Miracle-dz/UniFAR-FTUs huggingface dataset:
TAFII 250 Phosphorylates Human Transcription Factor IIA on Serine Residues Important for TBP Binding and Transcription Activity*

Transcription factor IIA (TFIIA) is a positive acting general factor that contacts the TATA-binding protein (TBP) and mediates an activator-induced conformational change in the transcription factor IID (TFIID) complex. Previously, we have found that phosphorylation of yeast TFIIA stimulates TFIIA·TBP·TATA complex formation and transcription activation in vivo. We now show that human TFIIA is phosphorylated in vivo on serine residues that are partially conserved between yeast and human TFIIA large subunits. Alanine substitution mutation of serine residues 316 and 321 in TFIIA αβ reduced TFIIA phosphorylation significantly in vivo. Additional alanine substitutions at serines 280 and 281 reduced phosphorylation to undetectable levels. Mutation of all four serine residues reduced the ability of TFIIA to stimulate transcription in transient transfection assays with various activators and promoters, indicating that TFIIA phosphorylation is required globally for optimal function. In vitro, holo-TFIID and TBP-associated factor 250 (TAFII250) phosphorylated TFIIA on the β subunit. Mutation of the four serines required for in vivophosphorylation eliminated TFIID and TAFII250 phosphorylation in vitro. The NH2-terminal kinase domain of TAFII250 was sufficient for TFIIA phosphorylation, and this activity was inhibited by full-length retinoblastoma protein but not by a retinoblastoma protein mutant defective for TAFII250 interaction or tumor suppressor activity. TFIIA phosphorylation had little effect on the TFIIA·TBP·TATA complex in electrophoretic mobility shift assay. However, phosphorylation of TFIIA containing a γ subunit Y65A mutation strongly stimulated TFIIA·TBP·TATA complex formation. TFIIA-γY65A is defective for binding to the β-sheet domain of TBP identified in the crystal structure. These results suggest that TFIIA phosphorylation is important for strengthening the TFIIA·TBP contact or creating a second contact between TFIIA and TBP that was not visible in the crystal structure.
Giant Magnetoimpedance of Cube/Feconi Electroplated Wires: Focus on Angular Sensoric

Giant magnetoimpedance effect (GMI) is a subject of special interest proved by applied electrodynamic and technological applications. GMI effect in ferromagnetic tubes is connected with the high sensitivity of the magnetic system to a circular magnetic field near the spin-reorientation magnetic phase transitions offering high sensitivity with respect to an external magnetic field. In this work the non-magnetic CuBe wires were covered by Fe20Co6Ni74 layers by electrodeposition. The thickness of 1 μm for magnetic layer was high enough in order to ensure the high GMI value. Longitudinal magnetic anisotropy was induced by post preparation annealing in a magnetic field of 160 A/m at 320℃ during 1 hour in order to obtain appropriate magnetisation process. Angular dependencies of GMI were measured in a frequency range of 1 to 10 MHz for driving currents of 2.5 to 20 mA. High longitudinal GMI of the order of 400% was observed at quite low frequency of 1 MHz. The highest value of the sensitivity of 520%/Oe was found for the active resistance: Linear sensitivities of 0.023 Ω/° and 0.05 Ω/° were observed for reasonably low fields of 240 and275 A/m respectively for small angles, where planar GMI elements are less effective.
Network Analysis to Support Navigation and Use of Ever-Changing Legislation

In this paper we first introduce the working context related to the under- standing of an heterogeneous network of references contained in the Italian regula- tory framework. We then present an extended analysis of a large network of laws, providing several types of analytical evaluation that can be used within a legal man- agement system for understanding the data through summarization, visualization, and browsing. In the legal domain, yet several tasks are strictly supervised by hu- mans, with strong consumption of time and energy that would dramatically drop with the help of automatic or semi-automatic supporting tools. We overview dif- ferent techniques and methodologies explaining how they can be helpful in actual scenarios.
LIN7 regulates the filopodium- and neurite-promoting activity of IRSp53

