Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytosine-to-Uracil Deamination by SssI DNA Methyltransferase

The prokaryotic DNA(cytosine-5)methyltransferase M.SssI shares the specificity of eukaryotic DNA methyltransferases (CG) and is an important model and experimental tool in the study of eukaryotic DNA methylation. Previously, M.SssI was shown to be able to catalyze deamination of the target cytosine to uracil if the methyl donor S-adenosyl-methionine (SAM) was missing from the reaction. To test whether this side-activity of the enzyme can be used to distinguish between unmethylated and C5-methylated cytosines in CG dinucleotides, we re-investigated, using a sensitive genetic reversion assay, the cytosine deaminase activity of M.SssI. Confirming previous results we showed that M.SssI can deaminate cytosine to uracil in a slow reaction in the absence of SAM and that the rate of this reaction can be increased by the SAM analogue 5’-amino-5’-deoxyadenosine. We could not detect M.SssI-catalyzed deamination of C5-methylcytosine (m5C). We found conditions where the rate of M.SssI mediated C-to-U deamination was at least 100-fold higher than the rate of m5C-to-T conversion. Although this difference in reactivities suggests that the enzyme could be used to identify C5-methylated cytosines in the epigenetically important CG dinucleotides, the rate of M.SssI mediated cytosine deamination is too low to become an enzymatic alternative to the bisulfite reaction. Amino acid replacements in the presumed SAM binding pocket of M.SssI (F17S and G19D) resulted in greatly reduced methyltransferase activity. The G19D variant showed cytosine deaminase activity in E. coli, at physiological SAM concentrations. Interestingly, the C-to-U deaminase activity was also detectable in an E. coli ung + host proficient in uracil excision repair.
Classification of dwellings into profiles regarding indoor air quality, and identification of indoor air pollution determinant factors

This study aims to identify the most relevant variables, among outdoor measures, building characteristics and socioeconomic situation, for predicting indoor air chemical pollution in dwellings. To achieve this, we propose a two-step plan: first, group the dwellings into classes according to the indoor measured concentrations, then use regression tools to express a dwelling's class as a function of the aforementioned variables. In the first step, we use modelbased clustering algorithms in a multivariate Gaussian mixture context; in the second step, we use binary decision trees in a discrimination context. This approach does not handle the pollutants individually, but considers them together as a multidimensional variable that must be summarized by a categorical variable (the dwelling's class).
An approach for Fuzzy Dominant Color Descriptor

In this paper, a new Dominant Color Descriptor is proposed. This descriptor is defined as a fuzzy set over a finite universe of fuzzy colors, in which membership degrees represent the dominance of each color. The fuzzy colors employed are fuzzy sets defined on an ordinary color space, filling the semantic gap between the color representation in computers and its human perception. The dominance of each fuzzy color is calculated on the basis of a fuzzy quantifier representing the notion of dominance, and a fuzzy histogram representing as a fuzzy quantity the percentage of pixels that match each fuzzy color. The obtained descriptor can be employed in a large amount of applications. We illustrate the usefulness of the descriptor by a particular application in image retrieval.
Characterization of the metabotropic glutamate receptors mediating phospholipase C activation and calcium release in cerebellar granule cells: calcium‐dependence of the phospholipase C response

