functional dissimilarity
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MR imaging-visible perivascular spaces (PVS) have been associated with disease phenotypes, risk factors, sleep measures, and overall brain health. We review avenues in the analysis of PVS quantified from brain MR imaging across dissimilar acquisition protocols, imaging modalities, scanner manufacturers and magnetic field strengths. We conduct a pilot analysis to evaluate different avenues to harmonise PVS assessments from using different parameters using brain MR imaging from 100 adult volunteers, acquired at two different magnetic field strengths with different sequence parameters. The 2024 MICCAI Enlarged Perivascular Spaces Segmentation Challenge provides a representative MRI dataset on which to test other harmonization methods.
- MeSH
- dospělí MeSH
- glymfatický systém * diagnostické zobrazování MeSH
- lidé MeSH
- magnetická rezonanční tomografie * metody MeSH
- magnetické pole MeSH
- mozek * diagnostické zobrazování MeSH
- neurozobrazování * metody MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
The genomic signature of an organism captures the characteristics of repeated oligonucleotide patterns in its genome 1, such as oligomer frequencies, GC content, and differences in codon usage. Viruses, however, are obligate intracellular parasites that are dependent on their host cells for replication, and information about genomic signatures in viruses has hitherto been sparse.Here, we investigate the presence and specificity of genomic signatures in 2,768 eukaryotic viral species from 105 viral families, aiming to illuminate dependencies and selective pressures in viral genome evolution. We demonstrate that most viruses have highly specific genomic signatures that often also differ significantly between species within the same family. The species-specificity is most prominent among dsDNA viruses and viruses with large genomes. We also reveal consistent dissimilarities between viral genomic signatures and those of their host cells, although some viruses present slight similarities, which may be explained by genetic adaptation to their native hosts. Our results suggest that significant evolutionary selection pressures act upon viral genomes to shape and preserve their genomic signatures, which may have implications for the field of synthetic biology in the construction of live attenuated vaccines and viral vectors.
PURPOSE: The aim of the study is to capture the difference between the groups in direct relation to the type of electrode array insertion during cochlear implantation (CI). The robotic insertion is expected to be a more gently option. As recent studies have shown, there is a difference in perception of visual vertical (SVV) and postural control related to the CI. We assume that there can be differences in postural control and space perception outcomes depending on the type of the surgical method. METHODS: In total, 37 (24 females, mean age ± SD was 42.9 ± 13.0) candidates for CI underwent an assessment. In 14 cases, the insertion of the electrode array was performed by a robotic system (RobOtol, Colin, France) and 23 were performed conventionally. In all of these patients, we performed the same examination before the surgery, the first day, and 3 weeks after the surgery. The protocol consists of static posturography and perception of visual vertical. RESULTS: The both groups, RobOtol and conventional, responded to the procedure similarly despite the dissimilar electrode insertion. There was no difference between two groups in the dynamic of perception SVV and postural parameters. Patients in both groups were statistically significantly affected by the surgical procedure, SVV deviation appeared in the opposite direction from the implanted ear: 0.90° ± 1.25; - 1.67° ± 3.05 and - 0.19° ± 1.78 PRE and POST surgery (p < 0.001). And this deviation was spontaneously adjusted in FOLLOW-UP after 3 weeks (p < 0.01) in the both groups. We did not find a significant difference in postural parameters between the RobOtol and conventional group, even over time. CONCLUSION: Although the robotic system RobOtol allows a substantial reduction in the speed of insertion of the electrode array into the inner ear, our data did not demonstrate a postoperative effect on vestibular functions (SVV and posturography), which have the same character and dynamics as in the group with standard manual insertion. REGISTRATION NUMBER: The project is registered on clinicaltrials.gov (registration number: NCT05547113).
