Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein threading using PROSPECT: Design and evaluation

The computer system PROSPECT for the protein fold recognition using the threading method is described and evaluated in this article. For a given target protein sequence and a template structure, PROSPECT guarantees to find a globally optimal threading alignment between the two. The scoring function for a threading alignment employed in PROSPECT consists of four additive terms: i) a mutation term, ii) a singleton fitness term, iii) a pairwise‐contact potential term, and iv) alignment gap penalties. The current version of PROSPECT considers pair contacts only between core (α‐helix or β‐strand) residues and alignment gaps only in loop regions. PROSPECT finds a globally optimal threading efficiently when pairwise contacts are considered only between residues that are spatially close (7 Å or less between the Cβ atoms in the current implementation). On a test set consisting of 137 pairs of target‐template proteins, each pair being from the same superfamily and having sequence identity ≤ 30%, PROSPECT recognizes 69% of the templates correctly and aligns 66% of the structurally alignable residues correctly. These numbers may be compared with the 55% fold recognition and 64% alignment accuracy for the same test set using only scoring terms i), ii), and (iv), indicating the significant contribution from the contact term. The fold recognition and alignment accuracy are further improved to 72% and 74%, respectively, when the secondary structure information predicted by the PHD program is used in scoring. PROSPECT also allows a user to incorporate constraints about a target protein, e.g., disulfide bonds, active sites, and NOE distance restraints, into the threading process. The system rigorously finds a globally optimal threading under the specified constraints. Test results have shown that the constraints can further improve the performance of PROSPECT. Proteins 2000;40:343–354. © 2000 Wiley‐Liss, Inc.
A Satisfiability Checker for Difference Logic

We present a constraint solver for difference logic, a logic whose formulae consist of Boolean combinations of difference inequalities of the form X − Y ≥ c where X and Y are numerical variables and c is a constant. Such formulae are encountered in many occasions, most notably in the definition of feasible solutions for scheduling problems and in the verification of timed automata. In both cases they express constraints on the time elapsed between pairs of events. While constraint solving for such formulae fits into more general frameworks such as of constraint propagation techniques, our aim is to provide a solver specialized for this class of formulae. To this end we take the general scheme of propositional SAT solving and extend it to difference logic.
Multi-task feature selection

We address the problem of joint feature selection across a group of related classification or regression tasks. We propose a novel type of joint regularization of the model parameters in order to couple feature selection across tasks. Intuitively, we extend the `1 regularization for single-task estimation to the multi-task setting. By penalizing the sum of `2-norms of the blocks of coefficients associated with each feature across different tasks, we encourage multiple predictors to have similar parameter sparsity patterns. To fit parameters under this regularization, we propose a blockwise boosting scheme that follows the regularization path. The algorithm introduces and updates simultaneously the coefficients associated with one feature in all tasks. We show empirically that this approach outperforms independent `1-based feature selection on several datasets.
Fifty Years of Economic Development : What Have we Learned ?

Before addressing the question of lessons of development, we must make clear at the outset the sense in which the term is used. Economic development, as distinct from mere economic growth, combines: (1) self-sustaining growth; (2) structural change in patterns of production; (3) technological upgrading; (4) social, political and institutional modernization; and (5) widespread improvement in the human condition. Kuznets used “development” in the sense of the first three elements; development historians, new institutional development theorists and the neoclassical development economists of the eighties added increasing the sphere in which markets guide economic decisions (institutional modernization) to the Kuznetsian definition of development. Modernization theorists have added social and political development to the list of transformations that development entails while the deficient entrepreneurship school has added socio cultural evolution to the necessary aspects of development. Finally, the deficiencies of the concentrated growth process of the first two decades of economic growth have led those concerned with the welfare of the poor ( Mc Namara 1973, Adelman and Morris 1973; Adelman 1973, Streeten and Stewart 1976, Sen 1988 and the UNDP,1990 onwards ) to add widespread improvements in national welfare explicitly to the list of characteristics of economic development which distinguish it from economic growth. When the notion of “development “ is used in this sense, less than half a dozen countries, mostly East Asian, have traveled the whole path from underdeveloped to developed. since the end of World War Two. Others have progressed part-way. The semi-industrial countries have achieved substantial transformation of their patterns of production, gone part-way in increasing the sway of markets and the democratization of their political institutions but failed to share the benefits of growth widely. And the Sub Saharan countries have accomplished some growth in human capital and infrastructure but are still relying on primary production and its processing for whatever growth they attain, if any.
Edinburgh System Description for the 2006 TC-STAR Spoken Language Translation Evaluation

