Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Gamma Differential Evolution Approach for Multiobjective Transformer Design Optimization

The differential evolution (DE) algorithm is a simple but powerful population-based stochastic search technique for solving global optimization problems. DE consists of three main operations: mutation, crossover and selection. The advantages of DE are simple structure, ease of use, speed and robustness. However, to achieve optimal performance with DE, time consuming parameter tuning is essential as its performance is sensitive to the choice of the mutation and crossover values. In this paper, a novel DE algorithm (NDE) based on truncated gamma probability distribution function is proposed for solving multiobjective optimization problems as the design of transformers. Simulations of transformer design optimization (TDO) demonstrate the effectiveness of the proposed optimization algorithm. The simulation results show that, compared with other multiobjective DE algorithm, the proposed NDE is able to find better spread of solutions with better convergence to the Pareto front and preserve the diversity of Pareto solutions more efficiently.
Single Molecule Imaging Deciphers the Relation between Mobility and Signaling of a Prototypical G Protein-coupled Receptor in Living Cells*

Background: The mobility of G protein-coupled receptors in the plasma membrane is of central importance to regulate transmembrane signaling. Results: In live cells, individual receptors show a broad mobility distribution with typical patterns for different phases of cellular signaling. Conclusion: Heterogeneity of receptor mobility is critical in regulation of receptor activity. Significance: These findings add further insights to the plasticity of receptor signaling. Lateral diffusion enables efficient interactions between membrane proteins, leading to signal transmission across the plasma membrane. An open question is how the spatiotemporal distribution of cell surface receptors influences the transmembrane signaling network. Here we addressed this issue by studying the mobility of a prototypical G protein-coupled receptor, the neurokinin-1 receptor, during its different phases of cellular signaling. Attaching a single quantum dot to individual neurokinin-1 receptors enabled us to follow with high spatial and temporal resolution over long time regimes the fate of individual receptors at the plasma membrane. Single receptor trajectories revealed a very heterogeneous mobility distribution pattern with diffusion constants ranging from 0.0005 to 0.1 μm2/s comprising receptors freely diffusing and others confined in 100–600-nm-sized membrane domains as well as immobile receptors. A two-dimensional representation of mobility and confinement resolved two major, broadly distributed receptor populations, one showing high mobility and low lateral restriction and the other showing low mobility and high restriction. We found that about 40% of the receptors in the basal state are already confined in membrane domains and are associated with clathrin. After stimulation with an agonist, an additional 30% of receptors became further confined. Using inhibitors of clathrin-mediated endocytosis, we found that the fraction of confined receptors at the basal state depends on the quantity of membrane-associated clathrin and is correlated to a significant decrease of the canonical pathway activity of the receptors. This shows that the high plasticity of receptor mobility is of central importance for receptor homeostasis and fine regulation of receptor activity.
Arabic text classification using linear discriminant analysis

The linear discriminant analysis (LDA) is a dimensionality reduction technique that is widely used in pattern recognition applications. The LDA aims at generating effective feature vectors by reducing the dimensions of the original data (e.g. bag-of-words textual representation) into a lower dimensional space. Hence, the LDA is a convenient method for text classification that is known by huge dimensional feature vectors. In this paper, we empirically investigated two LDA based methods for Arabic text classification. The first method is based on computing the generalized eigenvectors of the ratio (between-class to within-class) scatters, the second method includes linear classification functions that assume equal population covariance matrices (i.e. pooled sample covariance matrix). We used a textual data collection that contains 1,750 documents belong to five categories. The testing set contains 250 documents belong to five categories (50 documents for each category). The experimental results show that the linear classification functions method outperforms the eigenvalue decomposition method. We emphasize that the goal of this work is to demonstrate how to employ the LDA algorithm in text classification rather than comparing the performance with other well-known text classification algorithms.
Dominant Susceptibility Effect on the Murine Corneal Response to Pseudomonas aeruginosa

