A novel classification that defines the normal cervical spine: an analysis based on 632 asymptomatic Chinese volunteers.

PURPOSE: The "normal" cervical spine may be non-lordotic shapes and the cervical spine alignment targets are less well established. So, the study was to propose novel classification for cervical spine morphologies with Chinese asymptomatic subjects, and to address cervical balance status based on the classification. METHOD: An overall 632 asymptomatic individuals on cervical spine were selected from January 2020 to December 2022, with six age groups from 20-30 year to 70 plus group. Cervical alignment contained C2-7 cervical lordosis (C2-7 CL) and T1 slope (T1S), together with C1-2 CL, C2-4 CL, C5-7 CL, C2S, cervical sagittal vertical axis (CSVA), thoracic inlet angle (TIA) and neck tilt (NT). C2-7 cervical lordosis was regarded as primary outcomes. To identify groups with similar cervical alignment parameters, a 2-step cluster analysis was performed. RESULTS: C2-7 CL, T1S, CSVA, TIA and NT increased by age and mean value of them were larger in male than female group. Four unique clusters of female lordotic cluster, female kyphotic cluster, male lordotic cluster and male kyphotic cluster were classified mainly based on gender and C2-C7 CL. T1S was the independent influencing factor for C2-7 CL in all individuals and C2-7 CL = -28.65 + 0.57 × TIA, which varied from clusters. Although interactions among cervical parameters, it showed the alignment was more coordinated in lordotic groups. CONCLUSIONS: The cervical sagittal profile varied with age and gender. Four clusters were naturally classified based on C2-7 CL and gender. The cervical balance status was addressed by C2-7 CL = - 28.65 + 0.57 × TIA.

dPromoter-XGBoost: Detecting promoters and strength by combining multiple descriptors and feature selection using XGBoost.

Promoters play an irreplaceable role in biological processes and genetics, which are responsible for stimulating the transcription and expression of specific genes. Promoter abnormalities have been found in some diseases, and the level of promoter-binding transcription factors can be used as a marker before a disease occurs. Hence, detecting promoters from DNA sequences has important biological significance, particular, distinguishing strong promoters can help to elucidate differences in gene expression and the mechanisms of specific diseases. With the introduction of third-generation sequencing, it is difficult to match the speed of sequencing to the speed of labeling promoters experimentally. Many computing models have been designed to fill this gap and identify unlabeled DNA. However, their feature representation methods are very singular, which cannot reflect the information contained in the original samples. With the aim of avoiding information loss, we propose a computational model based on multiple descriptors and feature selection to jointly express samples. It is worth mentioning that a new feature descriptor called K-mer word vector is defined. The promoter model of multiple feature descriptors dominated by K-mer word vector achieves similar performance to existing methods, the sensitivity of 85.72% can distinguish the promoter more effectively than other methods. Furthermore, the performance of the promoter strength has surpassed published methods, and accuracy of 77.00% greatly improves the ability to distinguish between strong and weak promoters.

Let-7 mediated airway remodelling in chronic obstructive pulmonary disease via the regulation of IL-6.

BACKGROUND: Myofibroblast differentiation and extracellular matrix (ECM) deposition are observed in chronic obstructive pulmonary disease (COPD). However, the mechanisms of regulation of myofibroblast differentiation remain unclear. MATERIALS AND METHODS: We detected let-7 levels in peripheral lung tissues, serum and primary bronchial epithelial cells of COPD patients and cigarette smoke (CS)-exposed mice. IL-6 mRNA was explored in lung tissues of COPD patients and CS-exposed mice. IL-6 protein was detected in cell supernatant from primary epithelial cells by ELISA. We confirmed the regulatory effect of let-7 on IL-6 by luciferase reporter assay. Western blotting assay was used to determine the expression of α-SMA, E-cadherin and collagen I. In vitro, cell study was performed to demonstrate the role of let-7 in myofibroblast differentiation and ECM deposition. RESULTS: Low expression of let-7 was observed in COPD patients, CS-exposed mice and CS extract (CSE)-treated human bronchial epithelial (HBE) cells. Increased IL-6 was found in COPD patients, CS-exposed mice and CSE-treated HBE cells. Let-7 targets and silences IL-6 protein coding genes through binding to 3' untranslated region (UTR) of IL-6. Normal or CSE-treated HBE cells were co-cultured with human embryonic lung fibroblasts (MRC-5 cells). Reduction of let-7 in HBE cells caused myofibroblast differentiation and ECM deposition, while increase of let-7 mimics decreased myofibroblast differentiation phenotype and ECM deposition. CONCLUSION: We demonstrate that CS reduced let-7 expression in COPD and, further, identify let-7 as a regulator of myofibroblast differentiation through the regulation of IL-6, which has potential value for diagnosis and treatment of COPD.

