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Mutations in nuclear genes regulating mitochondrial DNA (mtDNA) replication are associated with mtDNA depletion syndromes. Using whole-genome sequencing, we identified a heterozygous mutation (c.272G>A:p.Arg91Gln) in single-stranded DNA-binding protein 1 (SSBP1), a crucial protein involved in mtDNA replisome. The proband manifested symptoms including sensorineural deafness, congenital cataract, optic atrophy, macular dystrophy, and myopathy. This mutation impeded multimer formation and DNA-binding affinity, leading to reduced efficiency of mtDNA replication, altered mitochondria dynamics, and compromised mitochondrial function. To correct this mutation, we tested two adenine base editor (ABE) variants on patient-derived fibroblasts. One variant, NG-Cas9-based ABE8e (NG-ABE8e), showed higher editing efficacy (≤30%) and enhanced mitochondrial replication and function, despite off-target editing frequencies; however, risks from bystander editing were limited due to silent mutations and off-target sites in non-translated regions. The other variant, NG-Cas9-based ABE8eWQ (NG-ABE8eWQ), had a safer therapeutic profile with very few off-target effects, but this came at the cost of lower editing efficacy (≤10% editing). Despite this, NG-ABE8eWQ-edited cells still restored replication and improved mtDNA copy number, which in turn recovery of compromised mitochondrial function. Taken together, base editing-based gene therapies may be a promising treatment for mitochondrial diseases, including those associated with SSBP1 mutations.

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With regards to the global continuous growth in consumption of base metals such as antimony (Sb), mining companies are currently looking to improve the productivity and extraction of Sb from low grade ore in order to economically process it. With this aim, in this study, an efficient protocol was developed to recover metallic Sb from the low grade Fe3Si2O5(OH)4. Sb3O6(OH). Sb2O3 ore of the Sefid-Abe mine in Zahedan province, Iran, utilizing selective acidic or alkaline leaching followed by Sb electrowinning. A process was developed to recover antimony from an Sb2O3 ore source, using selective acidic or alkaline leaching followed by antimony electrowinning. Sb could be leached with an efficiency of 85 % using 5 M NaOH and 87 % using 5 M hydrochloric acid/5 M sulfuric acid as the digestion solution at 80 °C for 8 h. The electrowinning process plays a significant role in recovery of highly pure Sb metal. Relying on this approach, a high deposition rate and current efficiency have been generated at a deposition potential 2 V at 30 °C (80 °C for alkaline medium). This was achieved by using anode electrode made of graphite and cathode electrode made of steel (two steel electrodes were used for alkaline electrowinning). Additionally, for acidic electrowinning, exploitation of Sb from the electrolyte solution was achieved by applying a current of 0.1 A, resulting in the highest yield equal to 89 %. On the other hand, for alkaline electrowinning, the highest efficiency corresponds to the current intensity of 0.5 A, which resulted in 97 % Sb extraction from the electrolyte solution. The XRD and ICP analysis performed for samples obtained from the electrolysis confirmed that the resulting antimony ingot has an exceptionally high purity.

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The objective of this study was to evaluate the effect of pretreatment and different technological conditions on the course of ABE fermentation of rye straw (RS) and the composition of volatile compounds in the distillates obtained. The highest concentration of ABE and butanol was obtained from the fermentation of pretreated rye straw by alkaline hydrolysis followed by detoxification and enzymatic hydrolysis. After 72 h of fermentation, the maximum butanol concentration, productivity, and yield from RS were 16.11 g/L, 0.224 g/L/h, and 0.402 g/g, respectively. Three different methods to produce butanol were tested: the two-step process (SHF), the simultaneous process (SSF), and simultaneous saccharification with ABE fermentation (consolidation SHF/SSF). The SHF/SSF process observed that ABE concentration (21.28 g/L) was higher than in the SSF (20.03 g/L) and lower compared with the SHF (22.21 g/L). The effect of the detoxification process and various ABE fermentation technologies on the composition of volatile compounds formed during fermentation and distillation were analyzed.