Abstract Natural host resistance to Pseudomonas aeruginosa corneal infection is regulated by two complementing dominant genes PsCR1 and PsCR2 (RS Berk, MA Leon, LD Hazlett. Infect Immun 26:1221-1223, 1979). In this study we have demonstrated a third dominant gene, which determines susceptibility to P. aeruginosa-induced eye damage. This gene was designated as PsCS. The F1 progeny from matings between the resistant DBA/2J strain and the susceptible strain C57BL/6J and C3H/HeJ displayed the susceptibility phenotype. Backcross and F2 studies using the C3H/HeJ and DBA/2J strains suggested the presence of two linked PsCS loci.
Combining dual tessellation and temporal opportunities for spectrum reuse in cellular systems

Cellular network operators usually have to maintain networks of different generations (2G, 3G, 4G, .) simultaneously. The progressive upgrade of users' terminals makes the spectrum of the legacy networks become gradually underused. An operator can enable cognitive radio techniques at its newest generation terminals to reuse the spectrum of its own legacy networks. We propose an hybrid access scheme for cellular networks combining secondary access over temporal and spatial opportunities. We show that, when considering a cell structure with frequency reuse, the spatial opportunities are characterized by a dual tessellation. Our results show that a randomized access strategy maximizes the capacity of the secondary network.
An improved active shape model method for facial landmarking based on relative position feature

Active Shape Model (ASM) is a most effective method of facial landmarking. It employs two models, profile model and shape model, to match the position of facial landmark. In this paper, we introduce a new model based on relative position feature (RPF) in local region to improve ASM. We found the fact that landmarks with larger matching error have more shape matching displacement. So, in our method, RPF model is used to adjust the position of landmarks with more shape matching displacement in every matching iteration. STASM (Stacked ASM) is practical standard of ASM and is proved to be the best method of locating face landmarks. Our experiments on STASM show significant performance improving, especially on databases in which faces are partially blocked by glasses or artificial black square.
The Salmonella enterica Serovar Typhimurium-Encoded Type III Secretion Systems Can Translocate Chlamydia trachomatis Proteins into the Cytosol of Host Cells

ABSTRACT Chlamydia trachomatis is an obligate, intracellular pathogen that is a major cause of preventable blindness and infertility worldwide. Although the published genome sequence suggests that C. trachomatis encodes a type III secretion system, the lack of genetic tools for studying Chlamydia has hindered the examination of this potentially important class of virulence genes. We have developed a technique to identify Chlamydia proteins that can be translocated into the host cell cytoplasm by a type III secretion system. We have selected several Chlamydia proteins and tagged them with a multiple peptide motif element called F8M4. Epitopes contained in the F8M4 tag allow us to use tools corresponding to different arms of the adaptive immune system to detect the expression and translocation of these proteins by Salmonella enterica serovar Typhimurium. In particular, CD8+-T-cell reactivity can be used to detect the translocation of F8M4-tagged proteins into the cytoplasm of host cells. We have found that CD8+-T-cell activity assays are sensitive enough to detect translocation of even a small amount of F8M4-tagged protein. We have used CD8+-T-cell activity to show that CopN, a Chlamydia protein previously shown to be translocated by Yersinia type III secretion, can be translocated by the Salmonella pathogenicity island 1 (SPI-1) type III secretion system. Additionally, we demonstrate that CopD and Pkn5, two Chlamydia proteins hypothesized to be substrates of a type III secretion system, are translocated via the SPI-2 type III secretion system of serovar Typhimurium. The epitope tag system described here can be used more generally to examine the expression and subcellular compartmentalization of bacterial proteins deployed during the interaction of pathogens with mammalian cells.
Glacial refugia of limber pine (Pinus flexilis James) inferred from the population structure of mitochondrial DNA

