Downscaling GRACE total water storage change using partial least squares regression.
Ontology highlight
ABSTRACT:
SUBMITTER: Vishwakarma BD
PROVIDER: S-EPMC7998002 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:[1] A long-standing challenge for hydrologists has been a lack of observational data on global-scale basin hydrological behavior. With observations from NASA's Gravity Recovery and Climate Experiment (GRACE) mission, hydrologists are now able to study terrestrial water storage for large river basins (>200,000 km(2)), with monthly time resolution. Here we provide results of a time series model of basin-averaged GRACE terrestrial water storage anomaly and Global Precipitation Climatology Project precipitation for the world's largest basins. We address the short (10 year) length of the GRACE record by adopting a parametric spectral method to calculate frequency-domain transfer functions of storage response to precipitation forcing and then generalize these transfer functions based on large-scale basin characteristics, such as percent forest cover and basin temperature. Among the parameters tested, results show that temperature, soil water-holding capacity, and percent forest cover are important controls on relative storage variability, while basin area and mean terrain slope are less important. The derived empirical relationships were accurate (0.54 ≤ Ef ≤ 0.84) in modeling global-scale water storage anomaly time series for the study basins using only precipitation, average basin temperature, and two land-surface variables, offering the potential for synthesis of basin storage time series beyond the GRACE observational period. Such an approach could be applied toward gap filling between current and future GRACE missions and for predicting basin storage given predictions of future precipitation.
| S-EPMC3925992 | biostudies-other
Project description:This Teaching Resource provides lecture notes, slides, and a problem set for a lecture introducing the mathematical concepts and interpretation of partial least squares regression (PLSR) that were part of a course entitled "Systems Biology: Mammalian Signaling Networks." PLSR is a multivariate regression technique commonly applied to analyze relationships between signaling or transcriptional data and cellular behavior.
| S-EPMC4965874 | biostudies-literature
Project description:Global Navigation Satellite System (GNSS) vertical displacements measuring the elastic response of Earth's crust to changes in hydrologic mass have been used to produce terrestrial water storage change (∆TWS) estimates for studying both annual ∆TWS as well as multi-year trends. However, these estimates require a high observation station density and minimal contamination by nonhydrologic deformation sources. The Gravity Recovery and Climate Experiment (GRACE) is another satellite-based measurement system that can be used to measure regional TWS fluctuations. The satellites provide highly accurate ∆TWS estimates with global coverage but have a low spatial resolution of ∼400 km. Here, we put forward the mathematical framework for a joint inversion of GNSS vertical displacement time series with GRACE ∆TWS to produce more accurate spatiotemporal maps of ∆TWS, accounting for the observation errors, data gaps, and nonhydrologic signals. We aim to utilize the regional sensitivity to ∆TWS provided by GRACE mascon solutions with higher spatial resolution provided by GNSS observations. Our approach utilizes a continuous wavelet transform to decompose signals into their building blocks and separately invert for long-term and short-term mass variations. This allows us to preserve trends, annual, interannual, and multi-year changes in TWS that were previously challenging to capture by satellite-based measurement systems or hydrological models, alone. We focus our study in California, USA, which has a dense GNSS network and where recurrent, intense droughts put pressure on freshwater supplies. We highlight the advantages of our joint inversion results for a tectonically active study region by comparing them against inversion results that use only GNSS vertical deformation as well as with maps of ∆TWS from hydrological models and other GRACE solutions. We find that our joint inversion framework results in a solution that is regionally consistent with the GRACE ∆TWS solutions at different temporal scales but has an increased spatial resolution that allows us to differentiate between regions of high and low mass change better than using GRACE alone.
| S-EPMC9287077 | biostudies-literature
Project description:With the growing availability of large-scale biological datasets, automated methods of extracting functionally meaningful information from this data are becoming increasingly important. Data relating to functional association between genes or proteins, such as co-expression or functional association, is often represented in terms of gene or protein networks. Several methods of predicting gene function from these networks have been proposed. However, evaluating the relative performance of these algorithms may not be trivial: concerns have been raised over biases in different benchmarking methods and datasets, particularly relating to non-independence of functional association data and test data. In this paper we propose a new network-based gene function prediction algorithm using a commute-time kernel and partial least squares regression (Compass). We compare Compass to GeneMANIA, a leading network-based prediction algorithm, using a number of different benchmarks, and find that Compass outperforms GeneMANIA on these benchmarks. We also explicitly explore problems associated with the non-independence of functional association data and test data. We find that a benchmark based on the Gene Ontology database, which, directly or indirectly, incorporates information from other databases, may considerably overestimate the performance of algorithms exploiting functional association data for prediction.
