CRISPR-like sequences association with antibiotic resistance and biofilm formation in Helicobacter pylori clinical isolates.

Role of clustered regularly interspaced short palindromic repeats (CRISPR)-like sequences in antibiotic resistance and biofilm formation isn't clear. This study investigated association of CRISPR-like sequences with antibiotic resistance and biofilm formation in H. pylori isolates. Thirty-six of H. pylori isolates were studied for existence of CRISPR-like sequences using PCR method and their correlation with biofilm formation and antibiotic resistance. Microtiter-plate technique was utilized for investigating antibiotic resistance profile of isolates against amoxicillin, tetracycline, metronidazole and clarithromycin. Biofilm formation of isolates was analyzed by microtiter-plate-based-method. Out of 23 CRISPR-like positive isolates, 19 had ability of biofilm formation and 7 of 13 CRISPR-like negative isolates were able to form biofilm (Pvalue = 0.445). In CRISPR-like positive isolates, 11 (48%), 18 (78%), 18 (78%) and 23 (100%) were resistant to amoxicillin, tetracycline, metronidazole and clarithromycin, respectively. Since CRISPR-like sequences have role in antibiotic resistance, may be applied as genetic markers of antibiotic resistance. But there was no substantial correlation between biofilm formation and existence of CRISPR-like sequences. These results indicate possible importance of CRISPR-like sequences on acquisition of resistance to antibiotics in this bacterium.

Analytical formulation of spatiotemporal modulated graphene-based waveguides using Floquet-Bloch theory.

In this work, an analytical model to study graphene-based spatiotemporal modulated structures is developed and verified through comparison with full wave numerical simulations. Graphene is an ideal material for realizing spatiotemporal modulated structures at high frequencies of THz and optics. In this analysis, the electromagnetic response of studied structures is expressed in terms of weighted Floquet-Bloch modes supported by the structure, while graphene is modeled by a spatiotemporal modulated surface current that imposes certain boundary conditions on the modes. The developed analytical technique is a comprehensive tool and can be used for accurate modeling of different kinds of spatiotemporal devices including lossy, guided, and leaky wave structures. To demonstrate the accuracy of the model, two plasmonic waveguides with space and time modulated graphene conductivity are analyzed and their interband and intraband transition between modes are thoroughly investigated. Using the developed analytical model, spatiotemporal modulation phenomena such as mode conversion, wave amplification and nonreciprocal response are explored and discussed for the studied structures.

Integrated optical beam steering device using switchable nanoantennas and a reflective metalens.

In this paper, an integrated optical device is proposed in which a reflective meta-lens and five switchable nano-antennas are combined to provide optical beam steering at the standard telecommunication wavelength of 1550 nm. For this purpose, a graphene-based switchable power divider is designed and integrated with nano-antennas to control the flow of the light entering the device. To achieve a higher angular accuracy in the radiated beams, a new algorithm is proposed and utilized to optimize the location of feeding nano-antennas in accordance with the reflective meta-lens. In order to achieve a minimum fluctuation in the light intensity when the beams are rotated in the space, an algorithm is developed to select optimum unit cells for the engineered meta-lens. The whole device is numerically analyzed using Electromagnetic full-wave simulations illustrating an optical beam steering with high accuracy (better than 1 degree) in the beam direction, and a low variation (less than 1 dB) in the radiated light intensity. The proposed integrated device can be used for many applications such as inter- and intra-chip optical interconnects, optical wireless communication systems, and advanced integrated LIDARs.

An analysis of retracted papers in Computer Science.

