Reproducible Analysis Research Articles

Electroencephalographic markers from routine sleep discriminate individuals who are vulnerable or resilient to sleep loss.

Sleep loss impairs cognition; however, individuals differ in their response to sleep loss. Current methods to identify an individual's vulnerability to sleep loss involve time-consuming sleep-loss challenges and neurobehavioural tests. Here, we sought to identify electroencephalographic markers of sleep-loss vulnerability obtained from routine night sleep. We retrospectively analysed four studies in which 50 healthy young adults (21 women) completed a laboratory baseline-sleep phase followed by a sleep-loss challenge. After classifying subjects as resilient or vulnerable to sleep loss, we extracted three electroencephalographic features from four channels during the baseline nights, evaluated the discriminatory power of these features using the first two studies (discovery), and assessed reproducibility of the results using the remaining two studies (reproducibility). In the discovery analysis, we found that, compared to resilient subjects, vulnerable subjects exhibited: (1) higher slow-wave activity power in channel O1 (p < 0.0042, corrected for multiple comparisons) and in channels O2 and C3 (p < 0.05, uncorrected); (2) higher slow-wave activity rise rate in channels O1 and O2 (p < 0.05, uncorrected); and (3) lower sleep spindle frequency in channels C3 and C4 (p < 0.05, uncorrected). Our reproducibility analysis confirmed the discovery results on slow-wave activity power and slow-wave activity rise rate, and for these two electroencephalographic features we observed consistent group-difference trends across all four channels in both analyses. The higher slow-wave activity power and slow-wave activity rise rate in vulnerable individuals suggest that they have a persistently higher sleep pressure under normal rested conditions.

SAT630 Analytical Validation Of A Telomerase Reverse Transcriptase (TERT) Promoter Mutation Assay

Abstract Disclosure: P. Iyer: None. R. Dadu: Advisory Board Member; Self; Exelixis, Inc., Bayer, Inc. Research Investigator; Self; Merck, Exelixis, Inc., AstraZeneca. A. Barque: Employee; Self; Veracyte, Inc. Stock Owner; Self; Veracyte, Inc. Z. Cleslei: Employee; Self; Veracyte, Inc. Stock Owner; Self; Veracyte, Inc. H. Jiang: Employee; Self; Veracyte, Inc. Stock Owner; Self; Veracyte, Inc. S. Walsh: Employee; Self; Veracyte, Inc. Stock Owner; Self; Veracyte, Inc. X. Zheng: Employee; Self; Veracyte, Inc. Stock Owner; Self; Veracyte, Inc. Y. Hao: Employee; Self; Veracyte, Inc. Stock Owner; Self; Veracyte, Inc. J. Huang: Employee; Self; Veracyte, Inc. Stock Owner; Self; Veracyte, Inc. J.P. Klopper: Employee; Self; Veracyte, Inc. Stock Owner; Self; Veracyte, Inc. R.T. Kloos: Employee; Self; Veracyte, Inc. Stock Owner; Self; Veracyte, Inc. M. Cabanillas: Advisory Board Member; Self; Exelixis, Inc., Bayer, Inc. Consulting Fee; Self; Lilly USA, LLC, Bayer, Inc. Research Investigator; Self; Genentech, Inc., Merck. TERT promoter mutations are relatively enriched in larger, aggressive thyroid cancers and these malignancies carry an independently decreased rate of disease free and disease specific survival when compared to thyroid cancers with wild type TERT promoter gene sequences. High quality analytical validation of a diagnostic test promotes confidence in the results which inform clinical decision making. TERT promoter mutation testing is now offered as a complement to Afirma Genomic Sequencing Classifier (GSC) testing in thyroid nodules that are not designated as molecularly benign. The Afirma TERT test was developed at Veracyte, Inc. based on the AmpliSeq-for-Illumina technology to detect TERT promoter variants C228T and C250T in genomic DNA (gDNA) extracted from patient thyroid fine needle aspirates (FNAs) sent for Afirma GSC testing, without any need for increased needle passes or sample volume. Herein, we describe the analytical performance of the Afirma TERT test. We examined the analytical sensitivity of the Afirma TERT test to varied input DNA amounts and the limit of detection (LOD) of variant allele frequency (VAF). We determined the negative percent agreement (NPA) and the positive percent agreement (PPA) of the Afirma TERT test against a reference primer pair. We also evaluated the analytical specificity from potential interfering substances such as RNA and blood gDNA. Further, the intra-run, inter-run and inter-laboratory reproducibility of the assay were examined. Analytical sensitivity analysis showed that the Afirma TERT test is tolerant to variation in DNA input amount (7-13 ng) and can detect expected positive TERT promoter variants down to 5% VAF LOD at 7ng DNA input with &amp;gt; 95% sensitivity. Both NPA and PPA were 100% against the reference primer pair. Analytical specificity studies demonstrated that the Afirma TERT test remains accurate in presence of 20% RNA or 80% blood gDNA for an average patient sample that typically has 30% VAF. The Afirma TERT test results are highly reproducible across different operators, runs, reagent lots, and laboratories. The Afirma TERT test also demonstrated a 100% confirmation rate when compared with an external NGS-based reference assay executed in a non-Veracyte laboratory. The analytical robustness and reproducibility of the Afirma TERT test support its routine clinical use among thyroid nodules with indeterminate cytology that are Afirma GSC suspicious or Bethesda V/VI nodules. Presentation: Saturday, June 17, 2023

