Ellipticity Bands Research Articles

Solid Phase Synthesis and TAR RNA-Binding Activity of Nucleopeptides Containing Nucleobases Linked to the Side Chains via 1,4-Linked-1,2,3-triazole.

Nucleopeptides (NPs) represent synthetic polymers created by attaching nucleobases to the side chains of amino acid residues within peptides. These compounds amalgamate the characteristics of peptides and nucleic acids, showcasing a unique ability to recognize RNA structures. In this study, we present the design and synthesis of Fmoc-protected nucleobase amino acids (1,4-TzlNBAs) and a new class of NPs, where canonical nucleobases are affixed to the side chain of L-homoalanine (Hal) through a 1,4-linked-1,2,3-triazole (HalTzl). Fmoc-protected 1,4-TzlNBAs suitable for HalTzl synthesis were obtained via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) conjugation of Fmoc-L-azidohomoalanine (Fmoc-Aha) and N1- or N9-propargylated nucleobases or their derivatives. Following this, two trinucleopeptides, HalTzlAAA and HalTzlAGA, and the hexanucleopeptide HalTzlTCCCAG, designed to complement bulge and outer loop structures of TAR (trans-activation response element) RNA HIV-1, were synthesized using the classical solid-phase peptide synthesis (SPPS) protocol. The binding between HalTzls and fluorescently labeled 5'-(FAM(6))-TAR UCU and UUU mutant was characterized using circular dichroism (CD) and fluorescence spectroscopy. CD results confirmed the binding of HalTzls to TAR RNA, which was evident by a decrease in ellipticity band intensity around 265 nm during complexation. CD thermal denaturation studies indicated a relatively modest effect of complexation on the stability of TAR RNA structure. The binding of HalTzls at an equimolar ratio only marginally increased the melting temperature (Tm) of the TAR RNA structure, with an increment of less than 2 °C in most cases. Fluorescence spectroscopy revealed that HalTzlAAA and HalTzlAGA, complementary to UUU or UCU bulges, respectively, exhibited disparate affinities for the TAR RNA structure (with Kd ≈ 30 and 256 µM, respectively). Hexamer HalTzlTCCCAG, binding to the outer loop of TARUCU, demonstrated a moderate affinity with Kd ≈ 38 µM. This study demonstrates that newly designed HalTzls effectively bind the TAR RNA structure, presenting a potential new class of RNA binders and may be a promising scaffold for the development of a new class of antiviral drugs.

Exploring the Antimicrobial Potential and Biofilm Inhibitory Properties of Hemocyanin from Hemifusus pugilinus (Born, 1778).

The seafood industry plays a huge role in the blue economy, exploiting the advantage of the enriched protein content of marine organisms such as shrimps and molluscs, which are cultured in aquafarms. Diseases greatly affect these aquatic organisms in culture and, hence, there is need to study, in detail, their innate immune mechanisms. Hemocyanin is a non-specific innate defense molecule present in the blood cells of several invertebrates, especially molluscs, arthropods, and annelids. It is concerned with oxygen transport, blood clotting, and immune enhancement. In the present study, this macromolecular metalloprotein was isolated from the hemolymph of the marine snail Hemifusus pugilinus (Born, 1778) using Sephadex G-100 gel filtration column chromatography. It occurred as a single band (MW 80 kDa) on SDS-PAGE. High-performance liquid chromatography (HPLC) of the purified hemocyanin showed a single peak with a retention time of 4.3 min. The secondary structure and stability of the protein were detected using circular dichroism (CD), and the spectra demonstrated negative ellipticity bands close to 208 nm and 225 nm, indicating β-sheets. Further exploration of the purified hemocyanin revealed remarkable antimicrobial and antibiofilm activities against Gram-positive (Enterococcus faecalis and Staphylococcus aureus) and Gram-negative bacteria (Pseudomonas aeruginosa and Proteus vulgaris) at a concentration of 1-5 μg/mL. Spectrophotometric and in situ microscopic analyses (CLSM) unveiled the potential of the purified hemocyanin to inhibit biofilm formation in these bacteria with a minimal inhibitory concentration of 40 μg/mL. Furthermore, H. pugilinus hemocyanin (10 μg/mL concentration) displayed antifungal activity against Aspergillus niger. The purified hemocyanin was also assessed for cytotoxicity against human cancer cells using cell viability assays. Altogether, the present study shows that molluscan hemocyanin is a potential antimicrobial, antibiofilm, antifungal, anticancer, and immunomodulatory agent, with great scope for application in the enhancement of the immune system of molluscs, thereby facilitating their aquaculture.

