Expression of Toll-like receptors in the cerebellum during pathogenesis of prion disease

Prion diseases, such as scrapie, entail the accumulation of disease-specific prion protein (PrPSc) within the brain. Toll-like receptors (TLRs) are crucial components of the pattern recognition system. They recognize pathogen-associated molecular patterns (PAMPs) and play a central role in orchestrating host innate immune responses. The expression levels of Toll-like receptors (TLRs) in the central nervous system (CNS) were not well-defined. To establish a model of prion diseases in BALB/C mice, the 22L strain was employed. The features of the 22L strain were analyzed, and the cerebellum exhibited severe pathological changes. TLR1-13 levels in the cerebellum were measured using quantitative polymerase chain reaction (qPCR) at time points of 60, 90, 120, and the final end point (145 days post-infection). During the pathogenesis, the expression levels of Toll-like receptors (TLRs) 1, 2, 7, 8, and 9 increased in a time-dependent manner. This trend mirrored the expression patterns of PrPSc (the pathological isoform of the prion protein) and glial fibrillary acidic protein. Notably, at the end point, TLR1-13 levels were significantly elevated. Protein level of TLR7 and TLR9 showed increasing at the end point of the 22L-infected mice. A deeper understanding of the increased Toll-like receptors (TLRs) in prion diseases could shed light on their role in initiating immune responses at various stages during pathogenesis. This insight is particularly relevant when considering TLRs as potential therapeutic targets for prion diseases.

[Role of mitochondrial autophagy and the curative effect of rehmannia glutinosa leaves total glycoside capsules on nucleos(t)ide drug-induced renal injury]

Objective: To study the curative effect of rehmannia glutinosa leaves total glycoside capsules and the role of mitochondrial autophagy on nucleos(t)ide drug-induced renal injury. Methods: Adefovir dipivoxil (ADV) was used to construct a hepatitis B virus (HBV) transgenic mouse model for renal injury. Renal function was measured in each group at one and two weeks of modeling. Mitochondrial autophagy indicators were measured at two weeks of modeling in renal tissue. Transmission electron microscopy was used to detect mitochondrial autophagy phenomena in renal tissue. The model was established for two weeks. Mouse with renal injury were treated with rehmannia glutinosa leaves total glycoside capsules or isotonic saline for eight weeks by intragastric administration. Renal function was measured. Renal tissue morphology was observed. Mitochondrial autophagy indicators were detected in renal tissue. The protective effect of different concentrations of verbascoside (the main active ingredient of rehmannia glutinosa capsule) was observed on HK-2 cell damage induced by ADV. HK-2 cells were divided into control, ADV, and ADV plus verbascoside groups. The effects of verbascoside at different times and concentrations were observed on the HK-2 mitochondrial autophagy indicators. Fifty patients with chronic hepatitis B were collected who presented with renal injury after treatment with nucleos(t)ide analogs. The random number method was used to divide 29 cases into a control group that received conventional treatment. The treatment group of 21 cases was treated with rehmannia glutinosa leaves total glycoside capsules on the basis of the control group. Serum creatinine (Scr) and urinary protein were detected at eight weeks.The χ(2) test or t-test was used for statistical analysis. Results: Compared with the control group, two weeks of modeling in the ADV group induced renal function injury in HBV mice. The expression of autophagy indicators was higher in the renal tissue of the ADV group than that of the control group. Transmission electron microscopy had revealed mitochondrial autophagy in the renal tissue of the ADV group. Compared with the control group, the renal function of HBV mice treated with rehmannia glutinosa leaves total glycoside capsules improved for two months, and the expressions of autophagy indicators were down-regulated.Verbascoside promoted proliferation in ADV-damaged HK-2 cells, and the expression of autophagy indicators was down-regulated compared with the ADV alone group. In 50 patients with renal function injury, the urinary protein improvement was significantly superior in the treatment group than that in the control group, with eighteen and three cases being effective and ineffective in the treatment group and 12 and 17 cases being effective and ineffective in the control group, with a statistically significant difference (χ(2) = 9.975 0, P = 0.001 6). Serum creatinine was decreased in the treatment group compared with the control group, with 11 and 10 cases being effective and ineffective in the treatment group and 12 and 17 cases being effective and ineffective in the control group, with no statistically significant difference (χ(2) = 0.593 5, P = 0.441 1). Conclusion: Rehmannia glutinosa leaves total glycoside capsule can improve the nucleos(t)ide drug-induced renal function injury in chronic hepatitis B, possibly playing a role via inhibiting PINK1/Parkin-mediated mitochondrial autophagy.

Optimization of binding affinities in chemical space with generative pre-trained transformer and deep reinforcement learning

Background

The key challenge in drug discovery is to discover novel compounds with desirable properties. Among the properties, binding affinity to a target is one of the prerequisites and usually evaluated by molecular docking or quantitative structure activity relationship (QSAR) models.

Methods

In this study, we developed SGPT-RL, which uses a generative pre-trained transformer (GPT) as the policy network of the reinforcement learning (RL) agent to optimize the binding affinity to a target. SGPT-RL was evaluated on the Moses distribution learning benchmark and two goal-directed generation tasks, with Dopamine Receptor D2 (DRD2) and Angiotensin-Converting Enzyme 2 (ACE2) as the targets. Both QSAR model and molecular docking were implemented as the optimization goals in the tasks. The popular Reinvent method was used as the baseline for comparison.

Results

The results on the Moses benchmark showed that SGPT-RL learned good property distributions and generated molecules with high validity and novelty. On the two goal-directed generation tasks, both SGPT-RL and Reinvent were able to generate valid molecules with improved target scores. The SGPT-RL method achieved better results than Reinvent on the ACE2 task, where molecular docking was used as the optimization goal. Further analysis shows that SGPT-RL learned conserved scaffold patterns during exploration.

Conclusions

The superior performance of SGPT-RL in the ACE2 task indicates that it can be applied to the virtual screening process where molecular docking is widely used as the criteria. Besides, the scaffold patterns learned by SGPT-RL during the exploration process can assist chemists to better design and discover novel lead candidates.

Phase I study of peposertib and avelumab with or without palliative radiotherapy in patients with advanced solid tumors

INTRODUCTION

We report results from a phase I, three-part, dose-escalation study of peposertib, a DNA-dependent protein kinase inhibitor, in combination with avelumab, an immune checkpoint inhibitor, with or without radiotherapy in patients with advanced solid tumors.

MATERIALS AND METHODS

Peposertib 100-400 mg twice daily (b.i.d.) or 100-250 mg once daily (q.d.) was administered in combination with avelumab 800 mg every 2 weeks in Part A or avelumab plus radiotherapy (3 Gy/fraction × 10 days) in Part B. Part FE assessed the effect of food on the pharmacokinetics of peposertib plus avelumab. The primary endpoint in Parts A and B was dose-limiting toxicity (DLT). Secondary endpoints were safety, best overall response per RECIST version 1.1, and pharmacokinetics. The recommended phase II dose (RP2D) and maximum tolerated dose (MTD) were determined in Parts A and B.

RESULTS

In Part A, peposertib doses administered were 100 mg (n = 4), 200 mg (n = 11), 250 mg (n = 4), 300 mg (n = 6), and 400 mg (n = 4) b.i.d. Of DLT-evaluable patients, one each had DLT at the 250-mg and 300-mg dose levels and three had DLT at the 400-mg b.i.d. dose level. In Part B, peposertib doses administered were 100 mg (n = 3), 150 mg (n = 3), 200 mg (n = 4), and 250 mg (n = 9) q.d.; no DLT was reported in evaluable patients. Peposertib 200 mg b.i.d. plus avelumab and peposertib 250 mg q.d. plus avelumab and radiotherapy were declared as the RP2D/MTD. No objective responses were observed in Part A or B; one patient had a partial response in Part FE. Peposertib exposure was generally dose proportional.

CONCLUSIONS

Peposertib doses up to 200 mg b.i.d. in combination with avelumab and up to 250 mg q.d. in combination with avelumab and radiotherapy were tolerable in patients with advanced solid tumors; however, antitumor activity was limited.

CLINICALTRIALS

GOV IDENTIFIER

NCT03724890.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024

The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulation of multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands and updates core database resources through big data archiving, integrative analysis and value-added curation. Importantly, NGDC collaborates closely with major international databases and initiatives to ensure seamless data exchange and interoperability. Over the past year, significant efforts have been dedicated to integrating diverse omics data, synthesizing expanding knowledge, developing new resources, and upgrading major existing resources. Particularly, several database resources are newly developed for the biodiversity of protists (P10K), bacteria (NTM-DB, MPA) as well as plant (PPGR, SoyOmics, PlantPan) and disease/trait association (CROST, HervD Atlas, HALL, MACdb, BioKA, BioKA, RePoS, PGG.SV, NAFLDkb). All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.

