Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of ProRoot MTA mixed with chlorhexidine on apoptosis and cell cycle of fibroblasts and macrophages in vitro.

AIM To compare the percentage of apoptotic cells and the cell cycle profile of fibroblasts and macrophages exposed to either ProRoot mineral trioxide aggregate (MTA) mixed with chlorhexidine (CHX), or exposed to ProRoot MTA mixed with sterile water. METHODOLOGY Mouse gingival fibroblasts or mouse macrophages were seeded in six-well plates and allowed to attach overnight. Freshly mixed or set (allowed to dry for 24 h) specimens of tooth-coloured (white) ProRoot MTA were prepared with 0.12% CHX gluconate (MTA/CHX) or with sterile water (MTA/H2O). The cells were exposed for 24 h to the MTA specimens, which were placed over permeable membrane inserts to avoid direct contact with the cells. Untreated cells served as controls. Propidium iodide staining followed by flow cytometry was used to evaluate the effects of ProRoot MTA on cell apoptosis and cell cycle. Statistical analyses were performed by one-way anova followed by post-hoc tests with the use of the SigmaStat 2.0 software, and significance was determined at P < or = 0.05. RESULTS MTA specimens containing CHX induced apoptosis of macrophages and fibroblasts (P < 0.05). In contrast, no change in the proportion of apoptotic cells was observed when sterile water was used to prepare the specimens (P > 0.05). Cell cycle analysis showed that exposure to MTA/CHX decreased the percentage of fibroblasts and macrophages in S phase (DNA synthesis) as compared with exposure to MTA/H2O (P < 0.05). CONCLUSION This in vitro study demonstrated that the substitution of CHX for sterile water in MTA increases its cytotoxicity. This suggests that the potentially beneficial antimicrobial effect of CHX may be accompanied by an increase in the cytotoxicity of the resulting MTA-based material.
Organizing Resources on Tagging Systems using TORG

Tagging systems (or folksonomies) like Flickr or Delicious are expanding tremendously. More and more resources are being added to them. As the resources present on these system increase in amount, it becomes difficult to explore these resources. For this purpose, we present a system T-ORG, which provides a mechanism to organize these resources by classifying the tags (or keywords) attached to them into predefined categories. Supervised classification in this case seems infeasible; therefore we also propose a new classification algorithm T-KNOW that does not require training data. For our experiments, we have downloaded images and their tags from groups present on Flickr website and then classified these tags into different categories. We have used Cohen’s Kappa and F-measure to evaluate the classification results of TKNOW. Results are encouraging and show that T-ORG can be used to explore resources in an effective manner.
A novel ontology for computer go knowledge management

In order to stimulate the development and research in computer Go, several Taiwanese Go players, including three professional Go players and four amateur Go players, were invited to play against the famous computer Go program, MoGo, in the Taiwan Open 2009. The MoGo program combines the online game values, offline values extracted from databases, and expert rules defined by Go expert that shows an excellent performance in the games. The results reveal that MoGo can reach the level of 3 Dan in Taiwan amateur Go environment. But there are still some drawbacks for MoGo that should be solved, for example, the weaknesses in semeai and how to flexibly practice the human knowledge through the embedded opening books. In this paper, a new game record ontology for computer Go knowledge management is proposed to solve the problems that MoGo is facing. It is hoped that the advances in intelligent agent and ontology model can provide much more knowledge to make a progress in computer Go and achieve as much as computer chess or Chinese chess in the future.
Walking through sight: Seeing the ability to see, in a 3-D augmediated reality environment

A 3-dimensional augmediated reality (AR) environment was designed, where users can physically walk through space, and by looking through AR glasses can see and interact with hidden veillance flux produced by cameras. Surveillance cameras, physically attached to a room, as well as handheld and body-worn cameras, each emit veillance flux and have a veillance field - a mathematical formulation of their capacity to see, as that capacity to see propagates through space. In this work, for the first time, we bring the mathematical veillance field into 3D augmediated reality, to "see sight".
Knowledge datawarehouse: Web usage OLAP application

Generally, OLAP analysis are based on both the observed data and a set of OLAP operators for restructuration and granularity modification. The goal is to discover patterns hidden into data. Unfortunately, this approach is also based on the analyst background. This latter assumes hypothesis according to his background and analyses data consequently: "hypothesis driven analysis". The integration of knowledge into data warehouse conduce to enriched analysis context where objects and their relations are explicitly represented, handled and visualized. We investigate a deep integration where the basic datawarehouse's operators consider both data and knowledge. This paper applies knowledge datawarehouse concept to Web usage analysis.
Output feedback guaranteed cost control of networked linear systems with random packet losses

