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Search Results: 1 - 10 of 299932 matches for " Aaron J Cummings "
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Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR – how well do they correlate?
Peter B Dallas, Nicholas G Gottardo, Martin J Firth, Alex H Beesley, Katrin Hoffmann, Philippa A Terry, Joseph R Freitas, Joanne M Boag, Aaron J Cummings, Ursula R Kees
BMC Genomics , 2005, DOI: 10.1186/1471-2164-6-59
Abstract: Correlations with qRT-PCR data were obtained using microarray data that were processed using robust multi-array analysis (RMA) and the MAS 5.0 algorithm. Our results indicate that when identical transcripts are targeted by the two methods, correlations between qRT-PCR and microarray data are generally strong (r = 0.89). However, we observed poor correlations between qRT-PCR and RMA or MAS 5.0 normalized microarray data for 13% or 16% of genes, respectively.These results highlight the complementarity of oligonucleotide microarray and qRT-PCR technologies for validation of gene expression measurements, while emphasizing the continuing requirement for caution in interpreting gene expression data.The use of microarray technology to assess gene expression levels is now widespread in biology and, particularly in the clinical setting, the applicability of the methodology is likely to broaden as the technology evolves, data analysis procedures improve, and costs decline [1-3]. Two distinct microarray platforms, cDNA and oligonucleotide, are currently in general use [4]. While the relative merits of the two systems continue to be discussed [5], the validation of microarray results using independent mRNA quantitation techniques, including Northern blotting, ribonuclease protection, in situ hybridization, or quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) remains a critical element of any microarray experiment [6,7]. Despite this, there have been few systematic validation studies of cDNA, or more noticeably, oligonucleotide microarray data using these independent approaches. For researchers to be confident with the interpretation of microarray results and for the establishment of consistent validation procedures in the microarray community for the purpose of data comparison, it is important that this issue be addressed.We have undertaken an extensive series of experiments examining gene expression profiles in pediatric cancer specimens and norm
The Strange Case of Privacy in Equilibrium Models
Rachel Cummings,Katrina Ligett,Mallesh M. Pai,Aaron Roth
Computer Science , 2015,
Abstract: We study how privacy technologies affect user and advertiser behavior in a simple economic model of targeted advertising. In our model, a consumer first decides whether or not to buy a good, and then an advertiser chooses an advertisement to show the consumer. The consumer's value for the good is correlated with her type, which determines which ad the advertiser would prefer to show to her---and hence, the advertiser would like to use information about the consumer's purchase decision to target the ad that he shows. In our model, the advertiser is given only a differentially private signal about the consumer's behavior---which can range from no signal at all to a perfect signal, as we vary the differential privacy parameter. This allows us to study equilibrium behavior as a function of the level of privacy provided to the consumer. We show that this behavior can be highly counter-intuitive, and that the effect of adding privacy in equilibrium can be completely different from what we would expect if we ignored equilibrium incentives. Specifically, we show that increasing the level of privacy can actually increase the amount of information about the consumer's type contained in the signal the advertiser receives, lead to decreased utility for the consumer, and increased profit for the advertiser, and that generally these quantities can be non-monotonic and even discontinuous in the privacy level of the signal.
Online Learning and Profit Maximization from Revealed Preferences
Kareem Amin,Rachel Cummings,Lili Dworkin,Michael Kearns,Aaron Roth
Computer Science , 2014,
Abstract: We consider the problem of learning from revealed preferences in an online setting. In our framework, each period a consumer buys an optimal bundle of goods from a merchant according to her (linear) utility function and current prices, subject to a budget constraint. The merchant observes only the purchased goods, and seeks to adapt prices to optimize his profits. We give an efficient algorithm for the merchant's problem that consists of a learning phase in which the consumer's utility function is (perhaps partially) inferred, followed by a price optimization step. We also consider an alternative online learning algorithm for the setting where prices are set exogenously, but the merchant would still like to predict the bundle that will be bought by the consumer for purposes of inventory or supply chain management. In contrast with most prior work on the revealed preferences problem, we demonstrate that by making stronger assumptions on the form of utility functions, efficient algorithms for both learning and profit maximization are possible, even in adaptive, online settings.
Privacy and Truthful Equilibrium Selection for Aggregative Games
Rachel Cummings,Michael Kearns,Aaron Roth,Zhiwei Steven Wu
Computer Science , 2014,
Abstract: We study a very general class of games --- multi-dimensional aggregative games --- which in particular generalize both anonymous games and weighted congestion games. For any such game that is also large, we solve the equilibrium selection problem in a strong sense. In particular, we give an efficient weak mediator: a mechanism which has only the power to listen to reported types and provide non-binding suggested actions, such that (a) it is an asymptotic Nash equilibrium for every player to truthfully report their type to the mediator, and then follow its suggested action; and (b) that when players do so, they end up coordinating on a particular asymptotic pure strategy Nash equilibrium of the induced complete information game. In fact, truthful reporting is an ex-post Nash equilibrium of the mediated game, so our solution applies even in settings of incomplete information, and even when player types are arbitrary or worst-case (i.e. not drawn from a common prior). We achieve this by giving an efficient differentially private algorithm for computing a Nash equilibrium in such games. The rates of convergence to equilibrium in all of our results are inverse polynomial in the number of players $n$. We also apply our main results to a multi-dimensional market game. Our results can be viewed as giving, for a rich class of games, a more robust version of the Revelation Principle, in that we work with weaker informational assumptions (no common prior), yet provide a stronger solution concept (ex-post Nash versus Bayes Nash equilibrium). In comparison to previous work, our main conceptual contribution is showing that weak mediators are a game theoretic object that exist in a wide variety of games -- previously, they were only known to exist in traffic routing games.
