Miracle-dz/UniFAR-FTUs huggingface dataset:
Runtime Goal Models

Goal models capture stakeholder requirements for a system-to-be, but also circumscribe a space of alternative specifications for fulfilling these requirements. Recent proposals for self-adaptive software systems rely on variants of goal models to support monitoring and adaptation functions. In such cases, goal models serve as mechanisms in terms of which systems reflect upon their requirements during their operation. We argue that existing proposals for using goal models at runtime are using design artifacts for purposes they were not intended, i.e., for reasoning about runtime system behavior. In this paper, we propose a conceptual distinction between Design-time Goal Models (DGMs)—used to design a system—and Runtime Goal Models (RGMs)—used to analyze a system’s runtime behavior with respect to its requirements. RGMs extend DGMs with additional state, behavioral and historical information about the fulfillment of goals. We propose a syntactic structure for RGMs, a method for deriving them from DGMs, and runtime algorithms that support their monitoring. Keywords—Runtime goal models; Requirements at runtime; Goal reasoning; Self-adaptive systems.
Gli1/DNA interaction is a druggable target for Hedgehog-dependent tumors

Hedgehog signaling is essential for tissue development and stemness, and its deregulation has been observed in many tumors. Aberrant activation of Hedgehog signaling is the result of genetic mutations of pathway components or other Smo‐dependent or independent mechanisms, all triggering the downstream effector Gli1. For this reason, understanding the poorly elucidated mechanism of Gli1‐mediated transcription allows to identify novel molecules blocking the pathway at a downstream level, representing a critical goal in tumor biology. Here, we clarify the structural requirements of the pathway effector Gli1 for binding to DNA and identify Glabrescione B as the first small molecule binding to Gli1 zinc finger and impairing Gli1 activity by interfering with its interaction with DNA. Remarkably, as a consequence of its robust inhibitory effect on Gli1 activity, Glabrescione B inhibited the growth of Hedgehog‐dependent tumor cells in vitro and in vivo as well as the self‐renewal ability and clonogenicity of tumor‐derived stem cells. The identification of the structural requirements of Gli1/DNA interaction highlights their relevance for pharmacologic interference of Gli signaling.
Robust stability of linear uncertain discrete-time systems with interval time-varying delay

This paper presents a robust stability problem for linear uncertain discrete-time systems with interval time-varying delay and norm-bounded uncertainties. First, a necessary and sufficient stability condition is obtained by employing a well-known lifting method and switched system approach for nominal discrete-time delay systems. Both the stability method of checking the characteristic values inside the unit circle and a Lyapunov function-based stability result are taken into consideration. Second, a simple Lyapunov--Krasovskii functional (LKF) is selected, and utilizing a generalized Jensen sum inequality, a sufficient stability condition is presented in the form of linear matrix inequalities. Third, a novel LKF is proposed together with the use of a convexity approach in the LKF. Finally, the proposed method is extended to the case when the system under consideration is subject to norm-bounded uncertainties. Three numerical examples are introduced to illustrate the effectiveness of the proposed approach, along with some numerical comparisons.
Enteropathogenic Escherichia coli inhibits butyrate uptake in Caco-2 cells by altering the apical membrane MCT 1 level

Borthakur, Alip, Ravinder K. Gill, Kim Hodges, Krishnamurthy Ramaswamy, Gail Hecht, and Pradeep K. Dudeja. Enteropathogenic Escherichia coli inhibits butyrate uptake in Caco-2 cells by altering the apical membrane MCT1 level. Am J Physiol Gastrointest Liver Physiol 290: G30–G35, 2006. First published September 8, 2005; doi:10.1152/ajpgi.00302. 2005. —Enteropathogenic Escherichia coli (EPEC), a food-borne human pathogen, is responsible for infantile diarrhea, especially in developing countries. The pathophysiology of EPEC-induced diarrhea, however, is not completely understood. Our recent studies showed modulation of Na /H and Cl / HCO3 exchange activities in Caco-2 cells in response to EPEC infection. We hypothesized that intestinal short-chain fatty acid absorption mediated by monocarboxylate transporter 1 (MCT1) might also be altered by EPEC infection. The aim of the current studies was to examine the effect of EPEC infection on butyrate uptake. Caco-2 cells were infected with wild-type EPEC, various mutant strains, or nonpathogenic E. coli HS4, and [C]butyrate uptake was determined. EPEC, but not nonpathogenic E. coli, significantly decreased butyrate uptake. Infection of cells with strains harboring mutations in escN, which encodes a putative ATPase for the EPEC type III secretion system (TTSS), or in the espA, espB, or espD genes encoding structural components of the TTSS, had no effect on butyrate uptake, indicating the TTSS dependence. On the other hand, strains with mutations in the effector protein genes espF, espG, espH, and map inhibited butyrate uptake, similar to the wild-type EPEC. Surface expression of MCT1 decreased considerably after EPEC but not after nonpathogenic E. coli infection. In conclusion, our studies demonstrate inhibition of MCT1-mediated butyrate uptake in Caco-2 cells in response to EPEC infection. This inhibition was dependent on a functional TTSS and the structural proteins EspA, -B, and -D of the translocation apparatus.
Control-based scheduling with QoS support for vehicle to infrastructure communications

