Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeting multiple targets in Pseudomonas aeruginosa PAO1 using flux balance analysis of a reconstructed genome-scale metabolic network

Constraint-based flux balance analysis (FBA) is a powerful tool for predicting target genes that can be engineered by analyzing the redistribution of metabolic fluxes on specific gene modifications. Specifically, the effects of metabolic gene deletions on flux distribution can be examined by forcing the fluxes of different reactions catalyzed by the corresponding gene product to zero. However, the target enzyme needs to be essential for survival of the organism to ensure that efficient chemical inhibition results in cell stasis or death. Here, we investigate the essentiality of enzymes in iMO1056 metabolic model of nosocomial pathogen Pseudomonas aeruginosa by performing in silico enzyme deletions using FBA. We identified 116/113 essential enzymes in rich medium in P. aeruginosa. These were then compared with human metabolic model to identify nonhomologous enzymes that could be possible drug targets. Here, we present a refined list of 41 novel potential targets for P. aeruginosa. These targets were then matched with the enzymes belonging to 97 correlated clusters through which we propose the concept of “one target per cluster. ” Our approach relates to the “single drug multiple target (SDMT)” concept and has potential in efficient drug target discovery.
Enhancement of Engine Performance and Reduction of Emissions by changing Piston Geometry

Internal combustion engines have been a relatively inexpensive and reliable source of power for applications ranging from domestic use to large scale industrial and transportation applications for most of the twentieth century. DI Diesel engines, having the evident benefit of a higher thermal efficiency than all other engines, have served for both lightduty and heavy-duty vehicles. In DI diesel engines, swirl can increase the rate of fuel-air mixing. Swirl interaction with compression induced squish flow increases turbulence levels in the combustion bowl, promoting mixing. It is evident that the effect of geometry has a negligible effect on the airflow during the intake stroke and early part of the compression stroke. But when the piston moves towards Top Dead Centre (TDC), the bowl geometry has a significant effect on air flow thereby resulting in better atomization, better mixing and better combustion. In CI engine piston shapes on crown is flat and concave combustion chamber, with this geometry we have been running the engine. But here air fuel ratio mixture cannot mix properly. To avoid this we make piston geometry changes. The main object of this project is to investigate the performance technique to enhance the air swirl to achieve betterment in engine performance and emission in a direct injection (DI) single cylinder diesel engine. In order to achieve the swirl intensities in the cylinder, changes on the piston crown has been selected. To increase the swirl, series of experiments were conducted like 2 toroidal grooves piston, 4 toroidal grooves piston, 6 toroidal grooves piston on piston crown and compare the results with normal piston values
Using thread-level speculation to simplify manual parallelization

In this paper, we provide examples of how thread-level speculation(TLS) simplifies manual parallelization and enhances itsperformance. A number of techniques for manual parallelizationusing TLS are presented and results are provided that indicate theperformance contribution of each technique on seven SPEC CPU2000benchmark applications. We also provide indications of theprogramming effort required to parallelize each benchmark. TLSparallelization yielded a 110% speedup on our four floating pointapplications and a 70% speedup on our three integer applications,while requiring only approximately 80 programmer hours and 150lines of non-template code per application. These results supportthe idea that manual parallelization using TLS is an efficient wayto extract fine-grain thread-level parallelism.
Defects localisation tool for wireless sensors network conception

The design, manufacture and deployment of embedded systems become increasingly complex and multidisciplinary process. Before the steps of manufacturing and deployment, and during the conception phase, we should have a tool to localize defects and to choose which modifications we can do to eliminate them. This procedure could be done by a simulation and validation phase. Given the increasing complexity of systems such as telecommunications systems, control systems and others, a specific simulation and validation process must take place. This simulation ideally made in a single development environment, should cover different areas and all components of the system. In this paper, we briefly describe the behavioral models of the elements of a large scale wireless sensors network (WSN) used to create our simulator, focusing specifically on the model of the transmission channel, and how we can detect the defects from the behavioral simulator. In side to legacy network simulator, for the testing and modeling of communication protocols, this simulator shouldn't omit WSN specific aspect, in accuracy it covers the modeling of node platforms, protocols, and real world phenomena.
Atmospheric vibration tests of an HTGR thermal barrier cover plate

Results are presented of a development program to experimentally determine the dynamic response parameters of a High-Temperature Gas-Cooled Reactor (HTGR) single cover plate thermal barrier assembly, and to improve the analytical techniques for predicting cover plate response to the HTGR vibration environment. Observations of changes in thermal barrier insulation blanket surface appearance as a result of cover plate vibration are also presented, as are recommendations for further work on cover plate vibration and on insulation blanket characteristics.
Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information

