Miracle-dz/UniFAR-FTUs huggingface dataset:
Time-dependent cross-correlations between different stock returns: a directed network of influence.

We study the time-dependent cross-correlations of stock returns, i.e., we measure the correlation as the function of the time shift between pairs of stock return time series using tick-by-tick data. We find a weak but significant effect showing that in many cases the maximum correlation appears at nonzero time shift, indicating directions of influence between the companies. Due to the weakness of this effect and the shortness of the characteristic time (of the order of a few minutes), our findings are compatible with market efficiency. The interaction of companies defines a directed network of influence.
Qualitative Possibilistic In ° uence Diagrams

|In°uence diagrams (IDs) are one of the most commonly used graphical decision models for reasoning under uncertainty. The quanti ̄cation of IDs which consists in de ̄ning conditional probabilities for chance nodes and utility functions for value nodes is not always obvious. In fact, decision makers cannot always provide exact numerical values and in some cases, it is more easier for them to specify qualitative preference orders. This work proposes an adaptation of standard IDs to the qualitative framework based on possibility theory.
Nickel-Responsive Induction of Urease Expression inHelicobacter pylori Is Mediated at the Transcriptional Level

ABSTRACT The nickel-containing enzyme urease is an essential colonization factor of the gastric pathogen Helicobacter pylori, as it allows the bacterium to survive the acidic conditions in the gastric mucosa. Although urease can represents up to 10% of the total protein content of H. pylori, expression of urease genes is thought to be constitutive. Here it is demonstrated that H. pyloriregulates the expression and activity of its urease enzyme as a function of the availability of the cofactor nickel. Supplementation of brucella growth medium with 1 or 100 μM NiCl2 resulted in up to 3.5-fold-increased expression of the urease subunit proteins UreA and UreB and up to 12-fold-increased urease enzyme activity. The induction was specific for nickel, since the addition of cadmium, cobalt, copper, iron, manganese, or zinc did not affect the expression of urease. Both Northern hybridization studies and a transcriptionalureA::lacZ fusion demonstrated that the observed nickel-responsive regulation of urease is mediated at the transcriptional level. Mutation of the HP1027 gene, encoding the ferric uptake regulator (Fur), did not affect the expression of urease in unsupplemented medium but reduced the nickel induction of urease expression to only twofold. This indicates that Fur is involved in the modulation of urease expression in response to nickel. These data demonstrate nickel-responsive regulation of H. pyloriurease, a phenomenon likely to be of importance during the colonization and persistence of H. pylori in the gastric mucosa.
On the achievable rates and degrees of freedom of causally cognitive MISO broadcast channels

This paper explores the problem of how a secondary transmitter could serve several users simultaneously by utilizing the spectrum of a primary system while imposing no impact on it (i.e. satisfying the coexistence constraint), even if the primary system keeps active all the time. The difficulty of this problem lies in that how the secondary system should tackle the interference encountered at multiple secondary receivers. In the cognitive transmission framework, the core of the above problem include two aspects: 1) How to learn quickly the message(s) of the primary system? 2) How to efficiently address the interference at multiple secondary receivers with the knowledge of the primary message? To solve these two problems, our main idea is to fully exploit the advantages of multiple antennas and the potential of transmitter cognition of the interfered message, in order to achieve the goal of fast exploration and full exploitation. In information theoretic terms, the above problem is equivalent to studying the achievable rate of the causally cognitive MISO broadcast channel under the so-called coexistence constraint. For this problem, we propose an efficient achievable scheme which is essentially based on the dirty paper coding and the zero-forcing beamforming and proves to be capable of realizing rather considerable sum rate and degrees of freedom for the secondary system. Our scheme exploits an interesting result regarding the capacity region of the MIMO Gaussian broadcast channel with states known only to the encoders.
Recommender System for E-Learning Based on Semantic Relatedness of Concepts

