Miracle-dz/UniFAR-FTUs huggingface dataset:
Theoretical Biology and Medical Modelling

Background: It is of particular interest to identify cancer-specific molecular signatures for early diagnosis, monitoring effects of treatment and predicting patient survival time. Molecular information about patients is usually generated from high throughput technologies such as microarray and mass spectrometry. Statistically, we are challenged by the large number of candidates but only a small number of patients in the study, and the right-censored clinical data further complicate the analysis. Results: We present a two-stage procedure to profile molecular signatures for survival outcomes. Firstly, we group closely-related molecular features into linkage clusters, each portraying either similar or opposite functions and playing similar roles in prognosis; secondly, a Bayesian approach is developed to rank the centroids of these linkage clusters and provide a list of the main molecular features closely related to the outcome of interest. A simulation study showed the superior performance of our approach. When it was applied to data on diffuse large B-cell lymphoma (DLBCL), we were able to identify some new candidate signatures for disease prognosis. Conclusion: This multivariate approach provides researchers with a more reliable list of molecular features profiled in terms of their prognostic relationship to the event times, and generates dependable information for subsequent identification of prognostic molecular signatures through either biological procedures or further data analysis.
The immediate effect of soft tissue manual therapy intervention on lung function in severe chronic obstructive pulmonary disease

Background and objective In chronic obstructive pulmonary disease (COPD), accessory respiratory muscles are recruited as a compensatory adaptation to changes in respiratory mechanics. This results in shortening and overactivation of these and other muscles. Manual therapy is increasingly being investigated as a way to alleviate these changes. The aim of this study was to measure the immediate effect on lung function of a soft tissue manual therapy protocol (STMTP) designed to address changes in the accessory respiratory muscles and their associated structures in patients with severe COPD. Methods Twelve medically stable patients (n=12) with an existing diagnosis of severe COPD (ten: GOLD Stage III and two: GOLD Stage IV) were included. Residual volume, inspiratory capacity and oxygen saturation (SpO2) were recorded immediately before and after administration of the STMTP. A Student’s t-test was used to determine the effect of the manual therapy intervention (P<0.05). Results The mean age of the patients was 62.4 years (range 46–77). Nine were male. Residual volume decreased from 4.5 to 3.9 L (P=0.002), inspiratory capacity increased from 2.0 to 2.1 L (P=0.039) and SpO2 increased from 93% to 96% (P=0.001). Conclusion A single application of an STMTP appears to have the potential to produce immediate clinically meaningful improvements in lung function in patients with severe and very severe COPD.
Simulation, animation, and shop-floor control

It is often desirable to link shop-floor hardware directly to a discrete-event simulation model or graphical animation. Four situations in which this type of arrangement may be beneficial are identified here, and several mechanisms for implementation are discussed. A primary application involves testing the planned control logic for a specific manufacturing system. In this case, a simulation model, linked directly to one or more programmable controllers, provides the controller(s) with system scenarios under which they are expected to perform and produce a response. A second application is system emulation, where real-time data is used to drive an animation. In this way, a visual representation of system status is provided to monitor shop-floor activity. This may be especially useful in situations where the system is monitored from a remote or central control area. The ability to simulate ahead from current shop-floor status is the foundation for the final two applications that are considered here. Used for contingency control, the effects of alternate control strategies which may be imposed when some critical event occurs, e.g. machine breakdown or expedited orders, may be studied and evaluated. Finally, alternate production schedules may be simulated and compared when the initial schedule is prepared, or updated and resimulated as the shop-floor situation changes.
Enterococcus faecium NCIMB 10415 Modulates Epithelial Integrity, Heat Shock Protein, and Proinflammatory Cytokine Response in Intestinal Cells

Probiotics have shown positive effects on gastrointestinal diseases; they have barrier-modulating effects and change the inflammatory response towards pathogens in studies in vitro. The aim of this investigation has been to examine the response of intestinal epithelial cells to Enterococcus faecium NCIMB 10415 (E. faecium), a probiotic positively affecting diarrhea incidence in piglets, and two pathogenic Escherichia coli (E. coli) strains, with specific focus on the probiotic modulation of the response to the pathogenic challenge. Porcine (IPEC-J2) and human (Caco-2) intestinal cells were incubated without bacteria (control), with E. faecium, with enteropathogenic (EPEC) or enterotoxigenic E. coli (ETEC) each alone or in combination with E. faecium. The ETEC strain decreased transepithelial resistance (TER) and increased IL-8 mRNA and protein expression in both cell lines compared with control cells, an effect that could be prevented by pre- and coincubation with E. faecium. Similar effects were observed for the increased expression of heat shock protein 70 in Caco-2 cells. When the cells were challenged by the EPEC strain, no such pattern of changes could be observed. The reduced decrease in TER and the reduction of the proinflammatory and stress response of enterocytes following pathogenic challenge indicate the protective effect of the probiotic.
The Crisis, Automatic Stabilisation, and the Stability Pact

