Faculty Opinions recommendation of Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies.

Author(s):  
Janet Thornton
Author(s):  
Pedro Gabriel Ferreira ◽  
Paulo Jorge Azevedo

Protein sequence motifs describe, through means of enhanced regular expression syntax, regions of amino-acids that have been conserved across several functionally related proteins. These regions may have an implication at the structural and functional level of the proteins. Sequence motif analysis can bring significant improvements towards a better understanding of the protein sequence-structure-function relation. In this chapter we review the subject of mining deterministic motifs from protein sequence databases. We start by giving a formal definition of the different types of motifs and the respective specificities. Then, we explore the methods available to evaluate the quality and interest of such patterns. Examples of applications and motif repositories are described. We discuss the algorithmic aspects and different methodologies for motif extraction. A briefly description on how sequence motifs can be used to extract structural level information patterns is also provided.


2019 ◽  
Vol 8 (5) ◽  
pp. 613 ◽  
Author(s):  
Juan Gómez-Salgado ◽  
Máximo Bernabeu-Wittel ◽  
Carmen Aguilera-González ◽  
Juan Antonio Goicoechea-Salazar ◽  
Daniel Larrocha ◽  
...  

It is unknown whether the digital application of automated ICD-9-CM codes recorded in the medical history are useful for a first screening in the detection of polypathological patients. In this study, the objective was to identify the degree of intra- and inter-observer concordance in the identification of in-patient polypathological patients between the standard clinical identification method and a new automatic method, using the basic minimum data set of ICD-9-CM codes in the digital medical history. For this, a cross-sectional multicenter study with 1518 administratively discharged patients from Andalusian hospitals during the period of 2013–2014 has been carried out. For the concordance between the clinical definition of a polypathological patient and the polypathological patient classification according to ICD-9-CM coding, a 0.661 kappa was obtained (95% confidence interval (CI); 0.622–0.701) with p < 0.0001. The intraclass correlation coefficient between both methods for the number of polypathological patient categories was 0.745 (95% CI; 0.721–0.768; p < 0.0001). The values of sensitivity, specificity, positive-, and negative predictive values of the automated detection using ICD-9-CM coding were 78%, 88%, 78%, and 88%, respectively. As conclusion, the automatic identification of polypathological patients by detecting ICD-9-CM codes is useful as a screening method for in-hospital patients.


Author(s):  
Irene Rechichi ◽  
Antonella Iadarola ◽  
Maurizio Zibetti ◽  
Alessandro Cicolin ◽  
Gabriella Olmo

Objectives: Rapid Eye Movement Sleep Behaviour Disorder (RBD) is regarded as a prodrome of neurodegeneration, with a high conversion rate to α–synucleinopathies such as Parkinson’s Disease (PD). The clinical diagnosis of RBD co–exists with evidence of REM Sleep Without Atonia (RSWA), a parasomnia that features loss of physiological muscular atonia during REM sleep. The objectives of this study are to implement an automatic detection of RSWA from polysomnographic traces, and to propose a continuous index (the Dissociation Index) to assess the level of dissociation between REM sleep stage and atonia. This is performed using Euclidean distance in proper vector spaces. Each subject is assigned a dissociation degree based on their distance from a reference, encompassing healthy subjects and clinically diagnosed RBD patients at the two extremes. Methods: Machine Learning models were employed to perform automatic identification of patients with RSWA through clinical polysomnographic scores, together with variables derived from electromyography. Proper distance metrics are proposed and tested to achieve a dissociation measure. Results: The method proved efficient in classifying RSWA vs. not-RSWA subjects, achieving an overall accuracy, sensitivity and precision of 87%, 93% and 87.5%, respectively. On its part, the Dissociation Index proved to be promising in measuring the impairment level of patients. Conclusions: The proposed method moves a step forward in the direction of automatically identifying REM sleep disorders and evaluating the impairment degree. We believe that this index may be correlated with the patients’ neurodegeneration process; this assumption will undergo a robust clinical validation process involving healthy, RSWA, RBD and PD subjects.


Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2750
Author(s):  
Zhuofu Ni ◽  
Xiaodong Cheng

Exchange proteins directly activated by cAMP (EPAC1 and EPAC2) are one of the several families of cellular effectors of the prototypical second messenger cAMP. To understand the origin and molecular evolution of EPAC proteins, we performed a comprehensive phylogenetic analysis of EPAC1 and EPAC2. Our study demonstrates that unlike its cousin PKA, EPAC proteins are only present in multicellular Metazoa. Within the EPAC family, EPAC1 is only associated with chordates, while EPAC2 spans the entire animal kingdom. Despite a much more contemporary origin, EPAC1 proteins show much more sequence diversity among species, suggesting that EPAC1 has undergone more selection and evolved faster than EPAC2. Phylogenetic analyses of the individual cAMP binding domain (CBD) and guanine nucleotide exchange (GEF) domain of EPACs, two most conserved regions between the two isoforms, further reveal that EPAC1 and EPAC2 are closely clustered together within both the larger cyclic nucleotide receptor and RAPGEF families. These results support the notion that EPAC1 and EPAC2 share a common ancestor resulting from a fusion between the CBD of PKA and the GEF from RAPGEF1. On the other hand, the two terminal extremities and the RAS-association (RA) domains show the most sequence diversity between the two isoforms. Sequence diversities within these regions contribute significantly to the isoform-specific functions of EPACs. Importantly, unique isoform-specific sequence motifs within the RA domain have been identified.


2020 ◽  
Vol 8 (1) ◽  
pp. 50
Author(s):  
Zbigniew Pietrzykowski ◽  
Miroslaw Wielgosz ◽  
Marcin Breitsprecher

One of the ways to prevent accidents at sea is to detect risks caused by humans and to counteract them. These tasks can be executed through an analysis of ship maneuvers and the identification of behavior considered to be potentially dangerous, e.g., based on data obtained online from the automatic identification system (AIS). As a result, additional measures or actions can be taken, e.g., passing at a distance greater than previously planned. The detection of risks at sea requires a prior definition of behavior patterns and the criteria assigned to them. Each pattern represents a specific navigator’s safety profile. The criteria assigned to each pattern for the identification of the navigator’s safety profile were determined from previously recorded AIS data. Due to a large amount of data and their complex relationships, these authors have proposed to use data mining tools. This work continues previous research on this subject. The conducted analysis covered data recorded in simulation tests done by navigators. Typical ship encounter situations were included. Based on additional simulation data, the patterns of behavior were verified for the determination of a navigator’s safety profile. An example of using the presented method is given.


2018 ◽  
Vol 72 (3) ◽  
pp. 777-794 ◽  
Author(s):  
Axel Hörteborn ◽  
Jonas W. Ringsberg ◽  
Martin Svanberg ◽  
Henrik Holm

When ships approach each other, they should keep a minimum area around them clear of other vessels in order to remain safe. The geometrical shape of this area has been studied since the early 1970s and is defined as the ship domain. The progress in computer capacity since then and the introduction of the Automatic Identification System (AIS) provides the potential to further investigate the size and the governing factors of the domain. This investigation revisits and proposes a method using data based on 600,000 ship encounters at 36 locations. It is concluded that the ship domain has the shape of an ellipse with half axis radii of 0.9 and 0.45 nautical miles. However, there are two factors that greatly affect the ship domain: how large the area is that is used to gather vessel intersections and whether they are constrained by water depth. In contradiction to some previous research, it is found that the ship domain is unrelated to the length of the ship.


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