CONTEXT: The retraction of research papers, for whatever reason, is a growing phenomenon. However, although retracted paper information is publicly available via publishers, it is somewhat distributed and inconsistent. OBJECTIVE: The aim is to assess: (i) the extent and nature of retracted research in Computer Science (CS) (ii) the post-retraction citation behaviour of retracted works and (iii) the potential impact upon systematic reviews and mapping studies. METHOD: We analyse the Retraction Watch database and take citation information from the Web of Science and Google scholar. RESULTS: We find that of the 33,955 entries in the Retraction watch database (16 May 2022), 2,816 are classified as CS, i.e., ≈ 8%. For CS, 56% of retracted papers provide little or no information as to the reasons. This contrasts with 26% for other disciplines. There is also some disparity between different publishers, a tendency for multiple versions of a retracted paper to be available beyond the Version of Record (VoR), and for new citations long after a paper is officially retracted (median = 3; maximum = 18). Systematic reviews are also impacted with ≈ 30% of the retracted papers having one or more citations from a review. CONCLUSIONS: Unfortunately, retraction seems to be a sufficiently common outcome for a scientific paper that we as a research community need to take it more seriously, e.g., standardising procedures and taxonomies across publishers and the provision of appropriate research tools. Finally, we recommend particular caution when undertaking secondary analyses and meta-analyses which are at risk of becoming contaminated by these problem primary studies.

Low profile multi-layered invisibility carpet cloak using quantum dot core-shell nanoparticles.

In this paper, a method to reduce the profile of layered carpet cloaks is proposed. We analytically prove and numerically demonstrate that using a Low Index Material (LIM), a material with a relative dielectric constant smaller than 1, in construction of carpet cloaks can remarkably reduce their profiles. Using the proposed technique, a carpet cloak consisting of alternating LIM and silicon layers is designed to provide invisibility at visible wavelengths. The designed cloak has a profile that is 2.3 times smaller than a carpet cloak without LIM layers. To realize low index materials at optical wavelengths, silver-coated CdSe/CdS quantum dots dispersed in a polymer host are used. Quantum dots are utilized to compensate the loss of Silver and to achieve a low index medium with neglectable loss. The designed low profile carpet cloak is numerically analyzed showing a good performance for a wide range of incident angles which is the advantage of the proposed structure in comparison with metasurface-based carpet cloaks which work only for a very narrow range of incident angles.

Developing a carpet cloak operating for a wide range of incident angles using a deep neural network and PSO algorithm.

Designing invisibility cloaks has always been one of the most fascinating fields of research; in this regard, metasurface-based carpet cloaks have drawn researchers' attention due to their inherent tenuousness, resulting in a lower loss and easier fabrication. However, their performances are dependent on the incident angle of the coming wave; as a result, designing a carpet cloak capable of rendering objects under it invisible for a wide range of angles requires advanced methods. In this paper, using the Particle Swarm Optimization (PSO) algorithm, along with a trained neural network, a metasurface-based carpet cloak is developed capable to operate for a wide range of incident angles. The deep neural network is trained and used in order to accelerate the process of calculation of reflection phases provided by different unit cell designs. The resultant carpet cloak is numerically analyzed, and its response is presented and discussed. Both near-field and far-field results show that the designed carpet cloak operates very well for all incident angles in the range of 0 to 65 degrees.

Comparing proteome changes involved in biofilm formation by Streptococcus mutans after exposure to sucrose and starch.

Streptococcus mutans is a main organism of tooth infections including tooth decay and periodontitis. The aim of this study was to assess the influence of sucrose and starch on biofilm formation and proteome profile of S. mutans ATCC 35668 strain. The biofilm formation was assessed by microtiter plating method. Changes in bacterial proteins after exposure to sucrose and starch carbohydrates were analyzed using matrix-assisted laser desorption/ionization mass spectrometry. The biofilm formation of S. mutans was increased to 391.76% in 1% sucrose concentration, 165.76% in 1% starch, and 264.27% in the 0.5% sucrose plus 0.5% starch in comparison to biofilm formation in the media without sugars. The abundance of glutamines, adenylate kinase, and 50S ribosomal protein L29 was increased under exposure to sucrose. Upregulation of lactate utilization protein C, 5-hydroxybenzimidazole synthase BzaA, and 50S ribosomal protein L16 was formed under starch exposure. Ribosome-recycling factor, peptide chain release factor 1, and peptide methionine sulfoxide reductase MsrB were upregulated under exposure to sucrose in combination with starch. The results demonstrated that the carbohydrates increase microbial pathogenicity. In addition, sucrose and starch carbohydrates can induce biofilm formation of S. mutans via various mechanisms such as changes in the expression of special proteins.

