Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA tertiary structure determination: NOE pathways construction by tabu search

MOTIVATION Liquid state nuclear magnetic resonance (NMR) spectroscopy has now been well established as a method for RNA tertiary structure determination. Most of the steps involved in the determination of RNA molecules are performed using computer programs. They however, do not apply to resonance assignment being the starting point of the whole procedure. We propose a tabu search algorithm as a tool for automating this step. Nuclear overhause effect (NOE) pathway, which determines the assignment, is constructed during an analysis of possible connections between resonances within aromatic/anomeric region of two-dimensional NOESY spectrum resulting from appropriate NMR experiment. RESULTS Computational tests demonstrate the superior performance of the tabu search algorithm as compared with the exact enumerative approach and genetic procedure applied to the experimental and simulated spectral data for RNA molecules. AVAILABILITY The software package can be obtained upon request from Marta Szachniuk.
Aggregative adherence fimbriae I of enteroaggregative Escherichia coli mediate adherence to HEp-2 cells and hemagglutination of human erythrocytes

Strains of enteroaggregative Escherichia coli (EAggEC) have been implicated in several studies as important agents of persistent diarrhea among infants in the developing world. We have previously shown that the aggregative adherence (AA) property of EAggEC is associated with the presence of a 60-MDa plasmid which confers AA when introduced into E. coli HB101. Here, we report the cloning of the AA determinant from EAggEC strain 17-2 into the 21.5-kb cosmid vector pCVD301. TnphoA mutagenesis of the AA cosmid clone pJPN31 implicated an AA region of approximately 12 kb. Transmission electron microscopy of HB101 (pJPN31) revealed the presence of bundle-forming fimbriae, which were absent in AA- TnphoA insertion mutants. The presence of these fimbriae, AA, and hemagglutination (HA) of human erythrocytes were all concurrently lost by single-insertion mutations. A 14-kDa protein was seen on polyacrylamide gel electrophoresis and Western blotting (immunoblotting) of surface shear preparations from fimbriated clones. Twelve of nineteen volunteers fed EAggEC 17-2 developed rises in antibodies to the 14-kDa protein as determined by Western blot. We have termed the cloned bundle-forming fimbriae aggregative adherence fimbriae I (AAF/I); positivity with a previously described EAggEC probe and human erythrocyte HA appear to correlate with the presence of AAF/I.
Plant Identification Based on Leaf Midrib Cross-Section Images Using Fractal Descriptors

The correct identification of plants is a common necessity not only to researchers but also to the lay public. Recently, computational methods have been employed to facilitate this task, however, there are few studies front of the wide diversity of plants occurring in the world. This study proposes to analyse images obtained from cross-sections of leaf midrib using fractal descriptors. These descriptors are obtained from the fractal dimension of the object computed at a range of scales. In this way, they provide rich information regarding the spatial distribution of the analysed structure and, as a consequence, they measure the multiscale morphology of the object of interest. In Biology, such morphology is of great importance because it is related to evolutionary aspects and is successfully employed to characterize and discriminate among different biological structures. Here, the fractal descriptors are used to identify the species of plants based on the image of their leaves. A large number of samples are examined, being 606 leaf samples of 50 species from Brazilian flora. The results are compared to other imaging methods in the literature and demonstrate that fractal descriptors are precise and reliable in the taxonomic process of plant species identification.
Analysis of generalised tit-for-tat strategies in evolutionary spatial n-player prisoner dilemmas: mr.

This work explores the evolution of a population of generalised tit-for-tat (TFT) strategies playing an N-player prisoner's dilemma on a regular lattice. We show that the generalised TFT can be robust to invasion by defectors in most cases. However, interestingly, the TFT strategies which are highly tolerant perform worse than totally cooperative strategies. Furthermore, although, the TFT strategies cannot guarantee the promotion of cooperation, the less tolerant TFT strategies obtain a stable and higher level of cooperation against defectors and populations containing both defectors and cooperators.
Defining Identification: A Theoretical Look at the Identification of Audiences With Media Characters

