Miracle-dz/UniFAR-FTUs huggingface dataset:
IDENTIFICATION OF HMG-CoA REDUCTASE INHIBITORS AS ACTIVATORS FOR HUMAN, MOUSE AND RAT CONSTITUTIVE ANDROSTANE RECEPTOR

Constitutive active (or androstane) receptor (CAR, NR1I3), a member of the nuclear receptor family, is a major regulator for induction of cytochrome P450 2B (CYP2B) genes by phenobarbital. Phenobarbital-like inducer, 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene is a potent mouse CAR ligand that has been used to study CAR target genes in mice but does not activate human CAR (hCAR) or rat CAR (rCAR). Although 6-(4-chlorophenyl) imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime (CITCO) was reported to be an hCAR agonistic ligand, activation of hCAR by CITCO in cell-based reporter assay was weak. Therefore, we performed a screening of 50 drugs and chemicals using cell-based reporter assays to identify activators of hCAR. Among them, HMG-CoA reductase inhibitors (cerivastatin, simvastatin, fluvastatin, and atorvastatin) enhanced the hCAR-mediated transcriptional activation of phenobarbital-responsive enhancer module reporter gene by up to 3-fold. Similar activation by HMG-CoA reductase inhibitors was also observed with mouse and rat CARs. On the other hand, pravastatin did not activate hCAR at the concentrations tested (up to 30 μM). The extent of activation by the HMG-CoA reductase inhibitors was stronger than that by CITCO. Cerivastatin, simvastatin, fluvastatin, and atorvastatin induced CYP2B6 mRNA in stable hCAR-expressed FLC7 cells but not in original FLC7 cells. Therefore, we concluded that CAR mediates the effects of HMG-CoA reductase inhibitors on the induction of CYP2B genes, although HMG-CoA reductase inhibitors also activate pregnane X receptor. HMG-CoA reductase inhibitors such as cerivastatin would be useful to study for elucidating molecular and cellular mechanisms of hCAR.
RPJ: producing fast join results on streams through rate-based optimization

We consider the problem of "progressively" joining relations whose records are continuously retrieved from remote sources through an unstable network that may incur temporary failures. The objectives are to (i) start reporting the first output tuples as soon as possible (before the participating relations are completely received), and (ii) produce the remaining results at a fast rate. We develop a new algorithm RPJ (<u>R</u>ate-based <u>P</u>rogressive <u>J</u>oin) based on solid theoretical analysis. RPJ maximizes the output rate by optimizing its execution according to the characteristics of the join relations (e.g., data distribution, tuple arrival pattern, etc.). Extensive experiments prove that our technique delivers results significantly faster than the previous methods.
Adaptive Man-Machine Interfaces MIT 9904-15 Progress Report : June 30 , 2000 — December 31 , 2000 Tomaso Poggio Project Overview

Project Overview In this project we aim to achieve two significant extensions of our recent work on developing a text-to-visualspeech (TTVS) system (Ezzat, 1998). The existing synthesis module may be trained to generate image sequences of a real human face synchronized to a text-to-speech system, starting from just a few real images of the person to be simulated. We proposed 1) to extend the system to use morphing of 3D models of faces — rather than face images — and to output a 3D model of a speaking face and 2) to enrich the context of each viseme to deal with coarticulation issues. The main applications of this work are for virtual actors and for very-low-bandwidth video communication. In addition, the project may contribute to the development of a new generation of computer interfaces more userfriendly than today's interfaces.
WikiTrip: animated visualization over time of geo-location and gender of Wikipedians who edited a page

In this short paper, we present WikiTrip, a web tool we created and released as open source which provides a visualization over time of two kinds of information about the Wikipedians who edited a selected page: their location in the world and their gender. We also describe evidence that pages on a language edition of Wikipedia which receive most attention in terms of edits from countries where the language is not primarily spoken are about TV shows and stars, football teams or specific geographic locations.
Simulating liquids and solid-liquid interactions with lagrangian meshes

This article describes a Lagrangian finite element method that simulates the behavior of liquids and solids in a unified framework. Local mesh improvement operations maintain a high-quality tetrahedral discretization even as the mesh is advected by fluid flow. We conserve volume and momentum, locally and globally, by assigning to each element an independent rest volume and adjusting it to correct for deviations during remeshing and collisions. Incompressibility is enforced with per-node pressure values, and extra degrees of freedom are selectively inserted to prevent pressure locking. Topological changes in the domain are explicitly treated with local mesh splitting and merging. Our method models surface tension with an implicit formulation based on surface energies computed on the boundary of the volume mesh. With this method we can model elastic, plastic, and liquid materials in a single mesh, with no need for explicit coupling. We also model heat diffusion and thermoelastic effects, which allow us to simulate phase changes. We demonstrate these capabilities in several fluid simulations at scales from millimeters to meters, including simulations of melting caused by external or thermoelastic heating.
Activation of brain NOP receptors attenuates acute and protracted alcohol withdrawal symptoms in the rat.

