Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions

Author(s) of this paper may load this reprint on their own web site provided that this cover page is retained. Republication of this article or its storage in electronic databases or the like is not permitted without prior permission in writing from the IUCr. The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone C atoms. The SSM results are compared with those obtained from other protein comparison servers, and the advantages and disadvantages of different scores that are used for structure recognition are discussed. A new score, balancing the r.m.s.d. and alignment length N align , is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and N align. 1. Introduction Protein function is in signi®cant part determined by spatial structure. It is commonly believed that the three-dimensional fold has a major impact on the ability of a protein to bind other proteins or ligands (drugs), stability and purely mechanical aspects of protein behaviour. The similarity analysis of protein structure is therefore a vital step in understanding that protein's role in the machinery of life. Comparison of protein structures is also essential for estimating the evolutionary distances between proteins and protein families. Currently, there are more than 28 000 structures in the Protein Data Bank (PDB) (Berman et al., 2000), 10±20 structures being deposited on a daily basis. Analysis of the ever-growing number of known structures requires ef®cient tools for protein structure alignment in three dimensions. In contrast to commonly known sequence alignment (Smith & Waterman, 1981), three-dimensional alignment is based on the comparison of geometrical positions, rather than biochemical properties, of amino-acid residues. Two residues are considered as aligned if they satisfy certain distance and orientation criteria at the best mutual superposition of the structures. While high sequence similarity almost always implies structural similarity, the opposite is not true. It is therefore expected that three-dimensional alignment will provide more signi®cant clues to protein function and properties than sequence alignment alone. Several approaches to protein structure alignment have been explored over the past decade. The techniques used include comparison of distance matrices (DALI; Holm & Sander, 1993), analysis of differences in vector distance plots (Orengo & Taylor, 1996), minimization of the …
Returns to Tenure and Experience Revisited -- Do Less Educated Workers Gain Less from Work Experience?

This paper explores whether within job and between job wage growth is lower for less-educated workers. While a simple model of heterogeneous learning ability predicts that individuals with low learning ability will have flatter wage profiles, this prediction has been largely ignored in the recent welfare reform debates. The key econometric problem in estimating returns to tenure and experience is that wages depend on the unobservable job match component, which is endogenous. We depart from the standard method for dealing with this problem in one important way. We show that this alternative implies that wages grow with the number of previous successful job matches. In our empirical work we show that this source of between job wage growth is large. Furthermore, we show that this source of wage growth, as well as the standard returns to tenure and experience, are substantially smaller for the least educated.
Endotoxin impairs agonist-induced calcium mobilization in rat mesangial cells.

We hypothesized that endotoxin would impair agonist-induced calcium (Ca2+) mobilization in rat mesangial cells, owing to the induction of nitric oxide synthase (NOS) and augmented nitric oxide (NO) synthesis. We measured basal and bradykinin-induced peak free cytosolic Ca2+ concentrations through microspectrofluorimetry with fura-2 in confluent mesangial cells, and assayed conditioned medium for nitrite accumulation. Prior to measurement, cells were incubated overnight in serum-supplemented medium, with or without endotoxin, 1-arginine, indomethacin, meclofenamate, or N omega-nitro-L-arginine methyl ester (L-NAME). Endotoxin (1 mg/ml) decreased bradykinin-induced peak Ca2+ responses by 35 to 60% (p < 0.0001) and increased nitrite accumulation > 6-fold (p < 0.01). Arginine supplementation further (> 9-fold, p < 0.0001) increased nitrite accumulation without changing the effect on Ca2+. Inhibition of NOS abolished increments in nitrite concentration but had no effect on impaired Ca2+ responses. Cyclooxygenase (COX) inhibitors, present during incubation with endotoxin, but not afterward, normalized bradykinin-stimulated calcium responses. Thrombin-stimulated Ca2+ responses were similarly affected. We conclude that neither NO nor prostaglandins act directly to impair agonist-induced Ca2+ mobilization following endotoxin exposure; however, this effect may be an indirect effect of COX products, including reactive oxygen intermediates.
Building Blocks for a Web Programming Language

The essential characteristics of a Web application are concurrency, distribution and XML processing. Excluding the emphasis on XML, these are the natural elements of normal distributed applications. This means that we should consider Web applications as distributed programs, where the special need for XML processing is explicit. Currently this is difficult, but we present a motivation and building blocks for a new Web programming language that targets the Web as an application platform. We also outline the structure of the necessary runtime environment and show where our language fits within the competitive landscape of programming languages aimed at developing Web applications and services.
Fast Blocked Clause Decomposition with High Quality