Periodic traveling waves in the ϕ^{4} model: Instability, stability, and localized structures.

We consider the instability and stability of periodic stationary solutions to the classical ϕ^{4} equationnumerically. In the superluminal regime, the model possesses dnoidal and cnoidal waves. The former are modulationally unstable and the spectrum forms a figureeight intersecting at the origin of the spectral plane. The latter can be modulationally stable, and the spectrum near the origin in that case is represented by vertical bands along the purely imaginary axis. The instability of the cnoidal states in that case stems from elliptical bands of complex eigenvalues far from the spectral plane origin. In the subluminal regime, there exist only snoidal waves which are modulationally unstable. Considering the subharmonic perturbations, we show that the snoidal waves in the subluminal regime are spectrally unstable with respect to all subharmonic perturbations, while for the dnoidal and cnoidal waves in the superluminal regime, the transition between the spectrally stable state and the spectrally unstable state occurs through a Hamiltonian Hopf bifurcation. The dynamical evolution of the unstable states is also considered, leading to some interesting localization events on the spatio-temporal backgrounds.

Design and Optimization of Butterworth and Elliptic Band Pass Filters in 5G Application

Filters are two-port networks that may pass or attenuate frequencies within defined ranges and can alter the frequency response of any system. In the present research study, the goals and optimization controller embedded with (ADS2019) are used to design Butterworth and Elliptic bandpass filters with frequency ranges of (18GHz – 38GHz), a bandwidth of (7GHz), stopband attenuation of (S21=-60dB), and passband attenuation of (S21=-1dB). Three types of each filter (Hp-Lp 6th order – 3rd order – 6th order) are simulated and optimized to choose the best (C, L) values. The selected filters are redesigned using the Design Filter Guide, and the simulation during this phase yields different values for (C, L). The designed circuit is then transformed into a microstrip model using transmission lines for open and short circuits. The study investigates the differences between each filter in BW-f center- attenuation at the stopband.In the last phase of the study, the circuit of each filter is transformed using a microstrip transmission line to obtain the (W, L) for each component of each filter. Finally, the study compares past studies and research projects in this field.

Fabrication and Characterization of Steel-Base Metal Matrix Composites Reinforced by Yttria Nanoparticles through Friction Stir Processing.

Friction Stir Processing (FSP) was used to fabricate metal matrix composite, based on steel and reinforced with nano-sized yttrium oxide powder. The powder was packed in a narrow longitudinal groove of 2 mm depth and 1 mm width cut in the steel plate’s rear surface. Different rotation speeds of 500–1500 rpm were used, at a fixed traveling speed of 50 mm·min−1. Single-pass and two passes, with the same conditions, were applied. The direction of the second pass was opposite to that of the first pass. After the first pass, complete nugget zones were obtained when the rotation speeds were more than 700 rpm with some particles agglomeration. The added particles showed as narrow elliptical bands, with a band pitch equal to the rotation speed over traveling speed. Performing the second FSP pass in the opposite direction resulted in better particles distributions. Almost defect-free composite materials, with homogenously distributed yttria nano-sized particles, were obtained after two passes when rotation speeds more than 700 rpm were used. The resulting steel matrix grains were refined from ~60 μm of the base metal to less than 3 μm of the processed nugget zone matrix. The hardness and the tensile strength of the fabricated materials improved almost two-fold over the base metal. Uniform microhardness values within the nugget areas were observed at higher rotational speeds. The ductility and toughness of the fabricated composites were reduced compared to the base metal.

High precision measurement for the chamfered hole radius and spacing of a large-size workpiece based on binocular vision combined with plane dynamic adjustment.

