Miracle-dz/UniFAR-FTUs huggingface dataset:
The relationship between N‐gram patterns and protein secondary structure

An n‐gram pattern (NP{n,m}) in a protein sequence is a set of n residues and m wildcards in a window of size n+m. Each window of n+m amino acids is associated with a collection of NP{n,m} patterns based on the combinatorics of n+m objects taken m at a time. NP{n,m} patterns that are shared between sequences reflect evolutionary relationships. Recently the authors developed an alignment‐independent protein classification algorithm based on shared NP{4,2} patterns that compared favorably to PSI‐BLAST. Theoretically, NP{4,2} patterns should also reflect secondary structure propensity since they contain all possible n‐grams for 1 ≤ n ≤ 4 and a window of 6 residues is wide enough to capture periodicities in the 2 ≤ n ≤ 5 range. This sparked interest in differentiating the information content in NP{4,2} patterns related to evolution from the content related to local propensity. The probability of α‐, β‐, and coil components was determined for every NP{4,2} pattern over all the chains in the Protein Data Bank (PDB). An algorithm exclusively based on the Z‐values of these distributions was developed, which accurately predicted 71–76% of α‐helical segments and 62–67% of β‐sheets in rigorous jackknife tests. This provided evidence for the strong correlation between NP{4,2} patterns and secondary structure. By grouping PDB chains into subsets with increasing levels of sequence identity, it was also possible to separate the evolutionary and local propensity contributions to the classification process. The results showed that information derived from evolutionary relationships was more important for β‐sheet prediction than α‐helix prediction. Proteins 2007. © 2007 Wiley‐Liss, Inc.
International Journal of Copd Dovepress Open Access to Scientific and Medical Research Open Access Full Text Article Dovepress Insights into Interventions in Managing Copd Patients: Lessons from the Torch and Uplift ® Studies

Influencing the progression of COPD has long been an elusive goal of drug therapy. Directly or indirectly, this has again been investigated in two of the largest, long-term drug trials in COPD: Towards a Revolution in COPD Health (TORCH) and Understanding Potential Long-Term Impacts on Function with Tiotropium (UPLIFT ®). Neither trial achieved statistical significance in their respective primary outcomes; however, both make considerable contributions to understanding of how the progression of COPD may be influenced. The objective of this article is to review the data from these different trials with a view to what can be learnt about the management of COPD. The long-term improvements in lung function, health-related quality of life, and possibly survival from the use of long-acting bronchodilators in these trials suggest an influence on progression of the disease. With the more optimistic view of benefits from drug treatment of COPD that these trials provide, a review of prescribing practices is warranted. Burden of COPD Chronic obstructive pulmonary disease (COPD) is a major cause of morbidity and mortality, and represents a substantial economic and social burden worldwide. Global prevalence of COPD in the general population has been reported to be between 7.5% and 10%, 1,2 and is predominantly associated with smoking. In a meta-analysis of 67 population-based studies (representing 111,000 cases of COPD from 28 countries), prevalence of COPD was significantly higher among smokers (15.4%) and ex-smokers (10.7%) than people who had never smoked (4.3%). 2 Prevalence of COPD is therefore highest in countries where cigarette smoking is common. Current prevalence data are likely to underestimate the true burden of COPD, since the disease is frequently misdiagnosed or not diagnosed until symptoms become clinically apparent at a more advanced stage. Of the people with COPD in Spain, for example, only an estimated 20% have their disease diagnosed. 3 In the US, it is believed that between 60% and 70% of patients with reduced forced expiratory volume in 1 second (FEV 1) have never been diagnosed with COPD. 4 The burden of morbidity and mortality due to COPD is predicted to increase. 4 COPD is the fourth leading cause of mortality in the US and Europe, 5 and approximately 2.7 million deaths worldwide were attributable to COPD in 2000. 4 Age-adjusted mortality due to COPD doubled between 1970 and 2002 in the US, 6 and total deaths from COPD are projected to increase by more than 30% …
Serial Persistence in Equity REIT Returns

