Efficiency of Algorithms in Phylogenetics

Phylogenetics is the study of evolutionary relationships between species. Phylogenetic trees have long been the standard object used in evolutionary biology to illustrate how a given set of species are related. There are some groups (including certain plant and fish species) for which the ancestral history contains reticulation events, caused by processes that include hybridization, lateral gene transfer, and recombination. For such groups of species, it is appropriate to represent their ancestral history by phylogenetic networks: rooted acyclic digraphs, where arcs represent lines of genetic inheritance and vertices of in-degree at least two represent reticulation events. This thesis is concerned with the efficiency, accuracy, and tractability of mathematical models for phylogenetic network methods. Three important and related measures for summarizing the dissimilarity in phylogenetic trees are the minimum number of hybridization events required to fit two phylogenetic trees onto a single phylogenetic network (the hybridization number), the (rooted) subtree prune and regraft distance (the rSPR distance) and the tree bisection and reconnection distance (the TBR distance) between two phylogenetic trees. The respective problems of computing these measures are known to be NP-hard, but also fixed-parameter tractable in their respective natural parameters. This means that, while they are hard to compute in general, for cases in which a parameter (here the hybridization number and rSPR/TBR distance, respectively) is small, the problem can be solved efficiently even for large input trees. Here, we present new analyses showing that the use of the “cluster reduction” rule – already defined for the hybridization number and the rSPR distance and introduced here for the TBR distance – can transform any O(f(p) · n)-time algorithm for any of these problems into an O(f(k) · n)-time one, where n is the number of leaves of the phylogenetic trees, p is the natural parameter and k is a much stronger (that is, smaller) parameter: the minimum level of a phylogenetic network displaying both trees. These results appear in [9]. Traditional “distance based methods” reconstruct a phylogenetic tree from a matrix of pairwise distances between taxa. A phylogenetic network is a generalization of a phylogenetic tree that can describe evolutionary events such as reticulation and hybridization that are not tree-like. Although evolution has been known to be more accurately modelled by a network than a tree for some time, only recently have efforts been made to directly reconstruct a phylogenetic network from sequence data, as opposed to reconstructing several trees first and then trying to combine them into a single coherent network. In this work, we present a generalisation of the UPGMA algorithm for ultrametric tree reconstruction which can accurately reconstruct ultrametric tree-child networks from the set of distinct distances between each pair of taxa. This result will also appear in [15]. Moreover, we analyse the safety radius of the NETWORKUPGMA algorithm and show that it has safety radius 1/2. This means that if we can obtain accurate estimates of the set of distances between each pair of taxa in an ultrametric tree-child network, then NETWORKUPGMA correctly reconstructs the true network

Investigation of Interfacial Effects in Ferromagnetic Thin-Films

The magnetic behaviour in thin-film structures has attracted considerable interest and also has importance for wide ranging technological applications. As the dimension of magnetic films reduce, they are able to exhibit different electrical and magnetic properties, where interfacial magnetism become more important. This thesis is centered on the interfacial effects in ferromagnetic thin-film structures with various adjacent materials. Within this framework, the ferromagnetic materials Co and CoFeB:Ta alloy have been investigated. A detailed investigation of the structural, magnetic and anisotropic magnetoresistance (AMR) properties of Co thin-films with Cu and Ir overlayers as a function of Co thickness was performed. Magnetic characterization of thin-films was performed to determine possible magnetic dead layer formations in these thin-films, where no magnetic dead layers were found to be present within these structures. Electrical resistivity measurements showed that the AMR is dependent upon on Co film thickness, where it decreases with decreasing of Co thickness, and it tends toward zero for Co thicknesses below 6 nm. The contribution to the AMR from a single Co/Ir interface is presented where the AMR is shown to vary inversely proportional to the Co film thickness with a Co/Ir interface. Interface magnetism and magnetic dead layers in amorphous CoFeB:Ta alloy thin-film multilayers were studied using polarized neutron reflectometry. Temperature dependent variations in the effective magnetic thickness of the film are found, and correlated with structural intermixing at interfaces. At the interface between ferromagnetic film and capping-layer the structurally graded interface appears to cause a concomitant grading of the local Curie temperature, and at the interface between ferromagnetic film and GaAs(001) substrate local interfacial alloying also creates a region where a magnetic dead-layer forms. The thickness of the magnetic dead layer at the ferromagnet-semiconductor interface is shown to be temperature dependent, which may have significant implications for room-temperature operation of hybrid ferromagnetic metal-semiconductor spintronic devices. Enhancement of Gilbert damping in Co thin-films of various thicknesses with Cu or Ir overlayers is studied under ferromagnetic resonance to understand the role of local interface structure in spin-pumping. Structural analysis indicates that Co films less than 6 nm have fcc(111)-dominated texture while thicker films are dominated by hcp(0001) structure. The intrinsic damping for Co thicknesses above 6 nm is weakly dependent on Co thickness for thin-films with both overlayers, and below 6 nm the Ir overlayers show higher intrinsic damping enhancement compared to Cu overlayers, as expected due to spin-pumping. The interfacial spin-mixing conductance is significantly enhanced in structures where both Co and Ir have fcc(111) structure in comparison to those where the Co layer has subtly different hcp(0001) texture at the interface

