RABC: Rheumatoid Arthritis Bioinformatics Center.

Advances in sequencing technologies have led to the rapid growth of multi-omics data on rheumatoid arthritis (RA). However, a comprehensive database that systematically collects and classifies the scattered data is still lacking. Here, we developed the Rheumatoid Arthritis Bioinformatics Center (RABC, http://www.onethird-lab.com/RABC/), the first multi-omics data resource platform (data hub) for RA. There are four categories of data in RABC: (i) 175 multi-omics sample sets covering transcriptome, epigenome, genome, and proteome; (ii) 175 209 differentially expressed genes (DEGs), 105 differentially expressed microRNAs (DEMs), 18 464 differentially DNA methylated (DNAm) genes, 1 764 KEGG pathways, 30 488 GO terms, 74 334 SNPs, 242 779 eQTLs, 105 m6A-SNPs and 18 491 669 meta-mQTLs; (iii) prior knowledge on seven types of RA molecular markers from nine public and credible databases; (iv) 127 073 literature information from PubMed (from 1972 to March 2022). RABC provides a user-friendly interface for browsing, searching and downloading these data. In addition, a visualization module also supports users to generate graphs of analysis results by inputting personalized parameters. We believe that RABC will become a valuable resource and make a significant contribution to the study of RA.

Wild species rice OsCERK1DY-mediated arbuscular mycorrhiza symbiosis boosts yield and nutrient use efficiency in rice breeding.

Meeting the ever-increasing food demands of a growing global population while ensuring resource and environmental sustainability presents significant challenges for agriculture worldwide. Arbuscular mycorrhizal symbiosis (AMS) has emerged as a potential solution by increasing the surface area of a plant's root system and enhancing the absorption of phosphorus, nitrogen nutrients, and water. Consequently, there is a longstanding hypothesis that rice varieties exhibiting more efficient AMS could yield higher outputs at reduced input costs, paving the way for the development of Green Super Rice (GSR). Our prior research study identified a variant, OsCERK1DY, derived from Dongxiang wild-type rice, which notably enhanced AMS efficiency in the rice cultivar "ZZ35." This variant represents a promising gene for enhancing yield and nutrient use efficiency in rice breeding. In this study, we conducted a comparative analysis of biomass, crop growth characteristics, yield attributes, and nutrient absorption at varying soil nitrogen levels in the rice cultivar "ZZ35" and its chromosome single-segment substitution line, "GJDN1." In the field, GJDN1 exhibited a higher AM colonization level in its roots compared with ZZ35. Notably, GJDN1 displayed significantly higher effective panicle numbers and seed-setting rates than ZZ35. Moreover, the yield of GJDN1 with 75% nitrogen was 14.27% greater than the maximum yield achieved using ZZ35. At equivalent nitrogen levels, GJDN1 consistently outperformed ZZ35 in chlorophyll (Chl) content, dry matter accumulation, major nutrient element accumulation, N agronomic efficiency (NAE), N recovery efficiency (NRE), and N partial factor productivity (NPFP). The performance of OsCERK1DY overexpression lines corroborated these findings. These results support a model wherein the heightened level of AMS mediated by OsCERK1DY contributes to increased nitrogen, phosphorus, and potassium accumulation. This enhancement in nutrient utilization promotes higher fertilizer efficiency, dry matter accumulation, and ultimately, rice yield. Consequently, the OsCERK1DY gene emerges as a robust candidate for improving yield, reducing fertilizer usage, and facilitating a transition towards greener, lower-carbon agriculture. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01459-8.

Epigenome-wide methylation haplotype association analysis identified HLA-DRB1, HLA-DRB5 and HLA-DQB1 as risk factors for rheumatoid arthritis.

