Abstract
Motivation
Protein model quality assessment is a key component of protein structure prediction. In recent research, the voxelization feature was used to characterize the local structural ...information of residues, but it may be insufficient for describing residue-level topological information. Design features that can further reflect residue-level topology when combined with deep learning methods are therefore crucial to improve the performance of model quality assessment.
Results
We developed a deep-learning method, DeepUMQA, based on Ultrafast Shape Recognition (USR) for the residue-level single-model quality assessment. In the framework of the deep residual neural network, the residue-level USR feature was introduced to describe the topological relationship between the residue and overall structure by calculating the first moment of a set of residue distance sets and then combined with 1D, 2D and voxelization features to assess the quality of the model. Experimental results on the CASP13, CASP14 test datasets and CAMEO blind test show that USR could supplement the voxelization features to comprehensively characterize residue structure information and significantly improve model assessment accuracy. The performance of DeepUMQA ranks among the top during the state-of-the-art single-model quality assessment methods, including ProQ2, ProQ3, ProQ3D, Ornate, VoroMQA, ProteinGCN, ResNetQA, QDeep, GraphQA, ModFOLD6, ModFOLD7, ModFOLD8, QMEAN3, QMEANDisCo3 and DeepAccNet.
Availability and implementation
The DeepUMQA server is freely available at http://zhanglab-bioinf.com/DeepUMQA/.
Supplementary information
Supplementary data are available at Bioinformatics online.
•A probabilistic framework of creep life assessment for components at elevated temperature is provided.•Effect of standard derivation of material parameters on creep reliability assessment is ...discussed.•Comparisons between probabilistic and deterministic creep design methods are conducted.
Current creep life assessment methods of components at elevated temperatures are mainly based on deterministic analysis strategies, which could not achieve the goal of probabilistic evaluation on creep failure. Based on this, a probabilistic framework of creep life assessment for components at elevated temperatures was provided. A method of determining distribution characteristics of material parameters was provided by randomly selecting a group of results at each stress level. Monte Carlo simulation was combined with finite element analysis technology to capture the distribution characteristic of creep rupture life of one typical structural component. Effect of standard derivation of material parameters on creep reliability assessment was discussed. Comparisons between probabilistic and deterministic creep design methods were made. Results indicated that the probabilistic analysis strategy can calculate the specific value of failure probability at various loading conditions, not two values of failure probability (i.e. 100% and 0%) by deterministic analysis strategy. The effect of standard derivation on mean values of effective stress and creep rupture life of the component is dependent on distribution characteristics of material parameters and related variables. A small standard derivation reduces the data scatter of effective stress and creep rupture life of the component.
For effective application of electrospinning and electrospun fibrous meshes in wound dressing, we have in situ electrospun poly(vinyl pyrrolidone)/iodine (PVP/I), PVP/poly(vinyl pyrrolidone)-iodine ...(PVPI) complex, and poly(vinyl butyral) (PVB)/PVPI solutions into fibrous membranes by a handheld electrospinning apparatus. The morphologies of the electrospun fibers were examined by SEM, and the hydrophobicity, gas permeability, and antibacterial properties of the as-spun meshes were also investigated. The flexibility and feasibility of in situ electrospinning PVP/I, PVP/PVPI, and PVB/PVPI membranes, as well as the excellent gas permeabilities and antibacterial properties of the as-spun meshes, promised their potential applications in wound healing.
In the study, zebrafish were exposed to 0 and 200 μg/L Zn for 8 weeks, and then both groups were transferred to water including 0, 100, and 200 μg/L Cd for 4 days, respectively. Acute Cd exposure ...caused negative effects on stress defense, immune, and metal transport systems by increasing lipid peroxidation, iNOS activity and mRNA levels of il-6 and inos, and decreasing Cu/Zn-SOD and HSP70 levels, and mRNA levels of sod1, cat, hsp70, p65, mtf-1, znt5, zip7, atp7a, and atp7b. Lipid peroxidation was significantly reduced by Zn pre-exposure under Cd exposure, which may be explained by the enhanced stress defense capacity and the weaken inflammatory response. Firstly, Zn pre-exposure increased MTs and HSP70 levels and CAT activity in Cd-free water, which may facilitate fish quick response to Cd. Secondly, Zn pre-exposure reduced Cd accumulation at 100 and 200 μg/L Cd, down-regulated il-6 and il-1β at 100 μg/L Cd and p65 at 200 μg/L Cd, and increased Cu/Zn-SOD and CAT activities at 200 μg/L Cd. Thirdly, Zn pre-exposure alone up-regulated transcription factors (hsf1, hsf2, and mtf-1, and nrf2) and their target genes (sod1, cat, hsp70, and mt2) under Cd exposure in a dose-dependent manner. It should be noted that Zn pre-exposure down-regulated several metal transport genes dramatically at 0 and 100 μg/L Cd, which may be an important mechanism for reducing Cd import into livers. Overall, long-term and environmental Zn pre-exposure mitigated Cd toxicity by the enhanced stress defense capacity and the down-regulated metal transport and inflammatory responses.