Dynamic evolution of emphysema and airway remodeling in two mouse models of COPD.

BACKGROUND: Establishment of a mouse model is important for investigating the mechanism of chronic obstructive pulmonary disease (COPD). In this study, we observed and compared the evolution of the pathology in two mouse models of COPD induced by cigarette smoke (CS) exposure alone or in combination with lipopolysaccharide (LPS). METHODS: One hundred eight wild-type C57BL/6 mice were equally divided into three groups: the (1) control group, (2) CS-exposed group (CS group), and (3) CS + LPS-exposed group (CS + LPS group). The body weight of the mice was recorded, and noninvasive lung function tests were performed monthly. Inflammation was evaluated by counting the number of inflammatory cells in bronchoalveolar lavage fluid and measuring the expression of the IL-6 mRNA in mouse lung tissue. Changes in pathology were assessed by performing hematoxylin and eosin and Masson staining of lung tissue sections. RESULTS: The two treatments induced emphysema and airway remodeling and decreased lung function. Emphysema was induced after 1 month of exposure to CS or CS + LPS, while airway remodeling was induced after 2 months of exposure to CS + LPS and 3 months of exposure to CS. Moreover, the mice in the CS + LPS group exhibited more severe inflammation and airway remodeling than the mice in the CS group, but the two treatments induced similar levels of emphysema. CONCLUSION: Compared with the single CS exposure method, the CS + LPS exposure method is a more suitable model of COPD in airway remodeling research. Conversely, the CS exposure method is a more suitable model of COPD for emphysema research due to its simple operation.

WITHDRAWN: Fracture line morphology of greater tuberosity fragments of Neer 3 and 4 part proximal humerus fractures.

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Phosphorylation of histone H3 on Ser-10 by Aurora B is essential for chromosome condensation in porcine embryos during the first mitotic division.

Phosphorylation of histone H3 on Ser-10 (H3S10ph) is involved in regulating mitotic chromosome condensation and decondensation, which plays an important regulatory role during mitotic cell cycle progression in mammalian cells. However, whether H3S10ph plays a similar role in early porcine embryos during the first mitotic division remains uncertain. In this study, the subcellular localization and possible roles of H3S10ph were evaluated in the first mitotic cell cycle progression of porcine embryos using western blot, indirect immunofluorescence and barasertib (H3S10ph upstream regulator Aurora-B inhibitor) treatments. H3S10ph exhibited a dynamic localization pattern and was localized to chromosomes from prometaphase to anaphase stages. Treatment of porcine embryos with barasertib inhibited mitotic division at the prophase stage and was associated with a defect in chromosome condensation accompanied by the reduction of H3S10ph. These results indicated that H3S10ph is involved in the first mitotic division in porcine embryos through its regulatory function in chromosome condensation, which further affects porcine embryo cell cycle progression during mitotic division.

Effects of anti-Helicobacter pylori concomitant therapy and probiotic supplementation on the throat and gut microbiota in humans.

