Miracle-dz/UniFAR-FTUs huggingface dataset:
PLAZA 3.0: an access point for plant comparative genomics

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.
Serum Trimethylamine-N-Oxide Is Strongly Related to Renal Function and Predicts Outcome in Chronic Kidney Disease

Background The microbial metabolite Trimethylamine-N-oxide (TMAO) has been linked to adverse cardiovascular outcome and mortality in the general population. Objective To assess the contribution of TMAO to inflammation and mortality in chronic kidney disease (CKD) patients ranging from mild-moderate to end-stage disease and 1) associations with glomerular filtration rate (GFR) 2) effect of dialysis and renal transplantation (Rtx) 3) association with inflammatory biomarkers and 4) its predictive value for all-cause mortality. Methods Levels of metabolites were quantified by a novel liquid chromatography/tandem mass spectrometry-based method in fasting plasma samples from 80 controls and 179 CKD 3–5 patients. Comorbidities, nutritional status, biomarkers of inflammation and GFR were assessed. Results GFR was the dominant variable affecting TMAO (β = -0.41; p<0.001), choline (β = -0.38; p<0.001), and betaine (β = 0.45; p<0.001) levels. A longitudinal study of 74 CKD 5 patients starting renal replacement therapy demonstrated that whereas dialysis treatment did not affect TMAO, Rtx reduced levels of TMAO to that of controls (p<0.001). Following Rtx choline and betaine levels continued to increase. In CKD 3–5, TMAO levels were associated with IL-6 (Rho = 0.42; p<0.0001), fibrinogen (Rho = 0.43; p<0.0001) and hsCRP (Rho = 0.17; p = 0.022). Higher TMAO levels were associated with an increased risk for all-cause mortality that remained significant after multivariate adjustment (HR 4.32, 95% CI 1.32–14.2; p = 0.016). Conclusion Elevated TMAO levels are strongly associated with degree of renal function in CKD and normalize after renal transplantation. TMAO levels correlates with increased systemic inflammation and is an independent predictor of mortality in CKD 3–5 patients.
Sure-fast bilateral filters

Edge-preserving smoothing is widely used in image processing and bilateral filtering is one way to achieve it. Bilateral filter is a nonlinear combination of domain and range filters. Implementing the classical bilateral filter is computationally intensive, owing to the nonlinearity of the range filter. In the standard form, the domain and range filters are Gaussian functions and the performance depends on the choice of the filter parameters. Recently, a constant time implementation of the bilateral filter has been proposed based on raised-cosine approximation to the Gaussian to facilitate fast implementation of the bilateral filter. We address the problem of determining the optimal parameters for raised-cosine-based constant time implementation of the bilateral filter. To determine the optimal parameters, we propose the use of Stein's unbiased risk estimator (SURE). The fast bilateral filter accelerates the search for optimal parameters by faster optimization of the SURE cost. Experimental results show that the SURE-optimal raised-cosine-based bilateral filter has nearly the same performance as the SURE-optimal standard Gaussian bilateral filter and the Oracle mean squared error (MSE)-based optimal bilateral filter.
Sentiment classification of customer reviews based on fuzzy logic

Nowadays, e-commerce is growing fast, so product reviews have grown rapidly on the web. The large number of reviews makes it difficult for manufacturers or businesses to automatically classify them into different semantic orientations (positive, negative, and neutral). Most existing method utilize a list of opinion words for sentiment classification. whereas, this paper propose a fuzzy logic model to perform semantic classifications of customers review into the following sub-classes: very weak, weak, moderate, very strong and strong by combinations adjective, adverb and verb to increase holistic the accuracy of lexicon approach. Fuzzy logic, unlike statistical data mining techniques, not only allows using non-numerical values also introduces the notion of linguistic variables. Using linguistic terms and variables will result in a more human oriented querying process.
Perception of simplification artifacts for animated characters

For real-time animation of characters, Level of Detail (LOD) techniques are usually deployed to achieve optimal efficiency and realism. Tools that can aid an application designer or developer to deploy simplification methods and LOD representations under different circumstances are therefore needed. In this paper we explore the perception of texture, silhouette and lighting artifacts on simplified character models, including the effect animation intensity has on the perceptibility of these artifacts. We propose novel methods to simulate each artifact separately, and test their effects in isolation and cumulatively. Our results provide useful insights and guidelines, including the importance of silhouette preservation. An adaptation of PerceptualDiff for predicting simplification detection has been developed, which can be used to guide automatic model placement and LOD selection in realtime character applications.
Healthcare continuity from hospital to territory in Lombardy: TELEMACO project.

