Miracle-dz/UniFAR-FTUs huggingface dataset:
For Flux Sake: The Confluence of Socially- and Biologically-Inspired Computing for Engineering Change in Open Systems

This position paper is concerned with the challenge of engineering multi-scale and long-lasting systems, whose operation is regulated by sets of mutually-agreed, conventional rules. The core of the problem is that there are multiple, inter-dependent dimensions of flux, with numerous contextual factors to take into account. These dimensions of flux include, on the one hand, the set of rules itself; and on the other, the system components (population), their social network, and the operating environment. However, there appears to be no `one size fits all' optimum ruleset for all combinations of population, social network and environment; nor (given the contextual factors) is there a planning-type algorithm that can compute an `ideal' ruleset for any particular combination of population, social network and environment. These features of the problem suggest that recent advances in machine learning and evolutionary computation can provide the instruments for facilitating self-adaptation of a rule-based system over different timescales. This paper proposes that the integration of concepts from socially- and biologically-inspired computing can pave the way for eventual development of a computational framework that will enable principled (methodological) development of sustainable adaptive rule-based systems.
Low-Rank Decomposition-Based Restoration of Compressed Images via Adaptive Noise Estimation

Images coded at low bit rates in real-world applications usually suffer from significant compression noise, which significantly degrades the visual quality. Traditional denoising methods are not suitable for the content-dependent compression noise, which usually assume that noise is independent and with identical distribution. In this paper, we propose a unified framework of content-adaptive estimation and reduction for compression noise via low-rank decomposition of similar image patches. We first formulate the framework of compression noise reduction based upon low-rank decomposition. Compression noises are removed by soft thresholding the singular values in singular value decomposition of every group of similar image patches. For each group of similar patches, the thresholds are adaptively determined according to compression noise levels and singular values. We analyze the relationship of image statistical characteristics in spatial and transform domains, and estimate compression noise level for every group of similar patches from statistics in both domains jointly with quantization steps. Finally, quantization constraint is applied to estimated images to avoid over-smoothing. Extensive experimental results show that the proposed method not only improves the quality of compressed images obviously for post-processing, but are also helpful for computer vision tasks as a pre-processing method.
Overview of drug data within French health insurance databases and implications for pharmacoepidemiological studies

In this study, we aimed to provide an updated overview of drug data contained in the French health insurance database (SNIIRAM) and its associated national representative sample (EGB). This study identified most common problems concerning drug data: (i) change in level of coverage of drugs of interest (drug no more eligible for reimbursement or no more prescription‐only), (ii) break in patients' eligibility (in connection with change of healthcare plan or patients' identifier), and (iii) technical and regulatory issues. We provide a brief checklist to enable a structured identification of these issues. The impact of gap in drug data availability on study validity will depend on the research question, drug, setting, and population of interest. The French health insurance database and associated sample are valuable resources for pharmacoepidemiological research. There is a need to pursue further methodological and validation studies to promote accurate and transparent use of French health insurance databases for pharmacoepidemiology.
Stability of a Class of Linear Switching Systems with Applications to Two Consensus Problems

In this paper, we first establish a stability result for a class of linear switched systems involving Kronecker product. The problem is interesting in that the system matrix does not have to be Hurwitz at any time instant. This class of linear switched systems arises in the control of multi-agent systems under switching network topology. As applications of this stability result, we give the solvability conditions for both the leaderless consensus problem and the leader-following consensus problem for general marginally stable linear multi-agent systems under switching network topology. In contrast with some existing results, our results only assume that the dynamic graph is uniformly connected.
Model Composition for Macromolecular Regulatory Networks

Models of regulatory networks become more difficult to construct and understand as they grow in size and complexity. Large models are usually built up from smaller models, representing subsets of reactions within the larger network. To assist modelers in this composition process, we present a formal approach for model composition, a wizard-style program for implementing the approach, and suggested language extensions to the Systems Biology Markup Language to support model composition. To illustrate the features of our approach and how to use the JigCell Composition Wizard, we build up a model of the eukaryotic cell cycle "engine¿ from smaller pieces.
Chromatin Association of Gcn4 Is Limited by Post-translational Modifications Triggered by its DNA-Binding in Saccharomyces cerevisiae