Digital publishing resources contain a lot of useful and authoritative knowledge. It may be necessary to reorganize the resources by concepts and recommend the related concepts for e-learning. A recommender system is presented in this paper based on the semantic relatedness of concepts computed by texts from digital publishing resources. Firstly, concepts are extracted from encyclopedias. Information in digital publishing resources is then reorganized by concepts. Secondly, concept vectors are generated by skip-gram model and semantic relatedness between concepts is measured according to the concept vectors. As a result, the related concepts and associated information can be recommended to users by the semantic relatedness for learning or reading. History data or users’ preferences data are not needed for recommendation in a specific domain. The technique may not be language-specific. The method shows potential usability for e-learning in a specific domain.
COMPOSITES IN BONE TISSUE ENGINEERING

B iomaterials play a critical role in the success of tissue engineering approaches, as they guide the shape and structure of developing tissues, provide mechanical stability, and present opportunities to deliver inductive molecules to transplanted or migrating cells. Therefore, the selection of the appropriate biomaterial can have a profound impact on the quality of newly formed tissue. A major challenge facing the field of tissue engineering is the development or identification of materials capable of promoting the desired cellular and tissue behavior. Given that few biomaterials possess all the necessary characteristics to perform ideally, engineers and clinicians alike have pursued the development of hybrid or composite biomaterials to synergize the beneficial properties of multiple materials into a superior matrix. The combination of natural and synthetic polymers with various other materials has demonstrated the ability to enhance cellular interaction, encourage integration into host tissue, and provide tunable material properties and degradation kinetics. In the current review, we describe the selection and utilization of numerous hybrid and composite materials to promote the formation of bone, vascular, and neural tissues. The continued development and implementation of hybrid biomaterials will lead to further successes in tissue engineering and regenerative medicine.
Conformational preferences of the amylin nucleation site in SDS micelles: An NMR study

Human islet amyloid polypeptide (hIAPP), or amylin, is a 37 amino acid hormone secreted by pancreatic β‐cells. hIAPP constitutes ∼90% of the amyloid deposits found in type II diabetic patients. It has been shown that the central region of the peptide (hIAPP20–29) constitutes the nucleation site for the amyloidogenic process with F23 playing a key role in the formation of the β‐pleated structures. In addition, it has been proposed that an important stage in the cytotoxicity of hIAPP is its interaction with the β‐cell membranes. As a first step toward the characterization of the interaction of hIAPP with cell membranes, we determined conformational preferences of hIAPP20–29 in membrane‐mimicking environments. We found that upon interacting with negatively charged micelles, the dominant conformation of hIAPP20–29 is a distorted type I β‐turn centered on residues F23 and G24, with F23, A25, and I26 forming a small hydrophobic cluster that may facilitate the interaction of this peptide with the membrane bilayer. Moreover, we were able to elucidate the topological orientation of the peptide that is absorbed on the micelle surface, with the hydrophobic cluster oriented toward the hydrocarbon region of the micelles and both N‐ and C‐termini exposed to the solvent. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 29–41, 2003
Modeling of Nafion-Pt composite actuators (ICPF) by ionic motion

In this paper, a white-box model of Nafion-Pt composite actuators considering the following physical phenomena is proposed: 1) ionic motion by electric field, 2) water motion by ion-drag, 3) swelling and contraction of the membrane, 4) momentum effect, 5) electrostatic force, and 6) conformation change. Computer simulation showed the following results. 1) The simulated motions agreed with experimental results improving the accuracy in comparison with the conventional models, especially on the time of the maximum displacement. 2) The nonlinear relation between input voltage and the maximum displacement was explained.
Cytochrome P4502C9-Derived Epoxyeicosatrienoic Acids Induce the Expression of Cyclooxygenase-2 in Endothelial Cells