In this paper we describe the Edinburgh University statisti cal machine translation system, as used for the TC-STAR 2006 evaluation campaign. We participated in the primary Final Text Edition track for the Spanish to English and English to Spanish translation tasks, using only the provided datasets for training our translati on and language models. We obtained the highest WNM/Recall score in both language pairs and had competitive results for all other evaluation metrics.
Bayesian image restoration for mosaic active imaging

In this paper, we focus on the restoration of images acquired with a new active imaging concept. This new instrument generates a mosaic of active imaging acquisitions. We first describe a simplified forward model of this so-called ''mosaic active imaging''. We also assume a prior on the distribution of images, using the \ac{TV}, and deduce a restoration algorithm. This algorithm iterates one step for the estimation of the restored image and one step for the estimation of the acquisition parameters. We then provide the details useful to the implementation of these two steps. In particular, we show that the image estimation can be performed with graph-cuts. This allows a fast resolution of this image estimation step. Finally, we detail numerical experiments showing that acquisitions made with a mosaic active imaging device can be restored even under severe noise levels, with few acquisitions.
The Construction of Local Grammars

Our programme is to use the model of W. Woods 1970 to attempt a full scale analysis of the language. It could be viewed as an attempt to revive the Markovian model, but this would be wrong, because previous Markovian models were aimed at giving a global description of a language, whereas the model we advocate, and which we call it finite-state for short, is of a strictly local nature. In this perspective, the global nature of language results from the interaction of a multiplicity of local finite-state schemes which we call finite-state local automata. To start with, we give elementary examples where the finite constraints can be exhaustively described in a local way, that is, without interferences from the rest of the grammar.
Speeding up random walks with neighborhood exploration

We consider the following marking process (rw-rand) made by a random walk on an undirected graph G. Upon arrival at a vertex v, it marks v if unmarked and otherwise it marks a randomly chosen unmarked neighbor of v. We also consider a variant of this process called rw-r-rank. Here each vertex is assigned a global random rank first and then in each step, the walk marks the lowest ranked unmarked neighbor of the currently visited vertex. Depending on the degree and the expansion of the graph, we prove several upper bounds on the time required by these processes to mark all vertices. For instance, if G is a hypercube or random graph, our processes mark all vertices in time O(n), significantly speeding up the Θ(n log n)-cover time of standard random walks.
A nonconvex regularized approach for phase retrieval

With the development of new imaging systems delivering large-size data sets, phase retrieval has become recently the focus of much attention. The problem is especially challenging due to its intrinsically nonconvex formulation. In addition, the applicability of many existing solutions may be limited either by their estimation performance or by their computational cost, especially in the case of non-Fourier measurements. In this paper, we propose a novel phase retrieval approach, which is based on a smooth nonconvex approximation of the standard data fidelity term. In addition, the proposed method allows us to employ a wide range of convex separable regularization functions. The optimization process is performed by a block coordinate proximal algorithm which is amenable to solving large-scale problems. An application of this algorithm to an image reconstruction problem shows that it may be very competitive with respect to state-of-the-art methods.
Internuclear exchange of an inner nuclear membrane protein (p55) in heterokaryons: in vivo evidence for the interaction of p55 with the nuclear lamina

