bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping Murine Corneal Neovascularization and Weight Loss Virulence Determinants in the Herpes Simplex Virus 1 Genome and the Detection of an Epistatic Interaction between the UL and IRS/US Regions
Authors: Lee Kyubin , Kolb Aaron W. , Larsen Inna , Craven Mark , Brandt Curtis R.
Published: July 2016

Herpes simplex virus 1 (HSV-1) most commonly causes recrudescent labial ulcers; however, it is also the leading cause of infectious blindness in developed countries. Previous research in animal models has demonstrated that the severity of HSV-1 ocular disease is influenced by three main factors: host innate immunity, host immune response, and viral strain. We have previously shown that mixed infection with two avirulent HSV-1 strains (OD4 and CJ994) results in recombinants with a wide range of ocular disease phenotype severity. Recently, we developed a quantitative trait locus (QTL)-based computational approach (vQTLmap) to identify viral single nucleotide polymorphisms (SNPs) predicted to influence the severity of the ocular disease phenotypes. We have now applied vQTLmap to identify HSV-1 SNPs associated with corneal neovascularization and mean peak percentage weight loss (MPWL) using 65 HSV-1 OD4-CJ994 recombinants. The vQTLmap analysis using Random Forest for neovascularization identified phenotypically meaningful nonsynonymous SNPs in the ICP4, UL41 (VHS), UL42, UL46 (VP11/12), UL47 (VP13/14), UL48 (VP22), US3, US4 (gG), US6 (gD), and US7 (gI) coding regions. The ICP4 gene was previously identified as a corneal neovascularization determinant, validating the vQTLmap method. Further analysis detected an epistatic interaction for neovascularization between a segment of the unique long (UL) region and a segment of the inverted repeat short (IRS)/unique short (US) region. Ridge regression was used to identify MPWL-associated nonsynonymous SNPs in the UL1 (gL), UL2, UL4, UL49 (VP22), UL50, and ICP4 coding regions. The data provide additional insights into virulence gene and epistatic interaction discovery in HSV-1.

IMPORTANCEHerpes simplex virus 1 (HSV-1) typically causes recurrent cold sores; however, it is also the leading source of infectious blindness in developed countries. Corneal neovascularization is critical for the progression of blinding ocular disease, and weight loss is a measure of infection severity. Previous HSV-1 animal virulence studies have shown that the severity of ocular disease is partially due to the viral strain. In the current study, we used a recently described computational quantitative trait locus (QTL) approach in conjunction with 65 HSV-1 recombinants to identify viral single nucleotide polymorphisms (SNPs) involved in neovascularization and weight loss. Neovascularization SNPs were identified in the ICP4, VHS, UL42, VP11/12, VP13/14, VP22, gG, US3, gD, and gI genes. Further analysis revealed an epistatic interaction between the UL and US regions. MPWL-associated SNPs were detected in the UL1 (gL), UL2, UL4, VP22, UL50, and ICP4 genes. This approach will facilitate future HSV virulence studies.
Prevailing PA Mutation K356R in Avian Influenza H9N2 Virus Increases Mammalian Replication and Pathogenicity
Authors: Xu Guanlong , Zhang Xuxiao , Gao Weihua , Wang Chenxi , Wang Jinliang , Sun Honglei , Sun Yipeng , Guo Lu , Zhang Rui , Chang Kin-Chow , Liu Jinhua , Pu Juan
Published: July 2016

Adaptation of the viral polymerase complex comprising PB1, PB2, and PA is necessary for efficient influenza A virus replication in new host species. We found that PA mutation K356R (PA-K356R) has become predominant since 2014 in avian H9N2 viruses in China as with seasonal human H1N1 viruses. The same mutation is also found in most human isolates of emergent avian H7N9 and H10N8 viruses whose six internal gene segments are derived from the H9N2 virus. We further demonstrated the mammalian adaptive functionality of the PA-K356R mutation. Avian H9N2 virus with the PA-K356R mutation in human A549 cells showed increased nuclear accumulation of PA and increased viral polymerase activity that resulted in elevated levels of viral transcription and virus output. The same mutant virus in mice also enhanced virus replication and caused lethal infection. In addition, combined mutation of PA-K356R and PB2-E627K, a well-known mammalian adaptive marker, in the H9N2 virus showed further cooperative increases in virus production and severity of infection
in vitro
and
in vivo
. In summary, PA-K356R behaves as a novel mammalian tropism mutation, which, along with other mutations such as PB2-E627K, might render avian H9N2 viruses adapted for human infection.

IMPORTANCE
Mutations of the polymerase complex (PB1, PB2, and PA) of influenza A virus are necessary for viral adaptation to new hosts. This study reports a novel and predominant mammalian adaptive mutation, PA-K356R, in avian H9N2 viruses and human isolates of emergent H7N9 and H10N8 viruses. We found that PA-356R in H9N2 viruses causes significant increases in virus replication and severity of infection in human cells and mice and that PA-K356R cooperates with the PB2-E627K mutation, a well-characterized human adaptive marker, to exacerbate mammalian infection
in vitro
and
in vivo
. Therefore, the PA-K356R mutation is a significant adaptation in H9N2 viruses and related H7N9 and H10N8 reassortants toward human infectivity.
Genetic Lineage and Reassortment of Influenza C Viruses Circulating between 1947 and 2014
Authors: Matsuzaki Yoko , Sugawara Kanetsu , Furuse Yuki , Shimotai Yoshitaka , Hongo Seiji , Oshitani Hitoshi , Mizuta Katsumi , Nishimura Hidekazu
Published: July 2016