In this study we have determined the metabotropic glutamate receptors (mGluRs) involved in the glutamate activation of phospholipase C (PLC) and Ca2+ mobilization in cerebellar granule cells at 9 days in vitro; and studied the Ca2+ modulation of the PLC response. Both PLC activation and Ca2+ signalling were found to be mediated exclusively by the mGluR1 subtype, although both group I mGluRs, mGluR1α and mGluR5, could be detected in cell extracts. Exposure of cells to medium devoid of Ca2+ for various times before agonist stimulation reduced the PLC response, which was quickly recovered following the re‐exposure of cells to Ca2+‐containing medium. The extent of the glutamate response correlated well with changes in the cytosolic Ca2+ concentration. On the other hand, loading of the intracellular Ca2+ stores by a transient depolarization followed by washing in nondepolarizing buffer, allowed glutamate to release stored Ca2+ in the majority of cells and enhanced glutamate activation of PLC. Under such conditions, the absence of extracellular Ca2+ during stimulation and the chelation of cytosolic Ca2+ with BAPTA/AM inhibited both glutamate‐elicited Ca2+ response and PLC activation. Overall, these results indicate that the mGluR‐mediated activation of PLC depends on the presence of extracellular Ca2+ and can be modulated by moderate changes of cytosolic Ca2+. Furthermore, ryanodine reduced PLC stimulation by glutamate in predepolarized cells but not in control cells, suggesting that ryanodine receptors could play a role in the potentiation of the mGluR‐mediated activation of PLC by Ca2+ release in predepolarized cells.
Document Type Definition ( DTD ) Metrics

In this paper, we present two complexity metrics for the assessment of schema quality written in Document Type Definition (DTD) language. Both “Entropy (E) metric: E(DTD)” and “Distinct Structured Element Repetition Scale (DSERS) metric: DSERS(DTD)” are intended to measure the structural complexity of schemas in DTD language. These metrics exploit a directed graph representation of schema document and consider the complexity of schema due to its similar structured elements and the occurrences of these elements. The empirical and theoretical validations of these metrics prove the robustness of the metrics. Key-words: XML schema, Document Type Definition, software metrics.
Constructing efficient certificate-based encryption scheme with pairing in the standard model

Certificate-based encryption (CBE) is a new asymmetric encryption paradigm which combines traditional public-key encryption (PKE) and identity-based encryption (IBE) while preserving some of their most attractive features. CBE provides an efficient implicit certificate mechanism and allows a form of automatic certificate revocation. It eliminates the third-party queries and simplifies the certificate revocation problem in the traditional PKI, while it is not subjected to the key escrow problem and key distribution problem inherent in IBE. In this paper, we propose an efficient pairing-based CBE scheme which is secure in the standard model under hardness of the mBDDH problem. When compared to the previous CBE schemes in the standard model, our scheme has obvious advantage in the computation and communication performance. It also offers performance competitive with those CBE schemes in the random oracle model.
The Interface Between Economic Development, Health and Environment in India: An Econometric Investigation

This paper analyses interrelationships between â€˜economic developmentâ€™, â€˜healthâ€™, and â€˜environmentâ€™ in a simultaneous equations framework. The endogenous variables chosen for the model are GDPPC (per capita gross domestic product), LE (life expectancy), NOCRD (number of cases of respiratory diseases) and PM10 (respirable suspended particulate matter). The four endogenous variables are supposed to be jointly determined in terms of several exogenous variables represented through indices of physical infrastructure (PI), social infrastructure (SI) and air pollution index (API). The three indices by the principal components method and thus effectively use only these three predetermined (exogenous) variables to simultaneously determine changes in the four endogenous variables listed above. The model is postulated in loglinear form and estimated by the two-stage least-squares method using data from the Indian economy 1980-81 to 2004-05.
A receding horizon control of a cooperative multi target tracking system

In this paper the problem of cooperative tracking of multiple targets for multi-agent systems is investigated. Defining problem of target tracking as gathering maximum rewards associated with the targets, an optimization-based algorithm is presented. A cooperative receding horizon controller for reaching moving targets is proposed. Agents are controlled by adjusting their headings toward the moving targets. A notable advantage of the proposed approach is the estimations of target's motion and planning the agent's heading based on them. Simulation results are provided to verify the efficiency of the proposed method.
Public debt sustainability in the northern countries of Latin America