Annual and monthly REIT returns display statistically significant serial persistence, although the two types of persistence behavior are qualitatively different. By contrast, quarterly REIT returns do not display serial persistence. This strongly suggests that linear multifactor market models cannot describe REIT investment behavior. Annual REIT returns fail to reflect corresponding persistence behavior in underlying real estate returns precisely when the REITs are large enough to attract institutional investor interest. Institutional investors move in and out of large-capitalization REITs in ways that negatively impact investment returns.
Heterogeneous Beliefs, Public Information, and Option Markets

In an incomplete market setting with heterogeneous prior beliefs, I show that public information and strike price of option have substantial infl? uence on asset pricing in option markets, by investigating an absolute option pricing model with negative exponential utility investors and normally distributed dividend. I demonstrate that heterogeneous prior variances give rise to the economic value of option markets. In- vestors speculate in option market and public information improves allocational efficiency of markets only when there is heterogeneity in prior variance. Heterogeneity in mean is neither a necessary nor sufficient condition for generating speculations in op- tion markets. With heterogeneous beliefs, options are non-redundant assets which can facilitate side-betting and enable investors to take advantage of the disagreements and the differences in con? dence. This fact leads to a higher growth rate in the investors? certainty equivalents and, thus, a higher equilibrium interest rate. The public infor- mation system facilitates improved dynamic trading opportunities in option markets based on the heterogeneously updated posterior beliefs. With an intermediate signal precision and the option with intermediate strike price, the highest efficiency of side- betting is achieved, re? ected by a unique maximum point of the ex ante equilibrium interest rate. The public signal precision affects ex ante equilibrium risk premium only via its relationship with option.
Governing from the Bench: The Supreme Court of Canada and the Judicial Role

Introduction 1 Studying Judicial Behaviour 2 The Evolution of the Court and Its Justices 3 Setting the Stage: Exploring Court Processes Leading to Decisions 4 The Decision: Collegiality, Conflict, and Consensus 5 A Question of Competence: Examining Judicial Policy Making 6 The Court in Government and Society: Dialogue, Public Opinion, and the Media Conclusion Notes Bibliography Index
The Macroeconomics of Finance-Dominated Capitalism - and its Crisis

In this timely and thought-provoking book, Eckhard Hein illustrates that the Great Recession, which hit the world economy in 2008/09, is rooted in the contradictions of finance-dominated capitalism. The author provides an in-depth exploration of the macroeconomics of finance-dominated capitalism, its problems and its crisis, and presents economic policy lessons and alternatives.
Negotiation Basics: Concepts, Skills, and Exercises

Transforming Problems into Negotiating Opportunities Identifying and Pursuing Useful Negotiating Goals Finding and Using Information Making Cost-Benefit Decisions Building Credibility to Enhance your Power Fitting Strategies to your Situation and Personal Style Choosing the Appropriate Tactics Organizing Constituents for Representative Bargaining Searching for Secrets to Break Impasses Using an Outside Party When You Need One Conclusion Creating a Positive Negotiating Climate
VEGFR-2 Expression in Glioblastoma Multiforme Depends on Inflammatory Tumor Microenvironment