Since influenza C virus was first isolated in 1947, the virus has been only occasionally isolated by cell culture; there are only four strains for which complete genome sequences are registered. Here, we analyzed a total of 106 complete genomes, ranging from the first isolate from 1947 to recent isolates from 2014, to determine the genetic lineages of influenza C virus, the reassortment events, and the rates of nucleotide substitution. The results showed that there are six lineages, named C/Taylor, C/Mississippi, C/Aichi, C/Yamagata, C/Kanagawa, and C/Sao Paulo. They contain both antigenic and genetic lineages of the hemagglutinin-esterase (HE) gene, and the internal genes PB2, PB1, P3, NP, M, and NS are divided into two major lineages, a C/Mississippi/80-related lineage and a C/Yamagata/81-related lineage. Reassortment events were found over the entire period of 68 years. Several outbreaks of influenza C virus between 1990 and 2014 in Japan consisted of reassortant viruses, suggesting that the genomic constellation is related to influenza C virus epidemics. The nucleotide sequences were highly homologous to each other. The minimum percent identity between viruses ranged from 91.1% for the HE gene to 96.1% for the M gene, and the rate of nucleotide substitution for the HE gene was the highest, at 5.20 × 10
−4
substitutions/site/year. These results indicate that reassortment is an important factor that increases the genetic diversity of influenza C virus, resulting in its ability to prevail in humans.

IMPORTANCE
Influenza C virus is a pathogen that causes acute respiratory illness in children and results in hospitalization of infants. We previously demonstrated (Y. Matsuzaki et al., J Clin Virol 61:87–93, 2014,
http://dx.doi.org/10.1016/j.jcv.2014.06.017
) that periodic epidemics of this virus occurred in Japan between 1996 and 2014 and that replacement of the dominant antigenic group occurred every several years as a result of selection by herd immunity. However, the antigenicity of the HE glycoprotein is highly stable, and antigenic drift has not occurred for at least 30 years. Here, we analyzed a total of 106 complete genomes spanning 68 years for the first time, and we found that influenza C viruses are circulating worldwide while undergoing reassortment as well as selection by herd immunity, resulting in an increased ability to prevail in humans. The results presented in this study contribute to the understanding of the evolution, including reassortment events, underlying influenza C virus epidemics.
Structure-Activity Relationships of the Human Immunodeficiency Virus Type 1 Maturation Inhibitor PF-46396
Authors: Murgatroyd Christopher , Pirrie Lisa , Tran Fanny , Smith Terry K. , Westwood Nicholas J. , Adamson Catherine S.
Published: July 2016

HIV-1 maturation inhibitors are a novel class of antiretroviral compounds that consist of two structurally distinct chemical classes: betulinic acid derivatives and the pyridone-based compound PF-46396. It is currently believed that both classes act by similar modes of action to generate aberrant noninfectious particles via inhibition of CA-SP1 cleavage during Gag proteolytic processing. In this study, we utilized a series of novel analogues with decreasing similarity to PF-46396 to determine the chemical groups within PF-46396 that contribute to antiviral activity, Gag binding, and the relationship between these essential properties. A spectrum of antiviral activity (active, intermediate, and inactive) was observed across the analogue series with respect to CA-SP1 cleavage and HIV-1 (NL4-3) replication kinetics in Jurkat T cells. We demonstrate that selected inactive analogues are incorporated into wild-type (WT) immature particles and that one inactive analogue is capable of interfering with PF-46396 inhibition of CA-SP1 cleavage. Mutations that confer PF-46396 resistance can impose a defective phenotype on HIV-1 that can be rescued in a compound-dependent manner. Some inactive analogues retained the capacity to rescue PF-46396-dependent mutants (SP1-A3V, SP1-A3T, and CA-P157S), implying that they can also interact with mutant Gag. The structure-activity relationships observed in this study demonstrate that (i) the
tert
-butyl group is essential for antiviral activity but is not an absolute requirement for Gag binding, (ii) the trifluoromethyl group is optimal but not essential for antiviral activity, and (iii) the 2-aminoindan group is important for antiviral activity and Gag binding but is not essential, as its replacement is tolerated.

IMPORTANCE
Combinations of antiretroviral drugs successfully treat HIV/AIDS patients; however, drug resistance problems make the development of new mechanistic drug classes an ongoing priority. HIV-1 maturation inhibitors are novel as they target the Gag protein, specifically by inhibiting CA-SP1 proteolytic cleavage. The lack of high-resolution structural information of the CA-SP1 target in Gag has hindered our understanding of the inhibitor-binding pocket and maturation inhibitor mode of action. Therefore, we utilized analogues of the maturation inhibitor PF-46396 as chemical tools to determine the chemical components of PF-46396 that contribute to antiviral activity and Gag binding and the relationship between these essential properties. This is the first study to report structure-activity relationships of the maturation inhibitor PF-46396. PF-46396 is chemically distinct from betulinic acid-derived maturation inhibitors; therefore, our data provide a foundation of knowledge that will aid our understanding of how structurally distinct maturation inhibitors act by similar modes of action.
How to Measure Export via Bacterial Multidrug Resistance Efflux Pumps
Authors: Blair Jessica M. A. , Piddock Laura J. V.
Published: July 2016

