Tree Damage in Mechanized Uneven-aged Selection Cuttings

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Reassessing the role of morphology in bryophyte phylogenetics : combined data improves phylogenetic inference despite character conflict

Morphological data has gained renewed attention and has been shown to be crucial in clarifying the phylogenetic relationship in a wide range of taxa. In the last decades, phylogenetic analyses of sequence-level data have radically modified the systematic schemes within bryophytes (early non-vascular land plants) and have revealed a widespread pattern of conflict with morphology-based classifications. Yet, a comprehensive evaluation of character conflict has not yet been performed in the context of combined matrices. In this study, we evaluate the impact of morphology on bryophyte phylogeny following a total-evidence approach across 10 published matrices. The analysed matrices span a wide range of bryophytes, taxonomic levels, gene sampling and number of morphological characters and taxa. Data conflict was addressed by measuring: (i) the topological congruence between individual partitions, (ii) changes in support values of the combined data relative to the molecular partition and (iii) clade stability. The association between these measures and the number of morphological characters per taxon (Nc/T ratio) and the proportion of non-fixed characters (i.e., inapplicable, polymorphic and missing data) was explored. In the individual partition analyses, the Nc/T ratio correlated positively with the topological congruence in six to seven datasets depending on the weighting scheme. The proportion of non-fixed cells had a minor influence on congruence between data partitions. The number of characters and proportion of non-fixed data varied significantly between morphological datasets that improved congruence between data types. This variation suggests that morphological datasets affect the results of combined analyses in different ways, depending on the taxa studied. Combined analyses revealed that, despite the low congruence values between partitions, integrating data types improves support values and stability. However, while non-fixed data had no negative effect on support values, stability was reduced as the proportion of non-fixed cells increased. Nc/T ratio was negatively associated with support values and it showed ambiguous responses in stability evaluations. Overall, the results indicate that adding morphology may contribute to the inference of phylogenetic relationships of bryophytes despite character conflict. Our findings suggest that merely comparing (a) morphology-based classifications with molecular phylogenies or (b) the outcome from individual data partitions can misestimate data conflict. These findings imply that analyses of combined data may provide conservative assessments of data conflict and, eventually, lead to an improved sampling of morphological characters in large-scale analyses of bryophytes.Peer reviewe

Using Biographical Texts as Linked Data for Prosopographical Research and Applications

This paper argues that representing texts as semantic Linked Data provides a useful basis for analyzing their contents in Digital Humanities research and for Cultural Heritage application development. The idea is to transform Cultural Heritage texts into a knowledge graph and a Linked Data service that can be used flexibly in different applications via a SPARQL endpoint. The argument is discussed and evaluated in the context of biographical and prosopographical research and a case study where over 13 000 life stories form biographical collections of Biographical Centre of the Finnish Literature Society were transformed into RDF, enriched by data linking, and published in a SPARQL endpoint. Tools for biography and prosopography, data clustering, network analysis, and linguistic analysis were created with promising first results.Peer reviewe

Epithermal Neutron Beam Interference with Cardiac Pacemakers

Peer reviewe

Integrating Historical Person Registers as Linked Open Data in the WarSampo Knowledge Graph

Semantic data integration from heterogeneous, distributed data silos enables Digital Humanities research and application development employing a larger, mutually enriched and interlinked knowledge graph. However, data integration is challenging, involving aligning the data models and reconciling the concepts and named entities, such as persons and places. This paper presents a record linkage process to reconcile person references in different military historical person registers with structured metadata. The information about persons is aggregated into a single knowledge graph. The process was applied to reconcile three person registers of the popular semantic portal "WarSampo -- Finnish World War 2 on the Semantic Web". The registers contain detailed information about some 100,000 people and are individually maintained by domain experts. Thus, the integration process needs to be automatic and adaptable to changes in the registers. An evaluation of the record linkage results is promising and provides some insight into military person register reconciliation in general.Peer reviewe

Genomic structure and transcript analysis of the Rapid Alkalinization Factor (RALF) gene family during host-pathogen crosstalk in Fragaria vesca and Fragaria x ananassa strawberry.