Glioblastoma multiforme (GBM) is one of the most angiogenic tumors. However, antiangiogenic therapy has not shown significant clinical efficacy. The aim of our study was to evaluate the impact of inflammatory tumor microenvironment on the expression of vascular endothelial growth factor receptor 2 (VEGFR-2). Surgically excised primary GBM tissues were histologically examined for overall extent of inflammation (score 1–3). After immunohistochemistry, the tissue expression of ICAM-1 (optical density), the number of VEGFR-2 positive (VEGFR-2+) blood vessels (per microscopic field), and the endothelial staining intensity of VEGFR-2 (score 0–3) were determined. In GBM, the extent of inflammation was 1.9 ± 0.7 (group mean ± SD). Mean optical density of inflammatory mediator ICAM-1 was 57.0 ± 27.1 (pixel values). The number of VEGFR-2+ blood vessels and endothelial VEGFR-2 staining intensity were 6.2 ± 2.4 and 1.2 ± 0.8, respectively. A positive association was found between endothelial VEGFR-2 staining intensity and the extent of inflammation (p = 0.005). Moreover, VEGFR-2 staining intensity correlated with the expression level of ICAM-1 (p = 0.026). The expression of VEGFR-2, one of the main targets of antiangiogenic therapy, depends on GBM microenvironment. Higher endothelial VEGFR-2 levels were seen in the presence of more pronounced inflammation. Target dependence on inflammatory tumor microenvironment has to be taken into consideration when treatment approaches that block VEGFR-2 signaling are designed.
A Long Run Perspective on Saving

Historical estimates of long-run gross savings rates are provided for eleven countries, which represent about 48 percent of world product in real terms and close to half of world savings. Even though savings rates declined over the past decade in nine of the eleven countries, present rates are usually well above their prewar levels. Factors that influence savings rates are also examined. Copyright 1992 by The editors of the Scandinavian Journal of Economics.
Absorptive Capacity and Firm Performance in SMEs: The Mediating Influence of Strategic Alliances

Absorptive capacity (ACAP) is a firm's ability to innovate by identifying, assimilating, and exploiting knowledge available in its environment. ACAP has been widely researched, but this research has not sufficiently analyzed the influence of ACAP on an interfirm level, especially regarding the multidimensional character of this construct. The present study intends to reveal whether the relationship between ACAP and firm performance in small and mediun sized enterprises (SMEs) is mediated by strategic alliances. Furthermore, different moderating characteristics such as age and size of the companies are taken into consideration. The findings indicate that strategic alliances of SMEs mediate both the relationship between ACAP and firm performance and the relationship between each dimension of ACAP and firm performance. However, these results might not be valid under certain circumstances since strategic alliances have no mediating influence when it comes to young SMEs, for example.
The Performance of ICDAS-II Using Low-Powered Magnification with Light-Emitting Diode Headlight and Alternating Current Impedance Spectroscopy Device for Detection of Occlusal Caries on Primary Molars

Early detection of occlusal caries in children is challenging for the dentists, because of the morphology of pit and fissures. The aim of this study was to compare in vitro the diagnostic performance of low-powered magnification with light-emitting diode headlight (LPMLED) using ICDAS-II criteria and AC Impedance Spectroscopy (ACIS) device, on occlusal surfaces of primary molars. The occlusal surfaces of 18 extracted primary molars were examined blindly by two examiners. The teeth were sectioned and examined under light microscopy using Downer's histological criteria as gold standard. Good to excellent inter- and intraexaminer reproducibility, higher sensitivity, specificity, and AUC values were achieved by LPMLED at D1 threshold. Also the relationship between histology and LPMLED was statistically significant. In conclusion visual aids have the potential to improve the performance of early caries detection and clinical diagnostics in children. Despite its potential, ACIS device should be considered as an adjunct method in detecting caries on primary teeth.
For Members Only

Although group membership has many privileges, members are expected to reciprocate those privileges. We tested whether in-group members would be punished more harshly than out-group members for marginal fairness norm violations within ultimatum game bargaining interactions. Participants considered monetary splits (of US$20) from in-group and out-group proposers, which ranged in proportion. Accepting an offer yielded the proposed payout; rejecting it caused each player to earn nothing—a punishment of the proposer at a personal cost. Participants exacted stricter costly punishment on racial in-group than out-group members for marginally unfair offers (Study 1), an effect that was replicated with college group membership and magnified among strong in-group identifiers (Study 2). Importantly, ultimatum game decisions were driven by fairness perceptions rather than proposer evaluations (Study 3), suggesting our effects reflected norm enforcement and not esteem preservation. These findings illuminate a previously unexplored process for maintaining group-based norms that may promote in-group favoritism.
Intraperiod and Intertemporal Substitution in Import Demand