To make inferences about the glacial refugia that harboured the limber pine, Pinus flexilis James, we examined the range‐wide population structure of mitochondrial DNA (mtDNA) with eight size variants in the second intron of nad1. The data consisted of haplotypes from 704 trees collected from 40 localities. The value of FST for these populations was 0.80, which is a much larger value than has been reported for allozymes and chloroplast DNA (cpDNA) in limber pine, and it suggests that the number of seeds moving among localities per generation is ≈ 0.12. Gene flow of this magnitude would allow mutation and subsequent genetic drift to have a substantial impact on the population structure of mtDNA. The majority of the mtDNA haplotypes are restricted to minor portions of the geographical range. The data are consistent with mtDNA differentiation in seven glacial refugia, followed by dispersal out of those refugia.
Synthesis and Characterization of Electropolymerized Nanostructured Aminophenylporphyrin Films

Porphyrins substituted at meso positions with aminophenyl groups undergo oxidative electropolymerization in a process analogous to the formation of polyaniline. Porphyrins that successfully generate polymer films on the electrode include those tetrasubstituted with four p-aminophenyl groups, trisubstituted, or trans-disubstituted, but not cis-disubstituted or monosubstituted. The polymerization process is monitored independently by cyclic voltammetry, absorption spectroscopy, and an electrochemical quartz crystal microbalance. The mechanism is considered analogous to aniline polymerization, except that attack of electrophilic nitrogens must occur at ortho positions of another aminophenyl group. Reflectance FT-IR and resonance Raman spectroscopy detect the presence of diphenylamine, dihydrophenazine, and phenazine linkages in the porphyrin polymer film from tetra(4-aminophenyl)porphyrin (TAPP). TAPP polymerized in dichloromethane (DCM) with added pyridine gradually passivates; i.e., electronic conductivity.
Rf coupling analysis via wire penetrating into an aperture

A metallic enclosure is used to provide effective radio frequency (RF) shielding for electronic circuits. However presence of apertures and wire penetrations in the enclosure degrades the Shielding effectiveness. The study of external electromagnetic coupling vi a wire penetration to elements inside a shielding enclosure have been performed in this paper. Two cases of coupling to a wire segment and a PCB present within the box have been considered. For external fields a plane wave and electromagnetic pulse (EMP) are used. The Computational Electromagnetic modelling is done using a software package.
Autophagy and the Effects of Its Inhibition on Varicella-Zoster Virus Glycoprotein Biosynthesis and Infectivity

ABSTRACT Autophagy and the effects of its inhibition or induction were investigated during the entire infectious cycle of varicella-zoster virus (VZV), a human herpesvirus. As a baseline, we first enumerated the number of autophagosomes per cell after VZV infection compared with the number after induction of autophagy following serum starvation or treatment with tunicamycin or trehalose. Punctum induction by VZV was similar in degree to punctum induction by trehalose in uninfected cells. Treatment of infected cells with the autophagy inhibitor 3-methyladenine (3-MA) markedly reduced the viral titer, as determined by assays measuring both cell-free virus and infectious foci (P < 0.0001). We next examined a virion-enriched band purified by density gradient sedimentation and observed that treatment with 3-MA decreased the amount of VZV gE, while treatment with trehalose increased the amount of gE in the same band. Because VZV gE is the most abundant glycoprotein, we selected gE as a representative viral glycoprotein. To further investigate the role of autophagy in VZV glycoprotein biosynthesis as well as confirm the results obtained with 3-MA inhibition, we transfected cells with ATG5 small interfering RNA to block autophagosome formation. VZV-induced syncytium formation was markedly reduced by ATG5 knockdown (P < 0.0001). Further, we found that both expression and glycan processing of VZV gE were decreased after ATG5 knockdown, while expression of the nonglycosylated IE62 tegument protein was unchanged. Taken together, our cumulative results not only documented abundant autophagy within VZV-infected cells throughout the infectious cycle but also demonstrated that VZV-induced autophagy facilitated VZV glycoprotein biosynthesis and processing.
Simultaneous analysis of the gene expression profiles of cancer and stromal cells in endometrial cancer