In this article I argue that although the notion of identification with media characters is widely discussed in media research, it has not been carefully conceptualized or rigorously tested in empirical audience studies. This study presents a theoretical discussion of identification, including a definition of identification and a discussion of the consequences of identification with media characters for the development of identity and socialization processes. It is suggested that a useful distinction can be made between identification and other types of reactions that media audiences have to media characters. A critical look at media research involving identification exposes the inherent conceptual problems in this research and leads to hypotheses regarding the antecedents and consequences of identification with media characters. The importance of a theory of identification to media research and communication research, more broadly, is presented.
Extensive tumor thrombus of hepatocellular carcinoma in the entire portal venous system detected on fluorodeoxyglucose positron emission tomography computed tomography

Detection of thrombus is usually an incidental finding on fluorodeoxyglucose positron emission tomography/computed tomography studies. Nevertheless this is an important finding in terms of disease prognostication and in planning the treatment strategy. We herein report a case of a 50-years-old male, a diagnosed case of hepatocellular carcinoma with extensive hypermetabolic thrombus involving the entire portal venous system.
The long-term effect of premier pay for performance on patient outcomes.

BACKGROUND Pay for performance has become a central strategy in the drive to improve health care. We assessed the long-term effect of the Medicare Premier Hospital Quality Incentive Demonstration (HQID) on patient outcomes. METHODS We used Medicare data to compare outcomes between the 252 hospitals participating in the Premier HQID and 3363 control hospitals participating in public reporting alone. We examined 30-day mortality among more than 6 million patients who had acute myocardial infarction, congestive heart failure, or pneumonia or who underwent coronary-artery bypass grafting (CABG) between 2003 and 2009. RESULTS At baseline, the composite 30-day mortality was similar for Premier and non-Premier hospitals (12.33% and 12.40%, respectively; difference, -0.07 percentage points; 95% confidence interval [CI], -0.40 to 0.26). The rates of decline in mortality per quarter at the two types of hospitals were also similar (0.04% and 0.04%, respectively; difference, -0.01 percentage points; 95% CI, -0.02 to 0.01), and mortality remained similar after 6 years under the pay-for-performance system (11.82% for Premier hospitals and 11.74% for non-Premier hospitals; difference, 0.08 percentage points; 95% CI, -0.30 to 0.46). We found that the effects of pay for performance on mortality did not differ significantly among conditions for which outcomes were explicitly linked to incentives (acute myocardial infarction and CABG) and among conditions not linked to incentives (congestive heart failure and pneumonia) (P=0.36 for interaction). Among hospitals that were poor performers at baseline, mortality was similar in the two groups of hospitals at the start of the study (15.12% and 14.73%; difference, 0.39 percentage points; 95% CI, -0.36 to 1.15), with similar rates of improvement per quarter (0.10% and 0.07%; difference, -0.03 percentage points; 95% CI, -0.08 to 0.02) and similar mortality rates at the end of the study (13.37% and 13.21%; difference, 0.15 percentage points; 95% CI, -0.70 to 1.01). CONCLUSIONS We found no evidence that the largest hospital-based pay-for-performance program led to a decrease in 30-day mortality. Expectations of improved outcomes for programs modeled after Premier HQID should therefore remain modest.
DECT: Distributed Evolving Context Tree for Understanding User Behavior Pattern Evolution

Internet user behavior models characterize user browsing dynamics or the transitions among web pages. The models help Internet companies improve their services by accurately targeting customers and providing them the information they want. For instance, specific web pages can be customized and prefetched for individuals based on sequences of web pages they have visited. Existing user behavior models abstracted as time-homogeneous Markov models cannot efficiently model user behavior variation through time. This demo presents DECT, a scalable time-variant variable-order Markov model. DECT digests terabytes of user session data and yields user behavior patterns through time. We realize DECT using Apache Spark and deploy it on top of Yahoo! infrastructure. We demonstrate the benefits of DECT with anomaly detection and ad click rate prediction applications. DECT enables the detection of higher-order path anomalies and provides deep insights into ad click rates with respect to user visiting paths.
Triple Percolation in Concrete Reinforced with Carbon Fiber