| S-EPMC4545790 | biostudies-literature
Project description:Background-subtracted fast-scan cyclic voltammetry (FSCV) provides a method for detecting molecular fluctuations with high spatiotemporal resolution in the brain of awake and behaving animals. The rapid scan rates generate large background currents that are subtracted to reveal changes in analyte concentration. Although these background currents are relatively stable, small changes do occur over time. These changes, referred to as electrochemical drift, result in background-subtraction artifacts that constrain the utility of FSCV, particularly when quantifying chemical changes that gradually occur over long measurement times (minutes). The voltammetric features of electrochemical drift are varied and can span the entire potential window, potentially obscuring the signal from any targeted analyte. We present a straightforward method for extending the duration of a single FSCV recording window. First, we have implemented voltammetric waveforms in pairs that consist of a smaller triangular sweep followed by a conventional voltammetric scan. The initial, abbreviated waveform is used to capture drift information that can serve as a predictor for the contribution of electrochemical drift to the subsequent full voltammetric scan using partial-least-squares regression (PLSR). This double-waveform partial-least-squares regression (DW-PLSR) paradigm permits reliable subtraction of the drift component to the voltammetric data. Here, DW-PLSR is used to improve quantification of adenosine, dopamine, and hydrogen peroxide fluctuations occurring >10 min from the initial background position, both in vitro and in vivo. The results demonstrate that DW-PLSR is a powerful tool for evaluating and interpreting both rapid (seconds) and gradual (minutes) chemical changes captured in FSCV recordings over extended durations.
| S-EPMC7357255 | biostudies-literature
Project description:Estimation of individuals' cognitive, behavioral and demographic (CBD) variables based on MRI has attracted much research interest in the past decade, and effective machine learning techniques are of great importance for these estimations. Partial least squares regression (PLSR) is an attractive machine learning technique that can accommodate both single- and multi-label learning in a simple framework, while its potential for MRI-based estimations of CBD variables remains to be explored. In this study, we systemically investigated the performance of PLSR in MRI-based estimations of individuals' CBD variables, especially its performance in simultaneous estimation of multiple CBD variables (multi-label learning). We performed the study on the dataset included in the HCP S1200 release. Resting state functional connections (RSFCs) were used as features, and a total of 10 CBD variables (e.g., age, gender, grip strength, and picture vocabulary) were estimated. The results showed that PLSR performed well in both single- and multi-label learning. In fact, the present estimations were better than those reported in literatures, as indicated by stronger correlations between the estimated and actual CBD variables, as well as high gender classification accuracy (97.8% in this study). Moreover, the RSFCs that contributed to the estimations exhibited strong correlations with the CBD variable estimated, that is, PLSR algorithm automatically selected the RSFCs closely related to one CBD variable to establish predictive models for the variable. Besides, the estimation accuracies based on RSFCs among 100, 200, and 300 regions of interest (ROIs) were higher than those based on RSFCs among 15, 25, and 50 ROIs; the estimation accuracies based on RSFCs evaluated using partial correlation were higher than those based on RSFCs evaluated using full correlation. In addition to the aforementioned virtues, PLSR is efficient in model training and testing, and it is simple and easy to use. Therefore, PLSR can be a favorable choice for future MRI-based estimations of CBD variables.
| S-EPMC6890557 | biostudies-literature
Project description:A fast and simple method to control variations in carbohydrate composition of Saccharomyces cerevisiae, baker's yeast, during fermentation was developed using mid-infrared (mid-IR) spectroscopy. The method allows for precise and accurate determinations with minimal or no sample preparation and reagent consumption based on mid-IR spectra and partial least squares (PLS) regression. The PLS models were developed employing the results from reference analysis of the yeast cells. The reference analyses quantify the amount of trehalose, glucose, glycogen, and mannan in S. cerevisiae. The selection and optimization of pretreatment steps of samples such as the disruption of the yeast cells and the hydrolysis of mannan and glycogen to obtain monosaccharides were carried out. Trehalose, glucose, and mannose were determined using high-performance liquid chromatography coupled with a refractive index detector and total carbohydrates were measured using the phenol-sulfuric method. Linear concentration range, accuracy, precision, LOD and LOQ were examined to check the reliability of the chromatographic method for each analyte.