Expression of ICAM-1 and E-selectin in different metabolic obesity phenotypes: discrepancy for endothelial dysfunction

OBJECTIVES

Endothelial dysfunction, the earliest vascular alteration, is a consequence of metabolic disorders associated with obesity. However, it is still unclear whether a proportion of obese individuals without metabolic alterations associated with obesity, defined as "metabolically healthy obesity (MHO)", exhibit better endothelial function. We therefore aimed to investigate the association of different metabolic obesity phenotypes with endothelial dysfunction.

METHODS

The obese participants without clinical cardiovascular disease from the MESA (Multi-Ethnic Study of Atherosclerosis) were allocated to the different metabolic obesity phenotypes based on their metabolic status, including MHO and metabolically unhealthy obesity (MUO). Associations of metabolic obesity phenotypes with the biomarkers of endothelial dysfunction, including soluble intercellular adhesion molecule-1 (sICAM-1) and soluble E-selectin (sE-selectin), were evaluated using multiple linear regression models.

RESULTS

Plasma levels of sICAM-1 and sE-selectin were respectively measured in 2371 and 968 participants. Compared to the non-obese participants, those with MUO were associated with higher concentrations of sICAM-1 (β 22.04, 95% CI 14.33-29.75, P < 0.001) and sE-selectin (β 9.87, 95% CI 6.00-13.75, P < 0.001) after adjusting for confounders. However, no differences were found for the concentrations of sICAM-1 (β 0.70, 95% CI - 8.91 to 10.32, P = 0.886) and sE-selectin (β 3.69, 95% CI - 1.13 to 8.51, P = 0.133) in the participants with MHO compared to the non-obese participants.

CONCLUSIONS

Individuals with MUO were associated with elevated biomarkers of endothelial dysfunction, but the association with endothelial dysfunction was not found in those with MHO, indicating that the individuals with MHO might exhibit better endothelial function.

A unified method to revoke the private data of patients in intelligent healthcare with audit to forget

Revoking personal private data is one of the basic human rights. However, such right is often overlooked or infringed upon due to the increasing collection and use of patient data for model training. In order to secure patients' right to be forgotten, we proposed a solution by using auditing to guide the forgetting process, where auditing means determining whether a dataset has been used to train the model and forgetting requires the information of a query dataset to be forgotten from the target model. We unified these two tasks by introducing an approach called knowledge purification. To implement our solution, we developed an audit to forget software (AFS), which is able to evaluate and revoke patients' private data from pre-trained deep learning models. Here, we show the usability of AFS and its application potential in real-world intelligent healthcare to enhance privacy protection and data revocation rights.

AB-Gen: Antibody Library Design with Generative Pre-trained Transformer and Deep Reinforcement Learning

Antibody leads must fulfill multiple desirable properties to be clinical candidates. Primarily due to the low throughput in the experimental procedure, the need for such multi-property optimization causes the bottleneck in preclinical antibody discovery and development, because addressing one issue usually causes another. We developed a reinforcement learning (RL) method, named AB-Gen, for antibody library design using a generative pre-trained transformer (GPT) as the policy network of the RL agent. We showed that this model can learn the antibody space of heavy chain complementarity determining region 3 (CDRH3) and generate sequences with similar property distributions. Besides, when using human epidermal growth factor receptor-2 (HER2) as the target, the agent model of AB-Gen was able to generate novel CDRH3 sequences that fulfill multi-property constraints. Totally, 509 generated sequences were able to pass all property filters, and three highly conserved residues were identified. The importance of these residues was further demonstrated by molecular dynamics simulations, consolidating that the agent model was capable of grasping important information in this complex optimization task. Overall, the AB-Gen method is able to design novel antibody sequences with an improved success rate than the traditional propose-then-filter approach. It has the potential to be used in practical antibody design, thus empowering the antibody discovery and development process. The source code of AB-Gen is freely available at Zenodo (https://doi.org/10.5281/zenodo.7657016) and BioCode (https://ngdc.cncb.ac.cn/biocode/tools/BT007341).

Effectiveness of Bladder Filling Control during Online MR-Guided Adaptive Radiotherapy for Rectum Cancer

PURPOSE/OBJECTIVE(S)

MR-guided adaptive radiotherapy (MRgART) treatment sessions at MR-Linac are time-consuming and changes in bladder filling during the session can impact the treatment dosimetry. In this work, we present the procedure implemented in the clinical workflow to stabilize bladder filling during the MR based adaptive radiotherapy sessions and evaluate its effectiveness and the resulting dosimetric impact on the adaptive plan.

MATERIALS/METHODS

Twenty-five rectum cancer patients treated at 1.5T MR-Linac with a short course radiotherapy (25 Gy in 5 fractions of 5 Gy each) were included in this retrospective study. Patients were treated with the adapt-to-shape workflow consisting of a plan adaptation based on the MRI acquired in each session and optimized on the corresponding MR-based synthetic CT. Considering the significant interval time between the acquisition of the first daily MRI used for plan adaptation, and the beam delivery, a bladder catheter was used to stabilize the bladder filling; the procedure consists of emptying the bladder and refilling it with a well-known amount of physiological solution before each MRI acquisition. Two MRIs were acquired at each session: the first was used for plan adaptation and the second was acquired while approving the adapted plan, to be rigidly registered with the first to ensure the appropriateness of the isodoses on the ongoing delivery treatment. A total of 125 sessions and 250 MRI images and bladder contours were analyzed; for each fraction, the time interval between the first and second MRI and the corresponding bladder volumes were recorded; the consistency of bladder volumes and shapes along each online session was assessed with the dice similarity index (DSC) and Hausdorff distance (HD); the impact on plan dosimetry was evaluated by comparing target and bladder DVH cut off points of the plan on the two different MRI datasets.

RESULTS

The time interval between the first and second MRI, averaged over the 125 sessions is 39.0 min, range (18.6-75.8) min. The changes in bladder volumes, DSC index, HD, and the differences between the bladder and target DVH cut-off points are shown in the table below. The DSC and HD are comparable to inter-observer variability in manual contour segmentation, with an average DSC of 0.91 and average HD of 2.13 mm; the average differences in bladder and target dosimetry remain under 0.63% and 0.10%, respectively.

CONCLUSION

The use of a procedure in the clinical workflow of MRgART to stabilize the bladder filling throughout the online session may be helpful to guarantee the accuracy of the ongoing delivered treatment.

Study on the Clinical Use of a Respiratory Navigator Combined with Breath-Hold for MRI- Guided Liver SBRT

PURPOSE/OBJECTIVE(S)

Respiratory movement strongly affects the accuracy of stereotactic body radiation therapy (SBRT) of liver malignancies treated without the use of a respiratory gating system. This study investigates the feasibility and advantages of using a respiratory navigator-guided combined with patient breath-hold for liver SBRT in an adaptive magnetic-resonance guided workflow.

MATERIALS/METHODS

Clinical datasets of 10 liver cancer patients treated with 1.5T MR-Linac with respiratory navigator-guided SBRT combined with patient breath-hold were retrospectively analyzed. All patients underwent simulation CT with and without contrast, and 4D-CT and 3D-T2w MRI without contrast. Patients received a prescription dose ranging from 36 to 50 Gy in 5 to 8 fractions and followed the adapt to shape (ATS) workflow including contours adjustment and a subsequent MR-based synthetic CT (sCT) calculation on the online MRI acquired. The reference treatment plan was optimized on the expiratory phase of the 4D-CT, and during the online session the contours and the adapted plans were performed using the 3D-T2w navigator MRI of the patient's end-expiratory signal; 2D-T2w real-time monitoring MRI was also used as support for the contour's definition. The radiation therapist instructed the patients to hold their breath at the end of the breathing cycle for the time of the beam on. A total of 59 fractions were analyzed. For each fraction the dosimetric parameters of the target and normal liver of the adaptive and reference plans were compared; particularly the volume, the conformity index (CI) and gradient index (GI) for the target, and V5, V10 and Dmean for the normal liver. T-student statistical analysis was performed; a p-value less than 0.05 was considered statistically significant.

RESULTS

In the free breathing state, the 3D-T2w navigator MRI images enable a clear visualization of the tumor and its boundaries. The average target CI of the adaptive and reference plans is not significantly different (p = 0.448), while the GI is significantly higher (p = 0.043). Normal liver V10 and Dmean are lower and V5 is slightly increased, but without statistical differences. The mean values and standard deviation of the dosimetric parameters of the reference and adapted plans are shown in the Table below.

CONCLUSION

The use of a respiratory navigator combined with the breath-hold for MRI- guided liver SBRT allows clear visualization of the tumor, ensures the accuracy of the delivered dose and may be considered an alternative when the respiratory gating system is not available during MRgART sessions.