The aim of this study was to compare nonrandom associations between physically adjacent single methylation polymorphism loci among rheumatoid arthritis (RA) and normal subjects for investigating RA-risk methylation haplotypes (meplotype). With 354 ACPA-positive RA patients and 335 normal controls selected from a case-control study based on Swedish population, we conducted the first RA epigenome-wide meplotype association study using our software EWAS2.0, mainly including (i) converted the ß value to methylation genotype (menotype) data, (ii) identified methylation disequilibrium (MD) block, (iii) calculated frequent of each meplotypes in MD block and performed case-control association test and (iv) screened for RA-risk meplotypes by odd ratio (OR) and p-values. Ultimately, 545 meplotypes on 334 MD blocks were identified significantly associated with RA (p-value < .05). These meplotypes were mapped to 329 candidate genes related to RA. Subsequently, combined with gene optimization, eight RA-risk meplotypes were identified on three risk genes: HLA-DRB1, HLA-DRB5 and HLA-DQB1. Our results reported the relationship between DNA methylation pattern on HLA-DQB1 and the risk of RA for the first time, demonstrating the co-demethylation of 'cg22984282' and 'cg13423887' on HLA-DQB1 gene (meplotype UU, p-value = 2.90E - 6, OR = 1.68, 95% CI = [1.35, 2.10]) may increase the risk of RA. Our results demonstrates the potential of methylation haplotype analysis to identify RA-related genes from a new perspective and its applicability to the study of other disease.

[Research on Management Efficiency of Hospital Low-value Consumables in Nursing Unit under Lean Management Mode].

Aiming at the management efficiency problems in the traditional medical low-value consumables management mode of the nursing unit, based on the perspective of supply chain management, this study uses lean management method to construct the lean management mode of low-value consumables with a whole cycle and whole process information monitoring, and analyzes the application effect of this mode. The results show that after the application of lean management mode, the low-value consumables of the nursing unit can achieve "consumables in use=priced consumables + un-priced consumables", the settlement cost is significantly reduced and its stability is high, and the efficiency of "supply-inventor-distribution" link is significantly enhanced. This model effectively improves the management efficiency of low-value consumables in the hospital, and also provides a reference for other hospitals to improve the management level of low-value consumables.

Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.).

Heterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice varieties, Taiyou 871 (TY871), and Taiyou 398 (TY398) and the parental grain endosperm using RNA-seq (three biological repeats per variety) and untargeted metabolomic (six biological repeats per variety) methods. TY871 and TY398 showed specific heterosis in yield and quality. Transcriptome analysis of the hybrids revealed 638 to 4059 differentially expressed genes in the grain when compared to the parents. Metabolome analysis of the hybrids revealed 657 to 3714 differential grain metabolites when compared to the parents. The honeydew1 and grey60 module core genes Os04g0350700 and Os05g0154700 are involved in the regulation of awn development, grain size, and grain number, as well as the regulation of grain length and plant height, respectively. Rice grain length may be an important indicator for improving the quality of three-line hybrid rice. In addition, the rice quality-related metabolite NEG_M341T662 was highly connected to the module core genes Os06g0254300 and Os03g0168100. The functions of Os06g0254300 and Os03g0168100 are EF-hand calcium binding protein and late embroideries absolute protein repeat containing protein, respectively. These genes may play a role in the formation of rice quality. We constructed a gene and metabolite coexpression network, which provides a scientific basis for the utilization of heterosis in producing high-yield and high-quality hybrid rice.

[Practice of Refined Management of in Vitro Diagnostic Reagents Based on SPD in Hospital].

The management of in vitro diagnostic reagents has always been a concern. This paper describes the application of SPD medical consumables fine management system in our hospital. Relying on the brand-new management mode, the whole process from supplier qualification certificate management, in vitro diagnostic reagent procurement management, secondary warehouse management, and then to the use process traceability was realized. The monthly cost of in vitro diagnostic reagents can be accurately counted, which effectively controls the cost of in vitro diagnostic reagents.

EWASdb: epigenome-wide association study database.

