Miracle-dz/UniFAR-FTUs huggingface dataset:
Bytecode Optimizer Using Side-eeect Analysis

This paper describes Cream, an optimizer for Java byte-code using side-eeect analysis to improve the optimizations. Dead code elimination and loop invariant removal is implemented and tested, as well as several variations of the side-eeect analysis. The optimizer is tested on real-world applications such as itself and JavaSoft's Java compiler. Results show that the optimizations beneet a lot from the side-eeect analysis. The best side-eeect analysis gives ve to ten times as many optimizations as without an analysis, and, in one case, makes a sped increase of 25 % possible.
Hidden Markov Models in Bioinformatics

Hidden Markov Models (HMMs) became recently important and popular among bioinformatics researchers, and many software tools are based on them. In this survey, we first consider in some detail the mathematical foundations of HMMs, we describe the most important algorithms, and provide useful comparisons, pointing out advantages and drawbacks. We then consider the major bioinformatics applications, such as alignment, labeling, and profiling of sequences, protein structure prediction, and pattern recognition. We finally provide a critical appraisal of the use and perspectives of HMMs in bioinformatics.
A DMT Modem Prototype for Broadband PLC

In this paper, the design and performance of a modem prototype for high hit-rate indoor power-line communications (PLC) are presented. The system architecture is based on two field programmable gate-arrays (FPGA) and a digital signal processor (DSP), in which the transmitter and receiver algorithms have been implemented. The modulation employed is discrete multitone (DMT) with bit-loading and adaptive equalization to channel selectivity both in frequency and time. The structure of the hardware and software used are explained, and the results obtained after testing the modem in some indoor PLC channels are discussed
A Recommendation System for Semantic Mashup Design

Techniques and tools for semantic description of mashup components are gaining more and more interest as an opportunity for a (semi-) automatic support of mashup design. We propose a recommendation system to design mashup applications, relying on the semantic description of mashup components for their proactive suggestion to the designer. A semantic organization of components is defined to propose ranked components, according to their similarity with designer's requirements and their mutual coupling.
Feature Location and Extraction using Landmarks and Barriers

Identifying and isolating the source code associated with a particular feature is a problem that frequently arises in many maintenance tasks. The delocalised nature of object-oriented systems, where the code associated with a feature is distributed across many interrelated objects, makes this problem particularly challenging. This paper presents an approach that combines landmark' methods that have a key role in the execution of a particular feature with slicing to create a call graph of related code. The size of this call graph is constrained by the identification of 'barrier' methods which exclude parts of the graph that are not of interest. The approach is supported by a tool, and the evaluation on three open-source systems yields encouraging results and demonstrates the practical applicability of the technique.
Sparse summarization of robotic grasping data

We propose a new approach for learning a summarized representation of high dimensional continuous data. Our technique consists of a Bayesian non-parametric model capable of encoding high-dimensional data from complex distributions using a sparse summarization. Specifically, the method marries techniques from probabilistic dimensionality reduction and clustering. We apply the model to learn efficient representations of grasping data for two robotic scenarios.
Impact of Market Risk Disclosures on Stock Price Sensitivity to Oil and Gas Prices

This study explores associations between U.S. firms' 10-K disclosures of market risk exposure, which were newly mandated by a 1997 SEC Release, and stock price sensitivity to underlying risk factors. Firms whose stock prices were more sensitive to oil and gas prices tended to have open year-end positions in commodity derivatives and disclose the value-at-risk or the sensitivity of their derivative contracts to commodity price changes. Firms whose stock prices were less sensitive to oil and gas prices tended not to have open year-end positions in commodity derivatives or, if they did, to give simple tabular disclosures of derivative contracts. On their SEC filing dates, firms that disclosed value-at-risk or sensitivity experienced more significant shifts than other firms did in stock-price sensitivity to oil and gas price changes. Firms disclosing that their material derivative contracts had zero net sensitivity to commodity price changes, given an assumed shift in commodity prices, experienced the most significant shifts in stock-price sensitivity to those same price changes. Preliminary tests on an oil-intensive sub-sample suggest a tentative economic interpretation of these results that is both intuitively appealing and consistent with the SEC's perceptions. Producers with naturally long oil exposure that disclosed the value-at-risk or sensitivity of their derivative contracts experienced a reduction in the sensitivity of their stock prices to oil price changes because such disclosures signaled to the market that they had implemented effective risk management strategies.
Structured visual markers for indoor pathfinding

We present a mobile augmented reality (AR) system to guide a user through an unfamiliar building to a destination room. The system presents a world-registered wireframe model of the building labeled with directional information in a see-through heads-up display, and a three-dimensional world-in-miniature (WIM) map on a wrist-worn pad that also acts as an input device. Tracking is done using a combination of wall-mounted ARToolkit markers observed by a head-mounted camera, and an inertial tracker. To allow coverage of arbitrarily large areas with a limited set of markers, a structured marker re-use scheme based on graph coloring has been developed.
Coupling analysis of transient cardiovascular dynamics