This article is concerned with the output feedback guaranteed cost control problem for a class of networked control systems (NCSs) with both packet losses and network-induced delays. The packet-loss processes in the forward channel and the backward channel are modelled as two Markov chains. The dynamic output feedback controllers are considered, and the closed-loop NCS is modelled as a discrete-time Markovian system with two modes and unit time delay. By using a properly constructed Lyapunov function and the state transformation technique, a sufficient condition is derived for the closed-loop NCS to be mean-square exponentially stable and ensure a decay rate that can be tuned according to the packet loss situations in the networks. Moreover, design procedures for the guaranteed cost controllers are also presented based on the obtained stability condition and guaranteed cost performance result. Finally, an illustrative example is given to demonstrate the effectiveness of the proposed results.
Authorship Identification for Online Text

Authorship identification for online text such as blogs and e-books is a challenging problem as these documents do not have a considerable amount of content. Therefore, identification is much harder than other documents such as books and reports. The paper investigates the choice of features and classifier accuracy which are suitable for such texts. Syntactic features are found to be good for large data sets, whereas lexical features are good for small data sets. The results can be used to customize and further improve authorship detection techniques according to the characteristics of the writing samples.
A model of Cdc25 phosphatase catalytic domain and Cdk-interaction surface based on the presence of a rhodanese homology domain.

Mammalian Cdc25 phosphatase is responsible for the dephosphorylation of Cdc2 and other cyclin-dependent kinases at Thr14 and Tyr15, thus activating the kinase and allowing cell cycle progression. The catalytic domain of this dual-specificity phosphatase has recently been mapped to the 180 most C-terminal amino acids. Apart from a CX3R motif, which is present at the active site of all known tyrosine phosphatases, Cdc25 does not share any obvious sequence similarity with any of those enzymes. Until very recently, the Cdc25 family was the only subfamily of tyrosine phosphates for which no three-dimensional structural data were available. Using the generalized profile technique, a sensitive method for sequence database searches, we found an extended and highly significant sequence similarity between the Cdc25 catalytic domain and similarly sized regions in other proteins: the non-catalytic domain of two distinct families of MAP-kinase phosphates, the non-catalytic domain of several ubiquitin protein hydrolases, the N and C-terminal domain of rhodanese, and a large and heterogeneous groups of stress-response proteins from all phyla. The relationship of Cdc25 to the structurally well-characterized rhodanese spans the entire catalytic domain and served as template for a structural model for human Cdc25a, which is fundamentally different from previously suggested models for Cdc25 catalytic domain organization. The surface positioning of subfamily-specific conserved residues allows us to predict the sites of interaction with Cdk2, a physiological target of Cdc25a. Based on the results of this analysis, we also predict that the budding yeast arsenate resistance protein Acr2 and the ORF Ygr203w encode protein phosphatases with catalytic properties similar to that of the Cdc25 family. Recent determination of the crystal structure of the Cdc25a catalytic domain supports the validity of the model and demonstrates the power of the generalized sequence profile technique in homology-based modeling of the three-dimensional structure of a protein having a weak but significant sequence similarity with a structurally characterized protein.
Problems with Traditional Science Publishing and Finding a Wider Niche for Post-Publication Peer Review

Science affects multiple basic sectors of society. Therefore, the findings made in science impact what takes place at a commercial level. More specifically, errors in the literature, incorrect findings, fraudulent data, poorly written scientific reports, or studies that cannot be reproduced not only serve as a burden on tax-payers’ money, but they also serve to diminish public trust in science and its findings. Therefore, there is every need to fortify the validity of data that exists in the science literature, not only to build trust among peers, and to sustain that trust, but to reestablish trust in the public and private academic sectors that are witnessing a veritable battle-ground in the world of science publishing, in some ways spurred by the rapid evolution of the open access (OA) movement. Even though many science journals, traditional and OA, claim to be peer reviewed, the truth is that different levels of peer review occur, and in some cases no, insufficient, or pseudo-peer review takes place. This ultimately leads to the erosion of quality and importance of science, allowing essentially anything to become published, provided that an outlet can be found. In some cases, predatory OA journals serve this purpose, allowing papers to be published, often without any peer review or quality control. In the light of an explosion of such cases in predatory OA publishing, and in severe inefficiencies and possible bias in the peer review of even respectable science journals, as evidenced by the increasing attention given to retractions, there is an urgent need to reform the way in which authors, editors, and publishers conduct the first line of quality control, the peer review. One way to address the problem is through post-publication peer review (PPPR), an efficient complement to traditional peer-review that allows for the continuous improvement and strengthening of the quality of science publishing. PPPR may also serve as a way to renew trust in scientific findings by correcting the literature. This article explores what is broadly being said about PPPR in the literature, so as to establish awareness and a possible first-tier prototype for the sciences for which such a system is undeveloped or weak.
Self-calibration and Euclidean reconstruction using motions of a stereo rig

