Protein lysine β-hydroxybutyrylation (Kbhb) is a newly discovered post-translational modification associated with a wide range of biological processes. Identifying Kbhb sites is critical for a better understanding of its mechanism of action. However, biochemical experimental methods for probing Kbhb sites are costly and have a long cycle. Therefore, a feature embedding learning method based on the Transformer encoder was proposed to predict Kbhb sites. In this method, amino acid residues were mapped into numerical vectors according to their amino acid class and position in a learnable feature embedding method. Then the Transformer encoder was used to extract discriminating features, and the bidirectional long short-term memory network (BiLSTM) was used to capture the correlation between different features. In this paper, a benchmark dataset was constructed, and a Kbhb site predictor, AutoTF-Kbhb, was implemented based on the proposed method. Experimental results showed that the proposed feature embedding learning method could extract effective features. AutoTF-Kbhb achieved an area under curve (AUC) of 0.87 and a Matthews correlation coefficient (MCC) of 0.37 on the independent test set, significantly outperforming other methods in comparison. Therefore, AutoTF-Kbhb can be used as an auxiliary means to identify Kbhb sites.
Protein Processing, Post-Translational ; Lysine/chemistry* ; Proteins/chemistry* ; Machine Learning ; Algorithms

ObjectiveTo provide a reference for the diagnosis of amyloidosis in experimental animals through the pathological diagnosis of systemic amyloidosis in a case of a New Zealand white rabbit. MethodsIn a 6-month repeated ocular toxicity study, an abnormal finding was noted during the routine gross anatomical examination of one New Zealand white rabbit. Its organs were prepared as paraffin sections and stained with hematoxylin-eosin (HE) staining and Congo red staining. The histopathological features were observed under optical and polarized light microscopy. ResultsGross anatomical examination of the animal revealed an enlarged spleen and changes in the color and texture of the lung. HE staining showed that the splenic tissue structure was destroyed, the white pulp of the spleen was surrounded by dense amyloid deposition in the form of nodular rings, along with pressure atrophy of the white pulp. Amyloid deposits were also observed in the submandibular lymph nodes, mesenteric lymph nodes, ileum, sacculus rotundus, vermiform appendix, jejunum, cecum, and rectum. Congo red staining showed that the amyloid deposition in the affected organs appeared salmon-pink, and exhibited characteristic apple green birefringence under polarized light microscopy.Conclusion The histo-pathological features of the New Zealand white rabbit are consistent with the diagnostic characteristics of systemic amyloidosis.

Objective:To explore the surgical efficacy of conductive deafness caused by otosclerosis and ossicular malformation with 980 nm fiber laser stapedial floor fenestration.Methods:Data of 58 patients (ears) who were diagnosed with conductive deafness caused by otosclerosis (49 ears) and ossicular malformation (9 ears) treated by 980 nm Diode laser small-fenestra stapedotomy were retrospectively analyzed. Air conduction (AC) thresholds, bone conduction (BC) thresholds, and air-bone gap (ABG) at 0.5, 1, 2, 4 kHz pure tone frequencies were compared before and 3 months after surgery, and the advantages and precautions of 980 nm fiber laser were summarized. Paired t-test (SPSS 26.0 software) was use to analyze the listening data. Results:Fiber optic laser stapes fenestration and artificial stapes implantation were successfully completed in all 57 cases (ears), the hearing of another one patient (ear) with floating malformation of detachment of stapedial floor was lower than that before surgery. Preoperative at 0.5, 1, 2, 4 kHz frequencies of AC thresholds, BC thresholds, and ABG were (65.4±9.7) dB, (27.2±8.9) dB, and (38.2±9.8) dB respectively. Postoperative 3 months at the same frequency of AC thresholds, BC thresholds, and ABG were (42.1±11.3) dB, (26.9±6.6) dB, and (15.2±9.1) dB. Preoperative and postoperative of AC threshold and ABG were statistically significant at 0.5, 1, 2, 4 kHz ( t value was 13.270 and13.948, both P<0.01), and yet the BC threshold was not statistically significant before and after surgery at the same frequency ( t=0.418, P>0.05). Conclusions:980 nm fiber laser stapes floor fenestration is an effective treatment for conductive deafness caused by otosclerosis and ossicular malformation.