Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring Condition-Specific Modulation of Transcription Factor Activity in Yeast through Regulon-Based Analysis of Genomewide Expression

Background A key goal of systems biology is to understand how genomewide mRNA expression levels are controlled by transcription factors (TFs) in a condition-specific fashion. TF activity is frequently modulated at the post-translational level through ligand binding, covalent modification, or changes in sub-cellular localization. In this paper, we demonstrate how prior information about regulatory network connectivity can be exploited to infer condition-specific TF activity as a hidden variable from the genomewide mRNA expression pattern in the yeast Saccharomyces cerevisiae. Methodology/Principal Findings We first validate experimentally that by scoring differential expression at the level of gene sets or “regulons” comprised of the putative targets of a TF, we can accurately predict modulation of TF activity at the post-translational level. Next, we create an interactive database of inferred activities for a large number of TFs across a large number of experimental conditions in S. cerevisiae. This allows us to perform TF-centric analysis of the yeast regulatory network. Conclusions/Significance We analyze the degree to which the mRNA expression level of each TF is predictive of its regulatory activity. We also organize TFs into “co-modulation networks” based on their inferred activity profile across conditions, and find that this reveals functional and mechanistic relationships. Finally, we present evidence that the PAC and rRPE motifs antagonize TBP-dependent regulation, and function as core promoter elements governed by the transcription regulator NC2. Regulon-based monitoring of TF activity modulation is a powerful tool for analyzing regulatory network function that should be applicable in other organisms. Tools and results are available online at http://bussemakerlab.org/RegulonProfiler/.
Can Network Linkage Effects Determine Return? Evidence from Chinese Stock Market

This study used the dynamic conditional correlations (DCC) method to identify the linkage effects of Chinese stock market, and further detected the influence of network linkage effects on magnitude of security returns across different industries. Applying two physics-derived techniques, the minimum spanning tree and the hierarchical tree, we analyzed the stock interdependence within the network of the China Securities Index (CSI) industry index basket. We observed that that obvious linkage effects existed among stock networks. CII and CCE, CAG and ITH as well as COU, CHA and REI were confirmed as the core nodes in the three different networks respectively. We also investigated the stability of linkage effects by estimating the mean correlations and mean distances, as well as the normalized tree length of these indices. In addition, using the GMM model approach, we found inter-node influence within the stock network had a pronounced effect on stock returns. Our results generally suggested that there appeared to be greater clustering effect among the indexes belonging to related industrial sectors than those of diverse sectors, and network comovement was significantly affected by impactive financial events in the reality. Besides, stocks that were more central within the network of stock market usually had higher returns for compensation because they endured greater exposure to correlation risk.
Less May Be More: Rethinking Adult Literacy Volunteer Tutor Training

This study analyzed the relation between volunteer tutor training and reading instruction in 4 adult literacy programs. The data focus on tutors' choices of reading materials and strategies for assisting in the development of comprehension and word identification skills. Tutor training did not always transfer to practice, and it did not always deal effectively with the complex topic of teaching reading to struggling adult learners. One implication might be that less initial training and more ongoing “just-in-time” training based on the specific needs and strengths of students and tutors working together on improving reading may be a more efficient use of resources than those traditionally expended on preservice training.
Statin Use Mitigate the Benefit of Omega-3 Fatty Acids Supplementation—A Meta-Regression of Randomized Trials

During last 2 decades, multiple studies have evaluated omega-3 polyunsaturated fatty acids (&ohgr;-3 PUFA) supplementation for cardiovascular prevention. The benefit found in previous studies was not demonstrated in more contemporary trials. We aimed to investigate effect of study characteristics, particularly concomitant statin therapy on results of randomized controlled trials. We systematically searched electronic databases for randomized controlled trials evaluating &ohgr;-3 PUFA supplementation and reporting clinical outcomes. A meta-analysis was performed using a random effect model, followed by a meta-regression of dose, docosahexaenoic acid/eicosapentaenoic acid (DHA/EPA) ratio, and duration of treatment and use of lipid-lowering/statin therapy in control group. Twenty-three studies with 77,776 patients (38,910 PUFA; 38,866 controls) were included. PUFA had no effect on total mortality [risk ratio (RR) = 0.96; 95% confidence interval (CI), 0.92–1.01] and myocardial infarction (RR = 0.87; 95% CI, 0.73–1.02), but marginally reduced cardiovascular mortality (RR = 0.93; 95% CI, 0.87–0.98). Lower control group statin use (b = 0.222, P = 0.027) and higher DHA/EPA (b = −0.105, P = 0.033) ratio was associated with higher reduction in total mortality. Duration and dose had no effect. None of the variables except duration had significant effect on reduction in cardiovascular mortality by PUFA supplementation. There was evidence of publication bias. Statin use may mitigate, and higher DHA/EPA ratio is associated with the beneficial effect of PUFA supplementation.
Network support for mobile multimedia using a self-adaptive distributed proxy