The movement between nuclei of an integral protein of the inner nuclear membrane has been studied in rat/mouse and rat/hamster heterokaryons. This protein, p55, was found to equilibrate between nuclei over a period of approximately 6 h in the absence of new protein synthesis. When rat/mouse heterokaryons were constructed using an undifferentiated murine embryonal carcinoma (P19), which lacks lamins A and C, no accumulation of p55 in the mouse cell nucleus was observed. However, P19 nuclei could be rendered competent to accumulate p55 by transfecting the parent cells with human lamin A before cell fusion, supporting the notion that p55 may interact with the nuclear lamina. Since p55 does not appear to be able to dissociate from the nuclear membrane, it is concluded that this exchange between nuclei does not occur in the aqueous phase and instead is probably membrane mediated. It is proposed that this protein may be free to move between the inner and outer nuclear membranes via the continuities at the nuclear pore complexes and that transfer between nuclei occurs via lateral diffusion through the peripheral ER, which appears to form a single continuous membrane system in these heterokaryons. One implication of these observations is that accumulation of at least some integral proteins in the inner nuclear membrane may be mediated by interactions with other nuclear components and may not require a single defined targeting sequence.
Graph-theoretical Bounds on the Entangled Value of Non-local Games

We introduce a novel technique to give bounds to the entangled value of non-local games. The technique is based on a class of graphs used by Cabello, Severini and Winter in 2010. The upper bound uses the famous Lovasz theta number and is efficiently computable; the lower one is based on the quantum independence number, which is a quantity used in the study of entanglement-assisted channel capacities and graph homomorphism games.
Automatic speechreading using genetic hybridization of Hidden Markov Models

In this paper, we present an Automatic SpeechReading system (ASR) that uses for modeling the visual speech an Hidden Markov Model (HMM) who is optimized by a Genetic Algorithm (GA). The idea is to combine a GA to explore the whole solution space with Baum-Welch algorithm in the training process to find the values of the exact parameters of the optimum. The experimental results show that the GA/HMM achieved higher rate recognition with less computation compared to the traditional HMM.
Opposite Effects of Gene Deficiency and Pharmacological Inhibition of Soluble Epoxide Hydrolase on Cardiac Fibrosis

Arachidonic acid-derived epoxyeicosatrienoic acids (EETs) are important regulators of cardiac remodeling; manipulation of their levels is a potentially useful pharmacological strategy. EETs are hydrolyzed by soluble epoxide hydrolase (sEH) to form the corresponding diols, thus altering and reducing the activity of these oxylipins. To better understand the phenotypic impact of sEH disruption, we compared the effect of EPHX2 gene knockout (EPHX2 −/−) and sEH inhibition in mouse models. Measurement of plasma oxylipin profiles confirmed that the ratio of EETs/DHETs was increased in EPHX2 −/− and sEH-inhibited mice. However, plasma concentrations of 9, 11, 15, 19-HETE were elevated in EPHX2 −/− but not sEH-inhibited mice. Next, we investigated the role of this difference in cardiac dysfunction induced by Angiotensin II (AngII). Both EPHX2 gene deletion and inhibition protected against AngII-induced cardiac hypertrophy. Interestingly, cardiac dysfunction was attenuated by sEH inhibition rather than gene deletion. Histochemical staining revealed that compared with pharmacological inhibition, EPHX2 deletion aggravated AngII-induced myocardial fibrosis; the mRNA levels of fibrotic-related genes were increased. Furthermore, cardiac inflammatory response was greater in EPHX2 −/− than sEH-inhibited mice with AngII treatment, as evidenced by increased macrophage infiltration and expression of MCP-1 and IL-6. In vitro, AngII-upregulated MCP-1 and IL-6 expression was significantly attenuated by sEH inhibition but promoted by EPHX2 deletion in cardiofibroblasts. Thus, compared with pharmacological inhibition of sEH, EPHX2 deletion caused the shift in arachidonic acid metabolism, which may led to pathological cardiac remodeling, especially cardiac fibrosis.
A Hybrid Approach for Data Clustering using Expectation-Maximization and Parameter Adaptive Harmony Search Algorithm