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The selective conversion of biomass fermentation derived from an acetone-butanol-ethanol (ABE) mixture into high-value biofuels is of paramount importance for industrial applications. However, challenges persist in effectively controlling the selectivity of long carbon chain ketones in elevated ABE conversion. In this research, a Ca-doped Ni-CaO-SiO2 catalyst was designed and employed to achieve a remarkable conversion of 89.9% into ketone products from the extracted ABE mixture. The selectivity for C8+ ketones reaches 41.8%, demonstrating exceptional performance. The reversible phase transition between Ca2SiO4 and CaCO3 enhances the recyclability, thereby improving the sustainability of the process. Additionally, the trace intermediate 3-hepten-2-one was successfully detected using two-dimensional GC×GC-MS, elucidating the conversion pathway in the catalytic upgrading of the ABE mixture. This finding offers a potential route for the efficient utilization of biomass and the highly selective production of value-added chemicals.

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Renewable and sustainable biofuel production, such as biobutanol, is becoming increasingly popular as a substitute for non-renewable and depleted petrol fuel. Many researchers have studied how to produce butanol cheaply by considering appropriate feedstock materials and bioprocess technologies. The production of biobutanol through acetone-butanol-ethanol (ABE) is highly sought after around the world because of its sustainable supply and lack of competition with food. The purpose of this study is to present the current biobutanol production research and to analyse the biobutanol research conducted during 2006 to 2023. The keyword used in this study is "Biobutanol," and the relevant data was extracted from the Web of Science database (WoS). According to the results, institutions and scholars from the People's Republic of China, the USA, and India have the highest number of cited papers across a broad spectrum of topics including acetone-butanol-ethanol (ABE) fermentation, biobutanol, various pretreatment techniques, and pervaporation. The success of biobutanol fermentation from biomass depends on the ability of the fermentation operation to match the microbial behaviour along with the appropriate bioprocessing strategies to improve the entire process to be suitable for industrial scale. Based on the review data, we will look at the biobutanol technologies and appropriate strategies that have been developed to improve biobutanol production from renewable biomass.

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BACKGROUND: Inhibitors that are released from lignocellulose biomass during its treatment represent one of the major bottlenecks hindering its massive utilization in the biotechnological production of chemicals. This study demonstrates that negative effect of inhibitors can be mitigated by proper feeding strategy. Both, crude undetoxified lignocellulose hydrolysate and complex medium supplemented with corresponding inhibitors were tested in acetone-butanol-ethanol (ABE) fermentation using Clostridium beijerinckii NRRL B-598 as the producer strain. RESULTS: First, it was found that the sensitivity of C. beijerinckii to inhibitors varied with different growth stages, being the most significant during the early acidogenic phase and less pronounced during late acidogenesis and early solventogenesis. Thus, a fed-batch regime with three feeding schemes was tested for toxic hydrolysate (no growth in batch mode was observed). The best results were obtained when the feeding of an otherwise toxic hydrolysate was initiated close to the metabolic switch, resulting in stable and high ABE production. Complete utilization of glucose, and up to 88% of xylose, were obtained. The most abundant inhibitors present in the alkaline wheat straw hydrolysate were ferulic and coumaric acids; both phenolic acids were efficiently detoxified by the intrinsic metabolic activity of clostridia during the early stages of cultivation as well as during the feeding period, thus preventing their accumulation. Finally, the best feeding strategy was verified using a TYA culture medium supplemented with both inhibitors, resulting in 500% increase in butanol titer over control batch cultivation in which inhibitors were added prior to inoculation. CONCLUSION: Properly timed sequential feeding effectively prevented acid-crash and enabled utilization of otherwise toxic substrate. This study unequivocally demonstrates that an appropriate biotechnological process control strategy can fully eliminate the negative effects of lignocellulose-derived inhibitors.

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Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.

