Evaluation of texture features for analysis of ovarian follicular development

Ovarian follicles in women are fluid-filled structures in the ovary that contain oocytes (eggs). A dominant follicle is physiologically selected and ovulates during the menstrual cycle. We examined the echotexture in ultrasonographic images of the follicle wall of dominant ovulatory follicles in women during natural menstrual cycles and dominant anovulatory follicles which developed in women using oral contraceptives (OC). Texture features of follicle wall regions of both ovulatory and anovulatory dominant follicles were evaluated over a period of seven days before ovulation (natural cycles) or peak estradiol concentrations (OC cycles). Differences in echotexture between the two classes of follicles were found for two co-occurrence matrix derived texture features and two edge-frequency based texture features. Co-occurrence energy and homogeneity were significantly lower for ovulatory follicles while edge density and edge contrast were higher for ovulatory follicles. In the each feature space, the two classes of follicle were adequately separable.This thesis employed several statistical approaches to analyses of texture features, such as plotting method and the Mann-Kendall method. A distinct change of feature trend was detected 3 or 4 days before the day of ovulation for ovulatory follicles in the two co-occurrence matrix derived texture features and two edge-frequency-based texture features. Anovulatory follicles, exhibited the biggest variation of the feature value 3 or 4 days before the day on which dominant follicles developed to maximum size. This discovery is believed to correspond to the ovarian follicles responding to system hormonal changes leading to presumptive ovulation

Predicting the outcomes of HIV treatment interruptions using computational modelling

In the past 30 years, HIV infection made a transition from fatal to chronic disease due to the emergence of potent treatment largely suppressing viral replication. However, this medication must be administered life-long on a regular basis to maintain viral suppression and is not always well tolerated. Any interruption of treatment causes residual virus to be reactivated and infection to progress, where the underlying processes occurring and consequences for the immune system are still poorly understood. Nonetheless, treatment interruptions are common due to adherence issues or limited access to antiretroviral drugs. Early clinical studies, aiming at application of treatment interruptions in a structured way, gave contradictory results concerning patient safety, discouraging further trials. In-silico models potentially add to knowledge but a review of the Literature indicates most current models used for studying treatment interruptions (equation-based), neglect recent clinical findings of collagen formation in lymphatic tissue due to HIV and its crucial role in immune system stability and efficacy. The aim of this research is the construction and application of so-called ‘Bottom-Up’ models to allow improved assessment of these processes in relation to HIV treatment interruptions. In this regard, a novel computational model based on 2D Cellular Automata for lymphatic tissue depletion and associated damage to the immune system was developed. Hence, (i) using this model, the influence of spatial distribution of collagen formation on HIV infection progression speed was evaluated while discussing aspects of computational performance. Further, (ii) direct Monte Carlo simulations were employed to explore the accumulation of tissue impairment due to repeated treatment interruptions and consequences for long-term prognosis. Finally, (iii) an inverse Monte Carlo approach was used to reconstruct yet unknown characteristics of patient groups. This is based on sparse data from past clinical studies on treatment interruptions with the aim of explaining their contradictory results

Insights into the function of short interspersed degenerated retroposons in the protozoan parasite Leishmania

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

The evolution of the mammal placenta — a computational approach to the identification and analysis of placenta-specific genes and microRNAs.

The presence of a placenta is an important synapomorphy that defines the mammal clade. From the fossil record we know that the first placental mammal lived approximately 125 million years ago, with the chorioallantoic placenta evolving not long after. In this thesis a set of 22 complete genomes from Eutherian, non-Eutherian and outgroup species are compared, the aim being to identify protein-coding and regulatory alterations that are likely to be implicated in the emergence of mammal placenta in the fossil record. To this end we have examined the roles played by positive selection and miRNA regulation in the evolution of the placenta. We have identified those genes that underwent functional shift uniquely in the ancestral placental mammal lineage and that are also heavily implicated in disorders of the placenta. Carrying out a thorough analysis of non-coding regions of the 22 genomes included in the study we identified a cohort of miRNAs that exist only in placental mammals. Many of the placenta related genes described above have multiple predicted “placenta-specific” miRNA binding sites. Together these results indicate a role for both adaptation in protein-coding regions and emergence of novel noncoding regulators in the origin and evolution of mammal placentation