OBJECTIVES To verify implementation and use of TELEMACO (TELEMedicina Ai piccoli COmunilombardi; http://www.telemaco.regione.lombardia.it/), which provides specialized continuity of care with innovative healthcare services in remote areas of the Lombardy region of Italy; to design a network in the territory for sharing of continuityof- care programs; and to allow the relevant health authorities to collect cost data to establish a model for sustainable pricing for implementing these services. METHODS TELEMACO provides home-based telemanagement services for patients with chronic heart failure and chronic obstructive pulmonary disease (COPD), as well as second-opinion teleconsultations in cardiology, dermatology, diabetology, and pulmonology for general practitioners and second-opinion teleconsultations on digital images in cases of traumatic brain injury and stroke. A total of 2 service centers, 10 cardiology and pneumology departments, 30 specialists, 176 general practitioners, 40 nurses, 2 emergency departments, and 2 consultant hospitals were involved. RESULTS A total of 166 patients with chronic heart failure and 474 patients with COPD were enrolled. There were 4830, 51, and 44 second-opinion teleconsultations for cardiologic, dermatologic, and diabetic conditions, respectively. There were 147 second-opinion teleconsultations on digital images, 68 for stroke, and 79 for traumatic brain injury. Implementation of TELEMACO introduced innovations in working methods and provided evidence to the health authorities for allocating funds for such services. CONCLUSIONS TELEMACO provided evidence that there is a growing need for home management of patients using telemedicine, a common and efficacious approach that can ensure care continuity, especially in chronic diseases.
Destruction and distress: using a quasi-experiment to show the effects of the September 11 attacks on subjective well-being in the UK

Using a longitudinal household panel dataset in the United Kingdom, where most interviews are conducted in September each year, we are able to show that the attacks of September 11 resulted in lower levels of subjective well-being for those interviewed after that date in 2001 compared to those interviewed before it. This quasi-experiment provides one of the first examples of the impact of a terrorist attack in one country on well-being in another country. We value this effect through a cost of illness approach, which is estimated to be between £170million and £380 million.
Biocompatibility of Intraocular Lenses

The performance of an intraocular lens is determined by several factors such as the surgical technique, surgical complications, intraocular lens biomaterial and design, and host reaction to the lens. The factor indicating the biocompatibility of an intraocular lens is the behavior of inflammatory and lens epithelial cells. Hence, the biocompatibility of intraocular lens materials is assessed in terms of uveal biocompatibility, based on the inflammatory foreign-body reaction of the eye against the implant, and in terms of capsular biocompatibility, determined by the relationship of the intraocular lens with residual lens epithelial cells within the capsular bag. Insufficient biocompatibility of intraocular lens materials may result in different clinical entities such as anterior capsule opacification, posterior capsule opacification, and lens epithelial cell ongrowth. Intraocular lenses are increasingly implanted much earlier in life in cases such as refractive lens exchange or pediatric intraocular lens implantation after congenital cataract surgery, and these lenses are expected to exhibit maximum performance for many decades. The materials used in intraocular lens manufacture should, therefore, ensure long-term uveal and capsular biocompatibility. In this article, we review the currently available materials used in the manufacture of intraocular lenses, especially with regard to their uveal and capsular biocompatibility, and discuss efforts to improve the biocompatibility of intraocular lenses.
Effects of Prior Exercise and Recovery Duration on Oxygen Uptake Kinetics During Heavy Exercise in Humans

