scholarly journals Simulation of Folding Kinetics for Aligned RNAs

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 347
Author(s):  
Jiabin Huang ◽  
Björn Voß
Keyword(s):  
Evolutionary Conservation ◽  
Folding Kinetics ◽  
New Approach ◽  
Computational Approaches ◽  
Reasonable Time ◽  
Valuable Method ◽  
Kinetics Of ◽  
Insight Into ◽  
Folding Space ◽  
Standing Problem

Studying the folding kinetics of an RNA can provide insight into its function and is thus a valuable method for RNA analyses. Computational approaches to the simulation of folding kinetics suffer from the exponentially large folding space that needs to be evaluated. Here, we present a new approach that combines structure abstraction with evolutionary conservation to restrict the analysis to common parts of folding spaces of related RNAs. The resulting algorithm can recapitulate the folding kinetics known for single RNAs and is able to analyse even long RNAs in reasonable time. Our program RNAliHiKinetics is the first algorithm for the simulation of consensus folding kinetics and addresses a long-standing problem in a new and unique way.

scholarly journals Decoding the Kinetic Limitations of Plasmon Catalysis: The Case of 4-Nitrothiophenol Dimerization

2020 ◽  
Author(s):  
Wouter Koopman ◽  
Radwan M. Sarhan ◽  
Felix Stete ◽  
Clemens N. Z. Schmitt ◽  
Matias Bargheer
Keyword(s):  
Thermal Effects ◽  
Dominant Role ◽  
Relative Importance ◽  
New Approach ◽  
Multistep Reaction ◽  
Kinetics Of ◽  
Complex Organic ◽  
Insight Into ◽  
Unique Ability

Plasmon-mediated chemistry presents an intriguing new approach to photocatalysis. However, the reaction enhancement<br>mechanism is not well understood. In particular, the relative importance of plasmon-generated hot charges and<br>photoheating are strongly debated. In this article, we evaluate the influence of microscopic photoheating on the kinetics of<br>a model plasmon-catalyzed reaction: the light-induced 4-nitrothiophenol (4NTP) to 4,4’-dimercaptoazobenzene (DMAB)<br>dimerization. Direct measurement of the reaction temperature by nanoparticle Raman-thermometry demonstrated that<br>the thermal effect plays a dominant role in the kinetic limitations of this multistep reaction. On the same time, no reaction<br>is possible by dark heating to the same temperature. This shows that plasmon nanoparticles have the unique ability to<br>enhance several steps of complex tandem reactions simultaneously. These results provide insight into the role of hot<br>electron and thermal effects in plasmonic catalysis of complex organic reactions, which highly important for the ongoing<br>development of plasmon based photosynthesis. <br>

scholarly journals Decoding the Kinetic Limitations of Plasmon Catalysis: The Case of 4-Nitrothiophenol Dimerization

2020 ◽  
Author(s):  
Wouter Koopman ◽  
Radwan M. Sarhan ◽  
Felix Stete ◽  
Clemens N. Z. Schmitt ◽  
Matias Bargheer
Keyword(s):  
Thermal Effects ◽  
Dominant Role ◽  
Relative Importance ◽  
New Approach ◽  
Multistep Reaction ◽  
Kinetics Of ◽  
Complex Organic ◽  
Insight Into ◽  
Unique Ability

Plasmon-mediated chemistry presents an intriguing new approach to photocatalysis. However, the reaction enhancement<br>mechanism is not well understood. In particular, the relative importance of plasmon-generated hot charges and<br>photoheating are strongly debated. In this article, we evaluate the influence of microscopic photoheating on the kinetics of<br>a model plasmon-catalyzed reaction: the light-induced 4-nitrothiophenol (4NTP) to 4,4’-dimercaptoazobenzene (DMAB)<br>dimerization. Direct measurement of the reaction temperature by nanoparticle Raman-thermometry demonstrated that<br>the thermal effect plays a dominant role in the kinetic limitations of this multistep reaction. On the same time, no reaction<br>is possible by dark heating to the same temperature. This shows that plasmon nanoparticles have the unique ability to<br>enhance several steps of complex tandem reactions simultaneously. These results provide insight into the role of hot<br>electron and thermal effects in plasmonic catalysis of complex organic reactions, which highly important for the ongoing<br>development of plasmon based photosynthesis. <br>

