Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Clean absorption mode NMR data acquisition based on time-proportional phase incrementation.

ABSTRACT: Clean absorption mode NMR data acquisition is presented based on mirrored time domain sampling and widely used time-proportional phase incrementation (TPPI) for quadrature detection. The resulting NMR spectra are devoid of dispersive frequency domain peak components. Those peak components exacerbate peak identification and shift peak maxima, and thus impede automated spectral analysis. The new approach is also of unique value for obtaining clean absorption mode reduced-dimensionality projection NMR spectra, which can rapidly provide high-dimensional spectral information for high-throughput NMR structure determination.

SUBMITTER: Wu Y

PROVIDER: S-EPMC2850597 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Clean absorption mode NMR data acquisition based on time-proportional phase incrementation.

Wu Yibing Y Ghosh Arindam A Szyperski Thomas T

Journal of structural and functional genomics 20090605 3

Clean absorption mode NMR data acquisition is presented based on mirrored time domain sampling and widely used time-proportional phase incrementation (TPPI) for quadrature detection. The resulting NMR spectra are devoid of dispersive frequency domain peak components. Those peak components exacerbate peak identification and shift peak maxima, and thus impede automated spectral analysis. The new approach is also of unique value for obtaining clean absorption mode reduced-dimensionality projection ...[more]

PMID: 19499349

Similar Datasets

Clean absorption-mode NMR data acquisition.

Project description:A new acquisition: Based on "phase-shifted mirrored sampling" (PMS) of indirect evolution periods of multi-dimensional experiments, new acquisition schemes eliminate, without application of a phase correction, dispersive signal components that exacerbate peak identification and shift peak maxima. The resulting enhanced resolution is of particular value for systems with high chemical shift degeneracy.

| S-EPMC3018340 | biostudies-literature

Continuous-Time Proportional Hazards Regression for Ecological Monitoring Data.

Project description:We consider a continuous-time proportional hazards model for the analysis of ecological monitoring data where subjects are monitored at discrete times and fixed sites across space. Since the exact time of event occurrence is not directly observed, we rely on dichotomous event indicators observed at monitoring times to make inference about the model parameters. We use autoregression on the response at neighboring sites from a previous time point to take into account spatial dependence. The interesting fact is utilized that the probability of observing an event at a monitoring time when the underlying hazards is proportional falls under the class of generalized linear models with binary responses and complementary log-log link functions. Thus, a maximum likelihood approach can be taken for inference and the computation can be carried out using standard statistical software packages. This approach has significant computational advantages over some of the existing methods that rely on Monte Carlo simulations. Simulation experiments are conducted and demonstrate that our method has sound finite-sample properties. A real dataset from an ecological study that monitored bark beetle colonization of red pines in Wisconsin is analyzed using the proposed models and inference. Supplementary materials that contain technical details are available online.

| S-EPMC3849820 | biostudies-literature

ANALYSIS OF MULTIVARIATE FAILURE TIME DATA USING MARGINAL PROPORTIONAL HAZARDS MODEL.

Project description:The marginal proportional hazards model is an important tool in the analysis of multivariate failure time data in the presence of censoring. We propose a method of estimation via the linear combinations of martingale residuals. The estimation and inference procedures are easy to implement numerically. The estimation is generally more accurate than the existing pseudo-likelihood approach: the size of efficiency gain can be considerable in some cases, and the maximum relative efficiency in theory is infinite. Consistency and asymptotic normality are established. Empirical evidence in support of the theoretical claims is shown in simulation studies.

| S-EPMC3846278 | biostudies-literature

New perspectives for neutron imaging through advanced event-mode data acquisition.

