Multimodality MRI Radiomics Based on Machine Learning for Identifying True Tumor Recurrence and Treatment-Related Effects in Patients with Postoperative Glioma.

INTRODUCTION: Conventional magnetic resonance imaging (MRI) features have difficulty distinguishing glioma true tumor recurrence (TuR) from treatment-related effects (TrE). We aimed to develop a machine-learning model based on multimodality MRI radiomics to help improve the efficiency of identifying glioma TuR. METHODS: A total of 131 patients were enrolled and randomly divided into the training set (n = 91) and the test set (n = 40). Radiomic features were extracted from the postoperative enhancement (PoE) region and edema (ED) region from four routine MRI sequences. After analyses of Spearman's rank correlation coefficient, and least absolute shrinkage and selection operator, the key radiomic features were selected to construct support vector machine (SVM) and k-nearest neighbor (KNN) models. Decision curve analysis (DCA) and receiver operating characteristic (ROC) curves were used to analyze the performance. RESULTS: The PoE model had a significantly higher area under curve (AUC) than the ED model (p < 0.05). Among the models constructed with a single sequence, the model using PoE regional features from CE-T1WI was superior to other models, with an AUC of 0.905 for SVM and 0.899 for KNN. In multimodality models, the PoE model outperformed the ED model with an AUC of 0.931 for SVM and 0.896 for KNN. The multimodality model, which combined routine sequences and the whole regional features, showed a slightly better performance with an AUC of 0.965 for SVM and 0.955 for KNN. Decision curve analysis showed the good clinical utility of multimodal radiomics models. CONCLUSIONS: Multimodality radiomics can identify glioma TuR and TrE, potentially aiding clinical decision-making for individualized treatment. And edematous regions may provide useful information for recognizing recurrence. RETROSPECTIVELY REGISTERED: 2021.04.15, No:2020039.

Comparison of Diffusion Kurtosis Imaging and Amide Proton Transfer Imaging in the Diagnosis and Risk Assessment of Prostate Cancer.

OBJECTIVES: This study aims to evaluate and compare the diagnostic value of DKI and APT in prostate cancer (PCa), and their correlation with Gleason Score (GS). MATERIALS AND METHODS: DKI and APT imaging of 49 patients with PCa and 51 patients with benign prostatic hyperplasia (BPH) were collected and analyzed, respectively. According to the GS, the patients with PCa were divided into high-risk, intermediate-risk and low-risk groups. The mean kurtosis (MK), mean diffusion (MD) and magnetization transfer ratio asymmetry (MTRasym, 3.5 ppm) values among PCa, BPH, and different GS groups of PCa were compared and analyzed respectively. The diagnostic accuracy of each parameter was evaluated by using the receiver operating characteristic (ROC) curve. The correlation between each parameter and GS was analyzed by using Spearman's rank correlation. RESULTS: The MK and MTRasym (3.5 ppm) values were significantly higher in PCa group than in BPH group, while the MD value was significantly lower than in BPH group. The differences of MK/MD/MTRasym (3.5 ppm) between any two of the low-risk, intermediate-risk, and high-risk groups were all statistically significant (p <0.05). The MK value showed the highest diagnostic accuracy in differentiating PCa and BPH, BPH and low-risk, low-risk and intermediate-risk, intermediate-risk and high-risk (AUC = 0.965, 0.882, 0.839, 0.836). The MK/MD/MTRasym (3.ppm) values showed good and moderate correlation with GS (r = 0.844, -0.811, 0.640, p <0.05), respectively. CONCLUSION: DKI and APT imaging are valuable in the diagnosis of PCa and demonstrate strong correlation with GS, which has great significance in the risk assessment of PCa.

Comparative analysis of the diagnostic values of T2 mapping and diffusion-weighted imaging for sacroiliitis in ankylosing spondylitis.

OBJECTIVE: To investigate the diagnostic values of T2 mapping and diffusion-weighted imaging (DWI) for active sacroiliitis in ankylosing spondylitis (AS) and to evaluate the correlations of T2 and ADC values with Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) and Spondyloarthritis Research Consortium of Canada (SPARCC) scores. METHODS: A total of 77 AS patients with sacroiliitis and 45 healthy controls were enrolled. All patients were scanned by standard magnetic resonance imaging longitudinal relaxation time (T1)-weighted imaging (T1WI), fat-saturated T2-weighted imaging (FS-T2WI)] and DWI, and T2 mapping of the sacroiliac joints. According to whether subchondral bone marrow edema was present in the FS-T2WI sequence, the 77 patients were divided into an active group (41 cases) and an inactive group (36 cases). The T2 and apparent diffusion coefficient (ADC) values of the subchondral bone marrow were measured in the active group, the inactive group, and the healthy control group. The average T2 and ADC values were compared among the three groups. Receiver operating characteristic (ROC) curves were used to analyze the diagnostic efficacy of T2 and ADC values for sacroiliitis. The correlations of T2 and ADC values with the BASDAI score and the SPARCC score were analyzed. RESULTS: The T2 and ADC values in the active group were higher than those in the inactive group, while that in the inactive group were significantly higher than those in the healthy control group (p < 0.0001). The T2 and ADC values of the AS patients were positively correlated with BASDAI scores, and the correlation coefficients (r) were 0.786 (p < 0.0001) and 0.842 (p < 0.0001), respectively. The areas under the ROC curves (AUCs) of T2 and ADC values between the active and inactive groups, the active group and the healthy control group, and the inactive group and the healthy control group were 0.889 (95% CI, 0.80-0.95) and 0.917 (95% CI, 0.83-0.97), 0.982 (95% CI, 0.93-1.00) and 0.984 (95% CI, 0.93-1.00), and 0.628 (95% CI, 0.51-0.73) and 0.871 (95% CI, 0.78-0.94), respectively. The T2 and ADC values of the AS patients in the active group were positively correlated with SPARCC scores, and the correlation coefficients (r) were 0.757 (p < 0.0001) and 0.764 (p < 0.0001), respectively. CONCLUSION: T2 and ADC values can be used to quantitatively assess the activity of AS, and the efficacy of the ADC value in the diagnosis of AS was higher than that of the T2 value.