The Saccharomyces cerevisiae transcription factor Gcn4 is expressed during amino acid starvation, and its abundance is controlled by ubiquitin-mediated proteolysis. Cdk8, a kinase component of the RNA polymerase II Mediator complex, phosphorylates Gcn4, which triggers its ubiquitination/proteolysis, and is thought to link Gcn4 degradation with transcription of target genes. In addition to phosphorylation and ubiquitination, we previously showed that Gcn4 becomes sumoylated in a DNA-binding dependent manner, while a nonsumoylatable form of Gcn4 showed increased chromatin occupancy, but only if Cdk8 was present. To further investigate how the association of Gcn4 with chromatin is regulated, here we examine determinants for Gcn4 sumoylation, and how its post-translational modifications are coordinated. Remarkably, artificially targeting Gcn4 that lacks its DNA binding domain to a heterologous DNA site restores sumoylation at its natural modification sites, indicating that DNA binding is sufficient for the modification to occur in vivo. Indeed, we find that neither transcription of target genes nor phosphorylation are required for Gcn4 sumoylation, but blocking its sumoylation alters its phosphorylation and ubiquitination patterns, placing Gcn4 sumoylation upstream of these Cdk8-mediated modifications. Strongly supporting a role for sumoylation in limiting its association with chromatin, a hyper-sumoylated form of Gcn4 shows dramatically reduced DNA occupancy and expression of target genes. Importantly, we find that Cdk8 is at least partly responsible for clearing hyper-sumoylated Gcn4 from DNA, further implicating sumoylation as a stimulus for Cdk8-mediated phosphorylation and degradation. These results support a novel function for SUMO in marking the DNA-bound form of a transcription factor, which triggers downstream processes that limit its association with chromatin, thus preventing uncontrolled expression of target genes.
The readiness self-assessment model for green IT implementation in organizations

Green IT is becoming an important concept for the organization, but unfortunately, not every organization is ready to apply green IT. Therefore, it is necessary to develop an easy-to-use but comprehensive self-assessment to evaluate organizational readiness to implement green IT. The Green IT implementation is also a form of business transformation. Thus, the development of the measurement will use four business transformational dimensions: Economy, Technology, Process, and People developed by Unhelkar. The assessment on this research is divided into two. First, there is a matrix to help managers determine whether the organization has used the right approach to implement green IT based on types of organization. Second, there are readiness factors consisting of strategy, technology, process, and human resources factors to determine how ready an organization is to implement green IT.
Associations of educational attainment and cognitive level of job with old age verbal ability and processing speed: The mediating role of chronic diseases

ABSTRACT We investigated whether the relation of educational attainment and cognitive level of job to performance in verbal ability and processing speed in old age was mediated via the number of chronic diseases. A total of 2,812 older adults participated. Psychometric tests on verbal ability and processing speed were administered. Individuals were interviewed regarding their education, midlife occupation, and chronic diseases in old age. Higher educational attainment and higher cognitive level of job were correlated with better performance in verbal ability and processing speed (.15 ≤ r ≤ .33, ps < .001). 1.4 to 7.3% of these relations was mediated via the number of chronic diseases (β = .01, ps < .026). In conclusion, individuals with higher educational attainment and higher cognitive level of job may possibly suffer from fewer chronic diseases later in life. Possibly, this may finally be related to better performance in verbal ability and processing speed in those individuals in old age.
Persistent synthesis of 5S RNA when production of 28S and 18S ribosomal RNA is inhibited by low doses of actinomycin D

