Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism

Topological filtering identifies biological networks compatible with known data and enables quantitative analysis of regulatory mechanisms. Reducing the Options Quantitative analysis of signaling systems is challenging because limited quantitative data are available and the data can be represented by many network models. Sunnåker et al. developed a computational approach called topological filtering to systematically and automatically integrate modeling and data acquisition to infer the set of mechanistically plausible models, thus vastly reducing the number of potential models. The approach iteratively eliminates reactions from the model to identify only those topological networks that fit the data. Application of their method to an extracellular signal–regulated kinase (ERK) pathway that could be represented by 512 possible network topologies reduced the possibilities to 16 and showed that a set of feedback reactions were necessary to quantitatively represent the results. Topological filtering applied to the regulation of the localization of Msn2, a yeast transcription factor controlled by phosphorylation by PKA (protein kinase A) in response to changes in glucose abundance, identified a single model that fit the data. Comparison of model predictions with experimental data showed that the nuclear phosphorylation rate was key to controlling Msn2 nuclear abundance in response to cAMP (cyclic adenosine monophosphate), a signal produced as cells recover from glucose starvation. Predictive dynamical models are critical for the analysis of complex biological systems. However, methods to systematically develop and discriminate among systems biology models are still lacking. We describe a computational method that incorporates all hypothetical mechanisms about the architecture of a biological system into a single model and automatically generates a set of simpler models compatible with observational data. As a proof of principle, we analyzed the dynamic control of the transcription factor Msn2 in Saccharomyces cerevisiae, specifically the short-term mechanisms mediating the cells’ recovery after release from starvation stress. Our method determined that 12 of 192 possible models were compatible with available Msn2 localization data. Iterations between model predictions and rationally designed phosphoproteomics and imaging experiments identified a single-circuit topology with a relative probability of 99% among the 192 models. Model analysis revealed that the coupling of dynamic phenomena in Msn2 phosphorylation and transport could lead to efficient stress response signaling by establishing a rate-of-change sensor. Similar principles could apply to mammalian stress response pathways. Systematic construction of dynamic models may yield detailed insight into nonobvious molecular mechanisms.
Removal of artifacts contaminated records from MEG records using a mixture of factor analyzers

Contamination of magnetoencephalogram (MEG) records by various artifacts seriously influences the estimation accuracy of magnetic sources. Although some methods have been proposed to reject contaminated records [1][2], most of them are ineffective when artifacts models are not available. In this study, we proposed to classify MEG records into contaminated records and others by mixture of factor analyzers (MFA). MFA provides a classification method which groups records into classes which are described by the model of factor analysis[3]. It is known that MFA is superior to conventional methods in its discrimination ability in a noisy environment [4]. It should be ideal in the classification of evoked responses on which large spontaneous waves are superimposed.We applied the proposed method to visual evoked fields (VEF) records.
Magnetically-guided manipulation of microfiber for fabrication of porous cell scaffold

As one of the most promising substitutes for regenerative medicine, the pore cell scaffold attracts great attentions in tissue engineering recently. In this study, we apply microfiber to assemble this kind of porous structure based on magnetically-guided manipulation. The microfiber is fabricated by biocompatible and biodegradable alginate solution inside a microfluidic device. To feasibly manipulate the microfiber, homogeneous magnetic nanoparticles are encapsulated into the alginate solution to improve controllability. Simultaneously, an external magnetic force generated by a round permanent magnet is provided to attract the microfibers on a magnetized device composed by pure iron wire arrays and wax. To provide a bionic environment, the magnetized device has been fabricated to allow the generation of optimal pore structure with submillimeter size and high density. As preliminary results, we have achieved to fabricate a one-layer cell scaffold through magnetically-guided micromanipulation.
Fragment molecular orbital study of the binding energy of ligands to the estrogen receptor

We examined the published data for the binding affinity of typical ligands to the α-subtype of the human estrogen receptor with use of an approximate molecular orbital method applicable to interacting molecular clusters. An ab initio procedure for "molecular fragments" proposed recently to deal with such macromolecules as proteins was applied to the molecular orbital calculations. The receptor protein was primarily modeled using 50 amino acid residues surrounding the ligand. For a few ligand-receptor complexes, the binding energy was also calculated with use of 241 amino acid residues contained in the entire binding domain. No significant difference was found in the calculated binding energy between the complex modeled with ligand-surrounding 50 amino acids and that with residues of the entire domain. The calculated binding energy was correlated very well with the published relative binding affinity for typical ligands.
Strong Parallel Repetition Theorem for Quantum XOR Proof Systems