To address the role of cancer‐stroma interactions, we performed gene expression profiling of both cancer and stroma, using matching samples of endometrial cancer (EC), and analyzed the relationship between the gene expression pattern and prognosis in EC. Sixty EC cases were included in this study (38 nonrecurrent and 22 recurrent). Cancer and stroma were separated by performing laser capture microdissection, and microarray analysis was performed separately on cancer and stromal cells. Genes related with progression‐free survival (PFS) in cancer and stroma were analyzed using the Cox regression model, and we established a formula, based on the gene expression pattern of cancer and stroma, to predict recurrence using logistic regression. We estimated the accuracy of the formula using the 0.632 method. All cases were classified based on the 79 selected genes of cancer and stroma related to PFS, based on unsupervised clustering. A total of 143 genes in cancer, and 79 genes in stroma were significantly related with PFS. The estimated area under the curve of receiver operating characteristics curve in cancer and stroma to predict recurrence were 0.800 and 0.758, respectively. Based on the 79 genes of cancer, the 22 recurrent cases were divided into two groups, which generally correlated with the histological grade. In contrast, based on the 79 genes of stroma, the 22 recurrent cases displayed homogeneous gene expression, unrelated to the histological grade. We conclude that gene expression profiles of cancer and stroma can predict the recurrence of EC and stromal that gene expression does not depend on the cancer grade. © 2014 Wiley Periodicals, Inc.
Hemodynamic responses and adverse effects associated with adenosine and dipyridamole pharmacologic stress testing: a comparison in 2,000 patients.

OBJECTIVE To compare the hemodynamic responses and the adverse effects associated with two coronary vasodilators used for pharmacologic stress testing. DESIGN We retrospectively studied the results of adenosine and dipyridamole perfusion imaging in a large group of patients who underwent pharmacologic stress radionuclide perfusion imaging. MATERIAL AND METHODS One thousand patients given dipyridamole between April 1989 and April 1991 (before adenosine became available) were compared with 1,000 patients given adenosine between April 1991 and October 1992. A standard protocol was used to infuse the drugs before myocardial perfusion imaging with 201Tl or 99mTc sestamibi. RESULTS Peak heart rate was higher (85 versus 83 beats/min; P = 0.02) and systolic blood pressure was lower (129 versus 133 mm Hg; P < 0.0001) with adenosine than with dipyridamole. More patients had a decrease in systolic blood pressure of 30 mm Hg or more with adenosine than with dipyridamole (P = 0.002). Horizontal or downsloping ST-segment depression of 1 mm or more occurred in 9% of patients who received adenosine and in 8% of those who received dipyridamole. Adverse effects occurred in 78% of the adenosine study group and in 50% of the dipyridamole group (P < 0.0001). Chest pain was the most common symptom with both drugs. Atrioventricular block occurred in 76 patients who received adenosine but in none who received dipyridamole. Because of adverse effects, 28% of patients who received dipyridamole required extra monitoring time (mean, 6 +/- 5 minutes beyond the standard protocol). Aminophylline was administered to 163 and 6 patients, respectively, in the dipyridamole and adenosine study groups. CONCLUSION Adenosine causes slightly greater systemic vasodilation than does dipyridamole. Adverse effects occur less often with dipyridamole but, in comparison with adenosine, are more difficult to manage and necessitate more monitoring time as well as fairly frequent intravenous use of aminophylline for reversal.
The First-Mover Disadvantage