This paper develops a comprehensive description of recent trends on the effectiveness of automatic stabilisers in the European Union, using both macro evidence on the cyclical sensitivity of budget deficits to economic activity and micro evidence on the tax and expenditure profiles. We conclude that there is increasing evidence of the declining importance of the automatic stabilisation. This points to a fundamental contradiction in the European Stability and Growth Pact, that relies almost exclusively on automatic stabilisation for the conduct of fiscal policy, We also argue, on the basis of past experience, that further increasing market flexibility does not seem a viable path to reduce aggregate fluctuations. The paper concludes by highlighting the complex relation between discretionary policies and automatic stabilisation .
Stock Market Valuations Of R&D And Electronics Firms During Taiwan'S Recent Economic Transition

The objective of the present study is to investigate the market valuation of Research and Development (R&D) investments in the Taiwanese stock market from July 1988 to June 2002. The motivation stems from Taiwan's recent economic transition from a labor‐intensive, then to a capital‐intensive, and currently to a technology‐based economy. The results support not only the existence, but also the persistence of R&D‐associated mispricing. More importantly, it has become stronger as the electronics industry gradually dominates the economy. First, R&D‐intensive stocks tend to outperform stocks with little or no R&D. Second, the R&D‐intensity effect cannot fully be attributed to firm size. Third, the R&D‐intensity effect is more pronounced for firms in the electronics industry after 1996.
WSMO-Lite based web service discovery algorithm for mobile environment

The advancement of mobile and wireless technologies has led to widespread access of web services in a mobile environment, where mobile devices can host web service as a web service provider or service requester. Due to rapid proliferation of web services with similar functionalities, discovering appropriate mobile web services that match service requester is still a major obstruction to its advancement, especially with the stringent constraints currently relating to mobile devices. This paper proposes an enhancement of WSMO-Lite to describe Non-Functional Properties (NFPs) as a context and Quality of Web Service (QoWS) information for mobile computing environment targeted to support the discovery of web services in a mobile environment. Then, the similarity of the service requester with each of the offered services is measured using semantic matchmaking algorithm based on WSMO-Lite was proposed. As a lightweight semantic web service description language, WSMOLite improves flexibility of web service description and enhances the web service discovery mechanism. The applicability of the enhancement and algorithm is applied through a simple case study to demonstrate the effectiveness of the idea.
Bringing the Social Sciences Alive: 10 Simulations for History, Economics, Government, and Geography

Chapters begin with "Teacher's Note" and conclude with "Using This Simulation," "How the Simulation Works," "Comments from Experience," "Possible Modifications," "Assessment," and "Appendix - Materials. " Foreword. Preface. 1.Introduction. What Simulations Can Add to Your Classroom? Some Practical Thoughts on Designing and Using Simulations. Layout of the Book. References. 2.Constructing a New American Government. Background on the Constitutional Convention. 3.The Mighty Dorito Cartel. Background on the Free Rider Syndrome, Oligopolies, and OPEC. 4.Letting the Bulls Run. Background on the Equity Markets. 5.Forging a Lasting Middle East Peace. Background on Middle East Conflict. 6.Choosing a President. Background on Political Party Conventions. 7.A Whirlwind American Tour. Background on Low-Budget Travel. 8.Passing a Crime Bill. Background on the Legislative Process. 9.Living on a Paycheck. Background on Budgeting. 10.The Delicate Balance of Power. Background on Europe Before World War I. 11.Making the United Nations Work. Background on the United Nations. 12.Final Thoughts. Assessing Simulations. Assessment Materials. Index.
Interactive Visual Profiling of Musicians

Determining similar objects based upon the features of an object of interest is a common task for visual analytics systems. This process is called profiling, if the object of interest is a person with individual attributes. The profiling of musicians similar to a musician of interest with the aid of visual means became an interesting research question for musicologists working with the Bavarian Musicians Encyclopedia Online. This paper illustrates the development of a visual analytics profiling system that is used to address such research questions. Taking musicological knowledge into account, we outline various steps of our collaborative digital humanities project, priority (1) the definition of various measures to determine the similarity of musicians' attributes, and (2) the design of an interactive profiling system that supports musicologists in iteratively determining similar musicians. The utility of the profiling system is emphasized by various usage scenarios illustrating current research questions in musicology.
The Value of Biodiversity: Markets, Society, and Ecosystems

