GSearcher: Agile Attribute Querying for Biological Networks

Summary: GSearcher provides a highly interactive user experience in navigating attribute data associated with large and complex biological networks. The user may either perform a quick search using keywords, phrases or regular expressions, or build a complex query with a group of filters for efficient and flexible exploration of large datasets

Needs for an Expanded Ontology‐Based Classification of Adverse Drug Reactions and Related Mechanisms

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110048/1/cptclpt201241.pd

Cross-domain neurobiology data integration and exploration

<p>Abstract</p> <p>Background</p> <p>Understanding the biomedical implications of data from high throughput experiments requires solutions for effective cross-scale and cross-domain data exploration. However, existing solutions do not provide sufficient support for linking molecular level data to neuroanatomical structures, which is critical for understanding high level neurobiological functions.</p> <p>Results</p> <p>Our work integrates molecular level data with high level biological functions and we present results using anatomical structure as a scaffold. Our solution also allows the sharing of intermediate data exploration results with other web applications, greatly increasing the power of cross-domain data exploration and mining.</p> <p>Conclusions</p> <p>The Flex-based PubAnatomy web application we developed enables highly interactive visual exploration of literature and experimental data for understanding the relationships between molecular level changes, pathways, brain circuits and pathophysiological processes. The prototype of PubAnatomy is freely accessible at:[<url>http://brainarray.mbni.med.umich.edu/Brainarray/prototype/PubAnatomy</url>]</p

Ground-layer wavefront reconstruction from multiple natural guide stars

Observational tests of ground layer wavefront recovery have been made in open loop using a constellation of four natural guide stars at the 1.55 m Kuiper telescope in Arizona. Such tests explore the effectiveness of wide-field seeing improvement by correction of low-lying atmospheric turbulence with ground-layer adaptive optics (GLAO). The wavefronts from the four stars were measured simultaneously on a Shack-Hartmann wavefront sensor (WFS). The WFS placed a 5 x 5 array of square subapertures across the pupil of the telescope, allowing for wavefront reconstruction up to the fifth radial Zernike order. We find that the wavefront aberration in each star can be roughly halved by subtracting the average of the wavefronts from the other three stars. Wavefront correction on this basis leads to a reduction in width of the seeing-limited stellar image by up to a factor of 3, with image sharpening effective from the visible to near infrared wavelengths over a field of at least 2 arc minutes. We conclude that GLAO correction will be a valuable tool that can increase resolution and spectrographic throughput across a broad range of seeing-limited observations.Comment: 25 pages, 8 figures, to be published in Astrophys.

Combined MASS-DIMM instrument for atmospheric turbulence studies

Several site-testing programs and observatories currently use combined MASS-DIMM instruments for monitoring parameters of optical turbulence. The instrument is described here. After a short recall of the measured quantities and operational principles, the optics and electronics of MASS-DIMM, interfacing to telescopes and detectors, and operation are covered in some detail. Particular attention is given to the correct measurement and control of instrumental parameters to ensure valid and well-calibrated data, to the data quality and filtering. Examples of MASS-DIMM data are given, followed by the list of present and future applications.Comment: Accepted by MNRAS, 11 pages, 8 figure

Ultimate Heat Sink Thermal Performance and Water Utilization: Measurements on Cooling and Spray Ponds

A data acquisition research program, entitled &quot;Ultimate Heat Sink Performance Field Experiments,&quot; has been brought to completion. The primary objective is to obtain the requisite data to characterize thermal performance and water utilization for cooling ponds and spray ponds at elevated temperature. Such data are useful for modeling purposes, but the work reported here does not contain modeling efforts within its scope. The water bodies which have been studied are indicative of nuclear reactor ultimate heat sinks, components of emergency core cooling systems. The data reflect thermal performance and water utilization for meteorological and solar influences which are representative of worst-case combinations of conditions. Constructed water retention ponds, provided with absolute seals against seepage, have been chosen as facilities for the measurement programs; the first pond was located at Raft River, Idaho, and the second at East Mesa, California. The data illustrate and describe, for both cooling ponds and spray ponds, thermal performance and water utilization as the ponds cool from an initially elevated temperature. To obtain the initial elevated temperature, it has been convenient to conduct the measurements at geothermal sites having large supplies and delivery rates of hot geothermal fluid. The data are described and discussed in the text, and presented in the form of data volumes as appendices

