High-quality label-free proteome quantification (LFQ) is valuable for clinical and pharmaceutical studies yet remains extremely challenging despite technical advances. Particularly, fluctuating ...precision, limited robustness, and compromised accuracy are known issues. Here, we described and validated a new strategy enabling the discovery of the LFQs of simultaneously enhanced precision, robustness, and accuracy from thousands of LFQ manipulation chains. In the proof-of-concept study, this strategy showed superior ability in identifying well-performing LFQs. An online tool incorporating this novel strategy was also developed.
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Highlights
•High-quality LFQ is valuable technique yet remains extremely challenging.•Fluctuating precision, limited robustness, and compromised accuracy are known issues.•We proposed a strategy collectively improving LFQ precision, robustness, and accuracy.•An online tool incorporating this novel strategy was also developed.
The label-free proteome quantification (LFQ) is multistep workflow collectively defined by quantification tools and subsequent data manipulation methods that has been extensively applied in current biomedical, agricultural, and environmental studies. Despite recent advances, in-depth and high-quality quantification remains extremely challenging and requires the optimization of LFQs by comparatively evaluating their performance. However, the evaluation results using different criteria (precision, accuracy, and robustness) vary greatly, and the huge number of potential LFQs becomes one of the bottlenecks in comprehensively optimizing proteome quantification. In this study, a novel strategy, enabling the discovery of the LFQs of simultaneously enhanced performance from thousands of workflows (integrating 18 quantification tools with 3,128 manipulation chains), was therefore proposed. First, the feasibility of achieving simultaneous improvement in the precision, accuracy, and robustness of LFQ was systematically assessed by collectively optimizing its multistep manipulation chains. Second, based on a variety of benchmark datasets acquired by various quantification measurements of different modes of acquisition, this novel strategy successfully identified a number of manipulation chains that simultaneously improved the performance across multiple criteria. Finally, to further enhance proteome quantification and discover the LFQs of optimal performance, an online tool (https://idrblab.org/anpela/) enabling collective performance assessment (from multiple perspectives) of the entire LFQ workflow was developed. This study confirmed the feasibility of achieving simultaneous improvement in precision, accuracy, and robustness. The novel strategy proposed and validated in this study together with the online tool might provide useful guidance for the research field requiring the mass-spectrometry-based LFQ technique.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
A novel core-shell structured Fe3O4@GO-CoPc magnetic catalyst, which is with magnetite (Fe3O4) as the core, graphene oxide (GO) as the interlayer and cobalt-phthalocyanine (CoPc) as the shell, was ...successfully prepared and used as a heterogeneous photo-Fenton catalyst for tetracycline (TC) degradation in this work. The core-shell structure of the catalyst was confirmed by XRD, FTIR, SEM and TEM. BET and magnetic hysteresis loops measurements indicated that Fe3O4@GO-CoPc catalyst owned large specific surface area and could be easily recovered under an external magnetic field. Meanwhile, the experimental results of TC degradation demonstrated that the photo-Fenton efficiency of Fe3O4@GO-CoPc was excellent. When the reaction time was 120 min, TC could be degraded almost completely in the photo-Fenton system with Fe3O4@GO-CoPc. The high photo-Fenton catalytic activity of Fe3O4@GO-CoPc could be resulted from the effective transfer of photo-generated electrons between CoPc and Fe3O4 by GO. Moreover, the main reaction species, •OH, O2•-, 1O2 and h+, were verified by the analysis of active species in this system. Finally, the mechanism analyses and quantitative analysis results of active species indicated that the introduction of GO accelerated the cycle between Fe(II) and Fe(III) as well as improved the effective utilization of H2O2 (the efficiency of conversion of H2O2 to •OH).
•Fe3O4@GO-CoPc was synthesized by simultaneous immobilized and synthesized methods.•Fe3O4@GO-CoPc showed superior photo-Fenton catalytic activity and stable structure.•Fe3O4@GO-CoPc system enhanced the conversion efficiency of H2O2 to .•OH.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
In this article, the uncertainty of a three-dimensional turbulent natural convection transient is quantified in a geometry representing an idealized spent fuel pool. The assessment is carried out ...through the creation of a surrogate fast model. This is build utilizing Proper Orthogonal Decomposition and Galerkin projection applied to a K-ϵ turbulent Navier–Stokes formulation. We discuss the uncertainties created by a uncertain heat release of the spent fuel elements. We consider the hypothesis of deviations that follow the normal distribution around a certain nominal value, with different standard deviations and sample size. The expected results and its uncertainty are henceforth computed by Monte–Carlo method, calculating hundreds of solutions of the Initial Value Problem with the surrogate model.
