Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods

Gene turnover rates and the evolution of gene family sizes are important aspects of genome evolution. Here, we use curated sequence data of the major chemosensory gene families from Drosophila-the gustatory receptor, odorant receptor, ionotropic receptor, and odorant-binding protein families-to conduct a comparative analysis among families, exploring different methods to estimate gene birth and death rates, including an ad hoc simulation study. Remarkably, we found that the state-of-the-art methods may produce very different rate estimates, which may lead to disparate conclusions regarding the evolution of chemosensory gene family sizes in Drosophila. Among biological factors, we found that a peculiarity of D. sechellia's gene turnover rates was a major source of bias in global estimates, whereas gene conversion had negligible effects for the families analyzed herein. Turnover rates vary considerably among families, subfamilies, and ortholog groups although all analyzed families were quite dynamic in terms of gene turnover. Computer simulations showed that the methods that use ortholog group information appear to be the most accurate for the Drosophila chemosensory families. Most importantly, these results reveal the potential of rate heterogeneity among lineages to severely bias some turnover rate estimation methods and the need of further evaluating the performance of these methods in a more diverse sampling of gene families and phylogenetic contexts. Using branch-specific codon substitution models, we find further evidence of positive selection in recently duplicated genes, which attests to a nonneutral aspect of the gene birth-and-death process.

ADVANCED NUMERICAL METHODS FOR SIMULATING MICROBUBBLE IN AN AERATED MIXING TANK

Fluid mixing in mechanically agitated tanks is one of the major unit operations in many industries. Bubbly flows have been of interest among researchers in physics, medicine, chemistry and technology over the centuries. The aim of this thesis is to use advanced numerical methods for simulating microbubble in an aerated mixing tank. Main components of the mixing tank are a cylindrical vessel, a rotating Rushton turbine and the air nozzle. The objective of Computational Fluid Dynamics (CFD) is to predict fluid flow, heat transfer, mass transfer and chemical reactions. The CFD simulations of a turbulent bubbly flow are carried out in a cylindrical mixing tank using large eddy simulation (LES) and volume of fluid (VOF) method. The Rushton turbine induced flow is modeled by using a sliding mesh method. Numerical results are used to describe the bubbly flows in highly complex liquid flow. Some of the experimental works related to turbulent bubbly flow in a mixing tank are briefly reported. Numerical simulations are needed to complete and interpret the results of the experimental work. Information given by numerical simulations has a major role in designing and scaling-up mixing tanks. The results of this work have been reported in the following scientific articles: ·Honkanen M., Koohestany A., Hatunen T., Saarenrinne P., Zamankhan P., Large eddy simulations and PIV experiments of a two-phase air-water mixer, in Proceedings of ASME Fluids Engineering Summer Conference (2005). ·Honkanen M., Koohestany A., Hatunen T., Saarenrinne P., Zamankhan P., Dynamical States of Bubbling in an Aerated Stirring Tank, submitted to J. Computational Physics.

Psychosexual development in men with congenital hypogonadotropic hypogonadism on long-term treatment: a mixed methods study.

INTRODUCTION: Congenital hypogonadotropic hypogonadism (CHH) is a rare, genetic, reproductive endocrine disorder characterized by absent puberty and infertility. Limited information is available on the psychosocial impact of CHH and psychosexual development in these patients. AIM: The aim of this study was to determine the impact of CHH on psychosexual development in men on long-term treatment. METHODS: A sequential mixed methods explanatory design was used. First, an online survey (quantitative) was used to quantify the frequency of psychosexual problems among CHH men. Second, patient focus groups (qualitative) were conducted to explore survey findings in detail and develop a working model to guide potential nursing and interdisciplinary interventions. MAIN OUTCOME MEASURES: Patient characteristics, frequency of body shame, difficulty with intimate relationships, and never having been sexually active were assessed. Additionally, we collected subjective patient-reported outcomes regarding the impact of CHH on psychological/emotional well-being, intimate relationships, and sexual activity. RESULTS: A total of 101 CHH men on long-term treatment (>1 year) were included for the analysis of the online survey (mean age 37 ± 11 years, range 19-66, median 36). Half (52/101, 51%) of the men had been seen at a specialized academic center and 37/101 (37%) reported having had fertility-inducing treatment. A high percentage of CHH men experience psychosexual problems including difficulty with intimate relationships (70%) and body image concerns/body shame (94/101, 93%), and the percentage of men never having been sexually active is five times the rate in a reference group (26% vs. 5.4%, P < 0.001). Focus groups revealed persisting body shame and low self-esteem despite long-term treatment that has lasting impact on psychosexual functioning. CONCLUSIONS: CHH men frequently experience psychosexual problems that pose barriers to intimate relationships and initiating sexual activity. These lingering effects cause significant distress and are not ameliorated by long-term treatment. Psychosexual assessment in CHH men with appropriate psychological support and treatment should be warranted in these patients. Dwyer AA, Quinton R, Pitteloud N, and Morin D. Psychosexual development in men with congenital hypogonadotropic hypogonadism on long-term treatment: A mixed methods study. Sex Med 2015;3:32-41.