Any CNF formula can be decomposed two blocked subsets such that both can be solved by BCE (Blocked Clause Elimination). To make the decomposition more useful, one hopes to have the decomposition as unbalanced as possible. It is often time consuming to achieve this goal. So far there have been several decomposition and post-processing algorithms such as PureDecompose, QuickDecompose, EagerMover etc. We found that these existing algorithms are often either inefficient or low-quality decomposition. This paper aims at improving the decomposition quality, while keeping the runtime of algorithms under control. To achieve this goal, we improve the existing BCE, and present two new variants of PureDecompose, a new heuristic decomposition called LessInterfereDecompose, and a new post-processing algorithm called RsetGuidedDecompose. Combining these new techniques results in a new algorithm called MixDecompose. In our experiments, there is no application formula where the quality of PureDecompose+EagerMover is better than MixDecompose. In terms of speed, MixDecompose is also very fast. Our average runtime is a little longer, but the worst-case runtime is shorter. In theory, our two variants of PureDecompose requires linear time in the number of clauses. By limiting the size of the touch list used by BCE, we can guarantee always that MixDecompose runs in linear time.
Dynamic user profile-based job recommender system

In this paper, we propose a dynamic user profile-based job recommender system. To address the challenge that the job applicants do not update the user profile in a timely manner, we update and extend the user profile dynamically based on the historical applied jobs and behaviors of job applicants. In particular, the statistical results of basic features in the applied jobs are used to update the job applicants'. In addition, feature selection is employed in the text information of jobs that applied by the job applicant for extending the feature. Then a hybrid recommendation algorithm is employed according to the characteristics of user profiles for achieving the dynamic recommendation.
Generating Lane-change Trajectories using the Dynamic Model of Emulating Driving Behavior

Modeling driving behavior and emulating driver control strategy is one of essential parts for risk assessment and auxiliary control in the driver assistance system and vehicle active safety system. In this paper, we propose a proposed model is intuitive and can clearly describe the habit and randomness of the lane-change behavior with limit parameters. Especially, by using the proposed model and method driver can choose the different driving scenes, such as slow or sudden, to generate different lane-change trajectories. Compared with the conventional polynomial lane-change path planning, the dynamic model can generate the feasible lane-change trajectories and show the good performance of approximating the real lane-change trajectories.
MoMut::UML Model-Based Mutation Testing for UML

Model-based mutation testing (MBMT) is a promising testing methodology that relies on a model of the system under test (SUT) to create test cases. Hence, MBMT is a so-called black-box testing approach. It also is fault based, as it creates test cases that are guaranteed to reveal certain faults: after inserting a fault into the model of the SUT, it looks for a test case revealing this fault. This turns MBMT into one of the most powerful and versatile test case generation approaches available as its tests are able to demonstrate the absence of certain faults, can achieve both, control-flow and data-flow coverage of model elements, and also may include information about the behaviour in the failure case. The latter becomes handy whenever the test execution framework is bound in the number of observations it can make and - as a consequence - has to restrict them. However, this versatility comes at a price: MBMT is computationally expensive. The tool MoMuT::UML (https://www.momut.org) is the result of a multi-year research effort to bring MBMT from the academic drawing board to industrial use. In this paper we present the current stable version, share the lessons learnt when applying two generations of MoMuT::UML in an industrial setting, and give an outlook on the upcoming, third,generation.
Self-organization of the Sound Inventories: Analysis and Synthesis of the Occurrence and Co-occurrence Networks of Consonants*

Abstract The sound inventories of the world's languages self-organize themselves, giving rise to similar cross-linguistic patterns. In this work, we attempt to capture this phenomenon of self-organization, which shapes the structure of the consonant inventories, through a complex network approach. For this purpose we define the occurrence and co-occurrence networks of consonants and systematically study some of their important topological properties. A crucial observation is that the occurrence as well as the co-occurrence of consonants across languages follows a power law distribution. This property is arguably a consequence of the principle of preferential attachment. In order to support this argument we propose a synthesis model, which reproduces the degree distribution for the networks to a close approximation. We further observe that the co-occurrence network of consonants shows a high degree of clustering and subsequently refine our synthesis model in order to explain this property. Finally, we discuss how preferential attachment manifests itself through the evolutionary nature of language.
Native and Non-Native Speech Perception

