Miracle-dz/UniFAR-FTUs huggingface dataset:
Significance testing for small microarray experiments

Which significance test is carried out when the number of repeats is small in microarray experiments can dramatically influence the results. When in two sample comparisons both conditions have fewer than, say, five repeats traditional test statistics require extreme results, before a gene is considered statistically significant differentially expressed after a multiple comparisons correction. In the literature many approaches to circumvent this problem have been proposed. Some of these proposals use (empirical) Bayes arguments to moderate the variance estimates for individual genes. Other proposals try to stabilize these variance estimate by combining groups of genes or similar experiments. In this paper we compare several of these approaches, both on data sets where both experimental conditions are the same, and thus few statistically significant differentially expressed genes should be identified, and on experiments where both conditions do differ. This allows us to identify which approaches are most powerful without identifying many false positives. We conclude that after balancing the numbers of false positives and true positives an empirical Bayes approach and an approach which combines experiments perform best. Standard t‐tests are inferior and offer almost no power when the sample size is small. Copyright © 2005 John Wiley & Sons, Ltd.
Low load latency through sum-addressed memory (SAM)

Load latency contributes significantly to execution time. Because most cache accesses hit, cache-hit latency becomes an important component of expected load latency. Most modern microprocessors have base+offset addressing loads; thus effective cache-hit latency includes an addition as well as the RAM access. This paper introduces a new technique used in the UltraSPARC III microprocessor Sum-Addressed Memory (SAM), which performs true addition using the decoder of the RAM array, with very low latency. We compare SAM with other methods for reducing the add part of load latency. These methods include sum-prediction with recovery, and bitwise indexing with duplicate-tolerance. The results demonstrate the superior performance of SAM.
Transatlantic transport of pollution and its effects on surface ozone in Europe and North America

[1] We examine the transatlantic transport of anthropogenic ozone and its impact on surface ozone in Europe and North America by using a 5-year (1993–1997) simulation with the GEOS-CHEM global three-dimensional model of tropospheric chemistry. Long-term time series of ozone and CO at Mace Head (Ireland) and Sable Island (Canada) are used to evaluate transatlantic transport in the model. North American anthropogenic emissions contribute on average 5 ppbv to surface ozone at Mace Head, and up to 10–20 ppbv during transatlantic transport events, which are forerunners of broader events in Europe. These events are associated with low-level westerly flow driven by an intense Icelandic low between Iceland and the British Isles. North American influence on ozone at Mace Head is strongly correlated with the North Atlantic Oscillation (NAO), implying that the NAO index can be used to forecast transatlantic transport of North American pollution to Europe. European anthropogenic emissions contribute on average less than 2 ppbv to surface ozone at Sable Island but up to 5–10 ppbv during transatlantic transport events. These events are associated with low-level easterly flow established by anomalous low pressure at 45°N over the North Atlantic. North American anthropogenic emissions enhance surface ozone in continental Europe by 2–4 ppbv on average in summer and by 5–10 ppbv during transatlantic transport events; transport in the boundary layer and subsidence from the free troposphere are both important mechanisms. We find in the model that 20% of the violations of the European Council ozone standard (55 ppbv, 8-hour average) in the summer of 1997 over Europe would not have occurred in the absence of anthropogenic emissions from North America. North American influence on surface ozone in Europe is particularly strong at the thresholds used for the European standards (55–65 ppbv).
Family‐Based Association Tests for Qualitative and Quantitative Traits Using Single‐Nucleotide Polymorphism and Microsatellite Data

Using the Genetic Analysis Workshop 12 simulated data, we contrasted results for association tests in nuclear families and extended pedigrees using single‐nucleotide polymorphism (SNP) data, and we compared results for different trait definitions, for outbred and isolate populations, and for SNP and microsatellite data. SNPs in major genes 1 and 6 were analyzed using transmission disequilibrium testing (TDT) [Spielman et al., Am J Hum Genet 52:506–16, 1993], sibship disequilibrium testing (SDT) [Horvath and Laird, Am J Hum Genet 63:1886–97, 1998], family‐based association testing (FBAT) [Horvath et al., Eur J Hum Genet 9:301–6, 2001], and a chi‐square analysis of founders. TDT and SDT were applied in a sample of independent nuclear families, while FBAT was applied in extended pedigrees. SNPs and microsatellites were analyzed with dichotomous and quantitative trait definitions using FBAT in the isolate and outbred populations. The results of the TDT, SDT, and FBAT analyses are comparable using SNP data to identify the disease gene. However, these tests of association were not helpful in discriminating between functional and non‐functional SNPs in disequilibrium. SNP data were able to identify association with affection status in a gene that influences the liability directly (MG6), but did not perform as well when assessing association with affection status in a gene that influences the outcome only through a quantitative trait (MGI). Association with MGI was observed using the SNP data when the outcome was defined quantitatively. Microsatellite data were relatively unsuccessful in identifying association with the markers in the region of a major gene. The magnitude of the associations between SNPs and the dichotomous or quantitative trait definitions were similar in the outbred and isolated populations. © 2001 Wiley‐Liss, Inc.
Activation of squid axon K+ channels. Ionic and gating current studies