BACKGROUND Alcohol withdrawal refers to a cluster of symptoms that may occur from suddenly ceasing the use of alcohol after chronic or prolonged ingestion. These symptoms make alcohol abstinence difficult and increase the risk of relapse in recovering alcoholics. In previous studies, we demonstrated that treatment with Nociceptin/orphanin FQ (N/OFQ) significantly reduces alcohol consumption and attenuates alcohol-seeking behavior induced by environmental conditioning factors or by stress in rats. In this study, we evaluated whether activation of brain NOP receptors may also attenuate alcohol withdrawal signs in rats. METHODS For this purpose, animals were subjected to a 6-day chronic alcohol intoxication (by intragastric administration), and at 8, 10, and 12 hours following cessation of alcohol exposure, they were treated intracerebroventricularly (ICV) with N/OFQ (0.0, 1.0, and 3.0 μg/rat). Somatic withdrawal signs were scored after ICV treatment. In a subsequent experiment, to evaluate N/OFQ effects on alcohol withdrawal-induced anxiety, another group of rats was subjected to ethanol intoxication and after 1 week was tested for anxiety behavior in the elevated plus maze (EPM). In the last experiment, an additional group of rats was tested for anxiety elicited by acute ethanol intoxication (hangover anxiety). For this purpose, animals received an acute dose (3.0 g/kg) of 20% alcohol and 12 hour later were tested in the EPM following ICV N/OFQ (0.0, 1.0, and 2.0 μg/rat). RESULTS Results showed that N/OFQ significantly reduced the expression of somatic withdrawal signs and reversed anxiety-like behaviors associated with both chronic and acute alcohol intoxication. N/OFQ did not affect anxiety scores in nondependent animals. CONCLUSIONS These findings suggest that the N/OFQ-NOP receptor system may represent a promising target for the development of new treatments to ameliorate alcohol withdrawal symptoms.
Serving the Grid: an Experimental Study of Server Clusters as Real-Time Demand Response Resources

Demand response is a crucial technology to allow large-scale penetration of intermittent renewable energy sources in the electric grid. This paper is based on the thesis that datacenters represent especially attractive candidates for providing flexible, real-time demand response services to the grid; they are capable of finely-controllable power consumption, fast power ramp-rates, and large dynamic range. This paper makes two main contributions: (a) it provides detailed experimental evidence justifying this thesis, and (b) it presents a comparative investigation of three candidate software interfaces for power control within the servers. All of these results are based on a series of experiments involving real-time power measurements on a lab-scale server cluster. This cluster was specially instrumented for accurate and fast power measurements on a time-scale of 100 ms or less. Our results provide preliminary evidence for the feasibility of large scale demand response using datacenters, and motivates future work on exploiting this capability.
Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASES1 and 2 Are Essential for Tapetum Development and Microspore Maturation[W][OA]

Among the >200 members of the leucine-rich repeat receptor kinase family in Arabidopsis thaliana, only a few have been functionally characterized. Here, we report a critical function in anther development for the SOMATIC EMBRYOGENESIS RECEPTOR KINASE1 (SERK1) and SERK2 genes. Both SERK1 and SERK2 are expressed widely in locules until stage 6 anthers and are more concentrated in the tapetal cell layer later. Whereas serk1 and serk2 single insertion mutants did not show developmental phenotypes, serk1 serk2 double mutants were not able to produce seeds because of a lack of pollen development in mutant anthers. In young buds, double mutant anthers developed normally, but serk1 serk2 microsporangia produced more sporogenous cells that were unable to develop beyond meiosis. Furthermore, serk1 serk2 double mutants developed only three cell layers surrounding the sporogenous cell mass, whereas wild-type anthers developed four cell layers. Further confocal microscopic and molecular analyses showed that serk1 serk2 double mutant anthers lack development of the tapetal cell layer, which accounts for the microspore abortion and male sterility. Taken together, these findings demonstrate that the SERK1 and SERK2 receptor kinases function redundantly as an important control point for sporophytic development controlling male gametophyte production.
Hillslope Hydrology in Global Change Research and Earth System Modeling