Regrowth-delay body as a bacterial subcellular structure marking multidrug-tolerant persisters.

Bacteria have long been recognized to be capable of entering a phenotypically non-growing persister state, in which the cells exhibit an extended regrowth lag and a multidrug tolerance, thus posing a great challenge in treating infectious diseases. Owing to their non-inheritability, low abundance of existence, lack of metabolic activities, and high heterogeneity, properties of persisters remain poorly understood. Here, we report our accidental discovery of a subcellular structure that we term the regrowth-delay body, which is formed only in non-growing bacterial cells and sequesters multiple key proteins. This structure, that dissolves when the cell resumes growth, is able to be viewed as a marker of persisters. Our studies also indicate that persisters exhibit different depth of persistence, as determined by the status of their regrowth-delay bodies. Our findings imply that suppressing the formation and/or promoting the dissolution of regrowth-delay bodies could be viable strategies for eradicating persisters.

Functional and cooperative stabilization of a two-metal (Ca, Zn) center in α-amylase derived from Flavobacteriaceae species.

Mesophilic α-amylase from Flavobacteriaceae (FSA) is evolutionary closely related to thermophilic archaeal Pyrococcus furiosus α-amylase (PWA), but lacks the high thermostability, despite the conservation of most residues involved in the two-metal (Ca, Zn) binding center of PWA. In this study, a disulfide bond was introduced near the two-metal binding center of FSA (designated mutant EH-CC) and this modification resulted in a slight improvement in thermostability. As expected, E204G mutations in FSA and EH-CC led to the recovery of Ca2+-binding site. Interestingly, both Ca2+- and Zn2+-dependent thermostability were significantly enhanced; 153.1% or 50.8% activities was retained after a 30-min incubation period at 50 °C, in the presence of Ca2+ or Zn2+. The C214S mutation, which affects Zn2+-binding, also remarkably enhanced Zn2+- and Ca2+- dependent thermostability, indicating that Ca2+- and Zn2+-binding sites function cooperatively to maintain protein stability. Furthermore, an isothermal titration calorimetry (ITC) analysis revealed a novel Zn2+-binding site in mutant EH-CC-E204G. This metal ion cooperation provides a possible method for the generation of α-amylases with desired thermal properties by in silico rational design and systems engineering, to generate a Zn2+-binding site adjacent to the conserved Ca2+-binding site.

Functional Interaction between the N and C Termini of NhaD Antiporters from Halomonas sp. Strain Y2.

Two NhaD-type antiporters, NhaD1 and NhaD2, from the halotolerant and alkaliphilic Halomonas sp. strain Y2, exhibit different physiological functions in regard to Na+ and Li+ resistance, although they share high sequence identity. In the present study, the truncation of an additional 4 C-terminal residues from NhaD2 or an exchange of 39 N-terminal residues between these proteins resulted in the complete loss of antiporter activity. Interestingly, combining 39 N-terminal residues and 7 C-terminal residues of NhaD2 (N39D2-C7) partially recovered the activity for Na+ and Li+ expulsion, as well as complementary growth following exposure to 300 mM Na+ and 100 mM Li+ stress. The recovered activity of chimera N39D2-C7 indicated that the N and C termini are structurally dependent on each other and function synergistically. Furthermore, fluorescence resonance energy transfer (FRET) analysis suggested that the N and C termini are relatively close in proximity which may account for their synergistic function in ion translocation. In the N-terminal region of N39D2-C7, the replacement of Glu38 with Pro abolished the recovered complementary and transport activities. In addition, this amino acid substitution in NhaD2 resulted in a drastically decreased complementation ability in Escherichia coli KNabc (level identical to that of NhaD1), as well as decreased activity and an altered pH profile.IMPORTANCE Limited information on NhaD antiporters supports speculation that these antiporters are important for resistance to high salinity and alkalinity. Moreover, only a few functional residues have been identified in NhaD antiporters, and there is limited literature on the molecular mechanisms of NhaD antiporter activity. The altered antiporter abilities of chimeras and mutants in this study implicate the functions of the N and C termini, especially Glu38, in pH regulation and ion translocation, and, most importantly, the essential roles of this negatively charged residue in maintaining the physiological function of NhaD2. These findings further our understanding of the molecular mechanism of NhaD antiporters for ion transport.