This article is focused on data transmission scheduling in V2I communications, where a central station, the roadside beacon, decides how to allocate system resources among the vehicles under coverage. We consider non-safety applications whose commercial appeal is expected to accelerate the deployment of VANETs. In this case the main objective is to deliver as much information as possible during the connection lifetime of the vehicles, which is limited by their speed and the length of the road sections under coverage. In this environment the contention free poll-based access mechanism of the 802.11e standard included in current VANET specifications is especially suitable. The design of a scheduling mechanism is addressed in this article from a control theory point of view with the additional novelty of using an optimal control formulation comprising resource constraints. This design strategy allows QoS differentiation, assuring a fixed amount of bandwidth for each QoS class. The resulting algorithm not only maximizes the amount of data delivered, but also reduces performance differences between users traveling along different roads.
Method of Edge Searching Considering Dynamics of Event Area for Wireless Sensor Networks

This paper targets the reduction in duplications of observations and unnecessary power consumption due to duplications in event-driven wireless sensor networks. Conventional research has proposed efficient scheme of data collection that only collect detected information from nodes located at the edges of event areas, which has eliminated the duplication of observation information in event-driven wireless sensor networks. However, it has not assumed temporal changes in event areas. Here, we propose an efficient scheme that utilizes changes in event areas and present the results obtained by evaluating its energy efficiency through simulation. We compared the power consumed by detecting edge nodes in changes after event areas between the proposed and conventional method to verify the effectiveness of the new approach.
Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile

The isolation of a new thermophilic bacterium, Thermus aquaticus gen. n. and sp. n. , is described. Successful enrichment requires incubation at 70 to 75 C, and the use of nutrient media relatively dilute with respect to the organic components. Strains of T. aquaticus have been isolated from a variety of thermal springs in Yellowstone National Park and from a thermal spring in California. The organism has also been isolated from man-made thermal habitats, such as hot tap water, in geographical locations quite distant from thermal springs. Isolates of T. aquaticus are gram-negative nonsporulating nonmotile rods which frequently form long filaments at supraoptimal temperatures or in the stationary phase. All isolates form a yellow cellular pigment, probably a carotenoid. A characteristic structure formed by all isolates is a large sphere, considerably larger than a spheroplast. These large spheres, as well as lysozyme-induced spheroplasts, are resistant to osmotic lysis. Deoxyribonucleic acid base compositions of four strains were determined by CsCl density gradient ultracentrifugation and found to be between 65.4 and 67.4 moles per cent guanine plus cytosine. The growth of all isolates tested is inhibited by fairly low concentrations of cycloserine, streptomycin, penicillin, novobiocin, tetracycline, and chloramphenicol. Nutritional studies on one strain showed that it did not require vitamins or amino acids, although growth was considerably faster in enriched than in synthetic medium. Several sugars and organic acids served as carbon sources, and either NH4+ or glutamate could serve as nitrogen source. The organism is an obligate aerobe and has a pH optimum of 7.5 to 7.8. The optimum temperature for growth is 70 C, the maximum 79 C, and the minimum about 40 C. The generation time at the optimum is about 50 min. The possible relationships of this new genus to the myxobacteria, flexibacteria, and flavobacteria are discussed.
Oncall Piano Sensei: Portable AR Piano Training System

We propose a portable AR piano training system that helps the user to learn piano with affordable cost and no space limitations. The optical music recognition (OMR) process is first applied so the system can automatically play the melody of a given sheet music. During the performance, the training system indicates which note is playing and which corresponding piano key should be pressed on the keyboard. Our system also detects which keys are pressed by the user and give sound/visual feed-back to correct the user. With no requirement of a physical piano and tutor, our system extends a great range of time and space for the user who wants to learn piano.
Evolving neural networks in compressed weight space

We propose a new indirect encoding scheme for neural networks in which the weight matrices are represented in the frequency domain by sets Fourier coefficients. This scheme exploits spatial regularities in the matrix to reduce the dimensionality of the representation by ignoring high-frequency coefficients, as is done in lossy image compression. We compare the efficiency of searching in this "compressed" network space to searching in the space of directly encoded networks, using the CoSyNE neuroevolution algorithm on three benchmark problems: pole-balancing, ball throwing and octopus arm control. The results show that this encoding can dramatically reduce the search space dimensionality such that solutions can be found in significantly fewer evaluations
Resolution of regulated secretion into sequential MgATP-dependent and calcium-dependent stages mediated by distinct cytosolic proteins