Effect of 5'-UTR mutations on HCV replication

Hepatitis C Virus (HCV) is an emerging and challenging virus due to the problematic understanding of its persistence mechanisms. In fact, for many years scientists have been trying to resolve the issue of HCV lymphotropism, as the virus has been detected in peripheral blood mononuclear cells (PBMCs), lymph nodes and brain tissue. HCV isolates detected in these extrahepatic sites have unique mutations at positions 107, 204 and 243, distinct from liver and serum, in the internal ribosomal entry site (IRES) located in the 5’ UTR, one of the most well conserved regions of the HCV genome. In this study, divergent IRES variants were detected in the PBMCs of HCV-infected patients. Differences were found among plasma and PBMC derived 5’ UTRs. Most of the PBMC-derived sequences contained the AAA mutations in the IRES affecting the aforementioned positions, a unique quasispecies population in PBMCs compared with plasma. The effect of mutations detected in the IRES was predicted based on its secondary structure. The three mutations alone and in combination detected in lymphotropic quasispecies were introduced in the 5’ UTR of HCV isolate JFH-1 and replicon genotype 1b to study the effect of these mutations on HCV replication in different cell lines. The replication capacity of HCV mutants was tested in the Huh7.5, Jurkat, EBV+ B and PBMC cell lines to examine whether such mutations had an effect on the efficiency of the virus to replicate in extrahepatic cell lines. All mutant constructs infected and showed robust replication in Huh7.5 cells. Jurkat cells failed to become infected while EBV+ B lymphocyte cells were shown to support HCV mutant replication. PBMCs failed to become infected with HCV mutants and transfection of such cells with siRNAs against IRF3 and NF-kB did not improve this outcome as they appeared to not have an impact on the innate immune response through failure to inhibit IRF3 and NF-kB gene expression. On the other hand, all cell lines were found to be susceptible to infection with HCV containing plasma. HCV mutants were able to target cells of the immune system but replicated with reduced efficiency compared to hepatocytes. Mutations that were detected in HCV mutants following replication in extrahepatic cells caused changes in the thermodynamic stability of the IRES that resulted in predicted structural changes.Open Acces

Research and Creative Activity, July 1, 2019-June 30, 2020: Major Sponsored Programs and Faculty Accomplishments in Research and Creative Activity, University of Nebraska-Lincoln

Foreword by Bob Wilhelm, Vice Chancellor for Research and Economic Development: This booklet highlights successes in research, scholarship and creative activity by University of Nebraska–Lincoln faculty during the fiscal year running July 1, 2019, to June 30, 2020. It lists investigators, project titles and funding sources on major grants and sponsored awards received during the year; fellowships and other recognitions and honors bestowed on our faculty; books published by faculty; performances, exhibitions and other creative activity; and patents and licensing agreements issued. Based on your feedback, the Office of Research and Economic Development expanded this publication to include peer-reviewed journal articles and conference presentations and recognize students and faculty mentors participating in the Undergraduate Creative Activities and Research Experience Program (UCARE) and the First-Year Research Experiences program (FYRE). While metrics cannot convey the full story of our work, they are tangible measures of impact. Nebraska achieved a record $317 million in total research expenditures in FY 2019, a 26$450 million in research expenditures by 2025. Husker researchers are stimulating economic growth through university-sponsored industry activity. Nebraska Innovation Campus created 1,657 jobs statewide and had a total economic impact of $324.1 million in FY 2019. NUtech Ventures brought in$6.6 million in licensing income in FY 2020. The University of Nebraska system now ranks 65th among the top 100 academic institutions receiving U.S. patents, jumping 14 spots from 2019. I am proud of the Nebraska Research community for facing the challenges of 2020 with grit and determination. Our researchers quickly adapted to develop solutions for an evolving pandemic — all while working apart and keeping themselves and their families safe. As an institution, we made a commitment to embrace an anti-racism journey and work toward racial equity. Advancing conversations and developing lasting solutions is among the most important work we can do as scholars. Against the backdrop of the pandemic, rising racial and social tensions, and natural disasters, Nebraska researchers worked diligently to address other pressing issues, such as obesity and related diseases, nanomaterials, agricultural resilience and the state’s STEM workforce. Let’s continue looking forward to what we can accomplish together. Thank you for participating in the grand challenges process and helping identify the wicked problems that Nebraska has unique expertise to solve. Soon, ORED will unveil a Research Roadmap that outlines how our campus will develop research expertise; enrich creative activity; bolster commitment to diversity, equity and inclusion; enhance economic development; and much more. Amidst the uncertainty of 2020, I remain confident in our faculty’s talent and commitment. I am pleased to present this record of accomplishments. Contents Awards of $5 Million or More Awards of$1 Million to $4,999,999 Awards of$250,000 to $999,999 Early Career Awards Arts and Humanities Awards of$250,000 or More Arts and Humanities Awards of $50,000 to$249,999 Arts and Humanities Awards of $5,000 to$49,999 Patents License Agreements Creative Activity Books Recognitions and Honors Journal Articles Conference Presentations UCARE and FYRE Projects Glossar