Transformer models have emerged as pivotal tools within the realm of drug discovery, distinguished by their unique architectural features and exceptional performance in managing intricate data landscapes. Leveraging the innate capabilities of transformer architectures to comprehend intricate hierarchical dependencies inherent in sequential data, these models showcase remarkable efficacy across various tasks, including new drug design and drug target identification. The adaptability of pre-trained transformer-based models renders them indispensable assets for driving data-centric advancements in drug discovery, chemistry, and biology, furnishing a robust framework that expedites innovation and discovery within these domains. Beyond their technical prowess, the success of transformer-based models in drug discovery, chemistry, and biology extends to their interdisciplinary potential, seamlessly combining biological, physical, chemical, and pharmacological insights to bridge gaps across diverse disciplines. This integrative approach not only enhances the depth and breadth of research endeavors but also fosters synergistic collaborations and exchange of ideas among disparate fields. In our review, we elucidate the myriad applications of transformers in drug discovery, as well as chemistry and biology, spanning from protein design and protein engineering, to molecular dynamics (MD), drug target identification, transformer-enabled drug virtual screening (VS), drug lead optimization, drug addiction, small data set challenges, chemical and biological image analysis, chemical language understanding, and single cell data. Finally, we conclude the survey by deliberating on promising trends in transformer models within the context of drug discovery and other sciences.

OBJECTIVE: This study aimed to evaluate the association between susceptibility genes and non-alcoholic fatty liver disease (NAFLD) in children with obesity. METHODS: We conducted a two-step case-control study. Ninety-three participants were subjected to whole-exome sequencing (exploratory set). Differential genes identified in the small sample were validated in 1,022 participants using multiplex polymerase chain reaction and high-throughput sequencing (validation set). RESULTS: In the exploratory set, 14 genes from the NAFLD-associated pathways were identified. In the validation set, after adjusting for sex, age, and body mass index, ECI2 rs2326408 (dominant model: OR = 1.33, 95% CI: 1.02-1.72; additive model: OR = 1.22, 95% CI: 1.01-1.47), C6orf201 rs659305 (dominant model: OR = 1.30, 95% CI: 1.01-1.69; additive model: OR = 1.21, 95% CI: 1.00-1.45), CALML5 rs10904516 (pre-ad dominant model: OR = 1.36, 95% CI: 1.01-1.83; adjusted dominant model: OR = 1.40, 95% CI: 1.03-1.91; and pre-ad additive model: OR = 1.26, 95% CI: 1.04-1.66) polymorphisms were significantly associated with NAFLD in children with obesity ( P < 0.05). Interaction analysis revealed that the gene-gene interaction model of CALML5 rs10904516, COX11 rs17209882, and SCD5 rs3733228 was optional ( P < 0.05), demonstrating a negative interaction between the three genes. CONCLUSION In the Chinese population, the CALML5 rs10904516, C6orf201 rs659305, and ECI2 rs2326408 variants could be genetic markers for NAFLD susceptibility.
Humans ; Non-alcoholic Fatty Liver Disease/genetics* ; Child ; Male ; Female ; Genetic Predisposition to Disease ; Case-Control Studies ; Exome Sequencing ; Adolescent ; Polymorphism, Single Nucleotide ; Obesity/complications* ; Pediatric Obesity/complications* ; China

Objective To observe the efficacy and safety of Morinda officinalis oligosaccharides in the continuation treatment of mild and moderate depression.Methods An open,single-arm,multi-center design was adopted in our study.Adult patients with mild and moderate depression who had received acute treatment of Morinda officinalis oligosaccharides were enrolled and continue to receive Morinda officinalis oligosaccharides capsules for 24 weeks,the dose remained unchanged during continuation treatment.The remission rate,recurrence rate,recurrence time,and the change from baseline to endpoint of Hamilton Depression Scale(HAMD),Hamilton Anxiety Scale(HAMA),Clinical Global Impression-Severity(CGI-S)and Arizona Sexual Experience Scale(ASEX)were evaluated.The incidence of treatment-related adverse events was reported.Results The scores of HAMD-17 at baseline and after treatment were 6.60±1.87 and 5.85±4.18,scores of HAMA were 6.36±3.02 and 4.93±3.09,scores of CGI-S were 1.49±0.56 and 1.29±0.81,scores of ASEX were 15.92±4.72 and 15.57±5.26,with significant difference(P＜0.05).After continuation treatment,the remission rate was 54.59％(202 cases/370 cases),and the recurrence rate was 6.49％(24 cases/370 cases),the recurrence time was(64.67±42.47)days.The incidence of treatment-related adverse events was 15.35％(64 cases/417 cases).Conclusion Morinda officinalis oligosaccharides capsules can be effectively used for the continuation treatment of mild and moderate depression,and are well tolerated and safe.