•Reduced model of k-ϵ Navier–Stokes equations utilizing POD-Galerkin.•Uncertainty quantification considering inaccuracy heat released by spent fuel elements.•Hundreds of solutions obtained with the surrogate fast model.•Uncertainty determined by mean solution, standard deviation and accuracy of the last.•Performance of the method studied.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Particle image velocimetry (PIV) has become the chief experimental technique for velocity field measurements in fluid flows. The technique yields quantitative visualizations of the instantaneous flow ...patterns, which are typically used to support the development of phenomenological models for complex flows or for validation of numerical simulations. However, due to the complex relationship between measurement errors and experimental parameters, the quantification of the PIV uncertainty is far from being a trivial task and has often relied upon subjective considerations. Recognizing the importance of methodologies for the objective and reliable uncertainty quantification (UQ) of experimental data, several PIV-UQ approaches have been proposed in recent years that aim at the determination of objective uncertainty bounds in PIV measurements. This topical review on PIV uncertainty quantification aims to provide the reader with an overview of error sources in PIV measurements and to inform them of the most up-to-date approaches for PIV uncertainty quantification and propagation. The paper first introduces the general definitions and classifications of measurement errors and uncertainties, following the guidelines of the International Organization for Standards (ISO) and of renowned books on the topic. Details on the main PIV error sources are given, considering the entire measurement chain from timing and synchronization of the data acquisition system, to illumination, mechanical properties of the tracer particles, imaging of those, analysis of the particle motion, data validation and reduction. The focus is on planar PIV experiments for the measurement of two- or three-component velocity fields. Approaches for the quantification of the uncertainty of PIV data are discussed. Those are divided into a-priori UQ approaches, which provide a general figure for the uncertainty of PIV measurements, and a-posteriori UQ approaches, which are data-based and aim at quantifying the uncertainty of specific sets of data. The findings of a-priori PIV-UQ based on theoretical modelling of the measurement chain as well as on numerical or experimental assessments are discussed. The most up-to-date approaches for a-posteriori PIV-UQ are introduced, highlighting their capabilities and limitations. As many PIV experiments aim at determining flow properties derived from the velocity fields (e.g. vorticity, time-average velocity, Reynolds stresses, pressure), the topic of PIV uncertainty propagation is tackled considering the recent investigations based on Taylor series and Monte Carlo methods. Finally, the uncertainty quantification of 3D velocity measurements by volumetric approaches (tomographic PIV and Lagrangian particle tracking) is discussed.
In this work, we propose a method to construct a uniform error bound for the SK predictor. In investigating the asymptotic properties of the proposed uniform error bound, we examine the convergence ...rate of SK’s predictive variance under the supremum norm in both fixed and random design settings. Our analyses reveal that the large-sample properties of SK prediction depend on the design-point sampling scheme and the budget allocation scheme adopted. Appropriately controlling the order of noise variances through budget allocation is crucial for achieving a desirable convergence rate of SK’s approximation error, as quantified by the uniform error bound, and for maintaining SK’s numerical stability. Moreover, we investigate the impact of noise variance estimation on the uniform error bound’s performance theoretically and numerically. We demonstrate the superiority of the proposed uniform bound to the Bonferroni correction-based simultaneous confidence interval under various experimental settings through numerical evaluations.
PASEF multiplies the sequencing speed without any loss in sensitivity and is implemented in the timsTOF Pro instrument introduced here. Sequencing speeds above 100 Hz enable single run proteome ...analysis at a depth of 6000 proteins, making the instrument particularly attractive for rapid and highly sensitive proteomics. Collisional cross sections can be determined with up to 0.1% precision and acquired on a scale of 100,000s, which opens exciting areas for proteomics exploration.
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Highlights
•Online PASEF achieves greater than 100 MS/MS per second at full sensitivity.•Accurate label-free quantification of over 6000 proteins in 2 h.•High throughput demonstrated on 50 ng digests measured in 5 min.•High-precision determination of 100,000 peptide collisional cross sections.
In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, whereas mass spectra are acquired in about 100 microseconds with time-of-flight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive because of its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation - serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al., PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 600,000 fragmentation spectra in standard 120 min LC runs are achievable, which can be used for near exhaustive precursor selection in complex mixtures or accumulating the signal of weak precursors. In 120 min single runs of HeLa digest, MaxQuant identified more than 6,000 proteins without matching to a library and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,500 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Background
Current molecular breast imaging (MBI) images are limited to qualitative evaluation, not absolute measurement, of 99mTc uptake in benign and malignant breast tissues.
Purpose
This work ...assesses the accuracy of previously‐published and newly‐proposed tumor and normal breast tissue 99mTc uptake MBI measurements using simulations of a commercial dual‐headed planar MBI system under typical clinical and acquisition protocols.
Methods
Quantification techniques were tested in over 4000 simulated acquisitions of spherical and ellipsoid tumors with clinically relevant uptake conditions using a validated Monte Carlo application of the GE Discovery NM750b system. The evaluated techniques consisted of four tumor total activity methodologies (two single‐detector‐based and two geometric‐mean‐based), two tumor MBI volume methodologies (diameter‐based and ROI‐based), and two normal tissue activity concentration methodologies (single‐detector‐based and geometric‐mean‐based). The most accurate of these techniques were then used to estimate tumor activity concentrations and tumor to normal tissue relative activity concentrations (RC).
