Variational Ensemble Kalman Filtering in Hydrology

The current thesis manuscript studies the suitability of a recent data assimilation method, the Variational Ensemble Kalman Filter (VEnKF), to real-life fluid dynamic problems in hydrology. VEnKF combines a variational formulation of the data assimilation problem based on minimizing an energy functional with an Ensemble Kalman filter approximation to the Hessian matrix that also serves as an approximation to the inverse of the error covariance matrix. One of the significant features of VEnKF is the very frequent re-sampling of the ensemble: resampling is done at every observation step. This unusual feature is further exacerbated by observation interpolation that is seen beneficial for numerical stability. In this case the ensemble is resampled every time step of the numerical model. VEnKF is implemented in several configurations to data from a real laboratory-scale dam break problem modelled with the shallow water equations. It is also tried in a two-layer Quasi- Geostrophic atmospheric flow problem. In both cases VEnKF proves to be an efficient and accurate data assimilation method that renders the analysis more realistic than the numerical model alone. It also proves to be robust against filter instability by its adaptive nature.

De novo transcriptome assembly and annotation of the isopod Idotea balthica

The Baltic Sea is a unique environment that contains unique genetic populations. In order to study these populations on a genetic level basic molecular research is needed. The aim of this thesis was to provide a basic genetic resource for population genomic studies by de novo assembling a transcriptome for the Baltic Sea isopod Idotea balthica. RNA was extracted from a whole single adult male isopod and sequenced using Illumina (125bp PE) RNA-Seq. The reads were preprocessed using FASTQC for quality control, TRIMMOMATIC for trimming, and RCORRECTOR for error correction. The preprocessed reads were then assembled with TRINITY, a de Bruijn graph-based assembler, using different k-mer sizes. The different assemblies were combined and clustered using CD-HIT. The assemblies were evaluated using TRANSRATE for quality and filtering, BUSCO for completeness, and TRANSDECODER for annotation potential. The 25-mer assembly was annotated using PANNZER (protein annotation with z-score) and BLASTX. The 25-mer assembly represents the best first draft assembly since it contains the most information. However, this assembly shows high levels of polymorphism, which currently cannot be differentiated as paralogs or allelic variants. Furthermore, this assembly is incomplete, which could be improved by sampling additional developmental stages.

Resolución No. 076. Por medio de la cual se dejan sin efecto las renovaciones de unas matriculas mercantiles por error operativo

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Calculation of nondifferential properties for atomic ground states /

A new method for sampling the exact (within the nodal error) ground state distribution and nondiflPerential properties of multielectron systems is developed and applied to firstrow atoms. Calculated properties are the distribution moments and the electronic density at the nucleus (the 6 operator). For this purpose, new simple trial functions are developed and optimized. First, using Hydrogen as a test case, we demonstrate the accuracy of our algorithm and its sensitivity to error in the trial function. Applications to first row atoms are then described. We obtain results which are more satisfactory than the ones obtained previously using Monte Carlo methods, despite the relative crudeness of our trial functions. Also, a comparison is made with results of highly accurate post-Hartree Fock calculations, thereby illuminating the nodal error in our estimates. Taking into account the CPU time spent, our results, particularly for the 8 operator, have a relatively large variance. Several ways of improving the eflSciency together with some extensions of the algorithm are suggested.

Autonomic prediction of error-related ERP components in perceptual and conceptual tasks in older and younger adults