Search for theta+(1540) in the Reaction K+ p -> K+ n pi+ at 11 GeV/c
J. Napolitano,J. Cummings,M. Witkowski
Physics , 2004,
Abstract: We have studied the reaction K+ p -> K+ n pi+ using an 11 GeV/c K+ beam and the Large Acceptance Superconducting Solenoid (LASS) multiparticle spectrometer facility at SLAC. We put limits on the production of narrow theta+ baryons in this reaction.
Autologous Natural Killer Cell/Natural Killer T Cell Immunotherapy of Malignant Diseases  [PDF]
Aaron J. Smith, John Oertle, Dino Prato
Open Journal of Medical Microbiology (OJMM) , 2014, DOI: 10.4236/ojmm.2014.43021
Abstract: Adoptive immunotherapy, the therapeutic infusion of ex vivo activated cancer-fighting white blood cells that was pioneered by Dr. Steven Rosenberg over 30 years ago, has become more widespread due to outstanding published research documenting the clinical efficacy of this strategy. Based on the well-established in vivo functions of NK and NKT cells, their integral role in the efficacy of certain chemotherapeutic and immunomodulatory agents, and their direct therapeutic action as displayed in clinical trials, the use of autologous natural killer cell infusions is an appropriate and warranted therapeutic option for the treatment of malignant diseases, especially in patients whose disease is refractory to standard treatments such as chemotherapy and radiation.
Immunotherapy in Cancer Treatment  [PDF]
Aaron J. Smith, John Oertle, Dino Prato
Open Journal of Medical Microbiology (OJMM) , 2014, DOI: 10.4236/ojmm.2014.43020
Abstract: Various kinds of immunotherapy treatment for cancer are either available to the public or are in the process of clinical trials. Immunotherapy treatments have the potential to treat cancer with significantly less toxicity than chemotherapy and radiation treatments. An emphasis on cellular infusion as a method of either enhancing the immune system by creating an environment for sequestering the host immune system to attack cancer cells or more directly inserting cells to directly attack cancer cells will be provided in this review. Various forms of cancer vaccines are also discussed in this paper as an important aspect in immunotherapy. This review seeks to describe various methodologies associated with administering immunotherapy in the treatment of cancer.
Cancer and Infectious Causes  [PDF]
Aaron J. Smith, John Oertle, Dino Prato
Open Journal of Medical Microbiology (OJMM) , 2014, DOI: 10.4236/ojmm.2014.43019
Abstract: Various kinds of organisms, including viruses, bacteria, trematodes and fungi are known carcinogens that cause cancer. Infectious identification related to cancer may lead to better treatment for both the prevention and targeting of cancer therapy. Although nearly 20% of all cancers are caused by an infection of a microbe, the amount of evidence and information regarding the mechanisms associated with oncogenesis varies dramatically from one organism to the next. This review cannot be exhaustive because we are not aware of all infections worldwide in addition to their potential mechanisms for oncogenesis. More research is required for all of the species mentioned in this review.
Borrelia burgdorferi: Cell Biology and Clinical Manifestations in Latent Chronic Lyme  [PDF]
Aaron J. Smith, John Oertle, Dino Prato
Open Journal of Medical Microbiology (OJMM) , 2014, DOI: 10.4236/ojmm.2014.44023
Abstract: Chronic Lyme disease is predicated by an infection with Borrelia burgdorferi via tick vector. B. burgdorferi has been extensively researched with regard to its genome and cell biology. There are many unique characteristics to the bacteria itself; however, serological diagnostics and diagnosis based on symptoms can be complicated and potentially misleading. Other promising diagnostics were also evaluated in this review. Treatment of the chronic Lyme disease can be complicated and at times ineffective. The purpose of this review is to examine B. burgdorferi from a biological and clinical perspective.
Chronic Lyme Disease: Persistent Clinical Symptoms Related to Immune Evasion, Antibiotic Resistance and Various Defense Mechanisms of Borrelia burgdorferi  [PDF]
Aaron J. Smith, John Oertle, Dino Prato
Open Journal of Medical Microbiology (OJMM) , 2014, DOI: 10.4236/ojmm.2014.44029
Abstract: There are several factors involved in the ability of Borrelia burgdorferi to retain a persistent infection within a mammalian host. These factors of immune evasion include regulation of membrane proteins, variable epitopes of surface proteins, protection against the immune system through tick saliva, the ability to migrate to regions where it is not exposed to the immune system or antibiotics, invagination or invasion within various cells, pleomorphic forms, and the potential to produce biofilms. The window of conventional treatment for Lyme disease is short and has the potential to display different symptoms depending on the strain of Borrelia bugdorferi. These symptoms are dependent on the localization of Borrelia burgdorferi which correlates to the significance of diagnosing Lyme disease early to prevent such a spread throughout the body. Such complications of Borrelia burgdorferi may demand new clinical treatment discoveries for patient fighting the chronic form.
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