In this paper, we study intraperiod and intertemporal substitution in U.S. import demand using a two-good version of the permanent-income model that allows for nonseparability between domestic and imported goods consumption. The intratemporal elasticity of substitution between the two goods is estimated to be about 1.09 while the intertemporal elasticity of substitution of the composite good is estimated to be statistically larger than the intraperiod measure and lie between 1.36 to 1.39. We then explore the implications of these estimates for intraperiod and intertemporal substitution in the presence of an exogenous real exchange rate movement. Dans ce papier, nous etudions la substitution intraperiode et intertemporelle de la demande d'importations des Etats-Unis en utilisant une version a deux biens du modele du revenu permanent qui permet de tenir compte de la non-separabilite entre les biens de consommation domestiques et importes. L'elasticite intratemporelle est estimee a environ 1.09 tandis que l'elasticite de substitution intertemporelle du bien compose est statistiquement plus elevee que la mesure intraperiode et se trouve entre 1.36 et 1.39. Par la suite, nous explorons les implications de ces estimations pour la substitution intraperiode et intertemporelle dans la presence d'un mouvement exogene du taux de change reel.
Optimization of interval type-2 fuzzy logic controllers with rule base size reduction using genetic algorithms

This paper presents optimization technique to develop type-2 fuzzy systems (FSs) through hybrid genetic algorithms (HGAs). The proposed optimization technique works as follows: (i) Optimize the type-2 membership functions (ii) Learn the rule base through genetic algorithms (iii) Apply the reducing technique to reduce the rule base. (iv) Build the FSs based on type-2 membership functions and the reduced rule base. For concurrently works step (i) and (ii), we used real and binary coded coupled GAs for the optimization technique. Real coded GAs is used to tune the type-2 membership functions and binary coded GAs is used to learn and reducing the fuzzy rules. For intelligent control of a two degree freedom inverted pendulum system, the control algorithm is used. Finally, the simulation studies show that the generated controller performance is better and comparable to the existing methods under normal conditions.
Corrugator muscle responses are associated with individual differences in positivity-negativity bias.

Corrugator supercilii muscle activity is considered an objective measure of valence because it increases in response to negatively valenced facial expressions (angry) and decreases to positive expressions (happy). The authors sought to determine if corrugator activity could be used as an objective measure of positivity-negativity bias. The authors recorded corrugator responses as participants rated angry, happy, and surprised faces as "positive" or "negative. " The critical measure of bias was the percentage of positive versus negative ratings assigned to surprised faces by each participant. Reaction times for surprise expressions were longer than for happy and angry expressions, consistent with their ambiguous valence. Participants who tended to rate surprised faces as negative showed increased corrugator activity to surprised faces, whereas those who tended to rate surprise as positive showed decreased activity. Critically, corrugator responses reflected the participants' bias (i.e., their tendency to rate surprise as positive or negative). These data show that surprised faces constitute a useful tool for assessing individual differences in positivity-negativity bias, and that corrugator activity can objectively reflect this bias.
Grid Architecture and implementation for ALICE experiment

According to the requirement of the Physics Data Challenge and many years of experiences from the actual operations, we propose the Grid Architecture for the ALICE Experiment. This architecture builds on AliEn2 framework and AliEn2 is the grid framework for the whole system's management and also provides the client interface for accessing the ALICE Grid platform. On the base of AliEn2, we adopt some middlewares to make the platform more flexible, availability and efficiency. At the end, the whole system has been worldwide deployed at around 88 sites for distributed production of raw data and Monte Carlo data, detector simulation, reconstruction and real data analysis. We observe the activities of the platform from different point of view and report the performance of the whole ALICE grid platform. The whole Grid Architecture for ALICE experiment plays an important role in High Energy Physics. It successfully manages the resources distributed all over the world and has a great efficiency system to make all peoples from and in different countries working together. The experiments show the whole system works fine and efficient.
A Multivariate Forward-Rate Mortality Framework

