This review provides a comprehensive summary of the latest advancements in high-throughput protein structural bioinformatics, a field that has undergone a revolutionary transformation with the advent of deep learning-based protein structure prediction systems like AlphaFold2. These systems have significantly increased the accuracy, speed, and scale of protein structure prediction, resulting in an exponential growth in the number of protein structures available for analysis. Notably, the AlphaFold Protein Structure Database (AFDB) has amassed over 214 million protein structures, surpassing the PDB’s 50-year cumulative data by over 1 000-fold within several months. Big data is driving the comprehensive upgrade of protein structural bioinformatics. This review focuses on three main areas: structure data management, tool development, and structure data mining. In the realm of structure data management, the review spotlights the optimization strategy of AlphaFold-like systems, which significantly reduces the resource requirements for protein folding, enabling more researchers to make custom structure predictions and further enlarging the data scale. The resulting “data explosion” has exerted increased pressure on storage and bandwidth, prompting the development of cutting-edge tools such as Foldcomp, PDC, and ProteStAr for compressing PDB files. Moreover, the review underscores the critical role of public repositories like ModelArchive and PDB-Dev in archiving and sharing third-party AlphaFold models. It also highlights the utilization of independent services like MineProt and 3D-Beacons to create more interactive and accessible data portals. In terms of tool development, the review spotlights recent breakthroughs in structure alignment algorithms, represented by Foldseek, which enable ultra-fast searching of large protein structure databases. It also covers tools for functional annotation of proteins based on their structures, including AlphaFill for ligand annotation, DeepFRI for Gene Ontology (GO) annotation, TT3D for protein-protein interaction (PPI) prediction, among others. It is proposed that 3Di sequences born concurrently with Foldseek can enhance many sequence-based deep learning models developed in the pre-AlphaFold era, enabling them to be applied to structure-based function prediction. The challenges on traditional molecular docking methods in the high-throughput era are mentioned at last, in a gesture to arouse the attention of researchers. Finally, the review explores the burgeoning field of structure data mining. Whole proteome structuring has become feasible in recent years, and scientists are processing large structure datasets from an omics viewpoint, continuously identifying analyzable elements and optimizing methodologies, as well as utilizing newly developed tools to push the boundaries. Notable examples include the identification of new protein families, the development of protein structure clustering, and the integration of AlphaFold with conventional experimental techniques to solve large structures. These advancements are paving the way for a deeper understanding of protein structure and function and have the potential to unlock new discoveries in the life sciences. However, the review also acknowledges the challenges and limitations that persist in the field, including the lack of diversity in high-throughput software for protein structural bioinformatics and the existing bottleneck in rapidly predicting protein complex structures. Overall, structural bioinformatics is expected to play an even more crucial role in the life sciences with the development of high-throughput methodology.

