Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple Mobile Promoter Regions for the Rare Carbapenem Resistance Gene of Bacteroides fragilis

ABSTRACT Two novel insertion sequences (IS), IS1187 and IS1188, are described upstream from the carbapenem resistance gene cfiA in strains of Bacteroides fragilis. Mapping, with the RACE procedure, of transcription start sites of cfiA in these and two other previously reported IS showed that transcription of this rarely encountered gene is initiated close to a variety of B. fragilis consensus promoter sequences, as recently defined (D. P. Bayley, E. R. Rocha, and C. J. Smith, FEMS Microbiol. Lett. 193:149–154, 2000). In the cases of IS1186 and IS1188, these sequences overlap with putative Eς70 promoter sequences, while in IS942 and IS1187 such sequences can be observed either upstream or downstream of the B. fragilispromoters.
Gravitational-Wave Limits from Pulsar Timing Constrain Supermassive Black Hole Evolution

Testing Black Holes Gravitational waves, predicted by General Relativity, are expected to be produced when very massive bodies, such as black holes, merge together. Shannon et al. (p. 334) used data from the Parkes Pulsar Timing Array project to estimate the gravitational wave background produced by pairs of supermassive black holes (those with masses between 106 and 1011 that of the Sun) in merging galaxies. The results can be used to test models of the supermassive black hole population. Analysis of pulsar timing data sets constraints on the gravitational-wave background produced by pairs of massive black holes. The formation and growth processes of supermassive black holes (SMBHs) are not well constrained. SMBH population models, however, provide specific predictions for the properties of the gravitational-wave background (GWB) from binary SMBHs in merging galaxies throughout the universe. Using observations from the Parkes Pulsar Timing Array, we constrain the fractional GWB energy density (ΩGW) with 95% confidence to be ΩGW(H0/73 kilometers per second per megaparsec)2 < 1.3 × 10−9 (where H0 is the Hubble constant) at a frequency of 2.8 nanohertz, which is approximately a factor of 6 more stringent than previous limits. We compare our limit to models of the SMBH population and find inconsistencies at confidence levels between 46 and 91%. For example, the standard galaxy formation model implemented in the Millennium Simulation Project is inconsistent with our limit with 50% probability.
Towards lenses for view synchronization in metamodel-based domain- specific workbenches

Model-driven engineering (MDE) advocates the use of different domainspecific languages (DSLs) for describing different aspects of a system, which is called multi-view modeling or multimodeling. Existing metamodel-based technologies like Xtext provide good support for defining a DSL and for creating a corresponding domainspecific workbench but do not support multimodeling, yet, i.e., they do not provide means to specify (non-bijective) relations between DSLs, so that models that are created using these DSLs are synchronized automatically. We present an approach to model synchronization that is based on asymmetric bidirectional transformations. Therefore, we implement lenses – a term-rewriting-based approach to bidirectional transformations – as an internal DSL in the Scala programming language and use lenses for model transformations. This way, our approach does not depend on special tool support and allows for seamless integration with Java-based MDE technologies.
Cole: compiler optimization level exploration

Modern compilers implement a large number of optimizations which all interact in complex ways, and which all have a different impact on code quality, compilation time, code size, energy consumption, etc. For this reason, compilers typically provide a limited number of standard optimization levels, such as -O1, -O2, -O3 and -Os, that combine various optimizations providing a number of trade-offs between multiple objective functions (such as code quality, compilation time and code size). The construction of these optimization levels, i.e., choosing which optimizations to activate at each level, is a manual process typically done using high-level heuristics based on the compiler developer's experience. This paper proposes COLE, Compiler Optimization Level Exploration, a framework for automatically finding Pareto optimal optimization levels through multi-objective evolutionary searching. Our experimental results using GCC and the SPEC CPU benchmarks show that the automatic construction of optimization levels is feasible in practice, and in addition, yields better optimization levels than GCC's manually derived (-Os, -O1, -O2 and -O3) optimization levels, as well as the optimization levels obtained through random sampling. We also demonstrate that COLE can be used to gain insight into the effectiveness of compiler optimizations as well as to better understand a benchmark's sensitivity to compiler optimizations.
Ultrasonic propagation of a metallic domain in Pr0.5Ca0.5CoO3 undergoing a photoinduced insulator-metal transition.