Far-field sub-wavelength imaging using high-order dielectric continuous metasurfaces.

Due to the wave nature of light, the resolution achieved in conventional imaging systems is limited to around half of the wavelength. The reason behind this limitation, called diffraction limit, is that part of the information of the object carried by the evanescent waves scattered from an abject. Although retrieving information from propagating waves is not difficult in the far-field region, it is very challenging in the case of evanescent waves, which decay exponentially as travel and lose their power in the far-field region. In this paper, we design a high-order continuous dielectric metasurface to convert evanescent waves into propagating modes and subsequently to reconstruct super-resolution images in the far field. The designed metasurface is characterized and its performance for sub-wavelength imaging is verified using full wave numerical simulations. Simulation results show that the designed continuous high-order metasurface can convert a large group of evanescent waves into propagating ones. The designed metasurface is then used to reconstruct the image of objects with sub-wavelength features, and an image with the resolution of λ/5.5 is achieved.

Design and analysis of multi-layer silicon nanoparticle solar cells.

We investigate the concept of nanoparticle-based solar cells composed of a silicon nanoparticle stack as a light trapping absorber for ultrathin photovoltaics. We study the potential of using these inherently nanotextured structures in enhancing the light absorption. For this, a detailed optical analysis is performed on dependency of the cell response to parameters such as the number of particle layers, lattice structure and angle of incidence; Optical response of these cells are then compared with the results in conventional silicon solar cells. Moreover, we propose various configurations to apply these submicron particles as a p-n junction solar cell. We also compute the electrical performance of selected configurations. In doing so, key issues including the effect of contact points between nanoparticles and impact of loss are addressed. In the end, we show how [Formula: see text] nanoparticles on top of the cell structure can enhance the photocurrent. The appropriate range of [Formula: see text] particle size is also obtained for the typical cell structures.

The clinical and paraclinical manifestations of tuberous sclerosis complex in children.

Tuberous sclerosis complex (TSC) is an autosomal-dominant, multi-system, neurocutaneous disorder characterized by hamartomas in multiple organs. This study aimed to evaluate the clinical and paraclinical manifestations of children with TSC. The clinical and paraclinical characteristics of 79 children with TSC were evaluated and the possible correlations between the factors were calculated. Among the studied children which composed of 41 females (51.9%) and 38 males (48.1%), skin manifestations as hypopigmented macules as well as the brain involvement as cortical tubers in all (100%) cases, seizure in 74 (93.7%), and sub-ependymal nodules in 73 (92.4%) patients were the most common findings. The renal angiomyolipoma was diagnosed in 36 (70.6%) out of 51 patients. Subependymal giant cell astrocytoma in 25 (3/54%) out of 46 patients, retinal hamartoma in 15 (42.9%) out of 35 patients, and cardiac rhabdomyoma in 17 (41.3%) out of 46 patients were diagnosed. Furthermore, 50 (63.3%) out of 79 patients had psychological disorders that had a significant correlation with the prevalence of seizures (p = 0.002). Given the multi-systemic involvement of TSC, it is necessary that all organs of the patients even without any related clinical symptom or sign be examined regularly for proper therapeutic intervention and prevent disease progression. The growth of hamartomas in the brain and kidneys can be life-threatening; therefore, these organs have more importance to be regularly followed up and examined.

Distributed silicon nanoparticles: an efficient light trapping platform toward ultrathin-film photovoltaics.