| S-EPMC3777185 | biostudies-literature
Project description:BackgroundThe presence of condensed tannins (CT) in tree fodders entails a series of productive, health and ecological benefits for ruminant nutrition. Current wet analytical methods employed for full CT characterisation are time and resource-consuming, thus limiting its applicability for silvopastoral systems. The development of quick, safe and robust analytical techniques to monitor CT's full profile is crucial to suitably understand CT variability and biological activity, which would help to develop efficient evidence-based decision-making to maximise CT-derived benefits. The present study investigates the suitability of Fourier-transformed mid-infrared spectroscopy (MIR: 4000-550 cm-1) combined with multivariate analysis to determine CT concentration and structure (mean degree of polymerization-mDP, procyanidins:prodelphidins ratio-PC:PD and cis:trans ratio) in oak, field maple and goat willow foliage, using HCl:Butanol:Acetone:Iron (HBAI) and thiolysis-HPLC as reference methods.ResultsThe MIR spectra obtained were explored firstly using Principal Component Analysis, whereas multivariate calibration models were developed based on partial least-squares regression. MIR showed an excellent prediction capacity for the determination of PC:PD [coefficient of determination for prediction (R2P) = 0.96; ratio of prediction to deviation (RPD) = 5.26, range error ratio (RER) = 14.1] and cis:trans ratio (R2P = 0.95; RPD = 4.24; RER = 13.3); modest for CT quantification (HBAI: R2P = 0.92; RPD = 3.71; RER = 13.1; Thiolysis: R2P = 0.88; RPD = 2.80; RER = 11.5); and weak for mDP (R2P = 0.66; RPD = 1.86; RER = 7.16).ConclusionsMIR combined with chemometrics allowed to characterize the full CT profile of tree foliage rapidly, which would help to assess better plant ecology variability and to improve the nutritional management of ruminant livestock.
| S-EPMC7866629 | biostudies-literature
Project description:The erythrocyte sedimentation rate (ESR) is a non-specific blood test for determining inflammatory conditions. However, the long measurement time (60 min) to obtain ESR is an obstacle for a prompt evaluation. In this study, to reduce the measurement time of ESR, deep neural networks (DNNs) were applied to the sedimentation tendency of blood samples. DNNs using multilayer perceptron (MLP), long short-term memory (LSTM), and gated recurrent unit (GRU) were assessed and compared to determine a suitable length of time for the input sequence. To avoid overfitting, a stacking ensemble learning was adopted, which combines multiple models by using a meta model. Four meta models were compared: mean, median, least absolute shrinkage and selection operator, and partial least squares regression (PLSR) schemes. From the empirical results, LSTM and GRU models have better prediction than MLP over sequence lengths of 5 to 20 min. The decrease in [Formula: see text] and [Formula: see text] of GRU and LSTM was attenuated after a sequence length of 15 min, so the input sequence length is determined as 15 min. In terms of the meta model, the statistical comparison suggests that GRU combined with PLSR (GRU-PLSR) is the best case. Then, the GRU-PLSR was tested for prediction of ESR data obtained from periodontitis patients to check its applicability to a specific disease. The Bland-Altman plot shows acceptable agreement between measured and predicted ESR values. Based on the results, the GRU-PLSR can predict ESR with improved performance within 15 min and has potential applicability to ESR data with inflammatory and non-inflammatory conditions.
| S-EPMC9666533 | biostudies-literature
Project description:Expression quantitative trait loci (eQTL) mapping concerns finding genomic variation to elucidate variation of expression traits. This problem poses significant challenges due to high dimensionality of both the gene expression and the genomic marker data. We propose a multivariate response regression approach with simultaneous variable selection and dimension reduction for the eQTL mapping problem. Transcripts with similar expression are clustered into groups, and their expression profiles are viewed as a multivariate response. Then, we employ our recently developed sparse partial least-squares regression methodology to select markers associated with each cluster of genes. We demonstrate with extensive simulations that our eQTL mapping with multivariate response sparse partial least-squares regression (M-SPLS eQTL) method overcomes the issue of multiple transcript- or marker-specific analyses, thereby avoiding potential elevation of type I error. Additionally, joint analysis of multiple transcripts by multivariate response regression increases power for detecting weak linkages. We illustrate that M-SPLS eQTL compares competitively with other approaches and has a number of significant advantages, including the ability to handle highly correlated genotype data and computational efficiency. We provide an application of this methodology to a mouse data set concerning obesity and diabetes.
| S-EPMC2674843 | biostudies-literature