Femtosecond optical response was investigated on a perovskite-type cobalt oxide, Pr0.5Ca0. 5CoO3 during an insulator-metal (I-M) transition accompanied with the change in spin configuration. After photoirradiation at 30 K, the reflectivity showed a sudden and large increase with subsequent variation depending on the observed photon energy. An exact calculation of Maxwell's equations for the Pr0.5Ca0. 5CoO3 after the photoirradiation enabled us to observe the ultrafast dynamics of I-M phase transition and the motion of the photonically created metallic domain at the velocity of ultrasonic wave.
Ethnic Minority-Majority Status and Mental Health: The Mediating Role of Perceived Discrimination

This study examines the role of perceived discrimination as a mediator of the relationship between ethnic minority-majority status and mental health in a sample of college students, of whom 246 were members of an ethnic minority (African American, Latino American, or Asian American) and 167 were European Americans. Ethnic minority students were significantly higher in perceived discrimination and significantly lower in mental health. African Americans were most likely to perceive racial discrimination, followed by Latino Americans, Asian Americans, and European Americans. Asian Americans reported the poorest mental health. Results of mediational analyses by ethnic status (minorities and majority) and across ethnic group pairings (Americans and European Americans, Latino Americans and European Americans, Asian Americans and European Americans) confirmed in every instance that perceived discrimination accounts for a modest part of the relationship between ethnic minority-majority status and mental health. W.
Language adaptation of multilingual phone models for vocabulary independent speech recognition tasks

This paper presents our new results on multilingual phone modeling and adaptation into a new target language which is not included in the trained multilingual models. The experiments were carried out with the SpeechDat(M) and MacroPhone databases including the languages of French, German, Italian, Portuguese, Spanish and American English. First, we constructed language-dependent and multilingual phone models. The recognition rate for an isolated word task decreased in average only by 3.2% using 95 multilingual instead of 232 language-dependent models. Second, we investigated adaptation techniques for cross-language transfer and showed that only 100 utterances from a new language were needed for adaptation. Using the MAP algorithm the recognition rate was improved from 79.9% to 84.3%. Finally, we defined a phonetic based dissimilarity measure between 2 languages and compared language-dependent and multilingual models for the purpose of cross-language transfer.
Interpersonal trust and common ground in electronically mediated communication

Communication and commerce by web or phone creates benefits and challenges for both buyer and seller. Websites provide convenience and visualization; telephones provide voice and real-time interaction. To combine key elements of these experiences, we developed PhoneChannel. Using PhoneChannel, a PC user while talking on the telephone can display visuals on the other person's television. How do these different media affect the consumer experience? In a recent laboratory study, prospective homebuyers selected houses of interest using web, telephone, or PhoneChannel. Using the telephone or PhoneChannel led to higher trust; but using web or PhoneChannel led to higher ratings on convenience, enjoyment, and 'good method' scales.
Campylobacter jejuni Colonization in Wild Birds: Results from an Infection Experiment

Campylobacter jejuni is a common cause of bacterial gastroenteritis in most parts of the world. The bacterium has a broad host range and has been isolated from many animals and environments. To investigate shedding patterns and putative effects on an avian host, we developed a colonization model in which a wild bird species, the European Robin Erithacus rubecula, was inoculated orally with C. jejuni from either a human patient or from another wild bird species, the Song Thrush Turdus philomelos. These two isolates were genetically distinct from each other and provoked very different host responses. The Song Thrush isolate colonized all challenged birds and colonization lasted 6.8 days on average. Birds infected with this isolate also showed a transient but significant decrease in body mass. The human isolate did not colonize the birds and could be detected only in the feces of the birds shortly after inoculation. European Robins infected with the wild bird isolate generated a specific antibody response to C. jejuni membrane proteins from the avian isolate, which also was cross-reactive to membrane proteins of the human isolate. In contrast, European Robins infected with the human isolate did not mount a significant response to bacterial membrane proteins from either of the two isolates. The difference in colonization ability could indicate host adaptations.
Class-based speech recognition using a maximum dissimilarity criterion and a tolerance classification margin

One of the difficult problems of Automatic Speech Recognition (ASR) is dealing with the acoustic signal variability. Much state-of-the-art research has demonstrated that splitting data into classes and using a model specific to each class provides better results. However, when the dataset is not large enough and the number of classes increases, there is less data for adapting the class models and the performance degrades. This work extends and combines previous research on un-supervised splits of datasets to build maximally separated classes and the introduction of a tolerance classification margin for a better training of the class model parameters. Experiments, carried out on the French radio broadcast ESTER2 data, show an improvement in recognition results compared to the ones obtained previously. Finally, we demonstrate that combining the decoding results from different class models leads to even more significant improvements.
Cyanogenic Pseudomonads Influence Multitrophic Interactions in the Rhizosphere

