Phylogram representing maximum-likelihood tree of gastric <i>Helicobacter</i> species based on 126 aligned and concatenated core genes.

<p>The tree was inferred using PhyML applying General Time Reversible (GTR) model, estimating the gamma shape parameter by setting the number of substitution rate categories at 6. Statistical tests for branch support were conducted via a Chi2-based parametric approximate likelihood-ratio test (aLRT). All nodes are supported with aLRT values > 99%. The topology, branch lengths and rate parameters of the starting tree were optimized. The enteric (non-gastric) species <i>H. hepaticus</i> was used as outgroup. The core genes used for this figure are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083177#pone.0083177.s001" target="_blank">Table S1</a>.</p

MAUVE alignment of representative <i>Helicobacter</i> chromosomes.

<p>For MAUVE software see <a href="http://gel.ahabs.wisc.edu/mauve/" target="_blank">http://gel.ahabs.wisc.edu/mauve/</a>. A. Two <i>H. cetorum</i> genomes. B. Two representative <i>H. pylori</i> genomes. For further illustration of the higher conservation of gene order and orientation in <i>H. pylori</i> relative to <i>H. cetorum</i>, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083177#pone.0083177-Kersulyte2" target="_blank">[23]</a>.</p

Strains and species used in this study.

<p>Strains and species used in this study.</p

<i>H. pylori</i> strain 26695 proteins⁽¹⁾ belonging to 22 GOs in <i>H. pylori/H. acinonychis</i> clade not in <i>H. cetorum</i>.

<p>⁽¹⁾ Gene names from original (1997) genome sequence deposition (NC_000915.1). The NCBI database also contains a recent deposition of a separately determined 26695 genome sequence with entirely different gene numbers (CP003904.1).</p><p>⁽²⁾ Designated as hypothetical in original 1997 publication; the function indicated here was suggested by other groups analyzing corresponding sequences in other strains.</p><p><i>H. pylori</i> genomes inspected (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083177#pone-0083177-t001" target="_blank">Table 1</a>), although its protein product was not identifiied in annotations of Shi417 and XZ274 because of apparent frameshift or nonsense mutations, which we suspect may result from DNA sequencing errors.⁽³⁾ The HP0692 gene sequence is present in all </p

General features of <i>H. cetorum</i> genomes.

<p>General features of <i>H. cetorum</i> genomes.</p

vacuolating cytotoxin (<i>vacA</i>) genes of <i>H. cetorum</i>.

<p>A, Chromosomal region containing <i>vacA</i> genes from the <i>H. cetorum</i> whale and dolphin strains. Arrows indicate gene orientation. B, Sequence conservation and divergence among <i>vacA</i> genes of <i>H. cetorum</i>. Lighter and darker shades of same color indicate ≥60% identity by BLASTP criteria. Completely different colors (black, green, blue, red) indicate ≤51% identity. To illustrate, amino acids (aa) 130–881 of gene HCD_01900 (<i>vacA</i> at normal location next to <i>cysS</i>) exhibit 40%, 50% and 65% identity to corresponding regions of HCD_01865, HCD_01875 and HCW_05035, respectively, and also 34–46% identity to corresponding regions of HCD_01870 (which itself has an internal divergent duplication with aa 1–694, just 67% identical to aa 734–1428). In contrast, aa 920–1342 of HCD_01900 exhibit 99% identity to corresponding carboxy terminal regions of HCD_01865 and HCD_01875, although only 58% and 69% identity to corresponding regions of HCD_01870 and HCW_04035. Similarly, the amino terminal ∼720 aa of HCD_01865 and HCD_01875 are each ≤50% identical to corresponding regions of other VacA proteins, whether from <i>H. cetorum</i> or <i>H. pylori</i>.</p

<i>H. cetorum</i> dolphin strain proteins distinct from those in <i>H. pylori</i> strains.

<p>–40% in multiple strains of <i>Actinobacillus, Leptotrichia, Haemophilus, Morganella, Providencia</i>, etc.⁽¹⁾ Homologs of HCD_02790 with aa identities of 35</p><p><i>H. felis, H. bizzozeronii</i>, and <i>H. fennelliae</i>.⁽²⁾ Distant homologs of HCD_03265 and HCD_03315 in </p><p><i>Campylobacter</i> strains.⁽³⁾ Homologs of HCD_04775 in many </p><p><i>H. pullorum</i>, <i>H. cinaedi</i> and <i>Campylobacter gracilis</i>.⁽⁴⁾ Homologs of HCD_08220 in several species including </p><p><i>Campylobacter</i> and <i>Helicobacter</i> species.⁽⁵⁾ Homologs of HCD_08225 in several </p

<i>H. cetorum</i> whale strain proteins distinct from those in <i>H. pylori</i> strains.