The biochemical events and components responsible for ATP-dependent Ca(2+)-activated secretion remain to be identified. To simplify the molecular dissection of regulated secretion, we have resolved norepinephrine (NE) secretion from semi-intact PC12 cells into two kinetically distinct stages, each of which was studied separately to discern its molecular requirements. The first stage consisted of MgATP- dependent priming of the secretory apparatus in the absence of Ca2+. MgATP-dependent priming was readily reversible and inhibited by a broad range of protein kinase inhibitors. The second stage consisted of Ca(2+)-triggered exocytosis which, in contrast to priming, occurred in the absence of MgATP. Both priming and triggering were found to be dependent upon or stimulated by cytosolic proteins. The priming and triggering activities of cytosol were functionally distinct as indicated by differing thermolability. Furthermore, active components in cytosol resolved by gel filtration were found to support either priming or triggering, but not both. For both priming and triggering reactions, several peaks of activity were detected; one of each type of factor was partially purified from rat brain cytosol, and found to be enriched for stage-specific activity. Two partially purified factors exhibiting stage-specific activity, a approximately 20-kD priming factor and approximately 300-kD triggering factor, were able to support regulated secretion as effectively as crude cytosol when used sequentially in the partial reactions. Further characterization of stage-specific cytosolic factors should clarify the nature of MgATP- and Ca(2+)-dependent events in the regulated secretory pathway.
Efficient histogram-based sliding window

Many computer vision problems rely on computing histogram-based objective functions with a sliding window. A main limiting factor is the high computational cost. Existing computational methods have a complexity linear in the histogram dimension. In this paper, we propose an efficient method that has a constant complexity in the histogram dimension and therefore scales well with high dimensional histograms. This is achieved by harnessing the spatial coherence of natural images and computing the objective function in an incremental manner. We demonstrate the significant performance enhancement by our method through important vision tasks including object detection, object tracking and image saliency analysis. Compared with state-of-the-art techniques, our method typically achieves from tens to hundreds of times speedup for those tasks.
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

Background A recent study of the gene expression patterns of Zika virus (ZIKV) infected human neural progenitor cells (hNPCs) revealed transcriptional dysregulation and identified cell-cycle-related pathways that are affected by infection. However deeper exploration of the information present in the RNA-Seq data can be used to further elucidate the manner in which Zika infection of hNPCs affects the transcriptome, refining pathway predictions and revealing isoform-specific dynamics. Methodology/Principal Findings We analyzed data published by Tang et al. using state-of-the-art tools for transcriptome analysis. By accounting for the experimental design and estimation of technical and inferential variance we were able to pinpoint Zika infection affected pathways that highlight Zika’s neural tropism. The examination of differential genes reveals cases of isoform divergence. Conclusions/Significance Transcriptome analysis of Zika infected hNPCs has the potential to identify the molecular signatures of Zika infected neural cells. These signatures may be useful for diagnostics and for the resolution of infection pathways that can be used to harvest specific targets for further study.
GABA Regulates the Multidirectional Tangential Migration of GABAergic Interneurons in Living Neonatal Mice

Cortical GABAergic interneurons originate from ganglionic eminences and tangentially migrate into the cortical plate at early developmental stages. To elucidate the characteristics of this migration of GABAergic interneurons in living animals, we established an experimental design specialized for in vivo time-lapse imaging of the neocortex of neonate mice with two-photon laser-scanning microscopy. In vesicular GABA/glycine transporter (VGAT)-Venus transgenic mice from birth (P0) through P3, we observed multidirectional tangential migration of genetically-defined GABAergic interneurons in the neocortical marginal zone. The properties of this migration, such as the motility rate (distance/hr), the direction moved, and the proportion of migrating neurons to stationary neurons, did not change through P0 to P3, although the density of GABAergic neurons at the marginal zone decreased with age. Thus, the characteristics of the tangential motility of individual GABAergic neurons remained constant in development. Pharmacological block of GABAA receptors and of the Na+-K+-Cl− cotransporters, and chelating intracellular Ca2+, all significantly reduced the motility rate in vivo. The motility rate and GABA content within the cortex of neonatal VGAT-Venus transgenic mice were significantly greater than those of GAD67-GFP knock-in mice, suggesting that extracellular GABA concentration could facilitate the multidirectional tangential migration. Indeed, diazepam applied to GAD67-GFP mice increased the motility rate substantially. In an in vitro neocortical slice preparation, we confirmed that GABA induced a NKCC sensitive depolarization of GABAergic interneurons in VGAT-Venus mice at P0-P3. Thus, activation of GABAAR by ambient GABA depolarizes GABAergic interneurons, leading to an acceleration of their multidirectional motility in vivo.
Soluble Heparin Binding Epidermal Growth Factor-Like Growth Factor Is a Regulator of GALGT2 Expression and GALGT2-Dependent Muscle and Neuromuscular Phenotypes

