Graph algorithms for machine learning: a case-control study based on prostate cancer populations and high throughput transcriptomic data

Background The continuing proliferation of high-throughput biological data promises to revolutionize personalized medicine. Confirming the presence or absence of disease is an important goal. In this study, we seek to identify genes, gene products and biological pathways that are crucial to human health, with prostate cancer chosen as the target disease. Materials and methods Using case-control transcriptomic data, we devise a graph theoretical toolkit for this task. It employs both innovative algorithms and novel two-way correlations to pinpoint putative biomarkers that classify unknown samples as cancerous or normal. Results and conclusion Observed accuracy on real data suggests that we are able to achieve sensitivity of 92% and specificity of 91%

MF2242

Daniel O'Brien et al., Economic comparison of SDI and center pivots for various field sizes, Kansas State University, October 1997

MF2587

Danny Rogers, et al, Fuel cost - an irrigation fuel cost evaluator, Kansas State University, August 2006

Differential rotation in giant planets maintained by density-stratified turbulent convection

The zonal winds on the surfaces of giant planets vary with latitude. Jupiter and Saturn, for example, have several bands of alternating eastward (prograde) and westward (retrograde) jets relative to the angular velocity of their global magnetic fields. These surface wind profiles are likely manifestations of the variations in depth and latitude of angular velocity deep within the liquid interiors of these planets. Two decades ago it was proposed that this differential rotation could be maintained by vortex stretching of convective fluid columns that span the interiors of these planets from the northern hemisphere surface to the southern hemisphere surface. This now classic mechanism explains the differential rotation seen in laboratory experiments and in computer simulations of, at best, weakly turbulent convection in rotating constant-density fluid spheres. However, these experiments and simulations are poor approximations for the density-stratified strongly-turbulent interiors of giant planets. The long thin global convective columns predicted by the classic geostrophic theory for these planets would likely not develop. Here we propose a much more robust mechanism for maintaining differential rotation in radius based on the local generation of vorticity as rising plumes expand and sinking plumes contract. Our high-resolution two-dimensional computer simulations demonstrate how this mechanism could maintain either prograde or retrograde surface winds in the equatorial region of a giant planet depending on how the density scale height varies with depth.Comment: Geophysical and Astrophysical Fluid Dynamics, in pres

MIL evaluation of center pivot irrigation systems

Presented at the 2006 Central Plains irrigation conference on February 21-22 in Colby, Kansas.Includes bibliographical references

Gravity Waves in the Sun

We present numerical simulations of penetrative convection and gravity wave excitation in the Sun. Gravity waves are self-consistently generated by a convective zone overlying a radiative interior. We produce power spectra for gravity waves in the radiative region as well as estimates for the energy flux of gravity waves below the convection zone. We calculate a peak energy flux in waves below the convection zone to be three orders of magnitude smaller than previous estimates for m=1. The simulations show that the linear dispersion relation is a good approximation only deep below the convective-radiative boundary. Both low frequency propagating gravity waves as well as higher frequency standing modes are generated; although we find that convection does not continually drive the standing g-mode frequencies.Comment: 22 pages, 14 figures, submitted to MNRA

Joint Maxiniurn Likelihood Estimation of Emission and Attenuation Densities in PET

Accurate attenuation correction can be performed in PET (positron emission tomography) using transmission scanning to estimate the survival probabilities along each coincidence line. However, since these measurements are typically corrupted by Poisson counting noise, they propagate additional uncertainty into reconstructed images and kinetic parameter estimates. This can be especially true in the thorax where the attenuating medium is heterogeneous and the statistical precision of the transmission scan may be approximately the same as that of the emission data. To account for the Poisson noise in the transmission measurement, the authors have developed a sieve-constrained maximum likelihood algorithm that jointly estimates both the survival probability and the emission intensity. They present some of their initial experiences in using the joint alternate and maximize algorithm with simulated PET data.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/85813/1/Fessler119.pd