In studies of cognitive processing, the allocation of attention has been consistently linked to subtle, phasic adjustments in autonomic control. Both autonomic control of heart rate and control of the allocation of attention are known to decline with age. It is not known, however, whether characteristic individual differences in autonomic control and the ability to control attention are closely linked. To test this, a measure of parasympathetic function, vagal tone (VT) was computed from cardiac recordings from older and younger adults taken before and during performance of two attentiondemanding tasks - the Eriksen visual flanker task and the source memory task. Both tasks elicited event-related potentials (ERPs) that accompany errors, i.e., error-related negativities (ERNs) and error positivities (Pe's). The ERN is a negative deflection in the ERP signal, time-locked to responses made on incorrect trials, likely generated in the anterior cingulate. It is followed immediately by the Pe, a broad, positive deflection which may reflect conscious awareness of having committed an error. Age-attenuation ofERN amplitude has previously been found in paradigms with simple stimulus-response mappings, such as the flanker task, but has rarely been examined in more complex, conceptual tasks. Until now, there have been no reports of its being investigated in a source monitoring task. Age-attenuation of the ERN component was observed in both tasks. Results also indicated that the ERNs generated in these two tasks were generally comparable for young adults. For older adults, however, the ERN from the source monitoring task was not only shallower, but incorporated more frontal processing, apparently reflecting task demands. The error positivities elicited by 3 the two tasks were not comparable, however, and age-attenuation of the Pe was seen only in the more perceptual flanker task. For younger adults, it was Pe scalp topography that seemed to reflect task demands, being maximal over central parietal areas in the flanker task, but over very frontal areas in the source monitoring task. With respect to vagal tone, in the flanker task, neither the number of errors nor ERP amplitudes were predicted by baseline or on-task vagal tone measures. However, in the more difficult source memory task, lower VT was marginally associated with greater numbers of source memory errors in the older group. Thus, for older adults, relatively low levels of parasympathetic control over cardiac response coincided with poorer source memory discrimination. In both groups, lower levels of baseline VT were associated with larger amplitude ERNs, and smaller amplitude Pe's. Thus, low VT was associated in a conceptual task with a greater "emergency response" to errors, and at the same time, reduced awareness of having made them. The efficiency of an individual's complex cognitive processing was therefore associated with the flexibility of parasympathetic control of heart rate, in response to a cognitively challenging task.

Variational Monte Carlo estimation of the dissociation energy of CuH using correlated sampling

A new approach to treating large Z systems by quantum Monte Carlo has been developed. It naturally leads to notion of the 'valence energy'. Possibilities of the new approach has been explored by optimizing the wave function for CuH and Cu and computing dissociation energy and dipole moment of CuH using variational Monte Carlo. The dissociation energy obtained is about 40% smaller than the experimental value; the method is comparable with SCF and simple pseudopotential calculations. The dipole moment differs from the best theoretical estimate by about 50% what is again comparable with other methods (Complete Active Space SCF and pseudopotential methods).

Developmental and individual differences in novelty and error detection in 10-year-old children and young adults /

Event-related potentials were recorded from 10-year-old children and young adults in order to examine the developmental dififerences in two frontal lobe functions: detection of novel stimuli during an auditory novelty oddball task, and error detection during a visual flanker task. All participants showed a parietally-maximal P3 in response to auditory stimuli. In children, novel stimuli generated higher P3 amplitudes at the frontal site compared with target stimuli, whereas target stimuli generated higher P3 amplitudes at the parietal site compared with novel stimuli. Adults, however, had higher P3 amplitude to novel tones compared with target tones at each site. Children also had greater P3 amplitude at more parietal sites than adults during the novelty oddball and flanker tasks. Furthermore, children and adults did not show a significant reduction in P3 amplitude from the first to second novel stimulus presentation. No age differences were found with respect to P3 latency to novel and target stimuli. These findings suggest that the detection of novel and target stimuli is mature in 10-year-olds. Error trials typically elicit a negative ERP deflection (the ERN) with a frontal-central scalp distribution that may reflect response monitoring. There is also evidence of a positive ERP peak (the Pe) with a posterior scalp distribution which may reflect subjective recognition of a response. Both children and adults showed an ERN and Pe maximal at frontal-central sites. Children committed more errors, had smaller ERN across sites, and had a larger Pe at the parietal site than adults. This suggests that response monitoring is still immature in 10-year-olds whereas recognition of and emotional responses to errors may be similar in children and adults.