This review examines research on speech perception by both native and non-native listeners. The development of speech perception in infancy is first considered and a theoretical model that accounts for this is introduced. A brief overview then follows of several research areas under the umbrella of non-native speech perception, namely cross-dialect, cross-language and second-language speech perception. It is shown that non-native and native speech perception is critically shaped by the specific ways in which speakers use acoustic cues in speech production.
Security and Privacy in Cloud Computing via Obfuscation and Diversification: A Survey

The development of cloud computing has facilitate the organizations with its services. This makes the security and privacy of the cloud even more significant. Diversification and obfuscation approaches are of the most promising proactive techniques that protect computers from harmful malware, by preventing them to take advantage of the security vulnerabilities. There is a large body of research on the use of diversification and obfuscation techniques for improving the security in various domains, including cloud computing. Cloud computing provides an excellent setting for applying diversification/obfuscation, as the computing platforms (virtual machines) are implemented in software. The main objective of this study is to determine in what ways obfuscation and diversification techniques are used to enhance the security and privacy of the cloud computing, and discover the potential avenues for the further research. To achieve this goal, we systematically review and report the papers that discuss/propose a technique to enhance the security and privacy of the cloud, using diversification and obfuscation techniques. As the result of the search we collected 43 papers published on the topic. In this report we present the process of data collection, analysis of the results, and classification of the related studies. The classification is done based on how the diversification/obfuscation techniques are used to enhance the security in cloud computing environment. The presented study gives a clear view of the state of the art of the existing works in the field, and sheds light on the areas remained intact which could be avenues for further research. The existing works cover surprisingly a small set of the wealth of opportunities for diversification/obfuscation.
VGRAM: Improving Performance of Approximate Queries on String Collections Using Variable-Length Grams

Many applications need to solve the following problem of approximate string matching: from a collection of strings, how to find those similar to a given string, or the strings in another (possibly the same) collection of strings? Many algorithms are developed using fixed-length grams, which are substrings of a string used as signatures to identify similar strings. In this paper we develop a novel technique, called VGRAM, to improve the performance of these algorithms. Its main idea is to judiciously choose high-quality grams of variable lengths from a collection of strings to support queries on the collection. We give a full specification of this technique, including how to select high-quality grams from the collection, how to generate variable-length grams for a string based on the preselected grams, and what is the relationship between the similarity of the gram sets of two strings and their edit distance. A primary advantage of the technique is that it can be adopted by a plethora of approximate string algorithms without the need to modify them substantially. We present our extensive experiments on real data sets to evaluate the technique, and show the significant performance improvements on three existing algorithms.
Incremental Discovery of Hidden Struct of Elementary

Discovering hidden structure is a challenging, universal research task in Physics, Chemistry, Biology, and other disciplines. Not only must the elements of hidden structure be postulated by the discoverer, but they can only be verified by indirect evidence, at the level of observable objects. In this paper we describe a framework for hidden structure discovery, built on a constructive definition of hidden structure. This definition leads to operators that build models of hidden structure step by step, postulating hidden objects, their combinations and properties, reactions described in terms of hidden objects, and mapping between the hidden and the observed structure. We introduce the operator dependency diagram, which shows the order of operator application and model evaluation. Different observational knowledge supports different evaluation criteria, which lead to different search systems with verifiable sequences of operator applications. Isomorphfree structure generation is another issue critical for efficiency of search. We apply our framework in the system GELL-MANN, that hypothesizes hidden structure for elementary particles and we present the results of a large scale search for quark models.
ACTIVITY BASED COSTING- DIFFUSION AND ADOPTION

Few new ideas in management accounting have achieved the same attention in terms of books, reports, conferences and implementation efforts, as has Activity Based Accounting (ABC). A lot of survey studies have been carried out describing the diffusion of ABC in different countries, for example Krumwiede (1998a) in USA, Gosselin in Canada (1997), Innes & Mitchell in Great Britain (1995), Sherrer in Germany (1996), Lukka & Grönlund in Finland (1996) and Björnenak in Norway (1997). The surveys give a general picture of the extent to which ABC has been considered and adopted at certain points in time. No such study has so far been made in Sweden. This paper reports on a survey conducted during autumn 1999. The sample contains 400 Swedish manufacturing firms with more than 50 employees with a response rate of 37%. The aim of the paper is to describe and explain the diffusion and the adoption of ABC in Swedish manufacturing industry and, wherever possible, compare the results with surveys from other countries. From a diffusion perspective, the survey shows that the majority of Swedish manufacturing firms (53%) never even discussed adopting ABC. In the end, however, 16% of the Swedish firms have implemented and are currently using ABC. Out of these, only 17% have chosen a complete implementation. In the adoption perspective 27 variables were tested, all generated from the ABC literature. The factor analysis reduced the 27 variables to 9 factors, which are size, competition, differentiation, system quality, automation, strategic importance of costing, budgetary control, product diversification and finally Relevance Lost variables. The results from the study show that only three of the factors were statistically significant and could explain why Swedish firms have adopted and are using ABC. Notably none of the classic “ABC factors”, e.g. product diversification (Cooper, 1988ab), was significant.
Oxygen Tension Is a Determinant of the Matrix-Forming Phenotype of Cultured Human Meniscal Fibrochondrocytes

