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  • 1
    Online Resource
    Online Resource
    Critical Assessment of Metagenome Interpretation: the second round of challenges
    Springer Science and Business Media LLC ; 2022
    In:  Nature Methods Vol. 19, No. 4 ( 2022-04), p. 429-440
    Details
    In: Nature Methods, Springer Science and Business Media LLC, Vol. 19, No. 4 ( 2022-04), p. 429-440
    Abstract: Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.
    Type of Medium: Online Resource
    ISSN: 1548-7091 , 1548-7105
    URL: Article
    DOI: 10.1038/s41592-022-01431-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2163081-1
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Validation of EuroSCORE II in atrial fibrillation heart surgery patients from the KROK Registry
    Springer Science and Business Media LLC ; 2023
    In:  Scientific Reports Vol. 13, No. 1 ( 2023-08-10)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2023-08-10)
    Abstract: The study aimed to validate the European System for Cardiac Operative Risk Evaluation score (EuroSCORE II) in patients with atrial fibrillation (AF). All data were retrieved from the National Registry of Cardiac Surgery Procedures (KROK). EuroSCORE II calibration and discrimination performance was evaluated. The final cohort consisted of 44,172 patients (median age 67, 30.8% female, 13.4% with AF). The in-hospital mortality rate was 4.14% (N = 1830), and 5.21% (N = 2303) for 30-day mortality. EuroSCORE II significantly underestimated mortality in mild- and moderate-risk populations [Observed (O):Expected (E)—1.1, 1.16). In the AF subgroup, it performed well [O:E—0.99), whereas in the very high-risk population overestimated mortality (O:E—0.9). EuroSCORE II showed better discrimination in AF (−) [area under curve (AUC) 0.805, 95% CI 0.793–0.817)] than in AF (+) population (AUC 0.791, 95%CI 0.767–0.816), P  〈  0.001. The worst discriminative performance for the AF (+) group was for coronary artery bypass grafting (CABG) (AUC 0.746, 95% CI 0.676–0.817) as compared with AF (−) population (AUC 0.798, 95% CI 0.774–0.822), P  〈  0.001. EuroSCORE II is more accurate for patients with AF. However, it underestimated mortality rates for low-to-moderate-risk patients and had a lower ability to distinguish between high- and low-risk patients with AF, particularly in those undergoing coronary artery bypass grafting.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-023-39983-w
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2615211-3
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  • 3
    Online Resource
    Online Resource
    Exploring the possibility of predicting human head hair greying from DNA using whole-exome and targeted NGS data
    Springer Science and Business Media LLC ; 2020
    In:  BMC Genomics Vol. 21, No. 1 ( 2020-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2020-12)
    Abstract: Greying of the hair is an obvious sign of human aging. In addition to age, sex- and ancestry-specific patterns of hair greying are also observed and the progression of greying may be affected by environmental factors. However, little is known about the genetic control of this process. This study aimed to assess the potential of genetic data to predict hair greying in a population of nearly 1000 individuals from Poland. Results The study involved whole-exome sequencing followed by targeted analysis of 378 exome-wide and literature-based selected SNPs. For the selection of predictors, the minimum redundancy maximum relevance (mRMRe) method was used, and then two prediction models were developed. The models included age, sex and 13 unique SNPs. Two SNPs of the highest mRMRe score included whole-exome identified KIF1A rs59733750 and previously linked with hair loss FGF5 rs7680591. The model for greying vs. no greying prediction achieved accuracy of cross-validated AUC = 0.873. In the 3-grade classification cross-validated AUC equalled 0.864 for no greying, 0.791 for mild greying and 0.875 for severe greying. Although these values present fairly accurate prediction, most of the prediction information was brought by age alone. Genetic variants explained 〈  10% of hair greying variation and the impact of particular SNPs on prediction accuracy was found to be small. Conclusions The rate of changes in human progressive traits shows inter-individual variation, therefore they are perceived as biomarkers of the biological age of the organism. The knowledge on the mechanisms underlying phenotypic aging can be of special interest to the medicine, cosmetics industry and forensics. Our study improves the knowledge on the genetics underlying hair greying processes, presents prototype models for prediction and proves hair greying being genetically a very complex trait. Finally, we propose a four-step approach based on genetic and epigenetic data analysis allowing for i) sex determination; ii) genetic ancestry inference; iii) greying-associated SNPs assignment and iv) epigenetic age estimation, all needed for a final prediction of greying.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-020-06926-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2041499-7
