BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

Allali, Julien; Saule, Cédric; Chauve, Cédric; d’Aubenton-Carafa, Yves; Denise, Alain; Drevet, Christine; Ferraro, Pascal; Gautheret, Daniel; Herrbach, Claire; Leclerc, Fabrice; Monte, Antoine de; Ouangraoua, Aïda; Sagot, Marie‐France; Termier, Michel; Thermes, Claude; Touzet, Hélène

doi:10.1155/2012/893048

Cited by 16 publications

(13 citation statements)

References 24 publications

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“…For the structure-comparative benchmarks, we took four different data sets from the Brasero (Allali et al 2012) collection, namely Cold Spring Harbor Laboratory Press on May 10, 2018 -Published by rnajournal.cshlp.org Downloaded from SRP, sRNA, miRNA, and tRNA. Each data set consists of three parts: The first one is a small number of RNAs together with their known structures R of the given RNA family F; the second is a set of RNA secondary structures T2 folded from a set of RNA sequences that belong to F using mfold (Zuker and Stiegler 1981) or RNAshapes; and the third, called noise, is a set of RNA secondary structures F2 folded from a set of RNA sequences that are either random segments from viral genomes or from encode sequences.…”

Section: Data Set and Benchmark Procedures For Structure Comparisonmentioning

confidence: 99%

Abstract folding space analysis based on helices

Huang

Backofen

Voß

2012

RNA

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RNA has many pivotal functions especially in the regulation of gene expression by ncRNAs. Identification of their structure is an important requirement for understanding their function. Structure prediction alone is often insufficient for this task, due to algorithmic problems, parameter inaccuracies, and biological peculiarities. Among the latter, there are base modifications, cotranscriptional folding leading to folding traps, and conformational switching as in the case of riboswitches. All these require more in-depth analysis of the folding space. The major drawback, which all methods have to cope with, is the exponential growth of the folding space. Therefore, methods are often limited in the sequence length they can analyze, or they make use of heuristics, sampling, or abstraction. Our approach adopts the abstraction strategy and remedies some problems of existing methods. We introduce a position-specific abstraction based on helices that we term helix index shapes, or hishapes for short. Utilizing a dynamic programming framework, we have implemented this abstraction in the program RNAHeliCes. Furthermore, we developed two hishape-based methods, one for energy barrier estimation, called HiPath, and one for abstract structure comparison, termed HiTed. We demonstrate the superior performance of HiPath compared to other existing methods and the competitive accuracy of HiTed. RNAHeliCes, together with HiPath and HiTed, are available for download at

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Section: Data Set and Benchmark Procedures For Structure Comparisonmentioning

confidence: 99%

Abstract folding space analysis based on helices

Huang

Backofen

Voß

2012

RNA

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“…The eye was long regarded an immune privileged organ, but emerging evidence has shown that the systemic immune system indeed has a crucial role in the pathophysiology of AMD 8 – 10 . In AMD, peripheral inflammatory/classical monocytes are recruited to the sites of retinal injury where they differentiate into macrophages 11 .…”

Section: Introductionmentioning

confidence: 99%

EX-vivo whole blood stimulation with A2E does not elicit an inflammatory cytokine response in patients with age-related macular degeneration

Durhuus¹,

Rozing²,

Nielsen³

et al. 2021

Sci Rep

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Age-related macular degeneration (AMD) is a highly prevalent degenerative disease and a leading cause of vision loss worldwide. Evidence for an inflammatory component in the development of AMD exists, yet the exact mechanisms remain unclear. Bisretinoid N-retinylidene-N-retinylethanolamine (A2E) in retinal pigmental epithelial (RPE) cells, and in extracellular deposits constitutes a hallmark of AMD, but its role in the pathology of AMD is elusive. Here, we tested the hypothesis that A2E is responsible for the heightened inflammatory activity in AMD. To this end, we measured ex vivo mRNA expression of the cytokines TNF-α, IL-6, and IL-10 in whole blood samples after stimulation with A2E in a clinical sample of 27 patients with neovascular AMD and 24 patients with geographic atrophy secondary to AMD. Patients’ spouses (n = 30) were included as non-affected controls. After stimulation with A2E, no statistical differences were found in the median expression level of TNF-α, IL-6, IL-10 between the control group, and the neovascular AMD and the geographic atrophy group. Our findings do not support evidence for the hypothesis, that A2E per se contributes to heightened inflammatory activity in AMD.

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“…Arterial stiffness describes properties of the arterial vascular system such as distensibility, compliance, and elastic modulus [5]. It can be assessed at different sites, such as systemically (pulse wave analysis), regionally (PWV), or locally (relating a change in the area of an artery to distending pressure) [6].…”

Section: Introductionmentioning

confidence: 99%

Arterial Function in Healthy Pregnant Women vs. Non-Pregnant Women—A 10-Year Study

et al. 2020

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Introduction. Maternal age for the first pregnancy is increasing and so, the prevalence of cardiovascular risk factors in pregnancy is also increasing. Heart disease is the main reason for maternal death during pregnancy in developed countries. Arterial stiffness is an independent risk factor for atherosclerosis and a predictor of cardiovascular morbidity and mortality. The most widespread parameters for detecting subclinical atherosclerosis are augmentation index (AIx) and pulse wave velocity (PWV). The objective of this prospective study was to assess the differences between arterial function in pregnant vs. non-pregnant women of the same age, and its changes throughout the gestation period. Materials and Methods. Between 2010–2019, 887 patients were enrolled into 2 groups: pregnant (N1 = 471) and non-pregnant (N2 = 416). Data about their anthropometric characteristics, arterial function (for group 1 in all three trimesters and 6 weeks post-partum), smoking status and physical activity were collected. Results. There were statistically significant differences (p < α, α = 0.05) between the two groups regarding the body mass index, brachial AIx, systolic, diastolic and central blood pressure, and pulse pressure values. In the first group, there was a decrease of both brachial AIx and PWV in the second and third trimester, followed by a post-partum increase; better outcomes were noticed in physically active women. Conclusions. Arterial function modifies during pregnancy and these alterations differ according to the trimester of gestation. Further research is needed to establish the cut-off values for this category. Pregnant women can have better outcomes through physical activity.

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BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

Cited by 16 publications

References 24 publications

Abstract folding space analysis based on helices

Abstract folding space analysis based on helices

EX-vivo whole blood stimulation with A2E does not elicit an inflammatory cytokine response in patients with age-related macular degeneration

Arterial Function in Healthy Pregnant Women vs. Non-Pregnant Women—A 10-Year Study

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