DNA methylation, the most intensively studied epigenetic modification, plays an important role in understanding the molecular basis of diseases. Furthermore, epigenome-wide association study (EWAS) provides a systematic approach to identify epigenetic variants underlying common diseases/phenotypes. However, there is no comprehensive database to archive the results of EWASs. To fill this gap, we developed the EWASdb, which is a part of 'The EWAS Project', to store the epigenetic association results of DNA methylation from EWASs. In its current version (v 1.0, up to July 2018), the EWASdb has curated 1319 EWASs associated with 302 diseases/phenotypes. There are three types of EWAS results curated in this database: (i) EWAS for single marker; (ii) EWAS for KEGG pathway and (iii) EWAS for GO (Gene Ontology) category. As the first comprehensive EWAS database, EWASdb has been searched or downloaded by researchers from 43 countries to date. We believe that EWASdb will become a valuable resource and significantly contribute to the epigenetic research of diseases/phenotypes and have potential clinical applications. EWASdb is freely available at http://www.ewas.org.cn/ewasdb or http://www.bioapp.org/ewasdb.

[Construction of Quality Control System for Medical Equipment under the Model of County Medical Service Community].

The construction of county and district medical community is an important measure for high-quality medical resources to "double sink and improve". In this study, we have initially constructed a medical equipment quality control system for members of the regional medical community. The current situation of lack of professional medical equipment management personnel and quality control equipment in primary medical institutions has been alleviated, the quality control level of medical equipment in primary medical institutions has been improved, and a new management model for quality control of primary medical equipment has been explored.

[The Traceability Management for Qualification Documents of Medical Instruments].

The management for qualification documents of medical instruments is very important work to management department of medical instruments. Because the number of qualification documents of medical instruments is very large and they have an expiry date, it is difficult to manage them. This article discussed how to manage qualification documents of medical instruments, and an information management system that has a function of traceability management has been developed. This information management system standardizes management for qualification documents of medical instruments, and ensures that qualification documents of medical instruments are available and can be traced. Besides, it can reduce the amount of work for medical instruments management.

[Refined Management of the Second Class Warehouse and Cost-benefit Analysis for In-vitro Diagnostic Reagent].

As the material basis of clinical examination, in -vitro diagnostic reagent could directly affect the timeliness and accuracy of clinical examination report if it was not uses properly. This article discusses about how to strengthen the management for the temperature monitoring, effect management, inventory management and cost-benefit analysis of in-vitro diagnostic reagents. An information management system that provides methods for fine management of in-vitro diagnostic reagents has been developed.

[A Medical Devices Management Information System Supporting Full Life-Cycle Process Management].

Medical equipments are essential supplies to carry out medical work. How to ensure the safety and reliability of the medical equipments in diagnosis, and reduce procurement and maintenance costs is a topic of concern to everyone. In this paper, product lifecycle management (PLM) and enterprise resource planning (ERP) are cited to establish a lifecycle management information system. Through integrative and analysis of the various stages of the relevant data in life-cycle, it can ensure safety and reliability of medical equipments in the operation and provide the convincing data for meticulous management.

[PTPN22 1858C/T polymorphism is associated with rheumatoid arthritis susceptibility in Caucasian population: a meta-analysis].

OBJECTIVE: To investigate the association of 1858C/T polymorphism of protein tyrosine phosphatase nonreceptor type 22 (PTPN22) and rheumatoid arthritis (RA) susceptibility. METHODS: CMB, wanfang (Chinese) and PubMed databases were searched to get the studies on the association between 1858C/T polymorphism and RA susceptibility, and odds ratio (OR) and 95% confidential interval (CI) were calculated under different genetic models. Then heterogeneity, stratified analysis, and publication bias test were conducted in the study. RESULTS: A total of 32 studies (40 separate comparisons) with 25 059 RA patients and 25 466 controls were included in this meta-analysis. No evidence for publication bias was found in these studies. Meta-analysis showed an association between PTPN22 1858C/T polymorphism and RA (OR=1.606, 95%CI: 1.518-1.699, P<0.001). When stratified by ethnicity, T allele of PTPN22 1858C/T polymorphism was a risk allele in Caucasian (OR=1.612, 95%CI: 1.544-1.683, P<0.001); however, the polymorphism was not detected in Asians (or allele frequencies was extremely low). PTPN22 1858C/T polymorphism was associated with rheumatoid factor (RF) and anti-cyclic citrullinated peptide antibody (ACCP). CONCLUSION: T allele of PTPN22 1858C/T polymorphism is associated with RA susaptibility in Caucasians. PTPN22 1858C/T polymorphism is significantly more prevalent in RF-positive or ACCP-positive patients than in RF-negative or ACCP-negative patients.

