Miracle-dz/UniFAR-FTUs huggingface dataset:
NTP-driven Translocation by Human RNA Polymerase II*

We report a “running start, two-bond” protocol to analyze elongation by human RNA polymerase II (RNAP II). In this procedure, the running start allowed us to measure rapid rates of elongation and provided detailed insight into the RNAP II mechanism. Formation of two bonds was tracked to ensure that at least one translocation event was analyzed. By using this method, RNAP II is stalled briefly at a defined template position before restoring the next NTP. Significantly, slow reaction steps are identified both before and after phosphodiester bond synthesis, and both of these steps can be highly dependent on the next templated NTP. The initial and final NTP-driven events, however, are not identical, because the slow step after chemistry, which includes translocation and pyrophosphate release, is regulated differently by elongation factors hepatitis δ antigen and transcription factor IIF. Because recovery from a stall and the processive transition from one bond to the next can be highly NTP-dependent, we conclude that translocation can be driven by the incoming substrate NTP, a model fully consistent with the RNAP II elongation complex structure.
Relational Framework and its Applications

This paper has, as its point of departure, the foundational axiomatic theory of E. De Giorgi (1996, Scuola Normale Superiore di Pisa, Preprints di Matematica 26, 1), based on two primitive notions of quality and relation. With the introduction of a unary relation, we develop a system totally based on the sole primitive notion of relation. Such a modification enables a definition of the concept of dynamic unary relation. In this way we construct a simple language capable to express other well known theories such as Robinson’s arithmetic or a piece of a theory of concatenation. A key role in this system plays an abstract relation designated by “( )”, which can be interpreted in different ways, but in this paper we will focus on the case when we can perform computations and obtain results. Keywords—language, unary relations, arithmetic, computability
Logic Programming Representation of the Compound Term Composition Algebra

The Compound Term Composition Algebra (CTCA) is an algebra with four algebraic operators, which can be used to generate the valid (meaningful) compound terms of a given faceted taxonomy, in an efficient and flexible manner. The positive operations allow the derivation of valid compound terms through the declaration of a small set of valid compound terms. The negative operations allow the derivation of valid compound terms through the declaration of a small set of invalid compound terms. In this paper, we show how CTCA can be represented in logic programming with negation-as-failure, according to both Clark's and well-founded semantics. Indeed, the SLDNF-resolution can be used for checking compound term validity and well-formedness of an algebraic expression in polynomial time w.r. t. the size of the expression and the number of terms in the taxonomy. This result makes our logic programming representation a competitive alternative to imperative algorithms. Embedding of our logic programming representation to the programming environment of a web portal for a computer sales company is demonstrated.
Geometric optimization for 3D pose estimation of quadratic surfaces

Our task is 3D pose estimation for on-line application in industrial robotics and machine vision. It involves the estimation of object position and orientation relative to a known model. Since most man made objects can be approximated by a small set of quadratic surfaces, in this paper we focus on pose estimation of such surfaces. Our optimization is of an error measure between the CAD model and the measured data. Most existing algorithms are sensitive to noise and occlusion or only converge linearly. Our optimization involves iterative cost function reduction on the smooth manifold of the Special Euclidean Group, SE/sub 3/. The optimization is based on locally quadratically convergent Newton-type iterations on this constraint manifold. A careful analysis of the underlying geometric constraint is required.
Desigualdade de rendimentos e pobreza: uma avaliação das regiões metropolitanas de Salvador e de São Paulo