GSP with General Independent Click-Through-Rates

The popular generalized second price (GSP) auction for sponsored search is built upon a separable model of click-through-rates that decomposes the likelihood of a click into the product of a "slot effect" and an "advertiser effect" --- if the first slot is twice as good as the second for some bidder, then it is twice as good for everyone. Though appealing in its simplicity, this model is quite suspect in practice. A wide variety of factors including externalities and budgets have been studied that can and do cause it to be violated. In this paper we adopt a view of GSP as an iterated second price auction (see, e.g., Milgrom 2010) and study how the most basic violation of separability --- position dependent, arbitrary public click-through-rates that do not decompose --- affects results from the foundational analysis of GSP (Varian 2007, Edelman et al. 2007). For the two-slot setting we prove that for arbitrary click-through-rates, for arbitrary bidder values, an efficient pure-strategy equilibrium always exists; however, without separability there always exist values such that the VCG outcome and payments cannot be realized by any bids, in equilibrium or otherwise. The separability assumption is therefore necessary in the two-slot case to match the payments of VCG but not for efficiency. We moreover show that without separability, generic existence of efficient equilibria is sensitive to the choice of tie-breaking rule, and when there are more than two slots, no (bid-independent) tie-breaking rule yields the positive result. In light of this we suggest alternative mechanisms that trade the simplicity of GSP for better equilibrium properties when there are three or more slots

Comparison of machine learning algorithms in restaurant revenue prediction

In this paper, we address several aspects of applying classical machine learning algorithms to a regression problem. We compare the predictive power to validate our approach on a data about revenue of a large Russian restaurant chain. We pay special attention to solve two problems: data heterogeneity and a high number of correlated features. We describe methods for considering heterogeneity—observations weighting and estimating models on subsamples. We define a weighting function via Mahalanobis distance in the space of features and show its predictive properties on following methods: ordinary least squares regression, elastic net, support vector regression, and random forest.</p

Risk factors for delay in symptomatic presentation: a survey of cancer patients

Background: Delay in symptomatic presentation leading to advanced stage at diagnosis may contribute to poor cancer survival. To inform public health approaches to promoting early symptomatic presentation, we aimed to identify risk factors for delay in presentation across several cancers. Methods: We surveyed 2371 patients with 15 cancers about nature and duration of symptoms using a postal questionnaire. We calculated relative risks for delay in presentation (time from symptom onset to first presentation >3 months) by cancer, symptoms leading to diagnosis and reasons for putting off going to the doctor, controlling for age, sex and deprivation group. Results: Among 1999 cancer patients reporting symptoms, 21% delayed presentation for >3 months. Delay was associated with greater socioeconomic deprivation but not age or sex. Patients with prostate (44%) and rectal cancer (37%) were most likely to delay and patients with breast cancer least likely to delay (8%). Urinary difficulties, change of bowel habit, systemic symptoms (fatigue, weight loss and loss of appetite) and skin symptoms were all common and associated with delay. Overall, patients with bleeding symptoms were no more likely to delay presentation than patients who did not have bleeding symptoms. However, within the group of patients with bleeding symptoms, there were significant differences in risk of delay by source of bleeding: 35% of patients with rectal bleeding delayed presentation, but only 9% of patients with urinary bleeding. A lump was a common symptom but not associated with delay in presentation. Twenty-eight percent had not recognised their symptoms as serious and this was associated with a doubling in risk of delay. Embarrassment, worry about what the doctor might find, being too busy to go to the doctor and worry about wasting the doctor’s time were also strong risk factors for delay, but were much less commonly reported (<6%). Interpretation: Approaches to promote early presentation should aim to increase awareness of the significance of cancer symptoms and should be designed to work for people of the lowest socioeconomic status. In particular, awareness that rectal bleeding is a possible symptom of cancer should be raised

Increasing Dominance - the Role of Advertising, Pricing and Product Design

Despite the empirical relevance of advertising strategies in concentrated markets, the economics literature is largely silent on the effect of persuasive advertising strategies on pricing, market structure and increasing (or decreasing) dominance. In a simple model of persuasive advertising and pricing with differentiated goods, we analyze the interdependencies between ex-ante asymmetries in consumer appeal, advertising and prices. Products with larger initial appeal to consumers will be advertised more heavily but priced at a higher level - that is, advertising and price discounts are strategic substitutes for products with asymmetric initial appeal. We find that the escalating effect of advertising dominates the moderating effect of pricing so that post-competition market shares are more asymmetric than pre-competition differences in consumer appeal. We further find that collusive advertising (but competitive pricing) generates the same market outcomes, and that network effects lead to even more extreme market outcomes, both directly and via the effect on advertising