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

Objective: This study evaluated the relationship between IVD degeneration and the vertebral body FSF in dogs and compared these factors between chondrodystrophic (CD) and nonchondrodystrophic (NCD) dogs. Methods: IVD degeneration in dogs was classified morphologically using the Pfirrmann grade, and the vertebral body FSF was evaluated quantitatively. Results: The vertebral body FSF showed a statistically significant difference among the age groups. The vertebral body FSF was significantly higher in Pfirrmann grades 3–5 than in grades 1 and 2. The mean Pfirrmann grade of CD dogs was higher than that of NCD dogs in the four-to-six-year-old group. The mean vertebral body FSF of CD dogs was higher than that of NCD dogs in the group of seven years and above. Conclusions and Relevance: In dogs, the vertebral body FSF increased significantly with age and Pfirrmann grade. The CD dogs showed a higher degree of IVD degeneration at a younger age than the NCD dogs. CD dogs appeared to experience more severe fat deposition of the vertebral body in old age than NCD dogs. MRI examinations are helpful for evaluating IVD degeneration and vertebral body fat deposition.

Objective: This study evaluated the relationship between IVD degeneration and the vertebral body FSF in dogs and compared these factors between chondrodystrophic (CD) and nonchondrodystrophic (NCD) dogs. Methods: IVD degeneration in dogs was classified morphologically using the Pfirrmann grade, and the vertebral body FSF was evaluated quantitatively. Results: The vertebral body FSF showed a statistically significant difference among the age groups. The vertebral body FSF was significantly higher in Pfirrmann grades 3–5 than in grades 1 and 2. The mean Pfirrmann grade of CD dogs was higher than that of NCD dogs in the four-to-six-year-old group. The mean vertebral body FSF of CD dogs was higher than that of NCD dogs in the group of seven years and above. Conclusions and Relevance: In dogs, the vertebral body FSF increased significantly with age and Pfirrmann grade. The CD dogs showed a higher degree of IVD degeneration at a younger age than the NCD dogs. CD dogs appeared to experience more severe fat deposition of the vertebral body in old age than NCD dogs. MRI examinations are helpful for evaluating IVD degeneration and vertebral body fat deposition.

Objective: This study evaluated the relationship between IVD degeneration and the vertebral body FSF in dogs and compared these factors between chondrodystrophic (CD) and nonchondrodystrophic (NCD) dogs. Methods: IVD degeneration in dogs was classified morphologically using the Pfirrmann grade, and the vertebral body FSF was evaluated quantitatively. Results: The vertebral body FSF showed a statistically significant difference among the age groups. The vertebral body FSF was significantly higher in Pfirrmann grades 3–5 than in grades 1 and 2. The mean Pfirrmann grade of CD dogs was higher than that of NCD dogs in the four-to-six-year-old group. The mean vertebral body FSF of CD dogs was higher than that of NCD dogs in the group of seven years and above. Conclusions and Relevance: In dogs, the vertebral body FSF increased significantly with age and Pfirrmann grade. The CD dogs showed a higher degree of IVD degeneration at a younger age than the NCD dogs. CD dogs appeared to experience more severe fat deposition of the vertebral body in old age than NCD dogs. MRI examinations are helpful for evaluating IVD degeneration and vertebral body fat deposition.

Objective: This study evaluated the relationship between IVD degeneration and the vertebral body FSF in dogs and compared these factors between chondrodystrophic (CD) and nonchondrodystrophic (NCD) dogs. Methods: IVD degeneration in dogs was classified morphologically using the Pfirrmann grade, and the vertebral body FSF was evaluated quantitatively. Results: The vertebral body FSF showed a statistically significant difference among the age groups. The vertebral body FSF was significantly higher in Pfirrmann grades 3–5 than in grades 1 and 2. The mean Pfirrmann grade of CD dogs was higher than that of NCD dogs in the four-to-six-year-old group. The mean vertebral body FSF of CD dogs was higher than that of NCD dogs in the group of seven years and above. Conclusions and Relevance: In dogs, the vertebral body FSF increased significantly with age and Pfirrmann grade. The CD dogs showed a higher degree of IVD degeneration at a younger age than the NCD dogs. CD dogs appeared to experience more severe fat deposition of the vertebral body in old age than NCD dogs. MRI examinations are helpful for evaluating IVD degeneration and vertebral body fat deposition.

