DIA Method Research Articles

Decision Support System For The Best Junior High School Using The Distance To The Ideal Alternative (Dia) Method At The Education And Culture Office Of The City Of Bengkulu

Decision Support System For The Best Junior High School Using The Distance To The Ideal Alternative (Dia) Method At The Education And Culture Office Of The City Of Bengkulu

Improved breast milk proteome coverage by DIA based LC-MS/MS method.

The breast milk composition includes a multitude of bioactive factors such as viable cells, lipids and proteins. Measuring the levels of specific proteins in breast milk plasma can be challenging because of the large dynamic range of protein concentrations and the presence of interfering substances. Therefore, most proteomic studies of breast milk have been able to identify under 1000 proteins. Optimised procedures and the latest separation technologies used in milk proteome research could lead to more precise knowledge of breast milk proteome. This study (n=53) utilizes three different protein quantification methods, including direct DIA, library-based DIA method and a hybrid method combining direct DIA and library-based DIA. On average we identified 2400 proteins by hybrid method. By applying these methods, we quantified body mass index (BMI) associated variation in breast milk proteomes. There were 210 significantly different proteins when comparing the breast milk proteome of obese and overweight mothers. In addition, we analysed a small cohort (n=5, randomly selected from 53 samples) by high field asymmetric waveform ion mobility spectrometry (FAIMS). FAIMS coupled with the Orbitrap Fusion Lumos mass spectrometer, which led to 41.7% higher number of protein identifications compared to Q Exactive HF mass spectrometer.

Robust, Precise, and Deep Proteome Profiling Using a Small Mass Range and Narrow Window Data-Independent-Acquisition Scheme.

In recent years, a plethora of different data-independent acquisition methods have been developed for proteomics to cover a wide range of requirements. Current deep proteome profiling methods rely on fractionations, elaborate chromatography, and mass spectrometry setups or display suboptimal quantitative precision. We set out to develop an easy-to-use one shot DIA method that achieves high quantitative precision and high proteome coverage. We achieve this by focusing on a small mass range of 430-670 m/z using small isolation windows without overlap. With this new method, we were able to quantify >9200 protein groups in HEK lysates with an average coefficient of variance of 3.2%. To demonstrate the power of our newly developed narrow mass range method, we applied it to investigate the effect of PGC-1α knockout on the skeletal muscle proteome in mice. Compared to a standard data-dependent acquisition method, we could double proteome coverage and, most importantly, achieve a significantly higher quantitative precision, as compared to a previously proposed DIA method. We believe that our method will be especially helpful in quantifying low abundant proteins in samples with a high dynamic range. All raw and result files are available at massive.ucsd.edu (MSV000092186).

Pelatihan IT Untuk Tenaga Pendidik dan Tenaga Kependidikan UPTD SMP Negeri 3 Towuti, Kec. Towuti, Kab. Luwu Timur, Prov. Sulawesi Selatan

Information technology training was carried out at UPTD SMP Negeri 3 Towuti, Towuti sub-district, East Luwu district, South Sulawesi province. The training was carried out for two days, namely from Friday to Saturday, precisely on 27 - 28 October 2023. The implementation of this activity was carried out using the DIA method. This method was chosen because it is considered quite effective in a teaching and learning process, considering that the participants in this activity are people who are adults in terms of reasoning, thinking and acting. DIA is an abbreviation for Delivery, Interaction, Assessment. Based on the activity evaluation, the results showed that 100% of the 24 teaching staff gained knowledge, 100% of the teaching staff thought that IT training was very useful and they hoped that the training would continue at another time.

A DIA method based on maximum a posteriori estimate for multiple outliers

A DIA method based on maximum a posteriori estimate for multiple outliers

Detection-only versus detection and identification of model misspecifications

It is common practice to use the well-known concept of the minimal detectable bias (MDB) to assess the performance of statistical testing procedures. However, such procedures are usually applied to a null and a set of multiple alternative hypotheses with the aim of selecting the most likely one. Therefore, in the DIA method for the detection, identification and adaptation of model misspecifications, rejection of the null hypothesis is followed by identification of the potential source of the model misspecification. With identification included, the MDBs do not truly reflect the capability of the testing procedure and should therefore be replaced by the minimal identifiable bias (MIB). In this contribution, we analyse the MDB and the MIB, highlight their differences, and describe their impact on the nonlinear DIA-estimator of the model parameters. As the DIA-estimator inherits all the probabilistic properties of the testing procedure, the differences in the MDB and MIB propagation will also reveal the different consequences a detection-only approach has versus a detection+identification approach. Numerical algorithms are presented for computing the MDB and the MIB and also their effect on the DIA-estimator. These algorithms are then applied to a number of examples so as to analyse and illustrate the different concepts.