Rapid Alkalinization Factors (RALFs) are cysteine-rich peptides ubiquitous within plant kingdom. They play multiple roles as hormonal signals in diverse processes, including root elongation, cell growth, pollen tube development, and fertilization. Their involvement in host-pathogen crosstalk as negative regulators of immunity in Arabidopsis has also been recognized. In addition, peptides homologous to RALF are secreted by different fungal pathogens as effectors during early stages of infection. Previous studies have identified nine RALF genes in the diploid strawberry (Fragaria vesca) genome. This work describes the genomic organization of the RALF gene families in commercial octoploid strawberry (Fragaria × ananassa) and the re-annotated genome of F. vesca, and then compares findings with orthologs in Arabidopsis thaliana. We reveal the presence of 15 RALF genes in F. vesca genotype Hawaii 4 and 50 in Fragaria x ananassa cv. Camarosa, showing a non-homogenous localization of genes among the different Fragaria x ananassa subgenomes. Expression analysis of Fragaria x ananassa RALF genes upon infection with Colletotrichum acutatum or Botrytis cinerea showed that FanRALF3-1 was the only fruit RALF gene upregulated after fungal infection. In silico analysis was used to identify distinct pathogen inducible elements upstream of the FanRALF3-1 gene. Agroinfiltration of strawberry fruit with deletion constructs of the FanRALF3-1 promoter identified a 5' region required for FanRALF3-1 expression in fruit, but failed to identify a region responsible for fungal induced expression

Impacts of winter feeding of reindeer on vegetation and soil in the sub-Arctic: insights from a feeding experiment

The overall impacts of winter feeding, including the effects of both forage and reindeer (Rangifer tarandus), were studied in an experiment in the Hammastunturi herding cooperative (68°N), Finland, with 300 reindeer in a sub-xeric heath forest (35 ha) during March/April 2009 and 2010. The feeding practices on the 50 plots were: (1) feeding with grass silage+hay with leftovers cleared in the spring; (2) feeding with grass silage+hay with leftovers not cleared; and (3) feeding with pellets. In addition, (4) unfenced and (5) fenced control plots were included, on which the reindeer were not fed. No invasive plant species introduced through grass silage+hay were observed on the plots. The coverage of Deschampsia flexuosa increased on grass silage+hay plots after the first winter, and both coverage and height of the grass increased after the second winter. The coverage of Dicranum sp. and Pleurozium schreberi was lower on plots where reindeer were fed with grass silage (leftover silage not cleared) vs. controls. Some dwarf shrubs, e.g., Calluna vulgaris, showed a similar response after the second winter. The N content of Empetrum nigrum was higher on grass silage plots (leftover silage not cleared) after the first winter vs. controls. After two winters, the N content of both E. nigrum and Vaccinium myrtillus was increased. Of the soil variables studied, C/N decreased on grass silage+hay plots vs. fenced controls. We conclude that even a moderate level of feeding may cause changes that can lead to a gradual shift from nutrient-poor heath forest towards a more nutrient-rich type

Association of Peripheral Membrane Proteins with Membranes: Free Energy of Binding of GRP1 PH Domain with Phosphatidylinositol Phosphate-Containing Model Bilayers

Understanding the energetics of peripheral protein-membrane interactions is important to many areas of biophysical chemistry and cell biology. Estimating free-energy landscapes by molecular dynamics (MD) simulation is challenging for such systems, especially when membrane recognition involves complex lipids, e.g., phosphatidylinositol phosphates (PIPs). We combined coarse-grained MD simulations with umbrella sampling to quantify the binding of the well-explored GRP1 pleckstrin homology (PH) domain to model membranes containing PIP molecules. The experimentally observed preference of GRP1-PH for PIP3 over PIP2 was reproduced. Mutation of a key residue (K273A) within the canonical PIP-binding site significantly reduced the free energy of PIP binding. The presence of a noncanonical PIP-interaction site, observed experimentally in other PH domains but not previously in GRP1-PH, was also revealed. These studies demonstrate how combining coarse-grained simulations and umbrella sampling can unmask the molecular basis of the energetics of interactions between peripheral membrane proteins and complex cellular membranes