An analysis of public debt indicators in eight northern countries of Latin America reveals that Nicaragua and Honduras are the most vulnerable; Panama, the Dominican Republic, Costa Rica, and El Salvador are moderately vulnerable; while Mexico and Guatemala have debt levels that are not considered dangerous. Nonetheless, a subsequent review of four indicators of fiscal sustainability shows only Mexico to be well positioned under all criteria; Costa Rica and Guatemala display a number of minor problems, while various special circumstances explain the favourable results obtained by Nicaragua and the Dominican Republic; and El Salvador, Honduras and Panama will be unable to sustain their 2004 fiscal policy for very long. Lastly, analysis of the sensitivity of the debt to a sudden stop in foreign capital inflows suggests the need for a cautious attitude towards the future trend of the public debt in the face of rising international interest rates.
Profile of a Serial Killer: Cellular and Molecular Approaches to Study Individual Cytotoxic T-Cells following Therapeutic Vaccination

T-cell vaccination may prevent or treat cancer and infectious diseases, but further progress is required to increase clinical efficacy. Step-by-step improvements of T-cell vaccination in phase I/II clinical studies combined with very detailed analysis of T-cell responses at the single cell level are the strategy of choice for the identification of the most promising vaccine candidates for testing in subsequent large-scale phase III clinical trials. Major aims are to fully identify the most efficient T-cells in anticancer therapy, to characterize their TCRs, and to pinpoint the mechanisms of T-cell recruitment and function in well-defined clinical situations. Here we discuss novel strategies for the assessment of human T-cell responses, revealing in part unprecedented insight into T-cell biology and novel structural principles that govern TCR-pMHC recognition. Together, the described approaches advance our knowledge of T-cell mediated-protection from human diseases.
Mineral and Matrix Changes in Brtl/+ Teeth Provide Insights into Mineralization Mechanisms

The Brtl/+ mouse is a knock-in model for osteogenesis imperfecta type IV in which a Gly349Cys substitution was introduced into one COL1A1 allele. To gain insight into the changes in dentin structure and mineral composition in these transgenic mice, the objective of this study was to use microcomputed tomography (micro-CT), scanning electron microscopy (SEM), and Fourier transform infrared imaging (FTIRI) to analyze these structures at 2 and 6 months of age. Results, consistent with the dental phenotype in humans with type IV OI, showed decreased molar volume and reduced mineralized tissue volume in the teeth without changes in enamel properties. Increased acid phosphate content was noted at 2 and 6 months by FTIRI, and a trend towards altered collagen structure was noted at 2 but not 6 months in the Brtl/+ teeth. The increase in acid phosphate content suggests a delay in the mineralization process, most likely associated with the defect in the collagen structure. It appears that in the Brtl/+ teeth slow maturation of the mineralized structures allows correction of altered mineral content and acid phosphate distribution.
TOWARD A COMPREHENSIVE FRAMEWORK OF THE CAUSES OF KNOWLEDGE MANAGEMENT SUCCESS OR FAILURE - A COMPARATIVE CASE STUDY

Knowledge management (KM) initiatives have been implemented with diverse results in many organizations. Although there has been substantial inquiry into the conditions for KM success or failure, prior findings need careful systematization before engaging into rigorous empirical investigation. Theory development is still emergent; interesting ideas can be found dispersedly, but signs of comprehensive, convergent theory are rather weak. Thus, the relevant literature can meet at the concept of ‘knowledge-leveraging processes’, the (at least desirable) ‘essence’ of KM interests. Accordingly, in order to tackle the deepest causes of KM outcomes, complex, underlying knowledge-related organizational dynamics ought to be considered. In this paper, a qualitativemethod based, exploratory case-supported comparison of two contrasting KM experiences is provided. After an integrated discussion of both cases, a comprehensive framework is tentatively suggested, encompassing a number of key issues for KM (project) effectiveness. Future research is needed to develop this framework and undertake further empirical analyses.
Own Your Android! Yet Another Universal Root