GALGT2 (also B4GALNT2) encodes a glycosyltransferase that is normally confined to the neuromuscular and myotendinous junction in adult skeletal muscle. GALGT2 overexpression in muscle can inhibit muscular dystrophy in mouse models of the disease by inducing the overexpression of surrogate muscle proteins, including utrophin, agrin, laminins, and integrins. Despite its well-documented biological properties, little is known about the endogenous regulation of muscle GALGT2 expression. ABSTRACT GALGT2 (also B4GALNT2) encodes a glycosyltransferase that is normally confined to the neuromuscular and myotendinous junction in adult skeletal muscle. GALGT2 overexpression in muscle can inhibit muscular dystrophy in mouse models of the disease by inducing the overexpression of surrogate muscle proteins, including utrophin, agrin, laminins, and integrins. Despite its well-documented biological properties, little is known about the endogenous regulation of muscle GALGT2 expression. Here, we demonstrate that epidermal growth factor receptor (EGFR) ligands can activate the human GALGT2 promoter. Overexpression of one such ligand, soluble heparin-binding EGF-like growth factor (sHB-EGF), also stimulated mouse muscle Galgt2 gene expression and expression of GALGT2-inducible surrogate muscle genes. Deletion analysis of the GALGT2 promoter identified a 45-bp region containing a TFAP4-binding site that was required for sHB-EGF activation. sHB-EGF increased TFAP4 binding to this site in muscle cells and increased endogenous Tfap4 gene expression. sHB-EGF also increased muscle EGFR protein expression and activated EGFR-Akt signaling. sHB-EGF expression was concentrated at the neuromuscular junction, and Hbegf deletion reduced Galgt2-dependent synaptic glycosylation. Hbegf deletion also mimicked Galgt2-dependent neuromuscular and muscular dystrophy phenotypes. These data demonstrate that sHB-EGF is an endogenous regulator of muscle Galgt2 gene expression and can mimic Galgt2-dependent muscle phenotypes.
Clustering of exchange rates and their dynamics under different dependence measures

This paper proposes an improvement to the method for clustering exchange rates given by D. J. Fenn et al, in Quantitative Finance, 12 (10) 2012, pp.1493-1520. To deal with the potentially non linear nature of currency time series dependence, we propose two alternative similarity metrics to use instead of the one used in the aforementioned paper based on Pearson correlation. Our proposed similarity metrics are based upon Kendall and distance correlations. We observe how each of the newly adapted clustering methods respond over several years of currency exchange data and find significant differences in the resulting clusters.
BRB: BetteR Batch Scheduling to Reduce Tail Latencies in Cloud Data Stores

A common pattern in the architectures of modern interactive web-services is that of large request fan-outs, where even a single end-user request (task) arriving at an application server triggers tens to thousands of data accesses (sub-tasks) to different stateful backend servers. The overall response time of each task is bottlenecked by the completion time of the slowest sub-task, making such workloads highly sensitive to the tail of latency distribution of the backend tier. The large number of decentralized application servers and skewed workload patterns exacerbate the challenge in addressing this problem. We address these challenges through BetteR Batch (BRB). By carefully scheduling requests in a decentralized and task-aware manner, BRB enables low-latency distributed storage systems to deliver predictable performance in the presence of large request fan-outs. Our preliminary simulation results based on production workloads show that our proposed design is at the 99th percentile latency within 38% of an ideal system model while offering latency improvements over the state-of-the-art by a factor of 2.
Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea

A structural and functional classification of H/ACA and H/ACA-like motifs is proposed from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide-target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum are presented as testable gene candidates which might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs.
Decision-Theoretic GOLOG with Qualitative Preferences

Personalization is becoming increasingly important in agent programming, particularly as it relates to the Web. We propose to develop underspecified, task-specific agent programs, and to automatically personalize them to the preferences of individual users. To this end, we propose a framework for agent programming that integrates rich, non-Markovian, qualitative user preferences expressed in a linear temporal logic with quantitative Markovian reward functions. We begin with DTGOLOG, a first-order, decision-theoretic agent programming language in the situation calculus. We present an algorithm that compiles qualitative preferences into GOLOG programs and prove it sound and complete with respect to the space of solutions. To integrate these preferences into DTGOLOG we introduce the notion of multi-program synchronization and restate the semantics of the language as a transition semantics. We demonstrate the utility of this framework with an application to personalized travel planning over the Web. To the best of our knowledge this is the first work to combine qualitative and quantitative preferences for agent programming. Further, while the focus of this paper is on the integration of qualitative and quantitative preferences, a side effect of this work is realization of the simpler task of integrating qualitative preferences alone into agent programming as well as the generation of GOLOG programs from LTL formulae.