OBJECTIVE: To compare the clinical efficacy between the combined therapy of fire needling and cupping, and western medication on herpes zoster of acute stage, as well as the effects on Th17 and Treg cells and inflammatory factors, i.e. IL-10 and IL-17 in the peripheral blood. METHODS: Eighty patients with herpes zoster of acute stage were randomly divided into a combined therapy (fire needling plus cupping) group and a western medication group, 40 cases in each one. In the combined therapy group, the pricking and scattering techniques with fire needle were used at ashi points and Jiaji (EX-B 2) corresponding to the affected spinal segments; afterwards, cupping therapy was delivered. The combined treatment was given once daily. In the western medication group, valaciclovir hydrochloride tablet and vitamin B₁ tablet were administered orally. The duration of treatment in each group was 10 days. Before each treatment from day 1 to day 10 and on day 11 , the score of symptoms and physical signs was observed in the two groups separately. Before each treatment from day 1 to day 10 and on day 11, 30, 60, the score of visual analogue scale (VAS) and skin lesion indexes were observed in the two groups. On day 60, the incidence of postherpetic neuralgia was recorded in the two groups. The levels of Th17 and Treg cells, Th17/Treg ratio in the peripheral blood, as well as serum levels of IL-10 and IL-17 were detected before and after treatment in the two groups. The clinical efficacy was compared between the two groups. RESULTS: From day 6 to day 10 during treatment and on day 11, the scores of symptoms and physical signs in the combined therapy group were lower than those of the western medication group (P<0.05, P<0.01). On day 3, day 6 to day 10 during treatment and day 11, day 30, VAS scores in the combined therapy group were lower than those of the western medication group (P<0.05, P<0.01). On day 60, the incidence of postherpetic neuralgia in the combined therapy group was lower compared with that in the western medication group (P<0.05). The blister arresting time and scabbing time in the combined therapy group were shorter than those of the western medication group (P<0.05). After treatment, the level of Th17, and Th17/Treg ratio in the peripheral blood, as well as the serum levels of IL-10 and IL-17 were all lower in comparison with those in the western medication group (P<0.05). The curative and remarkably effective rate was 82.5% (33/40) in the combined therapy group, higher than 62.5% (25/40) in the western medication group (P<0.05). CONCLUSION The early application of fire needling combined with cupping therapy can effectively treat herpes zoster of acute stage, relieve pain, and reduce the incidence of postherpetic neuralgia, which may be related to reducing the levels of Th17 and Treg cells, and Th17/Treg ratio in the peripheral blood, as well as the serum levels of IL-10 and IL-17 so that the cellular immune balance is modulated.
Humans ; Neuralgia, Postherpetic ; Acupuncture Therapy/methods* ; Interleukin-10 ; Interleukin-17 ; T-Lymphocytes, Regulatory ; Cupping Therapy ; Th17 Cells ; Herpes Zoster/therapy* ; Treatment Outcome ; Tablets

China/epidemiology* ; Forecasting ; Humans ; Incidence ; Scarlet Fever/epidemiology*

Objective:To characterize and compare the chemical information of four extracts of Qingre Chushi (QRCS) decoction by liquid chromatography-mass spectrometry (LC-MS), and combine the chemical information of the four extracts with their results of anti-inflammatory effect for a multivariate statistical analysis, in order to identify the compounds directly relating to the anti-inflammatory effects of QRCS decoction. Method:Four extracts of QRCS decoction were characterized by UPLC-Q-TOF-MS:①ethanol extract+water extract,② ethanol extract+supernatant after water extraction and alcohol precipitation, ③ ethanol extract+precipitation after water extraction and alcohol precipitation,and ④ standard decoction. On the basis of the results of inhibition of the four above extracts on xylene-induced ear swelling in mice,multivariate statistical analysis[principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA)] were carried out to lock the chromatographic peaks with significant differences between group ① (the best pharmacological action group) and group ④ (standard decoction group). According to the accuracy of quasi-molecular ion and fragment ion data,and the reference materials and literature data,those chromatographic peaks were identified. Result:PCA could cluster the four extracts of QRCS decoction,and the differences between groups was reflected in the distance between groups. Group ④ (standard decoction) had the most significant differences with the other three groups, especially in the first principal component; group ① (ethanol extract+water extract),group ② (ethanol extract+supernatant after water extraction and ethanol precipitation) and group ③ (ethanol extract+precipitation after water extraction and ethanol precipitation) had certain differences in the second principal component. OPLS-DA was used to compare group ① (the best pharmacological action group) and group ④ (standard decoction group). Eleven chromatographic peaks with great contribution and high reliability to group differences,were identified as gentiopicrin,skimmin,baicalin,baicalin isomer,wogonoside,5,6,7-trihydroxy-8-methoxyflavone-7-O-glucurodonaldehyde,5,6-dihydroxy-6,8,2',3'-tetramethoxyflavone,salicin-6-C-arabinose-8-C-glucoside,plantamajoside and glycyrrhizic acid. Conclusion:In the mode of pectrum-effect combination, this study explores and identifies compounds relating to the anti-inflammatory effect of QRCS decoction,so as to provide the basis for screening the extraction and purification process and optimizing the formulation of preparation of Qingre Chushi decoction.