In recent years, to find a universal root solution for Android becomes harder and harder due to rare vulnerabilities in the Linux kernel base and also the exploit mitigations applied on the devices by various vendors. In this paper, we will present our universal root solution. The related vulnerability CVE-2015-3636, a typical use-after-free bug in Linux kernel is discussed in detail. Exploiting such a use-after-free in Linux kernel is truly difficult due to the separated allocation from the kernel allocator. We will show how we leverage this kernel use-after-free bug to achieve privilege promotion on most popular Android devices on market which have a version not less than 4.3, including the first 64bit root case in the world. In short, we will present a generic way to exploit use-after-free vulnerabilities in Linux kernel, which means one exploit applies to devices of all brands. All the current mitigations in the kernel like PXN are circumvented by this approach. And most importantly our unique and undocumented exploitation technique targeting kernel use-after-free bugs features stability and accuracy.
Use of Adjunctive Aerosolized Antimicrobial Therapy in the Treatment of Pseudomonas aeruginosa and Acinetobacter baumannii Ventilator-Associated Pneumonia

BACKGROUND: Adjunctive aerosolized antibiotics (AAA) have been recommended in the setting of Gram-negative ventilator-associated pneumonia (VAP), but little is known about their influence on clinical outcomes. OBJECTIVE: To assess outcomes associated with AAA for the treatment of Pseudomonas aeruginosa (PA) and Acinetobacter baumannii (AB) VAP. METHODS: A retrospective, single-center cohort study at Barnes-Jewish Hospital in St Louis, Missouri. Consecutive subjects treated for bronchoalveolar lavage-confirmed PA or AB VAP between January 1, 2004 and December 31, 2009 were enrolled. Records of subjects treated with AAA were compared to those who did not receive AAAs (NAAA). RESULTS: Ninety-three patients were evaluated (NAAA n = 74, AAA n = 19, inhaled colistin n =9, inhaled tobramycin n =10). Patients receiving AAA were significantly more likely to be infected with multidrug-resistant bacteria (52.6% vs 14.9%, P < .001) and had greater Acute Physiology and Chronic Health Evaluation II scores (21.4 ± 5.7 vs 17.5 ± 5.3, P = .004) compared to patients receiving NAAA. NAAA subjects experienced a shorter time from VAP onset to appropriate intravenous antibiotic initiation (0.5 ± 0.9 d vs 2.6 ± 5.4 d, P = .038), but length of intravenous therapy was similar between groups (12.8 ± 8.5 d vs 17.8 ± 13.3 d, P = .16). The NAAA group demonstrated significantly shorter mechanical ventilation duration (18.9 ± 15.9 d vs 38.4 ± 32.4 days, P < .001), intensive care unit stay (37.5 ± 42.5 d vs 56.3 ± 31.3 d, P = .001), and hospital stay (39.0 ± 42.5 d vs 58.3 ± 33.4 d, P = .001). However, Kaplan-Meier curves for the probability of 30-day survival from VAP onset demonstrated that patients receiving AAA had statistically greater survival (P = .030 by the log rank test). CONCLUSIONS: Patients with PA and AB VAP may experience favorable survival when treated with AAA, despite greater severity of illness and a greater incidence of multidrug-resistant infection. Large randomized trials are needed to further explore this therapy.
Parallel Implementation of Smith-Waterman Algorithm using MPI, OpenMP and Hybrid Model

—Pairwise sequence alignment is often used to reveal similarities between sequences, locate patterns of conservation, study gene regulation, and infer evolutionary relationships [1]. Although the Smith–Waterman is the only algorithm guaranteed to find the optimal local alignment, it is also the slowest one as it costs O(mn) for computation & space. Also the volume of biological data is doubling about every six months so the total cost is O(kmn) where k is the size of the database [2, 3]. By using parallel hardware and software architecture accurate results can be achieved in reasonable time. In this paper we show a comparative study for parallelizing smith-waterman algorithm using different parallel models, pure MPI, pure OpenMP and hybrid MPI/OpenMP model. Based on the results it will be proved that hybrid programming which employ the coarse grain and fine grain parallelization, is more efficient compared with pure MPI and pure OpenMP.
A new graph-theoretic approach to clustering and segmentation