O trabalho avalia os determinantes dos rendimentos dos trabalhadores pobres nas regioes metropolitanas de Salvador e de Sao Paulo. A base de dados utilizada e a Pesquisa de Emprego e Desemprego para as duas regioes metropolitanas. Buscou-se eliminar os possiveis vieses de selecao da amostra, utilizando o procedimento de Heckman, com a inclusao da variavel lambda. Os resultados estatisticos mostram um diferencial positivo dos rendimentos dos trabalhadores pobres da regiao metropolitana de Sao Paulo. Os trabalhadores pobres nas duas regioes sao constituidos mais de mulheres, nao-chefes de familia e negros; a pobreza e crescente com a idade e decrescente com o nivel de escolaridade. A variavel que capta o movimento conjuntural da economia se mostrou positiva e estatisticamente significativa nas duas regioes, isso quer dizer que esses segmentos de mercados de trabalho respondem, em termos de remuneracao, aos movimentos conjunturais da economia. Por outro lado, a variavel que capta a aversao a desigualdade distributiva nao foi estatisticamente significativa, permitindo dizer que esses mercados de trabalho sao insensiveis ao aspecto distributivo, independentemente da conjuntura economica, dai a importância de politicas sociais dirigidas para diminuir a concentracao dos rendimentos.
Implementation of a transient-fault-tolerance scheme on DEOS-a technology transfer from an academic system to an industrial system

Fault tolerance is important in real time systems where correct execution of tasks must satisfy certain temporal constraints. Since transient faults occur more frequently than permanent faults, the paper focuses on a transient fault tolerance algorithm, FTRMS. The FORTS group of the University of Pittsburgh derived the FTRMS algorithm and implemented it on FT-RT-Mach. The same mechanism is transferred to a commercial system, DEOS, at the Honeywell Technology Center. By describing and contrasting the implementation of FTRMS on the two systems, the paper illustrates the difference between an academic system and an industrial system. An application example shows the effect of the new transient fault tolerance scheme on the system.
Reliability of Lightning Resistant Overhead Distribution Lines

ARFtrocr An assessment of the 32 year historical reliability of the 13.8 kV electrical distribution system at the Oak Ridge National Laboratory (ORNL) in Tennessee has yielded several conclusions useful in the planning of industrial power systems. The system configuration at ORNL has essentially remained unchanged in the last 32 years which allows a meaningful comparison of reliability trends for the plant's eight overhead distribution lines, two of which were built in the 1960% with lightning resistant construction techniques. Meticulous records indicating the cause, duration, and location of 135 electric outages in the plant's distribution system have allowed a reliability assessment to be performed. The assessment clearly shows Bow differences in voltage construction class, length, age, and maximum elevation above a reference elevation inff uence the reliability of overhead power distribution lines. Comparisons are also made between the ORNL historical data and predicted failure rates from ANSI and IEEE industry surveys.
Isothermal Microcalorimetry to Investigate Non Specific Interactions in Biophysical Chemistry

Isothermal titration microcalorimetry (ITC) is mostly used to investigate the thermodynamics of “specific” host-guest interactions in biology as well as in supramolecular chemistry. The aim of this review is to demonstrate that ITC can also provide useful information about non-specific interactions, like electrostatic or hydrophobic interactions. More attention will be given in the use of ITC to investigate polyelectrolyte-polyelectrolyte (in particular DNA-polycation), polyelectrolyte-protein as well as protein-lipid interactions. We will emphasize that in most cases these “non specific” interactions, as their definition will indicate, are favoured or even driven by an increase in the entropy of the system. The origin of this entropy increase will be discussed for some particular systems. We will also show that in many cases entropy-enthalpy compensation phenomena occur.
Phosphorylation of the myosin phosphatase targeting subunit and CPI‐17 during Ca2+ Sensitization in Rabbit Smooth Muscle

