Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA polymerase II.

PERSPECTIVES AND SUMMARY . 690 DEFINING THE ENZyME . 691 RNA Polymerase Purification . 691 General Properties . 692 The Subunit Problem . 692 Molecular Architecture of RNA Polymerase 11 693 YEAST RNA POLYMERASE II . 693 Eleven Unique Subunit Genes . 693 Subunit Features and Functions . 695 Subunit Stoichiometry and Phosphorylation . 701 Subunit Interactions and RNA Polymerase Structure . 702 HIGHER EliKARYOTIC RNA POLYMERASE II. 703 Conserved Features of Subunit Architecture . 703 Highly Conserved Subunit Sequences . 703 THE LARGE SUBUNIT CARBOXY TERMINAL DOMAIN . 704 Conserved Structure . 704 Essential Function . 706 Evidence for a Role in Initiation . 707 General Models for crD Function. 711 ACTIVATION OF RNA POLYMERASE II . 711 CONCLUDING REMARKS . 712
Closure to “Fracturing Pressure in Clay” by M. Marchi, G. Gottardi, and K. Soga

M. Marchi; G. Gottardi; and K. Soga Research Assistant, Dept. of Civil, Chemical, Environmental, and Materials Engineering (DICAM), Univ. of Bologna, Viale Risorgimento 2, 40136 Bologna, Italy (corresponding author). E-mail: michela.marchi@unibo.it Professor, Dept. of Civil, Chemical, Environmental, and Materials Engineering (DICAM), Univ. of Bologna, Viale Risorgimento 2, 40136 Bologna, Italy. E-mail: guido.gottardi2@unibo.it Professor, Dept. of Engineering, Univ. of Cambridge, Cambridge CB2 1PZ, U.K. E-mail: ks207@cam.ac. uk
Prevalence and predictors of dual antiplatelet therapy prolongation beyond one year in patients with acute coronary syndrome

There are limited real-world data on prevalence and predictors of dual antiplatelet therapy (DAPT) prolongation beyond one year after acute coronary syndrome (ACS). We have explored such issue in the START ANTIPLATELET Registry, which is a prospective, observational, multicenter, Italian registry performed in seven Italian cardiology institutions including patients admitted for ACS and followed up to one year. Out of a total population of 840 ACS patients, 596 patients had completed 12-month follow-up being on DAPT. Decision to prolong DAPT beyond one year was taken in 79 patients (13%), whereas in 517 patients DAPT was stopped. The strongest predictors of DAPT continuation were a new cardiovascular events after the index admission event (OR 3.3, 95% CI 1.4–7.7), no bleeding complications (OR 3.2, 95% CI 1.2–8.3) and no anemia during one-year follow-up (OR 2.6, 95% CI 1.1–5.9); other independent predictors were renal failure (OR 2.5, 95% CI 1.3–5.0) and peripheral artery disease (OR 1.8, 95% CI 1.1–3.0). The choice of DAPT prolongation was not correlated with younger ager, presence of diabetes mellitus, coronary angioplasty as initial treatment strategy or type of implanted stent (drug-eluting vs bare metal). In conclusion, this study provides a real-world snapshot on the factors influencing the option to continue DAPT beyond one year after ACS; a low bleeding risk seems to influence the choice to prolong DAPT more than a high ischemic risk.
Primary Care Patients’ Involvement in Decision-Making Is Associated With Improvement in Depression