- MeSH
- dospělí MeSH
- kochleární implantace * metody MeSH
- kochleární implantáty MeSH
- lidé středního věku MeSH
- lidé MeSH
- posturální rovnováha * fyziologie MeSH
- roboticky asistované výkony * metody MeSH
- vnímání prostoru * fyziologie MeSH
- výsledek terapie MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
BACKGROUND: The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy. Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. However, the role of the skin microbiome has not been well explored in the skin tumour microenvironment and the link between the gut microbiome and skin microbiome has not been investigated in melanoma progression. Therefore, the aim of the present study was to examine associations between dysbiosis in the skin and gut microbiome and the melanoma growth using MeLiM porcine model of melanoma progression and spontaneous regression. RESULTS: Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets. The bacterial composition of samples was analysed by high throughput sequencing of the V4-V5 region of the 16S rRNA gene. A significant difference in microbiome diversity and richness between melanoma tissue and healthy skin and between the faecal microbiome of MeLiM piglets and control piglets were observed. Both Principal Coordinate Analysis and Non-metric multidimensional scaling revealed dissimilarities between different bacterial communities. Linear discriminant analysis effect size at the genus level determined different potential biomarkers in multiple bacterial communities. Lactobacillus, Clostridium sensu stricto 1 and Corynebacterium 1 were the most discriminately higher genera in the healthy skin microbiome, while Fusobacterium, Trueperella, Staphylococcus, Streptococcus and Bacteroides were discriminately abundant in melanoma tissue microbiome. Bacteroides, Fusobacterium and Escherichia-Shigella were associated with the faecal microbiota of MeLiM piglets. Potential functional pathways analysis based on the KEGG database indicated significant differences in the predicted profile metabolisms between the healthy skin microbiome and melanoma tissue microbiome. The faecal microbiome of MeLiM piglets was enriched by genes related to membrane transports pathways allowing for the increase of intestinal permeability and alteration of the intestinal mucosal barrier. CONCLUSION: The associations between melanoma progression and dysbiosis in the skin microbiome as well as dysbiosis in the gut microbiome were identified. Results provide promising information for further studies on the local skin and gut microbiome involvement in melanoma progression and may support the development of new therapeutic approaches.
- MeSH
- Bacteria genetika MeSH
- dysbióza mikrobiologie MeSH
- feces mikrobiologie MeSH
- Fusobacterium MeSH
- melanom * MeSH
- mikrobiota * MeSH
- nádorové mikroprostředí MeSH
- prasata MeSH
- RNA ribozomální 16S genetika MeSH
- střevní mikroflóra * genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Structural variants (SVs) represent an important source of genetic variation. One of the most critical problems in their detection is breakpoint uncertainty associated with the inability to determine their exact genomic position. Breakpoint uncertainty is a characteristic issue of structural variants detected via short-read sequencing methods and complicates subsequent population analyses. The commonly used heuristic strategy reduces this issue by clustering/merging nearby structural variants of the same type before the data from individual samples are merged. RESULTS: We compared the two most used dissimilarity measures for SV clustering in terms of Mendelian inheritance errors (MIE), kinship prediction, and deviation from Hardy-Weinberg equilibrium. We analyzed the occurrence of Mendelian-inconsistent SV clusters that can be collapsed into one Mendelian-consistent SV as a new measure of dataset consistency. We also developed a new method based on constrained clustering that explicitly identifies these types of clusters. CONCLUSIONS: We found that the dissimilarity measure based on the distance between SVs breakpoints produces slightly better results than the measure based on SVs overlap. This difference is evident in trivial and corrected clustering strategy, but not in constrained clustering strategy. However, constrained clustering strategy provided the best results in all aspects, regardless of the dissimilarity measure used.