The value of biodiversity is discussed at different levels including market value, non-market values to humans, and the value of biodiversity to ecosystems. The main conclusion is that, although market exchange values of environmental services may be used to justify biodiversity protection measures, it must be stressed that exchange value constitutes a small portion of total biodiversity value. The total value of existing biodiversity is largely unknown but indications are that it is essential to human existence. The various levels of biodiversity value point to the need for a hierarchical and pluralistic methodology to determine appropriate policies for its preservation.
Modelling Contextualized Reasoning in Complex Societies with "Endorsements"

In many computational social simulation models only cursory reference to the foundations of the agent cognition used is made and computational expenses let many modellers chose simplistic agent cognition architectures. Both choices run counter to expectations framed by scholars active in the domain of rich cognitive modelling that see agent reasoning as socially inherently contextualized. The Manchester school of social simulation proposed a particular kind of a socially contextualized reasoning mechanism, so called endorsements, to implement the cognitive processes underlying agent action selection that eventually causes agent interaction. Its usefulness lies in its lightweight architecture and in taking into account folk psychological conceptions of how reasoning works. These and other advantages make endorsements an amenable tool in everyday social simulation modelling. A yet outstanding comprehensive introduction to the concept of endorsements is provided and its theoretical basis is extended and extant research is critically reviewed. Improvements to endorsements regarding memory and perception are suggested and tested against a case-study.
Privacy and the internet : differences in perspectives

This study examined results of a World Wide Web survey that used the framework of domain theory of moral development to examine attitudes of Internet users assuming perspectives of victims, aggressors and bystanders toward privacy issues. The effect of a monetary incentive was tested on two perspectives; effects of three moderating variables, employment status, newsgroup/mailing list membership and culture, were also tested. In the process of examining interactions, an evaluation determined if changes in attitudes indicated movement along a morality continuum. Results show that victims are more concerned than aggressors, and bystanders take a moralizing stance regardless of domain. Results of the monetary incentive test suggest that privacy is for sale. Employed respondents are more concerned than non-employed respondents; membership has little effect. Effects of culture do not support the hypotheses. Implications are that moral judgements are a function of perspective and domain, allowing flexibility along a morality continuum due to situational deviations.
CD8+ immunodominance among Epstein-Barr virus lytic cycle antigens directly reflects the efficiency of antigen presentation in lytically infected cells

Antigen immunodominance is an unexplained feature of CD8+ T cell responses to herpesviruses, which are agents whose lytic replication involves the sequential expression of immediate early (IE), early (E), and late (L) proteins. Here, we analyze the primary CD8 response to Epstein-Barr virus (EBV) infection for reactivity to 2 IE proteins, 11 representative E proteins, and 10 representative L proteins, across a range of HLA backgrounds. Responses were consistently skewed toward epitopes in IE and a subset of E proteins, with only occasional responses to novel epitopes in L proteins. CD8+ T cell clones to representative IE, E, and L epitopes were assayed against EBV-transformed lymphoblastoid cell lines (LCLs) containing lytically infected cells. This showed direct recognition of lytically infected cells by all three sets of effectors but at markedly different levels, in the order IE > E ≫ L, indicating that the efficiency of epitope presentation falls dramatically with progress of the lytic cycle. Thus, EBV lytic cycle antigens display a hierarchy of immunodominance that directly reflects the efficiency of their presentation in lytically infected cells; the CD8+ T cell response thereby focuses on targets whose recognition leads to maximal biologic effect.
The Published Extended Rotation Curves of Spiral Galaxies: Confrontation with Modified Dynamics

A sample of 22 spiral galaxy rotation curves, measured in the 21 cm line of neutral hydrogen, is considered in the context of Milgrom's modified dynamics (MOND). Combined with the previous, highly selected sample of Begeman et al., this constitutes the current total sample of galaxies with published (or available) extended rotation curves and photometric observations of the light distribution. This is the observational basis of present quantitative understanding of the discrepancy between the visible mass and classical dynamical mass in galaxies. It is found that the gravitational force calculated from the observed distribution of luminous material and gas by use of the simple MOND formula can account for the overall shape and amplitude of these 22 rotation curves, and in some cases, the predicted curve agrees with the observed rotation curve in detail. The fitted rotation curves have, in 13 cases, only one free parameter, which is the mass-to-light ratio of the luminous disk; in nine cases, there is an additional free parameter, which is M/L of a central bulge or light concentration. The values of the global M/L (bulge plus disk) are reasonable and, when the gas mass is also included, show a scatter consistent with that in the Tully-Fisher relation. The success of the MOND prescription in predicting the rotation curves in this larger, less stringently selected sample lends further support to the idea that dynamics or gravity is non-Newtonian in the limit of low acceleration and that it is unnecessary to invoke the presence of large quantities of unseen matter.
An Image Watermarking Scheme Based on Information Theoretic Principles