MOTIVATION There has been great expectation that the knowledge of an individual's genotype will provide a basis for assessing susceptibility to diseases and designing individualized therapy. Non-synonymous single nucleotide polymorphisms (nsSNPs) that lead to an amino acid change in the protein product are of particular interest because they account for nearly half of the known genetic variations related to human inherited diseases. To facilitate the identification of disease-associated nsSNPs from a large number of neutral nsSNPs, it is important to develop computational tools to predict the phenotypic effects of nsSNPs. RESULTS We prepared a training set based on the variant phenotypic annotation of the Swiss-Prot database and focused our analysis on nsSNPs having homologous 3D structures. Structural environment parameters derived from the 3D homologous structure as well as evolutionary information derived from the multiple sequence alignment were used as predictors. Two machine learning methods, support vector machine and random forest, were trained and evaluated. We compared the performance of our method with that of the SIFT algorithm, which is one of the best predictive methods to date. An unbiased evaluation study shows that for nsSNPs with sufficient evolutionary information (with not <10 homologous sequences), the performance of our method is comparable with the SIFT algorithm, while for nsSNPs with insufficient evolutionary information (<10 homologous sequences), our method outperforms the SIFT algorithm significantly. These findings indicate that incorporating structural information is critical to achieving good prediction accuracy when sufficient evolutionary information is not available. AVAILABILITY The codes and curated dataset are available at http://compbio.utmem. edu/snp/dataset/
Typing streams in the Λ μ-calculus : extended abstract

Λμ-calculus [11] has been built as an untyped extension of the λμ-calculus [10] in order to recover Böhm theorem which was known to fail in λμ-calculus since a result by David & Py [2]. An essential computational feature of Λμ-calculus for separation to hold is the unrestricted use of abstractions over continuation variables that provides the calculus with a construction of streams. In [11], Λμ-calculus was studied as a purely untyped calculus. Moreover, when one types Λμ-terms using standard λμ-calculus type system, the stream mechanism is desactivated because of typing constraints. This is deeply related with the failure of separation property in λμ-calculus and with the fact that λμ-calculus was rst designed as a typed calculus for classical logic. In this paper, we introduce a type system, ΛS , that unveils the stream mechanism at work in Λμ-calculus in the typed setting. We discuss some of its properties and argue it is a good candidate to study a typed separation result [5] for classical λ-calculi.
POPULATION STRUCTURE OF GRENADIER FISH COELORINCHUS CAELORHINCUS IN DEEP WATERS OF THE COLOMBIAN CARIBBEAN COAST

The objective of the study is to describe the patterns of spatial distribution and size structure of Coelorinchus caelorhincus in deep-sea waters of Colombian Caribbean. The samples were collected with trawling in depths between 200 and 550 m. Statistically significant differences in the sizes of the sexes were found, indicating sexual dimorphism. The length structure by depth strata showed a size increase with depth for both females and males. The length at sexual maturity in females was 17.238 cm TL. The spatial distribution indicates that in the northeastern area the higher aggregations were off the coast of the Magdalena River, off Santa Marta and Riohacha cities. In the southwestern area the higher aggregations were towards the northern part of the Urabá Gulf.
Training-Free Synthesized Face Sketch Recognition Using Image Quality Assessment Metrics

Face sketch synthesis has wide applications ranging from digital entertainments to law enforcements. Objective image quality assessment scores and face recognition accuracy are two mainly used tools to evaluate the synthesis performance. In this paper, we proposed a synthesized face sketch recognition framework based on full-reference image quality assessment metrics. Synthesized sketches generated from four state-of-the-art methods are utilized to test the performance of the proposed recognition framework. For the image quality assessment metrics, we employed the classical structured similarity index metric and other three prevalent metrics: visual information fidelity, feature similarity index metric and gradient magnitude similarity deviation. Extensive experiments compared with baseline methods illustrate the effectiveness of the proposed synthesized face sketch recognition framework. Data and implementation code in this paper are available online at www.ihitworld. com/WNN/IQA_Sketch. zip.
The Pneumococcal Polysaccharide Capsule and Pneumolysin Differentially Affect CXCL8 and IL-6 Release from Cells of the Upper and Lower Respiratory Tract

The polysaccharide capsule and pneumolysin toxin are major virulence factors of the human bacterial pathogen Streptococcus pneumoniae. Colonization of the nasopharynx is asymptomatic but invasion of the lungs can result in invasive pneumonia. Here we show that the capsule suppresses the release of the pro-inflammatory cytokines CXCL8 (IL-8) and IL-6 from the human pharyngeal epithelial cell line Detroit 562. Release of both cytokines was much less from human bronchial epithelial cells (iHBEC) but levels were also affected by capsule. Pneumolysin stimulates CXCL8 release from both cell lines. Suppression of CXCL8 homologue (CXCL2/MIP-2) release by the capsule was also observed in vivo during intranasal colonization of mice but was only discernable in the absence of pneumolysin. When pneumococci were administered intranasally to mice in a model of long term, stable nasopharyngeal carriage, encapsulated S. pneumoniae remained in the nasopharynx whereas the nonencapsulated pneumococci disseminated into the lungs. Pneumococcal capsule plays a role not only in protection from phagocytosis but also in modulation of the pro-inflammatory immune response in the respiratory tract.
Principle of nongravitating vacuum energy and some of its consequences.