•Acute Cd exposure affected negatively stress defense, immunity, and metal transporter of zebrafish.•Environmental Zn pre-exposure for 8 weeks reduced Cd-induced hepatic lipid peroxidaiton•Environmental Zn pre-exposure for 8 weeks slowed Cd-induced Cd accumulation.•Zn pre-exposure enhanced stress defense and reduced inflammatory and metal transport response.•Zn pre-exposure regulated activity, protein, and mRNA levels of related genes under Cd exposure.
Lead halide perovskite quantum dots (QDs) are known as prospective optoelectronic device materials because of their excellent luminescence, extraordinary photoelectric performance, and specific ...octahedron framework. Herein, we report a cost-effective approach for synthesizing highly stable CH3NH3PbBr3 QDs in low-polarity binary solvents without nitrogen protection. The CH3NH3PbBr3 QDs are tunable from 1.2 to 4.2 nm by adjusting the proportion of oleic acid and oleylamine as capping ligands. The photoluminescence quantum yield of CH3NH3PbBr3 QDs can reach 87.4%. The fluorescence can maintain over 80% of its earliest emission intensity under the atmosphere after 5 days, which is much better than that (∼10%) of QDs with ligand-assisted reprecipitation. The possible reaction mechanism of preparing CH3NH3PbBr3 QDs was also addressed. Notably, such a strategy can be applied extensively in the preparation of other lead halide perovskite QDs. Furthermore, the as-prepared thick PMMA-coated CH3NH3PbBr3 QDs were further conjoined with a red luminescence powder on a blue InGaN chip to obtain a powerful efficiency (45.4 lm W–1) warm white light-emitting diode.
Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, protists, remain poorly ...understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic protists and increased bacterivorous and omnivorous protists. The addition of individual biocontrol bacteria and fungi further altered the soil protist community composition, and eventually function. Network analysis integrating protist, bacterial and fungal community data, placed protists as a central hub in the soil microbiome, linking diverse bacterial and fungal populations. Given their dynamic response to soil management practices and key position in linking soil microbial networks, protists may provide the leverage between soil management and the enhancement of bacterial and fungal microbiota at the service of improved soil health.
New materials and manufacturing technologies require applicable non-destructive techniques for quality assurance so as to achieve better performance. This study comprehensively investigated the ...effect of influencing factors including excitation frequency, lift-off distance, defect depth and size, residual heat, and surface roughness on the defect EC signals of an Inconel 738LC alloy produced by selective laser melting (SLM). The experimental investigations recorded the impedance amplitude and phase angle of EC signals for each defect to explore the feasibility of detecting subsurface defects by merely analyzing these two key indicators. Overall, this study revealed preliminary qualitative and roughly quantitative relationships between influencing factors and corresponding EC signals, which provided a practical reference on how to quantitively inspect subsurface defects using eddy current testing (ECT) on SLMed parts, and also made solid progress toward on-line ECT in additive/subtractive hybrid manufacturing (ASHM) for fabricating SLMed parts with enhanced quality and better performance.
