Quality Control Standards Research Articles

Abstract 5705: Identifying DNA methylation quantitative trait loci across multi-ethnic populations

Abstract Objective: To date, genome-wide association studies (GWAS), which are primarily conducted in Europeans, have identified a large number of validated DNA methylation quantitative trait loci (meQTLs) acting in both cis and trans. However, it is recognized that there are racial differences in genetic architectures such as allele frequencies and linkage equilibrium patterns, which may differentially influence DNA methylation levels. This points to a critical need to conduct a methylome wide association study (MWAS) to identify meQTLs across multiethnic populations including understudied African Americans (AAs), Latinos, Japanese Americans (JAs), and Native Hawaiians (NHs). Methods: We are performing a GWAS to identify meQTLs in blood leukocytes in a multiethnic population using data from the Multiethnic Cohort Study (MEC). In MEC, “genome-wide” germline genetic variants and DNA methylation levels of blood leukocytes have been measured using the Illumina 1M and MethEPIC array, respectively, for 372 AAs, 408 Latinos, 531 JAs, 319 NHs, and 406 European Americans who were current smokers at time of blood draw. Genotyped data has been imputed with 1000 Genomes phase 3 dataset. For DNA methylation data, standardized quality control (QC) and normalization have been performed. We adjusted for the following potential confounders at time of blood draw: age, sex, body mass index, estimated cell type composition variables, genetic principal components, smoking pack-years, and urinary total nicotine equivalents (a biomarker for internal smoking dose). A stringent Bonferroni-corrected threshold (P<5×10-8/(850,355×6) = 9.80×10-15) was used to define statistical significance. An independent dataset of MEC participants including 114 AAs, 142 Latinos, 286 JAs, 108 NHs, and 270 European Americans will be used to replicate the identified meQTLs. Results: Our preliminary analyses for identifying cis-meQTL SNPs (residing within 1 Mb upstream or downstream of a CpG site of interest) found 169,823 CpG sites (20.0%) are associated with at least one nearby genetic variant in AAs. Similarly, 284,371 CpG sites (33.4%) in JAs, 168,580 CpG sites (19.8%) in Latinos, 123,032 CpG sites (14.5%) in NHs, and 234,822 CpG sites (27.6%) in European Americans are significantly associated with at least one nearby genetic variant. In the pan-ethnic analyses including all five ethnic/racial groups, 193,743 CpG sites (23.0%) are associated with at least one nearby genetic variant. Conclusion: Our preliminary findings identified ethnic-specific and pan-ethnic cis-meQTL SNPs across a multiethnic population that includes understudied AAs, Latinos, JAs, NHs, along with European Americans. If replicated in independent datasets, these findings will significantly improve our understanding of genetic regulation of DNA methylation levels in these populations. Citation Format: Lang Wu, Xiequn Xu, Dalia Ghoneim, Kayla Kim, Alexandra Binder, Yesha Patel, Daniel O. Stram, Loïc Le Marchand, Sungshim L. Park. Identifying DNA methylation quantitative trait loci across multi-ethnic populations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5705.

Abstract 1913: Quality control workflows developed for the NCI Patient-Derived Models Repository using low pass whole genome sequencing and whole exome sequencing

