The bombardment of surfaces by ions can lead to the spontaneous formation of nano-structures. Depending on the irradiation conditions, smoothening or roughening mechanisms can be the leading order in pattern formation which can result in the creation of dots, ripples or ultra-smoothening effects. Because ion bombardment is already ubiquitous in industrial settings, and is relatively inexpensive compared to other surface processing techniques, self-organized patterning by ion bombardment could enable a simple, economical means of inducing well-defined nanoscale structures in a variety of settings. Understanding the fundamental behavior of surfaces during ion bombardment is therefore a vital goal; however, a complete understanding of physical processes governing surface pattern formation has not been reached yet. In order to address this issue, my thesis research has utilized three primary approaches. First, I have done real-time non-coherent X-ray scattering experiments at Cornell High Energy Synchrotron Source (CHESS) for studying kinetics of structure formation of Silicon undergoing Ar⁺ bombardment over a range of wavenumbers 4-5 times larger than has previously been obtained. From our data, we were able to extract values of the angle-dependent thickness of the amorphous layer that forms under ion bombardment, the ion-enhanced fluidity within that film, the magnitude of the stress being generated by the ion beam, and the strength of prompt atomic displacement mechanisms. Second, to further deepen our knowledge of surface dynamics, I have performed coherent X-ray studies of Ar⁺ bombardment of SiO₂ at the Advanced Photon Source (APS) for investigating the dynamics more profoundly than can be done with traditional time-resolved experiments. When using a focused ion beam, an inhomogeneous ripple motion was generated, this phenomenon reflected as an oscillatory behavior in the two-time and corresponding g₂(t) correlation functions. By fitting the oscillations in the g₂(t) correlation function, we have determined the surface ripple velocity on SiO₂ driven by Ar⁺ sputter erosion. Finally, to support the results of coherent X-ray experiments, simulations of growth models such as linear Kuramoto-Sivashinsky (KS) and Kardar-Parisi-Zhang (KPZ) have been carried out in order to compare the simulated temporal correlation functions of the scattered intensity with those obtained from the coherent x-ray scattering experiments.

This diploma thesis assesses influence of treatment of feed components on feed compounds and related animal production. It is primarily focused on different degrees of disintegrating of particular feed components and comparison of various grinding machines. It also describes essential nutrients contained in feed and their function in organism, common types of engines used in compounded feed production. The goal of the diploma thesis' project is to evaluate an effect of various disintegrate of components in hammer and cylindric grinding machine. Another goal of diploma thesis' project is to approve or disapprove four hypotheses. H01 "All components used in compounded feed production can be ground by observed types of grinding machines". H02 "Economic demands of grinding is equal for all observed grinding machines". H03 "Uniformity of ground particles is the same for all observed grinding machines". H04 Quality of grinding does not affect nutritional value of compounded feed for observed grinding machines and observed animals. It was chosen 5 grinding machines for the purpose of research which are commonly used in agricultural companies and feed manufacturers. Data was collected from operators of grinding machines or feed manufacturer's experts. The thesis discuss some abroad researches for comparison of results. The results discover that most effective are cylindric grinding machines, but they are inappropriate for some feed components. Good results have also hammer grinding machines with upper load. All observed grinding machines except roller produced material with low uniformity. Hypotheses H01, H02 and H03 were disapproved by the research. Hypothesis H04 was neither approved nor disapproved.

