scholarly journals Large-scale parallelization of nanomechanical mass spectrometry with weakly-coupled resonators

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Stefano Stassi ◽  
Giulia De Laurentis ◽  
Debadi Chakraborty ◽  
Katarzyna Bejtka ◽  
Angelica Chiodoni ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Coupled Resonators ◽  
Nanomechanical Resonator ◽  
Technological Breakthrough ◽  
Physical Size ◽  
Vibrational Response ◽  
Physical Mechanisms ◽  
Real Time Analysis ◽  
Weakly Coupled

Abstract Nanomechanical mass spectrometry is a recent technological breakthrough that enables the real-time analysis of single molecules. In contraposition to its extreme mass sensitivity is a limited capture cross-section that can hinder measurements in a practical setting. Here we show that weak-coupling between devices in resonator arrays can be used in nanomechanical mass spectrometry to parallelize the measurement. This coupling gives rise to asymmetric amplitude peaks in the vibrational response of a single nanomechanical resonator of the array, which coincide with the natural frequencies of all other resonators in the same array. A rigorous theoretical model is derived that explains the physical mechanisms and describes the practical features of this parallelization. We demonstrate the significance of this parallelization through inertial imaging of analytes adsorbed to all resonators of an array, with the possibility of simultaneously detecting resonators placed at distances a hundred times larger than their own physical size.

Algorithm of combining chromatography mass spectrometry-untargeted profiling and multivariate analysis for identification of marker-substances in samples of complex composition

2020 ◽  
Vol 86 (7) ◽  
pp. 12-19
Author(s):  
I. V. Plyushchenko ◽  
D. G. Shakhmatov ◽  
I. A. Rodin
Keyword(s):  
Mass Spectrometry ◽  
Multivariate Analysis ◽  
Large Scale ◽  
Complex Composition ◽  
Unified Protocol ◽  
Chromatography Mass Spectrometry ◽  
Marker Substances ◽  
Selection Testing ◽  
Untargeted Profiling

A viral development of statistical data processing, computing capabilities, chromatography-mass spectrometry, and omics technologies (technologies based on the achievements of genomics, transcriptomics, proteomics, metabolomics) in recent decades has not led to formation of a unified protocol for untargeted profiling. Systematic errors reduce the reproducibility and reliability of the obtained results, and at the same time hinder consolidation and analysis of data gained in large-scale multi-day experiments. We propose an algorithm for conducting omics profiling to identify potential markers in the samples of complex composition and present the case study of urine samples obtained from different clinical groups of patients. Profiling was carried out by the method of liquid chromatography mass spectrometry. The markers were selected using methods of multivariate analysis including machine learning and feature selection. Testing of the approach was performed using an independent dataset by clustering and projection on principal components.

scholarly journals A Framework for International Collaboration on ITER Using Large-Scale Data Transfer to Enable Near-Real-Time Analysis

2021 ◽  
Vol 77 (2) ◽  
pp. 98-108
Author(s):  
R. M. Churchill ◽  
C. S. Chang ◽  
J. Choi ◽  
J. Wong ◽  
S. Klasky ◽  
...  
Keyword(s):  
Real Time ◽  
International Collaboration ◽  
Large Scale ◽  
Data Transfer ◽  
Time Analysis ◽  
Real Time Analysis ◽  
Large Scale Data ◽  
Scale Data

scholarly journals A Low-g MEMS Accelerometer with High Sensitivity, Low Nonlinearity and Large Dynamic Range Based on Mode-Localization of 3-DoF Weakly Coupled Resonators

Micromachines ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 310
Author(s):  
Muhammad Mubasher Saleem ◽  
Shayaan Saghir ◽  
Syed Ali Raza Bukhari ◽  
Amir Hamza ◽  
Rana Iqtidar Shakoor ◽  
...  
Keyword(s):  
Microelectromechanical Systems ◽  
Dynamic Range ◽  
Proof Mass ◽  
Amplitude Ratio ◽  
Silicon On Insulator ◽  
Coupled Resonators ◽  
Mode Localization ◽  
Mems Accelerometer ◽  
Weakly Coupled ◽  
Input Acceleration

This paper presents a new design of microelectromechanical systems (MEMS) based low-g accelerometer utilizing mode-localization effect in the three degree-of-freedom (3-DoF) weakly coupled MEMS resonators. Two sets of the 3-DoF mechanically coupled resonators are used on either side of the single proof mass and difference in the amplitude ratio of two resonator sets is considered as an output metric for the input acceleration measurement. The proof mass is electrostatically coupled to the perturbation resonators and for the sensitivity and input dynamic range tuning of MEMS accelerometer, electrostatic electrodes are used with each resonator in two sets of 3-DoF coupled resonators. The MEMS accelerometer is designed considering the foundry process constraints of silicon-on-insulator multi-user MEMS processes (SOIMUMPs). The performance of the MEMS accelerometer is analyzed through finite-element-method (FEM) based simulations. The sensitivity of the MEMS accelerometer in terms of amplitude ratio difference is obtained as 10.61/g for an input acceleration range of ±2 g with thermomechanical noise based resolution of 0.22 and nonlinearity less than 0.5%.