Prior heavy exercise (above the lactate threshold, LT) reduces the amplitude of the pulmonary oxygen uptake (V̇O2) slow component during heavy exercise, yet the precise effect of prior heavy exercise on the phase II V̇O2 response remains to be established. This study was designed to test the hypotheses that (1) prior heavy exercise increases the amplitude of the phase II V̇O2 response independently of changes in the baseline V̇O2 value and (2) the effect of prior exercise depends on the amount of external work done during prior exercise, irrespective of the intensity of the prior exercise. Nine subjects performed two 6 min bouts of heavy cycling exercise separated by 6 min baseline pedalling recovery (A), two 6 min heavy exercise bouts separated by 12 min recovery (6 min rest and 6 min baseline pedalling, B), and a bout of moderate exercise (below the LT) in which the same amount of external work was performed as during the prior heavy exercise, followed by 6 min heavy exercise (C). In both tests A and B, prior heavy exercise significantly increased the absolute V̇O2 amplitude at the end of phase II (by ∼150 ml min−1), and reduced the amplitude of the V̇O2 slow component by a similar amount. Following 12 min of recovery (B), baseline V̇O2, but not blood [lactate], had returned to pre‐exercise levels, indicating that these effects occurred independently of changes in baseline V̇O2. Prior moderate exercise (C) had no effect on either the V̇O2 or blood [lactate] responses to subsequent heavy exercise. The V̇O2 response to heavy exercise was therefore dependent on the intensity of prior exercise, and the effects on the amplitudes of the phase II and slow V̇O2 components persisted for at least 12 min following prior heavy exercise.
Testing subgraphs in large graphs

Let H be a fixed graph with h vertices, let G be a graph on n vertices and suppose that at least /spl epsi/n/sup 2/ edges have to be deleted from it to make it H-free. It is known that in this case G contains at least f (/spl epsi/, H)n/sup h/ copies of H. We show that the largest possible function f (/spl epsi/, H) is polynomial in /spl epsi/ if and only if H is bipartite. This implies that there is a one-sided error property tester for checking H-freeness, whose query complexity is polynomial in 1//spl epsi/, if and only if H is bipartite.
Cost and Outcomes of Medicare Reimbursement for HMO Preventive Services

Medicare beneficiaries enrolled in a health maintenance organization (HMO) were randomized to a preventive services benefit package for 2 years or to usual care. At 24- and 48-month followups, the treatment group had completed more advance directives, participated in more exercise, and consumed less dietary fat than the control group. Unexpectedly, more deaths occurred in the treatment group. Surviving treatment-group enrollees reported higher satisfaction with health, less decline in self-rated health status, and fewer depressive symptoms than surviving control participants. Despite these changes, the intervention did not yield lower cost per quality-adjusted life year in this historically prevention-oriented HMO.
Feasibility of the Olweus Bullying Prevention Program in Low-Income Schools

ABSTRACT This article examines school response to bullying and youth aggression in upper/middle-class and low socioeconomic neighborhoods, and the feasibility of successfully implementing the Olweus Bullying Prevention Program in schools located in impoverished communities. The Olweus Bullying Prevention Program is one of the few programs that has proven efficacy in upper/middle-class areas for reducing the incidence of bullying and improving attitudes towards school and academic achievement, but the effectiveness of the program has not been tested in low-income schools. However, research indicates that in both upper/middle-class and low socioeconomic neighborhoods, children are reluctant to seek assistance, and school teachers are not well-informed of effective bullying prevention measures. Researchers have pointed out that although children of low socioeconomic status (particularly minorities) have higher incidence of behavioral problems than their upper/middle-class counterparts, socioeconomic and cultural differences pose a major challenge to implementing effective anti-bullying interventions in schools that are located in impoverished communities. Suggestions for enhancing the applicability of anti-bullying programs to low-income schools are included.
Ground-based GPS remote sensing for precipitable water vapor: A case study of the heat-island effect in Taipei