Objective— Cytochrome P450 (CYP) epoxygenases metabolize arachidonic acid to epoxyeicosatrienoic acids (EETs). CYP2C9-derived EETs elicit endothelial cell proliferation and angiogenesis, but the signaling pathways involved are incompletely understood. Because cyclooxygenase-2 (COX-2) is involved in angiogenesis, we determined whether a link exists between CYP2C9 and COX-2 expression. Methods and Results— Human umbilical vein endothelial cells were infected with CYP2C9 sense or antisense adenoviral constructs. Overexpression of CYP2C9 increased COX-2 promoter activity, an effect accompanied by a significant increase in COX-2 protein expression and elevated prostacyclin production. The CYP2C9-induced expression of COX-2 was inhibited by the CYP2C9 inhibitor, sulfaphenazole, whereas 11,12-EET increased COX-2 expression. Overexpression of CYP2C9 and stimulation with 11,12-EET increased intracellular cAMP levels and stimulated DNA-binding of the cAMP-response element-binding protein. The protein kinase A inhibitor, KT5720, attenuated the CYP2C9-induced increase in COX-2 promoter activity and protein expression. Overexpression of CYP2C9 stimulated endothelial tube formation, an effect that was attenuated by the COX-2 inhibitor celecoxib. Identical responses were observed in cells preconditioned by cyclic strain to increase CYP2C expression. Conclusion— These data indicate that CYP2C9-derived EETs induce the expression of COX-2 in endothelial cells via a cAMP-dependent pathway and that this mechanism contributes to CYP2C9-induced angiogenesis.
Complexity and Expressive Power of Deterministic Semantics for DATALOG¬

Abstract Deterministic models are (partial) stable models which are not contradicted by any other stable model; i.e., M is a deterministic model if there is no stable model N such that M ∪ N is not an interpretation. For instanced the well-founded model, which coincides with the intersection of all partial stable models, is a deterministic model. As the well-founded model is deterministic and unique for each program, well-founded model semantics has been proposed as the canonical deterministic semantics for partial stable models. But the well-founded model is not the unique deterministic model; indeed the family of deterministic (partial stable) models is not, in general, a singleton and admits a minimum (the well-founded model) and a maximum, the max-deterministic model. The latter model is, another candidate for a deterministic semantics. The aim of this paper is to study the complexity and the expressive power of deterministic semantics. In coherence with the deterministic nature of the model, the expressive power of max-deterministic semantics is shown to be able to express problems with unique solutions, whereas the well-founded model only captures a proper subset of the queries computable in polynomial time, the so-called fixpoint queries.
Theoretical and mathematical models in polymer research : modern methods in polymer research and technology

D. Thirumalai and E. -Y. Ha, Statistical Mechanics of Semiflexible Chains: A Meanfield Variational Approach. A.N. Semenov, J.-F. Joanny, and A. Johner, Polymer Adsorption: Mean-Field Theory and Ground State DominanceApproximation. S.V. Panyukov and Y. Rabin, Replica Field Theory Methods in Physics of Polymer Networks. B. Drosel and M. Kardar, Winding Angle Distributions for Directed Polymers. B. OShaughnessy, Bulk and Interfacial Polymer Reaction Kinetics. Subject Index.
DNA Microarray-Mediated Transcriptional Profiling of the Escherichia coli Response to Hydrogen Peroxide

ABSTRACT The genome-wide transcription profile of Escherichia coli cells treated with hydrogen peroxide was examined with a DNA microarray composed of 4,169 E. coli open reading frames. By measuring gene expression in isogenic wild-type andoxyR deletion strains, we confirmed that the peroxide response regulator OxyR activates most of the highly hydrogen peroxide-inducible genes. The DNA microarray measurements allowed the identification of several new OxyR-activated genes, including thehemH heme biosynthetic gene; the six-genesuf operon, which may participate in Fe-S cluster assembly or repair; and four genes of unknown function. We also identified several genes, including uxuA, encoding mannonate hydrolase, whose expression might be repressed by OxyR, since their expression was elevated in the ΔoxyR mutant strain. In addition, the induction of some genes was found to be OxyR independent, indicating the existence of other peroxide sensors and regulators in E. coli. For example, theisc operon, which specifies Fe-S cluster formation and repair activities, was induced by hydrogen peroxide in strains lacking either OxyR or the superoxide response regulators SoxRS. These results expand our understanding of the oxidative stress response and raise interesting questions regarding the nature of other regulators that modulate gene expression in response to hydrogen peroxide.
Dual-optical-response photonic crystal fibre interferometer for multi-parameter sensing

