High altitude is one of the most extreme environments experienced by terrestrial mammals due to both low ambient temperatures and oxygen availability. Deer mice native to high altitude have a greater thermogenic capacity in hypoxia compared to a lowland population, likely as a consequence of both genetic adaptations and phenotypic plasticity. To understand the adaptive variation in phenotypic plasticity, F1 generation lab-reared mice were acclimated to chronic warm-hypoxia, cold-normoxia, and cold-hypoxia. Acclimation led to equal increases in thermogenic capacity in hypoxia for all stressors in high altitude deer mice. Low altitude mice also increased their thermogenic capacity after acclimation, with a distinct increase after acclimation to cold-hypoxia. The thermogenic capabilities of the high and low altitude mice tested in hypoxia were equal, suggesting that both populations of mice had reached a “metabolic ceiling”. Basal metabolic rate increased after acclimation to cold and cold-hypoxia. Nonshivering thermogenesis was not affected by acclimation or altitude ancestry. Shivering thermogenesis contributed 70 to 80 % of total heat produced during VO2summit across all acclimations, and in both populations. VO2summit in hypoxia was supported by lipids in deer mice even though carbohydrates would provide an oxygen saving advantage. Also, rates of lipid oxidation increased after acclimation to cold, and cold combined with hypoxia in the high altitude population. Together these findings suggest that the increased thermogenic capacity of the high altitude wild mice is based both on differences in phenotypic plasticity, and on differences in genotype from the low altitude mice. Adult phenotypic plasticity is pivotal in the thermogenic capabilities of both populations, and it is likely that developmental plasticity also plays an important role. / Thesis / Master of Science (MSc)

This thesis describes the development and application of the new software MAXCOVER that computes maximal covers and non-extendible repeats (a.k.a. “maximal repeats”). A string is a finite array x[1..n] of elements chosen from a set of totally ordered symbols called an alphabet. A repeat is a substring that occurs at least twice in x. A repeat is left/right extendible if every occurrence is preceded/followed by the same symbol; otherwise, it is non-left/non-right extendible (NLE/NRE). A non-extendible (NE) repeat is both NLE and NRE. A repeat covers a position i if x[i] lies within the repeat. A maximal cover (a.k.a. “optimal cover”) is a repeat that covers the most positions in x. For simplicity, we first describe a quadratic O(n2) implementation of MAXCOVER to compute all maximal covers of a given string based on the pseudocode given in [1]. Then, we consider the logarithmic O(n log n) pseudocode in [1], in which we identify several errors. We leave a complete correction and implementation for future work. Instead, we propose two improved quadratic algorithms that, shown through experiments, will execute in linear time for the average case. We perform a benchmark evaluation of MAXCOVER’s performance and demonstrate its value to biologists in the protein context [2]. To do so, we develop an extension of MAXCOVER for the closely related task of computing NE repeats. Then, we compare MAXCOVER to the repeat-match feature of the well-known MUMmer software [3] (600+ citations). We determine that MAXCOVER is an order-of-magnitude faster than MUMmer with much lower space requirements. We also show that MAXCOVER produces a more compact, exact, and user-friendly output that specifies the repeats. Availability: Open source code, binaries, and test data are available on Github at https://github.com/hollykoponen/MAXCOVER. Currently runs on Linux, untested on other OS. / Thesis / Master of Science (MSc) / This thesis deals with a simple yet essential data structure called a string, a sequence of symbols drawn from an alphabet. For example, a DNA sequence is a string comprised of four letters. We describe a new software called MAXCOVER that identifies maximal covers of a given string x (a repeating substring that ‘covers’ the most positions in x). This software is based on the algorithms in [1]. We propose two new algorithms that perform faster in practice. We also extended MAXCOVER for the closely related task of computing non-extendible repeats. We compare this extension to the well-known MUMmer software (600+ citations). We find that MAXCOVER is many times faster than MUMmer with much lower space requirements and produces a more compact, exact and user-friendly output.

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There are at least two reasons to have an efficient algorithm for identifying all maximal Lyndon substrings in a string: first, in 2015, Bannai et al. introduced a linear algorithm to compute all runs in a string that relies on knowing all maximal Lyndon substrings of the input string, and second, in 2017, Franek et al. showed a linear co-equivalence of sorting suffixes and sorting maximal Lyndon substrings of a string (inspired by a novel suffix sorting algorithm of Baier). In 2016, Franek et al. presented a brief overview of algorithms for com- puting the Lyndon array that encodes the knowledge of maximal Lyndon substrings of the input string. It discussed four different algorithms. Two known algorithms for computing the Lyndon array: a quadratic in-place algorithm based on iterated Duval’s algorithm for Lyndon factorization and a linear algorithmic scheme based on linear suffix sorting, computing the inverse suffix array, and applying the NSV (Next Smaller Value) algorithm. The overview also discusses a recursive version of Duval’s algorithm with a quadratic complexity and an algorithm emulating the NSV approach with a possible O(n log(n)) complexity. The authors at that time did not know of Baier’s algorithm. In 2017, Paracha proposed in her Ph.D. thesis an algorithm for the Lyndon array. The proposed algorithm was interesting as it emulated Farach’s recursive approach for computing suffix trees in linear time and introduced τ-reduction; which might be of independent interest. This was the starting point of this Ph.D. thesis. The primary aim is: (a) developing, analyzing, proving correct, and implementing in C++ a linear algorithm for computing the Lyndon array based on Baier’s suffix sorting; (b) analyzing, proving correct, and implementing in C++ the algorithm proposed by Paracha; and (c) empirically comparing the performance of these two algorithms with the iterative version of Duval’s algorithm. / Dissertation / Doctor of Philosophy (PhD)