We consider a class of two-prover interactive proof systems where each prover returns a single bit to the verifier and the verifier's verdict is a function of the XOR of the two bits received. We show that, when the provers are allowed to coordinate their behavior using a shared entangled quantum state, a perfect parallel repetition theorem holds in the following sense. The prover's optimal success probability for simultaneously playing a collection of XOR proof systems is exactly the product of the individual optimal success probabilities. This property is remarkable in view of the fact that, in the classical case (where the provers can only utilize classical information), it does not hold. The theorem is proved by analyzing parities of XOR proof systems using semidefinite programming techniques, which we then relate to parallel repetitions of XOR games via Fourier analysis.
Particle filter tracking method based on adaptive fusion of multiple features

An algorithm for fusing multiple features adaptively in particle filter tracking framework is proposed. The tracked object is represented by a set of submodels of each feature, and then the multiple cues are combined by linear weighting on particles to obtain a more satisfying approximation at the posterior distribution of object states. According to the discriminating contribution of each feature between object and background, the confidence on each feature is adjusted, and the feature weights are estimated and updated online in order to improve the complementary between multiple features. The analyses and experiments show good performance of the proposed method against appearance and background changes under complex scenes.
REAL-TIME QOS MEASUREMENTS

We propose a novel regressive principle to Admission Control (AC) assisted by real-time passive QoS monitoring. This measurement-based AC scheme accepts flows by default, but based on the changes in the network QoS, it makes regressive decisions on the possible flow rejection, thus bringing cognition to the network path. The REgressive Admission Control (REAC) system consists of three modules performing the necessary tasks: QoS measurements, traffic identification, and the actual AC decision making and flow control. There are two major advantages with this new scheme; (i) significant optimization of the connection start-up phase, and (ii) continuous QoS knowledge of the accepted streams. In fact, the latter combined with the REAC decisions can enable guaranteed QoS without requiring any QoS support from the network. REAC was tested on a video streaming test bed and proved to have a timely and realistic match between the network's QoS and the video quality.
Macroeconomic stability and the impact of foreign aid on economic growth in Nigeria

1. Identify unanticipated shocks in foreign aid. 2. Examining how macroeconomic stability constraints foreign aid and hinders the drives of growth. Vector Auto-regression Model 1. Estimates of the innovations of foreign aid shocks to macroeconomic variables shocks generates inconsistencies that distorts budget deficits. 2. Foreign aid shocks creates uncertainties that weakens current account balances and transmit negative shocks that has strong constraining effects on economic growth. 3. Foreign aid negative impacts reduce the tendencies for the economy to grow. 4. Macroeconomic strategies are inconsistent and lack the will to effectively utilize the gains of foreign aid.
The origin of deep ocean microseisms in the North Atlantic Ocean

Oceanic microseisms are small oscillations of the ground, in the frequency range of 0.05–0.3 Hz, associated with the occurrence of energetic ocean waves of half the corresponding frequency. In 1950, Longuet-Higgins suggested in a landmark theoretical paper that (i) microseisms originate from surface pressure oscillations caused by the interaction between oppositely travelling components with the same frequency in the ocean wave spectrum, (ii) these pressure oscillations generate seismic Stoneley waves on the ocean bottom, and (iii) when the ocean depth is comparable with the acoustic wavelength in water, compressibility must be considered. The efficiency of microseism generation thus depends on both the wave frequency and the depth of water. While the theory provided an estimate of the magnitude of the corresponding microseisms in a compressible ocean, its predictions of microseism amplitude heretofore have never been tested quantitatively. In this paper, we show a strong agreement between observed microseism and calculated amplitudes obtained by applying Longuet-Higgins' theory to hindcast ocean wave spectra from the North Atlantic Ocean. The calculated vertical displacements are compared with seismic data collected at stations in North America, Greenland, Iceland and Europe. This modelling identifies a particularly energetic source area stretching from the Labrador Sea to south of Iceland, where wind patterns are especially conducive to generating oppositely travelling waves of same period, and the ocean depth is favourable for efficient microseism generation through the ‘organ pipe’ resonance of the compression waves, as predicted by the theory. This correspondence between observations and the model predictions demonstrates that deep ocean nonlinear wave–wave interactions are sufficiently energetic to account for much of the observed seismic amplitudes in North America, Greenland and Iceland.
Miracle or misery? : understanding democratic participation in South Africa