Stochastic mortality models have been developed for a range of applications from demographic projections to financial management. Financial risk based models build on methods used for interest rates and apply these to mortality rates. They have the advantage of being applied to financial pricing and the management of longevity risk. Olivier and Jeffery (2004) and Smith (2005) proposed a model based on a forward-rate mortality framework with stochastic factors driven by univariate gamma random variables irrespective of age or duration. We assess and further develop this model. We generalize random shocks from a univariate gamma to a univariate Tweedie distribution and allow for the distributions to vary by age. Furthermore, since dependence between ages is an observed characteristic of mortality rate improvements, we formulate a multivariate framework using copulas. We find that dependence increases with age and introduce a suitable covariance structure, one that is related to the notion of a minimum. The resulting model provides a more realistic basis for capturing the risk of mortality improvements and serves to enhance longevity risk management for pension and insurance funds.
Activation Detection in Functional MRI Using Model-Free Technique Based On CCA-ICA Analysis

The model-based approach for detecting the fMRI activations involves assumptions about the hemodynamic response function. If such assumptions are incorrect or incomplete, this may result in biased estimates of the true response, posing a significant obstacle to the practicality of the technique. In this work, a simple yet robust model-free technique is proposed for detecting the fMRI activations. The idea of the proposed model is to convert one of the model-based fMRI tools, namely canonical correlation analysis (CCA), to model-free with help of independent component analysis (ICA). In particular, ICA provides accurate reference functions for CCA instead of the harmonics originally used. This combination enables the elimination of the limitations of both techniques and provides a model-free approach for data analysis. Results from both numerical simulations and real fMRI data sets confirm the practicality and robustness of the proposed method.
Structural Determinant and Its Underlying Molecular Mechanism of STPC2 Related to Anti-Angiogenic Activity

In this study, we aimed to use different strategies to further uncover the anti-angiogenic molecular mechanism of a fucoidan-like polysaccharide STPC2, isolated from brown alga Sargassum thunbergii. A desulfated derivative, STPC2-DeS, was successfully prepared and identified. The native polysaccharide and desulfated product were subjected to evaluate their anti-angiogenic effects. In the tube formation assay, STPC2 showed dose-dependent inhibition. In addition, STPC2 could distinctly inhibit the permeation of HUVEC cells into the lower chamber. Moreover, a significant reduction of microvessel density was observed in chick chorioallantoic membrane assay treated with STPC2. Meanwhile, STPC2 was found to repress the VEGF-induced neovessel formation in the matrigel plug assay in vivo. However, STPC2-DeS failed to suppress the anti-angiogenic activity via these in vitro and in vivo strategies. In addition, we demonstrated that STPC2 could significantly downregulate the phosphorylation of VEGFR2 and its related downstream Src family kinase, focal adhesion kinase, and AKT kinase. Furthermore, surface plasmon resonance assay revealed that STPC2 bound strongly to VEGF to interfere with VEGF–VEGFR2 interaction. Taken together, these results evidently demonstrated that STPC2 exhibited a potent anti-angiogenic activity through binding to VEGF via sulfated groups to impede VEGF–VEGFR2 interaction, thus affected the downstream signaling molecules.
From Stimulus to Consolidation: Revenue and Expenditure Policies in Advanced and Emerging Economies

This paper identifies policy tools that could be used for fiscal consolidation in advanced and emerging economies in the years ahead. The consolidation strategy, particularly in advanced countries, should aim to stabilize age-related spending in relation to GDP, reduce non-age-related expenditure ratios, and increase revenues. Bold reforms are needed to offset projected increases in age-related spending, particularly health care. On the revenue side, measures could include improving tax compliance, for example through better international cooperation, as well as increasing the yield from VAT by eliminating exemptions and reduced rates, further developing property taxes, and increasing excise rates within the range of rates already applicable in comparable countries.