scholarly journals Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice

2021 ◽  
Vol 20 (2) ◽  
pp. 1280-1295
Author(s):  
Aleksandr Gaun ◽  
Kaitlyn N. Lewis Hardell ◽  
Niclas Olsson ◽  
Jonathon J. O’Brien ◽  
Sudha Gollapudi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Real Time ◽  
Ion Mobility ◽  
Large Scale ◽  
Ion Mobility Mass Spectrometry ◽  
Plasma Proteomics ◽  
Rats And Mice

scholarly journals Atmospheric tropical modes are important drivers of Sahelian springtime heatwaves

2020 ◽  
Author(s):  
Kiswendsida H. Guigma ◽  
Françoise Guichard ◽  
Martin Todd ◽  
Philippe Peyrille ◽  
Yi Wang
Keyword(s):  
Large Scale ◽  
Geographic Location ◽  
Longwave Radiation ◽  
Potential Predictability ◽  
Modes Of Variability ◽  
Physical Mechanisms ◽  
Hot Air ◽  
Western Sahel ◽  
Maximum Temperatures ◽  
Sahel Region

AbstractHeatwaves pose a serious threat to human health worldwide but remain poorly documented over Africa. This study uses mainly the ERA5 dataset to investigate their large-scale drivers over the Sahel region during boreal spring, with a focus on the role of tropical modes of variability including the Madden–Julian Oscillation (MJO) and the equatorial Rossby and Kelvin waves. Heatwaves were defined from daily minimum and maximum temperatures using a methodology that retains only intraseasonal scale events of large spatial extent. The results show that tropical modes have a large influence on the occurrence of Sahelian heatwaves, and, to a lesser extent, on their intensity. Depending on their convective phase, they can either increase or inhibit heatwave occurrence, with the MJO being the most important of the investigated drivers. A certain sensitivity to the geographic location and the diurnal cycle is observed, with nighttime heatwaves more impacted by the modes over the eastern Sahel and daytime heatwaves more affected over the western Sahel. The examination of the physical mechanisms shows that the modulation is made possible through the perturbation of regional circulation. Tropical modes thus exert a control on moisture and the subsequent longwave radiation, as well as on the advection of hot air. A detailed case study of a major event, which took place in April 2003, further supports these findings. Given the potential predictability offered by tropical modes at the intraseasonal scale, this study has key implications for heatwave risk management in the Sahel.

Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence

2021 ◽  
Author(s):  
Lok Man ◽  
William P. Klare ◽  
Ashleigh L. Dale ◽  
Joel A. Cain ◽  
Stuart J. Cordwell
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Large Scale ◽  
Lipid A ◽  
Phenotypic Characterization ◽  
Post Translational Modification ◽  
Form Of Life ◽  
Antimicrobial Interventions

Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.

scholarly journals Challenges in Large-Scale Computational Mass Spectrometry and Multiomics

2016 ◽  
Vol 15 (3) ◽  
pp. 681-682
Author(s):  
Oliver Kohlbacher ◽  
Olga Vitek ◽  
Susan T. Weintraub
Keyword(s):  
Mass Spectrometry ◽  
Large Scale

scholarly journals New insights into Trypanosoma cruzi evolution and genotyping based on system-wide protein expression profiles (PhyloQuant)

2020 ◽  
Author(s):  
Simon Ngao Mule ◽  
Andrè Guillherme da Costa Martins ◽  
Livia Rosa-Fernandes ◽  
Gilberto Santos de Oliveira ◽  
Carla Monadeli Rodrigues ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Trypanosoma Cruzi ◽  
Protein Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Shotgun Proteomics ◽  
Close Correlation ◽  
Evolutionary Relationships ◽  
Trypanosome Species ◽  
Protein Expression Profiles

AbstractThe etiological agent of Chagas disease, Trypanosoma cruzi, is subdivided into seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution justifies the concerted efforts towards understanding the population structure of T. cruzi strains. In this study, we introduce a novel approach termed ‘phyloquant’ to infer the evolutionary relationships and assignment of T. cruzi strains to their DTUs based on differential protein expression profiles evidenced by bottom up large scale mass spectrometry-based quantitative proteomic features. Mass spectrometry features analyzed using parsimony (MS1, iBAQ and LFQ) showed a close correlation between protein expression and T. cruzi DTUs and closely related trypanosome species. Although alternative topologies with minor differences between the three MS features analyzed were demonstrated, we show congruence to well accepted evolutionary relationships of T. cruzi DTUs; in all analyses TcI and Tcbat were sister groups, and the parental nature of genotype TcII and the hybrid genotypes TcV/TcVI were corroborated. Character mapping of genetic distance matrices based on phylogenetics and phyloquant clustering showed statistically significant correlations. We propose the first quantitative shotgun proteomics approach as a complement strategy to the genetic-based assignment of T. cruzi strains to DTUs and evolutionary inferences. Moreover, this approach allows for the identification of differentially regulated and strain/DTU/species-specific proteins, with potential application in the identification of strain/DTU specific biomarkers and candidate therapeutic targets. In addition, the correlation between multi-gene protein expression and divergence of trypanosome species was evaluated, adding another level to understand the genetic subdivisions among T. cruzi DTUs.

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