Computational Approaches to Predict the Non-canonical DNAs

2019 ◽  
Vol 14 (6) ◽  
pp. 470-479 ◽  
Author(s):  
Nazia Parveen ◽  
Amen Shamim ◽  
Seunghee Cho ◽  
Kyeong Kyu Kim
Keyword(s):  
Computational Methods ◽  
Genetic Instability ◽  
Computational Prediction ◽  
Structure And Function ◽  
Sequence Motifs ◽  
Computational Approaches ◽  
Functional Roles ◽  
And Function ◽  
Genetic Events ◽  
Insight Into

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.

scholarly journals Can Economic Factors Improve Momentum Trading Strategies? The Case of Managed Futures during the COVID-19 Pandemic

Economies ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 86
Author(s):  
Renata Guobužaitė ◽  
Deimantė Teresienė
Keyword(s):  
Financial Markets ◽  
Risk Premium ◽  
Trading Strategies ◽  
Economic Factors ◽  
Momentum Strategies ◽  
New Approach ◽  
Managed Futures ◽  
Asset Classes ◽  
Momentum Trading ◽  
Insight Into

Systematic momentum trading is a prevalent risk premium strategy in different portfolios. This paper focuses on the performance of the managed futures strategy based on the momentum signal across different economic regimes, focusing on the COVID-19 pandemic period. COVID-19 had a solid but short-lived impact on financial markets, and therefore gives a unique insight into momentum strategies’ performance during such critical moments of market stress. We offer a new approach to implementing momentum strategies by adding macroeconomic variables to the model. We test a managed futures strategy’s performance with a well-diversified futures portfolio across different asset classes. The research concludes that constructing a portfolio based on academically/economically sound momentum signals with its allocation timing based on broader economic factors significantly improves managed futures strategies and adds significant diversification benefits to the investors’ portfolios.

scholarly journals Rapid systemic surge of IL-33 after severe human trauma: a prospective observational study

2021 ◽  
Vol 27 (1) ◽  
Author(s):  
Olav Sundnes ◽  
William Ottestad ◽  
Camilla Schjalm ◽  
Peter Lundbäck ◽  
Lars la Cour Poulsen ◽  
...  
Keyword(s):  
High Resolution ◽  
Prospective Observational Study ◽  
Tissue Injury ◽  
Trauma Patients ◽  
Decoy Receptor ◽  
Interleukin 33 ◽  
Injured Patients ◽  
First Time ◽  
Kinetics Of ◽  
Insight Into

Abstract Background Alarmins are considered proximal mediators of the immune response after tissue injury. Understanding their biology could pave the way for development of new therapeutic targets and biomarkers in human disease, including multiple trauma. In this study we explored high-resolution concentration kinetics of the alarmin interleukin-33 (IL-33) early after human trauma. Methods Plasma samples were serially collected from 136 trauma patients immediately after hospital admission, 2, 4, 6, and 8 h thereafter, and every morning in the ICU. Levels of IL-33 and its decoy receptor sST2 were measured by immunoassays. Results We observed a rapid and transient surge of IL-33 in a subset of critically injured patients. These patients had more widespread tissue injuries and a greater degree of early coagulopathy. IL-33 half-life (t1/2) was 1.4 h (95% CI 1.2–1.6). sST2 displayed a distinctly different pattern with low initial levels but massive increase at later time points. Conclusions We describe for the first time early high-resolution IL-33 concentration kinetics in individual patients after trauma and correlate systemic IL-33 release to clinical data. These findings provide insight into a potentially important axis of danger signaling in humans.

scholarly journals Individualized Hemodynamic Management in Sepsis

2021 ◽  
Vol 11 (2) ◽  
pp. 157
Author(s):  
Marcell Virág ◽  
Tamas Leiner ◽  
Mate Rottler ◽  
Klementina Ocskay ◽  
Zsolt Molnar
Keyword(s):  
Fluid Overload ◽  
Fluid Management ◽  
Multiple Organ ◽  
Treatment Protocols ◽  
Hemodynamic Management ◽  
New Approach ◽  
Hemodynamic Optimization ◽  
The Individual ◽  
Sepsis And Septic Shock ◽  
Insight Into