Scalable Infrastructure Supporting Reproducible Nationwide Healthcare Data Analysis toward FAIR Stewardship

Transparent and FAIR disclosure of meta-information about healthcare data and infrastructure is essential but has not been well publicized. In this paper, we provide a transparent disclosure of the process of standardizing a common data model and developing a national data infrastructure using national claims data. We established an Observational Medical Outcome Partnership (OMOP) common data model database for national claims data of the Health Insurance Review and Assessment Service of South Korea. To introduce a data openness policy, we built a distributed data analysis environment and released metadata based on the FAIR principle. A total of 10,098,730,241 claims and 56,579,726 patients’ data were converted as OMOP common data model. We also built an analytics environment for distributed research and made the metadata publicly available. Disclosure of this infrastructure to researchers will help to eliminate information inequality and contribute to the generation of high-quality medical evidence.

EP01.24: Reproducibility analysis of two speckle‐tracking software for antenatal semi‐automated assessment of fetal cardiac function

EP01.24: Reproducibility analysis of two speckle‐tracking software for antenatal semi‐automated assessment of fetal cardiac function

Free automatic software for quality assurance of computed tomography calibration, edges and radiomics metrics reproducibility

PurposeTo develop a QA procedure, easy to use, reproducible and based on open-source code, to automatically evaluate the stability of different metrics extracted from CT images: Hounsfield Unit (HU) calibration, edge characterization metrics (contrast and drop range) and radiomic features. MethodsThe QA protocol was based on electron density phantom imaging. Home-made open-source Python code was developed for the automatic computation of the metrics and their reproducibility analysis. The impact on reproducibility was evaluated for different radiation therapy protocols, and phantom positions within the field of view and systems, in terms of variability (Shapiro-Wilk test for 15 repeated measurements carried out over three days) and comparability (Bland-Altman analysis and Wilcoxon Rank Sum Test or Kendall Rank Correlation Coefficient). ResultsRegarding intrinsic variability, most metrics followed a normal distribution (88% of HU, 63% of edge parameters and 82% of radiomic features). Regarding comparability, HU and contrast were comparable in all conditions, and drop range only in the same CT scanner and phantom position. The percentages of comparable radiomic features independent of protocol, position and system were 59%, 78% and 54%, respectively. The non-significantly differences in HU calibration curves obtained for two different institutions (7%) translated in comparable Gamma Index G (1 mm, 1%, >99%). ConclusionsAn automated software to assess the reproducibility of different CT metrics was successfully created and validated. A QA routine proposal is suggested.

Clinical Reproducibility of the Stone Volume Measurement: A "Kidney Stone Calculator" Study.