- MeSH
- genom lidský * MeSH
- genomika MeSH
- lidé MeSH
- nejistota MeSH
- shluková analýza MeSH
- strukturální variace genomu * MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: The Cockcroft-Gault formula is recommended to determine a renal indication for dose reduction of dabigatran, edoxaban, and rivaroxaban. Nephrology guidelines now recommend the Modification of Diet in Renal Disease (MDRD) and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) formulae as more accurate estimates of glomerular filtration rate. METHODS: We analyzed anticoagulated patients with atrial fibrillation who were enrolled in the Prevention of Thromboembolic Events - European Registry in Atrial Fibrillation (PREFER in AF). The proportion of patients with dissimilar renal dosing indications was assessed when applying Cockcroft-Gault, MDRD, or CKD-EPI. Thromboembolic and major bleeding events at 1 year were compared in patients in whom Cockcroft-Gault and CKD-EPI provided concordant or discordant results around a threshold of 50 mL/minute. RESULTS: Out of 1288 patients with atrial fibrillation with chronic kidney disease in whom Cockcroft-Gault suggested a dose reduction of dabigatran, edoxaban, or rivaroxaban (creatinine clearance ≤50 mL/minutes), 19% and 16% were reclassified to the respective higher doses, and 24% and 23% to the respective lower doses by applying the MDRD and CKD-EPI formulae, respectively. In patients potentially receiving a different dose of dabigatran, edoxaban, or rivaroxaban when using CKD-EPI, we observed an excess of thromboembolic events (4.1% versus 0.8%; odds ratio, 5.5 [95% CI, 1.5-20.8]; P=0.01). Major bleeding rates were nonsignificantly different in the discordance versus concordance group (5.7% versus 2.7%; odds ratio, 2.2 [95% CI, 0.9-5.6]; P=0.09). CONCLUSIONS: The MDRD and CKD-EPI formulae suggest a different dosing in up to a quarter of anticoagulated patients with atrial fibrillation. This seems to impact hard outcomes.
- MeSH
- fibrilace síní * komplikace diagnóza farmakoterapie MeSH
- hodnoty glomerulární filtrace MeSH
- krvácení chemicky indukované diagnóza epidemiologie MeSH
- ledviny fyziologie MeSH
- lidé MeSH
- registrace MeSH
- tromboembolie * diagnóza epidemiologie etiologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Anthropogenically enhanced atmospheric sulphur (S) and nitrogen (N) deposition has acidified and eutrophied forest ecosystems worldwide. However, both S and N mechanisms have an impact on microbial communities and the consequences for microbially driven soil functioning differ. We conducted a two-forest stand (Norway spruce and European beech) field experiment involving acidification (sulphuric acid addition) and N (ammonium nitrate) loading and their combination. For 4 years, we monitored separate responses of soil microbial communities to the treatments and investigated the relationship to changes in the activity of extracellular enzymes. We observed that acidification selected for acidotolerant and oligotrophic taxa of Acidobacteria and Actinobacteria decreased bacterial community richness and diversity in both stands in parallel, disregarding their original dissimilarities in soil chemistry and composition of microbial communities. The shifts in bacterial community influenced the stoichiometry and magnitude of enzymatic activity. The bacterial response to experimental N addition was much weaker, likely due to historically enhanced N availability. Fungi were not influenced by any treatment during 4-year manipulation. We suggest that in the onset of acidification when fungi remain irresponsive, bacterial reaction might govern the changes in soil enzymatic activity.
- MeSH
- Bacteria genetika MeSH
- buk (rod) * MeSH
- dusík analýza MeSH
- houby MeSH
- koncentrace vodíkových iontů MeSH
- lesy MeSH
- půda * MeSH
- půdní mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Norsko MeSH
L-Tryptophan is an essential amino acid and a precursor of several physiologically active metabolites. In the placenta, the serotonin and kynurenine metabolic pathways of tryptophan metabolism have been identified, giving rise to various molecules of neuroactive or immunoprotective properties, such as serotonin, melatonin, kynurenine, kynurenic acid, or quinolinic acid. Current literature suggests that optimal levels of these molecules in the fetoplacental unit are crucial for proper placenta functions, fetal development and programming. Placenta is a unique endocrine organ that, being equipped with a battery of biotransformation enzymes and transporters, precisely orchestrates homeostasis of tryptophan metabolic pathways. However, because pregnancy is a dynamic process and placental/fetal needs are continuously changing throughout gestation, placenta must adapt to these changes and ensure proper communication in the feto-placental unit. Therefore, in this study we investigated alterations of placental tryptophan metabolic pathways throughout gestation. Quantitative polymerase chain reaction (PCR) analysis of 21 selected genes was carried out in first trimester (n = 13) and term (n = 32) placentas. Heatmap analysis with hierarchical clustering revealed differential gene expression of serotonin and kynurenine pathways across gestation. Subsequently, digital droplet PCR, Western blot, and functional analyses of the rate-limiting enzymes suggest preferential serotonin synthesis early in pregnancy with a switch to kynurenine production toward term. Correspondingly, increased function and/or protein expression of serotonin degrading enzyme and transporters at term indicates efficient placental uptake and metabolic degradation of serotonin. Lastly, gene expression analysis in choriocarcinoma-derived cell lines (BeWo, BeWo b30, JEG-3) revealed dissimilar expression patterns and divergent effect of syncytialization compared to primary trophoblast cells isolated from human term placentas; these findings show that the commonly used in vitro placental models are not suitable to study placental handling of tryptophan. Altogether, our data provide the first comprehensive evidence of changes in placental homeostasis of tryptophan and its metabolites as a function of gestational age, which is critical for proper placental function and fetal development.
