scholarly journals AI-based Spectroscopic Monitoring of Real-time Interactions between SARS-CoV-2 and Human ACE2

Author(s):  
Sheng Ye ◽  
Guozhen Zhang ◽  
Jun Jiang

<div> <p>Here we demonstrate by a proof-of-concept simulation of IR spectra of complex of spike protein of SARS-CoV-2 and human ACE2, that a time-resolved spectroscopy may monitor the real-time structural information of the protein-protein complexes of interest, with the help of a machine learning protocol. The significant speedup of our approach relative to conventional quantum chemistry approach suggests a promising way of accelerating the development of real-time spectroscopy study of protein dynamics.</p> </div>

2020 ◽  
Author(s):  
Sheng Ye ◽  
Guozhen Zhang ◽  
Jun Jiang

<div> <p>Here we demonstrate by a proof-of-concept simulation of IR spectra of complex of spike protein of SARS-CoV-2 and human ACE2, that a time-resolved spectroscopy may monitor the real-time structural information of the protein-protein complexes of interest, with the help of a machine learning protocol. The significant speedup of our approach relative to conventional quantum chemistry approach suggests a promising way of accelerating the development of real-time spectroscopy study of protein dynamics.</p> </div>


2021 ◽  
Vol 118 (26) ◽  
pp. e2025879118
Author(s):  
Sheng Ye ◽  
Guozhen Zhang ◽  
Jun Jiang

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), invades a human cell via human angiotensin-converting enzyme 2 (hACE2) as the entry, causing the severe coronavirus disease (COVID-19). The interactions between hACE2 and the spike glycoprotein (S protein) of SARS-CoV-2 hold the key to understanding the molecular mechanism to develop treatment and vaccines, yet the dynamic nature of these interactions in fluctuating surroundings is very challenging to probe by those structure determination techniques requiring the structures of samples to be fixed. Here we demonstrate, by a proof-of-concept simulation of infrared (IR) spectra of S protein and hACE2, that time-resolved spectroscopy may monitor the real-time structural information of the protein−protein complexes of interest, with the help of machine learning. Our machine learning protocol is able to identify fine changes in IR spectra associated with variation of the secondary structures of S protein of the coronavirus. Further, it is three to four orders of magnitude faster than conventional quantum chemistry calculations. We expect our machine learning protocol would accelerate the development of real-time spectroscopy study of protein dynamics.


2018 ◽  
Author(s):  
Sebastian Hoffmann ◽  
Daniele Fachinetti

i.Summary/AbstractMeasuring protein dynamics is essential to uncover protein function and to understand the formation of large protein complexes such as centromeres. Recently, genome engineering in human cells has improved our ability to study the function of endogenous proteins. By combining genome editing techniques with the Auxin Inducible Degradation (AID) system, we created a versatile tool to study protein dynamics. This system allows us to analyze both protein function and dynamics by enabling rapid protein depletion and re-expression in the same experimental set-up. Here, we focus on the dynamics of the centromeric histone-associated protein CENP-C, responsible for the formation of the kinetochore complex. Following rapid removal and re-activation of a fluorescent version of CENP-C by auxin treatment and removal, we could follow CENP-C de novo deposition at centromeric regions during different stages of the cell cycle. In conclusion, the auxin degradation system is a powerful tool to assess and quantify protein dynamics in real time.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sheetal Chaudhuri ◽  
Hao Han ◽  
Caitlin Monaghan ◽  
John Larkin ◽  
Peter Waguespack ◽  
...  

Abstract Background Inadequate refilling from extravascular compartments during hemodialysis can lead to intradialytic symptoms, such as hypotension, nausea, vomiting, and cramping/myalgia. Relative blood volume (RBV) plays an important role in adapting the ultrafiltration rate which in turn has a positive effect on intradialytic symptoms. It has been clinically challenging to identify changes RBV in real time to proactively intervene and reduce potential negative consequences of volume depletion. Leveraging advanced technologies to process large volumes of dialysis and machine data in real time and developing prediction models using machine learning (ML) is critical in identifying these signals. Method We conducted a proof-of-concept analysis to retrospectively assess near real-time dialysis treatment data from in-center patients in six clinics using Optical Sensing Device (OSD), during December 2018 to August 2019. The goal of this analysis was to use real-time OSD data to predict if a patient’s relative blood volume (RBV) decreases at a rate of at least − 6.5 % per hour within the next 15 min during a dialysis treatment, based on 10-second windows of data in the previous 15 min. A dashboard application was constructed to demonstrate how reporting structures may be developed to alert clinicians in real time of at-risk cases. Data was derived from three sources: (1) OSDs, (2) hemodialysis machines, and (3) patient electronic health records. Results Treatment data from 616 in-center dialysis patients in the six clinics was curated into a big data store and fed into a Machine Learning (ML) model developed and deployed within the cloud. The threshold for classifying observations as positive or negative was set at 0.08. Precision for the model at this threshold was 0.33 and recall was 0.94. The area under the receiver operating curve (AUROC) for the ML model was 0.89 using test data. Conclusions The findings from our proof-of concept analysis demonstrate the design of a cloud-based framework that can be used for making real-time predictions of events during dialysis treatments. Making real-time predictions has the potential to assist clinicians at the point of care during hemodialysis.