In the rhizosphere, plant roots cope with both pathogenic and beneficial bacterial interactions. The exometabolite production in certain bacterial species may regulate root growth and other root-microbe interactions in the rhizosphere. Here, we elucidated the role of cyanide production in pseudomonad virulence affecting plant root growth and other rhizospheric processes. Exposure of Arabidopsis thaliana Col-0 seedlings to both direct (with KCN) and indirect forms of cyanide from different pseudomonad strains caused significant inhibition of primary root growth. Further, we report that this growth inhibition was caused by the suppression of an auxin responsive gene, specifically at the root tip region by pseudomonad cyanogenesis. Additionally, pseudomonad cyanogenesis also affected other beneficial rhizospheric processes such as Bacillus subtilis colonization by biofilm formation on A. thaliana Col-0 roots. The effect of cyanogenesis on B. subtilis biofilm formation was further established by the down regulation of important B. subtilis biofilm operons epsA and yqxM. Our results show, the functional significance of pseudomonad cyanogenesis in regulating multitrophic rhizospheric interactions.
Sampling and Updating Higher Order Beliefs in Decision-theoretic Bargaining with Finite Interactive Epistemologies

In this paper we study the sequential strategic interactive setting of bilateral, two-stage, seller-offers bargaining under uncertainty. We model the epistemology of the problem in a finite interactive decision-theoretic framework and solve it for three types of agents of successively increasing (epistemological) sophistication (i.e. capacity to represent and reason with higher orders of beliefs). We relax typical common knowledge assumptions, which, if made, would be sufficient to imply the existence of a, possibly unique, game-theoretic equilibrium solution. We observe and characterize a systematic monotonic relationship between an agent’s beliefs and optimal behavior under a particular moment-based ordering of its beliefs. Based on this characterization, we present the spread-accumulatetechnique of sampling an agent’s higher order belief by generating “evenly dispersed” beliefs for which we (pre)compute offline solutions. Higher order prior belief identification is then approximated to arbitrary precision by identifying a (previously solved) belief “closest” to the true belief. These methods immediately suggest a mechanism for achieving a balance between efficiency and the quality of the approximation – either by generating a large number of offline solutions or by allowing the agent to search online for a “closer” belief in the vicinity of best current solution.
Self-Defeating Personality and Strategies for Coping with Stress

People who scored higher on a measure of self-defeating personality also scored low on ego-strength, showed an external locus of control, and used less adaptive coping strategies than those who scored lower. These strategies (denial, mental disengagement, alcohol and drug use) were viewed as helping to perpetuate their positions as victims.
Automatic registration of microarray images. I. Rectangular grid

MOTIVATION The analysis of high-throughput experiment data provided by microarrays becomes increasingly more and more important part of modern biological science. Microarrays allow to conduct genotyping or gene expression experiments on hundreds of thousands of test genes in parallel. Because of the large and constantly growing amount of experimental data the necessity of efficiency, robustness and complete automation of microarray image analysis algorithms is gaining significant attention in the field of microarray processing. RESULTS The author presents here an efficient and completely automatic image registration algorithm (that is an algorithm for spots and blocks indexing) that allows to process a wide variety of microarray slides with different parameters of grid and block spacing as well as spot sizes. The algorithm scales linearly with the grid size, the time complexity is O(M), where M is number of rows x number of columns. It can successfully cope with local and global distortions of the grid, such as focal distortions and non-orthogonal transformations. The algorithm has been tested both on CCD and scanned images and showed very good performance-the processing time of a single slide with 44 blocks of 200 x 200 grid points (or 1 760 000 grid points total) was about 10 s. AVAILABILITY The test implementation of the algorithm will be available upon request for academics. SUPPLEMENTARY INFORMATION http://fleece.ucsd. edu/~vit/Registration_Supplement. pdf
EEG signal classification for real-time brain-computer interface applications: A review

Brain-computer interface (BCI) is linking the brain activity to computer, which allows a person to control devices directly with his brain waves and without any use of his muscles. Recent advances in real-time signal processing have made BCI a feasible alternative for controlling robot and for communication as well. Controlling devices using BCI is a crucial aid for people suffering from severe disabilities and more than that, BCIs can replace human to control robots working in dangerous or uncongenial situations. Effective BCIs demand for accurate and real-time EEG signals processing. This paper is to review the current state of research and to compare the performance of different algorithms for real-time classification of BCI-based electroencephalogram signals.
Rho GTPase activity zones and transient contractile arrays

The Rho GTPases—Rho, Rac and Cdc42—act as molecular switches, cycling between an active GTP‐bound state and an inactive GDP‐bound state, to regulate the actin cytoskeleton. It has recently become apparent that the Rho GTPases can be activated in subcellular zones that appear semi‐stable, yet are dynamically maintained. These Rho GTPase activity zones are associated with a variety of fundamental biological processes including symmetric and asymmetric cytokinesis and cellular wound repair. Here we review the basic features of Rho GTPase activity zones, suggest that these zones represent a fundamental signaling mechanism, and discuss the implications of zone properties from the perspective of both their function and how they are likely to be controlled. BioEssays 28: 983–993, 2006. © 2006 Wiley Periodicals, Inc.
Oxidative Stress–Mediated Thrombospondin-2 Upregulation Impairs Bone Marrow–Derived Angiogenic Cell Function in Diabetes Mellitus