This report, presents an analytical framework for analyzing two-branch diversity systems for a Rayleigh fading channel. In many cases the fading received at both branches (i.e. a two-antenna element system) is correlated because of the proximity of the antenna elements to each other. It is also not uncommon for a diversity system to use antennas with different patterns or polarizations, this usually results in differences in average signal-to-noise ratios at both branches depending on which element is better matched to the signal environment. As will be shown, the performance of a diversity system depends greatly on the envelope correlation, average power imbalance and the combining scheme used on both branches. An analytical expression for the probability density function of the signal-to-noise ratio at the output of a two-branch maximal ratio and selection diversity system is developed in this report. The two branches are assumed to be Rayleigh fading, correlated, as well as of unequal signal-to-noise ratios. Measurements were made in Rayleigh fading channels and compared to the analytical results. The analytical cumulative distribution functions (derived using probability distributions) were found to be within 1 dB of the measured results (statistics obtained from time combining) for both maximal ratio and selection diversity attesting to the validity of the analytic results. Also developed in this report are the exact analytical average probabilities of symbol error for coherent BPSK and coherent QPSK before and after maximal ratio combining for this environment. The diversity gain for selection, maximal ratio, and equal gain combining for the 10% probability level is presented as a function of power imbalance and correlation between branches for a two-branch Rayleigh diversity system / Master of Science

No / In this paper, we study Bézier surfaces in View the MathML source three-dimensional Minkowski space. In particular, we focus on timelike and spacelike cases for Bézier surfaces. We also deal with the Plateau¿Bézier problem in View the MathML source, obtaining conditions over the control net to be extremal of the Dirichlet function for both timelike and spacelike Bézier surfaces. Moreover, we provide interesting examples showing the behavior of the Plateau¿Bézier problem in View the MathML source and illustrating the relationship between it and the corresponding Plateau¿Bézier problem in the Euclidean space R3.

Testosterone is a steroid and anabolic hormone found in all mammals. Previous research indicates that testosterone levels correlates with physical capacities related to physical performance. However, these studies refers only to men and boys. The aim of present study was therefore to investigate the potential relationship between body composition, strength, power and endurance capabilities in relation to blood levels of testosterone and DHEAS in young female football players. Seventeen female elite football (age: 15,4 ± 0,6, body mass: 57,2 ± 7,4kg, height 1,65 ±0,04m) players volunteered for the study. Morning levels of testosterone were plotted against results of Dual-energy X-ray absorptiometry, Biodex isokinetic dynamometer, maximal counter movement jump, drop jump, 10 and 20 meters sprints and aerobic fitness (Yo-Yo intermittent endurance test). Testosterone levels were significant correlated with DHEAS as well as bone density (BMD) in L1-L4 (p <0,01) and whole body (WB) BMD (p <0,05). DHEAS also correlated with BMD in L1-L4 and WB (p <0,05). No correlations were found between testosterone, DHEAS and performance capacities. These results suggest that DHEAS predict the level of testosterone and BMD in young women. However, more research is needed to clarify the relationship between testosterone, DHEAS and physical capacities in a larger group of women.

<p dir="ltr">This thesis advances the methodologies of quantum state tomography (QST) to validate and optimize quantum processing on Noisy Intermediate-Scale Quantum (NISQ) devices, crucial for the transition to practical quantum systems. Inspired by recent advancements in the field, we propose a novel QST method based on the maximal entropy formalism, specifically addressing scenarios with incomplete measurement sets to provide a robust framework for state reconstruction. We extend this formalism to an informationally complete (IC) set of observables and introduce a variational approach for quantum state preparation, easily implementable on near-term quantum devices. Our developed maximal entropy-based QST protocol is applied to ultrafast molecular dynamics specifically for studying photoexcited ammonia molecule, enabling direct measurement and manipulation of electronic quantum coherences and exploring entanglement effects in molecular systems. Through this approach, we achieve a groundbreaking milestone by, for the first time, constructing the entanglement entropy of the electronic subsystem - an otherwise inaccessible metric. In doing so it also provides the first physical interpretation of the maximal entropy parameters in an experimental setting and highlights the potential for feedback between time-resolved quantum dynamics and quantum information science. Furthermore, building upon our advancements in state tomography, we propose a variational quantum algorithm for Hamiltonian learning that leverages the time dynamics of observables. Additionally, we reverse engineer the maximal entropy approach and demonstrate the use of entropy to refine the traditional geometric Brownian motion (GBM) method for better capturing real system complexities by addressing its log-normality restrictions, which opens new avenues for quantum sampling techniques. Through these contributions, this thesis showcases the Maximal Entropy formalism’s efficacy in QST and set the stage for future innovations and applications in cutting-edge quantum research.</p>