- Publikační typ
- časopisecké články MeSH
A series of twenty-two novel N-(disubstituted-phenyl)-3-hydroxynaphthalene- 2-carboxamide derivatives was synthesized and characterized as potential antimicrobial agents. N-[3,5-bis(trifluoromethyl)phenyl]- and N-[2-chloro-5-(trifluoromethyl)phenyl]-3-hydroxy- naphthalene-2-carboxamide showed submicromolar (MICs 0.16-0.68 µM) activity against methicillin-resistant Staphylococcus aureus isolates. N-[3,5-bis(trifluoromethyl)phenyl]- and N-[4-bromo-3-(trifluoromethyl)phenyl]-3-hydroxynaphthalene-2-carboxamide revealed activity against M. tuberculosis (both MICs 10 µM) comparable with that of rifampicin. Synergistic activity was observed for the combinations of ciprofloxacin with N-[4-bromo-3-(trifluoromethyl)phenyl]- and N-(4-bromo-3-fluorophenyl)-3-hydroxynaphthalene-2-carboxamides against MRSA SA 630 isolate. The similarity-related property space assessment for the congeneric series of structurally related carboxamide derivatives was performed using the principal component analysis. Interestingly, different distribution of mono-halogenated carboxamide derivatives with the -CF3 substituent is accompanied by the increased activity profile. A symmetric matrix of Tanimoto coefficients indicated the structural dissimilarities of dichloro- and dimetoxy-substituted isomers from the remaining ones. Moreover, the quantitative sampling of similarity-related activity landscape provided a subtle picture of favorable and disallowed structural modifications that are valid for determining activity cliffs. Finally, the advanced method of neural network quantitative SAR was engaged to illustrate the key 3D steric/electronic/lipophilic features of the ligand-site composition by the systematic probing of the functional group.
Classical virulence analysis is based on discovering virulence phenotypes of isolates with regard to a composition of resistance genes in a differential set of host genotypes. With such a vision, virulence phenotypes are usually treated in a genetic manner as one of two possible alleles, either virulence or avirulence in a binary locus. Therefore, population genetics metrics and methods have become prevailing tools for analyzing virulence data at multiple loci. However, a basis for resolving binary virulence phenotypes is infection type (IT) data of host-pathogen interaction that express functional traits of each specific isolate in a given situation (particular host, environmental conditions, cultivation practice, and so on). IT is determined by symptoms and signs observed (e.g., lesion type, lesion size, coverage of leaf or leaf segments by mycelium, spore production and so on), and assessed by IT scores at a generally accepted scale for each plant-pathogen system. Thus, multiple IT profiles of isolates are obtained and can be subjected to analysis of functional variation within and among operational units of a pathogen. Such an approach may allow better utilization of the information available in the raw data, and reveal a functional (e.g., environmental) component of pathogen variation in addition to the genetic one. New methods for measuring functional variation of plant-pathogen interaction with IT data were developed. The methods need an appropriate assessment scale and expert estimations of dissimilarity between IT scores for each plant-pathogen system (an example is presented). Analyses of a few data sets at different hierarchical levels demonstrated discrepancies in results obtained with IT phenotypes versus binary virulence phenotypes. The ability to measure functional IT-based variation offers promise as an effective tool in the study of epidemics caused by plant pathogens.
