GenomeGraphs: integrated genomic data visualization with R.

BackgroundBiological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses.ResultsWe developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system.ConclusionGenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R

RADICAL EXPLORATIONS OF RADICAL EMPIRICISM: WILLIAM JAMES’S TRANSMISSIVE THEORY OF MIND IN THE CONTEXT OF VISIONARY EXPERIENCE

The dominant ontology in science is a form of materialism and it filters down into the social sciences in ways I will touch on throughout this paper. The influence of the current dominant ontology is especially apparent when it comes to experiences and phenomena that challenge its underlying assumptions which is why I will primarily focus on visionary experience and psi phenomena as studied by radical empiricists throughout the ages. The philosophical position of William James challenges materialist assumptions by championing the idea that the only world we can speak of is the world of our experience. William James affords academics the possibility of speaking from a place of personal experience when he argues that religious belief and visionary experience is psychologically “normal” and ripe grounds for rigorous academic consideration. Although James does not offer a systematic metaphysics, I will explore a series of analogies, metaphors, suggestions, and thick descriptions that are central to James’s effort to reclaim the intimacy and role of embodied experience in philosophy and James’s attempts to push empirical science into new territory that is currently assumed to be nonexistent in the dominant metaphysical episteme ruled by reductionary materialism. I will also visit radical empiricism within the broader context of his engagement with psychical research and various modalities of religious experience. I also draw on Edith Turner to show how James’s theory of mind can be productively extended to the methods of anthropology. Edith Turner’s anthropological method and interest in psychical research highlights intriguing parallels with James\u27s philosophy. Common to these approaches is the aim to reconcile religion and science; the adoption of a radical empiricist stance; acknowledgment of the inherent fallibility of hypotheses; a heavy reliance on personal and subjective epistemology; and a challenge to the traditional Cartesian mind-body dichotomy

Are there intergenerational differences in views on immigration?

This poster looks at intergenerational differences in the views on immigration. It evaluates the literature surrounding this and why these views may occur. Primary research in the form of semi-structured paired interviews were undertaken. 5 participants aged 20-23 and their grandparents were asked a series of questions on wider political opinions and then more specifically on immigration. The conclusion that was drawn was that in the literature and interviews, intergenerational differences can be seen, with the older generation being more negative. This may be as a result of several factors, with one being the life-cycle effect. This is when as people grow older their views shift to the right and as a result become more negative towards topics such as immigration

Satellite Communications Network Control in the Presence of Electronic Countermeasures

Satellite communications networks have supplanted other over-the-horizon communications systems because of their high capacity and high reliability. A key characteristic of satellite communications systems is that all communication links within a network share a common transponder and thus have the potential for deleterious interactions. This in turn gives rise to the need for a network control function that can establish and ensure appropriate transmission characteristics for each terminal with the goal of maximizing the communications capacity available to all network members. Because of the potential for electronic countermeasures in military satellite communications systems, an antijam mode of operations, which by its very nature is a reduced capacity mode, is often included in the network architecture. This in turn puts added burdens on the control function for the network. Both a clear mode of operation and an antijam mode of operation (often with different properties and characteristics) must be controlled and, furthermore, a timely mechanism for transitioning between the two modes must be provided. In this paper the generic top level requirements are defined for a military satellite communications control system. The control system function is then divided into its key components and generic requirements are provided for each component. Alternative strategies for both communicator and jammer are discussed leading to the flow of events that would result in the transitioning of the SATCOM network in response to a changing ECM environment

The Shared Experiences of Privilege and Oppression Among Black Females in Counselor Education and Supervision Programs: A Thematic Analysis

Because the United States has one of the most complex cultural identities in the Western world, it is essential that counselors and counselor educators develop the multicultural and social justice competencies needed to work within this diverse society. To this end, counselor educators must have awareness of their own knowledge, beliefs, attitudes, and behaviors related to privilege, oppressions, social group status, etc., as well as to be aware of the intersectionality of privilege and oppression across one’s various identities. This is particularly important given that research suggests that the intersectional privilege and oppression dynamics often experienced by Black females facing unique challenges affecting their success and performance. Yet historically, Black females have received minimal acknowledgement in research, praxis, practice, discourse, curriculum, and policies within institutional settings. To address this gap, a qualitative thematic analysis design was used to gain knowledge of the Black female doctoral students’ experiences with privilege and oppression in counselor education programs (CES). This study examined how Black females in CES programs described privilege and oppression; how they experienced privilege and oppression within their department, and with their interactions with faculty, and in the learning environment; and how they are impacted by their experiences as Black women. Several themes emerged for each of the five research questions examined. While most of the emergent themes were consistent with previous research, they also provided greater insight in understanding the experiences of privilege and oppression faced by Black females in CES programs. Implications and recommendations for future research are discussed

to be come

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Incentivized HIV Testing--Is It Needed and Effective? Developing an Evaluation Tool

The following is a case study of agencies in Seattle, WA who provide HIV testing followed by an evaluation tool for the agencies to determine the role of incentivizing HIV testing. Some agencies I interviewed provide incentives for the testing and others do not. This Capstone will focus on six agencies currently providing HIV testing and provides a tool for agencies to use to attempt to answer the following question: In the face of reduced funding for HIV prevention and a mandate to continue to push for increasingly getting more Men who have Sex with Men (MSM) tested for HIV, what role does providing an incentive play? Through key informant interviews with implementing agency staff it was discovered that none of the agencies are evaluating the effectiveness of providing an incentive for HIV testing. However all of them felt if funding were to be reduced the first thing to be cut would be the HIV testing incentive. None of the agencies interviewed were interested in implementing a monitoring and evaluation plan, inclusive of log-frames and budget. They all agreed that they did not have the time, budget or expertise to monitor a plan. They were also clear that they would not be interested if this plan was not going to be required by Public Health Seattle-King County, who funds most of the programs. Through discussions with the agencies that were interviewed and contract monitoring staff with Public Health, they all felt that if they had a simple tool to measure the effectiveness of incentivized HIV testing it would be valuable in their program planning. With feedback from implementing agencies, the author has developed a short, client administered survey in both English and Spanish, that will assist Community Based Organizations (CBOs) in determining the effectiveness of a client receiving an incentive, free testing or donation request for HIV testing. Knowing that most of the CBOs do not have extra funding, staff or expertise to implement a large-scale evaluation, the tool that has been developed does not require extra staff time, expertise or funding. This analysis links the author’s professional, graduate school course-work and practicum experience. Recommendations include utilizing the evaluation tool to determine the effectiveness of incentivized HIV testing. Question: In the face of reduced HIV prevention funding and pressure to continue to test MSM, especially Latino and Black MSM, does providing an incentive for testing increase the likelihood that MSM will get tested for HIV