This paper presents a novel hybrid data clustering algorithm based on parameter adaptive harmony search algorithm. The recently developed parameter adaptive harmony search algorithm (PAHS) is used to refine the cluster centers, which are further used in initializing Expectation-Maximization clustering algorithm. The optimal number of clusters are determined through four well-known cluster validity indices. The proposed algorithm is evaluated on three real life datasets and compared with the performance of K-Means, Fuzzy CMeans and HS initialize EM (HSEM). Experimental results reveal that the proposed approach provide better results in terms of precision, recall, weighted average, F-Measure and G-Measure.
Grit is Associated with Lower Depression via Meaning in Life among Filipino High School Students

Grit—passion and perseverance for long-term goals—has been linked to a wide array of positive academic and psychological outcomes. However, limited research has been conducted to explore the association of grit with different indicators of well-being and psychological health. The primary objective of this study was to assess the associations among grit, meaning in life, and depression. There were 447 Filipino high school students who participated in the study. Results of structural equation modeling showed that grit was linked to higher levels of meaning in life dimensions (i.e., presence of meaning and search for meaning in life) and presence of meaning was associated with lower depression. Bias-corrected bootstrapping revealed that grit had an indirect negative influence on depression through the intermediate variable—presence of meaning in life. Theoretical and practical implications are elucidated.
Motion correction of contrast-enhanced MRI time series of kidney

In this paper we focus on motion correction of cont rast enhanced kidney MRI time series, which is an important step towards accurate assessment of regional renal function. Due to respiratory motion and pulsations, the organ of interest undergoes complex movement and deformation, which disturb further renal function analysis. We propose geometric movement correction by image registration. We have compared rigid and nonrigid registration methods as well as registrati on of whole images and registration limited to ROI that defines the organ under investigation. The obtained results show that image registration methods benefi t to renal function analysis, i.e. to the assessment of intensity time courses. Furthermore, the comparison of the registration methods shows benefits of ROI limi ted methods and eventual problems of nonrigid methods.
HMNews: an integrated system for searching and browsing hypermedia news content

We describe HMNews (Hyper-Media News), a system designed and implemented for the collection, indexing and retrieval of hypermedia news content coming from Digital Television and the Web. The novelty of the approach relies in the ability of providing hierarchical and multi-resolution multimodal indexes based on the application of a novel generalised hybrid clustering technique. The system supports many functionalities: a) bi-directional news conceptual linking; b) relevant topics detection and tracking; c) integrated hypermedia browsing; d) integrated search and retrieval.
The European Large Area ISO Survey – IV. The preliminary 90‐μm luminosity function

We present the luminosity function of 90-mum-selected galaxies from the European Large Area ISO Survey (ELAIS), extending to z=0.3. Their luminosities are in the range 109 =100mJy data base, we have found optical, 15-mum or 1.4-GHz identifications for 24 (65 per cent). We have obtained 2dF and UK Schmidt FLAIR spectroscopy of 89 per cent of identifications to rigid multivariate flux limits. We construct a luminosity function assuming that (i) our spectroscopic subset is an unbiased sparse sample, and (ii) there are no galaxies that would not be represented in our spectroscopic sample at any redshift. We argue that we can be confident of both assumptions. We find that the luminosity function is well described by the local 100-mum luminosity function of Rowan-Robinson, Helou & Walker. Assuming this local normalization, we derive luminosity evolution of (1+z)2.45+/-0.85 (95 per cent confidence). We argue that star formation dominates the bolometric luminosities of these galaxies, and we derive comoving star formation rates in broad agreement with the Flores et al. and Rowan-Robinson et al. mid-infrared-based estimates.
A distributed cross-layer relay selection with fairness consideration based on buffer management