The microbiota within humans maintains homeostasis and plays important roles in human health. However, some situations such as the use of antibiotics may disrupt the microbiota balance and result in a series of adverse effects. This study aimed to investigate the effects of a commonly used anti-Helicobacter pylori concomitant therapy on the composition of the gut and throat microbiota and any antibiotic resistance that may develop. In addition to the standard regimen, two different supplementary probiotic regimens that both used Saccharomyces boulardii were included. Microbiological culture-based techniques were used to analyse the microbiota composition and antibiotic resistance. Our results showed marked quantitative and qualitative alterations in both the gut and throat microbiota after treatment with not only the standard concomitant therapy but also with either supplementary probiotic regimen. Nevertheless, most of the changes in the gut microbiota (except for yeast and Bacteroides spp. counts) reverted by Day 71, whereas the alterations in the throat microbiota appeared to persist. Patients treated with the eradication therapy in the absence of probiotic supplementation experienced the most pronounced disturbances in the throat microbiota, whereas changes in the throat microbiota appeared to stabilize in the groups that received probiotic supplementation. We also detected higher antibiotic resistance rates for Enterobacteriaceae, Enterococcus spp. and Bacteroides spp. after treatment with the eradication therapy. Co-administration of probiotics is likely to be more effective than post-antibiotic supplementation, and although some beneficial effects were observed, the probiotic combination did not exert significant effects on the unbalanced commensal gut and throat microbiota composition.

Plk1 is essential for proper chromosome segregation during meiosis I/meiosis II transition in pig oocytes.

BACKGROUND: Polo-like kinase 1 (Plk1), as a characteristic regulator in meiosis, organizes multiple biological events of cell division. Although Plk1 has been implicated in various functions in somatic cell mitotic processes, considerably less is known regarding its function during the transition from metaphase I (MI) to metaphase II (MII) stage in oocyte meiotic progression. METHODS: In this study, the possible role of Plk1 during the MI-to-MII stage transition in pig oocytes was addressed. Initially, the spatiotemporal expression and subcellular localization pattern of Plk1 were revealed in pig oocytes from MI to MII stage using indirect immunofluorescence and confocal microscopy imaging techniques combined with western blot analyses. Moreover, a highly selective Plk1 inhibitor, GSK461364, was used to determine the potential role of Plk1 during this MI-to-MII transition progression. RESULTS: Upon expression, Plk1 exhibited a specific dynamic intracellular localization, and co-localization of Plk1 with α-tubulin was revealed in the meiotic spindle of pig oocyte during the transition from MI to MII stage. GSK461364 treatment significantly blocked the first polar body (pbI) emission in a dose-dependent manner and resulted in a failure of meiotic maturation, with a larger percentage of the GSK461364-treated oocytes arresting in the anaphase-telophase I (ATI) stage. Further subcellular structure examination results showed that inhibition of Plk1 with GSK461364 had no visible effect on spindle assembly but caused a significantly higher proportion of the treated oocytes to have obvious defects in homologous chromosome segregation at ATI stage. CONCLUSIONS: Thus, these results indicate that Plk1 plays an essential role during the meiosis I/meiosis II transition in porcine oocytes, and the regulation is associated with Plk1's effects on homologous chromosome segregation in the ATI stage.

Plk1 inhibition leads to a failure of mitotic division during the first mitotic division in pig embryos.

PURPOSE: This study was conducted to examine the dynamic distribution of polo-like 1 kinase (Plk1) and the possible role it plays in first mitotic division during early porcine embryo development. METHODS: Indirect immunofluorescence and confocal microscopy imaging techniques combined with western blot analyses were used to study the dynamic expression and subcellular localization of Plk1 protein in pig parthenogenetic embryos. Finally, a selective Plk1 inhibitor, GSK461364, was used to evaluate the potential role of Plk1 during this special stage. RESULTS: The results showed that Plk1 upon expression exhibited specific dynamic intracellular localization, which closely correlated with the α-tubulin distribution during the first mitotic division. GSK461364 treatment resulted in cleavage failure, with majority of the GSK461364-treated embryos being arrested in prometaphase. Further results of the subcellular structure examination showed that GSK461364 treatment led to a significantly higher proportion of the treated embryos having abnormal spindles and misarranged chromosomes at the prometaphase stage. CONCLUSIONS: Thus, these results indicated that Plk1 is essential for porcine embryos to complete the first mitotic division. Furthermore, Plk1 regulation was associated with effects on spindle assembly and chromosome arrangement.

A miRNA-21-Mediated PTEN/Akt/NF-κB Axis Promotes Chronic Obstructive Pulmonary Disease Pathogenesis.

