Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome organization and molecular variability in Sweetpotato chlorotic fleck virus

The complete nucleotide sequence of the genomic RNA of a Ugandan isolate of Sweetpotato chlorotic fleck virus (SPCFV) was shown to be 9104 nt. The SPCFV RNA not only is very similar in genomic organisation to that of carlaviruses but also encodes proteins that showed strong homologies with those of carlaviruses. Open reading frame (ORF) 1 codes for a 238 kDa protein with characteristic motifs of replication-associated proteins. ORFs 2, 3 and 4 code for proteins of 27.5, 11.5, and 7.3 kDa, respectively, that form the multifunctional triple gene block proteins. ORF 5 encodes the capsid protein (CP) of 33 kDa and ORF 6 a 15-kDa protein with a nucleic acid binding zinc finger motif (NBP). Comparison with other carlaviruses showed 12-40% similarities. Based on CP sequences, the closest relatives of SPCFV among carlaviruses are Shallot latent virus (36.2%) and Kalanchoe latent virus (37.1%). However, the SPCFV genome (9.1 kb) differs from typical carlaviruses (7.4 8.5 kb) by being considerably larger as a result of a larger ORF 1 (238 vs. 200-223 kDa) and a long untranslated region between ORF 4 and 5 (213 vs. ca. 34 nt for Potato virus M). To obtain a better understanding of the molecular variability of the SPCFV genome, about 2000 nts of the 3' terminal genome part of a range of geographically diverse isolates were sequenced. Comparison of the deduced amino acid sequences revealed a considerable level of geographically associated diversity among SPCFV isolates. The CP and NBP amino acid sequence similarities ranged from 88 to 100 % and from 75 to 99%, respectively. In phylogenetic analysis of CP amino acid sequences, a major East African cluster with 92-99% intragroup identity and a non-East African cluster with 88-91% intragroup identity became evident.
Deep CNN Combined With Relevance Feedback for Trademark Image Retrieval

Abstract Trademark recognition and retrieval is a vital appliance component of content-based image retrieval (CBIR). Reduction in the semantic gap, attaining more accuracy, reduction in computation complexity, and hence in execution time, are the major challenges in designing and developing a trademark retrieval system. The direction of the proposed work takes into account these challenges by implementing trademark image retrieval through deep convolutional neural networks (DCNNs) integrated with a relevant feedback mechanism. The dataset features are optimized through particle swarm optimization (PSO), reducing the search space. These best/optimized features are given to the self-organizing map (SOM) for clustering at the preprocessing stage. The CNN model is trained on feature representations of relevant and irrelevant images, using the feedback information from the user bringing the marked relevant images closer to the query. Experimentation proved a significant performance when evaluated using FlickrLogos-27, FlickrLogos-32, and FlickrLogos-32 PLUS datasets, as illustrated in the performance results section.
On stabilized ®nite element methods for linear systems of convection±diusion-reaction equations

A stabilized ®nite element method for solving systems of convection±diusion-reaction equations is studied in this paper. The method is based on the subgrid scale approach and an algebraic approximation to the subscales. After presenting the formulation of the method, it is analyzed how it behaves under changes of variables, showing that it relies on the law of change of the matrix of stabilization parameters associated to the method. An expression for this matrix is proposed for the case of general coupled systems of equations that is an extension of the expression proposed for a one-dimensional (1D) model problem. Applications of the stabilization technique to the Stokes problem with convection and to the bending of Reissner±Mindlin plates are discussed next. The design of the matrix of stabilization parameters is based on the identi®cation of the stability de®ciencies of the standard Galerkin method applied to these two problems. Ó 2000 Elsevier Science S.A. All rights reserved. 1. Introduction The purpose of this paper is to study the application of a certain type of stabilized ®nite element methods to systems of convection±diusion-reaction equations of the form L U : o oxi AiU  ÿ o oxi  F in X; 1 U  0 on oX; 2 where X is the computational domain, U and F are vectors of nunk unknowns and Ai, K ij and S are nunk nunk matrices (i; j  1; . . . ; nsd). The usual summation convention is implied in (1), with indices running from 1 to the number of space dimensions nsd. We shall refer to the terms on the left-hand-side (LHS) of this equation as the convective, the diusive and the reactive term. The algebraic bilinear form associated to K ij, i; j  1; . ; nsd, is assumed to be positive-de®nite. Let W : H 1 0 X nunk . The weak form of the problem consists in ®nding U 2 W such that a U ;V ÿ l V  0 8V 2 W; 3 where the bilinear form a and the linear form l are de®ned as
Factor Analysis for Ranking Data