A novel, to the best of our knowledge, hole radius and spacing measurement method is presented based on binocular vision combined with dynamic local plane for the large-size workpiece with plane feature. The novel method overcomes the problem of the ariable working distance and large location error of an abrupt edge for conventional methods. Its measurement principle and model are introduced. Then, a chamfered inner edge extraction method based on the shrinkage of an elliptical band and an adaptive weight optimal calculation based on redundant measurement data are presented to improve the measurement accuracy. Experiments are carried out to validate the presented method, and a high measurement accuracy with a standard deviation of 0.017 mm in the hole radius and 0.021 mm in hole spacing have eventually been achieved for the actual measurement workpieces, respectively. Compared with the common method, the measurement accuracy is improved by at least 77% and 53% in radius and spacing, respectively.

Immunological and antibiofilm property of haemocyanin purified from grooved tiger shrimp (Penaeus semisulcatus): An in vitro and in silico approach

Haemocyanin (Hc) is a non-specific innate immune protein present in the haemolymph of arthropods and molluscs. In the current study, we characterized the structural and immunological properties of Hc from grooved tiger shrimp, Penaeus semisulcatus. Hc was isolated from the haemolymph of P. semisulcatus by gel filtration column chromatography using Sephadex G-100. High-performance liquid chromatography of the purified Hc emerged as a single peak through a retention time of 3.3 min demonstrating the homogeneity nature of the protein. X-ray diffraction analysis revealed a distinct peak at 31.7° indicating the crystalline character of the purified Hc. Circular dichroism spectra of the purified Hc displayed negative ellipticity bands close to 225 nm and 208 nm representing β-sheet secondary structure. The purified Hc agglutinated sheep RBCs, yeast Saccharomyces cerevisiae and fungal Candida albicans. In addition, the purified Hc displayed antibacterial activity against Gram-positive bacteria (Bacillus thuringiensis and Bacillus pumilis) and Gram-negative bacteria (Vibrio parahaemolyticus and Vibrio alginolyticus) with a minimal inhibitory concentration of 50 μg/ml. Antibiofilm activity revealed the potential of purified Hc to inhibit biofilm formation of both Gram-positive and Gram-negative bacterial pathogens. Furthermore, live/dead staining of biofilms demonstrated the reduced viability of bacterial cells after exposure to the purified Hc. In silico molecular modeling was carried out using the sequence of Hc from SwissProt and molecular docking was performed with the cell surface components found in Gram-positive and Gram-negative bacteria. Overall our study demonstrates the involvement of Hc in the native immune reaction of P. semisulcatus by eliciting pathogen recognition. Thus, Hc could enhance disease resistance against pathogenic infection in shrimp aquaculture.

Unique Banded Cylindrites of Polyoxymethylene/Poly(butylene succinate) Blends Induced by Interfacial Shear

Unique banded cylindrites of polyoxymethylene/poly(butylene succinate) blends were induced by the intense interfacial shear, which was applied by pulling a single glass fiber (GF) with non-nucleation ability. The crystalline morphology and structure of banded cylindrites were quantitively correlated with the shear rates to provide revealing insights in shear-induced nucleation and lamellar assembly. Densely packed row-nuclei emerged on the surface of pulled GF and the nucleation density increased dramatically with the shear rate. The subsequent lamellar extension and twisting were restricted perpendicularly to the GF axis, resulting in the formation of banded cylindrites. As the shear rate increased, the band spacing showed a linear decrease and the eccentricity of elliptical bands showed a linear increase. It was attributed to the augment of unbalanced surface stress caused by steric hindrance of serried nuclei. While the growth rate of banded cylindrites remained constant regardless of the shear rate, s...

