An API for dynamic estimation of reference intervals for functional abundances of gut microbiota
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA950343 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24015818_1.fastq.gz | Fastqsanger.gz | |||
| SRR24015818_2.fastq.gz | Fastqsanger.gz | |||
| SRR24015819_1.fastq.gz | Fastqsanger.gz | |||
| SRR24015819_2.fastq.gz | Fastqsanger.gz | |||
| SRR24015820_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 114 |
Similar Datasets
Project description:This study demonstrates the usefulness of the API by generating a baseline gut microbiota profile of a healthy population and estimating reference intervals for the functional abundance of manually selected KEGG pathways. API facilitates microbiome research by providing dynamic and customizable tools for estimating reference intervals for gut microbiota functional abundances. Through the API, researchers can rapidly generate gut microbiota functional profiles of healthy populations to use as a baseline for comparison. The API also allows users to manually select specific KEGG pathways and estimate reference intervals for the functional abundance of those pathways. By generating these customized reference intervals, researchers can better understand the expected range of gut microbiota functions in healthy individuals. API enables microbiome studies to go beyond simple taxonomic profiling and delve deeper into the functional potential of gut microbiome communities. In summary, API represents a valuable tool for microbiome researchers that enhances the ability to elucidate connections between gut microbial functions and human health.
2023-10-20 | GSE228552 | GEO
Project description:Benchmarking of available tools for the estimation of isoform-level transcript abundances from RNA-seq data
| PRJNA269376 | ENA
Project description:This study presents a mathematically rigorous approach that integrates peptide MS-signal and peptide-measurement agreement into an estimation of the true protein ratio and the associated confidence.We call our method BACIQ (Bayesian Approach to Confidence Intervals for protein Quantitation – pronounced BASIC).
2019-09-30 | PXD012285 | Pride
Project description:Images and gpr files were examined using a novel saturation reduction method to determine whether accuracy could be improved by extending dynamic range of saturated pixels Three immunosignatures from human Valley Fever (Coccidiodes) patients and three immunosignatures from human influenza vaccine recipients were examined to test an algorithm that extends the apparent dynamic range of a fluorescence image. These images had several saturated spots at 70PMT and 100% laser power. The program examined the differences between Valley Fever and influenza in terms of standard image processing vs. segmentation and intensity estimation.
2011-11-23 | E-GEOD-33899 | biostudies-arrayexpress
Project description:BackgroundReference intervals represent the expected range of physiological test results in a healthy population and are essential to support medical decision making. Particularly in the context of pediatric reference intervals, where recruitment regulations make prospective studies challenging to conduct, indirect estimation strategies are becoming increasingly important. Established indirect methods enable robust identification of the distribution of "healthy" samples from laboratory databases, which include unlabeled pathologic cases, but are currently severely limited when adjusting for essential patient characteristics such as age. Here, we propose the use of mixture density networks (MDN) to overcome this problem and model all parameters of the mixture distribution in a single step.ResultsEstimated reference intervals from varying settings with simulated data demonstrate the ability to accurately estimate latent distributions from unlabeled data using different implementations of MDNs. Comparing the performance with alternative estimation approaches further highlights the importance of modeling the mixture component weights as a function of the input in order to avoid biased estimates for all other parameters and the resulting reference intervals. We also provide a strategy to generate partially customized starting weights to improve proper identification of the latent components. Finally, the application on real-world hemoglobin samples provides results in line with current gold standard approaches, but also suggests further investigations with respect to adequate regularization strategies in order to prevent overfitting the data.ConclusionsMixture density networks provide a promising approach capable of extracting the distribution of healthy samples from unlabeled laboratory databases while simultaneously and explicitly estimating all parameters and component weights as non-linear functions of the covariate(s), thereby allowing the estimation of age-dependent reference intervals in a single step. Further studies on model regularization and asymmetric component distributions are warranted to consolidate our findings and expand the scope of applications.
| S-EPMC9336034 | biostudies-literature
Project description:BackgroundThe direct method for reference interval (RI) estimating is limited due to the requirement of resources, difficulties in defining a non-diseased population, or ethical problems in obtaining samples. We estimated the RI for inflammatory biomarkers using an indirect method (RII).MethodsC-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and presepsin (PSEP) data of patients visiting a single hospital were retrieved from April 2009 to April 2021. Right-skewed data were transformed using the Box-Cox transformation method. A mixed population of non-diseased and diseased distributions was assumed, followed by latent profile analysis for the two classes. The intersection point of the distribution curve was estimated as the RI. The influence of measurement size was evaluated as the ratio of abnormal values and adjustment (n×bandwidth) of the distribution curve.ResultsThe RIs estimated by the proposed RII method (existing method) were as follows: CRP, 0-4.1 (0-4.7) mg/L; ESR, 0-10.2 (0-15) mm/hr and PSEP, 0-411 (0-300) pg/mL. Measurement sizes ≥2,500 showed stable results. An abnormal-to-normal value ratio of 0.5 showed the most accurate result for CRP. Adjustment values ≤5 or >5 were applicable for a measurement size <25,000 or ≥25,000, respectively.ConclusionsThe proposed RII method could provide additional information for RI verification or estimation with some limitations.