It is known that there are severe heat-island effects in the urbanized area such as Taipei and that temperature increases are causing hydrological change. The city continues to develop, so it is urgent that the region creates early warning methods. In this study, we observed the influence of the heat-island effect on temperature, precipitable water vapor (PWV), and rainfall in a suburb in Taipei and confirmed that the urban area had a rising temperature trend during the period from 2006 - 2014, approximately 0.7 degrees higher than that in the suburb, which decreased by 1.1 degrees. The average PWV increased by approximately 6.7 mm and the cumulative rainfall increased approximately 54.7 mm. Two other high-temperature areas are in the development zone and in the northern mountainous area, which is lower in temperature, and a heat-island effect is obvious. Rainfall is greatest in the southern mountainous areas in summer. Due to wind direction in the winter, rain falls in the northeastern region of the windward side. Our results also show that there is a significant urban heat-island effect in the Taipei region and that PWV and rainfall are increasing in the urban area with global warming.
Interpreting Money-Supply and Interest-Rate Shocks as Monetary-Policy Shocks

In this paper two shocks are analysed using Canadian data: a money-supply shock (“M-shock”) and an interest-rate shock (“R-shock”). Money-supply shocks are derived using long-run restrictions based on long-run propositions of monetary theory. Thus, an M-shock is represented by an orthogonalized innovation in the trend shared by money and prices. An R-shock is represented by the orthogonalized innovation in the overnight interest rate. Either type of shock might be interpreted as a monetary-policy shock. A permanent increase in the nominal stock of M1 generates: a temporary fall in the interest rate, consistent with the liquidity effect; a temporary rise in real output; a permanent increase in the price level; and a permanent depreciation of the nominal exchange rate. Although the behaviour of M1 is not directly controlled by the central bank, the identifying assumption that the central bank controls the long-run trend in money and prices and has no long-run effect on real output appears to be quite reasonable. A temporary positive real-interest-rate shock generates a temporary fall in money and output, but prices rise initially (a “price puzzle”) before eventually declining. Both the Mshock and R-shock models are consistent with an active role for money in the transmission of monetary policy. Résumé Dans le présent document, l’auteur analyse deux types de choc au moyen de données canadiennes : un choc d’offre de monnaie (le choc M) et un choc de taux d’intérêt (le choc R). Pour identifier le premier type de choc, il recourt aux restrictions de long terme découlant de certaines propositions avancées par la théorie monétaire. Le choc M est représenté par une innovation orthogonale dans la tendance commune qu’affichent la monnaie et les prix, et le choc R, par une innovation orthogonale dans le taux d’intérêt à un jour. L’un ou l’autre de ces chocs peut être interprété comme un choc de politique monétaire. Une augmentation permanente du stock nominal de monnaie, M1, entraîne les conséquences suivantes: une chute temporaire du taux d’intérêt, conforme à l’effet de liquidité; une hausse passagère de la production exprimée en termes réels; une augmentation permanente du niveau des prix; et une dépréciation permanente du taux de change nominal. Bien que le comportement de M1 ne soit pas contrôlé directement par la banque centrale, l’hypothèse que cette dernière détermine la tendance de la monnaie et des prix à long terme mais qu’elle n’exerce aucune influence sur la production en termes réels en longue période semble fondée. Une hausse temporaire du taux d’intérêt réel provoque une baisse temporaire de la masse monétaire et de la production, mais les prix affichent un comportement plutôt déconcertant, puisqu’ils s’élèvent d’abord avant de redescendre. Les résultats obtenus à l’aide des modèles relatifs aux deux types de choc cadrent avec la thèse voulant que la monnaie joue un rôle actif dans la transmission de la politique monétaire.
Characteristics and performance of knowledge networks in the biotechnology sector

This research aimed to analyze the properties and typologies of a biotechnology sector network with regard to their relationships, attributes and performance in research and production of innovations. For this purpose, it had as its empirical field the Northeast Biotechnology Network, using patent reports produced by the network as a data source. In order to track the relationship networks between members, groups, institutions and projects, social networking analysis tools were used, making it possible to construct relationship matrices between the laboratories and companies and, lastly, researchers. In total, 117 researchers were identified, distributed among 18 research centers and 47 laboratories or companies. Their projects are distributed across three main areas: agriculture, industrial and health, the latter being the strongest of the three with more patents produced and more institutions involved in research. The weak density presented by the network, at all analysis levels, strengthens the necessity for integration strategies. Also, it indicates the possibility for new relationships between agents that are still isolated. However, it does not diminish its importance for economic development in the region in which it operates.
Computer Systems That Learn: Classification and Prediction Methods from Statistics, Neural Nets, Machine Learning and Expert Systems