Study on Lattice Radiotherapy Treatments (LRT) for Head and Neck Bulky Tumors

PURPOSE/OBJECTIVE(S)

Lattice radiotherapy (LRT) exploits various effects of radiation, such as the bystander effect and the abscopal effect, and consists on the administration of high dose fraction in small areas with large tumor masses, helping to solve the problem of treating bulky disease, especially if it is located in a critical anatomical area. The optimization of LRT treatment plans is challenging due to the difficulty to generate spots of high dose within the tumor with consequent high gradient. This study compares the plan dosimetry and delivery time of two delivery techniques VMAT and CyberKnife for LRT treatments of bulky head and neck lesions.

MATERIALS/METHODS

Six patients with giant head and neck tumors who received LRT at our institution were included in this study. Target and OARs were contoured following international guidelines; to allow easy identification of the desired high gradient zones, an artificial geometrical lattice structure with spherical vertices was arranged inside the target volume (GTV), and the vertices of the lattice representing the high dose boost volumes (GTVboost) were delineated. The GTVboost and GTV were prescribed to receive 12 Gy and 3 Gy, respectively in a single fraction. Separate VMAT and CyberKnife LRT plans were optimized for each patient with lattice vertex of 0.5 diameter and center-to-center distances of 1.5 cm (LRT1.5) and 3 cm (LRT3). The dose heterogeneity was measured as the peak-to-valley dose ratio (PVDR), with the traditional definition being replaced by the D10/D90 ratio, where D10 and D90 represent the doses covering 10% and 90% of the GTV, respectively. For each plan generated, the treatment delivery time, the monitor units (MU), and the PVDR were assessed. Pre-treatment plan verifications were performed with ArcCheck array and Gafchromics film for VMAT and CyberKnife, respectively, using gamma analysis criteria of 3%-3mm.

RESULTS

The mean PVDR obtained for VMAT LRT plans were 2.0 and 2.6 for LRT1.5 and LRT3, respectively, and 3.2 and 4.7, respectively for CyberKnife LRT plans. For each pre-treatment plan dose verification, the gamma passing rate (GPR) was higher than 95.0 %; CyberKnife delivery time and MU were more than 10 times higher than that of VMAT, nevertheless, VMAT had a lower PVDR. The detailed results are shown in the table below.

CONCLUSION

CyberKnife LRT has a strong ability to place the peak dose within the target, generating a higher peak-to-valley dose ratio, however its use is partially invalidated by the long beam delivery times and the resulting high MU number; the use of the VMAT LRT technique allows clinically adequate dosimetry with acceptable delivery times.

Repetitive DNA sequence detection and its role in the human genome

Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.

[A control study of steroid withdrawal protection strategy after kidney transplantation in children]

Objective: To study the influence of steroid withdrawal protection strategy on height growth in pediatric patients after kidney transplantation. Methods: The prospective cohort study enrolled 40 stage 5 chronic kidney disease children receiving kidney transplantation from July 2017 to September 2022 at Guangzhou Women and Children's Medical Center. Based on the primary preoperative disease, patients with immune abnormality-associated glomerular diseases or unknown causes were assigned to the steroid maintenance group, in which patients received steroid tapering within 3 months after surgery to a maintenance dose of 2.5 to 5.0 mg/d. While patients with hereditary kidney disease or congenital urinary malformations were assigned to the steroid withdrawal group, in which patients had steroids tapered off within 3 months. The characteristics of height catch-up growth and clinical data were compared between the 2 groups at baseline, 6, 12, 18 and 24 months after kidney transplantation. T-test, repeated measurement of variance analysis, Mann-Whitney U test, and Fisher exact test were used for the comparison between the 2 groups. Results: Among the 40 children, 17 were males, 23 were females, 25 were in the steroid withdraw group ((7.8±2.8) years old when receiving kidney transplantation) and 15 cases were in the steroid maintenance group ((7.6±3.5) years old when receiving kidney transplantation). The study population was followed up for (26±12) months. The total dose per unit body weight of steroids in the steroid withdrawal group was lower than that in the steroid maintenance group ((0.13±0.06) vs. (0.36±0.19) mg/(kg·d), t=5.83, P<0.001). The height catch-up rate (ΔHtSDS) in the first year after kidney transplantation in the steroid withdraw and steroid maintenance groups was 1.0 (0.7, 1.4) and 0.4 (0.1, 1.0), respectively; in the second year, the ΔHtSDS in the steroid withdraw group was significantly higher than that in the steroid maintenance group (1.1 (0.2, 1.7) vs. 0.3 (0, 0.8), U=28.00, P=0.039). The HtSDS in the steroid withdrawal group at the five follow-up time points was -2.5±0.8, -2.0±0.8, -1.5±0.8, -1.3±0.9 and -0.5±0.3, respectively, while in the steroid maintenance was -2.4±1.3, -2.2±1.1, -2.0±1.0, -1.8±1.0 and -1.6±1.0, respectively. There were statistically significant differences in HtSDS at different follow-up time points in both 2 groups (F=19.81, P<0.01), but no statistical differences in overall impact between the 2 groups (F=1.13, P=0.204). The steroid treatment was interaction with the increase of follow-up time (F=3.62, P=0.009). At the 24th month after transplantation, the HtSDS in the steroid withdrawal group was significantly higher than that in the steroid maintenance group (P=0.047). Six patients in the steroid withdrawal group experienced antibody-mediated immune rejection (AMR), while 3 did in the steroid maintenance group. Moreover, there was no significant difference in AMR between the two groups (χ2=0.06, P=0.814). Conclusion: The steroid withdrawal protection strategy favors the height catch-up growth in pediatric patients after kidney transplantation and does not increase the risk of postoperative antibody-mediated immune rejection.

The transmission of hepatitis B virus (HBV) infection from mother-to-infant (MTI) and the susceptibility of offspring to hepatitis B under intrauterine exposure to HBsAg

OBJECTIVE

Hepatitis B virus (HBV) causes long-term injury to the liver in patients with chronic hepatitis B. It was reported that nearly half of this disease's cases now result from mother-to-infant (MTI) transmission. Therefore, intervention during this period of transmission of HBV could effectively prevent HBV infection in infants.

MATERIALS AND METHODS

This study employed bioinformatics methods to analyze the datasets of MTI hepatitis B transmission obtained from the Gene Expression Omnibus (GEO) database. Through this analysis, we extracted valuable information to identify genes exhibiting differential expression and uncover the associated signal pathways. Ultimately, our investigations into alterations in immune function shed light on the underlying mechanisms of MTI HBV transmission.

RESULTS

There were 593 genes that were significantly differentially expressed (512 up-regulated genes and 81 down-regulated genes) in the offspring CD8+T cells with Hepatitis B surface antigen (HBsAg) intrauterine exposure. The pathways enriched for differentially expressed genes have been revealed. Furthermore, we performed a correlation analysis between differentially expressed genes and maternal hepatitis B inheritance via the weighted gene co-expression network analysis (WGCNA) and eventually found a high correlation between the cyan module and the shape. Among them, there were 166 genes in the cyan module, which were mainly enriched in the phosphatidylinositol signaling system, glycerolipid metabolism, and other types of O-Glycan biosynthesis.

CONCLUSIONS

Therefore, we speculated that these signaling pathways and the genes within may be closely related to hepatitis B susceptibility and maternal hepatitis B inheritance. In this study, we showed that differentially expressed genes and signaling pathways may be valuable in preventing MTI transmission of HBV.

Soil nutrients, enzyme activities, and bacterial communities in varied plant communities in karst rocky desertification regions in Wushan County, Southwest China

Vegetation restoration has become a common practice in karst rocky desertification (KRD) areas of southwestern China. The bacteria, which have made a connection between soil and plants, have been an important role in regulating the succession and restoration of karst vegetation. However, it is still unclear how soil bacterial communities and soil properties respond to natural vegetation restoration processes in karst areas. To address this gap, we investigated the soil nutrients, enzyme activity, and soil bacterial community among various plant communities, including farmland (FL), land with herbs only (SSI), herb-and-shrub land (SSII), woody thickets (SSIII), coniferous forest (SSIV), coniferous and broad-leaved mixed forest (SSV), and evergreen broad-leaved forest (SSVI). Our results found that SSII had the highest levels of soil organic matter, total nitrogen, available phosphorus, available nitrogen, sucrase, and β-glucosidase among all the plant communities. These results indicated that herb-and-shrub land have contributed to the rapid restoration of vegetation in KRD regions. FL exhibited the lowest levels of soil nutrients and enzyme activities, while showing the highest bacterial richness and diversity among all the plant communities. This suggested that appropriate human intervention can increase bacterial diversity and richness in the area. The predominant bacterial phylum also varied among the different plant communities, with Actinobacteria being the most abundant in SSI, SSII, SSIII, and SSIV, while Proteobacteria were the most abundant in SSV and SSVI. Furthermore, PCoA analysis demonstrated significant changes in the soil bacterial community structure, with SSI, SSII, SSIII, and SSIV had shared similar structures, while SSV and SSVI had comparable structures. As for soil characteristics, total phosphorus (TP) and total potassium (TK) were the primary factors affecting the soil bacterial community. SSV and SSVI had the most complex bacterial networks and were more stable than other groups. The genera Ktedonobacter, norank_f_Anaerolineaceae, and Vicinamibacter had the highest betweenness centrality scores and were identified as keystone genera in the co-occurrence network in KRD areas. In summary, our results have demonstrated that herb-and-shrub can promote community succession and increase soil nutrient levels in KRD regions.