Abstract Background: The National Cancer Institute's Patient-Derived Models Repository (NCI PDMR; pdmr.cancer.gov) is developing a variety of patient-derived xenograft (PDX) models for pre-clinical drug studies. All NCI PDMR models undergo quality control (QC) processes. Two unique QC challenges are: a) to assess genomic stability across PDX model passages; and b) to confirm the suitability of PDX-derived cancer associated fibroblasts (CAFs) as germline surrogates when blood is not available. Multiple bioinformatics QC assessments have been developed to measure the genomic fidelity in these PDX models using low-pass whole genome sequencing (LP-WGS) and in CAFs using whole exome sequencing (WES). Methods: LP-WGS was performed on 502 PDX samples from 38 models of rare cancer across passages 2 through 9 and WES was performed on 92 CAFs from 32 different histologies. In the QC workflow for estimating the genomic stability of passages within models, BBSplit was used for the assessment of human/mouse DNA content. CNVkit was utilized for copy number (CN) detection. The fraction of genome changed was calculated by comparing the copy numbers of each passage sample to the original patient sample. To evaluate purity of CAFs, three QC steps were constructed: a) plot of SNP variant allele frequency (ideogram); b) variant annotation using OncoKB (www.oncokb.org); c) percentage of genomic loss of heterozygosity (LOH), based on a set of ~800,000 heterozygous SNPs from a population-level genomic database (gnomAD) based on WES data. Results: PDX models showed genomic stability in CN profile when measured by LP-WGS. Human tumor DNA content remains stable ranging from 75-85% across different tiers of PDX passages from Donor +1 to Donor +6 and more. No models showed statistically significant evolution in CN profile, given the average 5 samples per model in each tier of passages. The QC workflow for CAFs generated five categories based on SNP ideograms, the presence/absence of oncogenic variants and LOH. Following observations were made: a) 72.5% CAFs were confirmed as matched diploid CAFs (category 1); b) 6.6% of CAFs were diploid and had >= 1 germline oncogenic variant - classified as category 2. CAFs in category 1&2 were suitable as germline surrogates; c) 12% of CAFs (category 3) showed putative polyploidy on SNP ideograms with no oncogenic variants and suitable for somatic variant calling; d) 8.8% of CAFs (category 4) had polyploidy and oncogenic variants present; e) LOH high CAF (category 5) - we identified a CAF with 42% LOH, later confirmed to be a tumor cell line by immunohistochemistry (IHC). Other CAFs (n=91) showed little variance, ranging from 0.6%-1.7% LOH. Conclusions: We developed standard QC workflows to evaluate genomic stability of PDX models during passaging and qualify CAFs as germline surrogates for pre-clinical study. Citation Format: Ting-Chia Chang, Li Chen, Biswajit Das, Yvonne A. Evrard, Chris A. Karlovich, Tomas Vilimas, Alyssa Chapman, Nikitha Nair, Luis Romero, Anna J. Lee Fong, Amanda Peach, Brandie Fullmer, Lindsay Dutko, Kelly Benauer, Gloryvee Rivera, Erin Cantu, Shahanawaz Jiwani, Nastaran Neishaboori, Tomas Forbes, Corinne Camalier, Luke Stockwin, Michael Mullendore, Michelle A. Eugeni, Dianne Newton, Melinda G. Hollingshead, Mickey P. Williams, James H. Doroshow. Quality control workflows developed for the NCI Patient-Derived Models Repository using low pass whole genome sequencing and whole exome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1913.

Evaluation of Radiation Protection Status of Diagnostic Radiology Departments of Hamadan University of Medical Sciences Hospitals

Purpose: The concept of Quality Control (QC) is considered a regular method to control, stabilize, and inspect the function of the diagnostic imaging system. The objective of implementing the QC program is to produce high-quality images by applying a minimum dose of radiation based on the As Low As Reasonably Achievable (ALARA) principle. Therefore, this study aimed to evaluate the status of radiation protection in diagnostic radiology wards of educational hospitals affiliated with Hamadan University of Medical Sciences.
 Materials and Methods: In order to implement the QC programs, standard QC tests were performed for 11 devices at educational hospitals affiliated with Hamadan University of Medical Sciences. A Sweden QC kit called Pirranha was used to carry out the QC tests of X-ray devices, and the dosimetry of controlled areas. Also, the measurement of ambient dose in different places was performed by Graetz dosimeter made in Germany.
 Results: Voltage Reproducibility, Exposure time reproducibility, tube outlet Linearity, and tube outlet reproducibility tests in all radiology departments which were in accordance with standard criteria were accepted; however, about 10% of the total filtration resulted in different centers needed to be corrected. In terms of radiation protection, 5% of the centers had problems related to warning signs, dimensions of radiology rooms were not standard at 7% of wards and also required protection was not sufficient at 9 percent. Moreover, there were problems with 12% of radiology centers in terms of dosimetry results and the efficiency of different parts of the radiology device.
 Conclusion: QC programs performed by authorized companies are costly. But if these programs are done by qualified physicists in addition to reducing costs, we will see a significant increase in the accuracy and precision of the obtained results.