Objective:To investigate the effect of single nucleotide polymorphism (SNP) of FCN gene on the susceptibility of pre-eclampsia (PE) in Han nationality pregnant women.Methods:A total of 274 PE pregnant women (PE group) and 154 healthy pregnant women (control group) admitted to Boai Hospital of Zhongshan, Affiliated Hospital to Southern Medical University from October 2020 to October 2022 were collected. The general information, medical history, reproductive history, blood pressure, body mass index and blood biochemical indicators before delivery were compared between the two groups. Twenty-three SNP loci of FCN gene family were genotyped by time-of-flight mass spectrometry, and the serum levels of ficolins (ficolin-1, -2 and -3) were detected by enzyme-linked immunosorbent assay.Results:(1) Compared with the control group, the body mass index, mean arterial pressure, gestational age at delivery, blood urea nitrogen, alanine aminotransferase, aspartate aminotransferase, direct bilirubin, albumin, and C-reactive protein in the PE group were significantly higher than those in the control group (all P<0.05). The levels of N-terminal pro-B type natriuretic peptide (NT-proBNP), placental growth factor (PlGF) and human soluble vascular endothelial growth factor receptor-1 (sFlt-1) were significantly different between the two groups (all P<0.05). (2) Among the 23 SNP loci in FCN gene family, 18 loci were in Hardy-Weinberg genetic equilibrium, including 5 loci in FCN1 gene, 10 loci in FCN2 gene, and 3 loci in FCN3 gene. Five loci that did not conform to Hardy-Weinberg genetic equilibrium were not included in the subsequent analysis. Compared with the control group, the genotype distribution of 3 loci of FCN2 gene (rs7872508, rs11103563, rs73664188) and 1 locus of FCN3 gene (rs3813800) in the PE group were significantly different (all P<0.05). After Bonferroni correction, only the genotype distribution of rs7872508 and rs73664188 in FCN2 gene were statistically different between the PE group and the control group (all P<0.05). Further analysis showed that for the rs7872508 locus of FCN2 gene, compared with GG genotype, genotype GT ( OR=3.025, 95% CI: 1.080-8.471) and TT ( OR=4.777, 95% CI: 1.758-12.979) both significantly increased the risk of PE (both P<0.05). For rs73664188 locus of FCN2 gene, compared with TT genotype, genotype TC ( OR=0.510, 95% CI: 0.334-0.778) significantly reduced the risk of PE ( P<0.05). (3) Compared with the control group, the serum levels of ficolin-1 and ficolin-2 in pregnant women in the PE group were significantly reduced (both P<0.05), while the level of ficolin-3 showed no significant change ( P=0.271). Correlation analysis showed that the serum levels of ficolin-2 in pregnant women in the PE group were significantly positively correlated with PlGF level ( r=0.321, P<0.001), and significantly negatively correlated with sFlt-1 level ( r=-0.187, P=0.002) and NT-proBNP level ( r=-0.392, P<0.001). Further analysis revealed that the serum levels of ficolin-2 in pregnant women of the PE group with GT and TT genotypes at rs7872508 locus of FCN2 gene were significantly reduced (both P<0.05), while the serum level of ficolin-2 in pregnant women of the PE group with TC genotype at the rs73664188 locus were significantly increased ( P<0.05). Conclusion:The SNP of FCN2 gene in FCN gene family might be related to the susceptibility to PE and have an effect on serum ficolin-2 level in PE pregnant women.