Temperature influences the physiological processes and ecology of both hosts and endophytes; however, it remains unclear how long noncoding RNAs (lncRNAs) modulate the consequences of ...temperature-dependent changes in host–pathogen interactions. To explore the role of lncRNAs in culm gall formation induced by the smut fungus Ustilago esculenta in Zizania latifolia, we employed RNA sequencing to identify lncRNAs and their potential cis-targets in Z. latifolia and U. esculenta under different temperatures. In Z. latifolia and U. esculenta, we identified 3194 and 173 lncRNAs as well as 126 and four potential target genes for differentially expressed lncRNAs, respectively. Further function and expression analysis revealed that lncRNA ZlMSTRG.11348 regulates amino acid metabolism in Z. latifolia and lncRNA UeMSTRG.02678 regulates amino acid transport in U. esculenta. The plant defence response was also found to be regulated by lncRNAs and suppressed in Z. latifolia infected with U. esculenta grown at 25 °C, which may result from the expression of effector genes in U. esculenta. Moreover, in Z. latifolia infected with U. esculenta, the expression of genes related to phytohormones was altered under different temperatures. Our results demonstrate that lncRNAs are important components of the regulatory networks in plant-microbe-environment interactions, and may play a part in regulating culm swelling in Z. latifolia plants.
In this study, female zebrafish (Danio rerio) were exposed to 26°C or 34°C, 0 or 197μg/L cadmium (Cd), singly or in combination for 7days. Multiple stress-related indicators were evaluated in the ...liver. Mortality, lipid peroxidation (LPO) and ultrastructural damage increased significantly by Cd exposure alone, and were not affected by heat alone. Interestingly, the combined exposure increased LPO, ultrastructural damage, and mortality compared with Cd exposure alone. The results indicated that elevated temperature increased Cd toxicity, which could be explained by several reasons. Firstly, Cd-exposed fish failed to activate the antioxidant defense system under heat stress. Secondly, expression levels of heat shock protein 70 (HSP70) were not significantly up-regulated by heat in Cd-exposed fish but increased by 117 times in Cd-free fish. Besides, hypermethylation of heat shock factor (HSF) binding motif in HSP70 promoter was observed during the combined exposure, indicating that simultaneous exposure may have partially suppressed the cytoprotective up-regulation of HSP70. Thirdly, heat induced an immunosuppressive effect in Cd-exposed fish, as reflected by the reduced mRNA and activity levels of nitric oxide synthase (iNOS) and interleukin-1β (IL-1β) expression levels. Finally, heat down-regulated Zir-, Irt-like protein 8 (ZIP8) and copper transporter 1 (CTR1) and up-regulated metallothioneins (MTs) in Cd-exposed fish, possibly suggesting Cu and Zn depletion and Cd accumulation. Hence, our data provide evidences that warmer temperatures can potentiate Cd toxicity, involved in the regulation of gene transcription, enzymatic activity, and DNA methylation. We found that heat indicators showed varied sensitivity between normal and Cd-exposed fish, emphasizing that the field metal pollution should be carefully considered when evaluating effects of climate change.
Display omitted
•Warming increased Cd toxicity in fish.•Mortality, lipid peroxidation and ultrastructure were examined.•Activity, transcription and methylation of stress-related genes were analyzed.•Sensitivity to warming varied between normal and Cd-exposed fish.
Metal matrix composites (MMCs) with specially designed structures can be fabricated by laser powder bed fusion (LPBF) time-efficiently and cost-effectively, but reinforcements pose enormous ...challenges to the technique. In this work, the effect of reinforcement on the formation of MMCs in LPBF is studied by taking diamond grinding wheels (GWs) as an example. Based on the balling phenomenon observed in the LPBF process, the formation characteristics of GWs such as surface morphology, porosity, and flexural strength are investigated. The balling size is increased with an increase in the linear energy density of the laser beam due to more intense diamond spattering. The acting forces applied by the plume and ambient gas flow generated around the melt pool on a diamond grain are analyzed to investigate the generation of diamond spatter. For MMCs with coarse reinforcements, spattering is the dominant cause of the balling phenomenon due to the induced discontinuous melt tracks and uneven powder layers. Furthermore, the performance of a cup-type diamond GW fabricated by LPBF in the electrical discharge grinding (EDG) process of reaction-bond silicon carbide (RB-SiC) is evaluated by the surface and subsurface quality. The grinding process removes the resolidified layer of RB-SiC induced during the electrical discharging process and suppresses crack generation in the subsurface. The results presented in this study reveal the influence of diamond grains on the formation mechanism of GWs, which is also suitable for MMCs with coarse reinforcements.
•Balling phenomenon affects the formation characteristics of MMCs.•Spattering is the dominant cause of the balling phenomenon.•Spattering is easily triggered in LPBF by the plume and induced ambient gas flow.•The as-built GW can improve the subsurface quality in EDG of RB-SiC.
PDF