Skill assessment of different quadruplet wave-wave interaction formulations in the WAVEWATCH-III model with application to the Gulf of Mexico

In this study, the Gaussian Quadrature Method (GQM) method was implemented in the WAVEWATCH-III model and used along with embedded formulations for estimating the nonlinear wave interactions. The results of DIA, GMD, GQM and WRT methods were compared for ideal test cases. The GQM was in good agreement with the exact WRT method while its medium resolution conjuration was ∼10 times faster than WRT. The GMD was more than 50 times faster than GQM but it could not reproduce WRT results for slanting fetch condition. Two different packages named ST3 and ST6, were employed for calculating the wind input and energy dissipation formulations over the Gulf of Mexico. The high quality ERA5 wind data from August to September in 2017 blended with Holland parametric model were used to run the wave model. The simulation period includes both fair weather condition and extreme events of Hurricanes Harvey and Irma. The performance of wave model using different nonlinear wave interaction terms was assessed against bulk wave parameters measured by in-situ buoys as well as altimeter-derived data by introducing a new error index. The general features of in-situ directional wave spectra were well captured by all DIA, GMD, GQM and WRT methods; however, the spectra produced by GMD and GQM were closer to the results by WRT method. Interestingly, the DIA method with calibrated whitecap dissipation term outperformed other methods in reproducing in-situ data (i.e. wave bulk parameters and wave spectra) during both fair weather and extreme events; indicating overfitting in the white capping or/and wind input terms in the wave model.

Sistem Pendukung Keputusan Pemilihan Tempat Kegiatan Olahraga di Medan dengan Metode Distance To The Ideal Alternative (DIA)

Exercise can provide a million benefits for your body. Not only for health, sports activities can also maintain fitness in carrying out daily activities in the midst of a pandemic (currently it is heading towards endemic). The advancement of the times and technology has made it easier for humans to exercise. Exercise can be done in various ways, either using tools or without using tools. Starting from expensive to no costs. Decision support system for the selection of sports venue activities in supporting users with assessments through a system that will be developed using PHP and MySQL programming languages as a database. The program was designed using the DIA method and designed the design using Flowchart, and UML. With the existence of a decision-making support system to make it easier for users to get the best sports venue according to their needs.

Control of Phase Morphology of Binary Polymer Grafted Nanoparticle Blend Films via Direct Immersion Annealing.

While the phase separation of binary mixtures of chemically different polymer-grafted nanoparticles (PGNPs) is observed to superficially resemble conventional polymer blends, the presence of a "soft" polymer-grafted layer on the inorganic core of these nanoparticles qualitatively alters the phase separation kinetics of these "nanoblends" from the typical pattern of behavior seen in polymer blends and other simple fluids. We investigate this system using a direct immersion annealing method (DIA) that allows for a facile tuning of the PGNPs phase boundary, phase separation kinetics, and the ultimate scale of phase separation after a sufficient "aging" time. In particular, by switching the DIA solvent composition from a selective one (which increases the interaction parameter according to Timmerman's rule) to an overall good solvent for both PGNP components, we can achieve rapid switchability between phase-separated and homogeneous states. Despite a relatively low and non-classical power-law coarsening exponent, the overall phase separation process is completed on a time scale on the order of a few minutes. Moreover, the roughness of the PGNP blend film saturates at a scale that is proportional to the in-plane phase separation pattern scale, as observed in previous blend and block copolymer film studies. The relatively low magnitude of the coarsening exponent n is attributed to a suppression of hydrodynamic interactions between the PGNPs. The DIA method provides a significant opportunity to control the phase separation morphology of PGNP blends by solution processing, and this method is expected to be quite useful in creating advanced materials.

Use of liquid chromatography-tandem mass spectrometry to perform urinary proteomic analysis of children with IgA nephropathy and Henoch-Schönlein purpura nephritis