[Prevalence of parasitic infections in human stool samples from a hospital in Chenzhou City of Hunan Province]

OBJECTIVE

To investigate the prevalence of parasitic infections in human stool samples from a hospital in Chenzhou City, Hunan Province, so as to provide insights into the management of intestinal parasitic diseases.

METHODS

Stool samples were collected from patients admitted to a hospital in Chenzhou City from September 2020 to March 2021, subjected to physiological saline smearing and microscopy for detection of intestinal parasites. The prevalence of parasitic infections and the species of parasites were descriptively analyzed.

RESULTS

The overall prevalence of intestinal parasitic infections was 1.61% in the 10 728 stool samples, and there were 3 samples with mixed infections of two parasite species. A total of seven parasite species were identified, including Blastocystis hominis (162 cases, 1.55%), Giardia lamblia (5 cases, 0.05%), Dientamoeba fragilis (5 cases, 0.05%), Endolimax nana (one case, 0.01%), Iodamoeba bütschlii (one case, 0.01%), Strongyloides stercoralis (one case, 0.01%) and Trichomonas hominis (one case, 0.01%). The prevalence of intestinal parasitic infection was significantly higher among women than in men (2.14% vs. 1.25%; χ² = 13.01, P < 0.01), and a high prevalence rate was seen among patients at ages of 20 to 30 years (2.99%) and 80 years and older (2.86%); however, no age-specific prevalence of intestinal parasitic infection was detected (χ² = 12.45, P > 0.05).

CONCLUSIONS

The overall prevalence of intestinal parasitic infection was low among patients admitted to a hospital in Chenzhou City, and gender-specific prevalence was found. Food-borne and opportunistic parasites were predominant intestinal parasites, including B. hominis, G. lamblia and D. fragilis.

LCAT: an isoform-sensitive error correction for transcriptome sequencing long reads

As the carrier of genetic information, RNA carries the information from genes to proteins. Transcriptome sequencing technology is an important way to obtain transcriptome sequences, and it is also the basis for transcriptome research. With the development of third-generation sequencing, long reads can cover full-length transcripts and reflect the composition of different isoforms. However, the high error rate of third-generation sequencing affects the accuracy of long reads and downstream analysis. The current error correction methods seldom consider the existence of different isoforms in RNA, which makes the diversity of isoforms a serious loss. Here, we introduce LCAT (long-read error correction algorithm for transcriptome sequencing data), a wrapper algorithm of MECAT, to reduce the loss of isoform diversity while keeping MECAT's error correction performance. The experimental results show that LCAT can not only improve the quality of transcriptome sequencing long reads but also retain the diversity of isoforms.

Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ

Alternative polyadenylation (APA) enables a gene to generate multiple transcripts with different 3' ends, which is dynamic across different cell types or conditions. Many computational methods have been developed to characterize sample-specific APA using the corresponding RNA-seq data, but suffered from high error rate on both polyadenylation site (PAS) identification and quantification of PAS usage (PAU), and bias toward 3' untranslated regions. Here we developed a tool for APA identification and quantification (APAIQ) from RNA-seq data, which can accurately identify PAS and quantify PAU in a transcriptome-wide manner. Using 3' end-seq data as the benchmark, we showed that APAIQ outperforms current methods on PAS identification and PAU quantification, including DaPars2, Aptardi, mountainClimber, SANPolyA, and QAPA. Finally, applying APAIQ on 421 RNA-seq samples from liver cancer patients, we identified >540 tumor-associated APA events and experimentally validated two intronic polyadenylation candidates, demonstrating its capacity to unveil cancer-related APA with a large-scale RNA-seq data set.

Effect of pulmonary function on bone mineral density in the United States: results from the NHANES 2007-2010 study

The relationship between pulmonary function (PF) and bone mineral density (BMD) remains controversial. In the US population, we found a positive association between PF and BMD. Mixed variables such as age, gender, and race may influence this association.

INTRODUCTION

Based on the data from the National Health and Nutrition Examination Survey (NHANES) from 2007 to 2010, this study explored whether there is a correlation between PF (1st second forceful expiratory volume as a percentage of expected value (FEV1(% predicted)), (one-second rate (FEV1/FVC)), and bone mineral density.

METHODS

We evaluated the relationship between PF and BMD in 6327 NHANES subjects (mean age 44.51 ± 15.64 years) from 2007 to 2010. The bone mineral density of the whole femur was measured by dual-energy X-ray absorptiometry (DXA). After adjusting for a wide range of confounders, we examined the relationship between PF and total femur BMD using a multiple linear regression model.

RESULTS

Correction of race, age, alcohol consumption, body mass index (BMI), height, poor income ratio (PIR), total protein, serum calcium, serum uric acid, cholesterol, serum phosphorus, blood urea nitrogen, FEV1(% predicted), and femur BMD were positively correlated (β = 0.032, 95% CI: 0.010-0.054, P = 0.004). FEV1/FVC was positively correlated with spine BMD (β = 0.275 95%CI: 0.102-0.448, P = 0.002).

CONCLUSIONS

Our study shows that PF is positively associated with BMD in the US population. A variety of factors such as race and age influence this relationship. the relationship between PF and BMD needs to be further investigated, including specific regulatory mechanisms and confounding factors.

A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics

Spatial transcriptomics technologies are used to profile transcriptomes while preserving spatial information, which enables high-resolution characterization of transcriptional patterns and reconstruction of tissue architecture. Due to the existence of low-resolution spots in recent spatial transcriptomics technologies, uncovering cellular heterogeneity is crucial for disentangling the spatial patterns of cell types, and many related methods have been proposed. Here, we benchmark 18 existing methods resolving a cellular deconvolution task with 50 real-world and simulated datasets by evaluating the accuracy, robustness, and usability of the methods. We compare these methods comprehensively using different metrics, resolutions, spatial transcriptomics technologies, spot numbers, and gene numbers. In terms of performance, CARD, Cell2location, and Tangram are the best methods for conducting the cellular deconvolution task. To refine our comparative results, we provide decision-tree-style guidelines and recommendations for method selection and their additional features, which will help users easily choose the best method for fulfilling their concerns.

ZnO@Carbon Dot Nanoparticles Stimulating the Antibacterial Activity of Polyvinylidene Fluoride-Hexafluoropropylene with a Higher Electroactive Phase for Multifunctional Devices

To further advance the application of flexible piezoelectric materials in wearable/implantable devices and robot electronic skin, it is necessary to endow them with a new function of antibacterial properties and with higher piezoelectric performance. Introducing a specially designated nanomaterial based on the nanocomposite effect is a feasible strategy to improve material properties and achieve multifunctionalization of composites. In this paper, carbon dots (CDs) were sensitized onto the surface of ZnO to form ZnO@CDs nanoparticles, which were then incorporated into polyvinylidene fluoride-hexafluoropropylene (PVDF-HFP) to obtain a multifunctional composite. On the one hand, the antibacterial property of ZnO was improved because CDs had good optical absorption of visible light and their surface functional groups were favorable for electrostatic adsorption with bacteria. Therefore, ZnO@CDs endowed the composite with an outstanding antibacterial rate of 69.1% for Staphylococcus aureus. On the other hand, CDs played a bridging role between ZnO and PVDF-HFP, reducing the negative effect of ZnO aggregation and interface incompatibility with PVDF-HFP. As a result, ZnO@CDs induced β-phase formation of 80.4% in PVDF-HFP with a d₃₃ value of 33.8 pC N^-1. The multifunctional device exhibited excellent piezoelectric and antibacterial performance in the application of energy harvesters and self-powered pressure sensors.