An accurate estimation of the stone burden is the key factor for predicting retrograde intra-renal surgical outcomes. Volumetric calculations better stratify stone burden than linear measurements. We developed a free software to assess the stone volume and estimate the lithotrity duration according to 3D-segmented stone volumes, namely the Kidney Stone Calculator (KSC). The present study aimed to validate the KSC's reproducibility in clinical cases evaluating its inter-observer and intra-observer correlations. Fifty patients that harbored renal stones were retrospectively selected from a prospective cohort. For each patient, three urologists with different experience levels in stone management made five measurements of the stone volume on non-contrast-enhanced computed tomography (NCCT) images using the KSC. the overall inter-observer correlation (Kendall's concordance coefficient) was 0.99 (p < 0.0001). All three paired analyses of the inter-observer reproducibility were superior to 0.8. The intra-observer variation coefficients varied from 4% to 6%, and Kendall's intra-observer concordance coefficient was found to be superior to 0.98 (p < 0.0001) for each participant. Subgroup analyses showed that the segmentation of complex stones seems to be less reproductible. The Kidney Stone Calculator is a reliable tool for the stone burden estimation. Its extension for calculating the lithotrity duration is of major interest and could help the practitioner in surgical planning.

Reproducibility in pharmacometrics applied in a phase III trial of BCG-vaccination for COVID-19

Large clinical trials often generate complex and large datasets which need to be presented frequently throughout the trial for interim analysis or to inform a data safety monitory board (DSMB). In addition, reliable and traceability are required to ensure reproducibility in pharmacometric data analysis. A reproducible pharmacometric analysis workflow was developed during a large clinical trial involving 1000 participants over one year testing Bacillus Calmette-Guérin (BCG) (re)vaccination in coronavirus disease 2019 (COVID-19) morbidity and mortality in frontline health care workers. The workflow was designed to review data iteratively during the trial, compile frequent reports to the DSMB, and prepare for rapid pharmacometric analysis. Clinical trial datasets (n = 41) were transferred iteratively throughout the trial for review. An RMarkdown based pharmacometric processing script was written to automatically generate reports for evaluation by the DSMB. Reports were compiled, reviewed, and sent to the DSMB on average three days after the data cut-off, reflecting the trial progress in real-time. The script was also utilized to prepare for the trial pharmacometric analyses. The same source data was used to create analysis datasets in NONMEM format and to support model script development. The primary endpoint analysis was completed three days after data lock and unblinding, and the secondary endpoint analyses two weeks later. The constructive collaboration between clinical, data management, and pharmacometric teams enabled this efficient, timely, and reproducible pharmacometrics workflow.

Novel HYDALJSS08 Polyherbal Formulation Development and Ultra-Performance Liquid Chromatographic Separation, Estimation of Gallic Acid in Terminalia chebula Dried Fruits, and a Marketed Siddha-based Polyherbal Formulation “Kabusura Kudineer”

The Siddha-based polyherbal formulation known as “Kabusura Kudineer (Marketed)” contains fifteen plants materials in dried raw form and The Ayush Ministry, Govt. of India highly endorsed for use of “Kabusura kudineer” during the pandemic of COVID-19, due to its immuno-booster properties. The current study aims to develop and document an analytical strategy for the estimation of gallic acid (GA) and methyl, ethyl acetate fraction of Terminalia chebula dried fruits and in polyherbal formulations (Marketed, &amp; Developed). One of the active substances of Kabusura Kudineer and developed “HYDALJSS08” Polyherbal formulation is Myrobalan (T. chebula dried fruit-Combretaceae). Myrobalan restrains active principal substances are GA. GA is proven for its Anti-viral and immunomodulatory activity. During the pandemic of, COVID-19 ministry of Ayush, Govt of India highly recommended the immuno-booster Siddha-based polyherbal formulation “Kabusura Kudineer” for immune-boosting and treatment of COVID-19. TLC, and FTIR carried out the preliminary identification of GA and the sample. The HPLC method was developed on an Inertsil C18 (150*4.6 mm and 5 μm) column. The mobile phase was enhanced for water: Acetonitrile (50:50). The flow rate was 1-mL/min and was GA tracked at 272 nm in a UV detector. The total run time of the chromatogram is 8 minutes and the retention time of GA is observed. The Rf value of GA and sample was found to be 0.27. Validation was carried out according to ICH guidelines. The retention time of GA was 2.2 min, and the Valid parameter of GA is system precision, SD (14247.75), %RSD (0.9), Regression equation y = 25511 x−947505, Correlation coefficient (R2) 0.9999. The adequate Linearity concentration was found to be 50 to 150 μg/mL, LoDs (1.70 μg/mL), LoQs (5.16 μg/mL), Method precision %RSD (0.8), SD (11626.7), Recovery 99.8, and 101.1%. GA content was found in a formulation (“Kabusura Kudineer”- 1.39 μg/mL, developed “HYDALJSS08” Polyherbal formulation-379.4 μg/mL), and ethyl, methyl acetate fraction of T. chebula dried fruits was 105.59 and 29.17 μg/mL. The developed (HPLC) UPLC methods have enabled novel, simple, accurate, rapid, easy, reproducible, rugged, and linear analysis in these two fractions, and Siddha-based formulation “Kabusura kudineer” (Marketed), a developed “HYDALJSS08” Polyherbal formulation.