Suppose in a random sample of n individuals, each individual is asked to rank a set of k items according to a certain preference criterion. In other words, individual i provides a ranking of k items, ri = (ri1; : : : ; rik) , where rij is the rank of item j from individual i. Smaller ranks refer to the more preferred items. To model the ranking data, we assume that each ranking ri is generated according to the ordering of k latent utilities xi1; ; xik assigned by each individual. For example, if ri = (2; 3; 1) is recorded, we have xi2 < xi1 < xi3. Then we impose the following d-factor model on xi: xij = zi aj + bj + "ij (i = 1; : : : ; n; j = 1; : : : ; k(> d))
PREVALENCE OF STAPHYLOCOCCUS AUREUS AMONG GINGIVITIS IN PATIENT WITH ORTHODONTIC WIRES IN KUFA CITY / IRAQ

This study aimed to investigate the role of orthodontic wire on bacterial community in oral cavity as well as its effectiveness on Staphylococcus aureus. A total of 78 gingival swab samples have been collected from patient with orthodontic wires suffering from gingivitis and 71 samples were collected from healthy without orthodontic wire during four months from private dental clinics. The results of conventional isolation and identification of bacterial isolates as well as biochemical test showed that S. aureus was the commonest causative pathogens among acute gingivitis (46%) followed by Granulicatella adiacens (29.6%) where 36 isolates were isolated from acute and chronic gingivitis in comparison with 27 isolates from healthy. A mutation experiment was carried out to explain the role of orthodontic wires on S. aureus. The results revealed the same change has been obtained when using both of Nikletitanium (NiTi) and stainless steel wire on S. aureus after 24-96 hr from incubation. Antibiotic sensitivity pattern of both original and treated isolates with NiTi and stainless steel wires explained increased in antibiotic resistance of S. aureus to bacitracin, ceftazidim, ogmentin, and erythromycin while other antibiotic remain sensitive such as cefotaxim and amikacin.
Design of interactive learning media to pronunciation characters and words English for blind children

This paper aims the study of designing an English learning system for blind children. Instrument designed is interactive learning media so hopefully blind child will be easy to be interested and active to learn. The processing hardware used is Raspberry Pi (as its main brain). Learning system mode is made of two kinds, namely learning mode (text to speech method) and question mode (speech to text method). The result of this research is a model for learning letters recognition and English pronunciation tool. The design of this tool using Raspberry Pi 3, because the Raspberry Pi 3 is a computer system that is integrated with the supporting components required in voice recognition processing and text to voice conversion. The design of this model does not cost much, because it only uses a mini PC that is Raspberry Pi 3 as the main component. However, in previous research, interactive learning of braille for children using linguistics requires a lot of hardware and requires teachers in its use. the learning media is expected to help the blind child in learning the characters and English words and also expected this instrument can be used for use in the school blind.
, aeruginosa from Australia Genetic Context in Pseudomonas , and Its UniqueAIM-1 bla-Lactamase Gene , β of an Acquired Subgroup B 3 Metallo-Genetic and Biochemical Characterization

Published Ahead of Print 17 September 2012. 10.1128/AAC.05654-11. 2012, 56(12):6154. DOI: Antimicrob. Agents Chemother. Rachael Pratt, Henry Ryley and Timothy R. Walsh Dongeun Yong, Mark A. Toleman, Jan Bell, Brett Ritchie, aeruginosa from Australia Genetic Context in Pseudomonas , and Its Unique AIM-1 bla -Lactamase Gene, β of an Acquired Subgroup B3 MetalloGenetic and Biochemical Characterization
Validity and Reliability of Green Skills Instrument