Background:Depression is undertreated in primary care settings. Little research investigates the impact of patient involvement in decisions on guideline-concordant treatment and depression outcomes. Objective:The objective of this study was to determine whether patient involvement in decision-making is associated with guideline-concordant care and improvement in depression symptoms. Design:Prospective cohort study. Setting:Multisite, nationwide randomized clinical trial of quality improvement strategies for depression in primary care. Subjects:Primary care patients with current symptoms and probable depressive disorder. Measurements:Patients rated their involvement in decision-making (IDM) about their care on a 5-point scale from poor to excellent 6 months after entry into the study. Depressive symptoms were measured every 6 months for 2 years using a modified version of theCenter for Epidemiologic Studies–Depression (CES-D) scale. We examined probabilities (Pr) of receipt of guideline-concordant care and resolution of depression across IDM groups using multivariate logistic regression models controlling for patient and provider factors. Results:For each 1-point increase in IDM ratings, the probability of patients’ report of receiving guideline-concordant care increased 4% to 5% (adjusted Pr 0.31 vs. 0.50 for the lowest and highest IDM ratings, respectively, P < 0.001). Similarly, for each 1-point increase in IDM ratings, the probability of depression resolution increased 2% to 3% (adjusted Pr 0.10 vs. 0.19 for the lowest and highest IDM ratings respectively, P = 0.004). Conclusions:Depressed patients with higher ratings of involvement in medical decisions have a higher probability of receiving guideline-concordant care and improving their symptoms over an 18-month period. Interventions to increase patient involvement in decision-making may be an important means of improving care for and outcomes of depression.
Down-regulation of Manganese-Superoxide Dismutase through Phosphorylation of FOXO3a by Akt in Explanted Vascular Smooth Muscle Cells from Old Rats*

Manganese-superoxide dismutase (MnSOD) is one of the major cellular antioxidant defense systems. To study the effect of age on the regulation of MnSOD in the vasculature, we compared MnSOD expression and its transcriptional regulation in explanted vascular smooth muscle cells (VSMC) isolated from old (24 months old) versus young (6 months old) rats and grown in a normal (5 mm) or high (12.5 and 25 mm) glucose or tumor necrosis factor α (5 ng/ml) environment to induce oxidative stress. Both MnSOD protein and activity were reduced in VSMC from old compared with young animals. FOXO3a, a member of the family of Forkhead transcription factors, interacted with the promoter of the rat MnSOD gene at a specific binding site. Inhibition of FOXO3a transcription with small interfering RNA led to a reduction in MnSOD gene expression. VSMC from old rats had increased phosphorylated FOXO3a at Ser253, which paralleled the reduction of MnSOD protein. Treatment of VSMC with 5 nm insulin-like growth factor-1 induced phosphorylation of Akt and FOXO3a over time, repressing FOXO3a DNA binding and consequently MnSOD gene expression. Furthermore, Akt activity was selectively increased in VSMC from the old, supporting the hypothesis that increased age-related Akt activity might be responsible for the phosphorylation and inactivation of FOXO3a, which in turn down-regulates MnSOD transcription.
CINEMÁTICA DE LA EXTENSIÓN JURÁSICA VINCULADA A LA PROVINCIA SILÍCEA CHON AIKE, SANTA CRUZ, ARGENTINA

La Provincia Silicea Chon-Aike, de vasta distribucion en Patagonia, Plataforma continental yPeninsula Antartica, representa un mega-evento volcanico ocurrido en tiempos jurasicos (188-152 Ma), cuyo emplazamiento estuvo controlado por una tectonica extensional.El analisis cinematico llevado a cabo a partir de fallas y zonas de cizalla fragil-ductil encuatro regiones (El Dorado – Monserrat, Norte de Cerro Vanguardia y El Fenix, en laComarca del Deseado; y Lago Ghio, en la Cordillera Patagonica Austral), permitio definir losejes cinematicos de la deformacion jurasica, reconocer dos eventos cinematicos diferentes(principal y secundario) e identificar la existencia de un regimen transtensional. En relacion ala oblicuidad que presentan los ejes cinematicos en estas localidades, se definieron en formapreliminar dos dominios: el oriental y el occidental. El dominio oriental (El Dorado –Monserrat, Norte de Cerro Vanguardia) presenta una direccion de extension ENE para elevento principal y NNO para el evento secundario, mientras que el dominio occidental (ElFenix y Lago Ghio) exhibe direcciones de extension NE y NO para los episodios principal ysecundario, respectivamente. Estos eventos cinematicos diferentes (principal y secundario)guardan estrecha correlacion con facies volcanicas definidas, ya que el episodio secundario seencuentra temporalmente restringido al momento del emplazamiento de la facies efusivariolitica (domos, coladas, cuerpos hipabisales). Dado el marcado diacronismo de esta provincia volcanica, las diferencias estructurales ycinematicas halladas entre ambos dominios podrian estar reflejando un emplazamientocontrolado por estructuras desarrolladas progresivamente que, a escala continental, estarianvinculadas a un regimen de deformacion no-coaxial mayor.
Quantitative Hydrogeology: Groundwater Hydrology for Engineers