We develop a framework for the image segmentation problem based on a new graph-theoretic formulation of clustering. The approach is motivated by the analogies between the intuitive concept of a cluster and that of a dominant set of vertices, a notion that generalizes that of a maximal complete subgraph to edge-weighted graphs. We also establish a correspondence between dominant sets and the extrema of a quadratic form over the standard simplex, thereby allowing us the use of continuous optimization techniques such as replicator dynamics from evolutionary game theory. Such systems are attractive as they can be coded in a few lines of any high-level programming language, can easily be implemented in a parallel network of locally interacting units, and offer the advantage of biological plausibility. We present experimental results on real-world images which show the effectiveness of the proposed approach.
A Flexible Load-Balancing Traffic Grooming Algorithm in Service Overlay Network

To overcome the unbalanced flow distribution problem caused by private routing on service overlay network, network service providers usually use load balancing strategy, but traditional methods do not consider making the load balance adapt to the status of the network, neither consider that load balancing may damage performance of some application links. In order to solve the two problems, based on Wardrop equilibrium theory, the paper proposes a flexible load-balancing traffic grooming strategy, which aims to achieve system optimization. According to the principle of stochastic user equilibrium, a network traffic optimization control model is proposed. The path impedance calculation formula is given based on the Logit stochastic add-in term, in which the value of the equilibrium parameter determines the level and scope of load balancing. Finally, we designed the elastic traffic grooming algorithm ElaGo. The simulation results verified the effectiveness of the proposed algorithm.
Constructing High-Precision Geometric Models from Sensed Position Data

The construction of geometric scene models from sensed data is a fundamental task in image understanding. The creation of such models is essential in computer vision systems for applications ranging from reconnaissance to robot navigation. Automated model construction using visual techniques can also provide important support for systems in manufacturing and simulation. Vision-based geometric modeling has typically emphasized generality, with little explicit concern for the accuracy of the models produced. When high-precision is required, domain-specific representations and processing can provide significant advantages. We describe such a system for reverse engineering mechanical parts as part of maintenance and repair activities. Many of the key components of this system are also applicable to the generation of models for simulation and virtual environment applications.
Framework for Energy efficiency in Wireless Sensor Networks Using Outlier Detection Methodology

Wireless sensor networks is one of the most important technologies in this 21st century. In Wireless Sensor Networks (WSNs), resource management and energy efficiency are important issues in the context of node interactions. This is presenting about the energy consumption in WSN without compromising the reliability. A service could be monitoring environmental parameters such as temperature, light and moisture etc. This framework follows the adaptive clustering algorithm, that improves the reliability when head node gets any problem without losing data. a clustering algorithm was provided to group the sensors of a network into clusters of different sizes. The nearest sensor to the geographical center of a cluster is called a clusterhead which receives the data from the neighboring nodes. The sizes of the clusters in the network were determined based on an input to the algorithm that contained the initial number of required clusters of each size. That clusterhead send that data to the sink node. sink node is the source node which may act as a gateway node to the user. A large number of non-sink nodes collects data and send the collected data to these sinks. Significantly cuts down on energy consumption by ensuring that a large number of sensor nodes can go into a deep sleep mode for a major part of their life time. By making the nodes in sleep mode its saving the lot of energy which is consumed by the silent nodes. So it reduces up to 50%of the energy and without compromising the reliable.
Automated Marking System for Short Answer examination (AMS-SAE)

Short answers essay typed examination requires the students to write their answers in short sentences. Marking the short answers essay typed examination requires lecturers to compare the similarity of sentences from the answer scripts and marking scheme. Sentence similarity is defined as sentences that have similar meaning but they are different because of the words used or their construction structure. Automatic Marking System for Short Answers Examination (AMS-SAE) is a system that has been developed to grade students' answers based on the given marking scheme. Marks are given to the essays based on the representation of the Grammatical Relations (GRs) extracted from the sentences. The average point different between the marks computed by AMS-SAE and human are 0.049, 0.028 and 0.18. The results show that the scores are low and AMS-SAE could award similar marks as the human awarded.