We have used data obtained from measurements of ionic and gating currents to study the process of K+ channel activation in squid giant axons. A marked improvement in the recording of K+ channel gating currents (IKg) was obtained by total replacement of Cl- in the external solution by NO-3, which eliminates approximately 50% of the Na+ channel gating current with no effect on IKg. The midpoint of the steady state charge-voltage (Qrel - V) relationship is approximately 40 mV hyperpolarized to that of the steady state activation (fo - V) curve, which is an indication that the channel has many nonconducting states. Ionic and gating currents have similar time constants for both ON and OFF pulses. This eliminates any Hodgkin-Huxley nx scheme for K+ channel activation. An interrupted pulse paradigm shows that the last step in the activation process is not rate limiting. IKg shows a nonartifactual rising phase, which indicates that the first step is either the slowest step in the activation sequence or is voltage independent. These data are consistent with the following general scheme for K+ channel activation: (formula; see text)
Predicting Influential Cross-lingual Information Cascades on Twitter

Social network services (SNSs) have become new global and multilingual information platforms due to their popularity. In SNSs with content-sharing functionality, such as "retweets'' in Twitter and "share'' in Facebook, posts are easily and quickly shared among users, and some grow into large information cascades. Accompanied with such growth, cascades can spread over regions and languages. The "ALS Ice Bucket Challenge'' is a good example of internationally influential information that are widely spread and internationally reshared. Analyzing and predicting these influential cross-lingual information cascades will help promote culture exchange and detect international news and issues. This type of research can also provide insights into internal and external relationships among countries and languages. Though there has been a large amount of research on information cascades, much has been focused on predicting just their growth, and little has been on cross-region/lingual information cascades. In this work, we aim to build a robust model and detect influential cross-lingual information diffusion on social networks. To the first attempt, we analyze and predict influential cross-lingual information cascades on Twitter. With a large Twitter dataset, we conducted statistical analysis of growth and language distribution of information cascades. Based on the analysis, we propose a feature-based model to detect influential cross-lingual information cascades and successfully predict their size and language distribution. Keyword Information cascades; cross-lingual cascades; cascade growth; multilingualism
Rich Internet Application Testing Using Execution Trace Data

The rapid and growing diffusion of Rich Internet Applications (RIAs) with their enhanced interactivity, responsiveness and dynamicity is sharpening the distance between Web applications and desktop applications, making the Web experience more and more appealing and user-friendly. This paper presents a technique for testing RIAs that generates test cases from application execution traces, and obtains more scalable test suites thanks to testing reduction techniques. Execution traces provide a fast and cheap way for generating test cases and can be obtained either from user sessions, or by crawling the application or by combining both approaches. The proposed technique has been evaluated by a preliminary experiment that investigated the effectiveness of different approaches for execution trace collection and of several criteria for reducing the test suites. The experimental results showed the feasibility of the technique and that its effectiveness can be improved by hybrid approaches that combine both manually and automatically obtained execution traces of the application.
The Role Of Cingulate Cortex In Spatial Learning And Pain Processing

(The Morris Team) for all their dedication to data collection. Another special thanks to the members of the 2006 neuroscience lab members and caretakers. I would also like to thank my mother and father for helping me get here, my children for occupying themselves when need be, and everyone else who helped along the way. I promise to make up for time missed with my family that supported me along this journey. I would also like to thank all the women that have touched my life in such a way that inspired who I am and who I am yet to become.
Comparison of Second-order Polynomial Model Selection Methods: an Experimental Survey

This abstract gives an overview of the work described in (Rumantir 1999). The paper compares some of the most commonly cited model selection criteria that claim to have the mechanism to balance between model complexity and goodness of fit. The model chosen by any of the methods is claimed to be a parsimonious description of the data at hand, therefore has predictive power for future data. This work tests the robustness of each method in support of the above claim in performing two tasks. First, to recover models from artificial data generated from known true models. Second, to parsimoniously select models from real data for the purpose of forecasting hurricane intensity change. The models selected are then compared with the benchmark models being used in operation. In addition to polynomials with single independent variables, the products of variables up to the second order are also considered. A method based on the Minimum Message Length (MML) principle has been formulated and is compared with the methods found in the literature. A common gradient descent search strategy has been developed and is used with all of the model selection criteria. The summary of the methods examined is given in the table below.
Journal of Graph Algorithms and Applications Np-completeness of the Planar Separator Problems