To determine whether transcription of the genes coding for 5S ribosomal RNA depends upon the concurrent activity of the genes for 28S and 18S ribosomal RNA we studied the synthesis of 5S RNA in cultured L cells when the synthesis of the 45S precursor of 28 and 18S RNA was inhibited with low doses of actinomycin D. Synthesis of 5S RNA was measured by following the incorporation of 3H uridine into components which, upon acrylamide gel electrophoresis, co‐migrated with markers of 5S RNA obtained from 32P labeled ribosomes. We observed that the synthesis of 5S RNA persists in the absence of detectable 28S and 18S RNA synthesis, continuing at the normal rate for several hours and at a reduced rate for at least a generation time. This strongly supports the concept that 45S RNA is not a precursor of 5S RNA, and indicates furthermore that neither the 45S component, nor any of the intermediates involved in its transition to 28S and 18S RNA, are involved in controlling the output of the 5S genes The 5S RNA which is made during actinomycin treatment is retained predominantly in the nucleoplasm and undergoes a turnover of about 3.5% per hour. It apparently cannot be utilized when ribosome synthesis resumes following removal of the actinomycin.
A Lattice Framework for Option Pricing with Two State Variables

Abstract A procedure is developed for the valuation of options when there are two underlying state variables. The approach involves an extension of the lattice binomial approach developed by Cox, Ross, and Rubinstein to value options on a single asset. Details are given on how the jump probabilities and jump amplitudes may be obtained when there are two state variables. This procedure can be used to price any contingent claim whose payoff is a piece-wise linear function of two underlying state variables, provided these two variables have a bivariate lognormal distribution. The accuracy of the method is illustrated by valuing options on the maximum and minimum of two assets and comparing the results for cases in which an exact solution has been obtained for European options. One advantage of the lattice approach is that it handles the early exercise feature of American options. In addition, it should be possible to use this approach to value a number of financial instruments that have been created in recent years.
Building a cooperative P2P-TV application over a wise network: the approach of the European FP-7 strep NAPA-WINE

Introduction TV services over the Internet can be provided by either exploiting IP multicast functionalities or relying on a pure peer-to-peer (P2P) approach. The first technique will only work on a network infrastructure controlled by a single broadband operator due to limitations of IP multicast facilities. The main goal of the project is the study of a future system suitable for HQTV live streaming over the Internet based on P2P technology, or a P2P-HQTV system. The major focus is on overcoming today's pure layered approach through a cooperative paradigm in which the application and network layers cooperate to optimize the quality of service offered to end users.
Synaptic GABAA Receptor Clustering without the γ2 Subunit

Rapid activation of postsynaptic GABAA receptors (GABAARs) is crucial in many neuronal functions, including the synchronization of neuronal ensembles and controlling the precise timing of action potentials. Although the γ2 subunit is believed to be essential for the postsynaptic clustering of GABAARs, synaptic currents have been detected in neurons obtained from γ2−/− mice. To determine the role of the γ2 subunit in synaptic GABAAR enrichment, we performed a spatially and temporally controlled γ2 subunit deletion by injecting Cre-expressing viral vectors into the neocortex of GABAARγ277Ilox mice. Whole-cell recordings revealed the presence of miniature IPSCs in Cre+ layer 2/3 pyramidal cells (PCs) with unchanged amplitudes and rise times, but significantly prolonged decays. Such slowly decaying currents could be evoked in PCs by action potentials in presynaptic fast-spiking interneurons. Freeze-fracture replica immunogold labeling revealed the presence of the α1 and β3 subunits in perisomatic synapses of cells that lack the γ2 subunit. Miniature IPSCs in Cre+ PCs were insensitive to low concentrations of flurazepam, providing a pharmacological confirmation of the lack of the γ2 subunit. Receptors assembled from only αβ subunits were unlikely because Zn2+ did not block the synaptic currents. Pharmacological experiments indicated that the αβγ3 receptor, rather than the αβδ, αβε, or αβγ1 receptors, was responsible for the slowly decaying IPSCs. Our data demonstrate the presence of IPSCs and the synaptic enrichment of the α1 and β3 subunits and suggest that the γ3 subunit is the most likely candidate for clustering GABAARs at synapses in the absence of the γ2 subunit.
Experiences in Data-Parallel Programming

