Background: The problem of finding the shortest absent words in DNA data has been recently addressed, and algorithms for its solution have been described. It has been noted that longer absent words might also be of interest, but the existing algorithms only provide generic absent words by trivially extending the shortest ones.

Given the wide range of methodologies employed, it is not possible to recommend the most appropriate for assessing MCo. Researchers should adopt recognized standards in future work. This is needed before consensus about the role that MCo plays in gait impairment in neurological diseases and its potential as a target for gait rehabilitation can be determined.

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we explore different sets of minimal absent words in the genomes of 22 organisms (one archaeota, thirteen bacteria and eight eukaryotes). We investigate if the mutational biases that may explain the deficit of the shortest absent words in vertebrates are also pervasive in other absent words, namely in minimal absent words, as well as to other organisms. We find that the compositional biases observed for the shortest absent words in vertebrates are not uniform throughout different sets of minimal absent words. We further investigate the hypothesis of the inheritance of minimal absent words through common ancestry from the similarity in dinucleotide relative abundances of different sets of minimal absent words, and find that this inheritance may be exclusive to vertebrates.

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Huanglongbing (HLB), the most important citrus disease worldwide, is associated with bacteria transmitted by the Asian citrus psyllid (ACP) preferably through new shoots present in the canopy. In a commercial citrus plant, the vegetative growth of the scion is influenced by the rootstock variety in which it is grafted. Although all commercial citrus varieties planted in recent years are susceptible to HLB, the dynamics of the rootstock in grafted plant could influence the progress of HLB, whether at the plant or grove scale. In this work, HLB incidence in 'Valencia' sweet orange grafted onto 16 rootstocks and its relationship to the tree canopy volume and flushing dynamics were evaluated in a field trial under ACP control. The experiment was conducted under rainfed conditions in Bebedouro, state of São Paulo, Brazil, from 2011 to 2019. 'Flying Dragon' trifoliate orange known for its dwarfing characteristics was used as the rootstock. A reduction in canopy volume by 77% at 8 years of age were observed compared to the most vigorous rootstocks. The frequency of flush shoots of 'Valencia' sweet orange was not influenced by the rootstock, but the abundance of flush shoots was lower on three semi-dwarfing rootstocks and as well as 'Flying Dragon'. Although HLB incidence on 'Flying Dragon' was lower than on 'Rangpur' lime and other three semi-standard rootstocks (trees with canopy volume between 51 and 75% of the 'Rangpur' lime canopy volume), all other combinations had similar HLB disease progress regardless of the canopy volume and flushing dynamics. Moreover, under field conditions, variations on the cumulative HLB incidence greater than 26% were necessary to significantly separate rootstocks. Therefore, the results suggest that true dwarfing rootstocks have potential to integrate the management program for HLB and that mechanisms in addition to tree vigor appear to be involved in the host-vector relationship.

Crackles are adventitious respiratory sounds that provide valuable information on different respiratory conditions. Crackles automatic detection in a respiratory sound file is challenging, and thus different signal processing methodologies have been proposed. However, limited testing of such methodologies, namely in respiratory sound files collected in clinical settings, has been conducted. This study aimed to develop an algorithm for automatic crackle detection and characterisation and to evaluate its performance and accuracy against a multi-annotator gold standard. The algorithm is based on three main procedures: i) extraction of a window of interest of a potential crackle (based on fractal dimension and box filtering techniques); ii) verification of the validity of the potential crackle considering computerised respiratory sound analysis established criteria; and iii) characterisation and extraction of crackle parameters. Twenty four 10-second files, acquired in clinical settings, were selected from 10 patients with pneumonia and cystic fibrosis. The algorithm performance was assessed by comparing its results with gold standard annotations (obtained by the agreement among three experts). A set of 7 parameters was optimised. High levels of sensitivity (SE=89%), positive predictive value (PPV=95%) and overall performance (F index=92%) were achieved. This promising result highlights the potential of the algorithm for automatic crackle's detection/characterisation in respiratory sounds acquired in clinical settings.

Summary We study the inter-dinucleotide distance distributions in the human genome, both in the whole-genome and protein-coding regions. The inter-dinucleotide distance is defined as the distance to the next occurrence of the same dinucleotide. We consider the 16 sequences of inter-dinucleotide distances and two reading frames. Our results show a period-3 oscillation in the protein-coding inter-dinucleotide distance distributions that is absent from the whole-genome distributions. We also compare the distance distribution of each dinucleotide to a reference distribution, that of a random sequence generated with the same dinucleotide abundances, revealing the CG dinucleotide as the one with the highest cumulative relative error for the first 60 distances. Moreover, the distance distribution of each dinucleotide is compared to the distance distribution of all other dinucleotides using the Kullback-Leibler divergence. We find that the distance distribution of a dinucleotide and that of its reversed complement are very similar, hence, the divergence between them is very small. This is an interesting finding that may give evidence of a stronger parity rule than Chargaff’s second parity rule.