What is integrative medicine? Establishing the decision criteria for an operational definition of integrative medicine for general practice health services research in Australia

BackgroundOperational definitions outline how a conceptual definition will be measured for consistent, reproducible data collection and analysis. This article reports the decision criteria that will be used for an operational definition of integrative medicine (IM) in a secondary analysis of an Australian national survey of general practitioner activity. MethodsA multidisciplinary team applied an iterative approach, informed by expert knowledge and literature reviews to establish decision criteria for categorizing the terms in the Australian clinical interface terminology of the International Classification of Primary Care, second edition (ICPC-2 PLUS) and the Coding Atlas for Pharmaceutical Substances, according to whether they reflected IM, conventional/mainstream medicine (MM), or both IM and MM (IM/MM). ResultsThe final decision criteria categorized all terms for examinations, investigations, advice/counselling, and drugs with synthetic ingredients, and terms for referrals to secondary care services and healthcare practitioners that are not a traditional or complementary medicine practitioner as MM. Terms that could apply to both styles of clinical practice (e.g., preventive health, lifestyle medicine, psychosocial and some drugs with natural ingredients) were categorised as IM/MM. The remaining terms, that mostly reflected the World Health Organization's theoretical definitions of traditional and complementary medicine, were categorized as IM. ConclusionDifferentiating between integrative and conventional/mainstream medicine in general practice is context specific and not always possible. The category IM/MM proposes integrative medicine as an extension, rather than an alternative. The rationale for the integrative medicine operational definition has relevance for researchers and health services in Australia, and internationally.

CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data.

Assay for transposase-accessible chromatin (ATAC) and chromatin immunoprecipitation (ChIP), coupled with next-generation sequencing (NGS), have revolutionized the study of gene regulation. A lack of standardization in the analysis of the highly dimensional datasets generated by these techniques has made reproducibility difficult to achieve, leading to discrepancies in the published, processed data. Part of this problem is due to the diverse range of bioinformatic tools available for the analysis of these types of data. Secondly, a number of different bioinformatic tools are required sequentially to convert raw data into a fully processed and interpretable output, and these tools require varying levels of computational skills. Furthermore, there are many options for quality control that are not uniformly employed during data processing. We address these issues with a complete assay for transposase-accessible chromatin sequencing (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) upstream pipeline (CATCH-UP), an easy-to-use, Python-based pipeline for the analysis of bulk ChIP-seq and ATAC-seq datasets from raw fastq files to visualizable bigwig tracks and peaks calls. This pipeline is simple to install and run, requiring minimal computational knowledge. The pipeline is modular, scalable, and parallelizable on various computing infrastructures, allowing for easy reporting of methodology to enable reproducible analysis of novel or published datasets.

BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data

BackgroundBisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generated by whole genome bisulfite sequencing (WGBS) requires several computational steps before it is ready for statistical analysis, and particular care is required to process data in a timely and memory-efficient manner. Alignment to a reference genome is one of the most computationally demanding steps in a WGBS workflow, taking several hours or even days with commonly used WGBS-specific alignment software. This naturally motivates the creation of computational workflows that can utilize GPU-based alignment software to greatly speed up the bottleneck step. In addition, WGBS produces raw data that is large and often unwieldy; a lack of memory-efficient representation of data by existing pipelines renders WGBS impractical or impossible to many researchers.ResultsWe present BiocMAP, a Bioconductor-friendly methylation analysis pipeline consisting of two modules, to address the above concerns. The first module performs computationally-intensive read alignment using Arioc, a GPU-accelerated short-read aligner. Since GPUs are not always available on the same computing environments where traditional CPU-based analyses are convenient, the second module may be run in a GPU-free environment. This module extracts and merges DNA methylation proportions—the fractions of methylated cytosines across all cells in a sample at a given genomic site. Bioconductor-based output objects in R utilize an on-disk data representation to drastically reduce required main memory and make WGBS projects computationally feasible to more researchers.ConclusionsBiocMAP is implemented using Nextflow and available at http://research.libd.org/BiocMAP/. To enable reproducible analysis across a variety of typical computing environments, BiocMAP can be containerized with Docker or Singularity, and executed locally or with the SLURM or SGE scheduling engines. By providing Bioconductor objects, BiocMAP’s output can be integrated with powerful analytical open source software for analyzing methylation data.

BRAVEHEART: Open-source software for automated electrocardiographic and vectorcardiographic analysis

Background and ObjectivesElectrocardiographic (ECG) and vectorcardiographic (VCG) analyses are used to diagnose current cardiovascular disease and for risk stratification for future adverse cardiovascular events. With increasing use of digital ECGs, research into novel ECG/VCG parameters has increased, but widespread computer-based ECG/VCG analysis is limited because there are no currently available, open-source, and easily customizable software packages designed for automated and reproducible analysis. Methods and ResultsWe present BRAVEHEART, an open-source, modular, customizable, and easy to use software package implemented in the MATLAB programming language, for scientific analysis of standard 12-lead ECGs acquired in a digital format. BRAVEHEART accepts a wide variety of digital ECG formats and provides complete and automatic ECG/VCG processing with signal denoising to remove high- and low-frequency artifact, non-dominant beat identification and removal, accurate fiducial point annotation, VCG construction, median beat construction, customizable measurements on median beats, and output of measurements and results in numeric and graphical formats. ConclusionsThe BRAVEHEART software package provides easily customizable scientific analysis of ECGs and VCGs. We hope that making BRAVEHART available will allow other researchers to further the field of ECG/VCG analysis without having to spend significant time and resources developing their own ECG/VCG analysis software and will improve the reproducibility of future studies. Source code, compiled executables, and a detailed user guide can be found at http://github.com/BIVectors/BRAVEHEART. The source code is distributed under the GNU General Public License version 3.

Methods of analyzing the long head of the biceps tendon in the management of distal supraspinatus tendon ruptures. Part 2: The role and validation of an arthroscopic exploration protocol of the long head of the biceps tendon

IntroductionInter-observer arthroscopic assessments of the Long head of the Biceps tendon (LHB) injuries, in the absence of predefined instructions, are poorly reproducible. There are several types of LHB injuries, of varying severity, which can make its intraoperative analysis subjective. HypothesisThe application of a precise arthroscopic exploration protocol, particularly dynamic, associated with an equally precise analysis of the possible tendon lesions, intrinsic or extrinsic, makes it possible to obtain a reproducible analysis of the lesions of the LHB and aid decision-making around its conservation or its resection, in distal supraspinatus tendon ruptures. Material and methodsThis was a prospective, multicenter study including 371 patients with a stage 1 rupture of the supraspinatus tendon, in accordance with the Patte classification. An exploration protocol with intraoperative video recording of the articular portion of the biceps was systematically performed by the operators. It included static intra-articular and extra-articular observation of the LHB, as well as a dynamic intra-articular hook test with mobilization in internal and external rotation, and in anterior elevation. An analysis of the lesion status of the LHB was then made by the principal operator (Op), after defining the various possible lesions: intrinsic or extrinsic. This initial diagnostic assessment was then compared with the analysis made by two independent observers (Obs1, Obs2) based on a replay of the recorded videos. The reliability of agreement was then measured using Cohen's Kappa coefficient (K) and Fleiss’ kappa. ResultsTwo hundred and fifty-seven videos were analyzable. The level of agreement between the two independent observers was strong (K=0.63) for applying the diagnosis of a healthy or pathological biceps. The agreement between the independent observers and the operator was weaker (respectively K Op-Obs1=0.51 - moderate and K Op-Obs2=0.39 - poor). ConclusionThe application of a precise protocol for the exploration of the LHB, associated with a previously defined lesion classification, makes it possible to obtain a high rate of agreement for the arthroscopic diagnostic analysis of the LHB. However, arthroscopy cannot be used as the only criterion for deciding which procedure to perform on the LHB. Other clinical and para-clinical factors must be taken into consideration. Level of evidenceIII; prospective inter-observer series.