Objective To investigate the effect of fluacrypyrim on the induction of apoptosis in human acute myeloid leuke-mia(AML)cell lines,NB4,THP-1 and HL-60,and explore the related mechanisms.Methods Trypan blue dye exclusion assay was used to estimate the growth of NB4,THP-1,and HL-60 cells after treatment with various concentrations of fluacrypyrim(1.25, 2.5,5 and 7.5 μmol/L)for 72 h.Cell apoptosis was evaluated by AnnexinⅤ-FITC/PI double stainning for the NB4 and THP-1 cells treated with fluacrypyrim(1.25,2.5 and 5 μmol/L)for 48 h as well as the HL-60 cells treated with fluacrypyrim(2.5,5 and 7.5 μmol/L) for 72 h.Western blotting was used to examine the protein expression of apoptotic regulators Bax,Mcl-1 and Caspase 3 in the NB4 cells treated with fluacrypyrim(1.25,2.5 and 5 μmol/L)for 24 h.Then,NB4 Cells were pretreated with Caspases inhibitor benzyloxy-carbonyl-Val-Ala-Asp-fluoromethylketone(Z-VAD-FMK)and exposed to fluacrypyrim at 2.5 μmol/L for 24 h,which was then evaluat-ed for the apoptosis using AnnexinⅤ-FITC/PI double stainning.Western blotting was used to examine the expression of the phosphory-lated and total proteins of mitogen-activated protein kinase(MAPK)signaling molecules,ERK,JNK and P38,in the NB4 cells treat-ed with fluacrypyrim(1.25,2.5 and 5 μmol/L)for 24 h. NB4 Cells were pretreated with ERK inhibitor U0126,JNK inhibitor SP600125,or P38 inhibitor SB203580 for 1 h and then exposed to fluacrypyrim at 2.5 μmol/L for 24 h,which was then analyzed for the apoptosis by the AnnexinⅤ-FITC/PI double stainning.Results The proliferation of NB4,THP-1 and HL-60 cells was inhibited by the treatment with fluacrypyrim(2.5,5 and 7.5 μmol/L)for 72 h.The apoptosis induced in the NB4 and THP-1 cells by the fluacry-pyrim treatment at 5 μmol/L for 48 h and in the HL-60 cells by the fluacrypyrim treatment at 7.5 μmol/L for 72 h were significant as compared with the control group(P<0.01).Mechanically,fluacrypyrim at the concentrations of 2.5 and 5 μmol/L effectively up-regu-lated the expression of Bax(P<0.01 and P<0.05)for the 2.5 and 5 μmol/L,respectively,down-regulated the expression of Mcl-1 (P<0.01)and activated Caspase 3(P<0.01)in the NB4 cells when compared with the control group(P<0.01).The pretreatment of the NB4 cells with Z-VAD-FMK blocked the apoptosis induced by fluacrypyrim.Furthermore,the fluacrypyrim(2.5 and 5 μmol/L) treatment increased the ERK,JNK and P38 phosphorylation(P<0.01),while the pretreatment of the NB4 cells with U0126 signifi-cantly inhibited the the fluacrypyrim-induced apoptosis(P<0.01),as compared with the control group.Conclusion Fluacrypyrim effectively inhibits the cell proliferation and induces caspase-dependent cell apoptosis in AML cells.Activation of ERK/MAPK signal-ing pathway might play an important role in the action of fluacrypyrim.

To know the status of Enterobius vermicularis infection in children in Jiangxi Province in 2014, so as to provide the evidence for the formulation of prevention and control measures.A survey was performed according to the scheme of the 3rd Principal Human Parasites of Jiangxi Province in 2014. Based on the ecological regions, a stratified cluster sampling method was applied by the economic and geographic situation. There were 84 survey sites from 28 counties, and the basic data were also collected in the different investigation sites, and the round-end tube adhesive cellophane anal swab was used to examine E. vermicularis eggs for the children aged 3–6 years.A total of 1 486 children aged 3-6 years were detected, the E. vermicularis infection rate was 13.73% (204/1 486), and the infection rates were 13.89% (114/821) and 13.53% (90/665) in the male and female, respectively. The infection rate in the different age groups showed a gradual rise then fall trend, the lowest infection rate was 10.05% (38/378) in the 3-year age group, and the highest infection rate was 18.24% (81/444) in the 5-year age group. The infection rates in the high, medium and low-income survey sites were 13.79% (87/631), 17.23% (51/296), and 11.81% (66/559), respectively. The E. vermicularis infection rates in the 4 ecological regions were from 12.34% to 17.74%, but there was no significant difference among the different ecological regions (P > 0.05).The status of E. vermicularis infection in children in Jiangxi Province is relatively serious, and therefore, the parasitic disease control sectors should continue to strengthen the monitoring and control work of E. vermicularis infection in children.