Project description:Imaging using scintillators is a widespread and cost-effective approach in radiography. While different types of scintillator and sensor configurations exist, it can be stated that the detection efficiency and resolution of a scintillator-based system strongly depend on the scintillator material and its thickness. Recently developed event-driven detectors are capable of registering spots of light emitted by the scintillator after a particle interaction, allowing to reconstruct the Center-of-Mass of the interaction within the scintillator. This results in a more precise location of the event and therefore provides a pathway to overcome the scintillator thickness limitation and increase the effective spatial resolution of the system. Utilizing this principle, we present a detector capable of Time-of-Flight imaging with an adjustable field-of-view, ad-hoc binning and re-binning of data based on the requirements of the experiment including the possibility of particle discrimination via the analysis of the event shape in space and time. It is considered that this novel concept might replace regular cameras in neutron imaging detectors as it provides superior detection capabilities with the most recent results providing an increase by a factor 3 in image resolution and an increase by up to a factor of 7.5 in signal-to-noise for thermal neutron imaging.

| S-EPMC8560941 | biostudies-literature

Sample size calculations for noninferiority trials for time-to-event data using the concept of proportional time.

Project description:Noninferiority trials intend to show that a new treatment is 'not worse' than a standard-of-care active control and can be used as an alternative when it is likely to cause fewer side effects compared to the active control. In the case of time-to-event endpoints, existing methods of sample size calculation are done either assuming proportional hazards between the two study arms, or assuming exponentially distributed lifetimes. In scenarios where these assumptions are not true, there are few reliable methods for calculating the sample sizes for a time-to-event noninferiority trial. Additionally, the choice of the non-inferiority margin is obtained either from a meta-analysis of prior studies, or strongly justifiable 'expert opinion', or from a 'well conducted' definitive large-sample study. Thus, when historical data do not support the traditional assumptions, it would not be appropriate to use these methods to design a noninferiority trial. For such scenarios, an alternate method of sample size calculation based on the assumption of Proportional Time is proposed. This method utilizes the generalized gamma ratio distribution to perform the sample size calculations. A practical example is discussed, followed by insights on choice of the non-inferiority margin, and the indirect testing of superiority of treatment compared to placebo.

| S-EPMC9042171 | biostudies-literature

Proportional exponentiated link transformed hazards (ELTH) models for discrete time survival data with application.

Project description:Discrete survival data are routinely encountered in many fields of study including behavior science, economics, epidemiology, medicine, and social science. In this paper, we develop a class of proportional exponentiated link transformed hazards (ELTH) models. We carry out a detailed examination of the role of links in fitting discrete survival data and estimating regression coefficients. Several interesting results are established regarding the choice of links and baseline hazards. We also characterize the conditions for improper survival functions and the conditions for existence of the maximum likelihood estimates under the proposed ELTH models. An extensive simulation study is conducted to examine the empirical performance of the parameter estimates under the Cox proportional hazards model by treating discrete survival times as continuous survival times, and the model comparison criteria, AIC and BIC, in determining links and baseline hazards. A SEER breast cancer dataset is analyzed in details to further demonstrate the proposed methodology.

| S-EPMC4676960 | biostudies-literature

A model checking method for the proportional hazards model with recurrent gap time data.

Project description:Recurrent events are the natural outcome in many medical and epidemiology studies. To assess covariate effects on the gaps between consecutive recurrent events, the Cox proportional hazards model is frequently employed in data analysis. The validity of statistical inference, however, depends on the appropriateness of the Cox model. In this paper, we propose a class of graphical techniques and formal tests for checking the Cox model with recurrent gap time data. The building block of our model checking method is an averaged martingale-like process, based on which a class of multiparameter stochastic processes is proposed. This maneuver is very general and can be used to assess different aspects of model fit. Numerical simulations are conducted to examine finite-sample performance, and the proposed model checking techniques are illustrated with data from the Danish Psychiatric Central Register.

| S-EPMC3138070 | biostudies-literature

Lipid-nanodiscs formed by paramagnetic metal chelated polymer for fast NMR data acquisition.