Background Meniscal cartilage displays a poor repair capacity, especially when injury is located in the avascular region of the tissue. Cell-based tissue engineering strategies to generate functional meniscus substitutes is a promising approach to treat meniscus injuries. Meniscus fibrochondrocytes (MFC) can be used in this approach. However, MFC are unable to retain their phenotype when expanded in culture. In this study, we explored the effect of oxygen tension on MFC expansion and on their matrix-forming phenotype. Methodology/Principal Findings MFC were isolated from human menisci followed by basic fibroblast growth factor (FGF-2) mediated cell expansion in monolayer culture under normoxia (21%O2) or hypoxia (3%O2). Normoxia and hypoxia expanded MFC were seeded on to a collagen scaffold. The MFC seeded scaffolds (constructs) were cultured in a serum free chondrogenic medium for 3 weeks under normoxia and hypoxia. Constructs containing normoxia-expanded MFC were subsequently cultured under normoxia while those formed from hypoxia-expanded MFC were subsequently cultured under hypoxia. After 3 weeks of in vitro culture, the constructs were assessed biochemically, histologically and for gene expression via real-time reverse transcription-PCR assays. The results showed that constructs under normoxia produced a matrix with enhanced mRNA ratio (3.5-fold higher; p<0.001) of collagen type II to I. This was confirmed by enhanced deposition of collagen II using immuno-histochemistry. Furthermore, the constructs under hypoxia produced a matrix with higher mRNA ratio of aggrecan to versican (3.5-fold, p<0.05). However, both constructs had the same capacity to produce a glycosaminoglycan (GAG) –specific extracellular matrix. Conclusions Our data provide evidence that oxygen tension is a key player in determining the matrix phenotype of cultured MFC. These findings suggest that the use of normal and low oxygen tension during MFC expansion and subsequent neo-tissue formation cultures may be important in engineering different regions of the meniscus.
EWMA control chart via multiple testing

This paper proposes a new type of multivariate EWMA control chart for detecting the process mean shift on the basis of a series of most recent T-squared statistics. We established a multiple hypothesis testing which uses the false discovery rate as the error to be controlled. Particularly, Benjamini–Hochberg procedure is applied to develop a new control scheme. A nonparametric density estimation based on the Parzen windows is adopted to approximate the distribution of the T-square statistics, from which the p-values are calculated. The performance of the proposed control charts is evaluated in terms of the outverage run length WMA ultiple testing ultivariate control chart of-control average run length and the in-control average run length according to various non-centrality parameters associated with the mean shifts. The result shows that the proposed control chart performs better than the existing multivariate EWMA chart for all mean shifts. The proposed method seems to be rigorous in the sense that error rates for the multiple hypotheses are considered in an integrated way via FDR rather than considering type I and II errors separately. © 2015 Elsevier Ltd. All rights reserved.
A comparison of matrix rewriting versus direct encoding for evolving neural networks

The intuitive expectation is that the scheme used to encode the neural network in the chromosome should be critical to the success of evolving neural networks to solve difficult problems. In 1990 Kitano published an encoding scheme based on context-free parallel matrix rewriting. The method allowed compact, finite, chromosomes to grow neural networks of potentially infinite size. Results were presented that demonstrated superior evolutionary properties of the matrix rewriting method compared to a simple direct encoding. The authors present results that contradict those findings, and demonstrate that a genetic algorithm (GA) using a direct encoding can find good individuals just as efficiently as a GA using matrix rewriting.
Bridging the Semantic Gap

Content-based image retrieval systems were introduced as an alternative to avoid the need of manual tagging in traditional keyword-based image retrieval systems. However, the representation of image using visual features only involves a loss of information which is referred to as semantic gap. A number of techniques have been proposed to deal with ‘semantic gap’. This paper reviews existing approaches to handle the well-known ‘semantic gap’ problem in image retrieval systems with a particular focus to approaches based on text and image fusion. Keywords— Image retrieval, Semantic Image Retrieval, CBIR, Text and Image fusion.