[Comparative study of decentration, tilt and visual quality after implantation of aspherical intraocular lenses]

Objective: To compare the difference of decentration and tilt among 4 kinds of aspherical intraocular lenses (IOLs), and to analyze their objective visual quality. Methods: Prospective non-randomized controlled clinical trial. Age-related cataract patients who planned to undergo phacoemulsification and IOL implantation in the Affiliated Hospital of North Sichuan Medical College from April to June in 2020 were divided into ZCB00 group, SN60WF group, A1-UV group, and AO group according to IOL types. Thirty right eyes and thirty left eyes were selected in each group. Before operation and at 1 day, 1 week and 1 month postoperatively, decentration and tilt values were measured by a new swept-source anterior-segment optical coherence tomography device (CASIA2), and wavefront aberrations, objective scatter index (OSI), modulation transfer function cut off frequency (MTF cut off) and Strehl ratio (SR) were also examined. Values of decentration, tilt and visual quality compared among 4 groups were took from the right eye. One-way analysis of variance was used for inter-group comparison, and repeated measurement one-way analysis of variance was used for intra-group comparison. Data between right eyes and left eyes from all the individuals were compared by independent sample t-test. Results: A total of 181 patients (240 eyes) were enrolled, and 169 patients (224 eyes) completed the follow-up (114 right eyes and 110 left eyes). There were 77 males and 92 females, with an age of (69±9) years. There was no significant difference in gender, age, axial length, decentration and tilt of crystalline lens and IOL power among 4 groups (all P>0.05). At 1 day, 1 week and 1 month postoperatively, there was significant difference in decentration value among 4 groups (F=7.11, 6.12, 4.66; all P<0.05). For further pairwise comparison, the decentration value of SN60WF group was higher than that of the other 3 groups at 1 day and 1 week postoperatively, and the decentration value of SN60WF group was (0.259±0.101) mm at 1 month postoperatively, which was higher than that of ZCB00 group (0.177±0.099) mm and AO group (0.163±0.122) mm, and the differences were statistically significant (using SNK-q test, both P<0.05). The IOL tilt value in the ZCB00 group, SN60WF group, A1-UV group, and AO group at 1 month postoperatively were (4.806±1.129)°, (5.080±1.309)°, (4.586±1.338)°, (5.112±1.406)°, respectively. No significant difference in tilt value among 4 groups was found at any time after surgery (all P>0.05). In each group, there was no significant difference in decentration and tilt value at different postoperative time points (all P>0.05). At 1 month postoperatively, there was no significant difference in decentration and tilt at horizontal and vertical directions respectively among 4 groups (all P>0.05), and in each group, there was no significant difference in decentration and tilt value between right eyes and left eyes (all P>0.05), and IOLs tended to tilt towards the inferonasal or inferotemporal direction in both eyes. With 4-mm and 6-mm pupil diameter, there was significant difference in internal (F=131.32, 85.17) and ocular (F=46.64, 47.55) spherical aberration among 4 groups (all P<0.01). For further pairwise comparison, the spherical aberration of AO group was higher than that of the other 3 groups, and the difference was statistically significant (using SNK-q test, all P<0.05). There was no significant difference in OSI, MTF cut off and SR among 4 groups (all P>0.05). Conclusions: The four types of IOLs show decentration and tilt in varying degrees after implantation in the capsular bag, but this difference do not lead to clinical significance. Human eyes have tolerance to mild decentration and tilt of aspheric IOLs, showing good visual quality.

POS0349 DECOY RECEPTOR 3 AND ITS SIGNAL PATHWAY CONTRIBUTE TO PATHOGENESIS IN PRIMARY GOUTY ARTHRITIS

Background

Gouty arthritis (GA) is an autoinflammatory disease caused by the deposition of monosodium urate crystal (MSU) in the joints and surrounding tissues, which lead to a series of complex inflammatory cascade amplification reactions.The clinical symptoms of acute GA attack rapidly, but often alleviate spontaneously within 7 ~ 10 days, which is one of the significant characteristics different from other joint diseases or autoimmune diseases. However, the exact molecular mechanism of its inflammatory self limitation is still unclear. The phenotypic imbalance of Th1 / Th2 cells and the M1/ M2 polarization of macrophages may be involved in the inflammatory self limitation of gout[1].Decoy receptor 3 (DCR3) can differentiate T cells into Th2 phenotype, promote M2 polarization of macrophages, and play the functions of immune regulation and repair[2].DCR3 and its Signal Pathway are involved in the pathogenesis of tumors and a variety of autoimmune diseases, and have become an important research target of tumors and immune related diseases.However, studies on DcR3 related molecular pathway and GA are scarce, and the specific regulatory mechanism is unknown.

Objectives

To assess the contribution of DcR3 and its signal pathway to gout and the clinical importance of these genes in primary gouty arthritis.

Methods

The mRNA expression levels of DCR3 and its signal pathway(DR3, TL1A, Fas, FasL, Ligth, LigthR, LTgthRNA expression levels of DCR3 and its signal pathway(DR3gout and the clinical importance of these genes in primary gouty arthritis.nt research target of tumors and immune related diseases.However, studies on DcR3 related moathway expression levels and laboratory features was analyzed in GA patients.

Results

The expression levels of DCR3, FasL were much lower in the AG and IG group than in the HC groups (p<0.05), and no significant difference was detected between AG and IG groups(P>0.05)(a,e). The expression levels of DR3 were much lower in the AG and IG group than in the HC groups (p<0.05), and much lower in the AG group than in the IG groups (p<0.05)(b). The expression levels of TL1A were much higher in the AG group than in the IG and HC groups (p<0.05), and no significant difference was detected between IG and HC groups(P>0.05)(c).The expression levels of Light, LightR were much lower in the AG group than in the HC groups (p<0.05), and no significant difference was detected between AG and IG groups, IG and HC groups(P>0.05)(f,g).The expression levels of LTlower in the AG and IG group than in the HC groups (p<0.05(p<0.05), and no significant difference was detected between AG and IG groups, IG and HC groups(P>0.05)(h).In GA patients, the levels of DcR3 related molecular pathway gene correlated with laboratory inflammatory and metabolic indexes.

Conclusion

Altered DCR3 and its signal pathway expression suggests that DCR3 related molecular pathway is involved in the pathogenesis of GA and participates in regulating inflammation and metabolism.

References

[1]Desai J, Steiger S, Anders HJ. Molecular Pathophysiology of Gout[J]. Trends Mol Med. 2017 Aug;23(8):756-768. DOI:10.1016/j.molmed.2017.06.005.

[2]Pan YG, Huang MT, Sekar P, et al. Decoy Receptor 3 Inhibits Monosodium Urate-Induced NLRP3 Inflammasome Activation via Reduction of Reactive Oxygen Species Production and Lysosomal Rupture[J]. Front Immunol. 2021 Mar 3;12:638676.DOI:10.3389/fimmu.2021.638676.

Figure 1.

Relative Expression of DcR3 related molecular pathway gene in the PBMCs of Patients.The expression levels of DCR3, FasL were much lower in the AG and IG group than in the HC groups (p<0.05)(a,e). The expression levels of DR3 were much lower in the AG and IG group than in the HC groups (p<0.05), and much lower in the AG group than in the IG groups (p<0.05)(b). The expression levels of TL1A were much higher in the AG group than in the IG and HC groups (p<0.05)(c).The expression levels of Light, LightR were much lower in the AG group than in the HC groups (p<0.05)(f,g).The expression levels of LTβR were much higher in the AG group than in the HC groups (p<0.05)(h).

Acknowledgements

Institute of Research Center of Gout and Hyperuricemia of the Affiliated Hospital, North Sichuan Medical College

Disclosure of Interests

None declared

AB0702 Coexistence of systemic sclerosis and microscopic polyangitis associated with pulmonary renal syndrome: a case report and literature review

Background

Systemic sclerosis is a chronic immune disease characterized by varying degrees of fibrosis of skin and internal organs. Microscopic polyangitis, as a subtype of ANCA associated vasculitis, mainly involves small blood vessels, often manifested as necrotizing glomerulonephritis and pulmonary capillary vasculitis. Pulmonary renal syndrome is characterized by diffuse alveolar hemorrhage based on pulmonary capillary vasculitis and rapidly progressive glomerulonephritis, which can be derived from a variety of autoimmune diseases, of which ANCA associated vasculitis accounts for about 60%[1]. The cases of coexistence of systemic sclerosis and microscopic polyangitis associated with pulmonary renal syndrome in clinic are rare, which is often dangerous and is easy to miss diagnosis or misdiagnosis.

Objectives

To investigate the clinical characteristics, diagnosis and treatment of coexistence of systemic sclerosis (SSC) and microscopic polyangitis（MPA）associated with pulmonary renal syndrome (PRS).

Methods

The clinical data, diagnosis and treatment process of a patient who has SSC combined with MPA and PRS were summarized and analyzed. And the literature was reviewed to explore the correlation of the pathogenesis and clinical experience of SSC complicated with MPA and PRS.