For a given graph G, the Separator Problem asks whether a vertex or edge set of small cardinality (or weight) exists whose removal partitions G into two disjoint graphs of approximately equal sizes. Called the Vertex Separator Problem when the removed set is a vertex set, and the Edge Separator Problem when it is an edge set, both problems are NP-complete for general unweighted graphs [6]. Despite the significance of planar graphs, it has not been known whether the Planar Separator Problem, which considers a planar graph and a threshold as an input, is NP-complete or not. In this paper, we prove that the Vertex Separator Problem is in fact NP-complete when G is a vertex weighted planar graph. The Edge Sep-arator Problem will be shown NP-complete when G is a vertex and edge weighted planar graph. In addition, we consider how to treat the constant α ∈ R + of the α-Separator Problem that partitions G into two disjoint graphs of size at most (1 − α) |V (G)|. The α-Separator Problem is not NP-complete for all real numbers α ∈ (0, 1/2], because it would imply uncountably many Non Deterministic Turing Machines. We will present a general scheme for treating a constant in computer arithmetic, by introducing the notion of real numbers comparable with rationals in polynomial time. This approach allows us to prove NP-completeness for each such real number α.
Mapping natura 2000 heathland in Belgium - an evaluation of ensemble classifiers for spaceborne angular CHRIS/Proba imagery

Natura 2000 is an ecological network of protected areas in the territory of the European Union (EU). With the introduction of the Habitats Directive in 1992, EU member states are obligated to report every six years the status of the Natura 2000 habitats so that better conservation policy can be formulated. This paper examines the use of angular hyperspectral CHRIS/Proba image for the mapping of heathland at a Belgian Natura 2000 site. We find that the use of angular images increases the overall classification rate as compared to using only the nadir image; with the incorporation of angular images the final mapping is also more homogenous with less salt and pepper effect. While the class accuracy of Calluna- and Erica-dominated heathlands are still low, class accuracy of Molinia-dominated heathland is generally more encouraging. Two tree-based ensemble classifiers, Random Forest (RF) and Adaboost, were compared with Support Vector Machines (SVM). When only the nadir image was used, SVM attained the highest accuracy. When angular images were included, all three classifiers obtained comparable accuracies though in general RF and Adaboost had faster training time. We also adopted an assessment approach which repeats the accuracy assessment in ten independent trials, instead of the common practice of having only one trial. Our results show that accuracy attainment can vary significantly among different trials and hence it is recommendable to have more than one trial in order that a more objective characterization of the classifiers is obtained. 1
Assessing Sale Strategies in Online Markets Using Matched Listings

We use data from eBay to identify hundreds of thousands of instances in which retailers posted otherwise identical product listings with targeted variation in pricing and auction design. We use these matched listings to measure the dispersion in auction prices for identical goods sold by the same seller, to estimate nonparametric auction demand curves, to analyze the effect of buy it now options, and to assess consumer sensitivity to shipping fees. The scale of the data allows us to show that the estimates are robust to narrower criteria for matching listings, thereby addressing plausible concerns about endogeneity and selection biases. (JEL D44, L11, L81)
The role of Greece as the gatekeeper of Fortress Europe

This thesis aims to explore the different aspects of the phenomenon of migration in Greece, as a case study. The choice of country is motivated by its geographical position at Europe’s external borders. In order to gain an insight into the reality that migrants are faced with when searching for a better life in Europe, a field study was conducted in Athens, Greece during a period of six weeks in the spring of 2010. The field work included interviews with various actors and individuals that are directly involved in migration issues, informal discussions with migrants and personal observations. Additionally, secondary sources such as previous studies were used. The framework used to approach the material included elements from neoinstitutionalism, hermeneutics as well as critical theory. The most important conclusions reached incorporate that the rights of migrants are not respected in any aspect of the societal sphere, or in other words the three institutional pillars, the regulative, normative and cultural-cognitive. As a result, there are double standards applied to Europeans respective migrants. As a possible cause of the problematic situation described, underlying perceptions of national identity versus “otherness” are identified. These perceptions derive from a deeply rooted acceptance of social constructions such as national borders, as undisputable facts.
Justifiable Arrests or Discretionary Justice