Background: This study sought to explore the underlying mechanism of miR-21 mediated apoptosis and inflammation in chronic obstructive pulmonary disease (COPD) induced by cigarette smoke (CS). Methods: We detected levels and PTEN/Akt/NF-κB axis protein levels in peripheral lung tissues of COPD patients and CS-exposed mice and HBE cells. Western blotting assay was used to determine the expression of cleaved caspase-3. IL-6 and IL-8 protein was detected in cell supernatant from cells by ELISA. HBE cells were transfected with a miR-21 inhibitor, and co-culture with A549. Results: Increased miR-21 expression, reduced PTEN expression and following activation of Akt in in peripheral lung tissues of COPD patients and CS-exposed mice and HBE cells. Inhibition of miR-21 showed enhanced PTEN levels and reduced the expression of phosphorylated form of Akt and NF-κB. Decreased expression of cleaved caspase-3, IL-6 and IL-8 in A549 cells co cultured with HBE cells transfected with miR-21 inhibitor compared with transfected with miR-21 control inhibitor. Conclusion: MiR-21 contributes to COPD pathogenesis by modulating apoptosis and inflammation through the PTEN/Akt/NF-κB pathway. Targeting miR-21 may increase PTEN expression and inhibit Akt/NF-κB pathway, offering potential diagnostic and therapeutic value in COPD management.

Validation of the China mortality prediction model in trauma based on the ICD-10-CM codes.

The China mortality prediction model in trauma, based on the International Classification of Diseases, Tenth Revision, Clinical Modification lexicon (CMPMIT-ICD-10), is a novel model for predicting outcomes in patients who experienced trauma. This model has not yet been validated using data acquired from patients at other trauma centers in China. This retrospective study used data retrieved from the Peking University People's Hospital discharge database and included all patients admitted for trauma between 2012 and 2022 for model validation. Model performance was categorized into discrimination and calibration. In total, 23,299 patients were included in this study, with an overall mortality rate of 1.2%. CMPMIT-ICD-10 showed good discrimination and calibration, with an area under the curve of 0.84 (95% confidence interval: 0.82-0.87) and a Brier score of 0.02. The performance of the CMPMIT-ICD-10 during validation was satisfactory, and the application of the model will be scaled up in future studies.

Tuning the Liquid-Vapour Interface of VLS Epitaxy for Creating Novel Semiconductor Nanostructures.

Controlling the morphology and composition of semiconductor nano- and micro-structures is crucial for fundamental studies and applications. Here, Si-Ge semiconductor nanostructures were fabricated using photolithographically defined micro-crucibles on Si substrates. Interestingly, the nanostructure morphology and composition of these structures are strongly dependent on the size of the liquid-vapour interface (i.e., the opening of the micro-crucible) in the CVD deposition step of Ge. In particular, Ge crystallites nucleate in micro-crucibles with larger opening sizes (3.74-4.73 µm2), while no such crystallites are found in micro-crucibles with smaller openings of 1.15 µm2. This interface area tuning also results in the formation of unique semiconductor nanostructures: lateral nano-trees (for smaller openings) and nano-rods (for larger openings). Further TEM imaging reveals that these nanostructures have an epitaxial relationship with the underlying Si substrate. This geometrical dependence on the micro-scale vapour-liquid-solid (VLS) nucleation and growth is explained within a dedicated model, where the incubation time for the VLS Ge nucleation is inversely proportional to the opening size. The geometric effect on the VLS nucleation can be used for the fine tuning of the morphology and composition of different lateral nano- and micro-structures by simply changing the area of the liquid-vapour interface.

Long Noncoding RNA AROD Inhibits Host Antiviral Innate Immunity via the miR-324-5p-CUEDC2 Axis.

Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs that are involved in multiple biological processes. Here, we report a mechanism through which the lnc-AROD-miR-324-5p-CUEDC2 axis regulates the host innate immune response, using influenza A virus (IAV) as a model. We identified that host lnc-AROD without protein-coding capability is composed of 975 nucleotides. Moreover, lnc-AROD inhibited interferon-ß expression, as well as interferon-stimulated genes ISG15 and MxA. Furthermore, in vivo assays confirmed that lnc-AROD overexpression increased flu virus pathogenicity and mortality in mice. Mechanistically, lnc-AROD interacted with miR-324-5p, leading to decreased binding of miR-324-5p to CUEDC2. Collectively, our findings demonstrated that lnc-AROD is a critical regulator of the host antiviral response via the miR-324-5p-CUEDC2 axis, and lnc-AROD functions as competing endogenous RNA. Our results also provided evidence that lnc-AROD serves as an inhibitor of the antiviral immune response and may represent a potential drug target. IMPORTANCE lnc-AROD is a potential diagnostic and discriminative biomarker for different cancers. However, so far the mechanisms of lnc-AROD regulating virus replication are not well understood. In this study, we identified that lnc-AROD is downregulated during RNA virus infection. We demonstrated that lnc-AROD enhanced CUEDC2 expression, which in turn inhibited innate immunity and favored IAV replication. Our studies indicated that lnc-AROD functions as a competing endogenous RNA that binds miR-324-5p and reduces its inhibitory effect on CUEDC2. Taken together, our findings reveal that lnc-AROD plays an important role during the host antiviral immune response.

NCOA4-Mediated Ferroptosis in Bronchial Epithelial Cells Promotes Macrophage M2 Polarization in COPD Emphysema.

Background: Macrophage polarization plays an important role in the pathogenesis of COPD emphysema. Changes in macrophage polarization in COPD remain unclear, while polarization and ferroptosis are essential factors in its pathogenesis. Therefore, this study investigated the relationship between macrophage polarization and ferroptosis in COPD emphysema. Methods: We measured macrophage polarization and the levels of matrix metalloproteinases (MMPs) in the lung tissues of COPD patients and cigarette smoke (CS)-exposed mice. Flow cytometry was used to determine macrophage (THP-M cell) polarization changes. Ferroptosis was examined by FerroOrange, Perls' DAB, C11-BODIPY and 4-HNE staining. Nuclear receptor coactivator 4 (NCOA4) was measured in the lung tissues of COPD patients and CS-exposed mice by western blotting. A cell study was performed to confirm the regulatory effect of NCOA4 on macrophage polarization. Results: Increased M2 macrophages and MMP9 and MMP12 levels were observed in COPD patients, CS-exposed mice and THP-M cells cocultured with CS extract (CSE)-treated human bronchial epithelial (HBE) cells. Increased NCOA4 levels and ferroptosis were confirmed in COPD. Treatment with NCOA4 siRNA and the ferroptosis inhibitor ferrostatin-1 revealed an association between ferroptosis and M2 macrophages. These findings support a role for NCOA4, which induces an increase in M2 macrophages, in the pathogenesis of COPD emphysema. Conclusion: In our study, CS led to the dominance of the M2 phenotype in COPD. We identified NCOA4 as a regulator of M2 macrophages and emphysema by mediating ferroptosis, which offers a new direction for research into COPD diagnostics and treatment.

Evaluation of NOTCH family genes' expression and prognostic value in prostate cancer.

Background: Abnormal regulation of the NOTCH signaling pathway in prostate cancer (PCa) can promote tumorigenesis, progression, and T cell exhaustion. However, there has not been a comprehensive analysis of NOTCH family genes (NOTCHs) as potential therapeutic targets and prognostic biomarkers for PCa patients. Methods: NOTCHs expressions in various types of cancer tissues and normal adjacent tissues in the TIMER and UALCAN database were screened. Immunohistochemistry (IHC) and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) were applied to validate the expression pattern of NOTCHs in clinical samples. The relationships of NOTCHs expression and clinicopathologic parameters or disease-free survival (DFS) were evaluated via GEPIA2 and UALCAN. A proteins network was built using STRING and GeneMANIA. Additionally, NOTCHs mutation status was analyzed by cBioportal. Finally, we used GDSC and TIMER to investigate NOTCH signaling-related drugs and immune cell infiltration. Results: The transcriptional levels of NOTCH1 and NOTCH4 in PCa tissues were significantly lower than in normal tissues, which was further validated in clinical patients' tissue samples. Furthermore, NOTCH1, NOTCH3, and NOTCH4 expressions in PCa were associated with worse DFS. Interestingly, there was a significant positive correlation between NOTCHs and androgen receptor (AR), but not with AR-related genes (KLK3 and TMPRSS2). Finally, we found that NOTCHs expressions were remarkably associated with infiltration of B cells, CD8+/CD4+ T cells, macrophages, neutrophils, and dendritic cells, which indicated that NOTCHs mutation status might be a potential therapeutic target for -tinib antineoplastic drugs. Conclusions: The expression and mutation of NOTCH1-4 in PCa were associated with disease progression, prognosis, immune cell infiltration, and drug sensitivity.

