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Search Results: 1 - 10 of 2393 matches for " Rick Jordan "
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Efficiency Analysis of Competing Tests for Finding Differentially Expressed Genes in Lung Adenocarcinoma
Rick Jordan,Satish Patel,Hai Hu,James Lyons-Weiler
Cancer Informatics , 2008,
Abstract: In this study, we introduce and use Efficiency Analysis to compare differences in the apparent internal and external consistency of competing normalization methods and tests for identifying differentially expressed genes. Using publicly available data, two lung adenocarcinoma datasets were analyzed using caGEDA (http://bioinformatics2.pitt.edu/GE2/GEDA. html) to measure the degree of differential expression of genes existing between two populations. The datasets were randomly split into at least two subsets, each analyzed for differentially expressed genes between the two sample groups, and the gene lists compared for overlapping genes. Efficiency Analysis is an intuitive method that compares the differences in the percentage of overlap of genes from two or more data subsets, found by the same test over a range of testing methods. Tests that yield consistent gene lists across independently analyzed splits are preferred to those that yield less consistent inferences. For example, a method that exhibits 50% overlap in the 100 top genes from two studies should be preferred to a method that exhibits 5% overlap in the top 100 genes. The same procedure was performed using all available normalization and transformation methods that are available through caGEDA. The ‘best’ test was then further evaluated using internal cross-validation to estimate generalizable sample classification errors using a Na ve Bayes classification algorithm. A novel test, termed D1 (a derivative of the J5 test) was found to be the most consistent, and to exhibit the lowest overall classification error, and highest sensitivity and specificity. The D1 test relaxes the assumption that few genes are differentially expressed. Efficiency Analysis can be misleading if the tests exhibit a bias in any particular dimension (e.g. expression intensity); we therefore explored intensity-scaled and segmented J5 tests using data in which all genes are scaled to share the same intensity distribution range. Efficiency Analysis correctly predicted the ‘best’ test and normalization method using the Beer dataset and also performed well with the Bhattacharjee dataset based on both efficiency and classification accuracy criteria.
Meiosis-Specific Cohesin Component, Stag3 Is Essential for Maintaining Centromere Chromatid Cohesion, and Required for DNA Repair and Synapsis between Homologous Chromosomes
Jessica Hopkins,Grace Hwang equal contributor,Justin Jacob equal contributor,Nicklas Sapp equal contributor,Rick Bedigian,Kazuhiro Oka,Paul Overbeek,Steve Murray,Philip W. Jordan
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004413
Abstract: Cohesins are important for chromosome structure and chromosome segregation during mitosis and meiosis. Cohesins are composed of two structural maintenance of chromosomes (SMC1-SMC3) proteins that form a V-shaped heterodimer structure, which is bridged by a α-kleisin protein and a stromal antigen (STAG) protein. Previous studies in mouse have shown that there is one SMC1 protein (SMC1β), two α-kleisins (RAD21L and REC8) and one STAG protein (STAG3) that are meiosis-specific. During meiosis, homologous chromosomes must recombine with one another in the context of a tripartite structure known as the synaptonemal complex (SC). From interaction studies, it has been shown that there are at least four meiosis-specific forms of cohesin, which together with the mitotic cohesin complex, are lateral components of the SC. STAG3 is the only meiosis-specific subunit that is represented within all four meiosis-specific cohesin complexes. In Stag3 mutant germ cells, the protein level of other meiosis-specific cohesin subunits (SMC1β, RAD21L and REC8) is reduced, and their localization to chromosome axes is disrupted. In contrast, the mitotic cohesin complex remains intact and localizes robustly to the meiotic chromosome axes. The instability of meiosis-specific cohesins observed in Stag3 mutants results in aberrant DNA repair processes, and disruption of synapsis between homologous chromosomes. Furthermore, mutation of Stag3 results in perturbation of pericentromeric heterochromatin clustering, and disruption of centromere cohesion between sister chromatids during meiotic prophase. These defects result in early prophase I arrest and apoptosis in both male and female germ cells. The meiotic defects observed in Stag3 mutants are more severe when compared to single mutants for Smc1β, Rec8 and Rad21l, however they are not as severe as the Rec8, Rad21l double mutants. Taken together, our study demonstrates that STAG3 is required for the stability of all meiosis-specific cohesin complexes. Furthermore, our data suggests that STAG3 is required for structural changes of chromosomes that mediate chromosome pairing and synapsis, DNA repair and progression of meiosis.