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The attentional boost effect (ABE) and action-induced memory enhancement (AIME) suggest that memory performance for target-paired items is superior to that for distractor-paired items when participants performed a target detection task and a memory encoding task simultaneously. Though the memory enhancement has been well established, the temporal dynamics of how the target detection task influenced memory encoding remains unclear. To investigate this, we manipulated the stimulus onset asynchrony (SOA) between detection stimuli and the words to be memorized using a remember/know study-test paradigm, and we focused primarily on memory performance for the words that appeared after the detection response. The results showed that target-paired memory enhancement was robust from SOA = 0 s to SOA = 0.75 s, but was not significant when examined by itself in Experiment 1A or weakened in Experiment 2 and the conjoint analysis when SOA = 1 s, which were only observed in R responses. The post-response memory enhancement still existed when there was no temporal overlap between the word and target, similar to the magnitude of memory enhancement observed with temporal overlap. These results supported the view that target-paired memory enhancement (recollection rather than familiarity) occurred irrespective of whether the items appeared simultaneously with the targets or within a short period after the response, and the temporal overlap of the word and target was not necessary for post-response memory enhancement.

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Argininosuccinate lyase deficiency (ASLD) is a recessive metabolic disorder caused by variants in ASL. In an essential step in urea synthesis, ASL breaks down argininosuccinate (ASA), a pathognomonic ASLD biomarker. The severe disease forms lead to hyperammonemia, neurological injury, and even early death. The current treatments are unsatisfactory, involving a strict low-protein diet, arginine supplementation, nitrogen scavenging, and in some cases, liver transplantation. An unmet need exists for improved, efficient therapies. Here, we show the potential of a lipid nanoparticle-mediated CRISPR approach using adenine base editors (ABEs) for ASLD treatment. To model ASLD, we first generated human-induced pluripotent stem cells (hiPSCs) from biopsies of individuals homozygous for the Finnish founder variant (c.1153C>T [p.Arg385Cys]) and edited this variant using the ABE. We then differentiated the hiPSCs into hepatocyte-like cells that showed a 1,000-fold decrease in ASA levels compared to those of isogenic non-edited cells. Lastly, we tested three different FDA-approved lipid nanoparticle formulations to deliver the ABE-encoding RNA and the sgRNA targeting the ASL variant. This approach efficiently edited the ASL variant in fibroblasts with no apparent cell toxicity and minimal off-target effects. Further, the treatment resulted in a significant decrease in ASA, to levels of healthy donors, indicating restoration of the urea cycle. Our work describes a highly efficient approach to editing the disease-causing ASL variant and restoring the function of the urea cycle. This method relies on RNA delivered by lipid nanoparticles, which is compatible with clinical applications, improves its safety profile, and allows for scalable production.

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To expand the scope of genomic editing, a C-to-G transversion-based editor called CGBE has been developed for precise single-nucleotide genomic editing. However, limited editing efficiency and product purity have hindered the development and application of CGBE. In this study, we introduced the Puromycin-Resistance Screening System, referred to as CGBE/ABE-PRSS, to select genetically modified cells via the CGBE or ABE editors. The CGBE/ABE-PRSS system significantly improves the enrichment efficiency of CGBE- or ABE-modified cells, showing enhancements of up to 59.6 % compared with the controls. Our findings indicate that the CGBE/ABE-PRSS, when driven by the CMV promoter, results in a higher enrichment of edited cells compared to the CAG and EF1α promoters. Furthermore, we demonstrate that this system is compatible with different versions of both CGBE and ABE, enabling various cell species and simultaneous multiplexed genome editing without any detectable random off-targets. In conclusion, our developed CGBE/ABE-PRSS system facilitates the selection of edited cells and holds promise in both basic engineering and gene therapy applications.