2021 ◽  
pp. neurintsurg-2021-017858
Author(s):  
Dee Zhen Lim ◽  
Melissa Yeo ◽  
Ariel Dahan ◽  
Bahman Tahayori ◽  
Hong Kuan Kok ◽  
...  

BackgroundDelivery of acute stroke endovascular intervention can be challenging because it requires complex coordination of patient and staff across many different locations. In this proof-of-concept paper we (a) examine whether WiFi fingerprinting is a feasible machine learning (ML)-based real-time location system (RTLS) technology that can provide accurate real-time location information within a hospital setting, and (b) hypothesize its potential application in streamlining acute stroke endovascular intervention.MethodsWe conducted our study in a comprehensive stroke care unit in Melbourne, Australia that offers a 24-hour mechanical thrombectomy service. ML algorithms including K-nearest neighbors, decision tree, random forest, support vector machine and ensemble models were trained and tested on a public WiFi dataset and the study hospital WiFi dataset. The hospital dataset was collected using the WiFi explorer software (version 3.0.2) on a MacBook Pro (AirPort Extreme, Broadcom BCM43x×1.0). Data analysis was implemented in the Python programming environment using the scikit-learn package. The primary statistical measure for algorithm performance was the accuracy of location prediction.ResultsML-based WiFi fingerprinting can accurately predict the different hospital zones relevant in the acute endovascular intervention workflow such as emergency department, CT room and angiography suite. The most accurate algorithms were random forest and support vector machine, both of which were 98% accurate. The algorithms remain robust when new data points, which were distinct from the training dataset, were tested.ConclusionsML-based RTLS technology using WiFi fingerprinting has the potential to streamline delivery of acute stroke endovascular intervention by efficiently tracking patient and staff movement during stroke calls.


Author(s):  
Marie Barth ◽  
Carla Schmidt

AbstractCross-linking, in general, involves the covalent linkage of two amino acid residues of proteins or protein complexes in close proximity. Mass spectrometry and computational analysis are then applied to identify the formed linkage and deduce structural information such as distance restraints. Quantitative cross-linking coupled with mass spectrometry is well suited to study protein dynamics and conformations of protein complexes. The quantitative cross-linking workflow described here is based on the application of isotope labelled cross-linkers. Proteins or protein complexes present in different structural states are differentially cross-linked using a “light” and a “heavy” cross-linker. The intensity ratios of cross-links (i.e., light/heavy or heavy/light) indicate structural changes or interactions that are maintained in the different states. These structural insights lead to a better understanding of the function of the proteins or protein complexes investigated. The described workflow is applicable to a wide range of research questions including, for instance, protein dynamics or structural changes upon ligand binding.


TAPPI Journal ◽  
2019 ◽  
Vol 18 (11) ◽  
pp. 679-689
Author(s):  
CYDNEY RECHTIN ◽  
CHITTA RANJAN ◽  
ANTHONY LEWIS ◽  
BETH ANN ZARKO

Packaging manufacturers are challenged to achieve consistent strength targets and maximize production while reducing costs through smarter fiber utilization, chemical optimization, energy reduction, and more. With innovative instrumentation readily accessible, mills are collecting vast amounts of data that provide them with ever increasing visibility into their processes. Turning this visibility into actionable insight is key to successfully exceeding customer expectations and reducing costs. Predictive analytics supported by machine learning can provide real-time quality measures that remain robust and accurate in the face of changing machine conditions. These adaptive quality “soft sensors” allow for more informed, on-the-fly process changes; fast change detection; and process control optimization without requiring periodic model tuning. The use of predictive modeling in the paper industry has increased in recent years; however, little attention has been given to packaging finished quality. The use of machine learning to maintain prediction relevancy under everchanging machine conditions is novel. In this paper, we demonstrate the process of establishing real-time, adaptive quality predictions in an industry focused on reel-to-reel quality control, and we discuss the value created through the availability and use of real-time critical quality.


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