Myosin phosphatase (MLCP) plays a critical regulatory role in the Ca2+ sensitivity of myosin phosphorylation and smooth muscle contraction. It has been suggested that phosphorylation at Thr695 of the MLCP regulatory subunit (MYPT1) and at Thr38 of the MLCP inhibitor protein CPI‐17 results in inhibition of MLCP activity. We have previously demonstrated that CPI‐17 Thr38 phosphorylation plays an important role in G‐protein‐mediated inhibition of MLCP in tonic arterial smooth muscle. Here, we attempted to evaluate the function of MYPT1 in phasic rabbit portal vein (PV) and vas deferens (VD) smooth muscles. Using site‐ and phospho‐specific antibodies, phosphorylation of MYPT1 Thr695 and CPI‐17 Thr38 was examined along with MYPT1 Thr850, which is a non‐inhibitory Rho‐kinase site. We found that both CPI‐17 Thr38 and MYPT1 Thr850 were phosphorylated in response to agonists or GTPγS concurrently with contraction and myosin phosphorylation in α‐toxin‐permeabilized PV tissues. In contrast, phosphorylation of MYPT1 Thr695 did not increase. Comparable results were also obtained in both permeabilized and intact VD. The Rho‐kinase inhibitor Y‐27632 and the protein kinase C (PKC) inhibitor GF109203X suppressed phosphorylation of MYPT1 Thr850 and CPI‐17 Thr38, respectively, in intact VD while MYPT1 Thr695 phosphorylation was insensitive to both inhibitors. These results indicate that phosphorylation of MYPT1 Thr695 is independent of stimulation of G‐proteins, Rho‐kinase or PKC. In the phasic PV, phosphorylation of CPI‐17 Thr38 may contribute towards inhibition of MLCP while the phasic visceral VD, which has a low CPI‐17 concentration, probably utilizes other Ca2+ sensitizing mechanisms for inhibiting MLCP besides phosphorylation of MYPT1 and CPI‐17.
The icmF3 locus is involved in multiple adaptation- and virulence-related characteristics in Pseudomonas aeruginosa PAO1

The type VI secretion system (T6SS) is widely distributed in Gram-negative bacteria. Three separate T6SSs called H1-, H2-, and H3-T6SS have been discovered in Pseudomonas aeruginosa PAO1. Recent studies suggest that, in contrast to the H1-T6SS that targets prokaryotic cells, H2- and H3-T6SS are involved in interactions with both prokaryotic and eukaryotic cells. However, the detailed functions of T6SS components are still uncharacterized. The intracellular multiplication factor (IcmF) protein is conserved in type VI secretion systems (T6SS) of all different bacterial pathogens. Bioinformatic analysis revealed that IcmF3 in P. aeruginosa PAO1 is different from other IcmF homologs and may represent a new branch of these proteins with distinct functions. Herein, we have investigated the function of IcmF3 in this strain. We have shown that deletion of the icmF3 gene in P. aeruginosa PAO1 is associated with pleiotropic phenotypes. The icmF3 mutant has variant colony morphology and an hypergrowth phenotype in iron-limiting medium. Surprisingly, this mutant is also defective for the production of pyoverdine, as well as defects in swimming motility and virulence in a C. elegans worm model. The icmF3 mutant exhibits higher conjugation frequency than the wild type and increased biofilm formation on abiotic surfaces. Additionally, expression of two phenazine biosynthetic loci is increased in the icmF3 mutant, leading to the overproduction of pyocyanin. Finally, the mutant exhibits decreased susceptibility to aminoglycosides such as tobramycin and gentamicin. And the detected phenotypes can be restored completely or partially by trans complementation of wild type icmF3 gene. The pleiotropic effects observed upon icmF3 deletion demonstrate that icmF3 plays critical roles in both pathogenesis and environmental adaptation in P. aeruginosa PAO1.
Catheter‐Related Bloodstream Infections in HIV‐Infected Patients

Abstract: Bloodstream infections (BSI) constitute a significant public health problem and represent an important cause of morbidity and mortality in hospitalized patients, with an approximate incidence of one episode per hundred hospital admissions. Studies on BSI in HIV+ patients have identified central venous catheters (CVC) as a risk factor, with an attributable mortality rate of 10–20%. The long‐term CVC‐related infection risk appeared to be 5 to 10‐fold higher with respect to the infection rates among HIV− patients. CVC associated infection rate ranges from 1.3 to 12 infections per 1,000 catheter‐days. Staphylococcus aureus is the most common etiologic agent causative of CVC‐related BSI, likely the result of the high skin and nasal carriage of this organism among HIV+ patients, mostly intravenous drug users. Coagulase‐negative staphylococci are also frequently identified as cause of CVC‐related BSI, likely the result of breaches in infection control measures and in antiseptic technique during CVC management. Treating bacteremia without catheter removal would be optimal, but the reported efficacy of systemic antibiotic therapy alone is only 25–32%. Conversely, recent studies have shown that, using an antibiotic‐lock procedure, up to 90% of HIV‐infected and uninfected patients achieved complete eradication of catheter‐related BSIs without catheter removal. Clinical trials using new materials such as covalently linked heparin on the CVC surface, electrically charged CVC, novel topical agents that interfere with bacterial colonization, antiadhesin molecules and agents that block the gene expression involved in the biofilm formation, are all needed to reduce the high catheter‐related infection risk among HIV+ patients.
Sparse Signal Recovery with Dynamic Update of Overcomplete Dictionary