This book contains: The water cycle; Rock porosity and fluid-solid relations in porous media; Darcy's Law; Aquifer systems; Steady state solutions of the diffusion equation; Flow of miscible fluids: dispersion, retention, and heat transfer; Geostatistic and stochastic approach in hydrogeology; and Index. The qualitative aspects is a description of one of the links in the chain of the water cycle inside the Earth's crust, the subsurface flow. The quantitative aspect is the quantification of the various types of subsurface flow, obtained by applying the principles of fluid mechanics in porous media.
QoS Control and Interworking of Overbooked Elastic and Brittle ATM Traffic

Early deployments of broadband ATM networks are likely to use ov rbooked Permanent Virtual Connections in which more connections are set up than Connection Admission Control (CAC) would ordinarily permit. Since, hopefully, not all users will simultaneously use their connections, the QoS levels required for each connection will be met. A critical problem concerns the behaviour when more than the expected maximum number of users are active does the network gracefully degrade? Internet type applications under the control of TCP posses a degree of elasticity that enable them to adjust, whereas others (often real time applications) are more brittle. Under such circumstances appropriate ATM level controls are required that maintain the differing QoS requirements. The interaction of these controls with higher layer protocols, notably TCP, is crucial. Various control mechanisms are described and compared. It is concluded that TCP performs well in conjunction with the ATM Forum’s Guaranteed Frame Rate and VBR.3 traffic classes. Both cases benefit from Partial Packet Discard and a mechanism that assures minimum bandwidth requirements. Network partitioning using PVCs gives additional control. When used together these controls can reduce undesirable interactions between elastic and brittle services thus enabling easier end-to-end service provision.
On computing the determinant and Smith form of an integer matrix

A probabilistic algorithm is presented to find the determinant of a nonsingular, integer matrix. For a matrix A/spl isin/Z/sup n/spl times/n/ the algorithm requires O(n/sup 3.5/(log n)/sup 4.5/) bit operations (assuming for now that entries in A have constant size) using standard matrix and integer arithmetic. Using asymptotically fast matrix arithmetic, a variant is described which requires O(n/sup 2+/spl theta//2//spl middot/log/sup 2/nloglogn) bit operations, where n/spl times/n matrices can be multiplied with O(n/sup /spl theta//) operations. The determinant is found by computing the Smith form of the integer matrix an extremely useful canonical form in itself. Our algorithm is probabilistic of the Monte Carlo type. That is, it assumes a source of random bits and on any invocation of the algorithm there is a small probability of error.
User, device and orientation independent human activity recognition on mobile phones: challenges and a proposal

Smart phones equipped with a rich set of sensors are explored as alternative platforms for human activity recognition in the ubiquitous computing domain. However, there exist challenges that should be tackled before the successful acceptance of such systems by the masses. In this paper, we particularly focus on the challenges arising from the differences in user behavior and in the hardware. To investigate the impact of these factors on the recognition accuracy, we performed tests with 20 different users focusing on the recognition of basic locomotion activities using the accelerometer, gyroscope and magnetic field sensors. We investigated the effect of feature types, to represent the raw data, and the use of linear acceleration for user, device and orientation-independent activity recognition.
A mutual reference shape based on information theory