Results

The case is a middle-aged male who was diagnosed as SSc due to the hardening of the skin of both hands，Reynolds phenomenon, the anti-scl-70 antibody are positive. The patient suffered from repeated hemoptysis, progressive dyspnea, severe anemia and renal insufficiency, so he was diagnosed as MPA with PRS. After giving glucocorticoid, immunosuppressant and anti-infection treatment, his condition has improved. A total of 7 case reports were retrieved by reviewing the relevant literature.A total of 7 patients were reported.They were first diagnosed as SSc and then MPA with PRS, of which 4 cases improved after treatment and 3 cases died. Among the dead patients, 1 case was treated with penicillamine for 3 years, and the remaining 2 cases were only treated with steroids without immunosuppressants.In SSc, P-ANCA is closely related to vasculitis, and the prognosis of PRS secondary to P-ANCA may be very poor. Most of the diagnosis of MPA is only after patients have kidney or lung diseases.There is a certain correlation between them in pathogenesis. Glucocorticoids, immunosuppressants, biological agents, hemodialysis and plasma exchange are the main treatments.

Conclusion

Although the cases of SSc combined with MPA and PRS are rare, there are still many cases reported,which reminds us: ①When SSc patients have new symptoms such as renal insufficiency or lungs, they should be alert to new entities that may be combined with other autoimmune diseases to avoid missed diagnosis or misdiagnosis.②ANCA should be detected in SSc patients at baseline, which may be related to disease activity.③PRS has rapid progress and high mortality, whcih is an emergency that needs urgent treatment. Such patients should be treated with glucocorticoid, immunosuppression and plasma exchange immediately. However, if patients are complicated with SSc, they need to be extra careful when using high-dose steroids, which increases the risk of renal crisis.

References

[1]de Groot K, Schnabel A. Das pulmorenale Syndrom [Pulmonary-renal syndrome]. Internist (Berl). 2005;46(7):769-782. doi:10.1007/s00108-005-1423-8.

Figure 1.

The contrast of chest CT before and after treatment showed that the exudative lesions of both lungs were significantly absorbed

Figure 2.

Clinical data of systemic sclerosis combined with microscopic polyangitis and pulmonary renal syndrome

Acknowledgements

Institute of Research Center of Gout and Hyperuricemia of the Affiliated Hospital, North Sichuan Medical College

Disclosure of Interests

None declared

AB0112 DECOY RECEPTOR 3 AND ITS SIGNAL PATHWAY CONTRIBUTE TO PATHOGENESIS IN ANKYLOSING SPONDYLITIS

Background

Ankylosing spondylitis (AS) is a chronic progressive disease with invasion of spine and sacroiliac joint as the main clinical manifestation, which can be combined with systemic inflammation or abnormalities in multiple parts at the same time. There are complex changes of immune function in patients with AS, and its immune and genetic pathogenesis is still unclear. Decoy receptor 3 (DcR3), as a new immune molecule discovered in recent years, plays an important role in regulating T cell activation, proliferation, differentiation and apoptosis.Studies have confirmed that DcR3 is involved in the immune disorder process of rheumatoid arthritis, SLE, AS and other autoimmune diseases, so that the role of DcR3 in AS has attracted attention. However, the expression of DcR3 related pathway genes[1-3].However, studies evaluating the DcR3 related pathway genes in AS are scarce.

Objectives

To assess the contribution of DcR3 and its signal pathway to AS and the clinical importance of these genes in AS.

Methods

The mRNA expression levels of DCR3 and its signal pathway(DR3、TL1A、Fas、FasL、Ligth、LigthR、LTgthRNA expresured in peripheral blood mononuclear cells (PBMCs) from 50 AS patients and 50 healthy subjects. The relationship between DCR3 related molecular pathway expression levels and laboratory features was analyzed in AS patients.

Results

The expression levels of DCR3、DR3、Fas、Light were much lower in the AS group than in the HC groups (p<0.05)(a,b,c,d), and the expression levels of LT The relationship between DCR3 related molecular pathway expression l

Conclusion

Compared with HC group, DCR3 and its signal pathway in PBMCs of AS patients are differentially expressed. It is speculated that DcR3 related molecular pathway gene may be involved in the pathogenesis of AS.

Figure 1.

Relative Expression of DcR3 related molecular pathway gene in the PBMCs of Patients. The mRNA levels in PBMCs from AS patients(n=50) and HCs(n=50) were measured by RT-qPCR. The expression levels of DCR3ˎDR3ˎFasˎLight were much lower in the AS group than in the HC groups (p<0.05)(a,b,c,d), and the expression levels of LTβR was much higher in the AS group than in the HC groups (p<0.05)(e).

References

[1]Lee CS, Hu CY, Tsai HF, et al. Elevated serum decoy receptor 3 with enhanced T cell activation in systemic lupus erythematosus. Clin Exp Immunol. 2008;151(3):383-390. doi:10.1111/j.1365-2249.2007.03579.x

[2]Hayashi S, Miura Y, Tateishi K, Takahashi M, Kurosaka M. Decoy receptor 3 is highly expressed in patients with rheumatoid arthritis. Mod Rheumatol. 2010;20(1):63-68. doi:10.1007/s10165-009-0240-7.

[3]Chen MH, Chen WS, Tsai CY, Liao HT, Chen CH, Chou CT. Overexpression of decoy receptor 3 in synovial tissues of inflammatory arthritis. Clin Exp Rheumatol. 2012;30(2):171-177.

Acknowledgements

Institute of Research Center of Gout and Hyperuricemia of the Affiliated Hospital, North Sichuan Medical College

Disclosure of Interests

None declared

Large amplitude vibration of a cantilever actuated by a high-frequency pulsed laser

Laser excitation based on the thermoelastic principle is effective for micro-scale actuation, enabled energy conversion from optical to mechanical. The major advantages lie in non-contact actuation, easy miniaturization, and integration. To avoid surface damage, the laser power per unit is limited, leading to several micrometers of the vibration. In this study, a pure nickel millimeter-sized cantilever is successfully actuated at a low-frequency resonance (around Hz) via a nanosecond pulsed laser. By modal interaction, the energy is transferred from a low-intensity, high-frequency (around kHz) excitation to a low-frequency response with millimeter amplitude. The stable low-frequency resonance of the cantilever was maintained by changing the laser pulse parameters and the illumination locations. We also present a method to control the vibration of the cantilever using a modulated wave (MW: the laser wave modulated by a rectangular wave). The cantilever's amplitude can be efficiently adjusted by changing the laser power or duty cycle of the MW. The resonance frequency of the cantilever also can be altered by optimizing the geometries to meet various actuation requirements. This study enables large actuation (up to tens of millimeters) by laser excitation, facilitating applications in precision manipulation, microfluidic mixing, lab-on-a-chip device, and other related micro actuation devices.

A37 EFFICACY AND SAFETY OF RISANKIZUMAB AS MAINTENANCE THERAPY IN PATIENTS WITH CROHN’S DISEASE: 52 WEEK RESULTS FROM THE PHASE 3 FORTIFY STUDY

Background

Risankizumab (RZB), an anti-IL-23 p19 inhibitor, was well-tolerated and superior to placebo (PBO) in inducing clinical remission and endoscopic response in patients (pts) with moderate-to-severe Crohn’s disease (CD) in two phase 3 studies at 12 weeks.

Aims

FORTIFY (NCT03105102), was a 52-week (wk) phase 3 double-blind, re-randomized responder withdrawal study that evaluated the efficacy and safety of continuing RZB as subcutaneous (SC) maintenance therapy versus withdrawal to placebo in pts achieving induction response to RZB

Methods

Week 12 IV RZB responders were re-randomized 1:1:1 to: RZB SC 360mg (N=141), RZB 180mg (N=157), or PBO (withdrawal from IV RZB; N=164) every 8wks for 52wks. Co-primary endpoints were clinical remission (per CD Activity Index [CDAI] (US); or stool frequency/abdominal pain score [SF/APS] (OUS) and endoscopic response at wk52. Other clinical and endoscopic endpoints, inflammatory biomarkers, RZB serum levels, and safety were assessed over time.

Results

Rates of clinical remission (CDAI, SF/APS) and clinical response were similar for RZB and PBO groups through wk24, with rates lower for PBO thereafter. At wk52, clinical remission (CDAI, SF/APS) and endoscopic response rates were significantly higher with RZB 360mg than PBO ( P<0.01); RZB 180mg was superior to PBO for clinical remission per CDAI and endoscopic response ( P<0.01). Endoscopic remission and deep remission rates increased over time with 360mg, remained steady with 180mg, and decreased with PBO. Mean fecal calprotectin (FCP) and C-reactive protein (CRP) levels decreased with SC RZB, but increased with PBO, over 52wks. Exposure-adjusted event rates (per 100 pts-years) of serious adverse event (AE) were generally similar among groups (360mg, 21.0 E/100PY and 180mg, 19.5 E/100PY vs PBO, 19.3 E/100PY), as were AEs leading to drug discontinuation (4.8 E/100PY and 2.4 E/100PY vs 3.7 E/100PY), and serious infections (6.0 E/100PY and 3.0 E/100PY vs 5.0 E/100PY).