Objective—Circulating angiogenic cells play an essential role in angiogenesis but are dysfunctional in diabetes mellitus characterized by excessive oxidative stress. We hypothesize that oxidative stress–mediated upregulation of thrombospondin-2 (TSP-2), a potent antiangiogenic protein, contributes to diabetic bone marrow–derived angiogenic cell (BMAC) dysfunction. Approach and Results—BMACs were isolated from adult male type 2 diabetic db/db mice and control db/+ (C57BLKS/J) mice. In Matrigel tube formation assay, angiogenic function was impaired in diabetic BMACs, accompanied by increased oxidative stress and nicotinamide adenine dinucleotide phosphate oxidase activity. BMAC angiogenic function was restored by overexpression of dominant negative Rac1 or by overexpression of manganese superoxide dismutase. TSP-2 mRNA and protein were both significantly upregulated in diabetic BMACs, mediated by increased oxidative stress as shown by a decrease in TSP-2 level after overexpression of dominant negative Rac1 or manganese superoxide dismutase. Silencing TSP-2 by its small interfering RNA in diabetic BMACs improved BMAC function in tube formation, adhesion, and migration assays. Notably, the upregulation of TSP-2 was also found in BMACs from streptozotocin-induced type 1 diabetic mice, and normal BMACs with high glucose treatment. let-7f, a microRNA which has been related to endothelial angiogenic function, is found to play key role in TSP-2 increase, but let-7f did not directly interact with TSP-2 mRNA. Conclusions—The upregulation of TSP-2 mediated by increased oxidative stress contributes to angiogenesis dysfunction in diabetic BMACs.
Quantitative Evaluation of User Simulation Techniques for Spoken Dialogue Systems

The lack of suitable training and testing data is currently a major roadblock in applying machine-learning techniques to dialogue management. Stochastic modelling of real users has been suggested as a solution to this problem, but to date few of the proposed models have been quantitatively evaluated on real data. In-deed, there are no established criteria for such an evaluation. This paper presents a systematic approach to testing user simulations and assesses the most prominent domain-independent techniques using a large DARPA Communica-tor corpus of human-computer dialogues. We show that while recent advances have led to signi(cid:2)cant improvements in simulation quality, simple statistical metrics are still suf(cid:2)cient to discern synthetic from real dialogues.
The Asymmetric Effects of Changes in Price and Income on Energy and Oil Demand

This paper estimates the effects on energy and oil demand of changes in income and oil prices, for 96 of the world’s largest countries, in per-capita terms. We examine three important issues: the asymmetric effects on demand of increases and decreases in oil prices; the asymmetric effects on demand of increases and decreases in income; and the different speeds of demand adjustment to changes in price and in income. Our main conclusions are the following: (1) OECD demand responds much more to increases in oil prices than to decreases; ignoring this asymmetric price response will bias downward the estimated response to income changes; (2) demand’s response to income decreases in many Non-OECD countries is not necessarily symmetric to its response to income increases; ignoring this asymmetric income response will bias the estimated response to income changes; (3) the speed of demand adjustment is faster to changes in income than to changes in price; ignoring this difference will bias upward the estimated response to income changes. Using correctly specified equations for energy and oil demand, the long-run response in demand for income growth is about 1.0 for Non-OECD Oil Exporters, Income Growers and perhaps all Non-OECD countries, and about 0.55 for OECD countries. These estimates for developing countries are significantly higher than current estimates used by the US Department of Energy. Our estimates for the OECD countries are also higher than those estimated recently by Schmalensee-Stoker-Judson (1998) and Holtz-Eakin and Selden (1995), who ignore the (asymmetric) effects of prices on demand. Higher responses to income changes, of course, will increase projections of energy and oil demand, and of carbon dioxide emissions.
Logical foundations of object-oriented and frame-based languages

We propose a novel formalism, called Frame Logic (abbr., F-logic), that accounts in a clean and declarative fashion for most of the structural aspects of object-oriented and frame-based languages. These features include object identity, complex objects, inheritance, polymorphic types, query methods, encapsulation, and others. In a sense, F-logic stands in the same relationship to the object-oriented paradigm as classical predicate calculus stands to relational programming. F-logic has a model-theoretic semantics and a sound and complete resolution-based proof theory. A small number of fundamental concepts that come from object-oriented programming have direct representation in F-logic; other, secondary aspects of this paradigm are easily modeled as well. The paper also discusses semantic issues pertaining to programming with a deductive object-oriented language based on a subset of F-logic.