Browsing by Subject "Multivariate analysis"

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  • Korkonen, Sanna; Weckström, Jan; Korhola, Atte (2020)
    The occurrence of various chrysophyte cyst morphotypes is unknown in Finland, with the exception of a few isolated lake studies. We set out to chart which cyst types are found in Finland and what their ecological preferences are, focusing on cyst-air temperature relationships that could be further utilized in reconstructing past winter/spring air temperatures and ice-free periods from sedimentary cyst assemblages. Surface sediment samples from lakes across Finland were analysed for their chrysophyte stomatocyst assemblages. Multivariate ecological techniques (e.g. canonical correspondence analysis, principal component analysis) were used to identify the environmental variables that most strongly affected the distribution of the cysts. This survey expanded the known geographical range for several cyst types. Lake water pH and ice-free periods (surrogate for air temperature) explained the statistically significant distribution and composition of the cyst assemblages studied. The results broaden our knowledge of cyst biogeography and strengthen the findings of previous studies of the environmental factors contributing to the occurrence of cysts. Highly variable and rich chrysophyte cyst assemblages in Finland are clearly associated with temperature, pH, electrical conductivity and total phosphorus, with good potential in contemporary and retrospective environmental assessment.
  • Pour-Aboughadareh, Alireza; Poczai, Péter (2021)
    The dataset herein indicated the novelty of the article entitled “Dataset on the use of MGIDI in screening drought-tolerant wild wheat accessions at the early growth stage”. Data were gathered during 2018-2019 on a set of wild wheat germplasm under two control and water deficit stress conditions. One hundred and forty-six accessions belonging to Ae. tauschii, Ae. cylindrica, and Ae. crassa were assessed under optimal glasshouse conditions to screen the drought-tolerant samples at the early growth stage. Nine drought tolerance and susceptibility indices along with the multi-trait genotype-ideotype distance index (MGIDI) were used to visualize the dataset. The obtained data can highlight the potential of the MGIDI index in accelerating screening of a large number of plant materials using multiple traits or selection indices in crop breeding programs, especially at the early growth stage.
  • Francis, Deanne; Ghazanfar, Shila; Havula, Essi; Krycer, James R.; Strbenac, Dario; Senior, Alistair; Minard, Annabel Y.; Geddes, Thomas; Nelson, Marin E.; Weiss, Fiona; Stöckli, Jacqueline; Yang, Jean Y.H.; James, David E. (2021)
    Genetic and environmental factors play a major role in metabolic health. However, they do not act in isolation, as a change in an environmental factor such as diet may exert different effects based on an individual's genotype. Here, we sought to understand how such gene-diet interactions influenced nutrient storage and utilization, a major determinant of metabolic disease. We subjected 178 inbred strains from the Drosophila genetic reference panel (DGRP) to diets varying in sugar, fat, and protein. We assessed starvation resistance, a holistic phenotype of nutrient storage and utilization that can be robustly measured. Diet influenced the starvation resistance of most strains, but the effect varied markedly between strains such that some displayed better survival on a high carbohydrate diet (HCD) compared to a high-fat diet while others had opposing responses, illustrating a considerable gene x diet interaction. This demonstrates that genetics plays a major role in diet responses. Furthermore, heritability analysis revealed that the greatest genetic variability arose from diets either high in sugar or high in protein. To uncover the genetic variants that contribute to the heterogeneity in starvation resistance, we mapped 566 diet-responsive SNPs in 293 genes, 174 of which have human orthologs. Using whole-body knockdown, we identified two genes that were required for glucose tolerance, storage, and utilization. Strikingly, flies in which the expression of one of these genes, CG4607 a putative homolog of a mammalian glucose transporter, was reduced at the whole-body level, displayed lethality on a HCD. This study provides evidence that there is a strong interplay between diet and genetics in governing survival in response to starvation, a surrogate measure of nutrient storage efficiency and obesity. It is likely that a similar principle applies to higher organisms thus supporting the case for nutrigenomics as an important health strategy.
  • Heikkinen, Janne Matias; Aalto, Juha; Rantamäki, Olli; Ruikkala, Toni; Soininen, Janne; Pajunen, Virpi (2022)
    Cold subarctic pond ecosystems will be threatened due to the increase in global temperatures. Therefore, it is important to gain more knowledge on how their biota may respond to global warming. The aim of this research was to illustrate the variability in diatom species richness and community composition along environmental gradients in northernmost Finland and Norway and reveal the variables most strongly associated with diatom biodiversity. We also compared diatom biodiversity among different biotope types and placed emphasis on the distribution of rare diatom taxa. A total of 100 subarctic ponds from the Finnish and Norwegian Lapland covering an elevational gradient of 8-887 m above sea level were sampled. A generalised linear model and hierarchical partitioning were used to identify variables associated with diatom species richness. To identify variables associated with diatom community composition, a non-metric multidimensional scaling ordination was performed. Finally, a principal component analysis and permutational multivariate analysis of variance were used for the investigation of environmental and biotic differences among biotope types. Water pH, aluminium concentration, and air temperature best explained the variation in species richness and community composition. Diatom species richness and community composition did not differ among the biotope types, but environmental variables in pine forests differed significantly from other biotope types. Many diatom species occupied the entire elevational gradient, while rare taxa seemed to appear at the ends of the elevational gradient as well around the mid-elevational zone. We found that elevation was not sufficient to explain the variation in diatom species richness and community composition, but diatom biodiversity was shaped by a variety of local-scale environmental variables, some of which are in turn correlated with elevation. Our findings suggest that local abiotic factors and especially water chemistry are important factors in describing the variability in diatom community composition and species richness in subarctic ponds. It seems that the lowest and the highest elevations provide suitable habitats for rare diatom taxa that have unique environmental preferences but some of the rare taxa were also constrained to mid elevations. Our study provides new insights into the role of local abiotic variables in shaping subarctic mountain pond biodiversity. We urge researchers not only to study elevational gradients per se in mountain areas, but also pay special attention to environmental covariates that may play a notable role in maintaining freshwater biodiversity in the subarctic.
  • Stevenson, Jonathan D.; Laitinen, Minna K.; Parry, Michael C.; Sumathi, Vaiyapuri; Grimer, Robert J.; Jeys, Lee M. (2018)
    Introduction: Chondrosarcoma (CS) is the second most common primary bone sarcoma with no clear role for adjuvant therapy. The purpose of this study was to investigate (1) the relationship between surgical excision margins and local recurrence free survival (LRFS), and (2) the role of local recurrence (LR) in disease specific survival (DSS) in CS of the extremity and pelvis. Material and methods: 341 pelvic and extremity CS diagnosed between 2003 and 2015 were studied retrospectively. Results: LR developed in 23% of cases. Pelvic location, pathologic fracture, margin and grade were significant factors for LR after univariate analysis. Multivariate analysis revealed surgical margin and pelvic location as positive factors for LR, and grade-1 and 2 CS as negative factors for LR. Pathologic fracture, central versus peripheral, grade, and LR were significant factors with univariate analysis for DSS; and grade was significant after multivariate analysis for all patients for DSS. After competing risk analysis, LR was statistically significant for DSS in grade-2 and grade-3 tumors. Conclusion: Surgical margins determine LR in all CS grades, but LR affects DSS only in grade-2 and grade 3 tumors. Although narrow margins are acceptable in grade-1 tumors, since biopsy is unreliable in predicting final grade, a minimum 4-mm margin should be the aim in all cases. (C) 2018 Elsevier Ltd, BASO similar to The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.