Conclusions

In pts with moderate-to-severe CD, a robust pharmacodynamic effect on the IL-23 pathway after 12wks RZB IV induction was maintained with RZB SC maintenance therapy. The durability of RZB was demonstrated with high rates of efficacy over the 52-wk study. RZB was superior to PBO for achieving clinical remission and endoscopic response at wk52. Results for the more stringent endpoints (endoscopic remission\deep remission) and persistent improvements in inflammatory biomarkers are consistent with a dose response relationship. Continued RZB SC maintenance treatment was generally safe and well-tolerated.

Funding Agencies

AbbVie

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.

msRepDB: a comprehensive repetitive sequence database of over 80 000 species

Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).

[Distribution and metabolism of toxicants in rats with phenol burn]

Objective: To study the distribution and metabolism of toxicants in rats after phenol burn. Methods: In February 2019, SPF-grade healthy SD male rats were transdermally exposed to 6 mg/kg phenol to create a 5% body surface burn model of rats. High performance liquid chromatography was used to determine phenol content in rat plasma and kidney tissues after 0.25, 0.75, 2, 4, 8, 16, and 32 h, respectively. The kinetic parameters of phenol were calculated by DAS 2.0 software, and the kidney targeting of phenol was evaluated. Results: The area under the blood concentration-time curve at 0-8 h (AUC(0-8)) of the rat after phenol burn was (28.741±6.485) μg/ml·h, and the area under the blood concentration-time curve from 0 to infinite time (AUC(0-∞)) was (30.354±6.424) μg/ml·h, half-life (t(1/2)) was (2.111±0.632) h, peak concentration (C(max)) was (16.287±4.870) μg/ml, mean residence time (MRT) was (1.854±0.148) h. The target efficiency (DTE) of rat kidney was 2.91. Conclusion: Phenol burn rats have fast percutaneous absorption, rapid elimination of phenol, and have high clearance rate, short MRT, and weak substance accumulation. Phenol has relatively obvious selectivity to the kidneys.

A sensitive repeat identification framework based on short and long reads

Numerous studies have shown that repetitive regions in genomes play indispensable roles in the evolution, inheritance and variation of living organisms. However, most existing methods cannot achieve satisfactory performance on identifying repeats in terms of both accuracy and size, since NGS reads are too short to identify long repeats whereas SMS (Single Molecule Sequencing) long reads are with high error rates. In this study, we present a novel identification framework, LongRepMarker, based on the global de novo assembly and k-mer based multiple sequence alignment for precisely marking long repeats in genomes. The major characteristics of LongRepMarker are as follows: (i) by introducing barcode linked reads and SMS long reads to assist the assembly of all short paired-end reads, it can identify the repeats to a greater extent; (ii) by finding the overlap sequences between assemblies or chomosomes, it locates the repeats faster and more accurately; (iii) by using the multi-alignment unique k-mers rather than the high frequency k-mers to identify repeats in overlap sequences, it can obtain the repeats more comprehensively and stably; (iv) by applying the parallel alignment model based on the multi-alignment unique k-mers, the efficiency of data processing can be greatly optimized and (v) by taking the corresponding identification strategies, structural variations that occur between repeats can be identified. Comprehensive experimental results show that LongRepMarker can achieve more satisfactory results than the existing de novo detection methods (https://github.com/BioinformaticsCSU/LongRepMarker).

EPGA-SC : A Framework for de novo Assembly of Single-Cell Sequencing Reads

Assembling genomes from single-cell sequencing data is essential for single-cell studies. However, single-cell assemblies are challenging due to (i) the highly non-uniform read coverage and (ii) the elevated levels of sequencing errors and chimeric reads. Although several assemblers for single-cell data have been proposed in recent years, most of them fail to construct correct long contigs. In this study, we present a new framework called EPGA-SC for de novo assembly of single-cell sequencing reads. The EPGA assembler has designed strategies to solve the problems caused by sequencing errors, sequencing biases, and repetitive regions. However, the extremely unbalanced and richer error types prevent EPGA to achieve high performance in single-cell sequencing data. In this study, we designed EPGA-SC based on EPGA. The main innovations of EPGA-SC are as follows: (i) classifying reads to reduce the proportion of false reads; (ii) using multiple sets of high precision paired-end reads generated from the high precision assemblies produced by other assembler such as SPAdes to overcome the impact of sequencing biases and repetitive regions; and (iii) developing novel algorithms for removing chimeric errors and extending contigs. We test EPGA-SC with seven datasets. The experimental results show that EPGA-SC can generate better assemblies than most current tools in most time in term of MAX contig, N50, NG50, NA50, and NGA50.

AB0197 EFFICACY AND SAFETY OF HLX01 COMBINED WITH METHOTREXATE IN CHINESE PATIENTS WITH MODERATELY TO SEVERELY ACTIVE RHEUMATOID ARTHRITIS WHO HAD INADEQUATE RESPONSES TO METHOTREXATE: RESULTS OF A RANDOMISED, DOUBLE-BLIND, PLACEBO-CONTROLLED PHASE 3 STUDY

Background:

Rituximab is an effective therapy for rheumatoid arthritis (RA) patients with inadequate responses to methotrexate (MTX)1, 2. However, it has not been registered or approved in China for the treatment of RA by far. HLX01, an approved rituximab biosimilar (demonstrated in Chinese patients with diffuse large B-cell lymphoma)3, is thus evaluated in this study for the benefits of Chinese RA patients.

Objectives:

This study aimed to evaluate the efficacy and safety of HLX01 plus MTX versus placebo plus MTX in Chinese patients with active RA who had inadequate responses to MTX.

Methods:

This was a randomised, double-blind, placebo-controlled phase 3 study conducted in China (NCT03522415). Eligible patients were randomised 2:1 to receive intravenous infusion of 2×1000 mg HLX01 or placebo on day 1 and day 15. Patients with inadequate responses at week 16 and 20 were allowed to receive rescue treatments. Patients were retreated with or switched to receive (if initially assigned to placebo) 2×1000 mg rituximab at the first day of week 24 and 26. The primary endpoint of this study was the American College of Rheumatology criteria (ACR) 20 response at week 24. Secondary efficacy endpoints were evaluated at week 12, 24, 36 and 48. The safety, pharmacokinetics, pharmacodynamics and immunogenicity of HLX01 were observed and analyzed throughout the study.

Results:

Between May 28, 2018 and Sep 11, 2020, a total of 275 patients (ITT set) were randomised and 263 patients without major protocol deviations were included in per-protocol set (PPS). At week 24, HLX01 showed statistically superior efficacy (p <0.001) to placebo (ACR20: 60.7% vs 35.9% in ITT set, 60.3% vs 37.1% in PPS). Secondary efficacy endpoints were also significantly improved in HLX01 group compared with placebo (Table 1). The overall incidence of serious treatment emergent adverse events (TEAEs), adverse drug reactions (ADRs), and TEAEs leading to drug discontinuation were similar among treatment groups, with the most common TEAE been upper respiratory tract infection before (18.1% vs 18.5%) or after (13.0% vs 12.3%) week 24. Serum concentrations, immunogenicity and pharmacodynamics were similar between HLX01 and placebo groups.

Table 1.

Results of secondary efficacy endpoints at week 12, 24, 36 and 48 in ITT set.

DurationSecondary efficacy endpointsACR20 (%)ACR50 (%)ACR70 (%)DAS28-CRP(mean)HAQ-DI(mean)HLX01PlaceboHLX01PlaceboHLX01PlaceboHLX01PlaceboHLX01PlaceboBaseline5.495.431.401.45Week 1248.132.621.910.94.45.43.894.471.021.22Week 2460.735.936.618.515.312.03.394.370.871.22Week 3660.148.946.431.532.217.42.883.510.710.97Week 4873.862.055.240.239.927.22.823.510.721.03

Conclusion:

Comparing with placebo plus MTX, HLX01 plus MTX showed significantly improved clinical outcomes and comparable safety profiles in Chinese patients with moderately to severely active RA who had inadequate responses to MTX, demonstrating HLX01 in combination with MTX as a well-tolerated, safe and efficient treatment option.

References:

[1]Emery P, Deodhar A, Rigby WF, et al. Efficacy and safety of different doses and retreatment of rituximab: a randomised, placebo-controlled trial in patients who are biological naive with active rheumatoid arthritis and an inadequate response to methotrexate (Study Evaluating Rituximab’s Efficacy in MTX iNadequate rEsponders (SERENE)). Ann Rheum Dis. Sep 2010;69(9):1629-35. doi:10.1136/ard.2009.119933.