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Familial hypercholesterolemia (FH) is one of the most prevalent monogenetic disorders leading to cardiovascular disease (CVD) worldwide. Mutations in Ldlr, encoding a membrane-spanning protein, account for the majority of FH cases. No effective and safe clinical treatments are available for FH. Adenine base editor (ABE)-mediated molecular therapy is a promising therapeutic strategy to treat genetic diseases caused by point mutations, with evidence of successful treatment in mouse disease models. However, due to the differences in the genomes between mice and humans, ABE with specific sgRNA, a key gene correction component, cannot be directly used to treat FH patients. Thus, we generated a knock-in mouse model harboring the partial patient-specific fragment and including the Ldlr W490X mutation. LdlrW490X/W490X mice recapitulated cholesterol metabolic disorder and clinical manifestations of atherosclerosis associated with FH patients, including high plasma low-density lipoprotein cholesterol levels and lipid deposition in aortic vessels. Additionally, we showed that the mutant Ldlr gene could be repaired using ABE with the cellular model. Taken together, these results pave the way for ABE-mediated molecular therapy for FH.

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Clostridia are known for their solvent production, especially the production of butanol. Concerning the projected depletion of fossil fuels, this is of great interest. The cultivation of clostridia is known to be challenging, and it is difficult to achieve reproducible results and robust processes. However, existing publications usually concentrate on the cultivation conditions of the main culture. In this paper, the influence of cryo-conservation and pre-culture on growth and solvent production in the resulting main cultivation are examined. A protocol was developed that leads to reproducible cultivations of Clostridium acetobutylicum. Detailed investigation of the cell conservation in cryo-cultures ensured reliable cell growth in the pre-culture. Moreover, a reason for the acid crash in the main culture was found, based on the cultivation conditions of the pre-culture. The critical parameter to avoid the acid crash and accomplish the shift to the solventogenesis of clostridia is the metabolic phase in which the cells of the pre-culture were at the time of inoculation of the main culture; this depends on the cultivation time of the pre-culture. Using cells from the exponential growth phase to inoculate the main culture leads to an acid crash. To achieve the solventogenic phase with butanol production, the inoculum should consist of older cells which are in the stationary growth phase. Considering these parameters, which affect the entire cultivation process, reproducible results and reliable solvent production are ensured. KEY POINTS: • Both cryo- and pre-culture strongly impact the cultivation of C. acetobutylicum • Cultivation conditions of the pre-culture are a reason for the acid crash • Inoculum from cells in stationary growth phase ensures shift to solventogenesis.

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Traditional cloud-centric approaches to medical data sharing pose risks related to real-time performance, security, and stability. Medical and healthcare data encounter challenges like data silos, privacy breaches, and transmission latency. In response to these challenges, this paper introduces a blockchain-based framework for trustworthy medical data sharing in edge computing environments. Leveraging healthcare consortium edge blockchains, this framework enables fine-grained access control to medical data. Specifically, it addresses the real-time, multi-attribute authorization challenge in CP-ABE through a Distributed Attribute Authorization strategy (DAA) based on blockchain. Furthermore, it tackles the key security issues in CP-ABE through a Distributed Key Generation protocol (DKG) based on blockchain. To address computational resource constraints in CP-ABE, we enhance a Distributed Modular Exponentiation Outsourcing algorithm (DME) and elevate its verifiable probability to "1". Theoretical analysis establishes the IND-CPA security of this framework in the Random Oracle Model. Experimental results demonstrate the effectiveness of our solution for resource-constrained end-user devices in edge computing environments.

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We present in this work a kinetic model of the acetone-butanol-ethanol (ABE) fermentation based on enzyme kinetics expressions. The model includes the effect of the co-substrate NADH as a modulating factor of cellular metabolism. The simulations obtained with the model showed an adequate fit to the experimental data reported by several authors, matching or improving the results observed with previous models. In addition, this model does not require artificial mathematical strategies such as on-off functions to achieve a satisfactory fit of the ABE fermentation dynamics. The parametric sensitivity allowed to identify the direct glucose → acetyl-CoA → butyryl-CoA pathway as being more significant for butanol production than the acid re-assimilation pathway. Likewise, model simulations showed that the increase in NADH, due to glucose concentration, favors butanol production and selectivity, finding a maximum selectivity of 3.6, at NADH concentrations above 55 mM and glucose concentration of 126 mM. The introduction of NADH in the model would allow its use for the analysis of electrofermentation processes with Clostridium, since the model establishes a basis for representing changes in the intracellular redox potential from extracellular variables.