The emerging technology of urinary proteomics has become an efficient biological approach for identifying biomarkers and characterizing pathogenesis in renal involvement. In this study, we attempted to elucidate the relationship between IgAN and HSPN in children, employing LC-MS/MS to perform urinary proteomic analyses using the DIA method. Early-morning spot urine was collected from patients with biopsy-proven IgAN (n = 19) and HSPN (n = 19) prior to treatment and renal biopsy in the Department of Pediatrics, Jinling Hospital, Nanjing, China, and did healthy volunteers (n = 14), from June 2018 to December 2019. Two hundred seventy-six urinary proteins and 125 urinary proteins were determined to be differentially expressed in children with IgAN (n = 4) and HSPN (n = 4), respectively, compared to the urinary proteins of healthy children (n = 4) (p < 0.05). GO analysis demonstrated that the differentially expressed proteins of the two groups, which were located in the extracellular matrix and cell membrane, were primarily involved in biological processes, including metabolic processes, immune system processes, cellular adhesion, cell proliferation, signaling, and biological regulation. KEGG analysis revealed that the differentially expressed proteins of the two groups were associated with cell adhesion molecules, ECM-receptor interactions, the PI3K-Akt signaling pathway, the complement and coagulation cascades, regulation of actin cytoskeleton, cholesterol metabolism, and platelet activation. The target proteins (alpha-1B-glycoprotein (A1BG) and afamin (AFM)), which participated in the complement and coagulation cascades and the regulation of complement activation, were further investigated in the independent validation cohort by ELISA. These proteins were significantly increased in children with IgAN (n = 15) and HSPN (n = 15) compared with the proteins observed in healthy controls (n = 10, P < 0.05). The validated results were consistent with the mass spectrometry results. SignificanceIgAN and HSPN both result from the glomerular deposition of abnormally glycosylated IgA1 with mesangial proliferative changes, and both diseases are common glomerulopathies in the pediatric population that are believed to be correlated. Interestingly, our data, by combining urinary proteomic analyses, showed that several uniform enrichment pathways played an important role in the progression of IgAN and HSPN, suggesting that we might reduce the renal involvement of the two diseases in children through these pathways. The same urinary proteins along these pathways were observed to be differentially expressed in children with IgAN and HSPN, implying that these proteins may be potential biomarkers to identify the two diseases. Future studies examining larger cohorts are warranted to confirm the validity of our findings.

Proteomic biomarkers in mid-trimester amniotic fluid associated with adverse pregnancy outcomes in patients with systemic lupus erythematosus.

We aimed to explore the proteomic profiles of mid-trimester amniotic fluid in pregnant women with systemic lupus erythematosus (SLE) according to the occurrence of adverse pregnancy outcome (APO). The study population included 35 pregnant women with SLE who underwent clinically indicated amniocentesis at 15–24 weeks of gestation. Patients were divided into two groups according to pregnancy outcomes: SLE patients without APO (Group 1) and SLE patients with APO (Group 2). Stored samples of amniotic fluid were analyzed using mass spectrometry (MS)-based proteomics with two-step approach, consisting of discovery and verification phase. In the discovery phase, 44 proteins were differentially expressed between Group 1 and Group 2. In the verification phase, differentially expressed proteins (DEPs) were verified in independent samples using DIA method. Four proteins including filamin A (FLNA), sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 (SVEP1), lecithin-cholesterol acyltransferase (LCAT), and transglutaminase 2 (TGM2) were differentially expressed both in discovery and verification phase. To select the best combination of proteins for discriminating two groups, three-fold cross validation (CV) with repetition of one hundred times was performed. The multi-marker model with three biomarkers (SVEP1, LCAT, TGM2) had a high discriminatory power to distinguish between the two groups (the area under the receiver operating characteristic, AUROC = 0.946, p <0.001). Our results indicate that the expression of FLNA, SVEP1, LCAT, and TGM2 in mid-trimester amniotic fluid was increased in SLE patients with APO (Group 2). A large-scale prospective study is warranted to verify this finding.

Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition.

Due to the technical advances of mass spectrometers, particularly increased scanning speed and higher MS/MS resolution, the use of data-independent acquisition mass spectrometry (DIA-MS) became more popular, which enables high reproducibility in both proteomic identification and quantification. The current DIA-MS methods normally cover a wide mass range, with the aim to target and identify as many peptides and proteins as possible and therefore frequently generate MS/MS spectra of high complexity. In this report, we assessed the performance and benefits of using small windows with, e.g., 5-m/z width across the peptide elution time. We further devised a new DIA method named RTwinDIA that schedules the small isolation windows in different retention time blocks, taking advantage of the fact that larger peptides are normally eluting later in reversed phase chromatography. We assessed the direct proteomic identification by using shotgun database searching tools such as MaxQuant and pFind, and also Spectronaut with an external comprehensive spectral library of human proteins. We conclude that algorithms like pFind have potential in directly analyzing DIA data acquired with small windows, and that the instrumental time and DIA cycle time, if prioritized to be spent on small windows rather than on covering a broad mass range by large windows, will improve the direct proteome coverage for new biological samples and increase the quantitative precision. These results further provide perspectives for the future convergence between DDA and DIA on faster MS analyzers.