Summary The insulin receptor substrate protein of 53 kDa (IRSp53) is crucially involved in the formation of filopodia and neurites through mechanisms that have only partially been clarified. We have investigated the role of the small scaffold protein LIN7, which interacts with IRSp53. We found that formation of actin-filled protrusions in neuronal NSC34 cells and neurites in neuroblastoma N2A cells depends on motifs mediating the LIN7:IRSp53 association, as both the coexpression of LIN7 with IRSp53 or the expression of the L27-IRSp53 chimera (a fusion protein between IRSp53 and the LIN7L27 domain for plasma membrane protein complexes association) prevented actin-deficient protrusions induced by overexpressed IRSp53, and enhanced the formation of actin-filled protrusions. The regulatory role of LIN7 in IRSp53-mediated extension of filopodia in neuronal N2A cells was demonstrated by live-cell imaging experiments. Moreover, LIN7 silencing prevented the extension of filopodia and neurites, induced by ectopic expression of IRSp53 or serum starvation, respectively, in undifferentiated and differentiated N2A cells. The expression of full-length IRSp53 or the LIN7&Dgr;PDZ mutant lacking the domain for association with IRSp53 was unable to restore neuritogenesis in LIN7-silenced cells. Conversely, defective neuritogenesis could be rescued by the expression of RNAi-resistant full-length LIN7 or chimeric L27-IRSp53. Finally, LIN7 silencing prevented the recruitment of IRSp53 in Triton X-100-insoluble complexes, otherwise occurring in differentiated cells. Collectively these data indicate that LIN7 is a novel regulator of IRSp53, and that the association of these proteins is required to promote the formation of actin-dependent filopodia and neurites.
Global Convergence of Augmented Lagrangian Methods Applied to Optimization Problems with Degenerate Constraints, Including Problems with Complementarity Constraints

We consider global convergence properties of the augmented Lagrangian methods on problems with degenerate constraints, with a special emphasis on mathematical programs with complementarity constraints (MPCC). In the general case, we show convergence to stationary points of the problem under an error bound condition for the feasible set (which is weaker than constraint qualifications), assuming that the iterates have some modest features of approximate local minimizers of the augmented Lagrangian. For MPCC, we first argue that even weak forms of general constraint qualifications that are suitable for convergence of the augmented Lagrangian methods, such as the recently proposed relaxed positive linear dependence condition, should not be expected to hold and thus special analysis is needed. We next obtain a rather complete picture, showing that, under this context's usual MPCC-linear independence constraint qualification, feasible accumulation points of the iterates are guaranteed to be C-stationary for MPC.
Uncertain Numerical Data Clustering Using VORONOI Diagram and R-Tree With Ensemble SVM

Recently data mining over the uncertain data grabed more attention of the data mining community. To classify or cluster the valid or certain data, there are different approaches like DTL, Rule based Classification, Naive Bayes Classification and many more techniques. Its easy to classify the certain data but classification of the uncertain data is bit difficult. The uncertainty occurs in the a data because of the impresize measurement of the results, like scientific results, data from sensor netowork, measuring temperature, humidity, pressure and so on. From such a sources there is possibility of getting the uncertainty in a data. Main task is to handle the uncertainty of the data in order to classify or cluster it. It comes under the NP-Hard problems. Solving this problem, different approaches are available. We study the problem of clustering and classification of uncertain objects whose locations are described by probability density functions (pdf) means valued uncertainty. We show that the averaging algorithm with KMean algorithm, which generalises the k-means algorithm to handle uncertain objects, is very inefficient. The inefficiency comes from the fact that it does the averaging of the range of uncertain attribute. In UK-means, an object is assigned to the cluster whose representative has the smallest expected distance to the object. For arbitrary pdfs, expected distances are computed by numerical integrations, which are costly operations. Previous literature has applied bounding-box-based techniques to reduce the number of Expected Distance(ED) calculation. We use pruning techniques that are based on Voronoi diagrams to further reduce the number of expected distance calculation. These techniques are analytically proven to be more effective than the basic boundingbox-based technique previously known in the literature. We use R-tree index to organise the uncertain objects in groups so as to reduce pruning overheads. We conduct experiments to evaluate the effectiveness of our novel techniques, and extend the studies to different datasets. We show that these techniques are additive and, when used in combination, significantly outperform previously known methods.
Densification and grain growth during sintering of nanosized particles