Objective To explore the effects of circ_100284 in affecting the invasion of esophageal squamous cell carcinoma(ESCC)cells and their sensitivity to 5-fluorouracil(5-FU)chemotherapy via regulating miR-217/mitogen-activated protein kinase 1(MAPK1)acting as a competing endogenous RNA(ceRNA).Methods The bioinformatics approach was used to analyze the differentially expressed circRNAs in ESCC.qRT-PCR was used to detect the expression of circ_100284 in ESCC tissues and cells.The 5-FU-resistant KYSE450 cell line(KYSE45-R)was established by increasing concentrations of 5-FU.The IC50 of 5-FU in KYSE450 and KYSE450-R cells was determined through MTT assay.qRT-PCR was used to detect the expression of circ_100284,miR-217,and MAPK1 mRNA in KYSE450 and KYSE450-R cells,while Western blotting detecting the protein expression of MAPK1.In the experiments with KYSE450-R cells,we set up the following groups:(1)blank group(without treatment),si-NC group(transfected with si-NC),si-circ_100284 group(transfected with si-circ_100284),pc-Control group(transfected with pc-Control),pc-circ_100284 group(transfected with pc-circ_100284),pc-circ_100284+mimic NC group(transfected with pc-circ_100284 and mimic NC),and pc-circ_100284+miR-217 mimic group(transfected with pc-circ_100284 and miR-217 mimic).These groups were subjected to MTT assay to detect cell viability,Transwell assay to detect cell invasion,and flow cytometry to detect cell apoptosis.(2)Blank group(without treatment),si-NC group(transfected with si-MAPK1 negative control),si-MAPK1 group(transfected with si-MAPK1),si-MAPK1+inhibitor NC group(transfected with si-MAPK1 and inhibitor NC),and si-MAPK1+miR-217 inhibitor group(transfected with si-MAPK1 and miR-217 inhibitor).We detected the mRNA and protein expression of MAPK1 using qRT-PCR and Western blotting.We evaluated cell viability using MTT assay,invasion with Transwell assay,and apoptosis by flow cytometry.circ_100284-WT or circ_100284-MUT reporter plasmids,as well as MAPK1-WT or MAPK1-MUT reporter plasmids,were co-transfected with miR-NC or miR-217 mimic into KYSE450-R cells for 48 h,and dual luciferase reporter assay was used to measure luciferase activity.Results The bioinformatics analysis revealed significant upregulation of circ_100284 in ESCC.Compared with adjacent normal tissues,the expression of circ_100284 in ESCC tissues is enhanced(P<0.05);compared with the HECC cells,the TE-11,ECA109 and KYSE450 ESCC cell lines showed enhanced expression of circ_100284(P<0.05).Compared with the KYSE450 cells,KYSE450-R cells demonstrated increased IC50 with enhanced expression of circ_100284 and MAPK1 but suppressed expression of miR-217(P<0.05).Compared with the si-NC group,the si-circ_100284 group demonstrated inhibited invasion and proliferation of cells with increased apoptosis(P<0.05).Compared with pc-Control group,the invasion and proliferation of cells in the pc-circ_100284 group are increased,and cell apoptosis is decreased(P<0.05).Over-expression of miR-217 reversed the malignant biological behavior of ESCC cells induced by pc-circ_100284(P<0.05).Compared with si-NC group,in the si-MAPK1 group,we observed decreased cell invasion and proliferation,and increased apoptosis(P<0.05),but miR-217 inhibitor reversed the effect of si-MAPK1 on the biological behavior of ESCC cells(P<0.05).The targeting relationship of circ_100284 and miR-217,miR-217 and MAPK1 is confirmed.Conclusion circ_100284 promotes ESCC cell invasion by regulating miR-217/MAPK1,inhibits the chemosensitivity of ESCC cells to 5-FU,and acts as a tumor-promoting factor in ESCC.