| S-EPMC9467833 | biostudies-literature
Project description:The generation of dynamic models of biological processes critically depends on the determination of precise cellular concentrations of biomolecules. Measurements of system-wide absolute protein levels are particularly valuable information in systems biology. Recently, mass spectrometry based proteomics approaches have been developed to estimate protein concentrations on a proteome-wide scale. However, for very complex proteomes, fractionation steps are required, increasing samples number and instrument analysis time. As a result, the number of full proteomes that can be routinely analyzed is limited. Here we combined absolute quantification strategies with the multiplexing capabilities of isobaric tandem mass tags to determine cellular protein abundances in a high throughput and proteome-wide scale even for highly complex biological systems, such as a whole human cell line. We generated two independent data sets to demonstrate the power of the approach regarding sample throughput, dynamic range, quantitative accuracy and proteome coverage in comparison to existing mass spectrometry based strategies.
2022-02-24 | PXD002021 | Pride
Project description:Reference intervals are essential for interpreting laboratory test results. Continuous reference intervals precisely capture physiological age-specific dynamics that occur throughout life, and thus have the potential to improve clinical decision-making. However, established approaches for estimating continuous reference intervals require samples from healthy individuals, and are therefore substantially restricted. Indirect methods operating on routine measurements enable the estimation of one-dimensional reference intervals, however, no automated approach exists that integrates the dependency on a continuous covariate like age. We propose an integrated pipeline for the fully automated estimation of continuous reference intervals expressed as a generalized additive model for location, scale and shape based on discrete model estimates using an indirect method (refineR). The results are free of subjective user-input, enable conversion of test results into z-scores and can be integrated into laboratory information systems. Comparison of our results to established and validated reference intervals from the CALIPER and PEDREF studies and manufacturers' package inserts shows good agreement of reference limits, indicating that the proposed pipeline generates high-quality results. In conclusion, the developed pipeline enables the generation of high-precision percentile charts and continuous reference intervals. It represents the first parameter-less and fully automated solution for the indirect estimation of continuous reference intervals.
| S-EPMC10439150 | biostudies-literature
Project description:Immunological aging type definition requires establishing reference intervals from the distribution of immunosenescence biomarkers conditional on age. For 1605 individuals (18-97 years), we determined the comprehensive immune age index IMMAX from flow-cytometry-based blood cell sub-populations and identified age-specific centiles by fitting generalized additive models for location, scale, and shape. The centiles were uncorrelated with age and facilitated the categorization of individuals as immunologically slow or fast aging types. Using its 50th percentile as a reference, we rescaled the IMMAX to equivalent years of life (EYOL) and computed the immunological age gap as the difference between EYOL and chronological age. Applied to preliminary baseline and follow-up measurements from 53 participants of the Dortmund Vital Study (Clinical-Trials.gov Identifier: NCT05155397), the averaged changes in the IMMAX and EYOL conformed to the 5-year follow-up period, whereas no significant changes occurred concerning IMMAX centiles and age gap. This suggested that the participants immunologically adapted to aging and kept their relative positions within the cohort. Sex was non-significant. Methodical comparisons indicated that future confirmatory analyses with the completed follow-up examinations could rely on percentile curves estimated by simple linear quantile regression, while the selection of the immunosenescence biomarker will greatly influence the outcome, with IMMAX representing the preferable choice.
| S-EPMC10487963 | biostudies-literature
Project description:<p>The age estimation of bloodstains measures the time-dependent changes in the levels of bloodstain biomolecules. Although several studies have identified bloodstain metabolites as markers for estimating bloodstain age, none has consider gender and age-related metabolomic differences or long-time bloodstain age. Therefore, we aimed to identify metabolite markers for estimating the age of bloodstains at weekly intervals within 28 d and validate them through the MRM technique. Interestingly, adenosine 5′-monophosphate (5′-AMP), choline and pyroglutamic acid were selected as markers. We validated a total of 7 metabolites, including 5 previously reported metabolites, ergothioneine, hypoxanthine, L-isoleucine, L-tryptophan and pyroglutamic acid. Choline and hypoxanthine might be used to differentiate between day 0 and day 14 at weekly intervals, while L-isoleucine and L-tryptophan might help distinguish between 7 d before and 14 d after. Evaluation of the changes in the levels of metabolites according to gender and age, revealed that the average level of all 7 metabolites was higher in women on day 0. Moreover, the level of ergothioneine was significantly higher in the elderly than the youth under all time conditions. In this study, we confirmed the potential effectiveness of metabolites in bloodstains as forensic markers, and provided a new perspective on metabolomic approaches linked to forensic science.</p>
2024-01-16 | MTBLS5208 | MetaboLights