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BACKGROUND: Nme2ABE8e has been constructed and characterized as a compact, accurate adenine base editor with a less restrictive dinucleotide protospacer-adjacent motif (PAM: N4CC) but low editing efficiency at challenging loci in human cells. Here, we engineered a subset of domain-inlaid Nme2Cas9 base editors to bring the deaminase domain closer to the nontarget strand to improve editing efficiency. RESULTS: Our results demonstrated that Nme2ABE8e-797 with adenine deaminase inserted between amino acids 797 and 798 has a significantly increased editing efficiency with a wide editing window ranging from 4 to 18 bases in mammalian cells, especially at the sites that were difficult to edit by Nme2ABE8e. In addition, by swapping the PAM-interacting domain of Nme2ABE8e-797 with that of SmuCas9 or introducing point mutations of eNme2-C in Nme2ABE8e-797, we created Nme2ABE8e-797Smu and Nme2ABE8e-797-C, respectively, which exhibited robust activities at a wide range of sites with N4CN PAMs in human cells. Moreover, the modified domain-inlaid Nme2ABE8e can efficiently restore or install disease-related loci in Neuro-2a cells and mice. CONCLUSIONS: These novel Nme2ABE8es with increased on-target DNA editing and expanded PAM compatibility will expand the base editing toolset for efficient gene modification and therapeutic applications.

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Multidrug resistance in bacterial strains known as superbugs is estimated to cause fatal infections worldwide. Migration and urbanization have resulted in overcrowding and inadequate sanitation, contributing to a high risk of superbug infections within and between different communities. The CRISPR-Cas system, mainly type II, has been projected as a robust tool to precisely edit drug-resistant bacterial genomes to combat antibiotic-resistant bacterial strains effectively. To entirely opt for its potential, advanced development in the CRISPR-Cas system is needed to reduce toxicity and promote efficacy in gene-editing applications. This might involve base-editing techniques used to produce point mutations. These methods employ designed Cas9 variations, such as the adenine base editor (ABE) and the cytidine base editor (CBE), to directly edit single base pairs without causing DSBs. The CBE and ABE could change a target base pair into a different one (for example, G-C to A-T or C-G to A-T). In this review, we addressed the limitations of the CRISPR/Cas system and explored strategies for circumventing these limitations by applying diverse base-editing techniques. Furthermore, we also discussed recent research showcasing the ability of base editors to eliminate drug-resistant microbes.

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Ciphertext policy-attribute-based encryption (CP-ABE), which provides fine-grained access control and ensures data confidentiality, is widely used in data sharing. However, traditional CP-ABE schemes often choose to outsource data to untrusted third-party cloud service providers for storage or to verify users' access rights through third parties, which increases the risk of privacy leakage and also suffers from the problem of opaque permission verification. This paper proposes an access control scheme based on blockchain and CP-ABE, which is based on multiple authorization centers and supports policy updating. In addition, blockchain technology's distributed, decentralized, and tamper-proof features are utilized to solve the trust crisis problem in the data-sharing process. Security analysis and performance evaluation show that the proposed scheme improves the computational efficiency by 18%, 26%, and 68% compared to previous references. The proposed scheme also satisfies the indistinguishability under chosen-plaintext attack (IND-CPA).