Recent advancements in video and audio codec technologies~(e.g., RealV ideo [18] make multimedia streaming possible across a wide range of network conditions. With an increasing trend of ubiquitous connectivity, more and more areas have overlapping coverage of multiple wired and wireless networks. Because the best network service changes as the user moves, to provide good multimedia application performance, the service needs to adapt to user movement as well as network and computational resource variations. For wireless multimedia applications, one must ensure smooth transitions when network connectivity changes. We argue that network adaptations for multimedia applications should be provided at the application layer with help from proxies in the network. The reasons are ease of programming, ease of deployment, better fault-tolerance, and greater scalability. We propose aself-adaptive distributed proxy systemthat provides streaming multimedia service to mobile wireless clients. Our system intelligently adapts to the real-time network variations and hides handoff artifacts using application protocol specific knowledge whenever possible. It also uses application-independent techniques such as dynamic relocation of transcoders and automatic insertion of forward error correction and compression into the data transcoding path. We advocate a composable, relocatable transcoding data path consisting of a directed acyclic graph ofstrongly-typedoperators to bridge any data format mismatch between the client and the data source. In this paper, we present the design, implementation, and evaluation of our system in the context of streaming video playback involving a series of transcoding proxies and a mobile client.
Cocaine Using Careers in Perspective

This article provides an integrative discussion of cocaine using careers based on a review of the articles included in this special issue of Addiction Research. It also attempts to place the findings from the article in context by examining the patterns of cocaine use among a representative sample of the U.S. population. Much of what we know about cocaine using careers has been obtained in studies of treatment or criminal justice populations. But studying cocaine users among “community-based” samples of users challenges common stereotypes about cocaine users. These studies conclude that although many cocaine users escalated use for some period of time, most also deescalated use. The frequency of cocaine use, the use of other drugs, and the mode of administration were found to be related to adverse consequences. Users employed a variety of rules to keep their cocaine use from becoming compulsive. Most importantly, many controlled users were socially fully integrated and placed great importance on their fam.
Design and control of high-speed solid-rotor synchronous reluctance drive with three-phase LC filter

Synchronous reluctance machines with solid rotor construction have advantages in certain high-speed applications such as flywheel energy storage systems. However, the solid rotor allows the flow of eddy currents, resulting in heat generation. A three-phase LC filter can reduce rotor losses due to the switching harmonics generated by a 3-phase inverter. This paper investigates the design and control of a high-speed synchronous reluctance drive with a three-phase LC filter. A two-phase dynamic model of the drive which incorporates the LC filter dynamics is presented. This model is used to predict rotor losses due to switching harmonics using phasor analysis. A feedforward-based current regulator is utilized, which is modified to include the effects of the LC filter. Simulation and experimental results validate the proposed approach.
Metatheoretical Prospects for the Field of Transformative Learning

This article examines the complex mosaic of first- and second-wave theories of transformative learning and recommends the development of a subfield of meta-inquiry. Central to this undertaking is the need for metatheorizing, to which this article outlines a rationale with specific criteria for developing a metatheoretical discourse and more comprehensive metatheoretical frameworks. It then goes on to examine the strengths and limitations of Wilber's AQAL model as a possible candidate for working with a meta-analysis of first- and second-wave contributions within the field.
Institution-based early intervention program

Cet article passe en detail un programme d'intervention precoce dans des orphelinats de Saint Petersbourg en Russie. Ce programme est base sur l'analyse du systeme de l'orphelinat et des premieres donnees statistiques sur les enfants, le personnel et leur interaction. Les resultats des observations faites avant l'intervention ont montre des deficits cruciaux du personnel de soin pour ce qui concerne la stabilite, la coherence, ainsi que l'attention et la disponibilite emotionnelle. Le personnel de soin met en fait l'attention sur le soin medical, l'education et le mode de soin quotidien et routinier. Cet article expose les principes directeurs d'un programme d'intervention precoce d'un niveau institutionnel, programme ayant pour but que chaque enfant ait une experience precoce d'interaction continue avec ses propres adultes, etant eux-memes proches et emotionnellement disponibles. Ces principes directeurs de ce programme sont soutenus par le projet collectif Saint Petersbourg (Federation de Russie) - Pittsburgh (USA) avec deux interventions principales: la formation de personnel de soin et des changements structurels dans l'orphelinat afin de promouvoir des conditions proches des conditions familiales pour les enfants. Un survol de l'intervention de formation est decrit dans un article parallele (Groark, Muhamedrahimov, Nikiforova, Palmov, & McCall, in press). L'intervention des changements structurels avait pour but d'ameliorer la stabilite et la coherence des modes de soin et d'offrir un milieu proche de celui d'une famille afin de promouvoir le developpement de relations. Plus particulierement, l'intervention a consiste en plus petits groupes, l'integration par âge et statut d'infirmite, les modes de soin primaires qui etaient presents tous les jours, une Heure Familiale, des groupes detachables, et une organisation du personnel basee sur le concept et l'esprit d'equipe. Les observations et l'analyse des donnees montrent que l'application efficace de l'intervention sur les changements structurels, une augmentation de la coherence et de la stabilite du personnel de mode de soin, et des changements chez les enfants et les modes de soin.
Is Breastfeeding Truly Cost Free? Income Consequences of Breastfeeding for Women