An all-fiber mode interferometer consisting of a short segment of photonic crystal fiber (PCF) fusion spliced to standard single mode optical fiber and pressed on localized regions is proposed for multi-parameter sensing. In our configuration, the physical parameter being sensed changes the fringe contrast (or visibility) of the interference pattern and also causes a shift to the same. To achieve this dual effect the device is pressed on localized regions over a few millimeters. In this manner we introduce losses and effective refractive index changes to the interference modes, hence visibility and shift to the interference pattern. Our interferometer is suitable for monitoring diverse physical parameters such as weight, force, pressure, load, etc. The advantage is that no temperature or power fluctuations compensation is required.
A window into the complexity of the dynamic rupture of the 2011 Mw 9 Tohoku‐Oki earthquake

The 2011 Mw 9 Tohoku‐Oki earthquake, recorded by over 1000 near‐field stations and multiple large‐aperture arrays, is by far the best recorded earthquake in the history of seismology and provides unique opportunities to address fundamental issues in earthquake source dynamics. Here we conduct a high resolution array analysis based on recordings from the USarray and the European network. The mutually consistent results from both arrays reveal rupture complexity with unprecedented resolution, involving phases of diverse rupture speed and intermittent high frequency bursts within slow speed phases, which suggests spatially heterogeneous material properties. The earthquake initially propagates down‐dip, with a slow initiation phase followed by sustained propagation at speeds of 3 km/s. The rupture then slows down to 1.5 km/s for 60 seconds. A rich sequence of bursts is generated along the down‐dip rim of this slow and roughly circular rupture front. Before the end of the slow phase an extremely fast rupture front detaches at about 5 km/s towards the North. Finally a rupture front propagates towards the south running at about 2.5 km/s for over 100 km. Key features of the rupture process are confirmed by the strong motion data recorded by K‐net and KIK‐net. The energetic high frequency radiation episodes within a slow rupture phase suggests a patchy image of the brittle‐ductile transition zone, composed of discrete brittle asperities within a ductile matrix. The high frequency is generated mainly at the down‐dip edge of the principal slip regions constrained by geodesy, suggesting a variation along dip of the mechanical properties of the mega thrust fault or their spatial heterogeneity that affects rise time.
Temporary inactivation of the anterior part of the bed nucleus of the stria terminalis blocks alarm pheromone-induced defensive behavior in rats

Rats emit an alarm pheromone in threatening situations. Exposure of rats to this alarm pheromone induces defensive behaviors, such as head out behavior, and increases c-Fos expression in brain areas involved in the mediation of defensive behaviors. One of these brain areas is the anterior bed nucleus of the stria terminalis (aBNST). The goal of the present study was to investigate if pharmacological inactivation of the aBNST by local microinjections of the GABAA receptor-agonist muscimol modulates alarm pheromone-induced defensive behaviors. We first established the behavioral paradigm of alarm pheromone-induced defensive behaviors in Sprague-Dawley rats in our laboratory. In a second experiment, we inactivated the aBNST, then exposed rats to one of four different odors (neck odor, female urine, alarm pheromone, fox urine) and tested the effects of the aBNST inactivation on the behavior in response to these odors. Our data show that temporary inactivation of the aBNST blocked head out behavior in response to the alarm pheromone. This indicates that the aBNST plays an important role in the mediation of the alarm pheromone-induced defensive behavior in rats.
Severe upper gastrointestinal polyposis associated with sparse colonic polyposis in a familial adenomatous polyposis family with an APC mutation at codon 1520