In this paper, a new architecture comprising silicon nanoparticles inside a hole transport layer laid on a thin silicon layer is proposed to develop ultrathin film solar cells. Using generalized Mie theory, a fast analytical approach is developed to evaluate the optical absorption of the proposed structure for various geometries, polarizations and angles of incidence. The analytical results are verified through comparison with full-wave simulations, illustrating a reasonable agreement. The electrical performance of a distributed silicon nanoparticle solar cell is determined for selected configurations. To be able to predict the light-trapping in a solar cell comprising randomly distributed nanospheres, a new technique based on probability theory is developed and validated through comparison with the simulation results. Both analytical and numerical results show that the excited Mie resonant modes in the proposed structure lead to a significant enhancement in both absorption and the photo-generated current, in comparison to a conventional silicon solar cell with an equivalent volume of the active layer. In the case of random distributions, other advantages, including the simple fabrication process, indicate that the cell is a promising structure for ultrathin photovoltaics.

Dysregulation of lncRNA in Helicobacter pylori-Infected Gastric Cancer Cells.

Helicobacter pylori (H. pylori) infection is the most common cause of gastric cancer (GC). This microorganism is genetically diverse; GC is caused by several genetic deregulations in addition to environmental factors and bacterial virulence factors. lncRNAs (long noncoding RNAs) are significant biological macromolecules in GC, have specific functions in diseases, and could be therapeutic targets. Altered lncRNAs can lead to the abnormal expression of adjacent protein-coding genes, which may be important in cancer development. Their mechanisms have not been well understood, so we are going to investigate the risk of GC in a population with both high lncRNA and H. pylori infection.

MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology.

There is a range of proteomics methods to spot and analyze bacterial protein contents such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), which give comprehensive information about the microorganisms that may be helpful within the diagnosis and coverings of infections. Microorganism identification by mass spectrometry is predicted on identifying a characteristic spectrum of every species so matched with an outsized database within the instrument. MALDI-TOF MS is one of the diagnostic methods, which is a straightforward, quick, and precise technique, and is employed in microbial diagnostic laboratories these days and may replace other diagnostic methods. This method identifies various microorganisms such as bacteria, fungi, parasites, and viruses, which supply comprehensive information. One of the MALDI-TOF MS's crucial applications is bacteriology, which helps identify bacterial species, identify toxins, and study bacterial antibiotic resistance. By knowing these cases, we will act more effectively against bacterial infections.

Novel Strategies to Combat Bacterial Biofilms.

Biofilms are considered as a severe problem in the treatment of bacterial infections; their development causes some noticeable resistance to antibacterial agents. Biofilms are responsible for at least two-thirds of all infections, displaying promoted resistance to classical antibiotic treatments. Therefore, finding new alternative therapeutic approaches is essential for the treatment and inhibition of biofilm-related infections. Therefore, this review aims to describe the potential therapeutic strategies that can inhibit bacterial biofilm development; these include the usage of antiadhesion agents, AMPs, bacteriophages, QSIs, aptamers, NPs and PNAs, which can prevent or eradicate the formation of biofilms. These antibiofilm agents represent a promising therapeutic target in the treatment of biofilm infections and development of a strong capability to interfere with different phases of the biofilm development, including adherence, polysaccharide intercellular adhesion (PIA), quorum sensing molecules and cell-to-cell connection, bacterial aggregation, planktonic bacteria killing and host-immune response modulation. In addition, these components, in combination with antibiotics, can lead to the development of some kind of powerful combined therapy against bacterial biofilm-related infections.

Tunable metasurfaces using phase change materials and transparent graphene heaters.

Tunable metasurfaces enable us to dynamically control light at subwavelength scales. Here, using phase change materials and transparent graphene heaters, a new structure is proposed to develop tunable metasurfaces which support first-order Mie-type resonance in the near-IR regime. In the proposed structure, by adjusting the bias voltages applied to transparent graphene heaters, the crystallization levels of the phase change materials are controlled, which in turn modifies the response of the metasurface. The proposed metasurface is able to modulate the phase of the reflected wave in the range of 0° to -270° at the telecommunication wavelength of λ = 1.55 µm. A comprehensive Joule heating analysis is performed to investigate the thermal characterizations of the proposed structure. The results of this analysis show that there is a suitable thermal isolation between adjacent unit cells, making individual control on unit cells possible. The potential ability of the proposed metasurface as a beam steering device is also demonstrated. By using the proposed unit cells, a beam-steering device is designed and numerically studied. This study shows that the device can reflect a light normally incident on it in the range of ±65° with reasonably low sidelobe levels. The proposed structure can be used in developing low-cost integrated LiDARs.