To efficiently parallelize a scientific application with a data-parallel compiler requires certain structural properties in the source program, and conversely, the absence of others. A recent parallelization effort of ours reinforced this observation and motivated this correspondence. Specifically, we have transformed a Fortran 77 version of GROMOS, a popular dusty-deck program for molecular dynamics, into Fortran D, a data-parallel dialect of Fortran. During this transformation we have encountered a number of difficulties that probably are neither limited to this particular application nor do they seem likely to be addressed by improved compiler technology in the near future. Our experience with GROMOS suggests a number of points to keep in mind when developing software that may at some time in its life cycle be parallelized with a data-parallel compiler. This note presents some guidelines for engineering data-parallel applications that are compatible with Fortran D or High Performance Fortran compilers.
DNA damage and replication stress induced transcription of RNR genes is dependent on the Ccr4–Not complex

Genetic experiments have indicated a role for the Ccr4–Not complex in the response to hydroxyurea (HU) induced replication stress and ionizing radiation in yeast. This response includes transcriptional induction of the four genes constituting the ribonucleotide reductase (RNR) enzymatic complex, RNR1-4 and degradation of its inhibitor, Sml1p. The Ccr4–Not complex has originally been described as a negative regulator of RNA polymerase II (pol II) transcription, but it has also been implicated in mRNA turnover and protein ubiquitination. We investigated the mechanism of the HU sensitivity conferred by mutation of CCR4-NOT genes. We found that the ubiquitin protein ligase activity of Not4p does not play a role in HU induced Sml1p degradation. We show, however, that the HU sensitivity of ccr4-not mutant strains correlated very well with a defect in accumulation of RNR2, RNR3 and RNR4 mRNA after HU or methyl-methane sulfonate (MMS) treatment. Chromatin immunoprecipitation (ChIP) experiments show that TBP, pol II and Set1p recruitment to the activated RNR3 locus is defective in cells lacking NOT4. Moreover, RNR3-promoter activity is not induced by HU in these cells. Our experiments show that induction of RNR gene transcription is defective in ccr4-not mutant strains, providing an explanation for their sensitivity to HU.
Recording Real Worlds for Playback in a Virtual Exercise Environment

Adhering to an exercise program is a challenge. Augmenting stationary exercise equipment with an immersive Virtual Exercise Environment may make adherence more fun. We describe a system for capturing real bicycle trails for playback in such a VEE. In particular we discuss instrumentation of an adult trike to record distance and tilt angle. Simultaneously we capture image sequences from a cylindrical 5 camera cluster which are merged offline into extended panoramic video sequences. These combined terrain and surround video recording techniques allow us to capture both physical aspects of the terrain and immersive visual information. This information can then be used to “play back” the trail both physically on the exercise equipment and visually on a tracked Head Mounted Display (HMD).
On the Benefits of Network Coding for Wireless Applications

We argue that the main benefits of network coding in a wireless environment might manifest in situations where the topology dynamically changes, and operation is restricted to distributed algorithms that do not employ knowledge about the network environment. We consider several problem instances in this set-up, that include broadcasting information to all nodes of the network and collecting sensor measurements. We show that in many such cases, under some simplifying assumptions, the problem is theoretically equivalent to simple variations of the coupon collector problem. Thus network coding can offer benefits of a factor of log n, where n is the number of nodes and the benefits are in terms of energy efficiency, as was proven in [3]. We present simulation results under more realistic conditions that support this claim.
Analytical galactic models with mild stellar cusps

In the past two decades, it has been established by high-resolution observations of early-type galaxies that their nuclear surface brightness and corresponding stellar mass densities are characterized by cusps. In this paper, we present a new spherical analytical model family describing mild cuspy centres. We study isotropic and anisotropic models of Osipkov-Merritt type. It is shown that the associated distribution functions and intrinsic velocity dispersions can be represented analytically in a unified way in terms of hypergeometric series, allowing thus a straightforward comparison of these important global quantities for galaxies having underlying mass densities which may differ significantly in their degree of central cuspiness or radial falloff.
4-Week repeated oral dose toxicity study of 1,4-dichlorobutane in rats