Preclinical study of human umbilical cord mesenchymal stem cell sheets for the recovery of ischemic heart tissue

BackgroundHuman umbilical cord mesenchymal stem cells (hUC-MSCs) have been widely used due to their multipotency, a broad range of sources, painless collection, and compliance with standard amplification. Cell sheet technology is a tissue engineering methodology requiring scaffolds free, and it provides an effective method for cell transplantation. To improve the therapeutic efficacy, we combined hUC-MSCs with cell sheet technology to evaluate the safety and efficacy of hUC-MSC sheets in preclinical studies using appropriate animal models.MethodshUC-MSC sheets were fabricated by hUC-MSCs from a cell bank established by a standard operation process and quality control. Cytokine secretion, immunoregulation, and angiopoiesis were evaluated in vitro. Oncogenicity and cell diffusion assays of hUC-MSC sheets were conducted to verify the safety of hUC-MSCs sheet transplantation in mice. To provide more meaningful animal experimental data for clinical trials, porcine myocardial infarction (MI) models were established by constriction of the left circumflex, and hUC-MSC sheets were transplanted onto the ischemic area of the heart tissue. Cardiac function was evaluated and compared between the experimental and MI groups.ResultsThe in vitro results showed that hUC-MSC sheets could secrete multiple cellular factors, including VEGF, HGF, IL-6, and IL-8. Peripheral blood mononuclear cells had a lower proliferation rate and lower TNF-α secretion when co-cultured with hUC-MSC sheets. TH1 cells had a smaller proportion after activation. In vivo safety results showed that the hUC-MSCs sheet had no oncogenicity and was mainly distributed on the surface of the ischemic myocardial tissue. Echocardiography showed that hUC-MSC sheets effectively improved the left ventricular ejection fraction (LVEF), and the LVEF significantly changed (42.25 ± 1.23% vs. 66.9 ± 1.10%) in the hUC-MSC transplantation group compared with the MI group (42.52 ± 0.65% vs. 39.55 ± 1.97%) at 9 weeks. The infarct ratio of the hUC-MSCs sheet transplantation groups was also significantly reduced (14.2 ± 4.53% vs. 4.00 ± 2.00%) compared with that of the MI group.ConclusionAllogeneic source and cell bank established by the standard operation process and quality control make hUC-MSCs sheet possible to treat MI by off-the-shelf drug with universal quality instead of individualized medical technology.

Interval Type-3 Fuzzy Control for Automated Tuning of Image Quality in Televisions

In this article, an intelligent system utilizing type-3 fuzzy logic for automated image quality tuning in televisions is presented. The tuning problem can be formulated as controlling the television imaging system to achieve the requirements of production quality. Previously, the tuning process has been carried out by experts, by manually adjusting the television imaging system on production lines to meet the quality control standards. In this approach, interval type-3 fuzzy logic is utilized with the goal of automating the tuning of televisions manufactured on production lines. An interval type-3 fuzzy approach for image tuning is proposed, so that the best image quality is obtained and, in this way, meet quality requirements. A system based on type-3 fuzzy control is implemented with good simulation results. The validation of the type-3 fuzzy approach is made by comparing the results with human experts on the process of electrical tuning of televisions. The key contribution is the utilization of type-3 fuzzy in the image tuning application, which has not been reported previously in the literature.

The quality control standards and principles of the application and training of critical ultrasonography

Critical ultrasonography is widely used in ICU and has become an indispensable tool for clinicians. However, besides operator-dependency of critical ultrasonography, lack of standardized training mainly result in the physicians' heterogenous ultrasonic skill. Therefore, standardized training as well as strict quality control plays the key role in the development of critical ultrasonography. We present this quality control standards to promote better development of critical ultrasonography.

Technological, Biochemical and Microbiological Evaluation of Dehydrated Pleurotus ostreatus Powder for Nutraceutical Applications