Further Properties of Reproducing Graphs  [PDF]
Jonathan Jordan, Richard Southwell
Applied Mathematics (AM) , 2010, DOI: 10.4236/am.2010.15045
Abstract: Many real world networks grow because their elements get replicated. Previously Southwell and Cannings introduced a class of models within which networks change because the vertices within them reproduce. This happens deterministically so each vertex simultaneously produces an offspring every update. These offspring could represent individuals, companies, proteins or websites. The connections given to these offspring depend upon their parent’s connectivity much as a child is likely to interact with their parent’s friends or a new website may copy the links of pre-existing one. In this paper we further investigate one particular model, ‘model 3’, where offspring connect to their parent and parent’s neighbours. This model has some particularly interesting features, including a degree distribution with an interesting fractal-like form, and was introduced independently under the name Iterated Local Transitivity by Bonato et al. In particular we show connections between this degree distribution and the theory of integer partitions and show that this can be used to explain some of the features of the degree distribution; we give exact formulae for the number of complete subgraphs and the global clustering coefficient and we show how to calculate the minimal cycle basis.
A Comparative Analysis of MMPI and Rorschach Findings Assessing Combat-Related PTSD in Vietnam Veterans—Analysis of MMPI and Rorschach Findings Assessing PTSD  [PDF]
Ioanna Katsounari, Jordan Jacobowitz
Psychology (PSYCH) , 2011, DOI: 10.4236/psych.2011.24053
Abstract: There has been a proliferation of assessment research on Post-traumatic Stress Disorder (PTSD) over the past twenty years. In spite of recent advances in the PTSD assessment research, there continues to be a controversy as to whether the MMPI or Rorschach is more useful in determining the presence of PTSD. The present comparative analysis of the research literature will carefully evaluate controlled empirical studies, which utilized psychometric measures such as the MMPI/2 and Rorschach to identify PTSD in Vietnam Veterans. This analysis is guided by the paucity of comparative data for standardized objective and projective instruments to assess combat-related PTSD. The analysis indicated that the MMPI as an assessment instrument focuses on symptom recognition of PTSD while the Rorschach seems to be more likely to identify chronic adaptations to trauma. The significance of pre-combat factors, such as preexisting personality, and their impact on the way individuals make meaning and express traumatic experiences needs to be further addressed in future research. The need for reliable and valid measures to assess combat-related PTSD is urgent as an increasing number of soldiers return from war zones.
Maximizing Sampling Efficiency  [PDF]
Harmon S. Jordan
Applied Mathematics (AM) , 2013, DOI: 10.4236/am.2013.411209
Abstract: Background and Goals: Although health care quality improvement has traditionally involved extensive work with paper records, the adoption of health information technology has increased the use of electronic record and administrative systems. Despite these advances, quality improvement practitioners now and for the foreseeable future need guidance in defining populations of individuals for study and in selecting and analyzing sample data from such populations. Statistical data analysis in health care research often involves using samples to make inferences about populations. The investigator needs to consider the goals of the study, whether sampling is to be used, and the type of population being studied. While there are numerous sampling strategies designed to conserve resources and yield accurate results, one of these techniques—use of the finite population correction (FPC)—has received relatively little attention in health care sampling contexts. It is important for health care quality practitioners to be aware of sampling options that may increase accuracy and conserve resources. This article describes common sampling situations in which the issue of the finite population correction decision often arises. Methods: This article describes 3 relevant sampling situations that influence the design and analysis phases of a study and offers guidance for choosing the most effective and efficient design. Situation 1: The study or activity involves taking a sample from a large finite target population for which enumerative inferences are needed. Situation 2: The population is finite and the study is enumerative. A complete enumerative count of “defects” in the process is needed so that remediation can occur. Here, statistical inference is unnecessary. Situation 3: The target population is viewed as infinite; such populations are “conceptual populations” [1] or “processes”. Results: The article shows how savings in resources can be achieved by choosing the correct analytic framework at the conceptualization phase of study design. Choosing the right sampling approach can produce accurate results at lower costs. Several examples are presented and the implications for health services research are discussed. Conclusion: By clearly specifying the objectives of a
Approaching the immunophysiology of steroid resistance
Rick Bucala
Arthritis Research & Therapy , 2012, DOI: 10.1186/ar3820
Abstract: In the current issue of Arthritis Research & Therapy, Wang and colleagues provide functional immunologic data on a molecular pathway for glucocorticoid resistance in systemic lupus erythematosus (SLE) [1]. Glucocorticoids have broad and powerful effects on the immune response and, despite the advent of biologic therapies, remain the most important and frequently used immunosuppressive agents in clinical practice [2]. Indeed, if it were not for their dose-limiting toxicity, glucocorticoids in all other respects would be ideal anti-inflammatory agents: orally absorbed, rapidly acting, and highly effective at shutting down a multitude of tissue-damaging, inflammatory pathways. Despite the clinical success of disease-modifying agents, concomitant steroid use remains an integral part of effective therapy as well as an established means for controlling disease exacerbations.Among practitioners focused on inflammatory disorders, whether rheumatologic or nonrheumatologic, there has long been the observation that some patients respond poorly to steroids or require high doses and prolonged treatment for disease control. These patients expectedly suffer most from the treatment-related complications of glucose intolerance, hypertension, obesity, osteoporosis, and myopathy. Even among patients maintained on low doses, the therapeutic objective remains the absolute minimalization or discontinuation of glucocorticoids. This goal has gained additional prominence with the recognition that accelerated atherosclerosis is an attendant consequence of systemic inflammation and a major cause of morbidity and mortality in rheumatoid arthritis and SLE [3]. The contributing effects of steroid-induced glucose intolerance and dyslipidemia add to the pathophysiology of atherogenesis and prompt continued investigation into more effective steroid-sparing agents and safer approaches to immunosuppression.Wang and colleagues provide evidence of a specific pathway for steroid resistance in patients w
Have microarrays failed to deliver for developmental biology?