<p><i>Campylobacter</i> species.⁽¹⁾ Homologs of HCW_01140 in many </p><p>% aa identity in many other <i>H. pylori</i> strains.⁽²⁾ Distant homologs of HCW_01270 with up to 29</p><p><i>Helicobacter</i> species such as <i>H. bilis, H. winghamensis</i>, and <i>H. fennelliae</i>.⁽³⁾ Distant homologs of HCW_01595 in other </p><p>% and 50% identity overall to HCD_02935 and HCD_05585, but >85% identity to these proteins starting at aa position ∼590 of the 752 aa long protein.⁽⁴⁾ For most OMPs in this table, distribution of identities throughout protein is distinctly non-random, with highest sequence conservation in carboxy terminal, and in some cases also amino terminal domains. For example, HCW_02225 exhibits 54</p><p>% aa identity in other <i>Helicobacter</i> species including <i>H. cinaedi</i>, <i>H. bizzozeronii</i>, and <i>H. hepaticus</i>.⁽⁵⁾ Homologs of HCW_03370 with up to 39</p><p>⁽⁶⁾ HCW_04255 is just one of four "integrases" annotated in the whale strain proteome.</p><p>–54% in H. bizzozeronii, H. felis, H. bilis, H. fennelliae, H. mustelae, H. hepaticus and Wolinella.⁽⁷⁾ Homologs of HCW_04530 with identities of 47</p><p>–38% in multiple strains of <i>Leptotrichia, Actinobacillus, Providencia, Haemophilus, Morganella</i>, etc.⁽⁸⁾ Homologs of HCW_07590 with aa identities of 35</p

Schematic representation of cysteine and methionine metabolism (based on KEGG pathway 00270).

<p>In blue, reactions predicted in <i>H. cetorum</i> but not <i>H. pylori</i> with locus tags of the unique <i>H. cetorum</i> rhodanese-related sulfurtransferase gene indicated. In red, reactions predicted in <i>H. pylori</i> but not <i>H. cetorum</i>. In black, reactions predicted in both <i>H. cetorum and H. pylori</i>. A reaction for which no predicted enzymes were found in <i>Helicobacter</i> genomes is indicated by the dotted line and arrowheads in gray. Of note, DNA sequences matching those of HP1045 (acetyl CoA synthetase) are missing by BLASTN criteria from each <i>H. cetorum</i> strain, and also from 14 of the 48 fully sequenced <i>H. pylori</i> genomes screened. HP1045 was not included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083177#pone-0083177-t005" target="_blank">Table 5</a> because of its absence from a significant minority of <i>H. pylori</i> strains.</p

Table_1_Enhancing spatial navigation skills in mild cognitive impairment patients: a usability study of a new version of ANTaging software.DOCX

IntroductionMild Cognitive Impairment (MCI) often presents challenges related to spatial navigation and retention of spatial information. Navigating space involves intricate integration of bodily and environmental cues. Spatial memory is dependent on two distinct frame of reference systems for organizing this information: egocentric and allocentric frames of reference. Virtual Reality (VR) has emerged as a promising technology for enhancing spatial navigation skills and spatial memory by facilitating the manipulation of bodily, environmental, and cognitive cues.MethodsThis usability study was based on a fully within-subjects design in which seven MCI patients underwent two kinds of VR conditions: participants were required to complete the ANTaging demo both in Oculus Rift S (immersive condition) and in Samsung UHD 4K monitor (semi-immersive condition). Participants were seated and they had to use a foot-motion pad to navigate and explore the environment to collect and relocate some objects in the virtual environment. Post-interaction, users provided feedback on their experiences. Additionally, usability, potential side effects, data analysis feasibility, and user preferences with immersive and semi-immersive technologies were assessed through questionnaires.ResultsResults indicated higher usability ratings for the semi-immersive setup, with fewer negative effects reported compared to the immersive counterpart. According to qualitative analyses of the interviews, patients do seem to like both VR apparatuses even though the semi-immersive condition was perceived as the most suitable choice because of the size of the screen. Patients generally found it difficult to remember object locations. Participants expressed the need for more practice with the foot-motion pad, despite an overall positive experience. They generally would like to use this system to improve their memory.DiscussionIdentifying these key aspects was crucial for refining the system before the upcoming clinical trial. This study sheds light on the potential of semi-immersive VR in aiding individuals with MCI, paving the way for enhanced spatial navigation interventions.</p