Bacterial multidrug resistance (MDR) efflux pumps are an important mechanism of antibiotic resistance and are required for many pathogens to cause infection. They are also being harnessed to improve microbial biotechnological processes, including biofuel production. Therefore, scientists of many specialties must be able to accurately measure efflux activity. However, myriad methodologies have been described and the most appropriate method is not always clear. Within the scientific literature, many methods are misused or data arising are misinterpreted. The methods for measuring efflux activity can be split into two groups, (i) those that directly measure efflux and (ii) those that measure the intracellular accumulation of a substrate, which is then used to infer efflux activity. Here, we review the methods for measuring efflux and explore the most recent advances in this field, including single-cell or cell-free technologies and mass spectrometry, that are being used to provide more detailed information about efflux pump activity.
Illuminating the Sites of Enterovirus Replication in Living Cells by Using a Split-GFP-Tagged Viral Protein
Authors: van der Schaar H. M. , Melia C. E. , van Bruggen J. A. C. , Strating J. R. P. M. , van Geenen M. E. D. , Koster A. J. , Bárcena M. , van Kuppeveld F. J. M.
Published: July 2016

Enteroviruses induce the formation of membranous structures (replication organelles [ROs]) with a unique protein and lipid composition specialized for genome replication. Electron microscopy has revealed the morphology of enterovirus ROs, and immunofluorescence studies have been conducted to investigate their origin and formation. Yet, immunofluorescence analysis of fixed cells results in a rather static view of RO formation, and the results may be compromised by immunolabeling artifacts. While live-cell imaging of ROs would be preferred, enteroviruses encoding a membrane-anchored viral protein fused to a large fluorescent reporter have thus far not been described. Here, we tackled this constraint by introducing a small tag from a split-GFP system into an RO-resident enterovirus protein. This new tool bridges a methodological gap by circumventing the need for immunolabeling fixed cells and allows the study of the dynamics and formation of enterovirus ROs in living cells.
My year as a Fulbrighter
Authors: Chandler Kate
Published: July 2016

In August 2015 Kate Chandler left London to embark on a masters degree in global policymaking as a Fulbright Scholar, studying first at New York University and then at University College London. As her year as a scholar draws to a close, Kate took time out from working on her dissertation to write for Vet Record Careers
Differences in photosynthetic capacity, chlorophyll fluorescence, and antioxidant system between invasive Alnus formosana and its native congener in response to different irradiance levels
Authors: Liu Shi-liang , Yang Rong-jie , Ren Bo , Wang Mao-hua , Ma Ming-dong
Published: July 2016

We compared the invasive Alnus formosana (Burk.) Makino with its native congener (Alnus cremastogyne Burk.) at three irradiances in terms of photosynthesis, chlorophyll fluorescence, and antioxidant system. The increased light-saturated photosynthetic rate (Amax) and light saturation point (LSP) contributed directly to the increased performance of the invasive. The invasive species had also higher plasticity in carotenoid and total chlorophyll than the native species at 100% irradiance, potentially contributing to invasion success in high-irradiance locations via photoprotection. Moreover, the diurnal photoinhibition of photosynthesis, as judged by the maximum photochemical efficiency of PSII (Fv/Fm) of dark-adapted leaves, was more severe in the native species than in the invasive species. With increasing irradiance, the invasive exhibited increased antioxidant activities and higher antioxidant levels to support the adverse conditions of both low- and high-irradiance acclimation. In contrast, the intercellular CO2 concentration (Ci) and stomatal limitation (Ls) decreased with increases in the net photosynthetic rate (An), stomatal conductance (Gs), and transpiration rate (Tr). We speculated that Ls was the main factor inhibiting the An for both studied species. These results first indicated that the invasive may occupy new habitats successfully through tolerating shading at low irradiance and out-compete native species through higher Amax and antioxidant levels when irradiance is increased.
Estimating light environment in forests with a new thresholding method for hemispherical photography
Authors: Zhao Kangning , He Fangliang
Published: July 2016

Light environment estimates derived from hemispherical photography are known to be affected by variations in sky illumination. During photo acquisition, rapid changes in sky illumination can occur and will result in changes in detected canopy gap size and frequency. Any resulting problems in image consistency will become more serious with increased time lags between setting the reference exposure and hemispherical photograph acquisition. We showed that if the camera exposure setting was kept constant during photo acquisition, the estimated diffuse transmittance would be greatly influenced by sky illumination change. We developed a new pixel thresholding method that calculated the optimal threshold value for the separation of sky and plant pixels as a function of the above-canopy photosynthetic photon flux density (PPFD). We tested the performance of our method for estimating transmittance against two established methods that assume exposure to be held constant to two stops higher than the reference exposure. Our method compensates for changes in sky illumination, producing a smaller pixel threshold value when sky illumination decreases and a larger pixel threshold value when photographs are taken under increased sky illumination. The new method achieved accurate and reproducible results, even in situations where under- or over-exposure was caused by changes in sky illumination during photo acquisition.
Probiotic Lactobacillus casei expressing porcine antimicrobial peptide PR39 elevates antibacterial activity in the gastrointestinal tract
Authors: Zhang Lei , Guo Dian , Liu Yangxin , Shao Yilan , Wang Yufeng , Xu Yigang , Jiang Yanping , Cui Wen , Li Yijing , Tang Lijie
Published: July 2016