For Einstein's General Relativity (GR) or the alternatives suggested up to date$ the vacuum energy gravitates. We present a model where a new measure is introduced for integration of the total action in the D-dimensional space-time. This measure is built from D scalar fields $\varphi_{a}$. As a consequence of such a choice of the measure, the matter lagrangian $L_{m}$ can be changed by adding a constant while no gravitational effects, like a cosmological term, are induced. Such Non-Gravitating Vacuum Energy (NGVE) theory has an infinite dimensional symmetry group which contains volume-preserving diffeomorphisms in the internal space of scalar fields $\varphi_{a}$. Other symmetries contained in this symmetry group, suggest a deep connection of this theory with theories of extended objects. In general {\em the theory is different from GR} although for certain choices of $L_{m}$, which are related to the existence of an additional symmetry, solutions of GR are solutions of the model. This is achieved in four dimensions if $L_{m}$ is due to fundamental bosonic and fermionic strings. Other types of matter where this feature of the theory is realized, are for example: scalars without potential or subjected to nonlinear constraints, massless fermions and point particles. The point particle plays a special role, since it is a good phenomenological description of matter at large distances. de Sitter space is realized in an unconventional way, where the de Sitter metric holds, but such de Sitter space is supported by the existence of a variable scalar field which in practice destroys the maximal symmetry. The only space - time where maximal symmetry is not broken, in a dynamical sense, is Minkowski space. The theory has non trivial dynamics in 1+1 dimensions, unlike GR.
A transformation based algorithm for reversible logic synthesis

A digital combinational logic circuit is reversible if it maps each input pattern to a unique output pattern. Such circuits are of interest in quantum computing, optical computing, nanotechnology and low-power CMOS design. Synthesis approaches are not well developed for reversible circuits even for small numbers of inputs and outputs. In this paper, a transformation based algorithm for the synthesis of such a reversible circuit in terms of n /spl times/ n Toffoli gates is presented. Initially, a circuit is constructed by a single pass through the specification with minimal look-ahead and no back-tracking. Reduction rules are then applied by simple template matching. The method produces very good results for larger problems.
MMPRO: A Methodology Based on ISO/IEC 15939 to Draw Up Data Quality Measurement Processes

Nowadays, data plays a key role in organizations, and management of its quality is becoming an essential activity. As part of such required management, organizations need to draw up processes for measuring the data quality (DQ) levels of their organizational units, taking into account the particularities of different scenarios, available resources, and characteristics of the data used in them. Given that there are not many works in the literature related to this objective, this paper proposes a methodology -abbreviated MMPROto develop processes for measuring DQ. MMPRO is based on ISO/IEC 15939. Despite being a standard of quality software, we believe it can be successfully applied in this context because of the similarities between software and data. The proposed methodology consists of four activities: (1) Establish and sustain the DQ measurement commitment, (2) Plan the DQ Measurement Process, (3) Perform the DQ Measurement Process, and (4) Evaluate the DQ Measurement Process. These four activities are divided into tasks. For each task, input and output products are listed, as well as a set of useful techniques and tools, many of them borrowed from the Software Engineering field.
Active stator winding thermal protection for AC motors

AC motors are the main workhorses in process industries. Their malfunction may not only lead to repair or replacement of the motor, but also cause significant financial losses due to unexpected process downtime. Reliable thermal protection of ac motors is crucial for reducing the motor failure rate and prolonging a motor's lifetime. In this paper, conventional thermal protection devices and state-of-the-art thermal protection techniques are reviewed with their advantages and limitations discussed. Since 2001, the research team at the author's company and at the Georgia Institute of Technology has been cooperatively developing a series of active motor thermal protection methods, as a low-cost alternative approach to the traditional passive and sensor-based methods. These active thermal protection methods monitor the average stator temperature via stator resistance estimation based on the dc equivalent model of ac motors, using only motor stator voltage and current measurements. In this paper, an overview of the active thermal protection techniques for line-started, soft-starter-connected and inverter-fed ac motors is presented, with their advantages and drawbacks discussed. The active thermal protection techniques are capable of providing accurate, and non-invasive thermal protection of ac motors.
Integration Versus Segregation in Functional Brain Networks

