Development of a Novel Algorithm to Remove Spurious Edges from Biological Networks Through Functional Enrichment

The field of systems biology has facilitated the modelling of large and complex biological networks. These networks, generated from prior knowledge contained in the corpus of medical and scientific literature, or from experimental data are being used to model differing macromolecule networks associated with distinct disease states. While these networks are vital in understanding disease pathology and possible treatment options, they are rife with spurious interactions. These interactions arise from the methods used to create such networks, where the ability to discriminate between direct and indirect relationships is a challenge. To combat these spurious interactions an algorithm that leverages functional enrichment in biological networks was developed. Here, functional enrichment refers to two or three node functional motifs that are ubiquitous in biological networks. The algorithm developed removes edges from an existing network based on that edge’s involvement in functional motifs relative to every other edge’s involvement. In this work, the application of this algorithm was explored using real-world clinical disease networks. Furthermore, a software package was developed to identify an edge’s membership in functional motifs with respect to the network being explored. The tools developed in this work are the first to critically analyze an edge’s relationship to functional motifs in terms of network inclusion. Therefore, the principles outlined in this work can be employed in future works aimed at removing spurious edges. These principles will also produce higher quality biological networks for the understanding of disease pathology and the development of more effective treatment options

Dynamics of some parabolic dunes in the Manawatu region, New Zealand : a thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Geography at Massey University

Parabolic dunes are U-shaped dunes which may be found in deserts and coastal locations around the world. They occur along much of the coastal area of the West Coast of the North Island of New Zealand, including the Manawatu Region. The parabolic dunes of the Manawatu coast comprise the largest parabolic dune fields in New Zealand. This research was conducted to identify the rates of movement of the parabolic dunes, and establish whether there is a relationship between parabolic dune development along the Manawatu coast and El Nino Southern Oscillation. Morphological changes in parabolic dunes over time are also examined, and a model of parabolic dune development which deals specifically with the parabolic dunes of the Manawatu coast is produced. Examination of the parabolic dunes was conducted by ground surveying using Global Positioning System (GPS) and through the use of aerial photographs and aerial photograph mapping. Rates of parabolic dune migration along the Manawatu coast were found to be significantly higher than has been recorded elsewhere in the world. By examining the wind regime and the El Nino Southern Oscillation, and comparing these with parabolic dune migration a pattern of increased parabolic dune activity under El Nino conditions was identified. A pattern of parabolic dune formation from blowout initiation through to parabolic dune maturity was identified and a model for parabolic dune development along the Manawatu coast designed

City of Elkhart - ADA Data Collection and Transition Plan Implementation

Over a 5-year period, the City of Elkhart col-lected detailed data on nearly 4,000 curb ramps. The City is now using that data to plan and fund ADA improvements within the public right-of-way. This presentation will discuss how to look at an overwhelming task such as ADA compli-ance in the right-of-way and develop a plan to manage it

An inventory of wild sandalwood stocks in Vanuatu

Characterizing sandalwood (S. austrocaledonicum) abundance in Vanuatu is challenging due to the broad, discontinuous yet highly modified distribution of sandalwood and the lack of systematic historical inventories or detailed harvest documentation. The preliminary distribution has been estimated from anecdotal ranges provided by the Vanuatu Department of Forests (VDoF), GIS spatial analyses and recorded sandalwood locations collected during the Oil Quality Survey (Page, 2005) and during the 2007 sandalwood inventory survey conducted for this project. Historic densities have been estimated from anecdotal descriptions and harvest data records. Current densities are based on the 2007 field survey of sandalwood populations on four Vanuatu islands. The surveys were conducted in regions of known sandalwood populations. The low aggregated density (0.4 trees/ha) of commercially sized trees found in these surveyed populations is a cause for concern. Based on the field data, we estimate that the current resource on the four islands surveyed is approximately 210 tonnes, with another 80 tonnes estimated on other islands of Vanuatu. At current harvest rates this resource may be quickly depleted and there will be a shortfall until plantation sandalwood is available in 10-15 years. Consideration should therefore be given to reducing the quota for wild sandalwood harvest to a sustainable level

Movement Behavior of Radio-Tagged European Starlings in Urban, Rural, and Exurban Landscapes