The performance of cooperative communications is highly dependent on careful resource allocation such as relay selection. Considering individual QoS requirements in a multi user system, traditional cross-layer relay selection schemes, failed to achieve an acceptable level of fairness considering limited buffer capacity of relays. To address this problem, in this paper, we propose a buffer management-based best relay selection algorithm considering both physical and MAC layer parameters. Our simulation results show that the proposed algorithm outperforms traditional ones significantly in terms of fairness, system spectrum efficiency, and average transmission time delay. Moreover, the proposed algorithm can be implemented in a distributed fashion with no need to a central processor and with minimum required signaling among the nodes.
Genome-Wide Transcriptional Profiling of the Cyclic AMP-Dependent Signaling Pathway during Morphogenic Transitions of Candida albicans

ABSTRACT Candida albicans is an opportunistic human fungal pathogen that causes systemic candidiasis as well as superficial mucosal candidiasis. In response to the host environment, C. albicans transitions between yeast and hyphal forms. In particular, hyphal growth is important in facilitating adhesion and invasion of host tissues, concomitant with the expression of various hypha-specific virulence factors. In previous work, we showed that the cyclic AMP (cAMP) signaling pathway plays a crucial role in morphogenic transitions and virulence of C. albicans by studying genes encoding adenylate cyclase-associated protein (CAP1) and high-affinity phosphodiesterase (PDE2) (Y. S. Bahn, J. Staab, and P. Sundstrom, Mol. Microbiol. 50:391-409, 2003; and Y. S. Bahn and P. Sundstrom, J. Bacteriol. 183:3211-3223, 2001). However, little is known about the downstream targets of the cAMP signaling pathway that are responsible for morphological transitions and the expression of virulence factors. Here, microarrays were probed with RNA from strains with hypoactive (cap1/cap1 null mutant), hyperactive (pde2/pde2 null mutant), and wild-type cAMP signaling pathways to provide insight into the molecular mechanisms of virulence that are regulated by cAMP and that are related to the morphogenesis of C. albicans. Genes controlling metabolic specialization, cell wall structure, ergosterol/lipid biosynthesis, and stress responses were modulated by cAMP during hypha formation. Phenotypic traits predicted to be regulated by cAMP from the profiling results correlated with the relative strengths of the mutants when tested for resistance to azoles and subjected to heat shock stress and oxidative/nitrosative stress. The results from this study provide important insights into the role of the cAMP signaling pathway not only in morphogenic transitions of C. albicans but also for adaptation to stress and for survival during host infections.
Efficient join processing on uncertain data streams

Join processing in the streaming environment has many practical applications such as data cleaning and outlier detection. Due to the inherent uncertainty in the real-world data, it has become an increasingly important problem to consider the join processing on uncertain data streams, where the incoming data at each timestamp are uncertain and imprecise. Different from the static databases, processing uncertain data streams has its own requirements such as the limited memory, small response time, and so on. To tackle the challenges with respect to efficiency and effectiveness, in this paper, we formalize the problem of join on uncertain data streams (USJ), which can guarantee the accuracy of USJ answers over uncertain data, and propose effective pruning methods to filter out false alarms. We integrate the pruning methods into an efficient query procedure for incrementally maintaining USJ answers. Extensive experiments have been conducted to demonstrate the efficiency and effectiveness of our approaches.
On the Identification of Relative Wage Rigidity Dynamics: A Proposal for a Methodology on Cross-Section Data and Empirical Evidence for Poland in Transition

We present a new and simple empirical methodology to identify relative wage rigidity dynamics. The methodology is applied to data from the Polish Labour Force Survey for the period 1994 to 1998. We estimate ceteris paribus changes in relative wage and unemployment differentials for various labour market defining characteristics. A simultaneous increase in the relative wage and the unemployment likelihood is defined as relative wage rigidity dynamic for a labour market characteristic. We find that the Polish wage structure generated hardly any rigidities between 1994 and 1998 nor did it reduce possibly existing rigidities during that period.