Nursing professionals\u27 mental well-being and workplace impairment during the COVID-19 crisis: A Network analysis

Aim: To investigate the effects of years of nursing experience and mental health on work impairment among nurses during the COVID-19 crisis. Background: During the COVID-19 crisis, nurses experience a greater psychological burden than other health care workers. Studies have not yet investigated the effects of years in nursing and mental health on potential work impairment during the COVID-19 crisis in nurses. Methods: A survey was administered to 83 nurses on active duty during the COVID-19 crisis. The graphical LASSO and the DAG helped estimate the associations between years of nursing experience, mental health and work impairment. Results: A moderate negative correlation emerged between years of nursing experience, avoidance and work impairment. A direct effect was observed between anxiety and work impairment. A moderate positive correlation emerged between anxiety, depression and work impairment. An indirect effect was observed between depression, burnout, insomnia, years of nursing experience and work impairment. Conclusions: In the present sample, nurses\u27 work impairment decreased with greater years of nursing experience and increased with higher anxiety, depression, burnout and avoidance levels. Implications for Nursing Management: These findings can help design effective infectious disease management programmes for students and professionals in nursing to prevent breakdowns and avoid work impairment

The Effects of Essential Oils on Perception of Exertion, Task Pleasantness and Time on Task

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Effects of Imagery on Effort Perception and Cycling Endurance

The effect of associative and dissociative imagery was tested on a range of psychological-, physiological-, and performance-related variables during a progressive cycling task using a quantitative approach. Participants (n ¼ 45) were randomly assigned to dissociative imagery, associative imagery, and no imagery conditions and performed a progressive cycling task at 10% above anaerobic threshold up to the point of volitional fatigue. Rate of perceived exertion (RPE), attention focus, and heart rate were monitored and assessed at 1-min intervals. Lactic acid (LA) accumulation was recorded at RPE ¼ 5 (i.e. “strong effort”) and at the point of volitional fatigue. A series of repeated measures analysis of variance indicated that relative to their counterparts who were not using imagery, participants who used imagery accumulated higher levels of LA in blood. Despite some of the non-significant results, present effect sizes seemed to indicate that dissociative imagery may help decrease perception of effort, and associative imagery may help increase time on tas

Effects of a Supportive Audience on a Handgrip Squeezing Task in Adults

International Journal of Exercise Science 9(1): 4-15, 2016. The role of social facilitation by way of audience effect in select exercise-related variables during an isometric handgrip task was assessed using a mixed design. Fifty three moderately active participants (Mage= 21.76 + 5.27) were recruited from the Midwestern United States. Participants were randomly assigned to one of two groups: supportive audience or control. Audience members provided positive verbal encouragement to participants in the experimental condition throughout the task performance. Participants in the control group performed the task in the absence of an audience and did not receive any verbal encouragement. Participants provided anxiety ratings pre- and post-task using the State-trait anxiety inventory for adults (STAI). Participants’ ratings of perceived exertion (RPE) and heart rate (HR) were monitored and assessed at 30-second intervals. Upon task completion, sustained effort in the form of time on task was recorded in seconds. A repeated measures analysis of variance (RM ANOVA) revealed that there was a time effect within groups of HR = ( F(2.64, 131.85) = 189.3 , p \u3c0.001) and within groups of RPE = (F(2.97, 139.42) = 2189.43 p \u3c0.001). An independent sample T-test revealed significant differences in HR at 0, 30 and 60 seconds between the groups. An independent sample T-test revealed no significant differences in anxiety and RPE between the groups. These results partially support the notion of social facilitation and may have implications for research and practice

Antecedents of Expatriate Spouse Adjustment: An Analysis of Japanese Spouses in the United States

This is one of the first studies investigating factors related to the adjustment of expatriate spouses. The study extends, both conceptually and methodologically, the limited research on spouse adjustment by testing the effects of language profciency and educational level on adjustment. Furthermore, it is the first study to survey non US respondents in their native language. In the end, we found that time since arrival, educational level, language proficiency, and willingness to communicate are directly related to spouse adjustment