Rick Livesey
Genome Biology , 2002, DOI: 10.1186/gb-2002-3-9-comment2009
Abstract: The cDNA microarray is a conceptually simple object, whether made on a glass slide within an academic lab or printed using complex technology in a commercial production setting. The best characterization of them is as glorified dot-blots (VG Cheung, personal communication), and this explains much of their appeal. Most life scientists have carried out a northern, Southern or in situ hybridization, and are therefore familiar with the main technology - hybridization - needed for microarray use. Yet it has proven difficult in some fields to translate the obvious promise of microarrays into tangible results. A pressing issue is why it appears that we are stuck in a 'proof of principle' stage, rather than a routine exploitation phase, especially in the field of developmental biology. The problem is that there have been few developmental biology microarray studies, indicating a very slow adoption of the technology in this field. Currently there appear to be two overriding concerns: access to the technology in a reliable form, and how best to apply the technology in a way that generates data that are useful in the short to medium term.Interesting and insightful developmental studies using microarrays have been published, but they are all the more striking for their infrequency. There have been several studies of Drosophila development [1,2,3], including one identifying targets of the mesoderm-specific transcription factor twist [4]. Similarly, there have been a number of genome-wide studies of worm development, almost all from the Kim lab at Stanford [5,6,7]. The situation appears more bleak when looking for published microarray studies of vertebrate development. Aside from some small-scale studies of retinal development in the mouse (including our own) [8,9] and mesoderm induction in Xenopus [10], there are very few. The predicted deluge of data has failed to materialize, and it is not immediately obvious why this is the case. Commercial arrays of worm, fly, human and mous
Tres proyectos en Arizona
ARQ (Santiago) , 2004, DOI: 10.4067/S0717-69962004005700008
Abstract: the dry air and gentle climate of certain parts of the american west made them an ideal setting for experimentation by architects like albert frey and rudolph schindler during the 20th century. various levels of relationship to the outside, innovative use of materials and new ways of handling light and shadow are some of the themes raised by these architectural incursions. the work of rick joy continues and expands upon these earlier explorations.
Reading with Methodological Perspective Bias: A journey into Classic Grounded Theory
Rick Deady
Grounded Theory Review : an International Journal , 2011,
Abstract: The following is a na ve narrative of my journey into classic grounded theory (CGT) and the consideration of the possible existence of methodological perspective bias when reviewing literature. Whilst research bias has been viewed from a number of differing perspectives, such as sample bias, interviewer bias, publication bias etc (Sica, 2006), there appears a dearth of discussion within the literature on methodological perspective bias, as well as, a reluctance to publicly acknowledge the existence of such bias. For the purpose of this paper the concept of bias is defined as “a source of systematic error … deriving from a conscious or unconscious tendency on the part of a researcher to produce data, and/or to interpret them, in a way that leans towards erroneous conclusions which are in line with his or her commitments” (Hammersley and Gomm, 1997, p.1).
The Evolution of an Activist
Rick Bass
Transatlantica : Revue d'études Américaines , 2012,
Abstract: IntroductionRick Bass, l’art de l’approche Nathalie CochoyAvant de devenir écrivain, Rick Bass fut ingénieur géologue, spécialisé dans l’étude et la détection des gisements pétroliers. De sa formation, il a sans doute gardé une fascination pour les profondeurs indicibles, littéralement incompréhensibles, du temps et de la terre. Dans ses essais, dans ses nouvelles, Rick Bass allie la rigueur et la minutie d’une approche scientifique et l’infini respect d’une démarche poétique éminemment consc...
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