The U.S. legal machinerysupposedly operates under the funda mental principle of impartial justice; however, legal sanctioning seems to contradict the notion of equality before the law. The American criminal justice system is based on an interdependent relationship between impartial laws and culturally influenced legal agents; therefore, the legal process may reflect the prevailing social structure of America, and the meaning of justice may depend on the social, economic, and cultural characteristics of the groups involved (Arrigo, 1999; Hagan, 1994). One of the more important and seemingly unsettled questions concerning the criminal justice system is whether the disproportionately high number of Blacks (compared to Whites) being processed through the system is the result of justifiable sanctions or discriminatory discretionary practices (Walker, Spohn, & Delone, 1996). Because the criminal justice system represents the state’s institu tionalized legal agent of social control, it is necessary to offer some brief theoretical discourse concerning the nature of social order. In simplest form, consensus theory postulates that equality is a funda mental value and that sanctions are imposed more or less objec tively on individuals who commit behavior that runs contrary to society’s collective conscience. It logically follows that sanctions will be applied to behavior without regard to demographic and social factors. The research indicating that criminal conduct and seriousness of offense are stronger predictors (than social, eco nomic, cultural, or demographic variables) of Black to White arrest
Evolution of acoustic and visual signals in Asian barbets

The study of animal communication systems is an important step towards gaining greater understanding of the processes influencing diversification because signals often play an important role in mate choice and can lead to reproductive isolation. Signal evolution can be influenced by a diversity of factors such as biophysical constraints on the emitter, the signalling environment, or selection to avoid heterospecific matings. Furthermore, because signals can be costly to produce, trade‐offs may exist between different types of signals. Here, we apply phylogenetic comparative analyses to study the evolution of acoustic and visual signals in Asian barbets, a clade of non‐Passerine, forest‐dependent birds. Our results suggest that evolution of acoustic and visual signals in barbets is influenced by diverse factors, such as morphology and signalling environment, suggesting a potential effect of sensory drive. We found no trade‐offs between visual and acoustic signals. Quite to the contrary, more colourful species sing significantly longer songs. Song characteristics presented distinct patterns of evolution. Song frequency diverged early on and the rate of evolution of this trait appears to be constrained by body size. On the other hand, characteristics associated with length of the song presented evidence for more recent divergence. Finally, our results indicate that there is a spatial component to the evolution of visual signals, and that visual signals are more divergent between closely related taxa than acoustic signals. Hence, visual signals in these species could play a role in speciation or reinforcement of reproductive isolation following secondary contacts.
The DELLA Domain of GA INSENSITIVE Mediates the Interaction with the GA INSENSITIVE DWARF1A Gibberellin Receptor of Arabidopsis[W]

Gibberellic acid (GA) promotes seed germination, elongation growth, and flowering time in plants. GA responses are repressed by DELLA proteins, which contain an N-terminal DELLA domain essential for GA-dependent proteasomal degradation of DELLA repressors. Mutations of or within the DELLA domain of DELLA repressors have been described for species including Arabidopsis thaliana, wheat (Triticum aestivum), maize (Zea mays), and barley (Hordeum vulgare), and we show that these mutations confer GA insensitivity when introduced into the Arabidopsis GA INSENSITIVE (GAI) DELLA repressor. We also demonstrate that Arabidopsis mutants lacking the three GA INSENSITIVE DWARF1 (GID1) GA receptor genes are GA insensitive with respect to GA-promoted growth responses, GA-promoted DELLA repressor degradation, and GA-regulated gene expression. Our genetic interaction studies indicate that GAI and its close homolog REPRESSOR OF ga1-3 are the major growth repressors in a GA receptor mutant background. We further demonstrate that the GA insensitivity of the GAI DELLA domain mutants is explained in all cases by the inability of the mutant proteins to interact with the GID1A GA receptor. Since we found that the GAI DELLA domain alone can mediate GA-dependent GID1A interactions, we propose that the DELLA domain functions as a receiver domain for activated GA receptors.
A Sound Idea: A Theory-Based Synthesis and Explanadum Supporting the Use of Music in Marketing Strategy

A review and synthesis of research literature regarding the role and influence of music on advertising effectiveness and in-store shopper moods and behavior is presented. A conceptual model is presented, with strong theoretical support found in classical conditioning, information processing, involvement, and mood states literature. The authors posit that a retailer should use a dual, concomitant music strategy as a component of an overall advertising and in-store marketing promotion plan. This strategy is presented in what the authors refer to as the Music Affect Model. While using the positive effects of music on consumer purchasing behavior as its core source of potency, the proposed strategy should likely lead to enhanced sales outcomes.
Testing Robustness of Real Time Embedded Systems

Embedded systems are constrained and critical. They need to be validated before their development. They handle time constraints to model important aspects (delays, timeouts). This issue has to be taken into account in every step during its development life cycle, in particular in the testing step. This paper presents a methodology for the development of reliable embedded systems. A system is described as a timed automaton. Since these systems have often to work in an hostile environment, they need to be able to react in presence of unexpected events, that is why the robustness testing issue has to be seriously considered. Key-words : Embedded Systems, Validation, Timed Automata, Robustness Testing.