Abstract The analysis of effects from coupling in and between systems is important in data-driven investigations as practiced in many scientific fields. It allows deeper insights into the mechanisms of interaction emerging among individual smaller systems when forming complex systems as in the human circulatory system. For systems featuring various regimes, usually only the epochs before and after a transition between different regimes are analyzed, although relevant information might be hidden within these transitions. Transient behavior of cardiovascular variables may emerge, on the one hand, from the recovery of the system after a severe disturbance or, on the other hand, from adaptive behavior throughout changes of states. It contains important information about the processes involved and the relations between state variables such as heart rate, blood pressure, and respiration. Therefore, we apply an ensemble approach to extend the method of symbolic coupling traces to time-variant coupling analysis. These new ensemble symbolic coupling traces are capable of determining coupling direction, strength, and time offset τ from transient dynamics in multivariate cardiovascular data. We use this method to analyze data recorded during an orthostatic test to reveal a transient structure that cannot be detected by classic methods.
Cost Growth and Stock Returns

This paper shows that investors do not fully incorporate cost behavior information into valuation. Firms with higher growth in operating costs generate substantially lower future stock returns and operating performance. An equal-weighted long-short spread portfolio earns an average return of 82 basis points per month that is robust to a number of specifications. The negative cost growth-return relation is much stronger around earnings announcement days and among firms with lower investor attention, higher idiosyncratic volatility, and higher transaction costs, suggesting that investor underreaction and limits to arbitrage mainly drive the effect. JEL Classification: G12, D21, G14
Immunophenotypic and Ultrastructural Analysis of Mast Cells in Hermansky-Pudlak Syndrome Type-1: A Possible Connection to Pulmonary Fibrosis

Hermansky-Pudlak Syndrome type-1 (HPS-1) is an autosomal recessive disorder caused by mutations in HPS1 which result in reduced expression of the HPS-1 protein, defective lysosome-related organelle (LRO) transport and absence of platelet delta granules. Patients with HPS-1 exhibit oculocutaneous albinism, colitis, bleeding and pulmonary fibrosis postulated to result from a dysregulated immune response. The effect of the HPS1 mutation on human mast cells (HuMCs) is unknown. Since HuMC granules classify as LROs along with platelet granules and melanosomes, we set out to determine if HPS-1 cutaneous and CD34+ culture-derived HuMCs have distinct granular and cellular characteristics. Cutaneous and cultured CD34+-derived HuMCs from HPS-1 patients were compared with normal cutaneous and control HuMCs, respectively, for any morphological and functional differences. One cytokine-independent HPS-1 culture was expanded, cloned, designated the HP proMastocyte (HPM) cell line and characterized. HPS-1 and idiopathic pulmonary fibrosis (IPF) alveolar interstitium showed numerous HuMCs; HPS-1 dermal mast cells exhibited abnormal granules when compared to healthy controls. HPS-1 HuMCs showed increased CD63, CD203c and reduced mediator release following FcɛRI aggregation when compared with normal HuMCs. HPM cells also had the duplication defect, expressed FcɛRI and intracytoplasmic proteases and exhibited less mediator release following FcɛRI aggregation. HPM cells constitutively released IL-6, which was elevated in patients’ serum, in addition to IL-8, fibronectin-1 (FN-1) and galectin-3 (LGALS3). Transduction with HPS1 rescued the abnormal HPM morphology, cytokine and matrix secretion. Microarray analysis of HPS-1 HuMCs and non-transduced HPM cells confirmed upregulation of differentially expressed genes involved in fibrogenesis and degranulation. Cultured HPS-1 HuMCs appear activated as evidenced by surface activation marker expression, a decrease in mediator content and impaired releasibility. The near-normalization of constitutive cytokine and matrix release following rescue by HPS1 transduction of HPM cells suggests that HPS-1 HuMCs may contribute to pulmonary fibrosis and constitute a target for therapeutic intervention.
Storytelling and design: the problem of leadership

“Stories provide a good first pass at what is important, from the point of view of the users; they provide the designer with a glimpse of what the user’s terrain feels like, and thus provide a starting point for further exploration. ” (Erickson, 1996: 3) This paper treats leadership essentially as a design problem. Taking Thomas Erickson’s study of the design of software for information systems as a somewhat unorthodox starting point we ask whether the production, telling and re-telling of stories can be used as a resource for making a ‘good first pass’ at what is important to those who are faced with the challenges of leadership in the UK learning and skills sector. Drawing upon a series of ethnographic studies of leadership in further education, we analyse the different ways in which everyday practices are made ‘storyable’ by participants and how different stories and storytelling practices are ‘occasioned’ through the practical accomplishment of everyday leadership work. In doing so we reflect on the extent to which the documenting and analysis of storytelling practices may provide 'teachable moments' through which to inform programmes of leadership development and create links between leadership training, research and everyday practice.
A Visual-interactive System for Prostate Cancer Stratifications