Oral spirochetes: Pathogenic mechanisms in periodontal disease.

Periodontitis is an infectious inflammatory disease resulting from infection of biofilm forming bacteria. Several bacterial factors regulate inflammatory response and cause to tissue damage and loss of connection between gingival and tooth. Since bacterial virulence factors and also host immune responses have role, understanding of periodontal disease is complex, in overall we can say that in this disease epithelium is deleted by bacteria. Oral spirochetes are related to periodontitis, among them, Treponema denticola, have been associated with periodontal diseases such as early-onset periodontitis, necrotizing ulcerative gingivitis, and acute pericoronitis. This review will analyse mechanisms of pathogenesis of spirochetes in periodontitis. Microorganisms cause destruction of gingival tissue by two mechanisms. In one, damage results from the direct action of bacterial enzymes and cytotoxic products of bacterial metabolism. In the other, only bacterial components have role, and tissue destruction is the inevitable side effect of a subverted and exaggerated host inflammatory response to plaque antigens.

Nanostructured graphene-based hyperbolic metamaterial performing as a wide-angle near infrared electro-optical switch.

We propose a nanostructured hyperbolic metamaterial (HMM) that can make the transition between elliptic and hyperbolic regimes in the near infrared (IR) frequency range. This switchable HMM is a slab made of a periodic stack of metal/Al(2)O(3)/graphene/Al(2)O(3)/metal nano-layers. By tuning the graphene conductivity via tuning its chemical potential, through a variable external bias, the response of this highly anisotropic medium to a monochromatic TM incident light can be switched between a positive/negative refraction regime and a negative refraction/no-transmission regime. The proposed structure is suitable for applications such as beam splitters, modulators, four-port devices, and optical gates.

Altered tubulin assembly dynamics with N-homocysteinylated human 4R/1N tau in vitro.

Tau isoforms promote neuronal integrity through binding and stabilization of microtubule proteins (MTP). It has been shown that hyperphosphorylation of tau contributes to Alzheimer's disease (AD) pathology and related tauopathies. However, other pathogenic modifications of tau have not been well characterized. It is well accepted that elevated level of homocysteine (Hcy) is associated with neurodegenerative diseases such as AD. As a result of N-homocysteinylation of lysine residues, Hcy becomes a component of proteins, as a protein-homocystamide adduct, which affects protein structure and function. Here we demonstrate that N-homocysteinylation of human tau (4R/1N isoform) inhibits its function via impaired tau-tubulin specific binding and MTP assembly dynamics in vitro.

Waveguide-fed optical hybrid plasmonic patch nano-antenna.

We propose a novel optical hybrid plasmonic patch nano-antenna for operation at the standard telecommunication wavelength of 1550 nm. The nano-antenna is designed to be compatible with a hybrid plasmonic waveguide through matching of both the operational mode and the wave impedance. The antenna is designed to receive the optical signal from a planar waveguide and redirect the signal out of plane, and is therefore useful for inter- or intra-chip optical communications and sensing. The transmission line model in conjunction with surface plasmon theory is used to develop analytical formulas for design and analysis, and a 3-dimensional full-wave numerical method is used to validate the design. The proposed device provides a bandwidth of more than 15 THz, a gain of 5.6 dB, and an efficiency of 87%. Furthermore, by designing an 8 × 8 array of the proposed antenna, a directivity of 20 dBi and steering of the beam angle are achieved by controlling the relative phase shift between elements of the array.