Project description:Lipid-nanodiscs have been shown to be an exciting innovation as a membrane-mimicking system for studies on membrane proteins by a variety of biophysical techniques, including NMR spectroscopy. Although NMR spectroscopy is unique in enabling the atomic-resolution investigation of dynamic structures of membrane-associated molecules, it, unfortunately, suffers from intrinsically low sensitivity. The long data acquisition often used to enhance the sensitivity is not desirable for sensitive membrane proteins. Instead, paramagnetic relaxation enhancement (PRE) has been used to reduce NMR data acquisition time or to reduce the amount of sample required to acquire an NMR spectra. However, the PRE approach involves the introduction of external paramagnetic probes in the system, which can induce undesired changes in the sample and on the observed NMR spectra. For example, the addition of paramagnetic ions, as frequently used, can denature the protein via direct interaction and also through sample heating. In this study, we show how the introduction of paramagnetic tags on the outer belt of polymer-nanodiscs can be used to speed-up data acquisition by significantly reducing the spin-lattice relaxation (T1) times with minimum-to-no alteration of the spectral quality. Our results also demonstrate the feasibility of using different types of paramagnetic ions (Eu3+, Gd3+, Dy3+, Er3+, Yb3+) for NMR studies on lipid-nanodiscs. Experimental results characterizing the formation of lipid-nanodiscs by the metal-chelated polymer, and their increased tolerance toward metal ions are also reported.

| S-EPMC7340147 | biostudies-literature

The Isotopic Ac-IP Tag Enables Multiplexed Proteome Quantification in Data-Independent Acquisition Mode.

Project description:Data-independent acquisition (DIA) is an increasingly used approach for quantitative proteomics. However, most current isotope labeling strategies are not suitable for DIA as they lead to more complex MS2 spectra or severe ratio distortion. As a result, DIA suffers from a lower throughput than data-dependent acquisition (DDA) due to a lower level of multiplexing. Herein, we synthesized an isotopically labeled acetyl-isoleucine-proline (Ac-IP) tag for multiplexed quantification in DIA. Differentially labeled peptides have distinct precursor ions carrying the quantitative information but identical MS2 spectra since the isotopically labeled Ac-Ile part leaves as a neutral loss upon collision-induced dissociation, while fragmentation of the peptide backbone generates regular fragment ions for identification. The Ac-IP-labeled samples can be analyzed using general DIA liquid chromatography-mass spectrometry settings, and the data obtained can be processed with established approaches. Relative quantification requires deconvolution of the isotope envelope of the respective precursor ions. Suitability of the Ac-IP tag is demonstrated with a triplex-labeled yeast proteome spiked with bovine serum albumin that was mixed at 10:5:1 ratios, resulting in measured ratios of 9.7:5.3:1.1.

| S-EPMC8209779 | biostudies-literature

Absorption Mode Fourier Transform Ion Mobility Mass Spectrometry Multiplexing Combined with Half-Window Apodization Windows Improves Resolution and Shortens Acquisition Times.

Project description:Fourier transform multiplexing enables the coupling of drift tube ion mobility to a wide array of mass spectrometers with improved ion utilization and duty cycles compared to dual-gate signal averaging methods. Traditionally, the data generated by this method is presented in the magnitude mode, but significant improvements in resolution and the signal-to-noise ratio (SNR) are expected if the data can be phase corrected and presented in the absorption mode. A method to simply and reliably determine and correct phase shifts in Fourier transform ion mobility mass spectrometry data using information readily available to any user is presented and evaluated for both small molecule and intact protein analyses with no modification to instrument hardware or experimental procedures. Additionally, the effects of apodization and zero padding are evaluated for both processing methods, and a strategy to use these techniques to reduce acquisition times is presented and evaluated. Resolution is improved by an average factor of 1.6, the SNR is improved by an average factor of 1.2, and acquisition times are reduced by up to 80% through the application of absorption mode processing combined with apodization and zero padding.

| S-EPMC9278813 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data