Validity and Reproducibility of Food Group-Based Food Frequency Questionnaires in Assessing Sugar-Sweetened Beverage Consumption Habits among Chinese Middle-School Students.

Assessing the intake of sugar-sweetened beverages (SSBs) is crucial for reducing obesity; however, a simple but relatively accurate method for determining added sugar consumption among school adolescents is lacking. The aim of this study was to evaluate the reproducibility and validity of a food group-based food frequency questionnaire (FG-FFQ) for SSBs in assessing SSB consumption and added sugar among middle-school students. A total of 242 school students completed the FG-FFQs twice and four discontinuous 24-h dietary records (24HDR) over a three-month period. A weighted average approach was used to obtain the average sugar content in the sugary drink food group (FG). Correlation coefficient, weighted kappa statistic, misclassification analysis, and Bland-Altman plot were used to evaluate the validity and reproducibility of the FG-FFQ. Linear regression was utilized to obtain the calibration formulas. The average content of added sugar in sugary drink FG was 8.1 g/100 mL. SSB consumption frequency, consumption amount, and added sugar had correlation coefficients of 0.81, 0.87, and 0.87, respectively, in the validity analysis (p < 0.05). The majority of scatter plots were covered by 95% confidence intervals in the Bland-Altman bias analysis. The intra-class correlation coefficient of SSB consumption frequency and Spearman correlation coefficient of SSB consumption amount and added sugar were 0.74, 0.81, and 0.90, respectively, in the reproducibility analysis (p < 0.05). Results produced by the FG-FFQ calibration formula were more comparable to 24HDR. The FG-FFQ for SSB consumption showed acceptable validity and reproducibility, making it a viable instrument for epidemiological studies on sugary drinks in adolescents.

Banff Human Organ Transplant Consensus Gene Panel for the Detection of Antibody Mediated Rejection in Heart Allograft Biopsies.

The molecular refinement of the diagnosis of heart allograft rejection based on whole-transcriptome analyses faces several hurdles that greatly limit its widespread clinical application. The targeted Banff Human Organ Transplant gene panel (B-HOT, including 770 genes of interest) has been developed to facilitate reproducible and cost-effective gene expression analysis of solid organ allografts. We aimed to determine in silico the ability of this targeted panel to capture the antibody-mediated rejection (AMR) molecular profile using whole-transcriptome data from 137 heart allograft biopsies (71 biopsies reflecting the entire landscape of histologic AMR, 66 non-AMR control biopsies including cellular rejection and non-rejection cases). Differential gene expression, pathway and network analyses demonstrated that the B-HOT panel captured biologically and clinically relevant genes (IFNG-inducible, NK-cells, injury, monocytes-macrophage, B-cell-related genes), pathways (interleukin and interferon signaling, neutrophil degranulation, immunoregulatory interactions, endothelial activation) and networks reflecting the pathophysiological mechanisms underlying the AMR process previously identified in whole-transcriptome analysis. Our findings support the potential clinical use of the B-HOT-gene panel as a reliable proxy to whole-transcriptome analysis for the gene expression profiling of cardiac allograft rejection.