Abstract: Mushroom-based products can serve as superior nutraceuticals in both preventing and alleviating human diseases. Dehydrated powder of Pleurotus ostreatus grown in Cuba has a rich nutritional composition and a large number of therapeutic properties. However, technological parameters (e.g. rheological), as well as biochemical and microbiological quality control standards for its use as a raw material in the manufacture of solid dosage forms with nutraceutical and biopharmaceutical applications have not been established yet. Objective: The study aims to determine the technological, biochemical and microbiological quality parameters of dehydrated Pleurotus ostreatus powder. Method: Rheological properties (Carr´s index, Hausner´s ratio, angle of repose and flow rate) were determined in seven batches of mushroom powder. Biochemical and microbiological analyses were performed using standard methods. Other physicochemical properties (mean particle size, pH and moisture) were also determined. Results: Technical parameters showed a mean particle size of 224.08±7.96 μm, Carr´s compressibility index (23.08-26.58%), Hausner´s ratio (1.30-1.36), angle of repose (36.6-41.90°) and flow rate (3.69-6.93 g cm-2 s-1), typical of materials with poor flowability. Biochemical analyses indicated significant nutraceutical composition: protein (25.0-30.4%), carbohydrate (45-60%), ash (6.1-9.8%), fiber (5-9%), β-D-Glucans (1.47-1.61%), iron (21-50 mg/100 g), zinc (3.8-8.0 mg/100 g), and polyphenols (123-160 mg/100 g). Moisture content was ≤3.50% and microbiological analyses were in agreement with ISO standards. Conclusion: Dehydrated P. ostreatus powder exhibits good nutraceutical composition and microbiological quality. Technological parameters evidenced poor flow properties, suggesting the need to include excipients to improve the rheological properties for applications as an active ingredient in solid dosage forms for health benefits.

Variation at the LRRK2 locus determines the rate of disease progression in pro- gressive supranuclear palsy

BackgroundThe genetic basis of variation in the rate of disease progression in primary tauopathies is poorly understood. Here, we have conducted a genome-wide association study (GWAS) of Progressive Supranuclear Palsy cases using survival as a marker of disease progression.MethodsTwo independent, deeply-phenotyped, PSP cohorts of European ancestry underwent genotyp- ing and SNP imputation. Standard data quality control steps were used, including a MAF threshold of 1%. We used a cox-proportional hazards survival model GWAS that adjusted for sex, age at motor symptom onset, PSP phenotype and ethnicity (first three principal components).Results1,001 PSP cases (2011 case-control GWAS, n=424; UCL PSP cohort, n=577) and 4,817,946 SNPs passed quality control steps and were available for analysis. We found a genome-wide significant signal on chromosome 12 with the lead SNP identified as rs2242367 (hazard ratio = 2.24, p-value = 7.5x10-10). This signal replicated when each independent cohort was analysed separately. The risk allele at this SNP was associated with a 1 year reduction in survival. eQTL analyses revealed that rs2242367 and its tagging SNPs are eQTLs for LRRK2 expression in whole blood and brain.ConclusionsWe hypothesise that the whole blood eQTL signal may impact on monocyte-derived micro- glia-like cells and that increased LRRK2 expression may result in a reactive microglia-induced pro-inflam- matory state which drives ongoing accumulation of misfolded tau protein and clinical disease progression.e.jabbari@ucl.ac.uk

Single-Cell Transcriptome Analysis Reveals the Importance of IRF1/FSTL1 in Synovial Fibroblast Subsets for the Development of Rheumatoid Arthritis

Objectives This study aimed to investigate the potential role of synovial fibroblasts (SFs) in the development of rheumatoid arthritis (RA) to identify potential molecular targets and provide a theoretical basis for the treatment of RA. Methods GSE109449, a fibroblast transcriptome dataset of synovial tissue from RA and osteoarthritis (OA), were obtained from the GEO database. After standard cell quality control, this single-cell transcriptome data was used to perform routine single-cell analysis processes. After completing dimensionality reduction, clustering, and cell subset identification of fibroblasts, the SCENIC analysis helped calculate the significant gene regulatory networks in fibroblasts and their subsets. From these computed gene regulatory networks, the regulon in which follistatin-like protein 1 (FSTL1) resides was extracted and used to analyze the transcriptional regulatory status of fibroblasts. Finally, the gene set enrichment analysis (GSEA) was used to calculate the respective enriched gene sets of IRF1 and FSTL1. Results Three SF subgroups were identified from the single-cell transcriptome analysis; SF subset 3 was more abundant in RA than in OA (p < 0.001). From the SCENIC analysis, we obtained 269 regulons and the corresponding gene regulatory networks in SF from the RA datasets. Next, we screened and obtained a regulon-containing FSTL1, where IRF1 was the major transcription factor. The top five regulons in SF subset 3 were TWIST1, MECOM, KLF6, MAFB, and RUNX1. Among the 3 SF subsets, IRF1 regulon was ranked the highest in SF subset 3. Differential analysis of pseudobulk RNA-seq showed that IRF1 was up-regulated in RA compared to OA. Between the three SF subgroups, IRF1 and FSTL1 expression was more up-regulated in SF subset 3 compared to the other two subgroups. Conclusions IRF1 was found to regulate the invasiveness of SFs by regulating FSTL1, which may influence the disease progression of RA.