BACKGROUNDMigrations have been reported to be associated with the high risk of tuberculosis (TB), but there is no systematic analysis of the available data for TB among migrant in China. The aim of this study was to examine the notification rate of active and sputum smear-positive TB by a systematic review and meta-analysis.

METHODSA systematic review and meta-analysis were performed to examine the notification rate of active and sputum smear-positive TB among migrants in China. Two reviewers searched the cross-sectional studies published in PubMed, EMBASE, SciFinder, and Web of Science in English and in CNKI and Wanfang databases in Chinese. Pooled estimates of notification rate of TB among migrants were calculated using a random effects model. Meta-regression analysis and subgroup analysis stratified by year, region were also performed.

RESULTSSeventy eligible studies met the inclusion criteria for the final analysis. The overall notification rate of active TB and sputum smear-positive cases among migrants were 53.12 (95% confidence interval [CI]: 47.32-59.63) and 24.53 (95% CI: 22.01-27.34) per 100,000 populations, respectively. The notification rate of active TB significantly increased from 50.95 (95% CI: 41.11-63.14) per 100,000 populations in 2005 to 84.62 (95% CI: 78.00-91.80) per 100,000 populations in 2014 while that of smear-positive TB was constant during the study time (P = 0.79). The geographic difference was identified both for active and sputum smear-positive TB, with the higher notification rates mainly distributing along the eastern coastal areas.

CONCLUSIONSThe pooled estimate of active TB and sputum smear-positive TB among migrants was lower than the national notification rate among general population, but the gap between our data and national notification rate among general population is narrowed down during 2005-2014.

China ; epidemiology ; Cross-Sectional Studies ; Female ; Humans ; Male ; Sputum ; microbiology ; Transients and Migrants ; statistics & numerical data ; Tuberculosis ; epidemiology

OBJECTIVETo investigate the effect of intermittent fasting on metabolize and gut microbiota in obese presenium rats fed with high-fat-sugar-diet.

METHODSWe fed the Wistar rats with high-fat and high-sugar diet to induce adiposity, and the rats for intermittent fasting were selected base on their body weight. The rats were subjected to fasting for 72 h every 2 weeks for 18 weeks. OGTT test was performed and fasting blood samples and fecal samples were collected for measurement of TC, TG, HDL-C and LDL-C and sequence analysis of fecal 16S rRNA V4 tags using Illumina. Gut microbial community structure was analyzed with QIIME and LEfSe.

RESULTSAfter the intervention, the body weight of the fasting rats was significantly lower than that in high-fat diet group (P<0.01). OGTT results suggested impairment of sugar tolerance in the fasting group, which showed a significantly larger AUC than compared with the high-fat diet group (P<0.05). Intermittent fasting significantly reduced blood HDL-C and LDL-C levels (P<0.05) and partially restored liver steatosis, and improved the gut microbiota by increasing the abundance of YS2, RF32 and Helicobacteraceae and reducing Lactobacillus, Roseburia, Erysipelotrichaceae and Ralstonia. Bradyrhizobiaceae was found to be positively correlated with CHOL and HDL-C, and RF39 was inversely correlated with the weight of the rats.

CONCLUSIONIntermittent fasting can decrease the body weight and blood lipid levels and restore normal gut microbiota but can cause impairment of glucose metabolism in obese presenium rats.