Efficient secretory expression of recombinant proteins in Escherichia coli with a novel actinomycete signal peptide.

In well-established heterologous hosts, such as Escherichia coli, recombinant proteins are usually intracellular and frequently found as inclusion bodies-especially proteins possessing high rare codon content. In this study, successful secretory expression of three hydrolases, in a constructed inducible or constitutive system, was achieved by fusion with a novel signal peptide (Kp-SP) from an actinomycete. The signal peptide efficiently enabled extracellular protein secretion and also contributed to the active expression of the intracellular recombinant proteins. The thermophilic α-amylase gene of Bacillus licheniformis was fused with Kp-SP. Both recombinants, carrying inducible and constitutive plasmids, showed remarkable increases in extracellular and intracellular amylolytic activity. Amylase activity was observed to be > 10-fold in recombinant cultures with the constitutive plasmid, pBSPPc, compared to that in recombinants lacking Kp-SP. Further, the signal peptide enabled efficient secretion of a thermophilic cellulase into the culture medium, as demonstrated by larger halo zones and increased enzymatic activities detected in both constructs from different plasmids. For heterologous proteins with a high proportion of rare codons, it is difficult to obtain high expression in E. coli owing to the codon bias. Here, the fusion of an archaeal homologue of the amylase encoding gene, FSA, with Kp-SP resulted in > 5-fold higher extracellular activity. The successful extracellular expression of the amylase indicated that the signal peptide also contributed significantly to its active expression and signified the potential value of this novel and versatile signal peptide in recombinant protein production.

Alkaline Response of a Halotolerant Alkaliphilic Halomonas Strain and Functional Diversity of Its Na+(K+)/H+ Antiporters.

Halomonas sp. Y2 is a halotolerant alkaliphilic strain from Na+-rich pulp mill wastewater with high alkalinity (pH >11.0). Transcriptome analysis of this isolate revealed this strain may use various transport systems for pH homeostasis. In particular, the genes encoding four putative Na+/H+ antiporters were differentially expressed upon acidic or alkaline conditions. Further evidence, from heterologous expression and mutant studies, suggested that Halomonas sp. Y2 employs its Na+/H+ antiporters in a labor division way to deal with saline and alkaline environments. Ha-NhaD2 displayed robust Na+(Li+) resistance and high transport activities in Escherichia coli; a ΔHa-nhaD2 mutant exhibited growth inhibition at high Na+(Li+) concentrations at pH values of 6.2, 8.0, and 10.0, suggesting its physiological role in osmotic homeostasis. In contrast, Ha-NhaD1 showed much weaker activities in ion exporting and pH homeostasis. Ha-Mrp displayed a combination of properties similar to those of Mrp transporters from some Bacillus alkaliphiles and neutrophiles. This conferred obvious Na+(Li+, K+) resistance in E. coli-deficient strains, as those ion transport spectra of some neutrophil Mrp antiporters. Conversely, similar to the Bacillus alkaliphiles, Ha-Mrp showed central roles in the pH homeostasis of Halomonas sp. Y2. An Ha-mrp-disrupted mutant was seriously inhibited by high concentrations of Na+(Li+, K+) but only under alkaline conditions. Ha-NhaP was determined to be a K+/H+ antiporter and shown to confer strong K+ resistance both at acidic and alkaline stresses.

Expression and functional analysis of two NhaD type antiporters from the halotolerant and alkaliphilic Halomonas sp. Y2.

Na(+)/H(+) antiporters play important roles in ion and pH homeostasis. In this study, two NhaD homologues that effectively catalyze Na(+)/H(+) antiporter were identified from Halomonas sp. Y2, a halotolerant and alkaliphilic strain isolated from sodium enriched black liquor. They exhibited high sequence identity of 72 % and similar binding affinities for Na(+) and Li(+) translocation, while having different pH profiles. Ha-NhaD1 was active at pH 6.0 and most active at pH 8.0-8.5, whereas Ha-NhaD2 lacked activity at pH 6.0 but exhibited maximum activity at pH 9.5 or higher. Based on multiple alignments, 11 partially conserved residues were selected and corresponding mutants were generated for Ha-NhaD1. As expected, replacement of most of the hydrophobic residues abolished the cation exchange activities. Three serine residues at positions 200, 282 and 353 in Ha-NhaD1 were replaceable by alanines with partial retention of activity. The S353A mutant exhibited significantly reduced binding affinity for Na(+) and Li(+), while S282 mutant exhibited an alkaline shift of about 1.5 pH units, as compared to the wild type Ha-NhaD1. Serine at position 282 was predicted to be located in transmembrane segment VIII and was found to be important in regulating pH sensitivity in concert with flanking residues.