Objective:To evaluate the efficacy and safety of oral anisodine hydrobromide tablets in the treatment of nonarteritic anterior ischemic optic neuropathy (NAION).Methods:A multicenter nonrandomized controlled trial was conducted.A total of 282 acute NAION patients (282 eyes) were recruited from 16 hospitals in China from July 2020 to May 2021.Patients were divided into two groups according to treatment methods, which were control group (124 cases, 124 eyes) receiving regular treatment including citicoline sodium plus Ginkgo biloba leaf liquid extract or Ginkgo biloba leaf extract tablets plus mecobalamin, and experimental group (158 cases, 158 eyes) receiving treatment in control group plus oral anisodine hydrobromide tablets 1 mg, twice daily for 2 to 3 months.Best corrected visual acuity (BCVA), visual field index (VFI), peripapillary retinal nerve fiber layer (pRNFL) and radial peripapillary capillary vessel density (RPC) were assessed at 1, 2, 3, and 6 months after enrollment using the standard decimal visual acuity chart, 750i Humphery visual field analyzer, Cirrus HD-OCT 4000/Cirrus HD-OCT 5000, RTVue-XR optical coherence tomography respectively.The primary outcomes were BCVA and VFI, and the secondary outcomes were pRNFL, RPC, and the side effects during the follow-up.The study adhered to the Declaration of Helsinki.All patients were fully informed about the treatment and purpose of this study and voluntarily signed the informed consent form.The study protocol was approved by Chinese PLA General Hospital (No.S2020-021-01). Results:In all, 242 patients (242 eyes) completed the follow-up of BCVA, and 98 patients (98 eyes) completed the VFI follow-up.In terms of visual function, BCVA and VFI improved significantly over time in the two groups, and BCVA and VFI were better in experimental group than in control group at various follow-up time points (all at P<0.05). In terms of structure, pRNFL gradually decreased in both groups with the extension of treatment, and pRNFL was significanthy thinner in experimental group than in control group at various follow-up time points (all at P<0.05). There was no significant difference in RPC between the two groups at the last follow-up ( P>0.05). There were two cases with side effects and one case was discontinued due to side effects 25 days after enrollment. Conclusions:Oral anisodine hydrobromide can improve visual acuity and visual field in NAION and accelerate the regression of optic disc edema, with good safety.

Objective:To observe the effect of interleukin-8 (IL-8) on the adhesion and migration of retinal vascular endothelial cells (RCEC).Methods:A cell experiment. Human RCEC (hRCEC) was divided into normal control group (N group), advanced glycation end product (AGE) treatment group (AGE group), and AGE-induced combined IL-8 antagonist SB225002 treatment group (AGE+SB group). The effect of AGE on IL-8 expression in hRCEC was observed by Western blot. The effect of SB225002 on hRCEC migration was observed by cell scratch assay. The effects of SB225002 on leukocyte adhesion and reactive oxygen species (ROS) on hRCEC were detected by flow cytometry. Student- t test was performed between the two groups. Oneway analysis of variance was performed among the three groups. Results:Compared with group N, the expression level of IL-8 in cells of AGE group was significantly increased, with statistical significance ( t=25.661, P<0.001). Compared with N group and AGE+SB group, cell mobility in AGE group was significantly increased ( F=29.776), leukocyte adhesion number was significantly increased ( F=38.159, 38.556), ROS expression level was significantly increased ( F=22.336), and the differences were statistically significant ( P<0.05). Conclusion:IL-8 antagonist SB225002 may down-regulate hRCEC adhesion and migration by inhibiting ROS expression.

Purpose: Colorectal cancer (CRC) is a common malignancy worldwide and the second leading cause of cancer-related deaths. In addition, lymph node metastasis in CRC is considered an important prognostic factor for predicting disease recurrence and patient survival. Recent studies demonstrated that the microbiome makes substantial contributions to tumor progression, however, there is still unknown about the microbiome associated with lymph node metastasis of CRC. Here, we first reported the microbial and tumor-infiltrating immune cell differences in CRC according to the lymph node metastasis status. Materials and Methods: Using Next Generation Sequencing data acquired from 368 individuals diagnosed with CRC (N0, 266; N1, 102), we applied the LEfSe to elucidate microbial differences. Subsequent utilization of the Kaplan-Meier survival analysis enabled the identification of particular genera exerting significant influence on patient survival outcomes. Results We found 18 genera in the N1 group and 3 genera in the N0 group according to CRC lymph node metastasis stages. In addition, we found that the genera Crenobacter (P=0.046), Maricaulis (P=0.093), and Arsenicicoccus (P=0.035) in the N0 group and Cecembia (P=0.08) and Asanoa (P=0.088) in the N1 group were significantly associated with patient survival according to CRC lymph node metastasis stages. Further, Cecembia is highly correlated to tumor-infiltrating immune cells in lymph node metastasized CRC.Concolusion: Our study highlights that tumor-infiltrating immune cells and intratumoral microbe diversity are associated with CRC. Also, this potential microbiome-based oncology diagnostic tool warrants further exploration.