On 27 April 1994 the most hated flag in Africa was lowered, signifying the end of the Apartheid regime. As the world watched the transformation of South Africa taking place – without the bloodshed that the state‟s direst cynics had predicted – words like "miracle" and "inspirational" abounded. Since then, the world has continued to watch South Africa‟s transition to democracy and even those who were its greatest supporters have begun to ask questions about the quality and quantity of democratic reforms. The increasing centralisation and monopolisation of power by the African National Congress, declining rates of formal participation by citizens and considerable failures in service delivery are major factors contributing to the concerns about the long-term prospects for democracy in South Africa, especially given the record of democratic failure across the rest of the continent. While significant contributions have been made to the study of South African democracy – both theoretical and empirical – there are few, if any, that have sought to combine both these methodologies and hence the scholarship is not, in my view, paying the dividends it should. This research thus explores contemporary politics in South Africa, examining its assets and liabilities in order to provide a clearer picture of the state of democracy in the country. It does so by measuring practices in South Africa in terms of the role accorded to participation in three conceptions of democracy: liberal representative accounts, deliberative accounts and what I term the "categorical" account. In so doing the research will show that although concerns about democracy in South Africa are justified, if we shift our focus from the instrumental value of participation to its categorical one we may find a way to ensure that the miracle continues.
The Rise of China and Its Implications for Emerging Markets - Evidence from a GVAR Model

This paper studies empirically the role of China in the world economy. We examine both the way the Chinese economy reacts to selected exogenous macroeconomic shocks and the repercussions for the world economy of a shock emanating from China. With regard to the latter, we focus on the responses of emerging markets, in particular those in Europe. Based on a global VAR (GVAR) model and a new data set that excels in country coverage and covers the most recent time period including the global financial crisis, our results are threefold: First, we show that a +1% shock to Chinese output translates to a permanent increase of 1.2% in Chinese real GDP and a 0.1% to 0.5% rise in output for most large economies. The countries of Central Eastern Europe (CEE) and the former Commonwealth of Independent States (CIS) also experience an output rise of 0.2%, while countries in South-Eastern Europe see a permanent 0.1% reduction in output. Secondly, to benchmark the shock to Chinese output, we examine the response to a +1% shock to US GDP. The results show that the US economy remains dominant in the world economy despite the rapid rise of China in recent years. In this vein, output rises in advanced economies by 1% to 1.4% and in the CIS and CEE regions by 1.5% and 0.7% respectively. By contrast China seems to be little affected by the US shock. Finally, we examine the effect of a +50% hike in oil prices on China and emerging economies. As one of the largest oil exporters, Russia's real output increases by about 6%. In contrast, the surge in oil prices puts a drag on Chinese output, amounting to 4.5% in the long-run. JEL Classification: C32, F44, E32, O54 Keywords: China, macroeconomic shocks, foreign shock, GVAR, great recession
Two-population replicator dynamics and number of Nash equilibria in matrix games

We study the connection between the evolutionary replicator dynamics and the number of Nash equilibria in large random bi-matrix games. Using techniques of disordered systems theory we compute the statistical properties of both, the fixed points of the dynamics and the Nash equilibria. Except for the special case of zero-sum games, one finds a transition as a function of the so-called co-operation pressure between a phase in which there is a unique stable fixed point of the dynamics coinciding with a unique Nash equilibrium, and an unstable phase in which there are exponentially many Nash equilibria with statistical properties different from the stationary state of the replicator equations. Our analytical results are confirmed by numerical simulations of the replicator dynamics, and by explicit enumeration of Nash equilibria.
Monitoring multi-tier clustered systems with invariant metric relationships

To ensure high availability, self-managing systems require self-monitoring and a system model against which to analyze monitoring data. Characterizing relationships between system metrics has been shown to model simple multi-tier transaction systems effectively, enabling failure detection and fault diagnosis. In this paper we show how to extend this invariant metric-relationships approach to clustered multi-tier systems. We show through analysis and experimentation that naive application of the approach increases cost dramatically while reducing diagnosis accuracy. We demonstrate that randomization at the load balancer during the invariant-identification phase will improve diagnosis accuracy, though it neither completely eliminates the problem nor reduces the cost; indeed, it may increase the cost, as this approach will require a long learning phase to remove all accidental correlations. Finally, we argue that knowing the system structure is necessary to effectively apply invariants to the clustered environment.
Counting bloom filters for pattern matching and anti-evasion at the wire speed

Standard pattern-matching methods used for deep packet inspection and network security can be evaded by means of TCP and IP fragmentation. To detect such attacks, intrusion detection systems must reassemble packets before applying matching algorithms, thus requiring a large amount of memory and time to respond to the threat. In the literature, only a few efforts proposed a method to detect evasion attacks at high speed without reassembly. The aim of this article is to introduce an efficient system for anti-evasion that can be implemented in real devices. It is based on counting bloom filters and exploits their capabilities to quickly update the string set and deal with partial signatures. In this way, the detection of attacks and almost all of the traffic processing is performed in the fast data path, thus improving the scalability of intrusion detection systems.
An Analysis Method for Sampling in Shift-invariant Spaces