Preface 1 Overview of Learning Systems 1.1 What is a Learning System? 1.2 Motivation for Building Learning Systems 1.3 Types of Practical Empirical Learning Systems 1.3.1 Common Theme: The Classification Model 1.3.2 Let the Data Speak 1.4 What's New in Learning Methods 1.4.1 The Impact of New Technology 1.5 Outline of the Book 1.6 Bibliographical and Historical Remarks 2 How to Estimate the True Performance of a Learning System 2.1 The Importance of Unbiased Error Rate Estimation 2.2. What is an Error? 2.2.1 Costs and Risks 2.3 Apparent Error Rate Estimates 2.4 Too Good to Be True: Overspecialization 2.5 True Error Rate Estimation 2.5.1 The Idealized Model for Unlimited Samples 2.5.2 Train-and Test Error Rate Estimation 2.5.3 Resampling Techniques 2.5.4 Finding the Right Complexity Fit 2.6 Getting the Most Out of the Data 2.7 Classifier Complexity and Feature Dimensionality 2.7.1 Expected Patterns of Classifier Behavior 2.8 What Can Go Wrong? 2.8. 1 Poor Features, Data Errors, and Mislabeled Classes 2.8. 2 Unrepresentative Samples 2.9 How Close to the Truth? 2.10 Common Mistakes in Performance Analysis 2.11 Bibliographical and Historical Remarks 3 Statistical Pattern Recognition 3.1 Introduction and Overview 3.2 A Few Sample Applications 3.3 Bayesian Classifiers 3.3.1 Direct Application of the Bayes Rule 3.4 Linear Discriminants 3.4.1 The Normality Assumption and Discriminant Functions 3.4.2 Logistic Regression 3.5 Nearest Neighbor Methods 3.6 Feature Selection 3.7 Error Rate Analysis 3.8 Bibliographical and Historical Remarks 4 Neural Nets 4.1 Introduction and Overview 4.2 Perceptrons 4.2.1 Least Mean Square Learning Systems 4.2.2 How Good Is a Linear Separation Network? 4.3 Multilayer Neural Networks 4.3.1 Back-Propagation 4.3.2 The Practical Application of Back-Propagation 4.4 Error Rate and Complexity Fit Estimation 4.5 Improving on Standard Back-Propagation 4.6 Bibliographical and Historical Remarks 5 Machine Learning: Easily Understood Decision Rules 5.1 Introduction and Overview 5.2 Decision Trees 5.2.1 Finding the Perfect Tree 5.2.2 The Incredible Shrinking Tree 5.2.3 Limitations of Tree Induction Methods 5.3 Rule Induction 5.3.1 Predictive Value Maximization 5.4 Bibliographical and Historical Remarks 6 Which Technique is Best? 6.1 What's Important in Choosing a Classifier? 6.1.1 Prediction Accuracy 6.1.2 Speed of Learning and Classification 6.1.3 Explanation and Insight 6.2 So, How Do I Choose a Learning System? 6.3 Variations on the Standard Problem 6.3.1 Missing Data 6.3.2 Incremental Learning 6.4 Future Prospects for Improved Learning Methods 6.5 Bibliographical and Historical Remarks 7 Expert Systems 7.1 Introduction and Overview 7.1.1 Why Build Expert Systems? New vs. Old Knowledge 7.2 Estimating Error Rates for Expert Systems 7.3 Complexity of Knowledge Bases 7.3.1 How Many Rules Are Too Many? 7.4 Knowledge Base Example 7.5 Empirical Analysis of Knowledge Bases 7.6 Future: Combined Learning and Expert Systems 7.7 Bibliographical and Historical Remarks References Author Index Subject Index