This article discusses how the electrical resistivity of carbon fiber (CF) reinforced concrete with electrical continuity within the cement paste and sand-cement ratio (s/c) 0.75 depends on the CF content and gravel-sand ratio (g/s). For resistivity ≤500 Ω. cm, the mortar must exceed 62 vol.% and the cement paste must exceed 44 vol.%. The minimum resistivities provided by double percolation (continuity provided by the cement paste in the mortar but no continuity of either paste or mortar), pseudo triple percolation (continuity provided by the cement paste of the mortar), and true triple percolation (continuity provided by the mortar) are 355, 36, and 7.6 Ω. cm, respectively. The true triple percolation threshold is 0.75% CF (by mass of cement) if g/s ≤1.50 and 1.5% CF if g/s ≤2.00. The pseudo triple percolation threshold is 1.5% CF if g/s = 2.50 and 1.75% CF if g/s = 2.50 to 3.00. The double percolation threshold is 0.75% CF if g/s = 2.00 to 3.00.
Malaria in Pregnancy

Pregnant women have a higher risk of malaria compared to non-pregnant women. This review provides an update on knowledge acquired since 2000 on P. falciparum and P.vivax infections in pregnancy. Maternal risk factors for malaria in pregnancy (MiP) include low maternal age, low parity, and low gestational age. The main effects of MIP include maternal anaemia, low birth weight (LBW), preterm delivery and increased infant and maternal mortality. P. falciparum infected erythrocytes sequester in the placenta by expressing surface antigens, mainly variant surface antigen (VAR2CSA), that bind to specific receptors, mainly chondroitin sulphate A. In stable transmission settings, the higher malaria risk in primigravidae can be explained by the non-recognition of these surface antigens by the immune system. Recently, placental sequestration has been described also for P.vivax infections. The mechanism of preterm delivery and intrauterine growth retardation is not completely understood, but fever (preterm delivery), anaemia, and high cytokines levels have been implicated. Clinical suspicion of MiP should be confirmed by parasitological diagnosis. The sensitivity of microscopy, with placenta histology as the gold standard, is 60% and 45% for peripheral and placental falciparum infections in African women, respectively. Compared to microscopy, RDTs have a lower sensitivity though when the quality of microscopy is low RDTs may be more reliable. Insecticide treated nets (ITN) and intermittent preventive treatment in pregnancy (IPTp) are recommended for the prevention of MiP in stable transmission settings. ITNs have been shown to reduce malaria infection and adverse pregnancy outcomes by 28–47%. Although resistance is a concern, SP has been shown to be equivalent to MQ and AQ for IPTp. For the treatment of uncomplicated malaria during the first trimester, quinine plus clindamycin for 7 days is the first line treatment and artesunate plus clindamycin for 7 days is indicated if this treatment fails; in the 2nd and 3rd trimester first line treatment is an artemisinin-based combination therapy (ACT) known to be effective in the region or artesunate and clindamycin for 7 days or quinine and clindamycin. For severe malaria, in the second and third trimester parenteral artesunate is preferred over quinine. In the first trimester, both artesunate and quinine (parenteral) may be considered as options. Nevertheless, treatment should not be delayed and should be started immediately with the most readily available drug.
Identification of cysteine and arginine residues essential for the phosphotransacetylase from Methanosarcina thermophila

Phosphotransacetylase catalyzes the following reaction: CoASH + CH3CO2PO3(2-) <==> CH3COSCoA + HPO4(2-) (where CoA is coenzyme A). Based on biochemical characterization of the enzyme from the obligate anaerobe Clostridium kluyveri, a ternary mechanism was proposed in which an unspecified cysteine abstracts a proton from CoASH forming a nucleophilic thiolate anion which attacks acetyl phosphate (J. Henkin and R. H. Abeles, Biochemistry 15:3472-3479, 1976). Heterologous production in Escherichia coli of the phosphotransacetylase from Methanosarcina thermophila, an obligately anaerobic methanoarchaeon, allowed site-specific replacements to identify essential residues. All four cysteines present in the sequence were individually replaced with alanine, and the kinetic constants of the altered enzymes were determined. The results indicated that only C159 is essential for activity; however, replacement with serine resulted in a fully active enzyme. Activity of the unaltered phosphotransacetylase was sensitive to N-ethylmaleimide. Inhibition kinetics of altered enzymes indicated that this sensitivity resulted from modification of C312, which is at the active site but itself is nonessential for catalysis. Five arginines were individually replaced with glutamine. Kinetic analysis of the altered enzymes identified R310 as essential for activity. Of the four nonessential for activity, R87 and R133 appear to be involved in binding CoA.
The 24-Month Changes in Body Fat Mass and Adipokines in Patients Starting Peritoneal Dialysis