Novel “HYDALJSS08” Hydroalcoholic Polyherbal Formulation Development and Ultra-performance Liquid Chromatographic Separation, Estimation of Andrographolides in Andrographis paniculata whole Plants and a Marketed Siddha-based Polyherbal Formulation “Kabusura Kudineer”

Background: The Siddha-based polyherbal formulation known as “Kabusura Kudineer (Marketed)" and developed as “HYDALJSS08” hydroalcoholic polyherbal formulation contains some fifteen plant materials in a dried raw form. Due to its immuno-booster properties, the Ministry of Ayush, Govt of India, highly recommended the use of "Kabusura Kudineer" during the pandemic of COVID-19. Objective: The present study intends to expand and validate the analytical profile for Andrographolides (AP), and isolated Andrographolides (AP) from the Andrographis Paniculata whole plant and in the Polyherbal Formulations (Marketed-Kabusura Kudineer, &amp; Developed “HYDALJSS08”). Methods: One of the active components of “Kabusura Kudineer” marketed and developed as “HYDALJSS08” Hydroalcoholic Polyherbal formulation is kalmegh, also known as the king of bitter (Andrographis Paniculata-Acanthaceae). Kalmegh composes active principal components of Andrographolides (AP), which are proven for their Anti-viral and immunomodulatory activity. The preliminary identification of AP and the sample was carried out by TLC and FT-IR. The liquid chromatography was performed on a Zorbaz SB C8 (250*4.6mm &amp; 5μm). The mobile phase incorporated pH 2.8 phosphate buffer with Acetonitrile: Methanol (60:30:10). The flow rate of the mobile phase was 1ml/min, and effluents were kept an eye on at 223 nm in a UV detector. The run time on the chromatogram was 10 min, and retention time was also observed. Results: The Rf value of Andrographolides (AP) was found to be 0.62. ICH guidelines were followed to carry out the Validation parameter. The retention time of AP was 2.5 min, and the Valid parameters of AP and system precision were as follows: SD (1831.11), % RSD (0.2), regression equations y = 41978 + x−10763, and correlation coefficient (R2) 0.9994. The adequate Linearity concentration was found to be 5 to 50 μg/ml, the value of LODs was 0.61μg /ml, LOQs was 2.01 μg/ml, method precision % RSD was 0.2, SD was 1597.1, and recovery was 99.9% and 101%. AP content found in a formulation (“Kabusura Kudineer” 1.48 μg/mL, developed “HYDALJSS08” Hydroalcoholic Polyherbal formulation-0.48 μg/ml) and isolated Andrographolides from Andrographis paniculata was 112.4μg/ml. Conclusion: The developed HPLC methods enabled simple, novel, rapid, easy, accurate, reproducible, and linear analysis of isolated andrographolides, and Siddha-based Polyherbal formulations.

Microscale Electrochemical Corrosion of Uranium Oxide Particles.

Understanding the corrosion of spent nuclear fuel is important for the development of long-term storage solutions. However, the risk of radiation contamination presents challenges for experimental analysis. Adapted from the system for analysis at the liquid-vacuum interface (SALVI), we developed a miniaturized uranium oxide (UO2)-attached working electrode (WE) to reduce contamination risk. To protect UO2 particles in a miniatured electrochemical cell, a thin layer of Nafion was formed on the surface. Atomic force microscopy (AFM) shows a dense layer of UO2 particles and indicates their participation in electrochemical reactions. Particles remain intact on the electrode surface with slight redistribution. X-ray photoelectron spectroscopy (XPS) reveals a difference in the distribution of U(IV), U(V), and U(VI) between pristine and corroded UO2 electrodes. The presence of U(V)/U(VI) on the corroded electrode surface demonstrates that electrochemically driven UO2 oxidation can be studied using these cells. Our observations of U(V) in the micro-electrode due to the selective semi-permeability of Nafion suggest that interfacial water plays a key role, potentially simulating a water-lean scenario in fuel storage conditions. This novel approach offers analytical reproducibility, design flexibility, a small footprint, and a low irradiation dose, while separating the α-effect. This approach provides a valuable microscale electrochemical platform for spent fuel corrosion studies with minimal radiological materials and the potential for diverse configurations.

Sagittal alignment in operative degenerative lumbar spondylolisthesis: a scoping review.