We report on the development of a system for the visual interactive stratification of prostate cancer patients. This system has been developed in collaboration with medical researchers. Our contribution to their analysis process is to short-cut the workflow of hypothesis building, selecting cases from the health record system by hand and statistical testing. Our system allows for the interactive selection of patient cohorts, which starts an ensemble calculation to determine the most promising correlations.
On the Lyapunov equation, coinvariant subspaces and some problems related to spectral factorizations

A geometric approach to stochastic realization theory, and hence to spectral factorization problems, has been developed by Lindquist and Picci (1985, 1991) and Lindquist et al. (1995). Most of this work was done abstractly. Fuhrmann and Gombani (1998) adopted an entirely Hardy space approach to this set of problems, studying the set of rectangular spectral factors of given size for a weakly coercive spectral function. The parametrization of spectral factors in terms of factorizations of related inner functions, as developed in Fuhrmann (1995), had to be generalized. This led to a further understanding of the partial order introduced by Lindquist and Picci in the set of stable spectral factors. In the present paper we study the geometry of finite dimensional coinvariant subspaces of a vectorial Hardy space H 2 via realization theory, emphasizing the role of the Lyapunov equation in lifting the Hardy space metric to the statespace domain. We follow this by deriving state space formulas for rectangular spectral factors as well as for related inner functions arising in Fuhrmann and Gombani (1998). Finally, we develop a state space approach to the analysis of the partial order of the set of rectangular spectral factors of a given spectral function and its representation in terms of inner functions.
Satisfying Arbitrary Delay Requirements in Multihop Networks

We consider the problem of scheduling in a multi- hop packet network so as to satisfy a set of arbitrary end-to-end delay requirements. A number of scheduling protocols are known for which end-to-end delay bounds can be derived. However, it is often the case that these end-to-end delay bounds are large for flows with small rate. This is clearly inappropriate for traffic types such as VoIP for which tight delay bounds are required but session rates are typically small. In this paper we study the problem of satisfying an arbitrary set of end-to-delay requirements. For a single server in isolation, precise conditions on whether or not a set of delay requirements can be satisfied are known. In contrast, for sessions in a multihop network, we show that deciding whether or not a set of delay requirements can be met is NP-hard. However, if the delay requirements satisfy a simple set of per-server and per- session conditions necessary for schedulability, we show that our proposed protocol can meet all the requirements up to some logarithmic factor. On the negative side, we construct examples in which some delay bound must be violated by a logarithmic factor even if the necessary conditions hold. We further demonstrate through simulation the advantage of our protocol against a counterpart that does not take delay requirements into consideration. We conclude the paper by extending our results to the problem of satisfying arbitrary delay bounds in an input-queued switch.
Empirical Analysis of CK Metrics for Object-Oriented Design Complexity: Implications for Software Defects

To produce high quality object-oriented (OO) applications, a strong emphasis on design aspects, especially during the early phases of software development, is necessary. Design metrics play an important role in helping developers understand design aspects of software and, hence, improve software quality and developer productivity. In this paper, we provide empirical evidence supporting the role of OO design complexity metrics, specifically a subset of the Chidamber and Kemerer (1991, 1994) suite (CK metrics), in determining software defects. Our results, based on industry data from software developed in two popular programming languages used in OO development, indicate that, even after controlling for the size of the software, these metrics are significantly associated with defects. In addition, we find that the effects of these metrics on defects vary across the samples from two programming languages-C++ and Java. We believe that these results have significant implications for designing high-quality software products using the OO approach.
Random topologies and the emergence of cooperation: the role of short-cuts

We study in detail the role of short-cuts in promoting the emergence of cooperation in a network of agents playing the Prisoner’s Dilemma game (PDG). We introduce a model whose topology interpolates between the one-dimensional Euclidean lattice (a ring) and the complete graph by changing the value of one parameter (the probability p of adding a link between two nodes not already connected in the Euclidean configuration). We show that there is a region of values of p in which cooperation is greatly enhanced, whilst for smaller values of p only a few cooperators are present in the final state, and for cooperation is totally suppressed. We present analytical arguments that provide a very plausible interpretation of the simulation results, thus unveiling the mechanism by which short-cuts contribute to promoting (or suppressing) cooperation.
Lattice-based signature schemes with additional features