This thesis provides analytical and forensic tools for data cabling, with particular focus on Ethernet cabling to assist designers and those involved in deployments in analyzing cable performance and the reasons behind the actual performance obtained. The need for higher bandwidth to accommodate increasing demand for multimedia services and data centers network infrastructure led to the formation of IEEE P802.3bq to create standards for 40GBASE-T over twisted pair cables. The 40GBASE-T is expected to offer bandwidth of up to 2000MHz over a maximum channel length of 30m. The research investigated means of predicting key performance parameters in Ethernet cabling standardization using the 40GBASE-T as an example. The performance parameters prediction method provided is equally applicable to ongoing and future high data rate Ethernet cabling standardization such as the 2.5/5GBASE-T and 50/100GBASE-T. Another problem in the Ethernet networking world is the availability of counterfeit and non-standards compliant twisted pair cables in the market. The significant amount of communications cables in the market containing copper clad aluminum cable or other non-standards compliant conductors disguised as Category 6 cables can pose serious problems to companies’ networks, the contractors or the installers. This is in view of the growing demand for internet of things (IOT) services that makes it imperative to have a reliable Ethernet driven communication network to support the required infrastructure. This thesis therefore, provides techniques that can be used to evaluate cables key performance parameters using the Feature Selective Validation method and the Kolmogorov-Smirnov (KS) test. The technique can help engineers avoid subjective judgement and make objective decisions in the selection of cables. The research provided a technique that can be used to reverse engineer impedance profile from the return loss measurement of Ethernet cables using genetic algorithms. The method can be applied in situations where time domain tests are inaccessible or only simple (magnitude) tests in the frequency domain are available and there is the need for impedance profiles of cables to evaluate their performance or physical integrity before or after installation. The method can also be useful where only simple (magnitude) tests are the only historical data available for the cables and facilities for time domain reflectometry measurements are inaccessible. This research also presented a method of evaluating and predicting NEXT in unshielded twisted pair (UTP) using Category 6 cables as an example. The results obtained from the evaluation were used to provide crosstalk parameters for fast NEXT prediction in Category 6 (UTP) cables. The research used the measured NEXT of three Category 6 (UTP) cables from different manufacturers for evaluation and validation. The evaluation and modeling method can thus be useful to engineers investigating NEXT in the design of data communication systems.

Big sagebrush (Artemisia tridentata) is one of the ecologically most important shrub species in western North America. The species serves as a major source of food and habitat for the near-threatened sage grouse and various other fauna. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is considered as a serious threat to sustainability of the big sagebrush ecosystem. Because of its importance, restoration of this species is very crucial to those dependent on big sagebrush community. However, restoration of big sagebrush carried out by using diverse seed source can lead to imbalance and degradation in the native ecosystem. Therefore, restoration works aided by understanding of adaptive traits of big sagebrush using molecular markers will aid successful restoration. The major objective of this research was to create a substantial resource of nuclear sequence data and identify markers that can be used in future studies in big sagebrush. We report the development and annotation of the first expressed sequence tag (EST) collection for big sagebrush based on 454 sequencing of leaf tissue. Expressed genes of subspecies tridentata and vaseyana were sequenced using the 454 GS-FLX titanium platform, which produced 823,392 reads with an average read length of 404 bp and 702,001 reads with an average read length of 333 bp for sspp. tridentata and vaseyana, respectively. Assembly of the reads resulted in 212,102 consensus sequences in ssp. tridentata and 199,439 in ssp. vaseyana. A combined assembly of both subspecies sequences generated 29,541 contigs with an average length of 796 bp and 275,866 singletons with an average length of 370 bp. A BLASTx search against the non-redundant (NR) protein database using the contigs obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e-15). Gene Ontology (GO) IDs were assigned to 18,397 sequences. A total of 20,952 SNPs were detected between the two subspecies and 1,182 SNPs were confirmed in tetraploid ssp. wyomingensis. In addition, 1,003 and 507 SSRs were detected in ssp. tridentata contigs and ssp. vaseyana contigs, respectively.