The benefit of surgical intervention over conservative treatment for degenerative lumbar spondylolisthesis (DLS) patients with neurologic symptoms is well-established. However, it is currently unclear what breadth of available evidence exists on regional and global sagittal alignment in DLS surgery. As such, the purpose of the current study is to conduct a scoping review to map and synthesize the DLS literature regarding the current radiographic assessment of sagittal spinal alignment in DLS surgery. A comprehensive search of the MEDLINE, EMBASE and Cochrane databases from January 1971 to January 2023 was performed for all DLS studies examining sagittal spinal alignment parameters with DLS surgery according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Review (PRISMA-ScR) protocol. From 2,222 studies, a total of 109 studies were included, representing 10,730 patients with an average age of 63.0 years old and average follow-up of 35.1 months postoperatively. Among included studies, 93 (85%), were largely published in the last decade and predominantly represented retrospective cohorts 70 (64%) or case series 22 (20%). A common theme among the reporting of radiographic parameters in the included investigations was the assessment of the magnitude and/or maintenance of a radiographic change postoperatively, with 92 (84%) studies reporting these findings. The majority of studies focused on index DLS level [33 (30%) studies] or lumbar spine radiographic imaging [33 (30%) studies] only. Thirty-seven (34%) studies reported spinopelvic parameters, with only 13 (12%) of included studies assessing 36-inch standing lateral radiographs and overall alignment. There is increasing prevalence of investigations assessing sagittal spinal alignment parameters in DLS surgery. Although, there is an increasing prevalence of studies investigating sagittal spinal alignment parameters in DLS surgery the quality of the currently available literature on this topic is of overall low evidence and largely retrospective in nature. Additionally, there is limited analysis of global sagittal spinal alignment in DLS suggesting that future investigational emphasis should prioritize longitudinally followed large prospective cohorts or multi-centre randomized controlled trials. Attempts at standardizing the radiographic and functional outcome reporting techniques across multi-centre investigations and prospective cohorts will allow for more robust, reproducible analyses of significance to be conducted on DLS patients.

ShIVA: a user-friendly and interactive interface giving biologists control over their single-cell RNA-seq data

Single-cell technologies have revolutionised biological research and applications. As they continue to evolve with multi-omics and spatial resolution, analysing single-cell datasets is becoming increasingly complex. For biologists lacking expert data analysis resources, the problem is even more crucial, even for the simplest single-cell transcriptomics datasets. We propose ShIVA, an interface for the analysis of single-cell RNA-seq and CITE-seq data specifically dedicated to biologists. Intuitive, iterative and documented by video tutorials, ShIVA allows biologists to follow a robust and reproducible analysis process, mostly based on the Seurat v4 R package, to fully explore and quantify their dataset, to produce useful figures and tables and to export their work to allow more complex analyses performed by experts.

Open Port Interface for Coupling Capillary Electrophoresis and Mass Spectrometry: Performance Evaluation for Capillary Isoelectric Focusing.

Capillary electrophoresis (CE) combined with mass spectrometry (MS) is a powerful analytical technique that utilizes the resolving power of CE and the mass-detection capabilities of MS. In many cases, CE is coupled to MS via a sheath-flow interface (SFI). This interface has a simple design and can be easily constructed; however, it often suffers from issues such as MS signal suppression, interference of MS and CE electrical circuits, and the inability to set an optical point of detection close to the capillary end due to the specific design of the coupling union. In this paper, we describe a novel coupling of CE and MS based upon the open port interface (OPI). The OPI differs from classical sheath flow interfaces by operating at flow rates at least 1 order of magnitude higher. In addition to the flow rate difference, the OPI provides more efficient mixing of the capillary eluates with the transport fluid and thus minimizes MS signal suppression. In this work, we compared the performance of OPI and SFI in a series of capillary isoelectric focusing (cIEF) experiments with 5 pI markers, carbonic anhydrase II and NIST antibody. The evaluation criteria for the comparison of the OPI and SFI were analytical sensitivity, reproducibility, and pI marker linearity. Given the extent of sample dilution in the OPI, we also compared the peak resolution determined using an upstream UV detector to those determined by the downstream mass spectrometer. The results suggested that the OPI configuration reduced signal suppression, with no adverse effect on peak resolution. In addition, the OPI provided better decoupling of the CE and MS potentials as well as reduced signal dependence upon the sheath liquid composition. While these results are preliminary, they suggest that the OPI is a viable approach for CE-MS coupling.