The sintering of nanosized particles is a scientific and technological topic that affects the manufacture of bulk nanocrystalline materials and the understanding of the stability of nanoparticles. Owing to their extremely small size and the high surface to volume ratio, nanoparticles during sintering exhibit a number of distinctively unique phenomena compared to the sintering of coarse powders. Particularly, it is generally found that the sintering temperatures of nanosized particles are dramatically lower than that of their micrometre or submicrometre sized counterparts. Research has also shown that the grain growth during nanosintering consists of an initial dynamic grain growth stage that occurs during heating up and the normal grain growth stage that occurs mostly during isothermal holding. For nanoparticles, the effect of the initial grain growth cannot be ignored because that it is sufficient to cause the material to lose nanocrystalline characteristics. This review aims to bring to focus the understanding of the fundamental issues of nanosinteirng, including the thermodynamic driving force of nanosintering, non-linear diffusion and the kinetics of nanosintering, and the relationships between agglomeration, densification and grain growth. This review will also examine the effects of microstructure and processing variables.
Comparison of Nasal Intermittent Positive Pressure Ventilation and Nasal Continuous Positive Airway Pressure Treatments Using Parametric Survival Models

Abstract Objective The Cox model is the dominant tool in clinical trials to compare treatment options. This model does not specify any specific form to the hazard function. On the other hand, parametric models allow the researcher to consider an appropriate shape of hazard function for the event of interest. The aim of this article is to compare performance of Cox and parametric models. Methods We used data collected in a prospective clinical trial that aimed to compare performance of nasal intermittent positive pressure ventilation (NIPPV) and nasal continuous positive airway pressure (NCPAP) treatments in terms of survival of newborn infants who had respiratory distress syndrome (RDS). Performance of Cox, exponential, Weibull, and log-logistic models were compared in terms of goodness of fit. Findings Fitting the Cox model, we have seen that infants who received NCPAP were 4.23 (Hazard Ratio= 4.23, 95% Confidence Interval: 1.87–9.59) times more likely to fail than those received NIPPV (P=0.001). Adequacy of the exponential model was rejected. We have seen a decreasing hazard rate over time, in both treatment groups. This decrease was sharper in NCPAP group. Akiake information criterion corresponded to the log-logistic model and was lower than all other models followed by Weibull model. Conclusion Our results demonstrate the benefit of parametric survival models over traditional Cox regression model in terms of modeling of shape of hazard function. We saw a decreasing hazard that confirms the flexibility of parametric models in terms of the modeling of hazard rate.
The Law and Economics of Costly Contracting

In most of the contract theory literature, contracting costs are assumed either to be high enough to preclude certain forms of contracting or low enough to permit any contract to be written. Similarly researchers usually treat renegotiation as either costless or prohibitively costly. This article addresses the middle ground between these extremes, in which the costs of contracting and renegotiation can take intermediate values and the contracting parties can themselves influence these costs. The context for our analysis is the canonical problem of inducing efficient relation-specific investment and efficient ex post trade. Among our principle results are: (i) The efficiency and complexity of the initial contract are decreasing in the cost to create a contract. Hence the best mechanism design contracts can be too costly to write. (ii) When parties use the simpler contract forms, they require renegotiation to capture ex post surplus and to create efficient investment incentives. In some cases, parties want low renegotiation costs. More interesting is that, in other cases, parties have a strict preference for moderate renegotiation costs. (iii) The effect of contract law on contract form is significant but has been overlooked. In particular, the law's interpretive rules raise the cost of enforcing complex contracts, and thus induce parties to use simple contracts. Worse, the law also lowers renegotiation costs, which further undermines complex contracts and is also inappropriate for some of the simpler contracts. Copyright 2004, Oxford University Press.
Blockade of Estrogen Action Upregulates Estrogen Receptor-α mRNA in the Fetal Brain