PR39, a 4.7 kDa proline-rich antimicrobial peptide, acts as a cationic host defense peptide. In addition to killing bacteria, PR39 mediates inflammatory reactions, including cell proliferation, migration, wound healing, and angiogenesis. Here, we examined the antibacterial effects of this peptide. The synthetic gene fragment PR39 was inserted into the secretory expression vector plasmid pPG:612 of Lactobacillus casei, yielding the recombinant strain pPG:612-PR39/L. casei 393. In vitro antibacterial tests showed that expression of the PR39 peptide in recombinant L. casei resulted in antibacterial activity against Escherichia coli and Salmonella but had only minor antibacterial effects in Staphylococcus aureus. In addition, BALB/c mice fed the recombinant pPG:612-PR39/L. casei 393 grew better and had increased peripheral blood lymphocyte percentages, white blood cell numbers, and spleen indices than mice in the control group. Scanning electron microscopy showed that jejunum and duodenum villus height, crypt depth, and the ratio of villus height/crypt depth in the intestinal villi also increased. Moreover, mice fed the recombinant strain showed significantly lower mortality rates than the control group mice when challenged with the enterotoxigenic E. coli K88+. Thus, this recombinant expression system had the beneficial characteristics of both L. casei and PR39, supporting its potential as an animal feed additive.
Improved Online Algorithms for 2-Space Bounded 2-Dimensional Bin Packing
Authors: Januszewski Janusz , Zielonka Łukasz
Published: July 2016

A 3.8165-competitive 2-space bounded 2-dimensional bin packing algorithm is described. Moreover, a 3.6-competitive online square packing algorithm with two active bins is presented.
A Parallel Approach in Computing Correlation Immunity up to Six Variables
Authors: Etherington Carole J. , Anderson Matthew W. , Bach Eric , Butler Jon T. , Stănică Pantelimon
Published: July 2016

We show the use of a reconfigurable computer in computing the correlation immunity of Boolean functions of up to 6 variables. Boolean functions with high correlation immunity are desired in cryptographic systems because they are immune to correlation attacks. The SRC-6 reconfigurable computer was programmed in Verilog to compute the correlation immunity of functions. This computation is performed at a rate that is 190 times faster than a conventional computer. Our analysis of the correlation immunity is across all n-variable Boolean functions, for 2 ≤ n ≤ 6, thus obtaining, for the first time, a complete distribution of such functions. We also compare correlation immunity with two other cryptographic properties, nonlinearity and degree.
Matrix inequalities from a two variables functional
Authors: Bourin Jean-Christophe , Lee Eun-Young
Published: July 2016

We introduce a two variables norm functional and establish its joint log-convexity. This entails and improves many remarkable matrix inequalities, most of them related to the log-majorization theorem of Araki. In particular: if[Formula: see text] is a positive semidefinite matrix and[Formula: see text] is a normal matrix,[Formula: see text] and[Formula: see text] is a subunital positive linear map, then[Formula: see text] is weakly log-majorized by[Formula: see text]. This far extension of Araki’s theorem (when [Formula: see text] is the identity and [Formula: see text] is positive) complements some recent results of Hiai and contains several special interesting cases, such as a triangle inequality for normal operators and some extensions of the Golden–Thompson trace inequality. Some applications to Schur products are also obtained.
The effect of induced strains on the optical band gaps in lanthanum-doped zinc ferrite nanocrystalline powders
Authors: Hamed Fathalla , Ramachandran Tholkappiyan , Kurapati Vishista
Published: July 2016

ZnFe[Formula: see text]La[Formula: see text]O4 nanocrystalline powders were synthesized by auto-combustion with the aid of glycine as fuel. The synthesized powders were subjected to heat treatment in air at constant temperatures (600–970[Formula: see text]C) for a period of 2 h. The annealed powders were characterized by X-ray diffraction (XRD), Fourier transformation infrared spectroscopy (FTIR), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS) and UV–Vis–NIR spectroscopy. The as-synthesized and annealed powders formed spongy porous network structure with voids and pores. All the powders were found to be single phase nanomaterial with cubic spinel crystal structure and the desired composition; however, they contained strains, dislocations and lattice distortions. Some of these strains and dislocations are relaxed as a function of annealing temperature. The powders displayed direct and indirect optical band gaps. The energies of these band gaps were found to vary as a function of the induced strains and dislocations. It is suggested that the energy of the optical band gap in lanthanum-doped zinc ferrite nanocrystalline powders can be varied as a function of induced strains if the initial preparation conditions and the following heat treatments are controlled.
Towards on Develop a Framework for the Evaluation and Benchmarking of Skin Detectors Based on Artificial Intelligent Models Using Multi-Criteria Decision-Making Techniques
Authors: Yas Qahtan M. , Zadain A. A. , Zaidan B. B. , Lakulu M. B. , Rahmatullah Bahbibi
Published: July 2016