This paper describes a method to upgrade projective reconstruction to affine and to metric reconstructions using rigid general motions of a stereo rig. We make clear the algebraic relationships between projective reconstruction, the plane at infinity (affine reconstruction), camera calibration, and metric reconstruction. We show that all the computations can be carried out using standard linear resolution methods and that these methods compare favorably with nonlinear optimization, methods in the presence of Gaussian noise. We carry out a theoretical error analysis which quantify the relative importance of the accuracies of projective-to-affine conversion and affine-to-Euclidean conversion. Experiments with with real data are consistent with the theoretical error analysis and with a sensitivity analysis performed with simulated data.
CENTRIN2 Modulates Homologous Recombination and Nucleotide Excision Repair in Arabidopsis

A genetic screen of a population of Arabidopsis thaliana lines exhibiting enhanced somatic homologous recombination yielded a mutant affected in expression of a gene encoding a caltractin-like protein (centrin). The hyperrecombinogenic phenotype could be reproduced using RNA interference (RNAi) technology. Both the original mutant and the RNAi plants exhibited a moderate UV-C sensitivity as well as a reduced efficiency of in vitro repair of UV-damaged DNA. Transcription profiling of the mutant showed that expression of components of the nucleotide excision repair (NER) pathway and of factors involved in other DNA repair processes were significantly changed. Our data suggest an indirect involvement of centrin in recombinational DNA repair via the modulation of the NER pathway. These findings thus point to a novel interconnection between an early step of NER and homologous recombination, which may play a critical role in plant DNA repair.
Feature-Preserving Simplification of Texture-Mapped Models

A feature-preserving multi-resolution simplification algorithm based on half-edge collapse operation for texture-mapped models is proposed. A new error metric based on the geometric importance the texture-attribute importance of a half-edge is presented. It can generate a low-polygon-count approximation model with shape preservation and texture attributes preservation. In addition, the half-edge based scheme is more efficient in memory usage and convenient for generating progressive meshes with texture attributes for real-time transmission of various surface data on the Web. The visual comparisons showing that the proposed algorithm results in higher quality approximations of original models with texture attribute preservation even at very low levels of detail than other algorithms in the literature
Finitary Deduction Systems

Cryptographic protocols are the cornerstone of security in distributed systems. The formal analysis of their properties is accordingly one of the focus points of the security community, and is usually split among two groups. In the first group, one focuses on trace-based security properties such as confidentiality and authentication, and provides decision procedures for the existence of attacks for an on-line attackers. In the second group, one focuses on equivalence properties such as privacy and guessing attacks, and provides decision procedures for the existence of attacks for an offline attacker. In all cases the attacker is modeled by a deduction system in which his possible actions are expressed. We present in this paper a notion of finitary deduction systems that aims at relating both approaches. We prove that for such deduction systems, deciding equivalence properties for on-line attackers can be reduced to deciding reachability properties in the same setting.
On the correlation between facial movements, tongue movements and speech acoustics

This study is a first step in a large-scale study that aims at quantifying the relationship between external facial movements, tongue movements, and the acoustics of speech sounds. The database analyzed consisted of 69 CV syllables spoken by two males and two females; each utterance was repeated four times. A Qualysis (optical motion capture system) and an EMA (electromagnetic midsaggital articulography) system were used to characterize facial and tongue movements, respectively. Acoustic features were represented by linear spectral pairs (LSP). To quantify the correlation between them, a multilinear regression technique was applied. The results were analyzed in terms of vowel context, place of articulation, and individual articulatory (EMA or Optical) or acoustic (LSP) channel.
Qualitative study on 3D face databases: A review

Recent researches in three-dimensional (3D) face recognition area have proved that, 3D face recognition methods, achieve better accuracy than its 2D counterpart. One of the main advantages of 3D face recognition methods is that it measures the geometry of rigid features on the human face, due to which it becomes an invariant to illumination, expressions and rotations of head (pose variation). But the main drawback of 3D face recognition methods is the acquisition of 3D face images which generally needs a range camera. It is where the research community is facing difficulty. Research in 3D face recognition also depends on available databases. In this paper, we present a qualitative review of all the available 3D face databases. A comparative table of all the databases is also given at the end with all the necessary parameters.
Adenine Aminohydrolase from Leishmania donovani