Building cryptographic schemes upon as many fundamentally different hard problems as possible, seems to be the best way to hedge against future threats such as quantum computers. Being mainly based on the hardness of factoring and computing discrete logarithms, the present security landscape is at risk. In contrast, problems in lattices, such as finding short non-zero vectors, seem to withstand quantum computer attacks and the best known algorithms run in exponential time. In sharp contrast to other fields of cryptography, lattices admit a worst-case to average-case reduction (Ajtai 1996). Instead of assuming that a problem is hard for randomly chosen instances, lattice-based cryptosystems merely require the existence of a single hard instance, i.e., hardness in the worst case. With such an additional "trust anchor", the resulting security guarantees are much more plausible. Quite recently, we have seen an increased interest in lattice-based cryptography with many striking results. In this thesis, we are particularly interested in signature schemes, which provide a supporting pillar for today's economy. While we have seen basic signature schemes from lattices, e.g., (Gentry, Peikert, Vaikuntanathan 2008), (Lyubashevsky, Micciancio 2008), (Lyubashevsky 2009), or (Cash, Hofheinz, Kiltz, Peikert 2009), there are hardly any results dealing with the specific needs of applications, where ordinary signatures often fall too short. In this thesis, we build upon the above results and equip them with additional features, motivated by an exemplary selection of application scenarios. Hence, we demonstrate the great versatility of lattices in cryptography. In particular, we facilitate privacy-friendly electronic elections, fair online contract signing, signature compression, secure signatures in the strongest sense, as well as identity-based primitives. As far as possible, we avoid simplifying assumptions, such as the random oracle model. We believe that our techniques can be transferred to other application scenarios as well. Independently of the these results, we discuss the practical hardness of lattice problems and provide a framework for estimating the security of essentially all modern lattice-based cryptography.
Optimal and Bidirectional optimal Empirical Mode Decomposition

The empirical mode decomposition (EMD) was recently proposed as a new time-frequency analysis tool for nonstationary and nonlinear signals. Although the EMD is able to find the intrinsic modes of the signal and is completely self-adaptive, it does not have any implication on optimality. In some situation, when certain optimality is considered, we need a more flexible signal decomposition and reconstruction scheme. We propose a modified version of the EMD, which enhances the capability of the EMD. The proposed modified EMD algorithm gives the best estimate to a given signal in the minimum mean square error sense. Two different formulations are proposed. The first one utilizes a linear weighting for the intrinsic mode functions (IMF). The second algorithm adopts a bidirectional weighting, namely, it not only uses weighting for IMF modes, but also exploits the correlations between samples in a specific window and carries out filtering in the window. These two new EMD methods extend the capability of the traditional EMD and is well suited for optimal signal recovery. Simulation studies are performed to show the application of the proposed optimal EMD algorithms to denoising problem.
Three dimensional structure of the closed conformation (active) of human merlin reveals masking of actin binding site in the FERM domain

We modelled the structure of human merlin using the structure of moesin from Spodoptera frugiperda as the template. The present model suggests an interaction of its extreme C-terminal region with the subdomains B and C of FERM domain, masking the binding site of beta II spectrin. Modelling the complete structure of merlin revealed a novel central alpha helical domain with a helix-coil-helix. The actin binding site in the carboxy terminal is absent in merlin and in its closed conformation the indirect actin binding site in the FERM domain is also not available for the interaction of other proteins with it.
Deepening Interdependence in the Asia-Pacific Region: An Empirical Study Using a Macro-Econometric Model

The development of an international division of labor across the Asia-Pacific basin was not only foundation for achieving the "East Asian Miracle," but also proved during the "Asian Currency Crisis" to be a possible trigger for an international chain reaction of economic bankruptcy. The purpose of this paper is to construct a macro-econometric model for the Asia-Pacific area, including Japan, the United States, Indonesia, Singapore, Thailand, the Philippines, Malaysia, South Korea, Hong Kong, and China. The model captures international specialization among regional neighbors in a simple way and enables us to quantify how their deepening interdependence affects economic activities in the area. Our main findings are as follows: (i) A Japanese recession may cause recession in East Asia and thereby rebound on Japanese exports. (ii) The depreciation of the Japanese yen favors its exports, but has a "beggar-thy-neighbor" effect on the East Asian economies. (iii) Foreign-demand shocks affect Japanese exports differently, depending on whether the shocks come from, say, the US or Asia. Moreover, the model includes policy rules (interest rate policy, exchange rate policy, and capital controls) to reflect the differing monetary policies observed in individual countries. These make it possible to simulate a change in a country's adopted policy rule and to quantify the effects of such a change, both on other countries and on itself. Using this model structure, we investigate which currency regime is most favorable for the East Asian economies. Our simulation results imply that (iv) it may be more desirable than the current policy regime or the US dollar peg that all the East Asian economies adopt the currency basket policy in order to preserve economic stability against turbulence arising inside or outside the East Asian economies.