Since their intentional introduction into the United States in the 1800s, European starlings (Sturnus vulgaris) have become the fourth most common bird species and a nuisance bird pest in both urban and rural areas. Managers require better information about starling movement and habit-use patterns to effectively manage starling populations and the damage they cause. Thus, we revisited 6 radio-telemetry studies conducted during fall or winter between 2005 and 2010 to compare starling movements (n = 63 birds) and habitat use in 3 landscapes. Switching of roosting and foraging sites in habitat-sparse rural landscapes caused daytime (0900–1500 hours) radio fixes to be on average 2.6 to 6.3 times further from capture sites than either urban or exurban landscapes (P \u3c 0.001). Roosts in urban city centers were smaller (100,000 birds) 6–13 km away in industrial zones. Radio-tagged birds from city-center roosts occasionally switched to the outlying major roosts. A multitrack railroad overpass and a treed buffer zone were used as major roosts in urban landscapes. Birds traveling to roosts from primary foraging sites in exurban and rural landscapes would often pass over closer-lying minor roosts to reach major roosts in stands of emergent vegetation in large wetlands. Daytime minimum convex polygons ranged from 101–229 km2 (x̄ = 154 km2). Anthropogenic food resources (e.g., concentrated animal feeding operations, shipping yards, landfills, and abattoirs) were primary foraging sites. Wildlife resource managers can use this information to predict potential roosting and foraging sites and average areas to monitor when implementing programs in different landscapes. In addition to tracking roosting flights, we recommend viewing high-resolution aerial images to identify potential roosting and foraging habitats before implementing lethal culls (e.g., toxicant baiting)

Fibroblasts derived from long-lived insulin receptor substrate 1 null mice are not resistant to multiple forms of stress

Reduced signalling through the insulin/insulin-like growth factor-1 signalling (IIS) pathway is a highly conserved lifespan determinant in model organisms. The precise mechanism underlying the effects of the IIS on lifespan and health is currently unclear, although cellular stress resistance may be important. We have previously demonstrated that mice globally lacking insulin receptor substrate 1 (Irs1−/−) are long-lived and enjoy a greater period of their life free from age-related pathology compared with wild-type (WT) controls. In this study, we show that primary dermal fibroblasts and primary myoblasts derived from Irs1−/− mice are no more resistant to a range of oxidant and nonoxidant chemical stressors than cells derived from WT mice

The Black Voice and Shaping Audacity

Throughout the course of the world history it has become very clear that the unrestrained black self is repugnant in the eyes of society, and as society demands that black culture strives for a more standardized aesthetic, theater can be used as a tool to educate and reshape these perceptions with a view to erasing reductions. I’m interested in how the process of thought, by black people, shapes the content and form of speech patterns and therefore art creation. How does a Eurocentric aesthetic and process of thought differ from African-based ideologies, and furthermore become implicitly forced and therefore standardized within our society? In what ways are black people affected by the expectation and need to unnaturally contort our bodies, voices, narratives, and philosophies to fit within an alien structure, and what might be the benefits of acknowledging, and therefore appreciating, our inherent differences. The state of being awake, whether literally or metaphorically, is the state of being aware of self. In this paper, I will further interpret the state of “being awake” to be active and attentively watchful of those entities that intend to reduce black development and self-actualization, and keep the black self in a spinning whirlwind of confusion, self-hate, lethargy, and self-doubt. I will also consider the position of self amongst a hostile and ever-changing environment that seeks to suppress and dehumanize in particular the black body. As black people, we must be watchful to resist believing that our inherent truths are inferior as compared to the images that we see around us, and that our actual being—thinking and speaking—is unsatisfactory and unacceptable, and, therefore, lacking a worthy sense of beauty and sophistication. Moving through the world as a black person, in this way—maintaining and managing the many variations of self that is needed to be accepted into society, can be taxing on one’s soul and can blur the ideas of where one’s authentic truth should begin and end. It is my intention in this paper to explore this dichotomy between the wider society’s negative perception of black people and culture together with the ensuing effects on their own lived reality through the medium of theater and using the plays Funnyhouse Of A Negro and The Death of the Last Black Man in the Whole Entire World as prisms to spell out these ideas