Verification of cell cycle-associated cyclin-dependent kinases facilitated prostate cancer progression by integrated bioinformatic analysis and experimental validation.

Introduction: Cell cycle-associated cyclin-dependent kinases (ccCDKs) are essential regulators known to control cell division and facilitate tumorigenesis and progression. However, there is currently no comprehensive study of distinct ccCDKs in prostate cancer (PCa). The purpose of this study was to determine the value of ccCDK expression in predicting the prognosis of patients with PCa and to identify the gene functions of ccCDK in PCa. Methods: The UALCAN databases were analyzed to examine the expression of CDKs in prostate cancer. The Human Protein Atlas was used to verify the expression of CDKs online. Then, we assessed the prognostic values of CDKs using GEPIA. GeneMANIA and Metascape analyses were used to predict biological functions. We analyzed the mutation of CDKs by cBioPortal. The TIMER database was used to evaluate the correlation of CDKs and immune infiltration. The expression of CDKs in tissue was examined through quantitative real-time polymerase chain reaction. After that, we focused on CDK3 and identified the expression of CDK3 by immunohistochemistry and western blot. The functions of CDK3 in C4-2 cell proliferation were determined by CCK-8 assays. C4-2 cells were tested for their ability to invade and migrate through transwell and wound healing assays. Results: The results showed that CDK1/3/4/5/6/16 was expressed at relatively higher levels in PCa tissues than in normal tissues. Patients with low expression of CDK1/3/5/16 exhibited significantly better disease-free survival than those with high expression. ccCDKs were enriched in the IL-18 signaling pathway and correlated with the infiltration of immune cells in PCa. Moreover, our cohort study data verified that there were significantly higher expression of CDK1/3/5/16 in PCa tissues compared to benign prostate hyperplasia tissues, and CDK3 was remarkably associated with a shorter progression-free survival for biochemical recurrence in PCa patients. CDK3 was positively expressed in PCa cells and tissues, and functional experiments demonstrated that silencing CDK3 inhibited PCa cell proliferation, migration, and invasion. Conclusions: Our study provides new evidence of ccCDKS in promoting PCa progression and implies that CDK3 may serve as an oncogene in PCa and may be valuable in the prognosis of biochemical recurrence in PCa patients.

Acremonium terricola Culture's Dose-Response Effects on Lactational Performance, Antioxidant Capacity, and Ruminal Characteristics in Holstein Dairy Cows.

Acremonium terricola culture (ATC) has similar bioactive constituents to Cordyceps and is known for its nutrient and pharmacological value, indicating the potential of ATC as a new feed additive in dairy cow feeding. The primary aim of this experiment was to investigate the effects of increasing amounts of ATC in diets on milk performance, antioxidant capacity, and rumen fermentation, and the secondary aim was to evaluate the potential effects of high doses of ATC. A total of 60 multiparous Holstein cows (110 ± 21 days in milk; 2.53 ± 0.82 parity) were assigned into 15 blocks and randomly assigned to one of four groups: 0, 30, 60, or 300 g/d of ATC per cow for 97 days. Data were analyzed using repeated measures in the Mixed procedure. Dry-matter intake was not changed (p > 0.05), while energy-corrected milk and fat-corrected milk yields increased linearly and quadratically, and somatic cell count in milk decreased linearly and quadratically (p < 0.05). The lactation efficiency and the yields of milk fat and protein increased linearly (p < 0.05). On day 90, serum catalase level, total oxidative capacity, glutathione peroxidase, immunoglobulin A, and immunoglobulin M concentrations were significantly higher in the 60 and 300 g/d groups than in the 0 g/d group (p < 0.05). ATC addition showed linear effects on total volatile fatty acid (VFA), acetate, branched VFA concentrations, and rumen pH (p < 0.05). Supplementing 60 and 300 g/d ATC significantly affected the bacterial composition (p < 0.05). The relative abundance of Christensenellaceae_R-7_group and Lachnospiraceae_NK3A20_group were significantly increased by 60 g/d supplementation, and the relative abundance of Erysipelotrichaceae_UCG_002, Acetitomaculum, Olsenella, and Syntrophococcus were significantly increased by 300 g/d supplementation (p < 0.05). ATC was effective in enhancing rumen fermentation and reducing somatic cell count in milk, thereby improving milk yield. The optimized dose of ATC was 60 g/d for lactating cows, and there were no risks associated with high doses of ATC.

