scholarly journals CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments

2020 ◽  
Vol 21 (11) ◽  
pp. 3852
Author(s):  
Martin Raden ◽  
Fabio Gutmann ◽  
Michael Uhl ◽  
Rolf Backofen
Keyword(s):  
Ad Hoc ◽  
State Of The Art ◽  
Compensatory Mutation ◽  
Guide Rna ◽  
Interaction Prediction ◽  
Interaction Partners ◽  
Compensatory Mutations ◽  
Rna Interaction ◽  
Selection Of

In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is non-trivial and typically based on subjective ad hoc decisions. To support the decision process, we introduce our COmPensatOry MUtation Selector CopomuS. CopomuS evaluates the effects of mutations on RNA-RNA interaction formation using a set of objective criteria, and outputs a reliable ranking of compensatory mutation candidates. For RNA-RNA interaction assessment, the state-of-the-art IntaRNA prediction tool is applied. We investigate characteristics of successfully verified RNA-RNA interactions from the literature, which guided the design of CopomuS. Finally, we evaluate its performance based on experimentally validated compensatory mutations of prokaryotic sRNAs and their target mRNAs. CopomuS predictions highly agree with known results, making it a valuable tool to support the design of verification experiments for RNA-RNA interactions. It is part of the IntaRNA package and available as stand-alone webserver for ad hoc application.

scholarly journals State-of-the-art methods and devices for generation, exposure, and collection of aerosols from e-vapor products

2020 ◽  
Vol 4 ◽  
pp. 239784732097975
Author(s):  
Stéphanie Boué ◽  
Didier Goedertier ◽  
Julia Hoeng ◽  
Anita Iskandar ◽  
Arkadiusz K Kuczaj ◽  
...  
Keyword(s):  
Ad Hoc ◽  
State Of The Art ◽  
Physicochemical Characterization ◽  
Objective Evaluation ◽  
Vapor Generation ◽  
Characterization Methods ◽  
Clinical Exposure ◽  
Aerosol Generation

E-vapor products (EVP) have become popular alternatives for cigarette smokers who would otherwise continue to smoke. EVP research is challenging and complex, mostly because of the numerous and rapidly evolving technologies and designs as well as the multiplicity of e-liquid flavors and solvents available on the market. There is an urgent need to standardize all stages of EVP assessment, from the production of a reference product to e-vapor generation methods and from physicochemical characterization methods to nonclinical and clinical exposure studies. The objective of this review is to provide a detailed description of selected experimental setups and methods for EVP aerosol generation and collection and exposure systems for their in vitro and in vivo assessment. The focus is on the specificities of the product that constitute challenges and require development of ad hoc assessment frameworks, equipment, and methods. In so doing, this review aims to support further studies, objective evaluation, comparison, and verification of existing evidence, and, ultimately, formulation of standardized methods for testing EVPs.

scholarly journals Integral methods for automatic quantification of fast-scan-cyclic-voltammetry detected neurotransmitters

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254594
Author(s):  
Leonardo X. Espín ◽  
Anders J. Asp ◽  
James K. Trevathan ◽  
Kip A. Ludwig ◽  
J. Luis Lujan
Keyword(s):  
Ad Hoc ◽  
Time Integration ◽  
Large Data ◽  
Data Sets ◽  
Oxidation Reactions ◽  
Fast Scan Cyclic Voltammetry ◽  
Integral Methods ◽  
Selection Of

Modern techniques for estimating basal levels of electroactive neurotransmitters rely on the measurement of oxidative charges. This requires time integration of oxidation currents at certain intervals. Unfortunately, the selection of integration intervals relies on ad-hoc visual identification of peaks on the oxidation currents, which introduces sources of error and precludes the development of automated procedures necessary for analysis and quantification of neurotransmitter levels in large data sets. In an effort to improve charge quantification techniques, here we present novel methods for automatic selection of integration boundaries. Our results show that these methods allow quantification of oxidation reactions both in vitro and in vivo and of multiple analytes in vitro.

Metrics in routing protocol for wireless mesh networks

2013 ◽  
Vol 18 (4) ◽  
pp. 7-20 ◽  
Author(s):  
Piotr Owczarek ◽  
Piotr Zwierzykowski
Keyword(s):  
Quality Assessment ◽  
Routing Protocol ◽  
Ad Hoc ◽  
Mesh Networks ◽  
State Of The Art ◽  
Routing Metrics ◽  
Wireless Mesh ◽  
Current State ◽  
Selection Of ◽  
Network Type