DIA+: A Data-Independent Acquisition Method Combining Multiple Precursor Charges to Improve Peptide Signal.

Data-independent acquisition methods that acquire fragment ions from virtually any peptide in a sample have expanded the benefits of low-throughput targeted proteomics to proteome-wide analyses. While these methods have increased the reproducibility of peptide quantification across multiple samples, their sensitivity is still limited, and the quantification of complete proteomes remains a challenge. Here we present DIA+, a DIA method that combines signals from identical peptides with different charge states, resulting in improved signal-to-noise, additional number of fragments, and therefore in a higher number of identified and quantified peptides in complex samples.

Detection of Functional Overreaching in Endurance Athletes Using Proteomics

There is a strong demand for diagnostic tools to identify athletes in various training states. PURPOSE: To determine if a cluster of proteins could be identified through proteomics procedures that are linked to functional overreaching (FOR) in male endurance athletes. METHODS: Participants (N=10, age 38.3±3.4 y, VO2max 41.3±1.7 ml.kg-1.min-1) served as their own controls and in random, counterbalanced order either ran/cycled 2.5 h (70.0±3.7% VO2max, 79.6±6.3% HRmax) three days in a row (FOR) or sat in the lab (rest) (separated by three weeks) (7:00 - 9:30 am, overnight fasted state). Participants provided fingerprick samples for dried blood spot samples (DBS) pre- and post-exercise/rest each of the three days, and then at 7:00 am during two additional recovery days. Participants also completed the Training Distress Scale (TDS) (19-items) at 7:00 am each of the five mornings during each trial (FOR and rest). Proteins were solubilized from DBS, digested into peptides and measured with nanoLC-MS in data independent acquisition mode (Q-Exactive, Thermo Fisher Scientific, Waltham, MA). The RAW MS data files were processed using SpectronautTM software (Biognosys, Schlieren, Switzerland). Following data independent acquisition (DIA method), 594 proteins were identified and quantified. Proteins were considered for the FOR cluster if they were elevated during one of the two recovery days but not more than one of the exercise days (compared to rest). The Generalized Estimating Equation (GEE) was used to identify proteins linked to FOR (between trial contrasts, P≤0.05 for proteins with CV<15%, P≤0.01 with CV>15%). RESULTS: TDS scores differed between FOR and rest trials, peaking on the first recovery day (9.8±3.8, 3.5±2.6, respectively, P=0.029). A total of 13 proteins was linked to FOR and of these, 11 were related to the immune system, and two to exercise-induced physiological responses. Immune-related proteins included those associated primarily with the acute phase response, complement activation, and granulocyte function. CONCLUSIONS: This study utilized targeted, DIA proteomics procedures to identify a cluster of 13 proteins linked to FOR (7.5 h of high intensity exercise over three days), and 85% of the proteins were related to immune system activation during the 2-day recovery period.

DIA-datasnooping and identifiability

In this contribution, we present and analyze datasnooping in the context of the DIA method. As the DIA method for the detection, identification and adaptation of mismodelling errors is concerned with estimation and testing, it is the combination of both that needs to be considered. This combination is rigorously captured by the DIA estimator. We discuss and analyze the DIA-datasnooping decision probabilities and the construction of the corresponding partitioning of misclosure space. We also investigate the circumstances under which two or more hypotheses are nonseparable in the identification step. By means of a theorem on the equivalence between the nonseparability of hypotheses and the inestimability of parameters, we demonstrate that one can forget about adapting the parameter vector for hypotheses that are nonseparable. However, as this concerns the complete vector and not necessarily functions of it, we also show that parameter functions may exist for which adaptation is still possible. It is shown how this adaptation looks like and how it changes the structure of the DIA estimator. To demonstrate the performance of the various elements of DIA-datasnooping, we apply the theory to some selected examples. We analyze how geometry changes in the measurement setup affect the testing procedure, by studying their partitioning of misclosure space, the decision probabilities and the minimal detectable and identifiable biases. The difference between these two minimal biases is highlighted by showing the difference between their corresponding contributing factors. We also show that if two alternative hypotheses, say {mathcal {H}}_{i} and {mathcal {H}}_{j}, are nonseparable, the testing procedure may have different levels of sensitivity to {mathcal {H}}_{i}-biases compared to the same {mathcal {H}}_{j}-biases.

Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of Aspergillus fumigatus with Azole and Echinocandin Antifungal Drugs.