A subspace V of L 2 (R) is called shift-invariant if it is the closed linear span of integer-shifted copies of a single function. As a complement to classical analysis techniques for sampling in such spaces, we propose a method which is based on a simple interpolation estimate of a certain coefficient mapping. Then we use this method for deriving both new results and relatively simple proofs of some previously known results. Among these are both some results of rather general nature and some more specialized results for B-spline wavelets. The main problem under study is to find a shift x 0 and an upper bound δ such that any function f ∈ V can be reconstructed from a sequence of sample values (f (x 0 + k + δ k)) k∈Z , either when all δ k = 0 or in the irregular sampling case with an upper bound sup k |δ k | < δ.
Gene Expression Changes Induced by Trypanosoma cruzi Shed Microvesicles in Mammalian Host Cells: Relevance of tRNA-Derived Halves

At present, noncoding small RNAs are recognized as key players in novel forms of posttranscriptional gene regulation in most eukaryotes. However, canonical small RNA pathways seem to be lost or excessively simplified in some unicellular organisms including Trypanosoma cruzi which lack functional RNAi pathways. Recently, we reported the presence of alternate small RNA pathways in T. cruzi mainly represented by homogeneous populations of tRNA- and rRNA-derived small RNAs, which are secreted to the extracellular medium included in extracellular vesicles. Extracellular vesicle cargo could be delivered to other parasites and to mammalian susceptible cells promoting metacyclogenesis and conferring susceptibility to infection, respectively. Here we analyzed the changes in gene expression of host HeLa cells induced by extracellular vesicles from T. cruzi. As assessed by microarray assays a large set of genes in HeLa cells were differentially expressed upon incorporation of T. cruzi-derived extracellular vesicles. The elicited response modified mainly host cell cytoskeleton, extracellular matrix, and immune responses pathways. Some genes were also modified by the most abundant tRNA-derived small RNAs included in extracellular vesicles. These data suggest that microvesicles secreted by T. cruzi could be relevant players in early events of the T. cruzi host cell interplay.
Seeking the Links between Telecommunications Investment and Competition

Using country-level time series and firm-level panel data, we show that telecommunications investment and competition have evolved quite independently, at least in OECD economies. The literature findings on this subject are quite mixed, but we here strengthen empirical evidence employing a set of models and methods. As a first analysis, unknown breakpoints were sought in the investment series of each country. Structural changes emerged, but they do not show a clear-cut relationship with liberalization and unbundling events. The incumbent’s investment was then focused on. Product market competition does not play an autonomous role, a result that was confirmed by both causality analyses and micro-econometric investment models. However, it moderates the impact of pro-entry regulation. The unbundling regime has been found to reduce the incumbent’s incentives to invest, unless a certain degree of competition has already emerged on the service market.
Straight talk about gays in the workplace

Establish inclusive policies to increase productivity and profitability! Until recently, the topic of diversity in the workplace had been limited to race and gender issues. In the past decade, however, there has been a growing awareness that sexual orientation is also a valid component of diversity. Even more importantly, the inclusion of this aspect of diversity and workplace education about it in organizational policy and programs are positive, revenue-enhancing actions for business organizations. This is true whether the organization in question is a municipal employer, a college/university, a nonprofit, or a private sector employer.The first edition of Straight Talk About Gays in the Workplace was the only book available to address sexual orientation for employers concerned about this aspect of diversity. This new edition is still the only book to do so. The book's approach is positive and practical, offering not only the 'why'and the 'what', but also the 'how-to', with strategies and tools to improve any workplace relative to this part of human resources. This new edition is fully updated with state-of-the-art information on: domestic partner benefits (DPBs) effective education regarding sexual orientation in the workplace marketing opportunities generated by full inclusion why full inclusion makes good business senseStraight Talk About Gays in the Workplace, Second Edition clarifies the details and impacts of: workplace education about sexual orientation tax codes concerning partner benefits the Employment Non-Discrimination Act (ENDA) the Hate Crimes Bill. and provides resources including: all applicable tax codes concerning partner benefits sample affidavit for partner benefits sample announcement for partner benefits sample termination form for partner benefits detailed information on the Employment Non-Discrimination Act (ENDA) detailed information about the Hate Crimes Bil a model for successful education focused on sexual orientation Web resources for more information . and more! After reading this volume, you will be able to write a business plan, proposal, or justification for policy/program improvements that will benefit your business. Straight Talk About Gays in the Workplace, Second Edition is especially valuable in today's job market where it is increasingly difficult to find and keep qualified job candidates.