses when compared to the wild-type receptor. These altered responses included loss- and gain-of-function activities related to STAT5 signalling, Akt and FOXO1 activity, as well as cell viability and apoptosis. These studies provide further insight into PRLR structure-function and indicate that rare germline PRLR variants may have diverse modulating effects on PRLR signalling, although the pathophysiologic relevance of such alterations remains to be defined.

Многоаспектное моделирование ситуаций в задачах обеспечения функциональной безопасности аппаратно-программных комплексов

Functional safety is a latent characteristic of hardware and software complexes (HSC) and is objectively characterized by consumer satisfaction with the HSC behavior. The paper considers an approach to solving project management problems based on the dynamic characteristics analysis of functional safety of conflict situations in the project management system. To analyze situations that arise when managing HSC projects, it is possible to use models known as system archetypes. The information essence of situations and the foundations of multi-aspect modeling are considered. The methodological basis of the research is a combination of dynamic models of parameters that characterize functional safety and structural models, corresponding to conflict situations that arise when ensuring the required level of functional safety. Examples of multi-aspect modeling of situations where manifestations of latent defects act as events are considered. As a result of the research, the information essences of situations are determined, the conceptual foundations of multi-aspect modeling of situations that arise when managing the HSC functional safety are proposed, and the basic stages of building a system of structural and dynamic models of situations at different stages of the HSC life cycle are identified. The results obtained can be used to make decisions about the advisability of making changes to the system structure for ensuring the functional safety of hardware and software complexes.

RootSlice-A novel functional-structural model for root anatomical phenotypes.

Root anatomy is an important determinant of root metabolic costs, soil exploration, and soil resource capture. Root anatomy varies substantially within and among plant species. RootSlice is a multicellular functional-structural model of root anatomy developed to facilitate the analysis and understanding of root anatomical phenotypes. RootSlice can capture phenotypically accurate root anatomy in three dimensions of different root classes and developmental zones, of both monocotyledonous and dicotyledonous species. Several case studies are presented illustrating the capabilities of the model. For maize nodal roots, the model illustrated the role of vacuole expansion in cell elongation; and confirmed the individual and synergistic role of increasing root cortical aerenchyma and reducing the number of cortical cell files in reducing root metabolic costs. Integration of RootSlice for different root zones as the temporal properties of the nodal roots in the whole-plant and soil model OpenSimRoot/maize enabled the multiscale evaluation of root anatomical phenotypes, highlighting the role of aerenchyma formation in enhancing the utility of cortical cell files for improving plant performance over varying soil nitrogen supply. Such integrative in silico approaches present avenues for exploring the fitness landscape of root anatomical phenotypes.

Analysis of the New Organizational Structure of the Kasepuhan Indigenous People through the Analytical Hierarchy Process (AHP) Method

An organizational structure that can realize the vision, mission, goals and strategies of any organization, including the Kasepuhan Banten Kidul indigenous people, is a critical factor in developing its existence. This structure facilitates communication and coordination, so that the tasks of empowering ancestral trusts in the form of preserving nature and agriculture (pamakayaan) can be accomplished properly. The qualitative descriptive method is used as an analytical knife which is then conducted by the hierarchical analysis process (AHP). The structure that has been owned and used for hundreds of years is in the form of a line (line organization).The most preferred organizational structure from the perspective of the Kasepuhan Banten Kidul indigenous people is the Divisional Organizational Structure with the highest score (0.68) compared to other alternative types of organizational structures, namely simple (line) and functional structural models. The Consistency Ratio (CI/IR) value is 0.02 which means below 10%.

A root functional-structural model allows assessment of the effects of water deficit on water and solute transport parameters.

Root water uptake is driven by a combination of hydrostatic and osmotic forces. Water transport was characterized in primary roots of maize seedlings grown hydroponically under standard and water deficit (WD) conditions, as induced by addition of 150 g l-1 polyethylene glycol 8000 (water potential= -0.336 MPa). Flow measurements were performed using the pressure chamber technique in intact roots or on progressively cut root system architectures. To account for the concomitant transport of water and solutes in roots under WD, we developed within realistic root system architectures a hydraulic tree model integrating both solute pumping and leak. This model explains the high spontaneous sap exudation of roots grown in standard conditions, the non-linearity of pressure-flow relationships, and negative fluxes observed under WD conditions at low external hydrostatic pressure. The model also reveals the heterogeneity of driving forces and elementary radial flows throughout the root system architecture, and how this heterogeneity depends on both plant treatment and water transport mode. The full set of flow measurement data obtained from individual roots grown under standard or WD conditions was used in an inverse modeling approach to determine their respective radial and axial hydraulic conductivities. This approach allows resolution of the dramatic effects of WD on these two components.

Functional Characterization and Structural Modeling of a Novel Glycine Oxidase from Variovorax paradoxus Iso1.

The N-acyl-d-amino acid amidohydrolase (N-d-AAase) of Variovorax paradoxus Iso1 can enantioselectively catalyze the zinc-assisted deacetylation of N-acyl-d-amino acids to yield consistent d-amino acids. A putative FAD-binding glycine/d-amino acid oxidase was located immediately upstream of the N-d-AAase gene. The gene encoding this protein was cloned into Escherichia coli BL21 (DE3)pLysS and overexpressed at 25°C for 6 h with 0.5 mM isopropyl β-d-1-thiogalactopyranoside induction. After purification, the tag-free recombinant protein was obtained. The enzyme could metabolize glycine, sarcosine, and d-alanine, but not l-amino acids or bulky d-amino acids. Protein modeling further supported these results, demonstrating that glycine, sarcosine, and d-alanine could fit into the pocket of the enzyme's activation site, while l-alanine and d-threonine were out of position. Therefore, this protein was proposed as a glycine oxidase, and we designated it VpGO. Interestingly, VpGO showed low sequence similarity to other well-characterized glycine oxidases. We found that VpGO and N-d-AAase were expressed on the same mRNA and could be transcriptionally induced by various N-acetyl-d-amino acids. Western blotting and zymography showed that both proteins had similar expression patterns in response to different types of inducers. Thus, we have identified a novel glycine oxidase that is co-regulated with N-d-AAase in an operon, and metabolizes N-acyl-d-amino acids in the metabolically versatile V. paradoxus Iso1. IMPORTANCE The Gram-negative bacterium Variovorax paradoxus has numerous metabolic capabilities, including the association with important catabolic processes and the promotion of plant growth. We had previously identified and characterized an N-acyl-d-amino-acid amidohydrolase (N-d-AAase) gene from the strain of V. paradoxus Iso1. The aim of this study was to isolate and characterize (both in vitro and in vivo) another potential gene found in the promoter region of this N-d-AAase gene. The protein was identified as a glycine oxidase, and the gene existed in an operon with N-d-AAase. The structural basis for its FAD-binding potential and substrate stereo-specificity were also elucidated. This study first reported a novel glycine oxidase from V. paradoxus. We believe that our study makes a significant contribution to the literature, because this enzyme has great potential for use as an industrial catalysis, as a biosensor, and in agricultural biotechnology.

SigFlow, a functional-structural model simulating floral induction based on inhibiting and activating signals transport in apple tree 3D structures

SigFlow, a functional-structural model simulating floral induction based on inhibiting and activating signals transport in apple tree 3D structures