3D FSS with multiple transmission zeros and pseudo elliptic response

The three-dimensional frequency selective surface (3D FSS) with band reject multiple transmission zeros and pseudo-elliptic response is designed from two-dimensional (2D) periodic array of shielded micro strip lines to realize wide out-of–band radio wave rejection. The 3D FSS array consists of multimode cavities whose coupling with air can be controlled to obtain a desired frequency range. The proposed FSS with shorting via to ground exhibits pseudo-elliptic band-reject response in the frequency range from 6GHz to 14GHz. As the plane wave of linear polarization incidents perpendicularly to the shielded micro strip line with perfect electric conductor (PEC) and perfect magnetic conductor (PMC) boundary walls, two quasi-TEM modes are obtained known as air mode and substrate mode. The first 3D FSS design is a combination of two or more resonators. Furthermore, second 3D FSS design with three shorting vias result more elliptic band reject frequency response and a pass band transmission pole. All in phase resonators of design give transmission poles and out of phase combination of resonators give transmission zeros respectively. The proposed 3D FSS is designed and simulated using Ansys HFSS software. These designs exhibit an improved performance for many practical applications such as antenna sub-reflector, and spatial filters.

Elliptical BandPassThree Dimensional Frequency Selective Surface with Multiple Transmission Zeros

An elliptic band pass response three-dimensional Frequency Selective Surface (3D FSS) is designed from a single unit cell of 2D array of two shielded microstrip lines. The designed FSS provides pseudo-elliptic band-pass frequency response (5.4 – 9.6) GHz with its application in long-distance radio telecommunications and space communications etc. The four transmission zeros at 5.4GHz, 9.6GHz, 12.4GHz and 15GHz provides wide out-of-band frequency rejection. The 3D FSS is independent of the variations in the incident angle of the plane wave up to 60 degree. Each unit cell is a combination of two shielded microstrip lines with one having an air gap and the other one having in between rectangular metallic plate. When a TE polarized plane wave incidents perpendicular to the perfect electric conductor (PEC) boundary walls shielded microstrip lines, it results in two quasi-TEM modes namely air and substrate mode. The 3D FSS consists of multiple resonators with a multimode cavity having number of propagating modes. These resonating modes in phase provide transmission poles and when out of phase give transmission zeros. The 3D FSS structure is simulated using Ansys HFSS software with improved performance over 2DFSS, for many practical applications such as antenna sub-reflector, radomes and spatial filters.

Design of Voltage Mode 6th Order Elliptic Band-pass Filter Using Z-Copy Current Follower Transconductance Amplifier )ZC-CFTA(

This paper describes the realization of the new configuration of an active element namely, Z Copy Current Follower Transconductance Amplifier (ZC-CFTA). In this study, the elliptic 6th order voltage-mode (VM) Band-pass filter was configured based on the ZC-CFTA, which operates at a high frequency of about 30 MHz. The active element also contains floated and grounded inductance with one capacitor. The ZC-CFTA which is an ABB (Active Building Block) is configured with a passive element that is the 6th order elliptic Band Pass Filter. The results LT-SPICE software simulation using 0.18µm CMOS processing parameter show that the designed filter could be operated at a supply voltage of 0.9V and it offers the advantages of a small size and high gain.

Circular Dichroism Spectroscopy of Collagen Fibrillogenesis: A New Use for an Old Technique

Type-I collagen assembles in a stepwise, hierarchic fashion from the folding of the triple helix to the assembly of fibrils into fibers. The mature assembled fibers are crucial for tissue structure and mechanics, cell interactions, and other functions in vivo. Although triple helix folding can be followed with the use of optical methods such as circular dichroism (CD) spectroscopy, fibrillogenesis is typically measured by alternative methods such as turbidity, rheology, and microscopy. Together, these approaches allow for investigation of the mechanical properties and architectures of collagen-based scaffolds and excised tissues. Herein, we demonstrate that CD spectroscopy, a technique that is used primarily to evaluate the secondary structure of proteins, can also be employed to monitor collagen fibrillogenesis. Type-I collagen suspensions demonstrated a strong, negative ellipticity band between 204 and 210 nm under conditions consistent with fibrillogenesis. Deconvolution of CD spectra before, during, and after fibrillogenesis identified a unique fibril spectrum distinct from triple helix and random coil conformations. The ability to monitor multiple states of collagen simultaneously in one experiment using one modality provides a powerful platform for studying this complex assembly process and the effects of other factors, such as collagenases, on fibrillogenesis and degradation.