Bio-inspired optimization & sampling technique for side-chain packing in MCCE

The prediction of proteins' conformation helps to understand their exhibited functions, allows for modeling and allows for the possible synthesis of the studied protein. Our research is focused on a sub-problem of protein folding known as side-chain packing. Its computational complexity has been proven to be NP-Hard. The motivation behind our study is to offer the scientific community a means to obtain faster conformation approximations for small to large proteins over currently available methods. As the size of proteins increases, current techniques become unusable due to the exponential nature of the problem. We investigated the capabilities of a hybrid genetic algorithm / simulated annealing technique to predict the low-energy conformational states of various sized proteins and to generate statistical distributions of the studied proteins' molecular ensemble for pKa predictions. Our algorithm produced errors to experimental results within .acceptable margins and offered considerable speed up depending on the protein and on the rotameric states' resolution used.

Generator Matrix Based Search for Extremal Self-Dual Binary Error-Correcting Codes

Self-dual doubly even linear binary error-correcting codes, often referred to as Type II codes, are codes closely related to many combinatorial structures such as 5-designs. Extremal codes are codes that have the largest possible minimum distance for a given length and dimension. The existence of an extremal (72,36,16) Type II code is still open. Previous results show that the automorphism group of a putative code C with the aforementioned properties has order 5 or dividing 24. In this work, we present a method and the results of an exhaustive search showing that such a code C cannot admit an automorphism group Z6. In addition, we present so far unpublished construction of the extended Golay code by P. Becker. We generalize the notion and provide example of another Type II code that can be obtained in this fashion. Consequently, we relate Becker's construction to the construction of binary Type II codes from codes over GF(2^r) via the Gray map.

A Study of Ordered Gene Problems Featuring DNA Error Correction and DNA Fragment Assembly with a Variety of Heuristics, Genetic Algorithm Variations, and Dynamic Representations

Ordered gene problems are a very common classification of optimization problems. Because of their popularity countless algorithms have been developed in an attempt to find high quality solutions to the problems. It is also common to see many different types of problems reduced to ordered gene style problems as there are many popular heuristics and metaheuristics for them due to their popularity. Multiple ordered gene problems are studied, namely, the travelling salesman problem, bin packing problem, and graph colouring problem. In addition, two bioinformatics problems not traditionally seen as ordered gene problems are studied: DNA error correction and DNA fragment assembly. These problems are studied with multiple variations and combinations of heuristics and metaheuristics with two distinct types or representations. The majority of the algorithms are built around the Recentering- Restarting Genetic Algorithm. The algorithm variations were successful on all problems studied, and particularly for the two bioinformatics problems. For DNA Error Correction multiple cases were found with 100% of the codes being corrected. The algorithm variations were also able to beat all other state-of-the-art DNA Fragment Assemblers on 13 out of 16 benchmark problem instances.

We need to have a conversation about OpenURL, a close look at a corpus of error reports from the 2013 academic year. Or, How I learned to stop worrying and give up on clean metadata.

Presented at Access 2014, winner of poster contest.

The effects of manipulated augmented sensory feedback on error detection when using a touch screen

The purpose of the present study was to determine which augmented sensory modality would best develop subjective error-detection capabilities of learners performing a spatial-temporal task when using a touch screen monitor. Participants were required to learn a 5-digit key-pressing task in a goal time of 2550 ms over 100 acquisition trials on a touch screen. Participants were randomized into 1 of 4 groups: 1) visual-feedback (colour change of button when selected), 2) auditory-feedback (click sound when button was selected), 3) visual-auditory feedback (both colour change and click sound when button was selected), and 4) no-feedback (no colour change or click sound when button was selected). Following each trial, participants were required to provide a subjective estimate regarding their performance time in relation to the actual time it took for them complete the 5-digit sequence. A no-KR retention test was conducted approximately 24-hours after the last completed acquisition trial. Results showed that practicing a timing task on a touch screen augmented with both visual and auditory information may have differentially impacted motor skill acquisition such that removal of one or both sources of augmented feedback did not result in a severe detriment to timing performance or error detection capabilities of the learner. The present study reflects the importance of multimodal augmented feedback conditions to maximize cognitive abilities for developing a stronger motor memory for subjective error-detection and correction capabilities.

Letter to S.D. Woodruff from an illegible signature stating that he suspects a clerical error in one of the columns, n.d.

Letter to S.D. Woodruff from an illegible signature stating that he suspects a clerical error in one of the columns, n.d.

Esta vida no es la vida o : el gran error del siglo XIX

UANL