Background—Familial adenomatous polyposis usually results in colonic polyposis with hundreds to thousands of polyps, congenital hypertrophy of the retinal pigment epithelium (CHRPE), and variable extracolonic features. Recent reports indicate that patients with distal mutations between codons 1445 and 1578 do not express CHRPE and have a high incidence of desmoid tumours. Patients—The family studied has an unusual phenotype of sparse colonic polyposis but profuse upper gastrointestinal polyposis. Affected subjects do not have CHRPE. Methods—The protein truncation test followed by sequencing identified a 2 base pair deletion at codon 1520 in the APC gene. This results in a frameshift creating a stop codon 13 codons downstream. Results—This family demonstrates that sparse colonic polyposis but severe upper tract polyposis may be associated with mutations between codons 1445 and 1578. Conclusions—Study of duodenal and colonic polyps in further cases with mutations in this region is warranted. Such mutations may preferentially cause duodenal adenomas and desmoid tumours as somatic mutations in these tumours also occur in this region, unlike colorectal tumours where somatic mutations occur more proximally. This study emphasises the importance of screening the upper gastrointestinal tract even when the colonic disease is mild.
Human Ebola virus infection results in substantial immune activation

Significance In 2014, Ebola virus became a household term. The ongoing outbreak in West Africa is the largest Ebola virus outbreak ever recorded, with over 20,000 cases and over 8,000 deaths to date. Very little is known about the human cellular immune response to Ebola virus infection, and this lack of knowledge has hindered development of effective therapies and vaccines. In this study, we characterize the human immune response to Ebola virus infection in four patients. We define the kinetics of T- and B-cell activation, and determine which viral proteins are targets of the Ebola virus-specific T-cell response in humans. Four Ebola patients received care at Emory University Hospital, presenting a unique opportunity to examine the cellular immune responses during acute Ebola virus infection. We found striking activation of both B and T cells in all four patients. Plasmablast frequencies were 10–50% of B cells, compared with less than 1% in healthy individuals. Many of these proliferating plasmablasts were IgG-positive, and this finding coincided with the presence of Ebola virus-specific IgG in the serum. Activated CD4 T cells ranged from 5 to 30%, compared with 1–2% in healthy controls. The most pronounced responses were seen in CD8 T cells, with over 50% of the CD8 T cells expressing markers of activation and proliferation. Taken together, these results suggest that all four patients developed robust immune responses during the acute phase of Ebola virus infection, a finding that would not have been predicted based on our current assumptions about the highly immunosuppressive nature of Ebola virus. Also, quite surprisingly, we found sustained immune activation after the virus was cleared from the plasma, observed most strikingly in the persistence of activated CD8 T cells, even 1 mo after the patients’ discharge from the hospital. These results suggest continued antigen stimulation after resolution of the disease. From these convalescent time points, we identified CD4 and CD8 T-cell responses to several Ebola virus proteins, most notably the viral nucleoprotein. Knowledge of the viral proteins targeted by T cells during natural infection should be useful in designing vaccines against Ebola virus.
Controllable coupling of an ultra-high-Q microtoroid cavity with monolayer graphene

We have demonstrated controllable coupling between an ultra-high-Q microcavity and monolayer graphene with tunability of the Q-factor from 1.59×10<sup>7</sup> to 1.20×10<sup>5</sup>. The Q-factor has been finely tuned by adjusting the gap between them.
Minimal-Energy Driving Strategy for High-Speed Electric Train With Hybrid System Model

This paper studies a minimal-energy driving strategy for high-speed electric trains with a fixed travel time. A hybrid system model is proposed to describe the new characteristics of high-speed electric trains, including the extended speed range, energy efficiency, and regenerative braking. Based on this model, train driving is characterized by the gear sequence and the switching locations. An approximate gradient information is derived via the variational principle. To avoid a combinatorial explosion, the gear sequence is fixed by a priori knowledge. Then, a gradient-based exterior point method is proposed to calculate the optimal driving. In the case study, the minimal-energy driving with a fixed travel time for CRH-3 is investigated, and the result reveals some new understandings for high-speed electric train drive. Additionally, the tradeoff relationship between energy consumption and travel time is quantitatively studied, which is helpful in assigning an appropriate travel time for high-speed trains.