Microscopical characterization of known postmortem root bands using light and scanning electron microscopy

A postmortem root band (PMRB) is a distinct microscopic feature that is postulated to occur in hair remaining in the follicle during the postmortem interval [1] (Petraco et al., 1998). The scientific validity of this premise has been highlighted in two recent high-profile criminal cases involving PMRBs [2,3] (State of Florida v. Casey Marie Anthony, 2008; People v. Kogut, 2005). To better understand the fundamental aspects of postmortem root banding, the microscopical properties of known PMRBs11In this paper, a known PMRB is defined as a dark elliptical band in a hair (when viewed in transmitted light) in the pre-keratin/keratogenous region of the hair root, which is also confirmed to have been recovered from the tissue of a deceased person during the postmortem interval. This is equivalent to a Stage 2 band as defined by Koch et al [4]. were characterized by light microscopy, and scanning electron microscope (SEM) imaging of microtomed sections of hairs showing root banding. The results from this study show that the appearance of the PMRB may be due to the degradation of the chemically labile, non-keratin intermacrofibrillar matrix (IMM) in the pre-keratin/keratogenous region of anagen hairs. In addition, this degradation is confined to the cortex of the hair, with no apparent damage to the layers of the cuticle. These results could provide valuable information for determining the mechanism of band formation, as well as identify a set of microscopic features that could be used to distinguish hairs with known PMRBs from similarly looking environmentally degraded hairs.

Electron mobility of a two-dimensional electron gas at the interface ofSrTiO3andLaAlO3

We calculate the mobility of a two-dimensional electron gas residing at the interface of LaAlO$_{3}$/SrTiO$_{3}$ following a three band Boltzmann approach at low temperature, where carrier-charged impurity scattering process is assumed to be dominant. We explain the anisotropic characteristic of the dielectric function, which is a consequence of elliptical bands close to Fermi surface. The screening effect, which weakens the long-range Coulomb interaction of the electron-impurity is considered within the random phase approximation. Working at carrier densities high enough to neglect the spin-orbit induced splitting of the bands, we find that the mobility varies inversely with the cubic power of the carrier density ($n_{2D}^{-3}$) in good agreement with the experimental results. We also investigate the role of variable dielectric constant of SrTiO$_{3}$, the multiband nature of the system and interband interactions in exploring this result.

Glycosaminoglycan and DNA Binding Induced Intra- and Intermolecular Exciton Coupling of the bis-4-Aminoquinoline Surfen.

Despite the diverse biological activities of the glycosaminoglycan (GAG) antagonist surfen, the molecular details of its interaction with biomacromolecules remain poorly understood. Therefore, heparin and DNA binding properties of surfen were studied by circular dichroism (CD) and UV absorption spectroscopy methods. High-affinity (Ka ~ 10(7) M(-1)) association of surfen to the chiral heparin chain gives rise to a characteristic biphasic CD pattern due to the conformational twist of the aminoquinoline moieties around the central urea bridge. At higher drug loading, intermolecular stacking of surfen molecules alters the induced CD profile and also provokes strong UV hypochromism. In contrast to the right-handed heparin template, binding of surfen to the left-helicity chondroitin sulfate chains produces inverted CD pattern. Large UV hypochromism as well as polyphasic induced ellipticity bands indicate that surfen intercalates between the base pairs of calf-thymus DNA. Extensive CD spectroscopic changes observed at higher drug binding ratios refer to cooperative binding interactions between the intercalated drug molecules. The inherent conformational flexibility of surfen demonstrated here for the first time is important in its binding to distinct macromolecular targets and should be considered for rational drug design of novel GAG antagonists.