Klinefelter syndrome (KS) (47,XXY) is the most common sex chromosomal anomaly in males with a prevalence of 1 in 650 males. This clinically relevant condition represents 3%-4% of the total patient population in male reproductive medicine practices. Klinefelter syndrome can manifest in different physical, cognitive, and behavioral phenotypes. The classical phenotypic descriptions are gynecomastia, hypotonia, tall stature, and hypogonadism. Currently there is no known treatment plan for adolescents who are diagnosed with this genetic condition. However, it has been hypothesized that early intervention through androgen replacement therapy can emulate a normal progression of puberty and improve the academic, social, and behavioral aspects of these adolescents. Using standardized instruments, in the form of the Children Behavior Checklist (CBCL) and the Youth Self Report (YSR), we captured data on the patient’s competence and behavior, as well as the parents’ views on their child’s competence and behavior. These data were converted into percentile scores, T scores, and categorical data (normal, intermediate, and clinical). Difference of means was used to test for statistically significant differences between the scores of the KS patients and their parents on competence and behavioral aspects. T test for equality of means was run to determine if there was a significant difference between group scores. Pearson correlation tests were done to see if there was an association between demographics of patients and competence/behavioral scores. We believed that there would be no statistically significant difference between how the parents score their child in the CBCL and how the child scores himself in the YSR in terms of demographics. We also believed that there would be no statistically significant difference or correlation between demographics and individual competence/behavioral scores. A total of 39 groups of surveys were collected, together with demographic information on the maternal and paternal ages when the child was born, patient age, patient age when starting testosterone, patient age when starting anastrazole, and patient height and weight. We examined concordance frequencies in specific areas of the competence and behavioral questionnaires. Concordance was when the parent and the child agreed and evaluated the child as normal, intermediate, or clinical. Discordance was when the parents and the child disagreed; for example, the parent evaluated the child as “clinical,” but the child evaluated himself as “normal.” This study, to our knowledge, is the first chart review study that involves a wide age range of males with KS. The study extends previous findings by providing data on how early hormonal intervention can improve the outlook of these patients’ lives. When taking aromatase inhibitors, the KS adolescents showed an overall reduction of aggression and rule-breaking behavior. When taking testosterone at an earlier age, the patient was less likely to have withdrawal depression. We also found the most discordance in total competence scores, suggesting that some parents may have unrealistic academic expectations for their child. Thus, when examining the data, we had to be aware that there were varying views of success, which can shape how parents and child answer their respective surveys. Our findings demonstrate the significance of early detection and treatment of Klinefelter syndrome, a disorder that is severely under-diagnosed throughout the world. The results also show that the desire of parents for their KS child to do well in school may affect their opinions on how their child is actually performing. Some limitations to this study include the decision to receive early hormonal intervention that was made exclusively between parents and their urologist. Furthermore, the socioeconomic status (SES) and educational characteristics of the families were not properly controlled, although the patient population was mostly likely similar because of the location of the clinic. Future Klinefelter syndrome studies will need to focus on identifying the factors that contribute to the variability of behavioral symptoms. In turn, these studies will support the continuing development of evidence-based treatments for adolescents with Klinefelter syndrome.

The topic of semestral thesis is methods to detect selection in DNA sequences. In the begining of the thesis we will describe molecular evolution. It will be written what made the evolution and how the evolution is shown. Moreover there are gen mutations and mechanisms of diffuse and fixation. It will be defined what pozitive, negative and neutral selection is. The thesis is focused on evolution distance of synonymous and nonsynonymous substitution. There will be described three methods – Nei-Gojobori, Li-Wu-Luo and Comeron. All these methods will be described with mathematic formulas. There will be statistic test to decide what kind of selection ti is – there will be used z-test. In the practical part, there will be information about developed software what counts selection pressure from sequences from databazes in format GenBank and it shows parts where selection is. The software will be used for two data sets with two different genetic codes. The result will be discussed. We will discuss results of all three methods of selection pressure and influence of input parametrs.