Irrigation and drainage in the new millennium

Presented at the 2000 USCID international conference, Challenges facing irrigation and drainage in the new millennium on June 20-24 in Fort Collins, Colorado.Irrigation scheduling has been promoted as management tool to minimize irrigation water application, however, few irrigators regularly followed any rigorous scheduling methodology. Kansas State University Research and Extension in conjunction with an irrigation association, Water PACK, began a long-term project to promote ET based irrigation scheduling and other management technology. Area irrigators serve as the focal point of the project and over time have been asked to assume responsibility of scheduling the project fields. A long-term commitment and on-farm activities such as variable water application tests and center pivot uniformity tests seems to have generated confidence and acceptance of ET-based irrigation scheduling

Facilitation of Task Performance and Removal of the Effects of Sleep Deprivation by an Ampakine (CX717) in Nonhuman Primates

The deleterious effects of prolonged sleep deprivation on behavior and cognition are a concern in modern society. Persons at risk for impaired performance and health-related issues resulting from prolonged sleep loss would benefit from agents capable of reducing these detrimental effects at the time they are sleep deprived. Agents capable of improving cognition by enhancing brain activity under normal circumstances may also have the potential to reduce the harmful or unwanted effects of sleep deprivation. The significant prevalence of excitatory α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) glutamatergic receptors in the brain provides a basis for implementing a class of drugs that could act to alter or remove the effects of sleep deprivation. The ampakine CX717 (Cortex Pharmaceuticals), a positive allosteric modulator of AMPA receptors, was tested for its ability to enhance performance of a cognitive, delayed match-to-sample task under normal circumstances in well-trained monkeys, as well as alleviate the detrimental effects of 30–36 h of sleep deprivation. CX717 produced a dose-dependent enhancement of task performance under normal alert testing conditions. Concomitant measures of regional cerebral metabolic rates for glucose (CMR(glc)) during the task, utilizing positron emission tomography, revealed increased activity in prefrontal cortex, dorsal striatum, and medial temporal lobe (including hippocampus) that was significantly enhanced over normal alert conditions following administration of CX717. A single night of sleep deprivation produced severe impairments in performance in the same monkeys, accompanied by significant alterations in task-related CMR(glc) in these same brain regions. However, CX717 administered to sleep-deprived monkeys produced a striking removal of the behavioral impairment and returned performance to above-normal levels even though animals were sleep deprived. Consistent with this recovery, CMR(glc) in all but one brain region affected by sleep deprivation was also returned to the normal alert pattern by the drug. The ampakine CX717, in addition to enhancing cognitive performance under normal alert conditions, also proved effective in alleviating impairment of performance due to sleep deprivation. Therefore, the ability to activate specific brain regions under normal alert conditions and alter the deleterious effects of sleep deprivation on activity in those same regions indicate a potential role for ampakines in sustaining performance under these types of adverse conditions

Using livestock wastewater with SDI: a status report after three seasons

Presented at the Central Plains irrigation short course and exposition on February 5-6, 2001 at the Holiday Inn in Kearney, Nebraska.Using subsurface drip irrigation (SDI) with lagoon wastewater has many potential advantages. The challenge is to design and manage the SDI system to prevent emitter clogging. A study was initiated in 1998 to test the performance of five types of driplines (with emitter flow rates of 0.15, 0.24, 0.40, 0.60, and 0.92 gal/hr-emitter) with lagoon wastewater. A disk filter (200 mesh, with openings of 0.003 inches) was used and shock treatments of chlorine and acid were injected periodically. Over the course of three seasons (1998-2000) a total of approximately 52 inches of irrigation water has been applied through the SDI system. The flow rates of the two smallest emitter sizes, 0.15 gal/hr-emitter and 0.24 gal/hr-emitter have decreased approximately 30% during the three seasons, indicating some emitter clogging. The three largest driplines (0.40, 0.60, and 0.92 gal/hr-emitters) have had less than 5% reduction in flow rate. The disk filter and automatic backflush controller have performed adequately with the beef livestock wastewater in all three years. Based on these results, the use of SDI with beef lagoon wastewater shows promise. However, the smaller emitter sizes normally used with groundwater sources in western Kansas may be risky for use with lagoon wastewater and the long-term (> 3 growing seasons) effects are untested