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  • 4
    Online Resource
    Online Resource
    The importance of prenol lipids in mitigating salt stress in the leaves of Tilia × euchlora trees
    Springer Science and Business Media LLC ; 2022
    In:  Trees Vol. 36, No. 1 ( 2022-02), p. 393-404
    Details
    In: Trees, Springer Science and Business Media LLC, Vol. 36, No. 1 ( 2022-02), p. 393-404
    Abstract: Plants use multiple mechanisms to deal with salt stress. Salt stress increases the content of polyprenols in Tilia ’s leaves, which may mitigate stress. Abstract De-icing salt has been used on streets and pavements in most northern countries since the 1960s. Salt stress limits all vital functions of trees. Tilia × euchlora is planted in many cities given its unique decorative qualities. The aim of this study was to determine the tree strategy to mitigate salt stress due to the synthesis of polyprenols in leaves. Many years of observations have demonstrated that trees of the same species growing in the same street conditions may have extremely different health statuses. The study consisted of two experiments: a field experiment with urban street trees growing in saline soils and a controlled pot experiment with young trees exposed to increasing doses of salt. The differences between the young trees from the pot experiment and older trees from the field experiment were expressed in their ability to synthesize polyprenols. In urban conditions, the tree leaves with less damage contained significantly more polyprenols than did those with more damage. The salt stress mitigation strategy may be related to the ability to synthesize polyprenols. This ability can be acquired through adaptation by older trees. The mechanism involves limiting the transport of Cl −  and Na + to leaves. In the pot experiment, the young trees did not exhibit this ability.
    Type of Medium: Online Resource
    ISSN: 0931-1890 , 1432-2285
    URL: Article
    DOI: 10.1007/s00468-021-02214-8
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 1463920-8
    SSG: 12
    SSG: 23
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  • 5
    Online Resource
    Online Resource
    Searching for improvements in predicting human eye colour from DNA
    Springer Science and Business Media LLC ; 2021
    In:  International Journal of Legal Medicine Vol. 135, No. 6 ( 2021-11), p. 2175-2187
    Details
    In: International Journal of Legal Medicine, Springer Science and Business Media LLC, Vol. 135, No. 6 ( 2021-11), p. 2175-2187
    Abstract: Increasing understanding of human genome variability allows for better use of the predictive potential of DNA. An obvious direct application is the prediction of the physical phenotypes. Significant success has been achieved, especially in predicting pigmentation characteristics, but the inference of some phenotypes is still challenging. In search of further improvements in predicting human eye colour, we conducted whole-exome (enriched in regulome) sequencing of 150 Polish samples to discover new markers. For this, we adopted quantitative characterization of eye colour phenotypes using high-resolution photographic images of the iris in combination with DIAT software analysis. An independent set of 849 samples was used for subsequent predictive modelling. Newly identified candidates and 114 additional literature-based selected SNPs, previously associated with pigmentation, and advanced machine learning algorithms were used. Whole-exome sequencing analysis found 27 previously unreported candidate SNP markers for eye colour. The highest overall prediction accuracies were achieved with LASSO-regularized and BIC-based selected regression models. A new candidate variant, rs2253104, located in the ARFIP2 gene and identified with the HyperLasso method, revealed predictive potential and was included in the best-performing regression models. Advanced machine learning approaches showed a significant increase in sensitivity of intermediate eye colour prediction (up to 39%) compared to 0% obtained for the original IrisPlex model. We identified a new potential predictor of eye colour and evaluated several widely used advanced machine learning algorithms in predictive analysis of this trait. Our results provide useful hints for developing future predictive models for eye colour in forensic and anthropological studies.
    Type of Medium: Online Resource
    ISSN: 0937-9827 , 1437-1596
    URL: Article
    DOI: 10.1007/s00414-021-02645-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 1459222-8
    SSG: 2
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