[A medical consumable material management information system].

Medical consumables material is essential supplies to carry out medical work, which has a wide range of varieties and a large amount of usage. How to manage it feasibly and efficiently that has been a topic of concern to everyone. This article discussed about how to design a medical consumable material management information system that has a set of standardized processes, bring together medical supplies administrator, suppliers and clinical departments. Advanced management mode, enterprise resource planning (ERP) applied to the whole system design process.

Prediction of aluminum, uranium, and co-contaminants precipitation and adsorption during titration of acidic sediments.

Batch and column recirculation titration tests were performed with contaminated acidic sediments. A generic geochemical model was developed combining precipitation, cation exchange, and surface complexation reactions to describe the observed pH and metal ion concentrations in experiments with or without the presence of CO2. Experimental results showed a slow pH increase due to strong buffering by Al hydrolysis and precipitation and CO2 uptake. The cation concentrations generally decreased at higher pH than those observed in previous tests without CO2. Using amorphous Al(OH)3 and basaluminite precipitation reactions and a cation exchange selectivity coefficient K(Na\Al) of 0.3, the model approximately described the observed (1) pH titration curve, (2) Ca, Mg, and Mn concentration by cation exchange, and (3) U concentrations by surface complexation with Fe hydroxides at pH < 5 and with liebigite (Ca2UO2(CO3)3·10H2O) precipitation at pH > 5. The model indicated that the formation of aqueous carbonate complexes and competition with carbonate for surface sites could inhibit U and Ni adsorption and precipitation. Our results suggested that the uncertainty in basaluminite solubility is an important source of prediction uncertainty and ignoring labile solid phase Al underestimates the base requirement in titration of acidic sediments.

U(VI) bioreduction with emulsified vegetable oil as the electron donor--microcosm tests and model development.

We conducted microcosm tests and biogeochemical modeling to study U(VI) reduction in contaminated sediments amended with emulsified vegetable oil (EVO). Indigenous microorganisms in the sediments degraded EVO and stimulated Fe(III), U(VI), and sulfate reduction, and methanogenesis. Acetate concentration peaked in 100-120 days in the EVO microcosms versus 10-20 days in the oleate microcosms, suggesting that triglyceride hydrolysis was a rate-limiting step in EVO degradation and subsequent reactions. Acetate persisted 50 days longer in oleate- and EVO- than in ethanol-amended microcosms, indicating that acetate-utilizing methanogenesis was slower in the oleate and EVO than ethanol microcosms. We developed a comprehensive biogeochemical model to couple EVO hydrolysis, production, and oxidation of long-chain fatty acids (LCFA), glycerol, acetate, and hydrogen, reduction of Fe(III), U(VI) and sulfate, and methanogenesis with growth and decay of multiple functional microbial groups. By estimating EVO, LCFA, and glycerol degradation rate coefficients, and introducing a 100 day lag time for acetoclastic methanogenesis for oleate and EVO microcosms, the model approximately matched observed sulfate, U(VI), and acetate concentrations. Our results confirmed that EVO could stimulate U(VI) bioreduction in sediments and the slow EVO hydrolysis and acetate-utilizing methanogens growth could contribute to longer term bioreduction than simple substrates (e.g., ethanol, acetate, etc.) in the subsurface.