SNAREs-SAP: SNARE Proteins Identification With PSSM Profiles.

Soluble N-ethylmaleimide sensitive factor activating protein receptor (SNARE) proteins are a large family of transmembrane proteins located in organelles and vesicles. The important roles of SNARE proteins include initiating the vesicle fusion process and activating and fusing proteins as they undergo exocytosis activity, and SNARE proteins are also vital for the transport regulation of membrane proteins and non-regulatory vesicles. Therefore, there is great significance in establishing a method to efficiently identify SNARE proteins. However, the identification accuracy of the existing methods such as SNARE CNN is not satisfied. In our study, we developed a method based on a support vector machine (SVM) that can effectively recognize SNARE proteins. We used the position-specific scoring matrix (PSSM) method to extract features of SNARE protein sequences, used the support vector machine recursive elimination correlation bias reduction (SVM-RFE-CBR) algorithm to rank the importance of features, and then screened out the optimal subset of feature data based on the sorted results. We input the feature data into the model when building the model, used 10-fold crossing validation for training, and tested model performance by using an independent dataset. In independent tests, the ability of our method to identify SNARE proteins achieved a sensitivity of 68%, specificity of 94%, accuracy of 92%, area under the curve (AUC) of 84%, and Matthew's correlation coefficient (MCC) of 0.48. The results of the experiment show that the common evaluation indicators of our method are excellent, indicating that our method performs better than other existing classification methods in identifying SNARE proteins.

VTP-Identifier: Vesicular Transport Proteins Identification Based on PSSM Profiles and XGBoost.

Vesicular transport proteins are related to many human diseases, and they threaten human health when they undergo pathological changes. Protein function prediction has been one of the most in-depth topics in bioinformatics. In this work, we developed a useful tool to identify vesicular transport proteins. Our strategy is to extract transition probability composition, autocovariance transformation and other information from the position-specific scoring matrix as feature vectors. EditedNearesNeighbours (ENN) is used to address the imbalance of the data set, and the Max-Relevance-Max-Distance (MRMD) algorithm is adopted to reduce the dimension of the feature vector. We used 5-fold cross-validation and independent test sets to evaluate our model. On the test set, VTP-Identifier presented a higher performance compared with GRU. The accuracy, Matthew's correlation coefficient (MCC) and area under the ROC curve (AUC) were 83.6%, 0.531 and 0.873, respectively.

AOPM: Application of Antioxidant Protein Classification Model in Predicting the Composition of Antioxidant Drugs.

Antioxidant proteins can not only balance the oxidative stress in the body, but are also an important component of antioxidant drugs. Accurate identification of antioxidant proteins is essential to help humans fight diseases and develop new drugs. In this paper, we developed a friendly method AOPM to identify antioxidant proteins. 188D and the Composition of k-spaced Amino Acid Pairs were adopted as the feature extraction method. In addition, the Max-Relevance-Max-Distance algorithm (MRMD) and random forest were the feature selection and classifier, respectively. We used 5-folds cross-validation and independent test dataset to evaluate our model. On the test dataset, AOPM presented a higher performance compared with the state-of-the-art methods. The sensitivity, specificity, accuracy, Matthew's Correlation Coefficient and an Area Under the Curve reached 87.3, 94.2, 92.0%, 0.815 and 0.972, respectively. In addition, AOPM still has excellent performance in predicting the catalytic enzymes of antioxidant drugs. This work proved the feasibility of virtual drug screening based on sequence information and provided new ideas and solutions for drug development.