Evaluation and benchmarking of skin detectors are challenging tasks because of multiple evaluation attributes and conflicting criteria. Although several evaluating and benchmarking techniques have been proposed, these approaches have many limitations. Fixing several attributes based on multi-attribute benchmarking approaches is particularly limited to reliable skin detection. Thus, this study aims to develop a new framework for evaluating and benchmarking skin detection on the basis of artificial intelligent models using multi-criteria analysis. For this purpose, two experiments are conducted. The first experiment consists of two stages: (1) discussing the development of a skin detector using multi-agent learning based on different color spaces to create a dataset of various color space samples for benchmarking and (2) discussing the evaluation and testing the developed skin detector according to multi-evaluation criteria (i.e. reliability, time complexity, and error rate within dataset) to create a decision matrix. The second experiment applies different decision-making techniques (AHP/SAW, AHP/MEW, AHP/HAW, AHP/TOPSIS, AHP/WSM, and AHP/WPM) to benchmark the results of the first experiment (i.e. the developed skin detector). Then, we discuss the use of the mean, standard deviation, and paired sample [Formula: see text]-test to measure the correlations among the different techniques based on ranking results.
Varieties satisfying semigroup identities: Algebras over a finite field and rings
Authors: Finogenova Olga B.
Published: July 2016

We study varieties of associative algebras over a finite field and varieties of associative rings satisfying semigroup or adjoint semigroup identities. We characterize these varieties in terms of “forbidden algebras” and discuss some corollaries of the characterizations.
The finite representation property for composition, intersection, domain and range
Authors: McLean Brett , Mikulás Szabolcs
Published: July 2016

We prove that the finite representation property holds for representation by partial functions for the signature consisting of composition, intersection, domain and range and for any expansion of this signature by the antidomain, fixset, preferential union, maximum iterate and opposite operations. The proof shows that, for all these signatures, the size of base required is bounded by a double-exponential function of the size of the algebra. This establishes that representability of finite algebras is decidable for all these signatures. We also give an example of a signature for which the finite representation property fails to hold for representation by partial functions.
Free path groupoid grading on Leavitt path algebras
Authors: Gonçalves Daniel , Yoneda Gabriela
Published: July 2016

In this work, we realize Leavitt path algebras as partial skew groupoid rings. This yields a free path groupoid grading on Leavitt path algebras. Using this grading, we characterize free path groupoid graded isomorphisms of Leavitt path algebras that preserves generators.
On addition of 1-handles with chart loops to 2-dimensional braids
Authors: Nakamura Inasa
Published: July 2016

A 2-dimensional braid over an oriented surface-knot [Formula: see text] is presented by a graph called a chart on a surface diagram of [Formula: see text]. We consider 2-dimensional braids obtained by an addition of 1-handles equipped with chart loops. We introduce moves of 1-handles with chart loops, called 1-handle moves, and we investigate how much we can simplify a 2-dimensional braid by using 1-handle moves. Further, we show that an addition of 1-handles with chart loops is an unbraiding operation.
Interacting ghost dark energy models in the higher dimensional cosmology
Authors: Sadeghi J. , Khurshudyan M. , Farahani H.
Published: July 2016

We investigate interacting ghost dark energy models in higher dimensional cosmology. We attempt to model dark matter within a barotropic fluid with [Formula: see text]. In this work, we consider four different models based on choosing equation of state (EoS) parameter and interaction term. We confirm that our models agree with observational data.
IRRADIATION AND SILVER DEPOSITION FOR IMPROVEMENT OF NASOPHARYNGEAL AIRWAY MEDICAL DEVICE PROPERTIES
Authors: ABDEL REHEEM A. M. , ATTA A. , ABD-ELMONEM MAHMMOUD S.
Published: July 2016

The thermal and mechanical properties of nasopharyngeal airway (NPA) samples are improved by irradiation using 4[Formula: see text]keV oxygen and nitrogen ion beams with different ion fluences varying from [Formula: see text] ions/cm2to [Formula: see text] ions/cm2. The thermal stability of NPA medical device increases with increasing nitrogen and oxygen ion fluences. The tensile strength increased from 48[Formula: see text]MPa for unirradiated sample to 74[Formula: see text]MPa for samples irradiated with nitrogen and to 58[Formula: see text]MPa for samples irradiated with oxygen ion, while the elongation at break decreases for irradiated samples. Silver thin films are deposited on NPA medical device samples using 4[Formula: see text]keV argon ion beam. The XRD spectra demonstrated that silver nanoparticles are deposited on NPA medical device substrate. The effects of Ag thin film on gram-positive and gram-negative bacteria are studied.
Sequential Measurement of Displacement and Conduction Currents in Electronic Devices
Authors: Albareda Guillermo , Traversa Fabio Lorenzo , Benali Abdelilah
Published: July 2016

The extension of the Ramo–Schockley–Pellegrini theorem for quantum systems allows to define a positive-operator valued measure (POVM) for the total conduction plus displacement electrical current. The resulting current operator is characterized by two parameters, viz. the width of the associated Gaussian functions and the lapse of time between consecutive measurements. For large Gaussian dispersions and small time intervals, the operator obeys to a continuous weak-measurement scheme. Contrarily, in the limit of very narrow Gaussian widths and a single-shot measurement, the operator corresponds to a standard von Neumann (projective) measurement. We have implemented the resulting measurement protocol into a quantum electron transport simulator. Numerical results for a resonant tunneling diode show the great sensibility of current–voltage characteristics to different parameter configurations of the total current operator.
A REALISTIC 3D COMPUTATIONAL MODEL OF THE CLOSURE OF SKIN WOUND WITH INTERRUPTED SUTURES
Authors: CHANDA ARNAB , UNNIKRISHNAN VINU
Published: July 2016