Background: Fetal neuroendocrine maturation in late gestation is critical for maintenance of fetal homeostasis, growth, and readiness for birth. Sheep express estrogen receptors (ERs) in various brain regions. However, little is known about the regulation of ER-α and ER-β in the ovine brain prenatally. Objective: The present study was designed to test the hypothesis that the expression of ER is influenced by circulating estrogens in the late-gestation sheep fetus. Methods: Six chronically-catheterized twin fetal sheep were treated with vehicle or the ER blocker ICI 182,780 i.c. v. (0.25 μg/day). Fetuses were sacrificed 6–14 days after surgery and start of infusion. Brain regions were rapidly isolated and snap-frozen for later extraction of mRNA and protein. ER-α and ER-β mRNA was measured using real-time PCR and protein was measured using Western blot. Results: Treatment with ICI 182,780 increased ER-α mRNA, especially in cerebellum and hippocampus. There were no changes in ER-α protein and no changes in ER-β at either the mRNA or protein level. Conclusion: Expression of ER-α is influenced by endogenous estrogens in the ovine fetal brain.
Increased Expression of Macrophage-Inducible C-type Lectin in Adipose Tissue of Obese Mice and Humans

OBJECTIVE We have provided evidence that saturated fatty acids, which are released from adipocytes via macrophage-induced adipocyte lipolysis, serve as a naturally occurring ligand for the Toll-like receptor (TLR) 4 complex in macrophages, thereby aggravating obesity-induced adipose tissue inflammation. The aim of this study was to identify the molecule(s) activated in adipose tissue macrophages in obesity. RESEARCH DESIGN AND METHODS We performed a cDNA microarray analysis of coculture of 3T3-L1 adipocytes and RAW264 macrophages. Cultured adipocytes and macrophages and the adipose tissue of obese mice and humans were used to examine mRNA and protein expression. RESULTS We found that macrophage-inducible C-type lectin (Mincle; also called Clec4e and Clecsf9), a type II transmembrane C-type lectin, is induced selectively in macrophages during the interaction between adipocytes and macrophages. Treatment with palmitate, a major saturated fatty acid released from 3T3-L1 adipocytes, induced Mincle mRNA expression in macrophages at least partly through the TLR4/nuclear factor (NF)-κB pathway. Mincle mRNA expression was increased in parallel with macrophage markers in the adipose tissue of obese mice and humans. The obesity-induced increase in Mincle mRNA expression was markedly attenuated in C3H/HeJ mice with defective TLR4 signaling relative to control C3H/HeN mice. Notably, Mincle mRNA was expressed in bone-marrow cell (BMC)-derived proinflammatory M1 macrophages rather than in BMC-derived anti-inflammatory M2 macrophages in vitro. CONCLUSIONS Our data suggest that Mincle is induced in adipose tissue macrophages in obesity at least partly through the saturated fatty acid/TLR4/NF-κB pathway, thereby suggesting its pathophysiologic role in obesity-induced adipose tissue inflammation.
Explicit Symmetries of Strict Feedforward Control Systems

We show that any symmetry of a smooth strict feedforward system is conjugated to a scaling translation and any 1-parameter family of symmetries to a family of scaling translations along the first variable. We compute explicitly those symmetries by finding the conjugating diffeomorphism. We deduce, in accordance with our previous work, that a smooth system is feedback equivalent to a strict feedforward form if and only if it gives rise to a sequence of systems, such that each element of the sequence, firstly, possesses an infinitesimal symmetry whose flow is conjugated to a 1-parameter families of scaling translations and, secondly, it is the factor system of the preceding one, that is, is reduced from the preceding one by its symmetry. We illustrate our results by computing the symmetries of the Cart-Pole system
LDPC for Physical Layer Security

This paper presents a coding scheme for the Gaussian wiretap channel based on low-density parity-check (LDPC) codes. The messages are transmitted over punctured bits to hide data from eavesdroppers. It is shown that this method is asymptotically effective in the sense that it yields a BER very close to 0.5 for an eavesdropper whose SNR is lower than the threshold SNRE , even if the eavesdropper has the ability to use a bitwise MAP decoder. Such codes also achieve high reliability for the friendly parties provided they have an SNR above a second threshold SNRB . It is shown how asymptotically optimized LDPC codes can be designed with differential evolution where the goal is to achieve high reliability between friendly parties and security against a passive eavesdropper while keeping the security gap SNRB/SNRE as small as possible. The proposed coding scheme is applicable at finite block lengths and can be combined with existing cryptographic schemes to deliver improved data security by taking advantage of the stochastic nature of many communication channels.
Isolation and characterization of an attenuated strain of Pseudomonas aeruginosa AC869, a 3,5-dichlorobenzoate degrader