[2]Rubbert-Roth A, Tak PP, Zerbini C, et al. Efficacy and safety of various repeat treatment dosing regimens of rituximab in patients with active rheumatoid arthritis: results of a Phase III randomized study (MIRROR). Rheumatology (Oxford). Sep 2010;49(9):1683-93. doi:10.1093/rheumatology/keq116.

[3]Shi Y, Song Y, Qin Y, et al. A phase 3 study of rituximab biosimilar HLX01 in patients with diffuse large B-cell lymphoma. J Hematol Oncol. Apr 16 2020;13(1):38. doi:10.1186/s13045-020-00871-9.

Acknowledgements:

The authors would like to thank participants in this study and their families. They would also like to acknowledge other investigators and staff at all clinical sites and the members of the Independent Data Monitoring Committee.

Disclosure of Interests:

None declared

High pressure homogenization inactivation of Escherichia coli and Staphylococcus aureus in phosphate buffered saline, milk and apple juice

High pressure homogenization (HPH) offers new opportunities for food pasteurization/sterilization. Escherichia coli and Staphylococcus aureus suspended in phosphate buffered saline (PBS) buffer, milk and apple juice at initial concentration of ~10⁶ log₁₀ CFU per ml were subjected to HPH treatments up to 200 MPa with inlet temperatures at 4-40°C. After HPH at 200 MPa with the inlet temperature at 40°C, the count of E. coli suspended in PBS, milk and apple juice reduced by 3·42, 3·67 and 3·19 log₁₀ CFU per ml respectively while the count of S. aureus decreased by 2·21, 1·02 and 2·33 log₁₀ CFU per ml respectively suggesting that S. aureus was more resistant. The inactivation data were well fitted by the polynomial equation. Milk could provide a protective effect for S. aureus against HPH. After HPH at 200 MPa with the inlet temperature at 20°C, the cell structure of E. coli was destroyed, while no obvious damages were found for S. aureus.

MultiNanopolish: Refined grouping method for reducing redundant calculations in nanopolish

MOTIVATION

Compared with the second generation sequencing technologies, the third generation sequencing technologies allows us to obtain longer reads (average ∼10kbps, maximum 900kbps), but brings a higher error rate (∼15% error rate). Nanopolish is a variant and methylation detection tool based on Hidden Markov Model (HMM), which uses Oxford Nanopore sequencing data for signal-level analysis. Nanopolish can greatly improve the accuracy of assembly, whereas it is limited by long running time since most executive parts of Nanopolish is a serial and computationally expensive process.

RESULTS

In this paper, we present an effective polishing tool, Multithreading Nanopolish (MultiNanopolish), which decomposes the whole process of iterative calculation in Nanopolish into small independent calculation tasks, making it possible to run this process in the parallel mode. Experimental results show that MultiNanopolish reduces running time by 50% with read-uncorrected assembler (Miniasm) and 20% with read-corrected assembler (Canu and Flye) based on 40 threads mode compared to the original Nanopolish.

AVAILABILITY

MultiNanopolish is available at GitHub: https://github.com/BioinformaticsCSU/MultiNanopolish.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads

Background

Repetitive sequences account for a large proportion of eukaryotes genomes. Identification of repetitive sequences plays a significant role in many applications, such as structural variation detection and genome assembly. Many existing de novo repeat identification pipelines or tools make use of assembly of the high-frequency k-mers to obtain repeats. However, a certain degree of sequence coverage is required for assemblers to get the desired assemblies. On the other hand, assemblers cut the reads into shorter k-mers for assembly, which may destroy the structure of the repetitive regions. For the above reasons, it is difficult to obtain complete and accurate repetitive regions in the genome by using existing tools.

Results

In this study, we present a new method called RepAHR for de novo repeat identification by assembly of the high-frequency reads. Firstly, RepAHR scans next-generation sequencing (NGS) reads to find the high-frequency k-mers. Secondly, RepAHR filters the high-frequency reads from whole NGS reads according to certain rules based on the high-frequency k-mer. Finally, the high-frequency reads are assembled to generate repeats by using SPAdes, which is considered as an outstanding genome assembler with NGS sequences.

Conlusions

We test RepAHR on five data sets, and the experimental results show that RepAHR outperforms RepARK and REPdenovo for detecting repeats in terms of N50, reference alignment ratio, coverage ratio of reference, mask ratio of Repbase and some other metrics.

An Efficient Trimming Algorithm based on Multi-Feature Fusion Scoring Model for NGS Data

Next-generation sequencing (NGS) has enabled an exponential growth rate of sequencing data. However, several sequence artifacts, including error reads (base calling errors and small insertions or deletions) and poor quality reads, which can impose significant impact on the downstream sequence processing and analysis. Here, we present PE-Trimmer, a sensitive and special trimming algorithm for NGS sequence. First, PE-Trimmer removes technical sequences in paired-end reads based on the characteristics of low quality reads in NGS data. Second, PE-Trimmer determines the range of reads that need to be trimmed according to the quality score statistics histogram of reads in the library. To improve the accuracy of this algorithm, we design a light-weight and easy-to-explain scoring model to evaluate candidates in the pattern of trimming step. Finally, PE-Trimmer selects the appropriate trimming strategy to process the low quality reads based on the location determined by the scoring model. PE-Trimmer is able to locate and remove adapter residues from the paired-end reads. It is easily configurable and offers superior throughput in the multi-threaded mode. We test PE-Trimmer on five datasets, and compare it with the current five latest methods. The experimental results demonstrate that PE-Trimmer produces more superior results, compared with other trimmers.

[Clinical analysis of seven cases with primary hyperoxaluria type 1 in children]

Objective: To investigate the clinical, imaging and molecular characteristics of primary hyperoxaluria type 1 (PH1) in children and to sum up existing evidence for further understanding the phenotype-genotype correlation of infantile PH1. Methods: This retrospective analysis was based on the medical records of children with PH1 diagnosed by gene test in the Department of Nephrology, Guangzhou Women and Children's Medical Center from June 2016 to May 2019. Targeted exome sequencing was performed on tubular disease-related genes of the probands and Sanger sequencing was conducted to validate suspected pathogenic variants of family members. Logistic regression analysis of NC and CCr was adopted to show the relation between NC and renal function. The literature review was conducted, and the clinical, imaging and molecular biogenetic characteristics of the disease were analyzed and summarized. Results: A total of 7 children from 6 families were enrolled. The median age of onset was 5 months. The median age of diagnosis was 8 months. Five cases had progressed to end-stage renal disease (ESRD), one case had chronic kidney disease (CKD) stage 1, and the other one had CKD stage 2. Four cases died, one case maintained on hemodialysis, and the other two non-dialysis cases were followed up. Among the 7 cases, 4 patients had infantile PH1, 1 patient had child and adolescent type, 1 patient had family type and the other one had unknown classification. There were two siblings (the younger brother had uremia and the sister had normal renal function) who had the delayed diagnosis for 5 and 3 years respectively. All patients in this cohort had proteinuria and microscopic hematuria, but no patients had gross hematuria. Three cases had hypercalciuria. Comprehensive diagnostic imaging evaluation include CT scan, MR scan, radiography and ultrasound led to the diagnosis of nephrocalcinosis (NC) in 5 cases, including 4 cases of simple NL and 1 case of NC with nephrolithiasis (NL), 1 case of multiple NL and 1 case of microcrystal deposition in renal medulla. However, only one case of NC was identified by ultrasound, the other 4 cases of NC were identified by radiograph examination. In the logistic regression analysis involving NC and creatinine clearnce rate (CCr), the results showed that NC was an independent risk factor for renal dysfunction (OR 2.5, 95%CI 0.7-1.2, P<0.05). All the 7 cases had AGXT gene variant, including homozygous variant in 4 cases and compound heterozygous variant in 3 cases. A total of 9 variant genotypes were found, and exon 6 variants were found in 4 children. Among them, there were 3 cases with c.679_680delAA. To our knowledge, both c.679_680delAA and c.190A>T in the cohort have not been reported previously. Conclusions: Infantile PH1 is the most common type of PH1 in children, which progresses rapidly or even begins with renal failure, with poor prognosis. It is also highly heterogeneous in phenotype and genotype. NC is an independent risk factor leading to renal failure. Radiograph examination showed high specificity for the diagnosis of NC. At present, the misdiagnosis and delayed diagnosis of PH1 are still common in China. It is of great significance to carry out quantitative determination of uric oxalate in order to reduce the misdiagnosis rate and enhance follow-up technologies for evaluating the therapeutic effect.