We propose a new methodology to evaluate the balance between segregation and integration in functional brain networks by using singular value decomposition techniques. By means of magnetoencephalography, we obtain the brain activity of a control group of 19 individuals during a memory task. Next, we project the node-to-node correlations into a complex network that is analyzed from the perspective of its modular structure encoded in the contribution matrix. In this way, we are able to study the role that nodes play I/O its community and to identify connector and local hubs. At the mesoscale level, the analysis of the contribution matrix allows us to measure the degree of overlapping between communities and quantify how far the functional networks are from the configuration that better balances the integrated and segregated activity.
A critical appraisal of the evidence for using cardiotocography plus ECG ST interval analysis for fetal surveillance in labor. Part II: the meta-analyses

We appraised the methodology, execution and quality of the five published meta‐analyses that are based on the five randomized controlled trials which compared cardiotocography (CTG)+ST analysis to cardiotocography. The meta‐analyses contained errors, either created de novo in handling of original data or from a failure to recognize essential differences among the randomized controlled trials, particularly in their inclusion criteria and outcome parameters. No meta‐analysis contained complete and relevant data from all five randomized controlled trials. We believe that one randomized controlled trial excluded in two of the meta‐analyses should have been included, whereas one randomized controlled trial that was included in all meta‐analyses, should have been excluded. After correction of the uncovered errors and exclusion of the randomized controlled trial that we deemed inappropriate, our new meta‐analysis showed that CTG+ST monitoring significantly reduces the fetal scalp blood sampling usage (risk ratio 0.64; 95% confidence interval 0.47–0.88), total operative delivery rate (0.93; 0.88–0.99) and metabolic acidosis rate (0.61; 0.41–0.91).
Optimization of Patient Selection for Gefitinib in Non–Small Cell Lung Cancer by Combined Analysis of Epidermal Growth Factor Receptor Mutation, K-ras Mutation, and Akt Phosphorylation

Purpose: Mutations in epidermal growth factor receptor (EGFR) are strongly predictive of gefitinib efficacy in non–small-cell lung cancer. However, the presence of EGFR mutant nonresponses and nonmutant responses points out the need for more comprehensive analysis. Patients and Methods: For 69 non–small-cell lung cancer patients treated with gefitinib, we have extended our analysis to EGFR gene copy number by fluorescence in situ hybridization, mutations in K-ras, HER2, and exon 20 of EGFR by direct sequencing, and phosphatase and tensin homologue expression by immunohistochemistry, in addition to EGFR exons 18, 19, and 21, and phosphorylations of Akt and extracellular signal–regulated kinase reported previously. Results: EGFR mutation and high gene copy number were associated with better objective response in univariate analysis. However, only gefitinib-sensitive EGFR mutation was independently predictive of both response (P = 0.011) and survival (P = 0.002) in multivariate analysis. No patients with K-ras mutation, including two EGFR mutants, showed response. In EGFR nonmutants, patients with either K-ras mutation or p-Akt overexpression exhibited poor response and time-to-progression whereas patients with high gene copy number tended to have better outcomes in univariate analysis. In multivariate analysis of time-to-progression in EGFR nonmutants, K-ras mutation or p-Akt overexpression was associated with shorter time-to-progression (P = 0.017). No patient with HER2 mutation showed response to gefitinib. Reduced phosphatase and tensin homologue expression was not associated with gefitinib sensitivity. Conclusion: Gefitinib-sensitive EGFR mutation is the single most important predictor of gefitinib sensitivity. In addition to EGFR mutation, K-ras mutation and Akt phosphorylation aid in better prediction of gefitinib responsiveness in non–small-cell lung cancer.
Ablation of BRaf Impairs Neuronal Differentiation in the Postnatal Hippocampus and Cerebellum

This study focuses on the role of the kinase BRaf in postnatal brain development. Mice expressing truncated, non-functional BRaf in neural stem cell-derived brain tissue demonstrate alterations in the cerebellum, with decreased sizes and fuzzy borders of the glomeruli in the granule cell layer. In addition we observed reduced numbers and misplaced ectopic Purkinje cells that showed an altered structure of their dendritic arborizations in the hippocampus, while the overall cornus ammonis architecture appeared to be unchanged. In male mice lacking BRaf in the hippocampus the size of the granule cell layer was normal at postnatal day 12 (P12) but diminished at P21, as compared to control littermates. This defect was caused by a reduced ability of dentate gyrus progenitor cells to differentiate into NeuN positive granule cell neurons. In vitro cell culture of P0/P1 hippocampal cells revealed that BRaf deficient cells were impaired in their ability to form microtubule-associated protein 2 positive neurons. Together with the alterations in behaviour, such as autoaggression and loss of balance fitness, these observations indicate that in the absence of BRaf all neuronal cellular structures develop, but neuronal circuits in the cerebellum and hippocampus are partially disturbed besides impaired neuronal generation in both structures.