Research status and prospects of integration of habitat processing and processing of Chinese medicinal decoction pieces

The integration of habitat processing and processing of Chinese medicinal decoction pieces(hereinafter referred to as &quot;integration&quot;) has changed the traditional processing mode and can ensure the quality of Chinese medicinal decoction pieces from the source. This paper introduced the background of integration from the connotation and denotation of integration, relevant policies and regulations, and variety development. The present situation of integration was analyzed from the existing problems and current research progress, and the development suggestions were proposed. It is considered that although the integration is in line with the development trend of the industry with the advantages of improving the quality and standardizing the management of decoction pieces, there are still some problems, such as the lack of variety selection principles and production technical specifications, imperfect quality control stan-dards in the production process, and inadequate integration of standards and supervision. Therefore, it is suggested to determine the integrated variety selection principles and variety range as soon as possible, establish relevant technical specifications, improve quality control standards in the production process, and strengthen policy guidance and supervision to promote the healthy and orderly development of integration.

A genome-wide association study (GWAS) of event-free survival in follicular lymphoma treated in first-line therapy with immunochemotherapy: study design and initial results using a leave-one-cohort-out cross-validation statistical approach

Relatively few studies have evaluated the role of germline genetics in predicting outcome in FL and most of these were small candidate gene studies. In addition, adapting statistical designs used in susceptibility GWAS for outcomes is challenging. In fact, at the genome-wide scale, discoveries from one cohort may fail to replicate in other cohorts due to both cohort heterogeneity, the « winner curse » phenomenon, and limited statistical power. To identify robust and reproducible SNPs associated with event-free survival (EFS) of FL patients, we developed a specific cross-validation statistical design in a multi-cohort study in order to better balance statistical power across cohorts and identify robust findings that replicate across cohorts. We conducted a GWAS study of FL patients treated with immunochemotherapy for EFS with adjustment for population stratification using, FLIPI score, and use of rituximab maintenance. Cohorts were from prospective clinical trials of the Lymphoma Study Association (LYSA, PRIMA [N=391], RELEVANCE [N=396], the Fondazione Italiana Linfomi (FIL, FOL05, [N=199]) and the Iowa/Mayo Clinic Lymphoma Specialized Program of Research Excellence (SPORE) (N=154), a prospective observational study. Genotyping for the GWAS was performed using Human Core exome (PRIMA, RELEVANCE, FOL05) and 660 Quad (SPORE) BeadChips (Illumina, San Diego, USA). Minimac4/1000G was used to impute additional SNPs. Statistical design is based on cross-validation statistical technique. Following a « leave-one-cohort-out » (LOCO) strategy, J train blocks are defined by combining iteratively the cohorts except cohort j which is left for validation purpose. A p-value threshold is defined to select the top SNPs from each train block, with subsequent validation based on p-value and hazard ratio estimate in the cohort that is left. Discordances between SNP hazard ratios from train and validation blocks indicates lack of reproducibility. At the end, SNPs are considered robust if they are discovered across several train blocks and validated with consistency. After standard quality control steps for genotyping, PCA for ancestry and population stratification (no exclusion) and imputation, 1,861,658 common SNPs for the five cohorts (N=1,140 patients) were analyzed. We will present in detail the cross-validation LOCO statistical design. Preliminary results for EFS indicated promising loci at chromosome 7 that replicated consistently across 4 out of the 5 train blocks in the unadjusted and adjusted Cox models. The LOCO design especially helps identifying SNPs with inconsistent results across cohorts. Some examples of divergent results across cohorts will be presented. The LOCO design can be used successfully to identify more robust results that are consistent across cohorts in GWAS, particularly in survival studies. Mots clés GWAS ; follicular lymphoma Déclaration de liens d'intérêts Les auteurs n'ont pas précisé leurs éventuels liens d'intérêts

Validation of a multiplexed and targeted lipidomics assay for accurate quantification of lipidomes