Background: Purine salvage in Leishmania is an indispensable nutritional process. Results: Adenine aminohydrolase, a key purine enzyme in Leishmania, has been characterized biochemically and genetically. Conclusion: Adenine aminohydrolase is a unique enzyme in purine salvage that converts 6-aminopurines into 6-oxypurines. Significance: Functional characterization of key enzymes is crucial for understanding purine salvage and ultimately for targeting the pathway with drugs. Adenine aminohydrolase (AAH) is an enzyme that is not present in mammalian cells and is found exclusively in Leishmania among the protozoan parasites that infect humans. AAH plays a paramount role in purine metabolism in this genus by steering 6-aminopurines into 6-oxypurines. Leishmania donovani AAH is 38 and 23% identical to Saccharomyces cerevisiae AAH and human adenosine deaminase enzymes, respectively, catalyzes adenine deamination to hypoxanthine with an apparent Km of 15.4 μm, and does not recognize adenosine as a substrate. Western blot analysis established that AAH is expressed in both life cycle stages of L. donovani, whereas subcellular fractionation and immunofluorescence studies confirmed that AAH is localized to the parasite cytosol. Deletion of the AAH locus in intact parasites established that AAH is not an essential gene and that Δaah cells are capable of salvaging the same range of purine nucleobases and nucleosides as wild type L. donovani. The Δaah null mutant was able to infect murine macrophages in vitro and in mice, although the parasite loads in both model systems were modestly reduced compared with wild type infections. The Δaah lesion was also introduced into a conditionally lethal Δhgprt/Δxprt mutant in which viability was dependent on pharmacologic ablation of AAH by 2′-deoxycoformycin. The Δaah/Δhgprt/Δxprt triple knock-out no longer required 2′-deoxycoformycin for growth and was avirulent in mice with no persistence after a 4-week infection. These genetic studies underscore the paramount importance of AAH to purine salvage by L. donovani.
Graph coloring: The more colors, the better?

In this paper, we investigate the algorithmic complexity of deciding colorability, as a function of the number of available colors. Intuitively, one may assume that the problem's complexity is highest around the chromatic number of the graph. We give substantial empirical evidence that this intuition is largely true, both for exact and heuristic graph coloring algorithms. We give a rigorous proof that the complexity of a class of exact algorithms is monotonously increasing in the number of available colors in the non-colorable case, and give a counter-example to demonstrate that the analogous claim does not always hold for colorable graphs.
Architecture Conformance Checking in Dynamically Typed Languages

Architectural erosion is a recurrent problem faced by software architects, which might be even more severe in systems implemented in dynamically typed languages. The reasons are twofold: (i) some features provided by such languages make developers more propitious to break the planned architecture (e.g., dynamic invocations and buildings), and (ii) the developers’ community lacks tool support for monitoring the implemented architecture. To address these shortcomings, this paper presents an architectural conformance and visualization approach based on static code analysis techniques and on a lightweight type propagation heuristic. The central idea is to provide the developers’ community with means to control the architectural erosion process by reporting architectural violations and visualizing them in high-level architectural models, such as reflexion models and DSMs. This paper also describes a tool—called ArchRuby—that implements our approach. We evaluate our solution in three real-world systems identifying 48 architectural violations of which the developers had no prior knowledge. We also measure the effectiveness of our type propagation heuristic reporting that (i) the number of analyzed types raises 5% on the average and (ii) certain violations are only detected due to our heuristic.
Generation of Attenuated Mycobacterium bovis Strains by Signature-Tagged Mutagenesis for Discovery of Novel Vaccine Candidates

ABSTRACT Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex, has a particularly wide host range and causes tuberculosis in most mammals, including humans. A signature tag mutagenesis approach, which employed illegitimate recombination and infection of guinea pigs, was applied to M. bovis to discover genes important for virulence and to find potential vaccine candidates. Fifteen attenuated mutants were identified, four of which produced no lesions when inoculated separately into guinea pigs. One of these four mutants had nine deleted genes including mmpL4 and sigK and, in guinea pigs with aerosol challenge, provided protection against tuberculosis at least equal to that of M. bovis BCG. Seven mutants had mutations near the esxA (esat-6) locus, and immunoblot analysis of these confirmed the essential role of other genes at this locus in the secretion of EsxA (ESAT-6) and EsxB (CFP10). Mutations in the eight other attenuated mutants were widely spread through the chromosome and included pks1, which is naturally inactivated in clinical strains of M. tuberculosis. Many genes identified were different from those found by signature tag mutagenesis of M. tuberculosis by use of a mouse infection model and illustrate how the use of different approaches enables identification of a wider range of attenuating mutants.