Based on studies showing health advantages for breastfeeding mothers and their infants, pediatricians and other breastfeeding advocates encourage new mothers to breastfeed their babies for at least the first six months of their infants’ lives, arguing that breast milk is best for infants, families, and society, and it is cost free. Few empirical studies, however, document how the decision to breastfeed instead of formula-feed is associated with women’s post-birth earnings. This is an important omission, given that the majority of women today work for pay, and many work in job environments incompatible with breastfeeding. Using data from the National Longitudinal Survey of Youth, our results show that mothers who breastfeed for six months or longer suffer more severe and more prolonged earnings losses than do mothers who breastfeed for shorter durations or not at all. The larger post-birth drop in earnings for long-duration breastfeeders is due to a larger reduction in labor supply. We discuss the implications of these findings for gender equality at home and at work.
Cultural Differences in Consumer Impatience

In this article, the authors examine cross-cultural variations in how people discount the future. Specifically, they predict that people from Western cultures are relatively less patient and therefore discount the future to a greater degree than do people from Eastern cultures, and thus Westerners value immediate consumption relatively more. Furthermore, on the basis of regulatory focus theory, the authors predict that when Easterners are faced with the threat of a delay in receiving a product (i.e., a prevention loss), they are more impatient, whereas when Westerners are faced with the threat of not being able to enjoy a product early (i.e., a promotion loss), their impatience increases. This enhanced impatience manifests in preference for expedited consumption of a product purchased online in two studies. In both studies, the authors used a priming methodology on “bicultural” Singaporean participants; the results support the predictions. In the second study, they also found evidence in support of the process-based explanation for the interaction between culture and message framing.
Design of artificial mains network for conducted disturbance from 2 kHz to 30 MHz

Power conversion equipment, such as power conditioning systems (PCSs), is known to generate conducted disturbance in a broad frequency range. Recently, the power capacity of the equipment has become larger because of the efficient use of them, and the conducted disturbances occur in the frequency range from 2 kHz to 9 kHz, where no measurement method and limit levels are regulated. In this paper, the design procedure and development of four types of artificial mains network (AMN) are studied in order to measure conducted disturbances and establish a reproducible measurement method that works in the frequency range from 2 kHz to 30 MHz. The impedance characteristics, isolation characteristics, and voltage conversion factor of each AMN are evaluated in both a circuit simulation and measurement to see if they can meet the required characteristics. As a result, it was found that the developed AMNs have a good agreement with the required characteristics.
Tolerating denial-of-service attacks: a system approach

Proxy network-based defense has recently emerged to address an open research challenge—protecting Internet service applications from Denial-of-Service (DoS) attacks. Such schemes use a proxy network as a mediator for a hidden application to prevent direct attacks on the application's physical infrastructure, while maintaining communication between users and the application. The proxy network provides a distributed front-end to disperse DoS attack traffic, thereby shielding the application. However, the basic feasibility and fundamental properties of such schemes remain unclear, posing critical challenges for their use. This dissertation addresses these challenges by exploring proxy networks' ability to resist important attacks: penetration, proxy depletion, and DoS attacks. We develop a generic analytic framework for proxy network-based systems, and use it to analyze proxy networks' resilience to penetration and proxy depletion attacks, characterizing how attacks, defenses, proxy network structure, and correlation in host vulnerabilities affect feasibility. Furthermore, using online simulation, we quantify the resistance to DoS attacks at an unprecedented scale and realism, by running real application, proxy network, and attack programs in a simulated network with a size comparable to tier-1 ISP networks. We show that proxy network-based DoS defense can effectively resist these attacks, and protect applications successfully. Specific results are the following. First, proactive defenses, such as proxy migration, are required for penetration resistance—proxy networks can be effectively impenetrable with proxy migration, but will be penetrated easily without proactive defenses. Second, correlation in host vulnerabilities makes proxy networks vulnerable to penetration. By exploiting host diversity and intelligent proxy network construction, effective resistance can be achieved. Third, topology is crucial for resisting proxy depletion attacks: when a topology's eigenvalue is smaller than the speed ratio between defense and attack, all compromised proxies will always be recovered; when a topology's Laplacian spectrum is larger than this ratio, compromised proxies will linger, making the proxy network unrecoverable. Last, proxy networks provide effective and scalable DoS defense. They can resist large-scale DoS attacks, while preserving performance for the majority (>90%) of users. Furthermore, increasing the proxy network size linearly improves the level of resistance to DoS attacks.
macroH2A1 histone variant represses rDNA transcription