Green Skills (GS) are the skills based on strong sustainability development from the aspects of technical, value knowledge and attitude that are needed by the workforce in developing economy and environment in the business, industry and society. The objective of this research was to validate the GS instrument. This research adopted the survey research method. Cluster random sampling and simple random sampling methods were utilised in selecting a total of 446 Secondary school students who enrolled the subject of Design all over Peninsular Malaysia. Structural Equation Modelling (SEM) analyses were used to determine validity and reliability in measurement model. Measurement model was fitted the data and was accepted base on suitability index (fit indices), that has been achieved namely CMIN χ2=595.204, with degrees of freedom (df) 132, CMIN/df=4.509 (≤5.0), incremental fit CFI & IFI (≤0.9), and absolute fit RMSEA=0.8(≤0.8). The instrument has been proven to be a good instrument and passed the psychometrics standards. The research findings showed there were a total of 10 elements must be present in the students. The research implicated that GS Model can be used as guidance in cultivating GS in the learning process. This GS Model is expected to cultivate a balanced environment from the aspects of attitude, knowledge and values that are needed in the students. This GS Model also can be used as the basis in developing curriculum as an added-value in training design. Furthermore, it can be used as a module in learning process that gives importance to environmental awareness among students
Simulation of NiMH Batteries via an Equivalent Circuit Model for Energy Storage Applications

Impedance measurement was conducted at the entire cell level for studying of the Ni-MH rechargeable batteries. An improved equivalent circuit model considering diffusion process is proposed for simulation of battery impedance data at different charge input levels. The cell capacity decay was diagnosed by analyzing the ohmic resistance, activation resistance, and mass transfer resistance of the Ni-MH cells with degraded capacity. The capacity deterioration of this type, Ni-MH cell, is considered in relation to the change of activation resistance of the nickel positive electrodes. Based on the report and surface analysis obtained from the energy dispersive X-ray spectroscopy, the composition formula of metal-hydride electrodes can be closely documented as the AB 5 type alloy and the “A” elements are recognized as lanthanum (La) and cerium (Ce). The capacity decay of the Ni-MH cell is potentially initiated due to starved electrolyte for the electrochemical reaction of active materials inside the Ni-MH battery, and the discharge product of Ni(OH) 2 at low state-of-charge level is anticipated to have more impeding effects on electrode kinetic process for higher power output and efficient energy delivery.
Interactive comment on “ Liquid marine cloud geometric thickness retrieved from OCO-2 ’ s oxygen A-band spectrometer ” by Mark Richardson

This manuscript presents a method for the joint retrieval of cloud optical thickness, top pressure and geometric thickness from passive hyperspectral shortwave IR measurements combined with lidar observations. Overall the paper is well written and the presented methodology appears sound. The retrieval of the cloud geometric thickness from O2 A-band measurements is an important novel element of this method, even though it must be acknowledged that the validation of cloud geometric thickness looks much less robust than that of the other parameters. In particular, I find it difficult to understand what is the additional added value of the retrieved cloud geometric thickness compared to a reasonably chosen prior. Below are my complete comments.
COLOR-TO-GRAY CONVERSION WITH PERCEPTUAL PRESERVATION AND DARK CHANNEL PRIOR

This paper aims to present a decolorization strategy based on perceptual consistency and dark channel prior. The proposed model consists of eﬀective ﬁdelity terms and a prior term. We use the (cid:96) 0 -norm to control the sparsity of the dark channel prior. To solve the non-convex minimization problem, we employ the split and penalty technique to simplify the minimization problem and then solve it by the carefully designed iteration scheme. Besides, we show the convergence of the algorithm using Kurdyka-(cid:32)Lojasiewicz property. The numerical evaluation in comparison with other state-of-the-art methods demonstrates the eﬀectiveness of the proposed method.
Supervised and unsupervised learning in processing myographic patterns