♦ Background: Peritoneal dialysis (PD) is characterized by a gain in fat mass. The fat tissue is a complex endocrine organ that releases various adipokines. In this study, we prospectively examined serial changes of fat composition and adipokines in patients undergoing PD. ♦ Methods: Body composition was assessed by computed tomography (CT). Nutrition status and adipokines (leptin, adiponectin, interleukin [IL]-6, and tumor necrosis factor [TNF]-α) were assessed on the 7th day and 6 months, 12 months, and 24 months after the start of PD. ♦ Results: Fifty-four patients (28 men), with a mean age of 53.2 ± 13.2 years, were enrolled. Baseline fat mass, especially subcutaneous fat mass, was correlated with baseline leptin (ρ = 0.612), adiponetin (ρ = -0.477), and interleukin-6 (IL-6) (ρ = 0.391). Visceral fat mass was correlated with leptin (ρ = 0.545) and adiponectin (ρ = -0.514). Baseline adiponectin was negatively correlated with baseline leptin (ρ = -0.363). While body weight and leptin increased during the 24 months, serum adiponectin decreased in that period. The changes in visceral and subcutaneous fat mass were greater in the first 12 months and 6 months, respectively. There was no difference in IL-6 and TNF-α. Eight patients died during the follow-up period (mean 47.4 months). Twenty-seven patients continued PD. Increased baseline and serial change of IL-6 level were risk factors for mortality. After adjusting for age, sex, diabetes mellitus (DM), and coronary vascular disease (CVD), the significance of the IL-6 level disappeared. ♦ Conclusions: Baseline subcutaneous fat in patients starting PD is correlated with baseline adipokine levels rather than visceral fat. The increase in subcutaneous fat was greatest in the first 6 months. While leptin and adiponectin increased and decreased respectively, IL-6 did not change in the first 24 months.
N‐cadherin restrains PTH repressive effects on sclerostin/SOST by regulating LRP6–PTH1R interaction

Sclerostin/SOST is a robust negative regulator of bone formation. Loss‐of‐function mutations of the sclerostin gene (SOST) cause sclerosteosis and Van Buchem disease characterized by bone overgrowth. Mediated by myocyte enhancer factor 2 (MEF2) transcription factors, parathyroid hormone (PTH) suppresses SOST expression through formation of complexes of parathyroid hormone–parathyroid hormone‐related peptide receptor 1 (PTH1R) and lipoprotein receptor–related protein 6 (LRP6). N‐cadherin has been shown to negatively regulate Wnt/β‐catenin and PTH induced, protein kinase‐dependent β‐catenin signaling. Here, we investigated whether N‐cadherin mediates the inhibitory effects of PTH on sclerostin/SOST. In vitro, overexpression of N‐cadherin resulted in blunted PTH suppressive effects on sclerostin/SOST expression, as detected by immunoblot and qPCR analysis; PTH‐induced downregulation of MEF2A, C, and D was impaired by N‐cadherin; and N‐cadherin reduced LRP6–PTHR1 interaction and endocytosis in response to PTH. In vivo, intermittent PTH (iPTH)–induced suppression of sclerostin/SOST was accentuated in Dmp1‐cre; Cdh2f/f (Cdh2ΔDmp1) mice, compared with Cdh2f/f mice. Additionally, iPTH had greater bone anabolic effects in Cdh2ΔDmp1 mice compared to Cdh2f/f mice. These data indicate that N‐cadherin negatively mediates PTH suppressive effects on sclerostin/SOST by regulating LRP6–PTHR1 interaction, ultimately influencing PTH anabolic effects on bone.
The deformation of plastically non-homogeneous materials