Calcineurin is a critical cell-signaling protein that orchestrates growth, stress response, virulence, and antifungal drug resistance in several fungal pathogens. Blocking calcineurin signaling increases the efficacy of several currently available antifungals and suppresses drug resistance. We demonstrate the application of a novel scanning quadrupole DIA method for the analysis of changes in the proteins coimmunoprecipitated with calcineurin during therapeutic antifungal drug treatments of the deadly human fungal pathogen Aspergillus fumigatus. Our experimental design afforded an assessment of the precision of the method as demonstrated by peptide- and protein-centric analysis from eight replicates of the study pool QC samples. Two distinct classes of clinically relevant antifungal drugs that are guideline recommended for the treatment of invasive "aspergillosis" caused by Aspergillus fumigatus, the azoles (voriconazole) and the echinocandins (caspofungin and micafungin), which specifically target the fungal plasma membrane and the fungal cell wall, respectively, were chosen to distinguish variations occurring in the proteins coimmunoprecipitated with calcineurin. Novel potential interactors were identified in response to the different drug treatments that are indicative of the possible role for calcineurin in regulating these effectors. Notably, treatment with voriconazole showed increased immunoprecipitation of key proteins involved in membrane ergosterol biosynthesis with calcineurin. In contrast, echinocandin (caspofungin or micafungin) treatments caused increased immunoprecipitation of proteins involved in cell-wall biosynthesis and septation. Furthermore, abundant coimmunoprecipitation of ribosomal proteins with calcineurin occurred exclusively in echinocandins treatment, indicating reprogramming of cellular growth mechanisms during different antifungal drug treatments. While variations in the observed calcineurin immunoprecipitated proteins may also be due to changes in their expression levels under different drug treatments, this study suggests an important role for calcineurin-dependent cellular mechanisms in response to antifungal treatment of A. fumigatus that warrants future studies.

Distributional theory for the DIA method

The DIA method for the detection, identification and adaptation of model misspecifications combines estimation with testing. The aim of the present contribution is to introduce a unifying framework for the rigorous capture of this combination. By using a canonical model formulation and a partitioning of misclosure space, we show that the whole estimation–testing scheme can be captured in one single DIA estimator. We study the characteristics of this estimator and discuss some of its distributional properties. With the distribution of the DIA estimator provided, one can then study all the characteristics of the combined estimation and testing scheme, as well as analyse how they propagate into final outcomes. Examples are given, as well as a discussion on how the distributional properties compare with their usage in practice.

Synthesis of Al-Fly Ash Composites by Modified Two Step Stir Casting Method

In the stir casting process, homogeneous dispersion of reinforcing particles within the matrix material is one such major problem, which influences on the properties of composites. In this research, an attempt has been made to study the influence of fly ash wt.% (10 ,15 and 20), ratio of the impeller outer dia to crucible inner dia (0.7,0.5 and 0.3) and processing method (liquid state stirring, two step stirring and modified two step stirring) on the mechanical properties and the distribution of fly ash particles in the Al matrix.Optimum parameters were identified for attaining the maximum mechanical properties such as hardness and tensile strength of composites by the application of Taguchi method, Analysis of Variance (ANOVA) and the results were validated by confirmation test.The present work could provide a guide for the industrial preparation of composites.

Colour change measurements of gravitational microlensing events by using the difference image analysis method

Detecting colour changes of a gravitational microlensing event induced by the limb-darkened extended source effect is important to obtain useful information both about the lens and source star. However, precise measurements of the colour changes are hampered by blending, which also causes colour changes of the event. In this paper, we show that although the colour change measured from the subtracted image by using the recently developed photometric method of the ``difference image analysis'' (DIA) differs from the colour change measured by using the conventional method based on the extraction of the individual source stars' point spread functions, the curve of the colour changes (colour curve) constructed by using the DIA method enables one to obtain the same information about the lens and source star, but with significantly reduced uncertainties due to the absence of blending. We investigate the patterns of the DIA colour curves for both single lens and binary lens events by constructing colour change maps.

Remarks on turbulent constitutive relations

The paper demonstrates that the concept of turbulent constitutive relations introduced by Lumley [1] can be used to construct general models for various turbulent correlations. Some of Generalized Cayley–Hamilton formulas for relating tensor products of higher Extension to tensor products of lower Extension are introduced. The combination of dimensional analysis and invariant theory can lead to “turbulent constitutive relations” (or general turbulence models) for, in principle, any turbulent correlations. As examples, the constitutive relations for Reynolds stresses and scalar fluxes are derived. The results are consistent with ones from RNG theory and two-scale DIA method, but with a more general form.