The present study investigated the potential subacute toxicity of 1,4-dichlorobutane by a 4-week repeated oral dose in Sprague-Dawley rats. The test article was administered once daily by gavage to male rats at dose levels of 0, 100, 300, and 1,000 mg/kg/day for 4 weeks. All rats were sacrificed at the end of the treatment period. During the test period, clinical signs, mortality, body weight, hematology, serum biochemistry, gross findings, and organ weight were examined. At 1,000 mg/kg/day, an increase in the clinical signs and weights of the liver and kidneys was observed in the male rats. Serum biochemical investigations revealed an increase in alanine aminotransferase, alkaline phosphatase, total cholesterol, total bilirubin, phospholipids, blood urea nitrogen, and gamma glutamyl transferase levels. There were no treatment-related adverse effects in the low and middle-dose groups. In the present experimental conditions, the target organs were determined to be liver and kidney. The no-observed-adverse-effect level was considered to be 300 mg/kg/day in rats.
Notch3 Is Dispensable for Thymocyte β-Selection and Notch1-Induced T Cell Leukemogenesis

Notch1 (N1) signaling induced by intrathymic Delta-like (DL) ligands is required for T cell lineage commitment as well as self-renewal during “β-selection” of TCRβ+ CD4−CD8− double negative 3 (DN3) T cell progenitors. However, over-expression of the N1 intracellular domain (ICN1) renders N1 activation ligand-independent and drives leukemic transformation during β-selection. DN3 progenitors also express Notch3 (N3) mRNA, and over-expression of ligand-independent mutant N3 (ICN3) influences β-selection and drives T cell leukemogenesis. However, the importance of ligand-activated N3 in promoting β-selection and ICN1-induced T cell leukemogenesis has not been examined. To address these questions we generated mice lacking functional N3. We confirmed that DN3 progenitors express N3 protein using a N3-specific antibody. Surprisingly however, N3-deficient DN3 thymocytes were not defective in generating DP thymocytes under steady state conditions or in more stringent competition assays. To determine if N3 co-operates with N1 to regulate β-selection, we generated N1;N3 compound mutants. However, N3 deficiency did not exacerbate the competitive defect of N1+/− DN3 progenitors, demonstrating that N3 does not compensate for limiting N1 during T cell development. Finally, N3 deficiency did not attenuate T cell leukemogenesis induced by conditional expression of ICN1 in DN3 thymocytes. Importantly, we showed that in contrast to N1, N3 has a low binding affinity for DL4, the most abundant intrathymic DL ligand. Thus, despite the profound effects of ectopic ligand-independent N3 activation on T cell development and leukemogenesis, physiologically activated N3 is dispensable for both processes, likely because N3 interacts poorly with intrathymic DL4.
An Integrative Approach to Stroop: Combining a Language Model and a Unififed Cognitive Theory

The rich empirical puzzle of the Stroop effect has traditionally been approached with narrowly focused and somewhat atheoretical models. A recent exception is a simulation model based on the WEAVER++ language theory. The present model, WACT, combines components of WEAVER++ with the memory and control processes of the ACT-R cognitive theory. WACT accounts for the time course of inhibition from incongruent word distractors, facilitation from congruent word distractors, the lack of effect of color distractors, and the semantic gradient in inhibition. WACT goes beyond WEAVER++ to account for Stroop performance errors as well as latencies, and its implementation in a unified cognitive theory opens doors to broader coverage of Stroop phenomena than standalone models are likely to attain. Documented and executable code for WACT is available for inspection and comment at www.msu. edu/~ema/stroop.
Island grid modeling and validation using single phase phasor measurement data

This paper discusses how the single phase phasor measurement data are used to validate the Oahu island grid model. The island system model is first established using available literature and proper assumptions. After validation via real system measurements, the physical model can truly represent the system dynamics. The model is used to study the integration of renewable source on the Oahu power grid.