Results
Single‐detector techniques for tumor total activity quantification achieved mean (standard deviation) relative errors of 0.2% (4.3%) and 1.6% (4.4%) when using the near and far detector images, respectively and were more accurate and precise than the measured 8.1% (5.8%) errors of a previously published geometric‐mean technique. Using these activity estimates and the true tumor volumes resulted in tumor activity concentration and RC errors within 10% of simulated values. The precision of tumor activity concentration and RC when using only MBI measurements were largely driven by the errors in estimating tumor MBI volume using planar images (± 30% inter‐quartile range).
Conclusions
Planar MBI images were shown to accurately and reliably be used to estimate tumor total activities and normal tissue activity concentrations in this simulation study. However, volumetric tumor uptake measurements (i.e., absolute and relative concentrations) are limited by inaccuracies in MBI volume estimation using two‐dimensional images, highlighting the need for either tomographic MBI acquisitions or anatomical volume estimates for accurate three‐dimensional tumor uptake estimates.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
This paper reviews recent research on the demand flexibility of residential buildings in regard to definitions, flexible loads, and quantification methods. A systematic distinction of the terminology ...is made, including the demand flexibility, operation flexibility, and energy flexibility of buildings. A comprehensive definition of building demand flexibility is proposed based on an analysis of the existing definitions. Moreover, the flexibility capabilities and operation characteristics of the main residential flexible loads are summarized and compared. Models and evaluation indicators to quantify the flexibility of these flexible loads are reviewed and summarized. Current research gaps and challenges are identified and analyzed as well. The results indicate that previous studies have focused on the flexibility of central air conditioning, electric water heaters, wet appliances, refrigerators, and lighting, where the proportion of studies focusing on each of these subjects is 36.7%, 25.7%, 14.7%, 9.2%, and 8.3%, respectively. These flexible loads are different in running modes, usage frequencies, seasons, and capabilities for shedding, shifting, and modulation, while their response characteristics are not yet clear. Furthermore, recommendations are given for the application of white-, black-, and grey-box models for modeling flexible loads in different situations. Numerous static flexibility evaluation indicators that are based on the aspects of power, temporality, energy, efficiency, economics, and the environment have been proposed in previous publications, but a consensus and standardized evaluation framework is lacking. This review can help readers better understand building demand flexibility and learn about the characteristics of different residential flexible loads, while also providing suggestions for future research on the modeling techniques and evaluation metrics of residential building demand flexibility.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
In quantitative PCR (qPCR), replicates can minimize the impact of intra-assay variation; however, inter-assay variations must be minimized to obtain a robust quantification method. The method ...proposed in this study uses Savitzky–Golay smoothing and differentiation (SGSD) to identify a derivative-maximum-based cycle of quantification. It does not rely on curve modeling, as is the case with many existing techniques. PCR fluorescence data sets challenged for inter-assay variations (different thermocycler units, different reagents batches, different operators, different standard curves, and different labs) were used for the evaluation. The algorithm was compared with a four-parameter logistic model (4PLM) method, the C
y
0 method, and the threshold method. The SGSD method compared favourably with all methods in terms of inter-assay variation. SGSD was statistically different from the 4PLM (P = 0.03), C
y
0 (P = 0.05), and threshold (P = 0.004) methods on relative error comparison basis. For intra-assay variations, SGSD outperformed the threshold method (P = 0.005) and equalled the 4PLM and C
y
0 methods (P > 0.05) on relative error basis. Our results demonstrate that the SGSD method could potentially be an alternative to sigmoid modeling based methods (4PLM and C
y
0) when PCR data are challenged for inter-assay variations.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Metal‐oxide photocatalysts have demonstrated great potential in photocatalytic H2O2 production. This review focuses on metal‐oxide‐based photocatalytic materials for H2O2 production and ...systematically discusses their pros and cons, modification strategies for enhanced performance, and prospects on future research directions. This review also summarizes the quantification methods for H2O2 and associated intermediates to provide guidance for future research in this area.
Hydrogen peroxide (H2O2) is a mild but versatile oxidizing agent with extensive applications in bleaching, wastewater purification, medical treatment, and chemical synthesis. The state‐of‐art H2O2 production via anthraquinone oxidation is hardly considered a cost‐efficient and environment‐friendly process because it requires high energy input and generates hazardous organic wastes. Photocatalytic H2O2 production is a green, sustainable, and inexpensive process which only needs water and gaseous dioxygen as the raw materials and sunlight as the power source. Inorganic metal oxide semiconductors are good candidates for photocatalytic H2O2 production due to their abundance in nature, biocompatibility, exceptional stability, and low cost. Progress has been made to enhance the photocatalytic activity toward H2O2 production, however, H2O2 photosynthesis is still in the laboratory research phase since the productivity is far from satisfaction. To inspire innovative ideas for boosting the H2O2 yield in photocatalysis, the most well‐studied metal oxide photocatalysts are selected and the modification strategies to improve their activity are listed. The mechanisms for H2O2 production over modified photocatalysts are discussed to highlight the facilitating role of the modification methods. Besides, methods for the quantification of H2O2 and associated radical intermediates are provided to guide future studies in this field.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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