Wide-Field Optic for Autonomous Acquisition of Laser Link

An innovation reported in Two-Camera Acquisition and Tracking of a Flying Target, NASA Tech Briefs, Vol. 32, No. 8 (August 2008), p. 20, used a commercial fish-eye lens and an electronic imaging camera for initially locating objects with subsequent handover to an actuated narrow-field camera. But this operated against a dark-sky background. An improved solution involves an optical design based on custom optical components for the wide-field optical system that directly addresses the key limitations in acquiring a laser signal from a moving source such as an aircraft or a spacecraft. The first challenge was to increase the light collection entrance aperture diameter, which was approximately 1 mm in the first prototype. The new design presented here increases this entrance aperture diameter to 4.2 mm, which is equivalent to a more than 16 times larger collection area. One of the trades made in realizing this improvement was to restrict the field-of-view to +80 deg. elevation and 360 azimuth. This trade stems from practical considerations where laser beam propagation over the excessively high air mass, which is in the line of sight (LOS) at low elevation angles, results in vulnerability to severe atmospheric turbulence and attenuation. An additional benefit of the new design is that the large entrance aperture is maintained even at large off-axis angles when the optic is pointed at zenith. The second critical limitation for implementing spectral filtering in the design was tackled by collimating the light prior to focusing it onto the focal plane. This allows the placement of the narrow spectral filter in the collimated portion of the beam. For the narrow band spectral filter to function properly, it is necessary to adequately control the range of incident angles at which received light intercepts the filter. When this angle is restricted via collimation, narrower spectral filtering can be implemented. The collimated beam (and the filter) must be relatively large to reduce the incident angle down to only a few degrees. In the presented embodiment, the filter diameter is more than ten times larger than the entrance aperture. Specifically, the filter has a clear aperture of about 51 mm. The optical design is refractive, and is comprised of nine custom refractive elements and an interference filter. The restricted maximum angle through the narrow-band filter ensures the efficient use of a 2-nm noise equivalent bandwidth spectral width optical filter at low elevation angles (where the range is longest), at the expense of less efficiency for high elevations, which can be tolerated because the range at high elevation angles is shorter. The image circle is 12 mm in diameter, mapped to 80 x 360 of sky, centered on the zenith

No change detected on Earth’s mid-latitude atmospheric ozone by the 2017 Total Solar Eclipse

Six high altitude balloon flights were completed during the summer of 2017 to measure the effect of the total solar eclipse on Earth’s ozone over the eastern Snake River Plain in Idaho. The stratospheric ozone layer undergoes a noisy diurnal pattern driven, primarily by photochemistry above 30km and by atmospheric dynamics for altitudes below 30km. The flights for this project rarely exceeded that boundary and were an attempt to detect photochemistry effects in the lower stratosphere. The first five flights determined a baseline for the distribution of ozone from ground level to the mid-stratosphere. The sixth flight was done during the total solar eclipse and was compared to the baseline. These data were also compared to multiple years’ data taken in the Uintah Basin in northeast Utah. All measurements were consistent with each other and show spatial and temporal variations in the ozone column that are expected. The balloon’s instrumentation payload was at the tropopause during eclipse totality and no change in either temperature or ozone was detected that was above the normal noise level in the previous data sets. The conclusion is that no photochemical processes are strong enough to clearly modify Earth’s ozone in the lower stratosphere on timescales shorter than three hours. This is consistent with previously reported satellite data of total column ozone

A Miniaturized Multi Sensor Array for Balloon-Borne Air Measurements, Phase I

Weber State University’s High-Altitude Ballooning team, HARBOR, has seen an opportunity for cooperative research among the many individual balloon teams based in North America. The Great American Solar Eclipse brought these teams into the spotlight as dozens of ballooning groups worked together to image the eclipse. Leveraging this collection of balloon teams to create a large-scale data set could make some valuable discoveries and give us a better understanding of the atmospheric dynamics that take place in the stratosphere. Our team has decided to facilitate the creation of such a data set by designing an atmospheric data collection tool, the mini-Multi Sensor Array, that can be flown by teams all over the nation, and potentially the world. Our goal is to create an inexpensive, lightweight, easy to assemble device which will measure gas concentrations, particulate matter, atmospheric turbulence, and meteorological parameters such as temperature, pressure, and humidity. We will also add features such as long distance telemetry, which will facilitate recovery of these payloads. Having a redundant, lightweight tracking device will increase the number of flight teams that are making a regular effort to fly our mini-MSA with their payload