Synaptic connections in neocortex are assumed to be formed by a self-organizing process leading to emergence of the so-called self-organized maps (SOMs). Formation of SOMs is based on the unsupervised Hebbian learning rule, according to which the weight of a synaptic connection depends on the co-activation of pre- and postsynaptic neurons. On the other hand, a variety of human-machine interfaces employ supervised learning based on the correction of synaptic weights in proportion to the network error. But this learning rule has not been verified as biologically relevant. In our work, we study artificial neural networks (ANN) that classify hand gestures through electromyographic recordings (EMG). We use eight-channel electromyographic (EMG) signals acquired by a Thalmic labs Myo device as an input to a multilayer perceptron (MLP) and Kohonen’s SOM. We compare supervised (MLP) and unsupervised (SOM) learning in the task of EMG-classification. The median value of recognition fidelity (F-measure) for SOM-based recognition is F = 0.87 and for MLP classification F = 0.96. Also we reveal strong correlation between F-measures for classification EMG patterns of 37 subjects by MLP and SOM. For estimation of clustering quality of SOM we introduce two indexes: the intra-cluster index describing the cluster “compactness” and the inter-cluster index measuring the degree of cluster overlapping. There are strong correlations between F-measures for SOM classification and introduced indexes. Differences in the significance level of the correlations suggest that the classification with SOM is more negatively affected by overlapping clusters than their large size.
Numl - A Strongly Typed Language for Numerical Accuracy

It is well-known that numerical computations may sometimes lead to wrong results because of roundoff errors. We propose an ML-like type system (strong, implicit, polymorphic) for numerical computations in finite precision, in which the type of an expression carries information on its accuracy. We use dependent types and a type inference which, from the user point of view, acts like ML type inference. Basically, our type system accepts expressions for which it may ensure a certain accuracy on the result of the evaluation and it rejects expressions for which a minimal accuracy on the result of the evaluation cannot be inferred. The soundness of the type system is ensured by a subject reduction theorem and we show that our type system is able to type implementations of usual simple numerical algorithms.
In vitro evaluation of antibacterial activity of bioactive compound of Bixa orellana L . ( Seed ) against five important species of bacteria

In vitro evaluation of antibacterial activity of bioactive compound of Bixa orellana L. seed were evaluated against five pathogens viz., Escherichia coli, Enterobacter aerogenes, Proteus vulgaris, Klebsiella pneumonia and Bacillus cereus tested at 100 to 1000 ppm concentration. Maximum inhibition was observed in E. coli, and recorded 39.0mm inhibition at 1000ppm concentration, followed by P. vulgaris and recorded 36.0mm at 1000ppm concentration. E. aerogenes and B. cereus recorded 31.0mm and 26.0mm inhibition at 1000ppm concentration and least activity was observed in K. pneumonia and recorded 23.0mm at 1000ppm concentration,. Compared to standard antibiotic gentamycein at a recommended concentration of 25mg.
Aerodynamic Shape Optimization of a Vertical-AxisWind Turbine Using Differential Evolution

The purpose of this study is to introduce and demonstrate a fully automated process for optimizing the airfoil cross-section of a vertical-axis wind turbine (VAWT). The objective is to maximize the torque while enforcing typical wind turbine design constraints such as tip speed ratio, solidity, and blade profile. By fixing the tip speed ratio of the wind turbine, there exists an airfoil crosssection and solidity for which the torque can be maximized, requiring the development of an iterative design system. The design system required to maximize torque incorporates rapid geometry generation and automated hybrid mesh generation tools with viscous, unsteady computational fluid dynamics (CFD) simulation software. The flexibility and automation of the modular design and simulation system allows for it to easily be coupled with a parallel differential evolution algorithm used to obtain an optimized blade design that maximizes the efficiency of the wind turbine.
Ho, Johnathan and Pelzel, Christin and Begitt, Andreas and Mee, Maureen and Elsheikha, Hany M. and Scott, David J. and Vinkemeier, Uwe (2016) STAT2 is a pervasive cytokine regulator due to its inhibition of STAT1 in multiple signaling