image watermarking, information hiding, side information In this report we investigate information hiding systems with non-malicious attack channels in which the decoder does not have access to the original source data. Recent works show that such information hiding systems can be viewed as communication systems with side information at the encoder. Based on this observation, we propose a novel watermarking scheme, named scaled bin encoding, which is based on capacity achieving random encoding scheme for an additive Gaussian channel with side information. This scheme out-performs previous watermarking techniques when applied to synthetic and imagery data. Furthermore, a theoretical and computational framework for the implementation of a family of information hiding schemes is proposed. This family, named binary modulation schemes, provides a computable expression for the theoretical information embedding rate, as well as fast encoding and decoding procedures. The decoding procedure is based on the maximum likelihood principle that improves upon the standard correlation based decoding techniques. We describe experimental results of implementing various binary modulation schemes for the additive Gaussian information hiding system and for DCT domain image watermarking .
A Comparative Study of Chebyshev Functional Link Artificial Neural Network, Multi-layer Perceptron and Decision Tree for Credit Card Fraud Detection

With introduction of online transaction the fraudulent activities through World Wide Web have increased rapidly. It's not only affecting common people but also making them lose huge amount of money. Online transaction basically takes place between merchant and customer, and in this case neither customer nor the card needs to be present at the time of transaction so merchant does not know that whether the customer in the other end is an authorized person or fraudster, so it may lead to an unusual transaction. This kind of online transaction can be easily done using stolen credit card information of a cardholder. To detect status of the current transaction it is imperative to analyze all the previous transactions made by a genuine card holder to know the kind of pattern he/she uses. Based on these patterns new transaction can be categorized as either fraud or legal. There are few data mining techniques which help us to detect a certain pattern on complex and large data sets. In this paper it is proposed to compare Decision Tree, Multi-Layer Perceptron (MLP) and Chebyshev functional link artificial neural network (CFLANN) in terms of their classification accuracy and elapsed time for credit card fraud detection.
Thelytokous worker reproduction and lack of Wolbachia infection in the harvesting ant Messor capitatus

In hymenopteran societies, workers are not always sterile, and may produce parthenogenetically either males (arrhenotoky) or females (thelytoky). Thelytoky however is exceptional, and has been recorded in only four ant species. Here we provide evidence for worker thelytoky in an additional species, the harvesting ant Messor capitatus (Latreille) (Hymenoptera Formicidae Myrmicinae). Two orphaned colonies produced a large amount of worker offspring during 10 months in the laboratory. Dissections showed that reproduction was performed by workers and not by mated worker-like individuals (ergatoids). In some parasitoid wasps, parthenogenetic reproduction is caused by the maternally transmitted bacterium Wolbachia. Using a PCR-based assay we showed that Wolbachia can not be involved in parthenogenesis induction in this species. Finally, we point out reasons for the low Wolbachia susceptibility of parthenogenetic ant species.
Essays in Robust and Data-Driven Risk Management

Risk defined as the chance that the outcome of an uncertain event is different than expected. In practice, the risk reveals itself in different ways in various applications such as unexpected stock movements in the area of portfolio management and unforeseen demand in the field of new product development. In this dissertation, we present four essays on data-driven risk management to address the uncertainty in portfolio management and capacity expansion problems via stochastic and robust optimization techniques. The third chapter of the dissertation (Portfolio Management with Quantile Constraints) introduces an iterative, data-driven approximation to a problem where the investor seeks to maximize the expected return of his/her portfolio subject to a quantile constraint, given historical realizations of the stock returns. Our approach involves solving a series of linear programming problems (thus) quickly solves the large scale problems. We compare its performance to that of methods commonly used in finance literature, such as fitting a Gaussian distribution to the returns. We also analyze the resulting efficient frontier and extend our approach to the case where portfolio risk is measured by the inter-quartile range of its return. Furthermore, we extend our modeling framework so that the solution calculates the corresponding conditional value at risk (CVaR) value for the given quantile level. The fourth chapter (Portfolio Management with Moment Matching Approach) focuses on the problem where a manager, given a set of stocks to invest in, aims to minimize the probability of his/her portfolio return falling below a threshold while keeping the expected portfolio return no worse than a target, when the stock returns are assumed to be Log-Normally distributed. This assumption, common in finance literature, creates computational difficulties. Because the
Cancer Salivary Biomarkers for Tumours Distant to the Oral Cavity

The analysis of saliva as a diagnostic approach for systemic diseases was proposed just two decades ago, but recently great interest in the field has emerged because of its revolutionary potential as a liquid biopsy and its usefulness as a non-invasive sampling method. Multiple molecules isolated in saliva have been proposed as cancer biomarkers for diagnosis, prognosis, drug monitoring and pharmacogenetic studies. In this review, we focus on the current status of the salivary diagnostic biomarkers for different cancers distant to the oral cavity, noting their potential use in the clinic and their applicability in personalising cancer therapies.