Wounds or cuts are the most common form of skin injuries. While a shallow wound may heal over time, deep wounds often require clinical interventions such as suturing to ensure the wound closure and timely healing. To date, suturing practices are based on a surgeon's experience and there is no benchmark to what is right or wrong. In the literature, there have been few attempts to characterize wound closure and suture mechanics using simple 2D computational models. In our current work, for the first time, a realistic three-dimensional (3D) computational model of the skin with the two layers, namely the epidermis and dermis, have been developed. A 3D diamond shaped wound with a varying cross-section has been modeled, and interrupted sutures have been placed numerically in multiple steps to close the wound. Nonlinear hyperelastic material properties have been adopted for the skin and a skin pre-stress was applied bi-axially. The force requirements for each suture were estimated numerically using a novel suture pulling technique. The suture forces were found to lie in the range of 0–5 N with a maximum value at the center. Also, the center suture was observed to require an approximately four times pull force compared to the first end suture. All these findings provide important guidelines for suturing. Additionally, the suture force can be approximated as a polynomial function of the displacement. Given a wound geometry, wound depth, skin material properties, skin pre-stress, suture wire material and cross-sectional area, using our computational model, such a relationship can be used to estimate and characterize the suture force requirements accurately. To our knowledge, such a 3D computational model of skin wound closure with interrupted sutures have not been developed till date, and would be indispensable for planning robotic surgeries and improving clinical suturing practices in the future.
Multivariate sampling-type approximation
Authors: Krivoshein A. , Skopina M.
Published: July 2016

Approximation properties of the expansions [Formula: see text], where [Formula: see text] is a linear differential operator and [Formula: see text] is a matrix dilation, are studied. The sampling expansions are a special case of such differential expansions. Error estimations in [Formula: see text]-norm, [Formula: see text], are given in terms of the Fourier transform of [Formula: see text]. The approximation order depends on the smoothness of [Formula: see text], the order of [Formula: see text], the order of Strang–Fix condition for [Formula: see text] and [Formula: see text]. A wide class of [Formula: see text] including both band-limited and compactly supported functions is considered, but a special condition of compatibility [Formula: see text] with [Formula: see text] is required. Such differential expansions may be useful for engineers.
Vibrational and electronic profiles, molecular docking and biological prediction of 5-methoxy-1-[(5-methoxy-1H-indol-2-yl)methyl]-1H-indole: Experimental and theoretical investigations
Authors: Haress Nadia G. , Manimaran Devarasu , Joe Isaac Hubert , EL-Azzouny Aida A. , Al-Wabli Reem I. , Attia Mohamed I.
Published: July 2016

Indole derivatives represent an important class of privileged structures. Spectroscopic (Fourier transform infrared (FT-IR), FT-Raman,1H and [Formula: see text]C nuclear magnetic resonance (NMR)) investigations of the indole-bearing title compound, namely 5-methoxy-1-[(5-methoxy-1[Formula: see text]-indol-2-yl)methyl]-1[Formula: see text]-indole (MMIMI) have been carried out. The corresponding data of the MMIMI molecule were analyzed to understand its optimized geometry, and inter/intra-molecular interactions. The equilibrium geometry, harmonic vibrational wavenumbers, Frontier orbital energy, and natural bond orbital (NBO) analyses have been performed with the help of density functional theory (DFT) with B3LYP/6-311[Formula: see text]G([Formula: see text],[Formula: see text]) level of theory. The vibrational modes have been unequivocally assigned using potential energy distribution analysis. The theoretically predicted wavenumbers have good agreement with the experimental values. NBO has confirmed the intra-molecular charge transfer interactions. HOMO–LUMO analysis was carried out to explore charge delocalization on the MMIMI molecule. The immunomodulatory activity of the title molecule was predicted using molecular docking approach.
Behavioral pattern exploration of single guest, hexadecane-1,16-diol and hexadecane in urea inclusion compounds via molecular dynamics simulation
Authors: Mustafa Siti Fatimah Zaharah , Maarof Hasmerya , Naser Mohammed Abu , Abdallah Hassan H. , Irfan Ahmad , Ahmed Rashid
Published: July 2016

The urea inclusion compounds, a unique polar organic crystalline complex, are considered as a potential candidate for a molecular separator of long chain alkane molecule. A well-defined structure of the crystalline channel systems constructed from hydrogen bonding arrangement of the urea molecules, can be used to understand the fundamental aspects of the processes involving ions or molecules transportation. To do so, in our work, molecular dynamics approach is implemented to understand the behavioral pattern of the hexadecane-1,16-diol and hexadecane guests’ related to translational and rotational orientation along the urea tunnel. Our obtained results reveal that high interaction of hexadecane-1,16-diol with urea host molecules offers a restricted environment inside urea tunnel, resulting in slowing down the guest movement. Hexadecane guest system, on the contrary, exhibits lower interaction whereby the translational and rotational movement is faster. Moreover, as the distance increases (along [Formula: see text]-axis) in the urea tunnel, both guest systems favor a clockwise rotational orientation. Preference of the respected orientation indicates the influence of chiral urea tunnel on achiral guests that is clathrate inside the tunnel structure.
Coefficient-based regularized regression with dependent and unbounded sampling
Authors: Guo Qin , Ye Peixin
Published: July 2016