A major challenge of lipidomics is to determine and quantify the precise content of complex lipidomes to the exact lipid molecular species. Often, multiple methods are needed to achieve sufficient lipidomic coverage to make these determinations. Multiplexed targeted assays offer a practical alternative to enable quantitative lipidomics amenable to quality control standards within a scalable platform. Herein, we developed a multiplexed normal phase liquid chromatography-hydrophilic interaction chromatography multiple reaction monitoring method that quantifies lipid molecular species across over 20 lipid classes spanning wide polarities in a single 20-min run. Analytical challenges such as in-source fragmentation, isomer separations, and concentration dynamics were addressed to ensure confidence in selectivity, quantification, and reproducibility. Utilizing multiple MS/MS product ions per lipid species not only improved the confidence of lipid identification but also enabled the determination of relative abundances of positional isomers in samples. Lipid class-based calibration curves were applied to interpolate lipid concentrations and guide sample dilution. Analytical validation was performed following FDA Bioanalytical Method Validation Guidance for Industry. We report repeatable and robust quantitation of 900 lipid species measured in NIST-SRM-1950 plasma, with over 700 lipids achieving inter-assay variability below 25%. To demonstrate proof of concept for biomarker discovery, we analyzed plasma from mice treated with a glucosylceramide synthase inhibitor, benzoxazole 1. We observed expected reductions in glucosylceramide levels in treated animals but, more notably, identified novel lipid biomarker candidates from the plasma lipidome. These data highlight the utility of this qualified lipidomic platform for enabling biological discovery.

Non-targeted analysis with high-resolution mass spectrometry for investigation of riverbank filtration processes

A fully non-targeted analytical workflow for the investigation of a riverbank filtration site located at the river Danube has been developed and applied. Variations of compound intensities at different sampling locations of the riverbank filtration site and, for a single production well, over a monitoring period of one year have been investigated using liquid chromatography combined with time-of-flight-mass spectrometry followed by evaluation via non-targeted data analysis. Internal standardization and appropriate quality control strategies have been implemented into the workflow for reduction of possible methodological biases influencing data interpretation. Emphasis was placed on the assessment of different blank elimination steps and the final blank elimination strategy is reported. The spatial study of the selected riverbank filtration site revealed a homogenous composition of the filtered water sampled at 11 different locations across the 32,000 m2 site, except for one sampling location in a zone of the aquifer, which was only weakly connected to the well field in terms of hydrogeological conditions. The examination of time-dependent changes of the composition of surface and groundwater obtained at the riverbank filtration system revealed that the non-targeted workflow is fit-for-purpose regarding the assessment the stability of filtration efficiency and compound residence time in the riverbank filtration compartment. In total, 677 compounds were selected for the investigation of the time-dependent variations of the filtration process. Analysis of the signal intensities of these compounds revealed that the riverbank filtration is significantly reducing the intensity and number of compounds present in surface water over a wide polarity range. In addition, the method enabled the determination of compound residence times in the riverbank filtration system ranging from 5 to 7 days.

Kratom (Mitragyna speciosa) Validation: Quantitative Analysis of Indole and Oxindole Alkaloids Reveals Chemotypes of Plants and Products.

Many consumers are turning to kratom ( Mitragyna speciosa ) to self-manage pain and opioid addiction. In the United States, an array of capsules, powders, and loose-leaf kratom products are readily available. Additionally, several online sites supply live kratom plants. A prerequisite to establishing quality control and quality assurance standards for the kratom industry, or understanding how alkaloid levels effect clinical outcomes, is the identification and quantitation of major and minor alkaloid constituents within available products and preparations. To this end, an ultra-high performance liquid chromatography-high resolution mass spectrometry method was developed for the analysis of 8 indole alkaloids (7-hydroxymitragynine, ajmalicine, paynantheine, mitragynine, speciogynine, isopaynantheine, speciociliatine, and mitraciliatine) and 6 oxindole alkaloids (isomitraphylline, isospeciofoleine, speciofoline, corynoxine A, corynoxeine, and rhynchophylline) in US-grown kratom plants and commercial products. These commercial products shared a qualitatively similar alkaloid profile, with 12 – 13 detected alkaloids and high levels of the indole alkaloid mitragynine (13.9 ± 1.1 – 270 ± 24 mg/g). The levels of the other major alkaloids (paynantheine, speciociliatine, speciogynine, mitraciliatine, and isopaynantheine) and the minor alkaloids varied in concentration from product to product. The alkaloid profile of US-grown M. speciosa “Rifat” showed high levels of the indole alkaloid speciogynine (7.94 ± 0.83 – 11.55 ± 0.18 mg/g) and quantifiable levels of isomitraphylline (0.943 ± 0.033 – 1.47 ± 0.18 mg/g). Notably, the alkaloid profile of a US-grown M. speciosa seedling was comparable to the commercial products with a high level of mitragynine (15.01 ± 0.20 mg/g). This work suggests that there are several M. speciosa chemotypes.