2-(4-Methylthiazol-5-yl) ethyl nitrate hydrochloride (W1302) is a nitro containing derivative of clomethiazole, which is a novel neuroprotective agent with both carbon monoxide (NO) donor and weak γ-aminobutyric acid type A (GABA_A) receptor allosteric regulatory excitatory effect. The current study used a rat model of transient middle cerebral arteryocclusion (tMCAO) brain injury to evaluate the therapeutic effect of W1302 on ischemic stroke and explore its potential mechanisms of action. This experiment has been reviewed and approved by the Laboratory Animal Management and Use Committee of the Institute of Materia Medica, Chinese Academy of Medical Sciences (ethical review forms No. 620, 632, 5013). The results showed that gavage administration of 1, 3, and 10 mg·kg^-1 of W1302 can significantly reduce the volume of cerebral infarction in rats with ischemia for 2 h and reperfusion for 24 h, and the therapeutic effect was better than that of 200 mg·kg^-1 of DL-3n-butylphthalide. W1302 significantly increased NO levels in blood and brain tissue. It increased cerebral blood flow and brain adenosine triphosphate (ATP) content after reperfusion, as well as, inhibited the expressions of inflammatory factors tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) in brain tissue. The time window of W1302 was between 120-180 min after ischemia. These research results demonstrated that W1302 could increase NO release, dilate blood vessels, and increase cerebral blood flow, improve energy supply to brain tissue and increase ATP levels, and inhibit neuro-inflammation, which playing the protective roles in tMCAO stroke model rats. This provides theoretical support for the clinical application of W1302 in the treatment of ischemic stroke.

Objective:To analyze clinical, immunopathological, therapeutic, and prognostic features of epidermolysis bullosa acquisita (EBA) .Methods:A retrospective study was conducted on patients with confirmed EBA at the Department of Dermatology, West China Hospital, Sichuan University from January 1, 2015 to July 30, 2022. Their clinical, immunopathological, therapeutic and prognostic features were analyzed. The autoimmune bullous skin disorder intensity score (ABSIS) was used to assess the severity of lesions in patients with EBA, and the visual analogue scale (VAS) to assess itch intensity. Descriptive statistical analysis was primarily carried out, and the correlation between disease severity scores and itch scores was analyzed using Pearson correlation analysis.Results:A total of 13 patients with EBA were included, including 9 males and 4 females, with the age at the clinic visit being 49.0 ± 20.6 years and ABSIS scores being 24.2 ± 10.7 points. One patient was diagnosed with classical EBA, while the remaining 12 patients with inflammatory EBA. Mucosal involvement was observed in 6 cases, whose oral mucosae were all affected. All patients had itching to varying degrees, with VAS scores of 5.6 ± 2.2 points; 9 of the 12 inflammatory EBA patients had VAS scores of ≥ 5 points, whereas 1 classical EBA patient had a VAS score of 2 points; there was no significant correlation between the ABSIS scores and VAS scores ( r = -0.02, P > 0.05). Histopathological examination showed subepidermal cleavages or blister formation and varying degrees of perivascular inflammatory cell infiltration in the superficial dermis of patients with inflammatory EBA. Direct immunofluorescence assay demonstrated linear IgG deposits along the basement membrane zone in all 13 patients, including 12 with concomitant linear C3 deposits in the basement membrane zone, 5 with linear IgA deposits, and 2 with IgM deposits. Indirect immunofluorescence on salt-split skin showed IgG deposition on the dermal side of the salt-split skin in the 13 patients. An elevated eosinophil count in the peripheral blood was observed in 1 out of 11 patients, while increased total IgE levels were noted in 3 out of 9 patients. Among the 13 EBA patients, 11 were treated with systemic glucocorticoids (equivalent to 10 - 100 mg/d of prednisone), and the other 2 were treated with compound glycyrrhizin tablets, sulfasalazine, hydroxychloroquine sulfate, and minocycline hydrochloride alone or in combination. During the follow-up period of 34.0 (27.5, 66.0) months in the 13 patients, 8 achieved complete remission after drug withdrawal, 2 achieved complete remission on therapy, 1 achieved partial remission on minimal therapy, and 2 presented with uncontrolled condition. The time to complete remission off/on therapy was 6.0 (3.8, 17.5) months. Conclusions:The inflammatory phenotype seems to be relatively common in EBA patients, with itching to varying degrees, and oral mucosa was the most commonly involved mucosa in those with mucosal damage. After treatment with systemic glucocorticoids alone or in combination with immunomodulators, most patients could achieve complete remission.