Pseudomonas aeruginosa AC869, a 3,5-dichlorobenzoate degrader, is a mouse pathogen and has a reported 50% lethal dose (LD50) of 1.05 x 10(7) CFU when given intranasally to C3H/HeJ mice (S.E. George, M.J. Kohan, M.I. Gilmour, M.S. Taylor, H.G. Brooks, J.P. Creason, and L.D. Claxton, Appl. Environ, Microbiol. 59:3585-3591, 1993). AC869 was serotyped as O6 when grown in CD-1 mouse cecal and lung mucus but could not be assigned an O serotype when grown in Luria broth (LB). After growth in mouse cecal mucus, a less virulent mutant, AC869-11, was isolated from AC869 by using bacteriophage E79, which adsorbs to the O side chain of lipopolysaccharide (LPS). AC869-11 produced significantly less O antigen on its LPS than AC869 when grown in mouse lung and cecal mucus. The mutant also produced half the amount of exoenzyme S and 16-fold less extracellular protease than AC869 and was more sensitive than its parent to a number of antibiotics when grown either in LB or in mouse lung mucus. AC869-11 had ninefold higher LD50 than AC869 in CD-1 mice when administered intranasally. AC869-11 was found in the lungs, small intestine, cecum, and large intestine in numbers at least 100-fold below AC869, 3 h after intranasal exposure of mice to a sublethal dose of the two strains. Moreover, AC869-11 induced a decreased pulmonary inflammatory response relative to AC869. In contrast to AC869, AC869-11 did not translocate to the mesenteric lymph nodes, liver, and spleen following a sublethal dose. Despite attenuation, AC869-11 grew as well as AC869 with 3,5-dichlorobenzoate as the sole carbon and energy source. However, although AC869-11 survived in 3,5-dichlorobenzoate-contaminated soil as well as AC869 for 1 week, it failed to survive as well thereafter. These results suggest the possibility that mutations that lead to pulmonary attenuation of P. aeruginosa in mice also lead to weakness in the environment, despite such mutants maintaining the ability to degrade toxic substances under laboratory conditions.
Towards Exascale Scientific Metadata Management

Author(s): Blanas, Spyros; Byna, Surendra | Abstract: Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability of metadata that describe the scientific datasets. Existing workflow engines have been capturing a limited form of metadata to provide provenance information about the identity and lineage of the data. However, much of the data produced by simulations, experiments, and analyses still need to be annotated manually in an ad hoc manner by domain scientists. Systematic and transparent acquisition of rich metadata becomes a crucial prerequisite to sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and domain-agnostic metadata management infrastructure that can meet the demands of extreme-scale science is notable by its absence. To address this gap in scientific data management research and practice, we present our vision for an integrated approach that (1) automatically captures and manipulates information-rich metadata while the data is being produced or analyzed and (2) stores metadata within each dataset to permeate metadata-oblivious processes and to query metadata through established and standardized data access interfaces. We motivate the need for the proposed integrated approach using applications from plasma physics, climate modeling and neuroscience, and then discuss research challenges and possible solutions.
A gender difference in the false recall of negative words: Women DRM more than men

Gender differences in susceptibility to associative memory illusions in the Deese/Roediger–McDermott paradigm were investigated using negative and neutral word lists. Women (n=50) and men (n=50) studied 20 lists of 12 words that were associates of a non-presented critical lure. Ten lists were associates of negatively valenced lures (e.g., cry, evil) and ten were associates of neutral lures (e.g., chair, slow). When asked to recall the words after each list, women falsely recalled more negative lures than men, but there was no gender difference in the false recall of neutral lures. These findings suggest that women reflect on associations within negative lists to a greater degree than men and are thereby more likely to generate the negative critical lures.