U(VI) bioreduction with emulsified vegetable oil as the electron donor--model application to a field test.

We amended a shallow fast-flowing uranium (U) contaminated aquifer with emulsified vegetable oil (EVO) and subsequently monitored the biogeochemical responses for over a year. Using a biogeochemical model developed in a companion article (Tang et al., Environ. Sci. Technol.2013, doi: 10.1021/es304641b) based on microcosm tests, we simulated geochemical and microbial dynamics in the field test during and after the 2-h EVO injection. When the lab-determined parameters were applied in the field-scale simulation, the estimated rate coefficient for EVO hydrolysis in the field was about 1 order of magnitude greater than that in the microcosms. Model results suggested that precipitation of long-chain fatty acids, produced from EVO hydrolysis, with Ca in the aquifer created a secondary long-term electron donor source. The model predicted substantial accumulation of denitrifying and sulfate-reducing bacteria, and U(IV) precipitates. The accumulation was greatest near the injection wells and along the lateral boundaries of the treatment zone where electron donors mixed with electron acceptors in the groundwater. While electron acceptors such as sulfate were generally considered to compete with U(VI) for electrons, this work highlighted their role in providing electron acceptors for microorganisms to degrade complex substrates thereby enhancing U(VI) reduction and immobilization.

In situ bioremediation of uranium with emulsified vegetable oil as the electron donor.

A field test with a one-time emulsified vegetable oil (EVO) injection was conducted to assess the capacity of EVO to sustain uranium bioreduction in a high-permeability gravel layer with groundwater concentrations of (mM) U, 0.0055; Ca, 2.98; NO3(-), 0.11; HCO3(-), 5.07; and SO4(2-), 1.23. Comparison of bromide and EVO migration and distribution indicated that a majority of the injected EVO was retained in the subsurface from the injection wells to 50 m downgradient. Nitrate, uranium, and sulfate were sequentially removed from the groundwater within 1-2 weeks, accompanied by an increase in acetate, Mn, Fe, and methane concentrations. Due to the slow release and degradation of EVO with time, reducing conditions were sustained for approximately one year, and daily U discharge to a creek, located approximately 50 m from the injection wells, decreased by 80% within 100 days. Total U discharge was reduced by 50% over the one-year period. Reduction of U(VI) to U(IV) was confirmed by synchrotron analysis of recovered aquifer solids. Oxidants (e.g., dissolved oxygen, nitrate) flowing in from upgradient appeared to reoxidize and remobilize uranium after the EVO was exhausted as evidenced by a transient increase of U concentration above ambient values. Occasional (e.g., annual) EVO injection into a permeable Ca and bicarbonate-containing aquifer can sustain uranium bioreduction/immobilization and decrease U migration/discharge.

Integrated 16S and metabolomics revealed the mechanism of drought resistance and nitrogen uptake in rice at the heading stage under different nitrogen levels.

The normal methods of agricultural production worldwide have been strongly affected by the frequent occurrence of drought. Rice rhizosphere microorganisms have been significantly affected by drought stress. To provide a hypothetical basis for improving the drought resistance and N utilization efficiency of rice, the study adopted a barrel planting method at the heading stage, treating rice with no drought or drought stress and three different nitrogen (N) levels. Untargeted metabolomics and 16S rRNA gene sequencing technology were used to study the changes in microorganisms in roots and the differential metabolites (DMs) in rhizosphere soil. The results showed that under the same N application rate, the dry matter mass, N content and N accumulation in rice plants increased to different degrees under drought stress. The root soluble protein, nitrate reductase and soil urease activities were improved over those of the no-drought treatment. Proteobacteria, Bacteroidota, Nitrospirota and Zixibacteria were the dominant flora related to N absorption. A total of 184 DMs (98 upregulated and 86 downregulated) were identified between low N with no drought (LN) and normal N with no drought (NN); 139 DMs (83 upregulated and 56 downregulated) were identified between high N with no drought (HN) and NN; 166 DMs (103 upregulated and 63 downregulated) were identified between low N with drought stress (LND) and normal N with drought stress (NND); and 124 DMs (71 upregulated and 53 downregulated) were identified between high N with drought stress (HND) and NND. Fatty acyl was the metabolite with the highest proportion. KEGG analysis showed that energy metabolism pathways, such as D-alanine metabolism and the phosphotransferase system (PTS), were enriched. We conclude that N-metabolism enzymes with higher activity and higher bacterial diversity have a significant effect on drought tolerance and nitrogen uptake in rice.