Abstract The interest in services offered by wireless network has been growing for many years. It has encouraged the development of wireless technologies. New solutions are able to satisfy the ever-increasing demands concerning wireless services. It is also evident in the diversification of quality assessment methods employed with reference to connections used in such networks. One of the basic elements used in connection quality assessment are metrics. The use of metrics is directly linked to the type of the routing protocol applied in a given network. The selection of a given routing protocol is often determined by its specific properties that might be advantageous in a certain network type, or that are important in terms of the type or scope of services provided. Therefore, it is easy to identify a relationship between metrics and the area of application of a given routing protocol. The significance and diversity of metrics is also reflected inWireless Mesh Networks (WMNs). The proposed paper presents a review of the current state-of-the-art routing metrics for Ad-hoc and WMN networks

Selection of Reference Genes for Transcription Studies on Adventitious Root Induction in Olive (Olea Europaea L.) Microshoots Considering Co-expression and Average Transcriptional Stability

2020 ◽  
Author(s):  
Carlos Noceda ◽  
Augusto Peixe ◽  
Birgit Arnholdt-Schmitt
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Reference Genes ◽  
Ad Hoc ◽  
Root Induction ◽  
Expression Data ◽  
Internal Reference ◽  
Experimental Conditions ◽  
Selection Of

Abstract BackgroungSelection of reference genes (RGs) for normalization of PCR-gene expression data includes two crucial steps: determination of the among-sample transcriptionally more stable genes and subsequent choosing of the most suitable genes as internal controls. Both steps can be carried-out through generally accepted strategies each having different strengths and weaknesses. The present study proposes to reinforce normalization of gene expression data by integrating and adding analytical revision at critical steps of those accepted procedures. Especially crucial is to counterbalance a higher representative number of RGs with a correspondent increase in their average transcriptional instability or a generalised co-expression trend among the samples. This methodological study used in vitro olive adventitious rooting as an experimental system, since the underlying morphogenetic process -wich is common to diverse species- is still not completely understood.ResultsFirstly, RG candidates were ranked according to transcriptional stability following a simple statistical method that reduces biasing effects of concomitant, systematic biological variations associated to experimental conditions, such as the variations caused by gene co-regulation. Those types of systematic co-variation are unconsidered by several popular ad hoc informatics programmes. To select the adequate genes among those already ranked, an algorithm of one of the ad hoc informatics programmes (GeNorm) was adapted to allow partial automatization of RG selection for any strategy of transcriptional-gene stability ordering. In order to delve into the resulting possible RG sets suitability for inter-assay comparisons and technical-error compensation, separate statistics were formulated. The achieved results were compared with those obtained by standard stability ranking methods. Finally, a double evaluation was performed to accurately contrast two choice RG sets. The whole strategy was applied to a panel considering several independent factors, but the suitability of the obtained putative RG sets was tested for cases restricted to fewer variables. H2B, OUB and ACT are valid for normalization in transcriptional studies on olive microshoot rooting when comparing treatments, time points and assays.ConclusionsThe set of genes identified as internal reference is now available for wider expression studies on any target gene in similar biological systems. The overall methodology aims to constitute a guide for general application.

An Optimal Fuzzy Load Balanced Adaptive Gateway Discovery for Ubiquitous Internet Access in MANET

2016 ◽  
Vol 9 (4) ◽  
pp. 45-63 ◽  
Author(s):  
Prakash Srivastava ◽  
Rakesh Kumar
Keyword(s):  
Ad Hoc Network ◽  
Ad Hoc ◽  
Mobile Ad Hoc Network ◽  
State Of The Art ◽  
Internet Access ◽  
Analytical Validation ◽  
Multiple Parameters ◽  
Gateway Discovery ◽  
Mobile Ad Hoc ◽  
Selection Of

A mobile ad hoc network (MANET) is an autonomous collection of independent nodes cooperating together to form an infrastructure less network spontaneously. For increasing usability of MANET domain which finds application in natural disaster such as earthquake, floods etc. it is also desired to be connected with Internet through Internet gateways. Therefore, an efficient gateway discovery mechanism is required for MANET-Internet integration. Existing schemes use one or multiple parameters for optimal selection of gateway which causes a particular gateway to be selected many times which results in higher delay latency and packet drops due to prevailing congestion at a particular gateway. To avoid this situation, the authors have utilized the potential of fuzzy logic to ascertain the decision of load balancing at the Internet gateway. Besides this, their scheme also incorporates an effective adaptive gateway discovery mechanism. Consequently, enhanced performance is achieved as compared to existing state-of-the-art related schemes. The proposed approach is evaluated by simulation and analytical validation.

scholarly journals RNA structure through multidimensional chemical mapping

2016 ◽  
Author(s):  
Siqi Tian ◽  
Rhiju Das
Keyword(s):  
Structure Determination ◽  
Rna Structure ◽  
De Novo ◽  
Compensatory Mutation ◽  
Chemical Mapping ◽  
Rna Molecules ◽  
Viral Genomes ◽  
Rna Interaction