Lossless Compression Methods for Multispectral Images: Development and Comparisons

Main purpose of this thesis is to introduce a new lossless compression algorithm for multispectral images. Proposed algorithm is based on reducing the band ordering problem to the problem of finding a minimum spanning tree in a weighted directed graph, where set of the graph vertices corresponds to multispectral image bands and the arcs’ weights have been computed using a newly invented adaptive linear prediction model. The adaptive prediction model is an extended unification of 2–and 4–neighbour pixel context linear prediction schemes. The algorithm provides individual prediction of each image band using the optimal prediction scheme, defined by the adaptive prediction model and the optimal predicting band suggested by minimum spanning tree. Its efficiency has been compared with respect to the best lossless compression algorithms for multispectral images. Three recently invented algorithms have been considered. Numerical results produced by these algorithms allow concluding that adaptive prediction based algorithm is the best one for lossless compression of multispectral images. Real multispectral data captured from an airplane have been used for the testing.

Kysynnän ennustaminen leipomotuotteille ja ennusteen tarkkuuden arviointi

Tässä diplomityössä tutkittiin kysynnän ennustamista Vaasan & Vaasan Oy:n tuotteille. Ensin työssä perehdyttiin ennustamiseen ja sen tarjoamiin mahdollisuuksiin yrityksessä. Erityisesti kysynnän ennustamisesta saatavat hyödyt käytiin läpi. Kysynnän ennustamisesta haettiin ratkaisua erityisesti ongelmiin työvuorosuunnittelussa.Työssä perehdyttiin ennustemenetelmiin liittyvään kirjallisuuteen, jonka oppien perusteella tehtiin koe-ennustuksia yrityksen kysynnän historiadatan avulla. Koe-ennustuksia tehtiin kuudelle eri Turun leipomon koe-tuotteelle. Ennustettavana aikavälinä oli kahden viikon päiväkohtainen kysyntä. Tämän aikavälin erityisesti peruskysynnälle etsittiin ennustetarkkuudeltaan parasta kvantitatiivista ennustemenetelmää. Koe-ennustuksia tehtiin liukuvilla keskiarvoilla, klassisella aikasarja-analyysillä, eksponentiaalisen tasoituksen menetelmällä, Holtin lineaarisella eksponenttitasoituksen menetelmällä, Wintersin kausittaisella eksponentiaalisella tasoituksella, autoregressiivisillä malleilla, Box-Jenkinsin menetelmällä ja regressioanalyysillä. Myös neuroverkon opettamista historiadatalla ja käyttämistä ongelman ratkaisun apuna kokeiltiin.Koe-ennustuksien tulosten perusteella ennustemenetelmien toimintaa analysoitiin jatkokehitystä varten. Ennustetarkkuuden lisäksi arvioitiin mallin yksinkertaisuutta, helppokäyttöisyyttä ja sopivuutta yrityksen monien tuotteiden ennustamiseen. Myös kausivaihteluihin, trendeihin ja erikoispäiviin kiinnitettiin huomiota. Ennustetarkkuuden huomattiin parantuvan selvästi peruskysyntää ennustettaessa, jos ensin historiadata esikäsittelemällä puhdistettiin erikoispäivistä ja –viikoista.