Earth System Models (ESMs) are essential tools for understanding and predicting global change, but they cannot explicitly resolve hillslope‐scale terrain structures that fundamentally organize water, energy, and biogeochemical stores and fluxes at subgrid scales. Here we bring together hydrologists, Critical Zone scientists, and ESM developers, to explore how hillslope structures may modulate ESM grid‐level water, energy, and biogeochemical fluxes. In contrast to the one‐dimensional (1‐D), 2‐ to 3‐m deep, and free‐draining soil hydrology in most ESM land models, we hypothesize that 3‐D, lateral ridge‐to‐valley flow through shallow and deep paths and insolation contrasts between sunny and shady slopes are the top two globally quantifiable organizers of water and energy (and vegetation) within an ESM grid cell. We hypothesize that these two processes are likely to impact ESM predictions where (and when) water and/or energy are limiting. We further hypothesize that, if implemented in ESM land models, these processes will increase simulated continental water storage and residence time, buffering terrestrial ecosystems against seasonal and interannual droughts. We explore efficient ways to capture these mechanisms in ESMs and identify critical knowledge gaps preventing us from scaling up hillslope to global processes. One such gap is our extremely limited knowledge of the subsurface, where water is stored (supporting vegetation) and released to stream baseflow (supporting aquatic ecosystems). We conclude with a set of organizing hypotheses and a call for global syntheses activities and model experiments to assess the impact of hillslope hydrology on global change predictions.
Performance Assessment of SVM Modulation Techniques for Losses Reduction in Induction Motor Drives

This paper analyses the switching losses in high power level induction machine drives and investigates how to improve their efficiency using suitably chosen space vector modulation (SVM) techniques. Three different SVM strategies to control the inverter have been compared and contrasted: the two-phase modulation, the symmetrical modulation and a strategy obtained by a combination of both of the previous techniques. The losses of the inverter are estimated using a simulation model and then compared with experimental measures on a 200 kW oil cooled induction motor drive. The efficiency of the whole drive is simulated and experimentally measured in order to evaluate the overall losses and accurately assess the modulation performance in the view of a rational optimization of different system aspects.
Tight control in the treatment of rheumatoid arthritis: efficacy and feasibility

Objective: To evaluate the available evidence on the efficacy and feasibility of the new concept of tight control in randomised trials in patients with rheumatoid arthritis (RA). Tight control is a treatment strategy tailored to the individual patient with RA, which aims to achieve a predefined level of low disease activity or remission within a certain period of time. Methods: The literature database PubMed was searched and yielded four trials: the FIN-RACo trial, the TICORA study, the BeSt study and the CAMERA study. Results: Tight control resulted in greater improvement and a higher percentage of patients meeting the preset aim of low disease activity or remission when compared to the control intervention. In the FIN-RACo trial, aimed at DAS28<2.6, 51% of patients in the tight control group achieved remission versus 16% in the contrast group (p<0.001). In the TICORA study, 65% of patients in the tight control group versus 16% of the contrast group achieved remission, based on DAS<1.6 (p<0.0001). In the CAMERA study, 50% of patients in the tight control group using a computer decision model achieved remission, versus 37% in the contrast group (p = 0.029). The BeSt study consisted of only tight control groups aimed at a DAS<1.6; remission was achieved in 38–46% of patients. This is higher than the range of remission in earlier trials of 13–36%. Conclusion: Tight control aiming for low disease activity or even better still, remission, seems a promising option in treating patients with RA in clinical trials and probably also in daily practice.
Spatio-temporal analysis of Greenhouse Gas data via clustering techniques

Data mining allows for hidden patterns to be brought to light in large data sets. This paper aims to apply data mining on real-life data showing Greenhouse Gas Emissions for countries within the European Union. Greenhouse Gasses are gasses which are released into the atmosphere, trapping the infrared radiation from the sun and causing an effect called the Greenhouse Effect. This effect contributes to global Climate Change and is a topical issue. Using the K-means clustering algorithm, a model is produced in order to provide a deeper insight into the emissions of the industrial sectors of the UK, France and Italy. The model is intended to be of use to those in governmental authority when decisions on emissions within individual industries are to be made.
Screen space cone tracing for glossy reflections

Indirect lighting (also Global Illumination (GI)) is an important part of photo-realistic imagery and has become a widely used method in real-time graphics applications, such as Computer Aided Design (CAD), Augmented Reality (AR) and video games. Path tracing can already achieve photo-realism by shooting thousands or millions of rays into a 3D scene for every pixel, which results in computational overhead exceeding real-time budgets. However, with modern programmable shader pipelines, a fusion of ray-casting algorithms and rasterization is possible, i.e. methods, which are similar to testing rays against geometry, can be performed on the GPU within a fragment (or rather pixel-) shader. Nevertheless, many implementations for real-time GI still trace perfect specular reflections only. In this work the advantages and disadvantages of different reflection methods are exposed and a combination of some of these is presented, which circumvents artifacts in the rendering and provides a stable, temporally coherent image enhancement. The benefits and failings of this new method are clearly separated as well. Moreover the developed algorithm can be implemented as pure post-process, which can easily be integrated into an existing rendering pipeline.
The Influence of Uncertainty and Social Support on Information Seeking Concerning Illicit Stimulant Use Among Young Adults