Animals ; Body Weight ; Diet, High-Fat ; Fasting ; Fatty Liver ; microbiology ; physiopathology ; Gastrointestinal Microbiome ; Lipids ; blood ; Obesity ; microbiology ; physiopathology ; RNA, Ribosomal, 16S ; Rats ; Rats, Wistar

BACKGROUNDDihydropyrimidine dehydrogenase (DPD), a key enzyme involved in the catabolism of 5-fluorouracil (5-FU), is the attractive candidate for pharmacogenetic research on efficacies and toxicities of 5-FU. The aim of this study is to explore the association between polymorphisms of dihydropyrimidine dehydrogenase gene (DPYD) and clinical outcomes of gastric cancer patients treated with fluorouracil-based adjuvant chemotherapy in the Chinese population.

METHODSThree hundred and sixty-two patients with gastric cancer in the Chinese population were treated with fluorouracil-based adjuvant chemotherapy. The single nucleotide polymorphic genotypes of DPYD were determined by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) using DNA samples isolated from peripheral blood collected before treatment.

RESULTSThe average response rate for chemotherapy was 46.7%. A significantly different distribution of the rs1801159 (c2=8.76, P=0.012) genotypes was observed. Homozygous genotype rs1801159A/A was over-represented in responsive patients. Conversely, carriers of the rs1801159A/G genotype were prevalent in non-responsive patients. In the haplotype association analysis, there was significant difference in global haplotype distribution between the groups (c2=3.96, P=0.0465).

CONCLUSIONSThese results suggest that polymorphisms of rs1801159 in DPYD may be used as valuable predictors of the response to fluorouracil-based chemotherapy for gastric cancer patients in the Chinese population. Well-designed, comprehensive, and prospective studies on determining these polymorphisms of DPYD as predictive markers for gastric cancer in response to fluorouracil-based therapies are warranted.

Adolescent ; Adult ; Aged ; Aged, 80 and over ; Asian Continental Ancestry Group ; Chemotherapy, Adjuvant ; methods ; Dihydrouracil Dehydrogenase (NADP) ; genetics ; Female ; Fluorouracil ; therapeutic use ; Genotype ; Humans ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; genetics ; Stomach Neoplasms ; drug therapy ; genetics ; Treatment Outcome ; Young Adult

BACKGROUNDThe cytosine arabinoside (Ara-C)-based chemotherapy is the major remedial measure for acute myeloid leukemia (AML). Deoxycytidine kinase (DCK) and cytidine deaminase (CDA) are the key enzymes in the metabolism of Ara-C. Many single nucleotide polymorphisms (SNPs) and haplotypes of DCK and CDA, which contribute to susceptibility to Ara-C, have been identified in Africans and Europeans. However, there has been no report about the relation among three SNPs in DCK (rs115543896, rs72552079, and rs111454937) and two SNPs in CDA (rs2072671 and rs60369023), and their clinical response to Ara-C for a Chinese population. In this study, we aimed to investigate whether these five SNPs are associated with the therapeutic outcomes of Ara-C-based chemotherapy regimens in patients with AML.

METHODSA total of 151 Chinese patients with AML were enrolled in our study. SNPs genotyping were performed using the MassARRAY system by means of the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) method.

RESULTSThe results illustrated that DCKrs111454937 AA genotype was more frequent in patients with higher platelet count, and A allele frequency was significantly higher in the group £40 years, lower white blood cell (WBC) count patients group and the group with platelet counts > 60'10(9)/L. Meanwhile, both DCKrs72552079 TC (OR = 1.225, 95%CI = 1.225 - 9.851, P = 0.0192) and CDArs60369023 GA (OR = 9.851, 95%CI = 1.31 - 77.93, P = 0.0263) significantly improved Ara-C-based chemotherapy response. While DCKrs11554389 AA (OR = 0.147, 95%CI = 0.027 - 0.801, P = 0.0267) was associated with the decrease of Ara-C-based chemotherapy response.

CONCLUSIONIt is evident that the DCK and CDA polymorphisms might be the important markers for the AML patients' therapy outcomes in a Chinese population.

Adolescent ; Adult ; Aged ; Aged, 80 and over ; Cytarabine ; therapeutic use ; Cytidine Deaminase ; genetics ; Deoxycytidine Kinase ; genetics ; Female ; Gene Frequency ; genetics ; Humans ; Leukemia, Myeloid, Acute ; drug therapy ; genetics ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Treatment Outcome ; Young Adult