The current research establishes a first-mover disadvantage in negotiation. We propose that making the first offer in a negotiation will backfire when the sender reveals private information that an astute recipient can leverage to his or her advantage. In two experiments, we manipulated whether the first offer was purely distributive or revealed that the sender’s preferences were compatible with the recipient’s preferences (i.e., the negotiators wanted the same outcome on an issue). When first offers contained only distributive issues, the classic first-mover advantage occurred, and first offers predicted final prices. However, a first-mover disadvantage emerged when senders opened with offers that revealed compatible preferences. These effects were moderated by negotiators’ social value orientation: Proself negotiators were more likely to take advantage of compatible information than were prosocial negotiators. Overall, the key factor that determined whether the first-mover advantage or disadvantage emerged was whether the offer revealed compatible preferences. These results demonstrate that first offers not only provide numerical value but also convey qualitative information.
Fund Flows and Market States

This paper establishes a new empirical fact: Mutual funds’ flow-performance sensitivity is a hump-shaped function of aggregate risk-factor realizations. Explanations based on extant theories can explain only a fraction of the pattern. We thus develop a new parsimonious model. It assumes Bayesian investors who are uncertain about the degree to which fund returns are exposed to systematic risk. Fund performance is then less informative about manager skill when factor realizations are larger in absolute value. The data also support the out-of-sample prediction that the hump shape is more pronounced for funds with more uncertain risk loadings.Received October 24, 2014; editorial decision October 11, 2016 by Editor Itay Goldstein.
The Highly Conserved Arginine Residues at Positions 76 through 78 of Influenza A Virus Matrix Protein M1 Play an Important Role in Viral Replication by Affecting the Intracellular Localization of M1

ABSTRACT Influenza A virus matrix protein (M1) plays an important role in virus assembly and budding. Besides a well-characterized basic amino acid-rich nuclear localization signal region at positions 101 to 105, M1 contains another basic amino acid stretch at positions 76–78 that is highly conserved among influenza A and B viruses, suggesting the importance of this stretch. To understand the role of these residues in virus replication, we mutated them to either lysine (K), alanine (A), or aspartic acid (D). We could generate viruses possessing either single or combination substitutions with K or single substitution with A at any of these positions, but not those with double substitutions with A or a single substitution with D. Viruses with the single substitution with A exhibited slower growth and had lower nucleoprotein/M1 quantitative ratio in virions compared to the wild-type virus. In cells infected with a virus possessing the single substitution with A at position 77 or 78 (R77A or R78A, respectively), the mutated M1 localized in patches at the cell periphery where nucleoprotein and hemagglutinin colocalized more often than the wild-type did. Transmission electron microscopy showed that virus possessing M1 R77A or R78A, but not the wild-type virus, was present in vesicular structures, indicating a defect in virus assembly and/or budding. The M1 mutations that did not support virus generation exhibited an aberrant M1 intracellular localization and affected protein incorporation into virus-like particles. These results indicate that the basic amino acid stretch of M1 plays a critical role in influenza virus replication.
Study of Secnidazole-Serratiopeptidase Alginate/HPMC Gels For Periodontal Delivery

The main goal of this study was to develop a controlled release periodontal formulation of Secnidazole Serratiopeptidase that can be used in the treatment of periodontitis by direct intrapocket administration, thus ensuring a high effective concentration of antimicrobial agent at the site of infection. This minimizes the occurrence of systemic side effects and bacterial resistance. Serratiopeptidase, a proteolytic enzyme with anti- inflammatory activity, is widely used in dental treatment. The topical use of enzymes is also associated with a significant increase in the concentration of antibiotic at the wound and decrease in the rate of infection. Therefore, localized delivery of the enzyme along with antibiotic may provide better relief than antibiotic alone. The pH sensitive and mucoadhesive formulations consist of non-toxic polymer, Sodium alginate (1%), HPMC E50Lv (1- 8%w/w). To modulate the gel strength and the bioadhesive force of gel HPMC E50Lv was used as viscosity enhancer. Viscosity studies indicated pseudo plastic (shear thinning) behavior of gel. Increase in polymer concentration showed increase in the viscosity thereby affecting the drug release. Dissolution studies demonstrate diffusion release of drug and enzyme from the gel thus alginate/HPMC gels can be used as an in-situ gelling vehicle to enhance periodontal drug delivery.