Quality Control Standardization and in-vitro Antioxidant Activity of Marsilea quadrifolia Linn.

Pharmacognosy Research,2022,14,2,140-145.DOI:10.5530/pres.14.2.20Published:April 2022Type:Original ArticleAuthors:Kancharla Bhanukiran, Tarkeshwar Dubey, and Siva Hemalatha Author(s) affiliations:Kancharla Bhanukiran, Tarkeshwar Dubey, Siva Hemalatha* Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, INDIA. Abstract:Background: The species Marsilea quadrifolia L. belonging to the family Marsileaceae is a semi-aquatic plant widely distributed in the tropical and sub-tropical regions of India. The whole plant of Marsilea quadrifolia L. is extensively used for its eminent medicinal properties. Objectives: Despite promising therapeutic benefits, the plant seems to be less explored, and consequently, the present investigation focuses on exploring pharmacognostical parameters, quality control standardization and antioxidant studies. Materials and Methods: The microscopical (transverse sections of leaves, petiole, stem, and root.) studies, leaf constants (stomatal number, vein islet number, etc.), and powder microscopic examination were performed. All physicochemical evaluations, like swelling index, foaming index, etc. were accomplished as per the World health organization (WHO) guidelines. TLC profiling and HPLC standardization of ethanolic extract was also performed. In vitro, antioxidant activities of ethanolic extract were carried out by various methods. Results: The transverse sections of all parts of the plant, leaf constants, and powder microscopy were reported with clear identification. Physicochemical parameters, i.e., foaming index (<100), Loss on drying (13.99 w/w), moisture content (13.75 w/w), total ash value (13.5 w/w) were done. Ethanolic extract was standardized with reference to quercetin and quantified HPLC data was calculated to be 2.1805±0.02089 mg/g. The antioxidant potential of ethanolic extract and its IC50 values are reported. Conclusion: We have reported complete pharmacognostical standardization of Marsilea quadrifolia L. as per WHO guidelines. We have reported the antioxidant potential of ethanolic extract of the whole plant of Marsilea quadrifolia L. along with quantitative estimation of quercetin using HPLC. Keywords: Quercetin, HPLC, Pharmacognosy, Phytopharmaceuticals, Sushni, European water clover. View:PDF (495.6 KB)

OA24 Predicting drug immunogenicity to tumour necrosis factor inhibitors in patients with rheumatoid arthritis