Objective: To develop a quantitative evaluation software for three-dimensional morphology of pathological scars based on photo modeling technology, and to verify its accuracy and feasibility in clinical application. Methods: The method of prospective observational study was adopted. From April 2019 to January 2022, 59 patients with pathological scars (totally 107 scars) who met the inclusion criteria were admitted to the First Medical Center of Chinese PLA General Hospital, including 27 males and 32 females, aged 33 (26, 44) years. Based on photo modeling technology, a software for measuring three-dimensional morphological parameters of pathological scars was developed with functions of collecting patients' basic information, and scar photography, three-dimensional reconstruction, browsing the models, and generating reports. This software and the clinical routine methods (vernier calipers, color Doppler ultrasonic diagnostic equipment, and elastomeric impression water injection method measurement) were used to measure the longest length, maximum thickness, and volume of scars, respectively. For scars with successful modelling, the number, distribution of scars, number of patients, and the longest length, maximum thickness, and volume of scars measured by both the software and clinical routine methods were collected. For scars with failed modelling, the number, distribution, type of scars, and the number of patients were collected. The correlation and consistency of the software and clinical routine methods in measuring the longest length, maximum thickness, and volume of scars were analyzed by unital linear regression analysis and the Bland-Altman method, respectively, and the intraclass correlation coefficients (ICCs), mean absolute error (MAE), and mean absolute percentage error (MAPE) were calculated. Results: A total of 102 scars from 54 patients were successfully modeled, which located in the chest (43 scars), in the shoulder and back (27 scars), in the limb (12 scars), in the face and neck (9 scars), in the auricle (6 scars), and in the abdomen (5 scars). The longest length, maximum thickness, and volume measured by the software and clinical routine methods were 3.61 (2.13, 5.19) and 3.53 (2.02, 5.11) cm, 0.45 (0.28, 0.70) and 0.43 (0.24, 0.72) cm, 1.17 (0.43, 3.57) and 0.96 (0.36, 3.26) mL. The 5 hypertrophic scars and auricular keloids from 5 patients were unsuccessfully modeled. The longest length, maximum thickness, and volume measured by the software and clinical routine methods showed obvious linear correlation (with r values of 0.985, 0.917, and 0.998, P<0.05). The ICCs of the longest length, maximum thickness, and volume of scars measured by the software and clinical routine methods were 0.993, 0.958, and 0.999 (with 95% confidence intervals of 0.989-0.995, 0.938-0.971, and 0.998-0.999, respectively). The longest length, maximum thickness, and volume of scars measured by the software and clinical routine methods had good consistency. The Bland-Altman method showed that 3.92% (4/102), 7.84% (8/102), and 8.82% (9/102) of the scars with the longest length, maximum thickness, and volume respectively were outside the 95% consistency limit. Within the 95% consistency limit, 2.04% (2/98) scars had the longest length error of more than 0.5 cm, 1.06% (1/94) scars had the maximum thickness error of more than 0.2 cm, and 2.15% (2/93) scars had the volume error of more than 0.5 mL. The MAE and MAPE of the longest length, maximum thickness, and volume of scars measured by the software and clinical routine methods were 0.21 cm, 0.10 cm, 0.24 mL, and 5.75%, 21.21%, 24.80%, respectively. Conclusions: The quantitative evaluation software for three-dimensional morphology of pathological scars based on photo modeling technology can realize the three-dimensional modeling and measurement of morphological parameters of most pathological scars. Its measurement results were in good consistency with those of clinical routine methods, and the errors were acceptable in clinic. This software can be used as an auxiliary method for clinical diagnosis and treatment of pathological scars.