In this paper, we consider the estimation of a reference shape from a set of different segmentation results using both active contours and information theory. The reference shape is defined as the minimum of a criterion that benefits from both the mutual information and the joint entropy of the input segmentations and is then called a mutual shape. This energy criterion is here justified using similarities between information theory quantities and area measures, and presented in a continuous variational framework. This framework brings out some interesting evaluation measures such as the specificity and sensitivity. In order to solve this shape optimization problem, shape derivatives are computed for each term of the criterion and interpreted as an evolution equation of an active contour. Some synthetical examples allow us to cast the light on the difference between our mutual shape and an average shape. Our framework has been considered for the estimation of a mutual shape for the evaluation of cardiac segmentation methods in MRI.
Practical Box Splines for Reconstruction on the Body Centered Cubic Lattice

We introduce a family of box splines for efficient, accurate, and smooth reconstruction of volumetric data sampled on the body-centered cubic (BCC) lattice, which is the favorable volumetric sampling pattern due to its optimal spectral sphere packing property. First, we construct a box spline based on the four principal directions of the BCC lattice that allows for a linear C0 reconstruction. Then, the design is extended for higher degrees of continuity. We derive the explicit piecewise polynomial representations of the C0 and C2 box splines that are useful for practical reconstruction applications. We further demonstrate that approximation in the shift-invariant space - generated by BCC-lattice shifts of these box splines - is twice as efficient as using the tensor-product B-spline solutions on the Cartesian lattice (with comparable smoothness and approximation order and with the same sampling density). Practical evidence is provided demonstrating that the BCC lattice not only is generally a more accurate sampling pattern, but also allows for extremely efficient reconstructions that outperform tensor-product Cartesian reconstructions.
3 Recent Literature on Time-inconsistent Portfolio Optimization

The explicit results for the classical Merton optimal investment/consumption problem rely on the use of constant risk aversion parameters and exponential discounting. However, many studies have suggested that individual investors can have different risk aversions over time, and they discount future rewards less rapidly than exponentially. While state-dependent risk aversions and non-exponential type (e.g. hyperbolic) discounting align more with the real life behavior and household consumption data, they have tractability issues and make the problem time-inconsistent. We analyze the cases where these problems can be closely approximated by time-consistent ones. By asymptotic approximations, we are able to characterize the equilibrium strategies explicitly in terms of the corrections to solutions for the base problems with constant risk aversion and exponential discounting. We also explore the effects of hyperbolic discounting under proportional transaction costs.
Learning Morphological Disambiguation Rules for Turkish

In this paper, we present a rule based model for morphological disambiguation of Turkish. The rules are generated by a novel decision list learning algorithm using supervised training. Morphological ambiguity (e.g. lives = live+s or life+s) is a challenging problem for agglutinative languages like Turkish where close to half of the words in running text are morphologically ambiguous. Furthermore, it is possible for a word to take an unlimited number of suffixes, therefore the number of possible morphological tags is unlimited. We attempted to cope with these problems by training a separate model for each of the 126 morphological features recognized by the morphological analyzer. The resulting decision lists independently vote on each of the potential parses of a word and the final parse is selected based on our confidence on these votes. The accuracy of our model (96%) is slightly above the best previously reported results which use statistical models. For comparison, when we train a single decision list on full tags instead of using separate models on each feature we get 91% accuracy.
Accumulo di carbonio e produttività delle piantagioni legnose (Kyoto forests) del Friuli Venezia Giulia

Abstract: Aboveground biomass, increment and carbon stock in a 36 forest plantations chronosequence of different ages were quantified. Results have been extrapolated in time using the Richard’s model. Maximum carbon stock was measured in 23 years old plantations (37 tC ha-1) and annual carbon stock rate occurs at 9 years (3.4 tC ha-1 year-1). After this age it decreases to reach 0.40 tC ha-1 year-1 at 23 years after plantation.
Recent advances in efficient learning of recurrent networks

Recurrent neural networks (RNNs) carry the promise of implementing efficient and biologically plausible signal processing. They both are optimally suited for a wide area of applications when dealing with spatiotemporal data or causalities and provide explanation of cog- nitive phenomena of the human brain. Recently, a few new fundamental paradigms connected to RNNs have been developed which allow insights into their potential for information processing. They also pave the way towards new efficient training algorithms which overcome the well-known problem of long-term dependencies. This tutorial gives an overview of this recent developments in efficient, biologically plausible recurrent informa- tion processing.
LR-tree: a Logarithmic Decomposable Spatial Index Method