Identification of novel meQTLs strongly associated with rheumatoid arthritis by large-scale epigenome-wide analysis.

Rheumatoid arthritis (RA) is highly heritable, and previous studies have suggested that genetic variation may affect susceptibility to RA by altering epigenetic modifications (e.g. DNA methylation). Here we examined how genetic variation influences DNA methylation (DNAm) in RA by integrating individual genetic variation and DNAm data. Epigenome-wide meQTL (methylation quantitative trait loci) analysis was performed on 354 RA patients and 335 controls, scanning 30,101,744 relationships between 62 SNPs and 485,512 DNA methylation sites. Two regulatory relationship pairs (FDR < 0.05) showed very strong associations with RA risk. One was rs10796216-cg00475509, and the DNAm decreased by 0.0168 per addition of allele rs10796216-A. The other was rs6546473-cg13358873, for which a 0.0365 reduction of DNAm at cg13358873 was observed for each addition of allele rs6546473-A, and lower DNAm was found to be significantly associated with RA risk (P = 2.0407e-28). Moreover, both pairs of meQTL showed a strong regulatory relationship only in RA samples, so they can be subsequently considered as risk markers for RA. In conclusion, our integrated analysis of genetic and epigenetic variation suggests that genetic variation may affect the risk of RA by regulating DNA methylation levels. Alterations of DNAm at cg00475509 and cg13358873 loci conferred by rs10796216-A and rs6546473-A allele may suggest a potential risk for RA. Our results deepen our understanding of the genetic and epigenetic mechanisms of RA and provide novel associations that can be further investigated in future studies.

Mobile-Based and Self-Service Tool (iPed) to Collect, Manage, and Visualize Pedigree Data: Development Study.

BACKGROUND: Pedigree data (family history) are indispensable for genetics studies and the assessment of individuals' disease susceptibility. With the popularity of genetics testing, the collection of pedigree data is becoming more common. However, it can be time-consuming, laborious, and tedious for clinicians to investigate all pedigree data for each patient. A self-service robot could inquire about patients' family history in place of professional clinicians or genetic counselors. OBJECTIVE: The aim of this study was to develop a mobile-based and self-service tool to collect and visualize pedigree data, not only for professionals but also for those who know little about genetics. METHODS: There are 4 main aspects in the iPed construction, including interface building, data processing, data storage, and data visualization. The user interface was built using HTML, JavaScript libraries, and Cascading Style Sheets (version 3; Daniel Eden). Processing of the submitted data is carried out by PHP programming language. MySQL is used to document and manage the pedigree data. PHP calls the R script to accomplish the visualization. RESULTS: iPed is freely available to all users through the iPed website. No software is required to be installed, no pedigree files need to be prepared, and no knowledge of genetics or programs is required. The users can easily complete their pedigree data collection and visualization on their own and through a dialogue with iPed. Meanwhile, iPed provides a database that stores all users' information. Therefore, when the users need to construct new pedigree trees for other genetic traits or modify the pedigree trees that have already been created, unnecessary duplication of operations can be avoided. CONCLUSIONS: iPed is a mobile-based and self-service tool that could be used by both professionals and nonprofessionals at any time and from any place. It reduces the amount of time required to collect, manage, and visualize pedigree data.