Sparse signal priors help in a variety of modern signal processing tasks. In a typical sparse recovery problem, a sparse signal needs to be recovered from an underdetermined system of equations. For example, sparse representation of signal in an overcomplete dictionary or reconstruction of a sparse signal from a small number of linear measurements. In recent years, several results have been presented which guarantee reliable reconstruction under certain conditions. In this paper we investigate the problem of recovering sparse signals when elements are added to (or removed from) the overcomplete dictionary. We propose a dynamic update algorithm for basis pursuit denoising (BPDN), when new columns are added to (or removed from) the dictionary. We use this update procedure to iteratively update the working set of basis elements, chosen from a large library of basis elements, to compute the sparse solution. We also discuss the extension of the same ideas for the analysisbased BPDN.
Primary sensory deficits after right brain damage – an attentional disorder by any other name?

This chapter provides a review of primary sensory deficits after right brain damage. It begins by presenting the historical basis for the conceptual divide between ‘primary’ and ‘high-level’ deficits. A number of converging studies have demonstrated that impairments such as visual field deficits, somatosensory disorders, and motor disorders, traditionally conceived as primary deficits, involve impairments of higher-order cognitive processes. The mere clinical fact that some patients show deficits on one set of tasks whereas others show deficits on other tasks does not in itself provide sufficient reason to justify a qualitative distinction between visual field deficit (VFD) and visual-spatial neglect (VSN).
The Ergodic Capacity of the Multiple Access Channel Under Distributed Scheduling - Order Optimality of Linear Receivers

Consider the problem of a multiple-input multiple-output multiple-access channel at the limit of large number of users. Clearly, in practical scenarios, only a small subset of the users can be scheduled to utilize the channel simultaneously. Thus, a problem of user selection arises. However, since solutions which collect channel state information from all users and decide on the best subset to transmit in each slot do not scale when the number of users is large, distributed algorithms for user selection are advantageous. In this paper, we analyze a distributed user selection algorithm, which selects a group of users to transmit without coordinating between users and without all users sending CSI to the base station. This threshold-based algorithm is analyzed for both zero-forcing and minimum mean square error receivers, and its expected sum rate in the limit of large number of users is investigated. It is shown that for large number of users, it achieves the same scaling laws as the optimal centralized scheme.
Existence of aa 3-Type Ubiquinol Oxidase as a Terminal Oxidase in Sulfite Oxidation of Acidithiobacillus thiooxidans

It was found that Acidithiobacillus thiooxidans has sulfite:ubiquinone oxidoreductase and ubiquinol oxidase activities in the cells. Ubiquinol oxidase was purified from plasma membranes of strain NB1-3 in a nearly homogeneous state. A purified enzyme showed absorption peaks at 419 and 595 nm in the oxidized form and at 442 and 605 nm in the reduced form. Pyridine ferrohaemochrome prepared from the enzyme showed an α-peak characteristic of haem a at 587 nm, indicating that the enzyme contains haem a as a component. The CO difference spectrum of ubiquinol oxidase showed two peaks at 428 nm and 595 nm, and a trough at 446 nm, suggesting the existence of an aa 3-type cytochrome in the enzyme. Ubiquinol oxidase was composed of three subunits with apparent molecular masses of 57 kDa, 34 kDa, and 23 kDa. The optimum pH and temperature for ubiquinol oxidation were pH 6.0 and 30 °C. The activity was completely inhibited by sodium cyanide at 1.0 mM. In contrast, the activity was inhibited weakly by antimycin A1 and myxothiazol, which are inhibitors of mitochondrial bc 1 complex. Quinone analog 2-heptyl-4-hydoroxyquinoline N-oxide (HOQNO) strongly inhibited ubiquinol oxidase activity. Nickel and tungstate (0.1 mM), which are used as a bacteriostatic agent for A. thiooxidans-dependent concrete corrosion, inhibited ubiquinol oxidase activity 100 and 70% respectively.
Exploration for Polish-* bi-lingual translation equivalents from comparable and quasi-comparable corpora