STAT2 is the quintessential transcription factor for type 1 interferons (IFNs), where it functions as a heterodimer with STAT1. However, the human and murine STAT2-deficient phenotypes suggest important additional and currently unidentified type 1 IFN-independent activities. Here, we show that STAT2 constitutively bound to STAT1, but not STAT3, via a conserved interface. While this interaction was irrelevant for type 1 interferon signaling and STAT1 activation, it precluded the nuclear translocation specifically of STAT1 in response to IFN-γ, interleukin-6 (IL-6), and IL-27. This is explained by the dimerization between activated STAT1 and unphosphorylated STAT2, whereby the semiphosphorylated dimers adopted a conformation incapable of importin-α binding. This, in turn, substantially attenuated cardinal IFN-γ responses, including MHC expression, senescence, and antiparasitic immunity, and shifted the transcriptional output of IL-27 from STAT1 to STAT3. Our results uncover STAT2 as a pervasive cytokine regulator due to its inhibition of STAT1 in multiple signaling pathways and provide an understanding of the type 1 interferon-independent activities of this protein.
International trade with social comparisons

As consumers in countries around the world become increasingly aware of and sensitive to the products that their foreign counterparts consume, a natural question is what predictions do classic trade frameworks hold when incorporating social comparison-based preferences? We analyze this question in a general equilibrium framework for a two-country, two-good world, in which the gap between domestic and foreign consumption of a product can enter into the representative consumer's utility function. We consider nine exhaustive social comparison scenarios, which differ based upon the combination and origin of products that consumers of each country hold a social comparison over. We show that Home Comparison preference (social comparison over the home-produced good) unilaterally brings consumption and welfare bene fits to the home country, and global welfare is enhanced when both countries maintain such preferences. On the other hand, Foreign Envy (social comparison over the foreign-produced good) is disadvantageous to the home country, contributing negatively to welfare when the other country either prefers its own produced good or has no particular social preference. Mutual Foreign Envy however, tends to contribute positively to global welfare. Our analysis helps to explain the social welfare incentives of policy-makers in promoting cross-country comparisons of domestic goods among their own consumers, while advocating domestically-produced goods as status symbols abroad.
Phytomedicine In Vitro Evaluation of Free Radical Scavenging and Antioxidant Activities of Averrhoa bilimbi Fruit Extracts

The phytochemicals are biologically active compounds and have therapeutic potential for free radical associated disorders. Free radicals are implicated in the development of various chronic and degenerative diseases including diabetes mellitus, coronary heart disease, arthritis, cancer, ageing etc. The present study evaluates the antioxidant potential of different solvent fractions of Averrhoa bilimbi Linn. (Oxalidaceae) fruits. Antioxidant activity was assessed by various in vitro methods such as 1, 1-Diphenyl-2-Picrylhydrazyl (DPPH) radical scavenging assay, superoxide radical scavenging assay, nitric oxide radical scavenging assay, total reducing power and total antioxidant activity. Total phenolic and flavonoid contents of different solvent fractions (petroleum ether, ethyl acetate, butanol and water) were also determined and expressed in gallic acid and quercetin equivalents respectively. The results of the study show that the ethyl acetate fraction (ABE) of the lyophilized aqueous extract of Averrhoa bilimbi fruits has superior antioxidant properties than the other fractions. IC50values of the ethyl acetate fraction for superoxide radical scavenging and nitric oxide radical scavenging activities were 72 and 61.5 μg/ml, respectively. Total phenolic content (31.26 ± 1.16 mg%) and flavonoid content (6.15 ± 0.23 mg%) of ABE was significantly higher than other fractions. The results of the present study indicate that Averrhoa bilimbi fruits are a rich source of natural antioxidants and might be utilized as a functional food/nutraceutical.