Using the Theory of Motivated Information Management (TMIM) and the concept of desired informational support as a framework, this project examined factors in the information management process young adults employ in potential information seeking about illicit stimulant drug use with members of their social networks. One hundred and seventy-three individuals participated in the study. Results indicated that (a) uncertainty discrepancy and the desire for informational support covaried, and (b) uncertainty discrepancy, anxiety, and outcome expectancy had significant impacts on the efficacy judgments made by individuals with regard to potential information seeking with their social networks about their stimulant drug use. The study thus provides further evidence for the utility of TMIM as a framework for understanding health communication in regard to drug use, and suggests that desired informational support may be a useful addition to the model for this health issue.
Efficient pinpointing of misplaced tags in large RFID systems

The Radio-Frequency Identification (RFID) technology has stimulated many innovative applications. Misplaced-tag pinpointing (MTP) is important to RFID applications in production economics because optimal inventory placement can significantly increase profit. Previous research from the database perspective needs to process a large amount of data which is time-consuming to collect (and energy-consuming if active tags are used). How to efficiently address the MTP problem from the protocol design perspective however has not been investigated. In this paper, we propose a series of protocols toward efficient MTP solution in large RFID systems. The proposed protocols detect misplaced tags based on reader positions instead of tag positions to guarantee the efficiency and scalability as system scale grows, because the number of readers is much smaller than that of tags. Considering applications to employ more and more popular active tags, we further propose a solution requiring responses from only partial tags in favor of energy saving. We analyze the optimal performances of proposed protocols to demonstrate their efficiency potential and conduct extensive simulation experiments to evaluate their performance under various scenarios. The results show that the proposed protocols can significantly increase the time efficiency and the energy efficiency by over 70% on average when compared with the state of the art.
Dominance Move: A Measure of Comparing Solution Sets in Multiobjective Optimization

One of the most common approaches for multiobjective optimization is to generate a solution set that well approximates the whole Pareto-optimal frontier to facilitate the later decision-making process. However, how to evaluate and compare the quality of different solution sets remains challenging. Existing measures typically require additional problem knowledge and information, such as a reference point or a substituted set of the Pareto-optimal frontier. In this paper, we propose a quality measure, called dominance move (DoM), to compare solution sets generated by multiobjective optimizers. Given two solution sets, DoM measures the minimum sum of move distances for one set to weakly Pareto dominate the other set. DoM can be seen as a natural reflection of the difference between two solutions, capturing all aspects of solution sets' quality, being compliant with Pareto dominance, and does not need any additional problem knowledge and parameters. We present an exact method to calculate the DoM in the biobjective case. We show the necessary condition of constructing the optimal partition for a solution set's minimum move, and accordingly propose an efficient algorithm to recursively calculate the DoM. Finally, DoM is evaluated on several groups of artificial and real test cases as well as by a comparison with two well-established quality measures.
Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri

Whereas genomes can be rapidly sequenced, the functions of many genes are incompletely or erroneously annotated because of a lack of experimental evidence or prior functional knowledge in sequence databases. To address this weakness, we describe here a model-enabled gene search (MEGS) approach that (i) identifies metabolic functions either missing from an organism's genome annotation or incorrectly assigned to an ORF by using discrepancies between metabolic model predictions and experimental culturing data; (ii) designs functional selection experiments for these specific metabolic functions; and (iii) selects a candidate gene(s) responsible for these functions from a genomic library and directly interrogates this gene's function experimentally. To discover gene functions, MEGS uses genomic functional selections instead of relying on correlations across large experimental datasets or sequence similarity as do other approaches. When applied to the bioluminescent marine bacterium Vibrio fischeri, MEGS successfully identified five genes that are responsible for four metabolic and transport reactions whose absence from a draft metabolic model of V. fischeri caused inaccurate modeling of high-throughput experimental data. This work demonstrates that MEGS provides a rapid and efficient integrated computational and experimental approach for annotating metabolic genes, including those that have previously been uncharacterized or misannotated.
Space-efficient local computation algorithms

Recently Rubinfeld et al. (ICS 2011, pp. 223--238) proposed a new model of sublinear algorithms called local computation algorithms. In this model, a computation problem F may have more than one legal solution and each of them consists of many bits. The local computation algorithm for F should answer in an online fashion, for any index i, the ith bit of some legal solution of F. Further, all the answers given by the algorithm should be consistent with at least one solution of F. In this work, we continue the study of local computation algorithms. In particular, we develop a technique which under certain conditions can be applied to construct local computation algorithms that run not only in polylogarithmic time but also in polylogarithmic space. Moreover, these local computation algorithms are easily parallelizable and can answer all parallel queries consistently. Our main technical tools are pseudorandom numbers with bounded independence and the theory of branching processes.