We consider the coefficient-based least squares regularized regression learning algorithm for the strongly and uniformly mixing samples. We obtain the capacity independent error bounds of the algorithm by means of the integral operator techniques. A standard assumption in theoretical study of learning algorithms for regression is the uniform boundedness of output sample values. We abandon this boundedness assumption and carry out the error analysis with output sample values satisfying a generalized moment hypothesis.
Effects of COM Vertical Oscillation on Joint Torques During 3D Walking of Humanoid Robots
Authors: Omran Sahab , Sakka Sophie , Aoustin Yannick
Published: July 2016

This paper proposes an analysis of the effect of vertical motion of the center of mass (COM) during humanoid walking. The linear inverted pendulum (LIP) model is classically used to deal with humanoid balance during walking. The effects on energy consumption of the COM height remaining constant for humanoid robots, or varying like human beings are studied here. Two approaches are introduced for the comparison: the LIP which offers the great advantage of analytical solving (i.e., fast and easy calculations), and a numerical solving of the IP dynamics, which allows varying the height of the center of mass during walking. The results are compared using a sthenic criterion in a 3D dynamics simulation of the humanoid robot Romeo (Aldebaran Robotics Company) and show a consequent reduction of the robot torque solicitation when the COM oscillates vertically.
EFFECT OF TRIVALENT CHROMIUM ON GROWTH HORMONE AND INSULIN-LIKE GROWTH FACTOR-I IN OVARIOHYSTERECTOMIZED RATS
Authors: Su Wei-Ling , Cheng Ching-Chang , Shia Wei-Yau , Hsu Tien-Huan , Chen Kuan-Sheng , Wang Hsien-Chi , Lee Wei-Ming
Published: July 2016

Changes in sex hormones following neutering appear to influence development of obesity by directly affecting satiety and metabolism, and indirectly affecting cell metabolism and hormone regulation. Trivalent chromium (Cr[Formula: see text]), an essential trace element in humans and animals, plays an important role in the metabolism and regulation of hormones such as growth hormone (GH) and insulin-like growth factor 1 (IGF-1). This study is to observe whether the effect of Cr[Formula: see text] on body weight gain and regulation of GH and IGF-1 after estradiol deprivation in rat model. All 8-week-old Sprague Dawley (SD) female rats were divided into four groups ([Formula: see text]): control, ovariohysterectomy (OHE), chromium (Cr) and OHE with Cr groups. GH and IGF-1 were determined at 14-, 18- and 22-week-old, respectively. In results, the body weights of ovariohysterectomized rats had been significantly higher ([Formula: see text]0.05) than that of intact rats since 12-week-old. The GH levels in OHE with Cr[Formula: see text] supplement group were decreased gradually and even reached to significantly lower in comparison to control group at 22 week-old. The IGF-1 levels in both OHE groups were significantly higher ([Formula: see text]0.05) than that in control group at 14- and 18-week-old, respectively. The results of this study did not provide the evidence concerning that the daily Cr[Formula: see text] supplement can regulate the GH and IGF-1 levels due to estradiol deprivation in ovariohysterectomized rats.
The Effects of pH and Ionic Strength of Swelling of Cationic Gels
Authors: Drozdov A. D. , Christiansen J. Declaville
Published: July 2016

A model is reported for the mechanical response of a cationic polyelectrolyte gel subjected to swelling in a water bath with an arbitrary pH and an arbitrary concentration of a monovalent salt. A gel is treated as a three-phase medium consisting of a polymer network, solvent (water), and solute (mobile ions). Transport of solvent and solute is thought of as their diffusion through the network accelerated by the electric field formed by mobile ions and bound charges and accompanied by chemical reactions (self-ionization of water molecules, protonation of functional groups, and formation of ion pairs between fixed cations and mobile anions). Material constants in the governing equations are determined by fitting equilibrium swelling diagrams on several copolymer gels with vinylimidazole component. Simulation demonstrates that the anti-polyelectrolyte effect (nonmonotonic changes in degree of swelling with molar fraction of salt) can be observed in cationic gels and core-shell microgels.
Logarithmic Spin, Logarithmic Rate and Material Frame-Indifferent Generalized Plasticity
Authors: Soldatos D. , Triantafyllou S. P.
Published: July 2016

In this work, we present a new rate type formulation of large deformation generalized plasticity which is based on the consistent use of the logarithmic rate concept. For this purpose, the basic constitutive equations are initially established in a local rotationally neutralized configuration which is defined by the logarithmic spin. These are then rephrased in their spatial form, by employing some standard concepts from the tensor analysis on manifolds. Such an approach, besides being compatible with the notion of (hyper)elasticity, offers three basic advantages, namely:

(i) The principle of material frame-indifference is trivially satisfied.

(ii) The structure of the infinitesimal theory remains essentially unaltered.

(iii) The formulation does not preclude anisotropic response.