Objective:To observe clinical phenotypes and analyze the pathogenic genes of Leber congenital amaurosis (LCA).Methods:A retrospective clinical study. From 2019 to 2020, 2 patients diagnosed with LCA by genetic testing in Tianjin Medical University Eye Hospital and their 6 unaffected family members were enrolled in the study. Two patients were from 2 unrelated families, both were probands. The patient's medical history was inquired in detail, slit lamp microscopy, ultra-widefield fundus photography, autofluorescence, and flash visual evoked potential (F-VEP) were performed. Peripheral vein blood (3-5 ml) was collected and genomic DNA was extracted from all study subjects. A total of 381 pathogetic genes associated with inherited retinal diseases, were selected by targeted exome sequencing capture strategy. Sanger sequencing was used to verify suspected pathogenic mutations. Candidate pathogenic mutations were identified after bioinformatics analysis. Sanger sequencing, real-time quantitative polymerase chain reaction and family co-identification were used to confirm the final mutations.Results:Two patients were male, aged 3 and 27 years. One case had vision loss in both eyes, accompanied by nystagmus and acupressure eye sign since childhood. The clinical hallmark of the proband (F1-Ⅱ-3) in F1 includes clearly boundary of optic disc, normal retinal blood vessels and macular fovea. The implied period of the maximum forward wave in both eyes of F-VEP was roughly normal, and its amplitude decreased significantly. The phenotype of the proband (F2-Ⅱ-1) in F2 includes optic nerve head pallor, bone-spicule intraretinal pigmentation, "gold-foil maculopathy" , retina patchy hypo-autofluorescence in both eyes. There was no abnormal phenotype in the eyes of the family members. According to the genetic diagnosis, the proband (F1-Ⅱ-3) carried the GUCY2D gene c.835G>A (p.D279N) (M1) and exon 9-19 deletion (M2) compound heterozygous mutations, in which M1 was derived from healthy mother and M2 was derived from healthy father. The proband (F2-Ⅱ-1) carried CRB1 gene c.1576C>T(R526X) (M3) and c.1522T>C (C508R) (M4) compound heterozygous mutations, in which M3 from the healthy father, M4 from the healthy mother. M2 and M4 were novel mutations. Conclusion:GUCY2D gene mutations lead to LCA1 type in the F1 family, CRB1 gene mutations lead to LCA8 type in the F2 family; there are significant different phenotypes caused by different pathogenic genes.

Background::Compared with human leukocyte antigen (HLA)-matched sibling donor (MSD) transplantation, it remains unclear whether haploidentical donor (HID) transplantation has a superior graft-versus-leukemia (GVL) effect for Philadelphia-negative (Ph-) high-risk B-cell acute lymphoblastic leukemia (B-ALL). This study aimed to compare the GVL effect between HID and MSD transplantation for Ph- high-risk B-ALL.Methods::This study population came from two prospective multicenter trials (NCT01883180, NCT02673008). Immunosuppressant withdrawal and prophylactic or pre-emptive donor lymphocyte infusion (DLI) were administered in patients without active graft-versus-host disease (GVHD) to prevent relapse. All patients with measurable residual disease (MRD) positivity posttransplantation (post-MRD+) or non-remission (NR) pre-transplantation received prophylactic/pre-emptive interventions. The primary endpoint was the incidence of post-MRD+.Results::A total of 335 patients with Ph- high-risk B-ALL were enrolled, including 145 and 190, respectively, in the HID and MSD groups. The 3-year cumulative incidence of post-MRD+ was 27.2% (95% confidence interval [CI]: 20.2%-34.7%) and 42.6% (35.5%-49.6%) in the HID and MSD groups (P = 0.003), respectively. A total of 156 patients received DLI, including 60 (41.4%) and 96 (50.5%), respectively, in the HID and MSD groups ( P= 0.096). The 3-year cumulative incidence of relapse was 18.6% (95% CI: 12.7%-25.4%) and 25.9% (19.9%-32.3%; P = 0.116) in the two groups, respectively. The 3-year overall survival (OS) was 67.4% (95% CI: 59.1%-74.4%) and 61.6% (54.2%-68.1%; P = 0.382), leukemia-free survival (LFS) was 63.4% (95% CI: 55.0%-70.7%) and 58.2% (50.8%-64.9%; P= 0.429), and GVHD-free/relapse-free survival (GRFS) was 51.7% (95% CI: 43.3%-59.5%) and 37.8% (30.9%-44.6%; P= 0.041), respectively, in the HID and MSD groups. Conclusion::HID transplantation has a lower incidence of post-MRD+ than MSD transplantation, suggesting that HID transplantation might have a superior GVL effect than MSD transplantation for Ph- high-risk B-ALL patients.Trial registration::ClinicalTrials.gov: NCT01883180, NCT02673008.