Female ; Humans ; Male ; Asian People ; Cicatrix, Hypertrophic/diagnostic imaging* ; Extremities ; Keloid/diagnostic imaging* ; Prospective Studies ; Adult

Obstructive sleep apnea hypopnea syndrome (OSAHS) is a common sleep respiratory disorder characterized by upper respiratory collapse during sleep, with a high prevalence and potentially fatal complications. Currently, maxillary transverse deficiency are considered to be an important pathogenic factor of OSAHS. For patients with poor compliance with positive airway pressure therapy, rapid maxillary expansion can increase the volume and ventilation of the upper respiratory tract, which is an alternative treatment. This paper reviewed the current research on surgically assisted rapid palatal expansion, miniscrew assisted rapid palatal expansion, and distraction osteogenesis maxillary expansion in the treatment of adult OSAHS. By comparing the indications, contraindications, complications, efficacy and long-term stability of the three treatment methods, it provided reference for treatment of patients with OSAHS.
Adult ; Humans ; Nose ; Palatal Expansion Technique ; Palate ; Sleep Apnea, Obstructive/surgery* ; Syndrome

OBJECTIVE: To analyze the characteristics and prognosis of acute leukemia(AL) with SET-NUP214 fusion gene. METHODS: The clinical data of 17 patients over 14 years old newly diagnosed with SET-NUP214 positive AL admitted in Institute of Hematology and Blood Diseases Hospital from August 2017 to May 2021 were analyzed retrospectively. RESULTS: Among the 17 SET-NUP214 positive patients, 13 cases were diagnosed as T-ALL (ETP 3 cases, Pro-T-ALL 6 cases, Pre-T-ALL 3 cases, Medullary-T-ALL 1 case), AML 3 cases (2 cases M5, 1 case M0) and ALAL 1 case. Thirteen patients presented extramedullary infiltration at initial diagnosis. All 17 patients received treatment, and a total of 16 cases achieved complete remission (CR), including 12 cases in patients with T-ALL. The total median OS and RFS time were 23 (3-50) months and 21 (0-48) months, respectively. Eleven patients received allogeneic hematopoietic stem cell transplantation(allo-HSCT), with median OS time of 37.5 (5-50) months and median RFS time of 29.5 (5-48) months. The median OS time of 6 patients in chemotherapy-only group was 10.5 (3-41) months, and median RFS time of 6.5 (3-39) months. The OS and RFS of patients with transplantation group were better than those of chemotherapy-only group (P=0.038). Among the 4 patients who relapsed or refractory after allo-HSCT, the SET-NUP214 fusion gene did not turn negative before transplantation. While, in the group of 7 patients who have not relapsed after allo-HSCT till now, the SET-NUP214 fusion gene expression of 5 patients turned negative before transplantation and other 2 of them were still positive. CONCLUSION The fusion site of SET-NUP214 fusion gene is relatively fixed in AL patients, often accompanied by extramedullary infiltration. The chemotherapy effect of this disease is poor, and allo-HSCT may improve its prognosis.
Humans ; Adolescent ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ; Retrospective Studies ; Leukemia, Myeloid, Acute/therapy* ; Hematopoietic Stem Cell Transplantation ; Acute Disease ; Prognosis ; Leukemia-Lymphoma, Adult T-Cell/therapy* ; Nuclear Pore Complex Proteins