Abstract Many two-phase alloys work-harden much faster than do pure single crystals. This is because the two phases are not equally easy to deform. One component (often dispersed as small particles) deforms less than the other, or not at all, so that gradients of deformation form with a wavelength equal to the spacing between the phases or particles. Such alloys are ‘plastically non-homogeneous’, because gradients of plastic deformation are imposed by the microstructure. Dislocations are stored in them to accommodate the deformation gradients, and so allow compatible deformation of the two phases. We call these ‘geometrically-necessary’ dislocations to distinguish them from the ‘statistically-stored’ dislocations which accumulate in pure crystals during straining and are responsible for the normal 3-stage hardening. Polycrystals of pure metals are also plastically non-homogeneous. The density and arrangement of the geometrically-necessary dislocations can be calculated fairly exactly and checked by electr.
Estimation of the defective IDDQ caused by shorts in deep-submicron CMOS ICs

The defective IDDQ in deep-submicron full complementary MOS circuits with shorts is estimated. High performance and also low power scenarios are considered. The technology scaling, including geometry reductions of the transistor dimensions, power supply voltage reduction, carrier mobility degradation and velocity saturation, is modeled. By means of the characterization of the saturation current of a simple MOSFET, a lower bound of IDDQ defective consumption versus Leff is found. Quiescent current consumption lower bound for shorts intragate, and shorts intergate affecting at least one logic node is evaluated. The methodology is used to estimate the IDDQ distribution, for a given input vector, of defective circuits. This IDDQ estimation allows the determination of the threshold value to be used for the faulty/fault-free circuit classification
Multidiscipline Modeling in Materials and Structures

A simple interaction‐potential model has been established to calculate the higher order elastic constants of intermetallic YbAl2 in the temperature range from 10‐300K. Temperature dependent second and third order elastic constants are used for the determination of the ultrasonic attenuation, velocity, Gruneisen numbers, Acoustic‐coupling constants, and thermal relaxation time at the different temperatures. Temperature dependency of the ultrasonic properties of YbAl2 is similar at low temperatures to that of pure metals and the low carrier heavy fermion systems ‐ LaSb, YbAs and YbP having simple NaCl‐type structures. Thermal energy density makes significant contribution to the total attenuation in the compound at the higher temperatures from 100‐300K. Effect of the magnetic field on the ultrasonic attenuation is also evaluated using the magneto resistance data. At 100K, the effect of the magnetic field becomes insignificant. The attenuation decreases with the field at 3K to 50K.
A method for measuring switching frequency using complex asynchronous logic circuits

In order to optimize logic libraries for high-speed operation, and be able to compare new library designs with existing ones, a method that allows switching frequency measurement on-chip is required. In this paper we present a measurement technique to evaluate the switching frequency (and therefore the maximum speed) of digital circuits. The method utilizes asynchronous logic, and is flexible - allowing measurements and comparison to be performed on digital circuits of varying complexity. This measurement method was integrated onto an IC in a 65nm CMOS technology. We provide simulation results that show that the technique is not only able to provide switching frequency measurements but can also identify the critical path through the circuit under test. Such information is critical for logic library optimization.
Modeling Compression Failure of laminated Composites Containing Multiple Through-the-Width Delaminations

An analytical and experimental investigation was performed to study the compression response of laminated composites containing multiple delaminations. It was of particular interest to determine the effects of delaminations on the residual stiffness and strength of delaminated composite structures and on the ability of the structures to sustain compression. An analytical model was developed for simulating the compression re sponse, from initial loading to final collapse, of laminated composites containing multiple through-the-width delaminations. The model is comprised of three parts: a stress analysis, a failure analysis, and a contact analysis. The stress analysis was developed for simulating the buckling and post-buckling response of the structures, the failure analysis was pro posed for predicting delamination growth and fiber-matrix failure, and the contact analysis was developed for analyzing delamination interface condition during loading. A nonlinear finite element code based on the updated Lagrangian formulation was developed for the model. Extensive experiments on T300/976 graphite/epoxy composites were also per formed to verify the model. Laminates with one or two delaminations were tested. Good agreements were obtained between the predictions and the test data from the initial loading to the final collapse of the specimens. Numerical simulations were also performed to dem onstrate the effect of size, location, and distribution of multiple delaminations on the com pression response of composites.