Master of Regional and Community Planning / Department of Landscape Architecture/Regional and Community Planning / Ray B. Weisenburger / This report examines how 17th Street on the Kansas State University campus, initially a service road on the west edge of the campus, has become a major point of public campus access while retaining its function as a service road. In addition, this report conducts interviews with 10 persons with various backgrounds and experiences involving 17th Street to understand public impressions and interests regarding 17th Street. Finally, this report reviews future development scenarios of 17th Street that allow 17th Street to be a contributor with a distinctive character to the university. When Kansas State University was transferred from old Bluemont Central College to its current location in 1875, 17th Street, which now crosses the middle of the campus on a North-South axis, was outside of the campus’ core facility areas. As various university programs have grown throughout the late 20th Century, the campus of Kansas State University has expanded toward the west. As a result, the relative proximity of 17th Street to the center of campus has changed. Now, 17th Street is recognized as one of the major entrances to campus from the south; yet because of the street’s initial and ongoing service function and its service-related facilities, there are parts of the corridor that are not attractive. It is desired for 17th Street to become a more appealing and functional part of the university experience for guiding and welcoming visitors to the campus.

Single-molecule localisation microscopy (SMLM), has allowed for optical microscopy to probe biological systems beyond the diffraction limit. The intrinsic 3D nature of biology has motivated the development of 3D-SMLM with novel techniques, including the double-helix point spread function (DHPSF). A bespoke microscope platform employing the DHPSF transformation was built, achieving ~10 nm lateral and ~20 nm axial localisation precision over a ~4 μm axial depth. Until recently, the DHPSF has been limited by spherical aberration present when imaging away from coverslip surfaces to the study of small volumes close to the coverslip. By matching the refractive index of the objective lens immersion liquid to that of the imaging media, this aberration can be minimised, facilitating large-volume imaging away from unphysiological flat surfaces. The work presented in this thesis illustrates the capabilities of the DHPSF for 3D-SMLM and single-particle tracking (SPT) in previously inaccessible areas of biological samples (e.g. in the nucleus and on the apical cell surface). Application of the DHPSF for SPT in eukaryotic cells are presented; tracking the motion of T-cell membrane proteins on the apical surface and components of the chromosome remodelling complex in the nucleus of embryonic stem cells. For these applications, meansquared displacement and jump distance diffusion analysis methodologies were extended into 3D and benchmarked against simulated datasets. A variety imaging applications that are facilitated by the extended depth of focus of the DHPSF are presented, focusing on quantification of T-cell membrane protein reorganisation upon immunological activation. Finally, the clustering distribution of the T-cell receptor is investigated by Ripley’s K analysis enabled by duel labelling of its position and the outer membrane in primary T cells.

No description available.

Yes / KSHV is the causative agent of commonly fatal malignancies of immuno-compromised individuals, including primary effusion lymphoma (PEL) and Kaposi's sarcoma (KS). A hallmark of all herpesviruses is their biphasic lifecycle – viral latency and the productive lytic cycle, and it is well established that reactivation of the KSHV lytic cycle is associated with KS pathogenesis. Therefore, a thorough appreciation of the mechanisms that govern reactivation is required to better understand disease progression. The viral protein, replication and transcription activator (RTA), is the KSHV lytic switch protein due to its ability to drive the expression of various lytic genes, leading to reactivation of the entire lytic cycle. While the mechanisms for activating lytic gene expression have received much attention, how RTA impacts on cellular function is less well understood. To address this, we developed a cell line with doxycycline-inducible RTA expression and applied SILAC-based quantitative proteomics. Using this methodology, we have identified a novel cellular protein (AT-rich interacting domain containing 3B, ARID3B) whose expression was enhanced by RTA and that relocalised to replication compartments upon lytic reactivation. We also show that siRNA knockdown or overexpression of ARID3B led to an enhancement or inhibition of lytic reactivation, respectively. Furthermore, DNA affinity and chromatin immunoprecipitation assays demonstrated that ARID3B specifically interacts with A/T-rich elements in the KSHV origin of lytic replication (oriLyt), and this was dependent on lytic cycle reactivation. Therefore, we have identified a novel cellular protein whose expression is enhanced by KSHV RTA with the ability to inhibit KSHV reactivation.