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Supplementation or limitation of some micronutrients during acetone-butanol-ethanol (ABE) fermentation has led to improvement in butanol yield and productivity. A mechanistic model of ABE fermentation offers insights in understanding these complex interactions and improving productivity through optimal culture conditions. This study proposes a mechanistic kinetic model of ABE fermentation by two Clostridium Acetobutylicum strains, L7 and ATCC 824 using glucose as sole carbon source without zinc and with various zinc doses. The model incorporates enzyme regulation by zinc on several glycolytic, acidogenesis and solventogenesis enzymes. The model was fitted and validated to experimental data collected from the published literature. The simulated results were in compliance with the experimental data, most importantly indicating higher glucose consumption and butanol productivity when supplemented with zinc compared to the control culture. The average squared correlation factor (R2) between the experimental and the simulated results, without and with zinc, were 0.99 and 0.96 for glucose, and 0.89 and 0.95 for butanol, respectively. A sensitivity analysis performed on the fitted and validated model indicated that the glucose consumption and growth parameters most influenced the model outputs. The developed model can be used as a template for modeling ABE fermentation under different combinations of micronutrients that may offer improved butanol yield and productivity.

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Canonical splice site variants affecting the 5' GT and 3' AG nucleotides of introns result in severe missplicing and account for about 10% of disease-causing genomic alterations. Treatment of such variants has proven challenging due to the unstable mRNA or protein isoforms that typically result from disruption of these sites. Here, we investigate CRISPR-Cas9-mediated adenine base editing for such variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We validate a CFTR expression minigene (EMG) system for testing base editing designs for two different targets. We then use the EMG system to test non-standard single-guide RNAs with either shortened or lengthened protospacers to correct the most common cystic fibrosis-causing variant in individuals of African descent (c.2988+1G>A). Varying the spacer region length allowed placement of the editing window in a more efficient context and enabled use of alternate protospacer adjacent motifs. Using these modifications, we restored clinically significant levels of CFTR function to human airway epithelial cells from two donors bearing the c.2988+1G>A variant.

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BACKGROUND: On the basis of visual-dependent reading method, radiological recognition and assessment of neonatal hyperbilirubinemia (NH) or acute bilirubin encephalopathy (ABE) on conventional magnetic resonance imaging (MRI) sequences are challenging. Prior studies had shown that radiomics was possible to characterize ABE-induced intensity and morphological changes on MRI sequences, and it has emerged as a desirable and promising future in quantitative and objective MRI data extraction. To investigate the utility of radiomics based on T1-weighted sequences for identifying neonatal ABE in patients with hyperbilirubinemia and differentiating between those with NH and the normal controls. METHODS: A total of 88 patients with NH were enrolled, including 50 patients with ABE and 38 ABE-negative individuals, and 70 age-matched normal neonates were included as controls. All participants were divided into training and validation cohorts in a 7:3 ratio. Radiomics features extracted from the basal ganglia of T1-weighted sequences on magnetic resonance imaging were evaluated and selected to set up the prediction model using the K-nearest neighbour-based bagging algorithm. A receiver operating characteristic curve was plotted to assess the differentiating performance of the radiomics-based model. RESULTS: Four of 744 radiomics features were selected for the diagnostic model of ABE. The radiomics model yielded an area under the curve (AUC) of 0.81 and 0.82 in the training and test cohorts, with accuracy, precision, sensitivity, and specificity of 0.82, 0.80, 0.91, and 0.69 and 0.78, 0.8, 0.8, and 0.75, respectively. Six radiomics features were selected in this model to distinguish those with NH from the normal controls. The AUC for the training cohort was 0.97, with an accuracy of 0.92, a precision of 0.92, a sensitivity of 0.93, and a specificity of 0.90. The performance of the radiomics model was confirmed by testing the test cohort, and the AUC, accuracy, precision, sensitivity, and specificity were 0.97, 0.92, 0.96, 0.89, and 0.95, respectively. CONCLUSIONS: The proposed radiomics model based on traditional TI-weighted sequences may be used effectively for identifying ABE and even differentiating patients with NH from the normal controls, which can provide microcosmic information beyond experience-dependent vision and potentially assist in clinical diagnosis and treatment.

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