Robust Pitch Detection Based on Recurrence Analysis and Empirical Mode Decomposition

A new pitch detection method is designed by the recurrence analysis in this paper, which is combined of Empirical Mode Decomposition (EMD) and Elliptic Filter (EF). The Empirical Mode Decomposition (EMD) of Hilbert-Huang Transform (HHT) are utilized tosolve the problem, and a noisy voice is first filtered on the elliptic band filter. The two Intrinsic Mode Functions (IMF) are synthesized by EMD with maximum correlation of voice, and then the pitch be easily divided. The results show that the new method performance is better than the conventional autocorrelation algorithm and cepstrum method, especially in the part that the surd and the sonant are not evident, and get a high robustness in noisy environment. DOI: http://dx.doi.org/10.11591/telkomnika.v14i1.7216

Performance Improvement for PAPR Reduction in LTE Downlink System with Elliptic Filtering

This paper is concerned with the performance improvement of PAPR reduction of orthogonal frequency division multiplexing (OFDM) signal using amplitude clipping & filtering based design. Note that OFDM is one of the well adept multi-carrier multiplexing transmission scheme which has been implemented in long term evolution (LTE) downlink. Nonetheless peak to average power ratio (PAPR) is the more rattling problem with OFDM, consequently in this paper a reduction procedure of the PAPR by using amplitude clipping and filtering is proposed. Here we used IIR bandpass elliptic filter after amplitude clipping to reduce the PAPR. The performance of the system in terms of bit error rate (BER) is also canvased as a new filter based clipping method. Our results show that the proposed methodology of clipping method with the IIR elliptic band pass filter significantly reduces the PAPR value.

Bifunctional role of a pattern recognition molecule β-1,3 glucan binding protein purified from mangrove crab Episesarma tetragonum

β-1,3-Glucan binding protein (β-GBP) was purified from the haemolymph of Episesarma tetragonum by affinity chromatography with epoxy-activated laminarin-sepharose CL-6B column. E. tetragonum β-GBP exhibits a single band with a molecular weight of 100kDa on SDS-PAGE and a pI of 5.9 in isoelectric focusing (IEF). The circular dichroism (CD) spectra result of E. tetragonum β-GBP indicates that the negative ellipticity bands near 220nm and 208nm correspond to the β-sheets in the secondary structure. Functional analysis results demonstrate that the purified E. tetragonum β-GBP agglutinates fungal cells (Candida albicans) containing β-glucan. This recognition and binding specificity leads to the activation of the prophenoloxidase (ProPO) cascade and enhance the phenoloxidase (PO) activity in a dose-dependent manner. Our finding discloses new insights in the ProPO activation and fungal agglutination of purified E. tetragonum β-GBP. It seems to play a significant role in microbial uncovering mechanism in invertebrates.

Empirical Mode Decomposition and Robust Pitch Detection Based on Recurrence Analysis

A new pitch detection method is designed by the recurrence analysis in this paper, which is combined of Empirical Mode Decomposition (EMD) and Elliptic Filter (EF). The Empirical Mode Decomposition (EMD) of Hilbert-Huang Transform (HHT) are utilized tosolve the problem, and a noisy voice is first filtered on the elliptic band filter. The two Intrinsic Mode Functions (IMF) are synthesized by EMD with maximum correlation of voice, and then the pitch be easily divided. The results show that the new method performance is better than the conventional autocorrelation algorithm and cepstrum method, especially in the part that the surd and the sonant are not evident, and get a high robustness in noisy environment.

Statistical Analysis of Spectral Entropy Features for the Detection of Alcoholics Based on Elecroencephalogram (EEG) Signals

EEG happens to be an important tool for brain study providing a non- invasive and cost effective method to detect the effects of alcohol on the human brain. This paper highlights the importance of statistical analysis to determine the usefulness of spectral entropy features for discriminating alcoholics from healthy subjects. The open source EEG database consisting of 10 alcoholic and 10 control subjects recordings under visual stimulus is considered for the study. The EEG signal is preprocessed to remove eye blink artefact using independent component analysis (ICA) and the gamma sub band is extracted by using an elliptic band pass filter to obtain the visually evoked pattern (VEP) signal. The spectral entropy (SEN) coefficients are computed on all the 61 VEP signals of each subject. To obtain a statistical measure of SEN coefficients suitability for classifying the alcoholic EEG, ANOVA tests are performed. Results show that the test exhibits interesting observations in the form of p-value <0.05 (accepted significance level) for most of the channels and p-value >0.05 for the remaining channels. This study may help in identifying those significant channels (p<0.05) which contribute to the classification of both the groups.