Hemodynamic optimization remains the cornerstone of resuscitation in the treatment of sepsis and septic shock. Delay or inadequate management will inevitably lead to hypoperfusion, tissue hypoxia or edema, and fluid overload, leading eventually to multiple organ failure, seriously affecting outcomes. According to a large international survey (FENICE study), physicians frequently use inadequate indices to guide fluid management in intensive care units. Goal-directed and “restrictive” infusion strategies have been recommended by guidelines over “liberal” approaches for several years. Unfortunately, these “fixed regimen” treatment protocols neglect the patient’s individual needs, and what is shown to be beneficial for a given population may not be so for the individual patient. However, applying multimodal, contextualized, and personalized management could potentially overcome this problem. The aim of this review was to give an insight into the pathophysiological rationale and clinical application of this relatively new approach in the hemodynamic management of septic patients.

Atomic-level insight into reasonable design of metal-based catalysts for hydrogen oxidation in alkaline electrolytes

2021 ◽  
Author(s):  
Lulu An ◽  
Xu Zhao ◽  
Tonghui Zhao ◽  
Deli Wang
Keyword(s):  
Fuel Cell ◽  
Anion Exchange ◽  
Hydrogen Oxidation ◽  
Anion Exchange Membrane ◽  
Atomic Level ◽  
Alkaline Electrolytes ◽  
Exchange Membrane ◽  
Kinetics Of ◽  
Insight Into ◽  
Hydrogen Utilization

Anion exchange membrane fuel cell (AEMFC) is becoming highly attractive for hydrogen utilization owing to the advantages of employing economic catalysts in alkaline electrolytes. Nevertheless, the kinetics of anodic hydrogen...

scholarly journals Modulation of Folding Kinetics of Repeat Proteins: Interplay between Intra- and Interdomain Interactions

2012 ◽  
Vol 103 (7) ◽  
pp. 1555-1565 ◽  
Author(s):  
Tzachi Hagai ◽  
Ariel Azia ◽  
Emmanuel Trizac ◽  
Yaakov Levy
Keyword(s):  
Folding Kinetics ◽  
Repeat Proteins ◽  
Interdomain Interactions ◽  
Kinetics Of

An Insight into the Mechanism and Kinetics of Reactions In BOF Steelmaking: Theory vs Practice

2010 ◽  
Vol 81 (11) ◽  
pp. 940-948 ◽  
Author(s):  
A. K. Shukla ◽  
B. Deo ◽  
S. Millman ◽  
B. Snoeijer ◽  
A. Overbosch ◽  
...  
Keyword(s):  
Mechanism And Kinetics ◽  
Kinetics Of ◽  
Insight Into

Comparison of New Telescopic Video Microlaryngoscopic and Standard Microlaryngoscopic Techniques

1992 ◽  
Vol 101 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Eiji Yanagisawa ◽  
Ken Yanagisawa ◽  
Jay B. Horowitz ◽  
Lawrence J. Mambrino
Keyword(s):  
Video Camera ◽  
New Method ◽  
Depth Of Field ◽  
Microscopic Technique ◽  
New Approach ◽  
Advantages And Disadvantages ◽  
Laryngeal Surgery ◽  
Valuable Method ◽  
Microlaryngeal Surgery ◽  
Television Image

A new approach to microlaryngeal surgery using a specially designed video microlaryngoscope with a rigid endoscopic telescope and an attached video camera was introduced by Kantor et al in 1990. The ability to video document and perform surgery of the larynx by viewing a high-resolution television image was demonstrated. This method was recommended over the standard microscopic technique for increased visibility with greater depth of field, unimpeded instrument access, instant documentation, and superior teaching value. The authors tried this new method and the standard microscopic technique at the same sitting on a series of patients. This paper will compare these two different techniques and discuss their advantages and disadvantages. Although the new method has many advantages, the standard microscopic technique remains as a valuable method in laryngeal surgery.

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