Since its introduction in 1984, R-tree has been proven to be one of the most practical and well-behaved data structures for accommodating dynamic massive sets of geometric objects and conducting a very diverse set of queries on such datasets in real-world applications. This success has led to a variety of versions, each one trying to tune the performance parameters of the original proposal. Among them, the most prominent one is R ∗ -tree, which employs a number of carefully designed heuristicsand is widely accepted as achieving the best performance in most cases. However, in the presence of actively changing datasets, R ∗ -tree still does not avoid performance tuning with forced reinsertion, i.e. a process that performs a kind of local rebuilding. The latter fact has motivated the investigation of the adaptation of a known dynamization technique, based on carefully triggered local rebuildings, for converting static or semi-dynamic, main memory data structures to dynamic ones onto R ∗ -trees. In this paper, we present LR-trees, a new efficient scheme for dynamic manipulation of large datasets, which combines the search performance of the bulkloaded R-trees with the updated performance of R ∗ -trees. Experimental results provide evidence on the latter statement and illustrate the superiority of the proposed method.
Noun Faithfulness: Evidence from Accent in Japanese Dialects

Kusumoto, John McCarthy, Rachel Walker, and the members of the UMass Phonology Reading Group for helpful discussion related to the topics considered here, and to Teruhiro Hayata for first introducing me to the variety of accent patterns to be found in Japanese dialects. This research was supported by the National Science Foundation under grant SBR-9420424 and by an NSF Graduate Research Fellowship.
Distribution of Heparan Sulfate Oligosaccharides in Murine Mucopolysaccharidosis Type IIIA

Heparan sulfate (HS) catabolism begins with endo-degradation of the polysaccharide to smaller HS oligosaccharides, followed by the sequential action of exo-enzymes to reduce these oligosaccharides to monosaccharides and inorganic sulfate. In mucopolysaccharidosis type IIIA (MPS IIIA) the exo-enzyme, N-sulfoglucosamine sulfohydrolase, is deficient resulting in an inability to hydrolyze non-reducing end glucosamine N-sulfate esters. Consequently, partially degraded HS oligosaccharides with non-reducing end glucosamine sulfate esters accumulate. We investigated the distribution of these HS oligosaccharides in tissues of a mouse model of MPS IIIA using high performance liquid chromatography electrospray ionization-tandem mass spectrometry. Oligosaccharide levels were compared to total uronic acid (UA), which was used as a measure of total glycosaminoglycan. Ten oligosaccharides, ranging in size from di- to hexasaccharides, were present in all the tissues examined including brain, spleen, lung, heart, liver, kidney and urine. However, the relative levels varied up to 10-fold, suggesting different levels of HS turnover and storage. The relationship between the di- and tetrasaccharides and total UA was tissue specific with spleen and kidney showing a different disaccharide:total UA ratio than the other tissues. The hexasaccharides showed a stronger correlation with total UA in all tissue types suggesting that hexasaccharides may more accurately reflect the storage burden in these tissues.
Multireservoir system optimization in the Han River basin using multi‐objective genetic algorithms

In this study, NSGA‐II is applied to multireservoir system optimization. Here, a four‐dimensional multireservoir system in the Han River basin was formulated. Two objective functions and three cases having different constraint conditions are used to achieve nondominated solutions. NSGA‐II effectively determines these solutions without being subject to any user‐defined penalty function, as it is applied to a multireservoir system optimization having a number of constraints (here, 246), multi‐objectives, and infeasible initial solutions. Most research by multi‐objective genetic algorithms only reveals a trade‐off in the objective function space present, and thus the decision maker must reanalyse this trade‐off relationship in order to obtain information on the decision variable. Contrastingly, this study suggests a method for identifying the best solutions among the nondominated ones by analysing the relation between objective function values and decision variables. Our conclusions demonstrated that NSGA‐II performs well in multireservoir system optimization having multi‐objectives. Copyright © 2005 John Wiley & Sons, Ltd.