A general integration scheme for the computational implementation of generalized plasticity models which are based on the logarithmic rate is also discussed. The performance of the scheme is tested by two representative numerical examples.
Numerical and Experimental Characterization of the Dynamic Properties of Flax Fiber Reinforced Composites
Authors: Daoud Hajer , Rebière Jean-Luc , Makni Amine , Taktak Mohamed , El Mahi Abderrahim , Haddar Mohamed
Published: July 2016

In this paper, the damping properties of flax fiber reinforced composites were investigated. Throughout a series of resonance vibration tests, the natural frequencies and the modal damping were evaluated. A numerical modelling was also produced by using a finite element model to determine the energies dissipated in each layer of the laminate structure in order to calculate the damping factors. The results obtained for the dynamic properties of flax fiber reinforced composites from experimental data and numerical analysis method show close agreement. The effect of fiber orientations on the damping behavior for this material was investigated. Another part of our work was to insert a thin viscoelastic layer within the flax fiber laminate. The interposition of this viscoelastic layer had a significant influence on the vibration behavior, bending stiffness and damping factors.
Numerical Solution for Dissimilar Confocally Elliptic Layers in Antiplane Elasticity
Authors: Chen Y. Z.
Published: July 2016

This paper provides a general solution for confocally elliptic layers in antiplane elasticity. The studied medium is composed of many layers with different shear moduli. The remote stresses are applied at infinity. Complex variable method is used to study the problem. The continuity conditions for the displacement and the resultant force along the interfaces are suggested. By using the complex variable, the matrix transfer technique, and the boundary condition, the final solution is obtainable. Numerical examples are carried out to show the influence of the different shear moduli defined on different layers to the stress distribution.
Nanoparticles of Ni-Co Alloy Derived from Layered Double Hydroxides and Their Catalytic Performance for CO Methanation
Authors: Liu Jingge , Cao Ang , Si Jing , Zhang Lihong , Hao Qinglan , Liu Yuan
Published: July 2016

Sintering of the active metallic nanoparticles and carbon deposition are the key problems faced for CO methanation catalysts. For overcoming those problems, bimetallic nanocatalyst is a promising route. In this work, a series of Al2O3 supported Ni-Co alloy catalysts were prepared by reducing NiCoAl layered double hydrotalcite (LDHs), and characterized with X-ray diffraction (XRD), temperature programmed reduction TPR, N2 adsorption-desorption, transmission electron microscopy (TEM) and temperature programed oxidation (TPO) techniques. The resultant catalysts were mesoporous with nanoparticles of Ni-Co alloy ranging from 7.9[Formula: see text]nm to 9.2[Formula: see text]nm which were highly dispersed in alumina matrix. The sample Ni7Co3-Al2O3 catalysts showed very good catalytic performance during the stability test at 500/600[Formula: see text]C for 300[Formula: see text]h, meanwhile exhibited excellent anti-sintering ability and anti-carbon deposition ability, owing to the formation of Ni-Co alloy and the feature of LDHs. This strategy for improving anti-sintering and anti-carbon deposition should be extendable for catalysts of other reactions.
Highly Efficient and Recyclable g-C3N4/CuO Hybrid Nanocomposite Towards Enhanced Visible-Light Photocatalytic Performance
Authors: Hong Shiquan , Yu Yong , Yi Zhijie , Zhu Haijun , Wu Wencheng , Ma Peiyan
Published: July 2016

A highly efficient visible-light-driven g-C3N4/CuO hybrid nanocomposite catalyst with different molar contents of CuO are successfully fabricated via a simple liquid phase synthesis process and applied to the degradation of Rhodamine B (RhB) solution. The results reveal that monodisperse CuO nanoparticles with a size of less than 10[Formula: see text]nm are uniformly distributed on the surface of g-C3N4nanosheets. Compared with the pure g-C3N4and CuO, the as-prepared nanocomposite displays significantly enhanced photocatalytic performance under visible-light irradiation. Attractively, the photocatalytic activities of the nanocomposite catalysts can be tuned by adjusting the molar ratio of g-C3N4and CuO. When the molar ratio reaches 2:1, the nanocomposite exhibits the highest photocatalytic activity, which can decompose RhB completely in 5[Formula: see text]min. The improved performance could be ascribed to the formation of heterostructure between g-C3N4and CuO as well as the decreased particle size of CuO, the presence of H2O2, large surface-exposure area and the suitable band position of g-C3N4/CuO nanocomposite. Interestingly, the nanocomposite shows excellent stability and recyclable property toward the photodegradation of RhB. Finally, a possible photocatalytic mechanism is proposed.
Applying singular value decomposition technique for quantifying the insects in commercial Thai Hommali Rice from NIR Spectrum
Authors: Jarruwat Puttinun , Choomjaihan Prasan
Published: July 2016

Insect infestation in rice stock is a significant issue in rice exporting business, resulting in the loss of product quality, nutrient as well as the economic losses. However, detecting the insect contamination with the traditional sorting techniques were destructive, inaccurate, time consuming and unable to detect the internal insect infestation. This study used near infrared (NIR) spectroscopy for obtaining the absorbent spectra from the insect contamination in two kinds of rice samples, Milled Hommali rice (MHR) and Brown Hommali rice (BHR). The mathematical methods of partial least squares (PLSs) regression and singular value decomposition (SVD) were employed to construct the predicting model. The statistical analysis results, R2, RMSEP, RPD and bias, concluded that the predictive models from PLS for MHR and BHR were 0.95 and 0.90, 0.014 and 0.019, 4.79 and 3.11, as well as [Formula: see text]0.007 and −0.008, respectively; while the statistical analysis results from SVD for MHR and BHR were 0.97 and 0.96, 0.012 and 0.013, 5.71 and 5.39, as well as [Formula: see text]0.003 and 0.002, respectively. It showed that SVD technique performed better than PLS technique which shows that using the advantage of SVD technique required less amounts of wave numbers for predicting and was possible to construct the low cost handheld equipment for detecting the insects in rice samples.