CT radiomics nomogram predicts pathological response after induced chemotherapy and overall survival in patients with advanced laryngeal cancer: A single-center retrospective study.

Purpose: This study aimed to develop a radiomics nomogram to predict pathological response (PR) after induction chemotherapy (IC) and overall survival (OS) in patients with advanced laryngeal cancer (LC). Methods: This retrospective study included patients with LC (n = 114) who had undergone contrast computerized tomography (CT); patients were randomly assigned to training (n = 81) and validation cohorts (n = 33). Potential radiomics scores were calculated to establish a model for predicting the PR status using least absolute shrinkage and selection operator (LASSO) regression. Multivariable logistic regression analyses were performed to select significant variables for predicting PR status. Kaplan-Meier analysis was performed to assess the risk stratification ability of PR and radiomics score (rad-score) for predicting OS. A prognostic nomogram was developed by integrating radiomics features and clinicopathological characteristics using multivariate Cox regression. All LC patients were stratified as low- and high-risk by the median CT radiomic score, C-index, calibration curve. Additionally, decision curve analysis (DCA) of the nomogram was performed to test model performance and clinical usefulness. Results: Overall, PR rates were 45.6% (37/81) and 39.3% (13/33) in the training and validation cohorts, respectively. Eight features were optimally selected to build a rad-score model, which was significantly associated with PR and OS. The median OS in the PR group was significantly shorter than that in the non-PR group in both cohorts. Multivariate Cox analysis revealed that volume [hazard ratio, (HR) = 1.43], N stage (HR = 1.46), and rad-score (HR = 2.65) were independent risk factors associated with OS. The above four variables were applied to develop a nomogram for predicting OS, and the DCAs indicated that the predictive performance of the nomogram was better than that of the clinical model. Conclusion: For patients with advanced LC, CT radiomics score was an independent biomarker for estimating PR after IC. Moreover, the nomogram that incorporated radiomics features and clinicopathological factors performed better for individualized OS estimation.

Modeling amide-I vibrations of alanine dipeptide in solution by using neural network protocol.

Infrared spectroscopy is a powerful tool for the understanding of molecular structure and function of polypeptides. Theoretical interpretation of IR spectra relies on ab initio calculations may be very costly in computational resources. Herein, we developed a neural network (NN) modeling protocol to evaluate a model dipeptide's backbone amide-I spectra. DFT calculations were performed for the amide-I vibrational motions and structural parameters of alanine dipeptide (ALAD) conformers in different micro-environments ranging from polar to non-polar ones. The obtained backbone dihedrals, C = O bond lengths and amide-I frequencies of ALAD were gather together for NN architecture. The applications of built NN protocols for the prediction of amide-I frequencies of ALAD in other solvation conditions are quite satisfactory with much less computational cost comparing with electronic structure calculations. The results show that this cost-effective way enables us to decipher the polypeptide's dynamic secondary structures and biological functions with their backbone vibrational probes.

Structural dynamics and vibrational feature of N-Acetyl-d-glucosamine in aqueous solution.

Molecular dynamics simulations and DFT calculations were performed for the demonstration of the structural dynamics and vibrational feature of N-Acetyl-d-glucosamine (NAG) in solution phase. The interactions between NAG and solvent molecules were evaluated through spatial distribution function and radial distribution function, and the preferred conformations of NAG in aqueous solution were revealed by cluster analysis. Results from normal mode analysis show that the solvent induced structural fluctuation of NAG could be reflected in the vibrational feature of specific chromophores, thus we can evaluate the molecular structure with the help of its vibrational signature based on the built correlation between molecular structure and vibrational frequencies of specific groups.

DNA-binding protein phosphatase AtDBP1 acts as a promoter of flowering in Arabidopsis.

MAIN CONCLUSION: We provide evidence that AtDBP1 promotes flowering by regulating the transcript levels of several important integrators and floral meristem identity genes, including FLC, CO, SOC1, LFY, FT and FD. DNA-binding protein phosphatases (DBP) which exhibit both sequence specific DNA-binding and protein phosphatase 2C activities are important regulators that are involved in both the transcriptional and post-translational regulations. DBP factors are known to mediate susceptibility to potyviruses; however, whether they are involved in other processes is still unclear. In this study, under both long day (LD) and short day conditions, AtDBP1 overexpressing plants displayed early flowering, while the knock out mutants, atdbp1, exhibited a delay in flowering relative to the wild-type plants; both the overexpressing lines and atdbp1 mutants remained photoperiodic sensitive, indicating that AtDBP1 was involved in the autonomous pathway. AtDBP1 does not respond to vernalization at transcript level, and both AtDBP1 overexpressing plants and atdbp1 mutants remain responsive to vernalization, indicating that AtDBP1 may not be directly involved in vernalization. Real-time PCR analysis showed that AtDBP1 can suppress FLOWERING LOCUC C (FLC) expression, a key integrator of the autonomous and vernalization pathways, and enhance the expression levels of CONSTANS and FLOWERING LOCUC T, key regulators of the LD pathway. Furthermore, expression of floral meristem identity genes including SUPPRESSOR OF OVEREXPRESSION OF CO 1, LEAFY and FD was also promoted in AtDBP1 overexpressing plants. AtDBP1 transcription can be detected in root, leaf, stem, flower and silique. AtDBP1-GFP and YFP-AtDBP1 fusion protein were localized in the cytosol and nucleus. Our results provide the evidence demonstrating the effective role of AtDBP1 for flowering time regulation and report a novel function of DBP factors in planta besides in plant defense.

[Sequence polymorphism of the promoter region of gene STK11 in patients with Peutz-Jeghers syndrome].

OBJECTIVE: To explore the relationship between the sequence variation of the promoter region (-1543 approximately -1160) of STK11 gene and the risk of developing Peutz-Jeghers syndrome (PJS). METHODS: The sequences of the promoter region of 14 PJS patients (7 patients are inherited and the other 7 patients are sporadic) and 42 normal individuals were PCR amplified and then sequenced. RESULTS: A new single nucleotide polymorphism (SNP) G/T (-1275) in STK11 promoter region was identified. The frequency of genotype GG, GT, and TT was 53.3%, 26.7%, and 20%, respectively among PJS patients and 33.3%, 64.3%, and 2.4%, respectively among the normal individuals. The frequency of genotype GG and TT among patients was significantly higher than that among the normal individuals, and the frequency of genotype GT among patients was significantly lower than that among the normal individuals (chi(2)=8.521, P<0.05). CONCLUSION: G/T(-1275) in STK11 promoter region is a new SNP. The genotype of this new SNP may relate to the risk of developing Peutz-Jeghers syndrome (PJS) deserve further research.