The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire transcriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure determination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M2), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed .OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide. A growing body of in vitro blind tests and compensatory mutation/rescue experiments indicate that MCM methods give consistently accurate secondary structures and global tertiary structures for ribozymes, ribosomal domains and ligand-bound riboswitch aptamers up to two hundred nucleotides in length. Importantly, MCM analyses provide detailed information on structurally heterogeneous RNA states, such as ligand-free riboswitches, that are functionally important but difficult to resolve with other approaches. The sequencing requirements of currently available MCM protocols scale at least quadratically with RNA length, precluding general application to transcriptomes or viral genomes at present. We propose a modify-crosslink-map expansion to overcome this and other current limitations to resolving the in vivo "RNA structurome".

scholarly journals RNA structure through multidimensional chemical mapping

2016 ◽  
Vol 49 ◽  
Author(s):  
Siqi Tian ◽  
Rhiju Das
Keyword(s):  
Structure Determination ◽  
Rna Structure ◽  
De Novo ◽  
Compensatory Mutation ◽  
Chemical Mapping ◽  
Rna Molecules ◽  
Viral Genomes ◽  
Rna Interaction

AbstractThe discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire transcriptomesin vivo, but the resulting one-dimensional data generally remain too information-poor to allow accuratede novostructure determination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M2), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed •OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide. A growing body ofin vitroblind tests and compensatory mutation/rescue experiments indicate that MCM methods give consistently accurate secondary structures and global tertiary structures for ribozymes, ribosomal domains and ligand-bound riboswitch aptamers up to 200 nucleotides in length. Importantly, MCM analyses provide detailed information on structurally heterogeneous RNA states, such as ligand-free riboswitches that are functionally important but difficult to resolve with other approaches. The sequencing requirements of currently available MCM protocols scale at least quadratically with RNA length, precluding general application to transcriptomes or viral genomes at present. We propose a modify-cross-link-map (MXM) expansion to overcome this and other current limitations to resolving thein vivo ‘RNA structurome’.

scholarly journals Integral methods for automatic quantification of fast-scan-cyclic-voltammetry detected neurotransmitters

2020 ◽  
Author(s):  
Leonardo X. Espín ◽  
Anders J. Asp ◽  
James K. Trevathan ◽  
Kip A. Ludwig ◽  
J. Luis Lujan
Keyword(s):  
Ad Hoc ◽  
Time Integration ◽  
Large Data ◽  
Data Sets ◽  
Fast Scan Cyclic Voltammetry ◽  
Integral Methods ◽  
Automated Procedures ◽  
Selection Of

AbstractModern techniques for estimating basal levels of electroactive neurotransmitters rely on the measurement of oxidative charges. This requires time integration of oxidation currents at certain intervals. Unfortunately, the selection of integration intervals relies on ad-hoc visual identification of peaks on the oxidation currents, which introduces sources of error and precludes the development of automated procedures necessary for analysis and quantification of neurotransmitter levels in large data sets. In an effort to improve charge quantification techniques, here we present novel methods for automatic selection of integration boundaries. Our results show that these methods allow quantification of oxidation and reduction reactions, for multiple analytes, both in vitro and in vivo.

scholarly journals Investigating the concept of accessibility for predicting novel RNA-RNA interactions

2021 ◽  
Author(s):  
Sabine Reisser ◽  
Irmtraud M Meyer
Keyword(s):  
Free Energy ◽  
Thermodynamic Model ◽  
Rna Structure ◽  
State Of The Art ◽  
Minimum Free Energy ◽  
Prediction Performance ◽  
Interaction Prediction ◽  
Energy Penalty ◽  
Rna Interaction

State-of-the-art methods for predicting novel trans RNA-RNA interactions use the so-called accessibility as key concept. It estimates whether a region in a given RNA sequence is accessible for forming trans interactions, using a thermodynamic model which quantifies its secondary structure features. RNA-RNA interactions are then predicted by finding the minimum free energy base pairing between the two transcripts, taking into account the accessibility as energy penalty. We investigated the underlying assumptions of this approach using the two methods RNAPLEX and INTARNA on two datasets, containing sRNA-mRNA and snoRNA-rRNA interactions, respectively. We find that (1) known trans RNA-RNA interactions frequently overlap regions containing RNA structure features, (2) the estimated accessibility reflects sRNA structures fairly well, but often disagrees with structures of longer transcripts, (3) the prediction performance of RNA-RNA interaction prediction methods is independent of the quality of the estimated accessibility profiles, and (4) one important overall effect of accessibility profiles is to prevent the thermodynamic model from predicting too long interactions. Based on our findings, we conclude that the accessibility concept to the minimum free energy approach to predicting novel RNA-RNA interactions has conceptual limitations and discuss potential ways of improving the field in the future.

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