Abstract Background/Aims Rheumatoid arthritis (RA) is a chronic immune-mediated inflammatory disease that irreversibly damages synovial joints. Tumour necrosis factor inhibitors (TNFi) may be prescribed for patients with moderate to severe RA. However, approximately 40% of patients do not respond well to TNFi, with a lack of effectiveness underpinned by immunogenicity (development of anti-drug antibodies) in some patients. A recent well-powered study by Sazonovs et al. (2020) reported a strong genetic association between the HLA-DQA1 locus and immunogenicity to TNFi in a cohort of Crohn's disease patients treated with either infliximab or adalimumab. The current study aimed to investigate the association between HLA alleles, primarily HLA-DQA1, and immunogenicity to adalimumab in RA patients. Methods Anti-adalimumab antibody titres were measured using radioimmunoassay in serum samples from RA patients following six months of treatment. Genetic datasets were generated using the Illumina OmniExpress genotyping array and, following standard quality control filtering, variants were imputed using SNP2HLA statistical software. Following imputation, filtering was performed to exclude variants in linkage disequilibrium or with low minor allele frequency. Logistic regression models were developed to explore the association between HLA alleles and amino acids and immunogenicity (all models were adjusted for sex). Amino acid positions of interest were annotated using P2Rank; a ligand binding site prediction tool. Results A total of 171 HLA alleles and 339 amino acid positions were analysed in 226 RA patients. The strongest association observed between HLA alleles and immunogenicity was for HLA-DQB1*02 (coefficient = 0.87; 95% CI, 0.31-1.43; p value = 2.10E-3), followed by HLA-DQA1*05 (coefficient = 0.91; 95% CI, 0.29-1.53; p value = 3.95E-3). The strongest associated amino acid positions were amino acids 66 and 67 within the ligand binding domain of the HLA-DQB1 protein. Conclusion In keeping with previous findings in Crohn's disease, variants within HLA-DQ molecules confer the strongest evidence for immunogenicity risk in RA patients receiving adalimumab. RA patients carrying these variants could be redirected to receive etanercept, an effective alternative to monoclonal antibodies that is not immunogenic. Further well-powered studies in RA are now warranted to replicate these findings. Disclosure M. Alshehri: None. N. Nair: None. C. Yap: None. J.D. Isaacs: None. K. Hyrich: Honoraria; Abbvie. A.W. Morgan: None. A.G. Wilson: None. A. Barton: None. D. Plant: None.

Deep learning-enabled mobile application for efficient and robust herb image recognition

With the increasing popularity of herbal medicine, high standards of the high quality control of herbs becomes a necessity, with the herb recognition as one of the great challenges. Due to the complicated processing procedure of the herbs, methods of manual recognition that require chemical materials and expert knowledge, such as fingerprint and experience, have been used. Automatic methods can partially alleviate the problem by deep learning based herb image recognition, but most studies require powerful and expensive computation hardware, which is not friendly to resource-limited settings. In this paper, we introduce a deep learning-enabled mobile application which can run entirely on common low-cost smartphones for efficient and robust herb image recognition with a quite competitive recognition accuracy in resource-limited situations. We hope this application can make contributions to the increasing accessibility of herbal medicine worldwide.

Production and quality control of NICA-MPD shashlik electromagnetic calorimeter in Tsinghua University

The Multi Purpose Detector (MPD) is one of the detectors at the NICA collider and the Electromagnetic Calorimeter (ECal) is an important part of MPD. The cylindrical ECal system consists of 2400 ECal modules. In the first stage (2020–2024), Tsinghua University (THU) will produce 460 ECal modules for MPD project. This article mainly introduces the production, quality control and cosmic ray test of ECal modules in THU. The process flow, quality control standards, and testing system of ECal production have been established, which guarantees the high-quality completion of mass production on schedule. Up to now, nearly 360 modules have been manufactured, and a total of 460 modules will be produced by June 2022.

Advancing Near-Real-Time Quality Controls of Meteorological Observations

Abstract Meteorological observations from ground weather stations are of the upmost importance to implement and run sectoral climate services and to perform scientific activities, such as models’ evaluation and data assimilation. However, meteorological observations may be affected by errors deteriorating the quality and the reliability of the products based on these data. To avoid such a cascade of effects, it is essential to quality check meteorological observations in near–real time. A new system based on several levels of increasing complexity checks is proposed here. Besides the standard quality controls, this system applies dynamic and adaptive checks targeting exactly the locations and the data under analysis. The proposed system is designed to be flexible and easily modifiable thanks to its combined R and XML implementation. To facilitate its applicability, the proposed system is made available as a free open-source software: QuackMe.

Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data

Single-cell RNA sequencing (scRNA-seq) can be used to gain insights into cellular heterogeneity within complex tissues. However, various technical artifacts can be present in scRNA-seq data and should be assessed before performing downstream analyses. While several tools have been developed to perform individual quality control (QC) tasks, they are scattered in different packages across several programming environments. Here, to streamline the process of generating and visualizing QC metrics for scRNA-seq data, we built the SCTK-QC pipeline within the singleCellTK R package. The SCTK-QC workflow can import data from several single-cell platforms and preprocessing tools and includes steps for empty droplet detection, generation of standard QC metrics, prediction of doublets, and estimation of ambient RNA. It can run on the command line, within the R console, on the cloud platform or with an interactive graphical user interface. Overall, the SCTK-QC pipeline streamlines and standardizes the process of performing QC for scRNA-seq data.