In contemporary world, translation becomes a critical need of the time. Parallel dictionaries have now become a most accessible source by humans, but confines are there as they do not offer good quality translation function, because of neologisms and words that are out of vocabulary. To overcome this problem in the usage of statistical translation systems is becoming more and more important in maintaining the eminence and quantity of the training data. But due to the limitations in these systems they have very limited availability for few languages and very limited narrow text areas. The purpose of this research is to bring calculation time up gradation via GPU acceleration, tuning script introduction and the enhancement and improvements in the methodologies of the contemporary comparable corpora mining through re-implementation of analogous algorithms through Needleman-Wunch algorithm. Experiments have been conducted on multiple language data which were extracted on numerous domains from Wikipedia. For the sake of Wikipedia, multiple cross-lingual contrasts and comparison were established. Optimistic impact on the both quantity and quality of mined data was observed due to such changes and adaptation. The solution is language independent and highly practical especially for under-resourced languages.
A Novel Visualization Method of Power Transmission Lines

Visualization plays an important role in the analysis of grid circuit topological structure. The traditional line visualization method based on geographical position usually contains such problems that the nodes density distribution is uneven and the lines are too complex to understand. Some other methods completely neglect the real geographic location information. In this paper, we propose a new visualization method by adjustment of the nodes' location and optimization of drawing lines. Initially, the scheduling substation node is designed as the central node, the other nodes are divides into different groups by k-means++ cluster algorithm. Next, the location of the nodes is adjusted and optimized after clustering, and the data density is balanced. Finally, the nodes are connected with the colored lines of ring or radial structure. Experimental results show that our visualization method can more clearly show the topological structure of the current power transmission lines and retain the main geographical location information.
3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase Inhibitors Interfere With Angiogenesis by Inhibiting the Geranylgeranylation of RhoA

Angiogenesis is implicated in the pathogenesis of cancer, rheumatoid arthritis, and atherosclerosis and in the treatment of coronary artery and peripheral vascular disease. Here, cholesterol-lowering agents, 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors, are shown to interfere with angiogenesis. In vivo, the HMG-CoA reductase inhibitor simvastatin dose-dependently inhibited capillary growth in both vascular endothelial growth factor–stimulated chick chorioallantoic membranes and basic fibroblast growth factor–stimulated mouse corneas. In vitro, the development of tubelike structures by human microvascular endothelial cells cultured on 3D collagen gels was inhibited at simvastatin concentrations similar to those found in the serum of patients on therapeutic doses of this agent. HMG-CoA reductase inhibitors interfered with angiogenesis via inhibition of the geranylgeranylation and membrane localization of RhoA. Simvastatin inhibited membrane localization of RhoA with a concentration dependence similar to that for the inhibition of tube formation, whereas geranylgeranyl pyrophosphate, the substrate for the geranylgeranylation of Rho, reversed the effect of simvastatin on tube formation and on the membrane localization of RhoA. Furthermore, tube formation was inhibited by GGTI, a specific inhibitor of the geranylgeranylation of Rho; by C3 exotoxin, which inactivates Rho; and by the adenoviral expression of a dominant-negative RhoA mutant. The expression of a dominant-activating RhoA mutant reversed the effect of simvastatin on tube formation. Finally, HMG-CoA reductase inhibitors inhibited signaling by vascular endothelial growth factor, Akt, and focal adhesion kinase, three RhoA-dependent pathways known to be involved in angiogenesis. This study demonstrates a new relationship between lipid metabolism and angiogenesis and an antiangiogenic effect of HMG-CoA reductase inhibitors with possible important therapeutic implications.