The regulation of ribosomal DNA transcription is an important step for the control of cell growth. Epigenetic marks such as DNA methylation and posttranslational modifications of canonical histones have been involved in this regulation, but much less is known about the role of histone variants. In this work, we show that the histone variant macroH2A1 is present on the promoter of methylated rDNA genes. The inhibition of the expression of macroH2A1 in human HeLa and HepG2 cells and in a mouse ES cell line resulted in an up to 5-fold increase of pre-rRNA levels. This increased accumulation of pre-rRNA is accompanied by an increase of the loading of RNA polymerase I and UBF on the rDNA without any changes in the number of active rDNA genes. The inhibition of RNA polymerase I transcription by actinomycin D or by knocking down nucleolin, induces the recruitment of macroH2A1 on the rDNA and the relocalization of macroH2A1 in the nucleolus. Interestingly, the inhibition of rDNA transcription induced by nucleolin depletion is alleviated by the inactivation of macroH2A1. These results demonstrate that macroH2A1 is a new factor involved in the regulation of rDNA transcription.
The third public : hermeneutical key to the theological debate on church and development?

The aim of the paper is to answer the question whether the proposal for a third public mode of theological involvement represents the key to overcoming the current deficiency in theological thinking about the strategic role of the churches in addressing the problems of poverty and underdevelopment in South Africa. In the light of a twofold exploration into (i) historical ecumenical development discourse and (ii) the so-called generational perspective in the NGO development debate, the paper concludes with a positive answer. At the same time, however, it is argued that there is also an important role to play for the modes of the first and second publics, and that a greater interplay between the various publics is required in order for Christian theology to be effective in the field of development.
PROPER FILTER DESIGN PROCEDURE FOR VIBRATION SUPPRESSION USING DELAY-ERROR-ORDER CURVES

Vibration suppression can be performed by digital filtering the input to the flexible system. Traditional digital filters have been proved to be efficient for vibration suppression, when they are properly designed. In order to ensure the proper filter design, the Delay-ErrorOrder (DEO) curves are introduced, to be used as a filter design tool. Based on the DEO curves, the vibration suppression properties and capabilities of the filter can be related with the design parameters involved in the traditional filter design methods. Using the DEO curves, the filters designed by means of conventional design methods posses excellent vibration suppression capabilities. This design procedure is presented in detail in this paper and an example of the application of the method is included.
Spectrum bandit optimization

We consider the problem of allocating radio channels to links in a wireless network. Links interact through interference, modelled as a conflict graph (i.e., two interfering links cannot be simultaneously active on the same channel). We aim at identifying the channel allocation maximizing the total network throughput over a finite time horizon. Should we know the average radio conditions on each channel and on each link, an optimal allocation would be obtained by solving an Integer Linear Program (ILP). When radio conditions are unknown a priori, we look for a sequential channel allocation policy that converges to the optimal allocation while minimizing on the way the throughput loss or regret due to the need for exploring suboptimal allocations. We formulate this problem as a generic linear bandit problem, and analyze it in a stochastic setting where radio conditions are driven by a i.i. d. stochastic process, and in an adversarial setting where radio conditions can evolve arbitrarily. We provide, in both settings, algorithms whose regret upper bounds outperform those of existing algorithms.
High-Level Optimization by Combining Retiming and Shannon Decomposition

Applying Shannon decomposition can reshape sequential circuits and improve opportunities for retiming. Both Shannon decomposition and retiming only rely on limited information about combinational blocks (timing estimates), so both techniques are suitable for high-level synthesis. We describe an efficient algorithm to preprocess a circuit using Shannon decomposition to increase retiming efficacy. It assembles complex chains of Shannon decompositions while carefully avoiding parallel ones in order to limit the area overhead due to logic duplication. We compare a traditional retiming flow with the same flow augmented with our algorithm. Although our algorithm provides no improvement on half of our benchmarks, for the other half we obtain a 25% speed-up on average (7% to 61%), while only increasing area by 5% (3% to 12%).