Novel on-chip applications using silicon photonics

The emerging field of silicon photonics offers solutions to designing CMOScompatible optical devices. By taking advantage of the immense fabrication infrastructure offered by the silicon industry, it would be possible to design optical structures that are smaller, faster, less-power consuming and cheaper than traditional, non-silicon-based optical devices. In this dissertation, the design and performance testing of two novel silicon photonic structures are presented: 1) Silicon nanowire ridge waveguide for sensing applications at the optical transmission frequency. 2) Doped silicon plasmonic structures for negative-index, epsilon-near-zero and sensing applications at the mid-infrared. For the first design, silicon nanowires are arranged in a ridge shape to act as a sensitive medium. Most conventional optical sensors rely on evanescent field detection, where only the tail of the incident wave contributes to the sensing process. Silicon nanowires, on the other hand, allow a large portion of the light wave to be present in the low-index-region, which is comprised of the gaps between the nanowires. This feature provides an opportunity for the optical wave to be vastly affected by the refractive index of the gaps between the nanowires. Thus, by introducing materials-under-test, or analytes, to the gaps, the optical signal response is heavily altered, hence, providing a much larger sensitivity than evanescent field sensors. Previous literature has reported on rib-shaped silicon nanowire sensors. We show that the proposed design is more superior in several areas. Firstly, simulations show that ridge-shaped sensors respond slightly more strongly to refractive-index changes than rib-shaped sensors. This could be due to their slightly larger optical overlap with their surroundings, provided by the inherently larger dimensions of the ridge shape. They can also detect up to a 1e-8 refractive-index-changes in the surrounding environment. Secondly and more importantly, single-mode operation, which is usually mandatory for most optical sensor configurations, can be guaranteed using more flexible dimensions for the ridge-shaped nanowire waveguide than for its rib-shaped counterpart. This provides a fabrication convenience, since devices with larger dimensions are generally cheaper and easier to manufacture. Additionally, since the ridge waveguide sports a wide low-thickness region, it can cover the substrate and safe-guard it against erosion during the fabrication process. To further characterize our design, the ridge-shaped silicon nanowire waveguide was put in a bimodal interferometer sensor configuration. The sensitivity obtained through FDTD simulations proved to be very high; its value was comparable to recently reported sensitivities using much larger footprints. This very high sensitivity-to-footprint ratio, along with the CMOS compatibility of the proposed design, deems it as a suitable candidate for on-chip integration. In the second portion of this dissertation, we aim to model and characterize highconfinement plasmonic devices using doped silicon in the mid-infrared range. The midinfrared range is home to some important applications such as molecular sensing, environmental monitoring and security applications. Traditional plasmonic devices possess some much desired features that may be utilized in the mid-infrared. These include hosting a high surface sensitivity, and having the ability to guide and confine light through subwavelength structures, including sharp bends. However, much of these features are exclusive to the near-infrared and visible frequencies, where the plasma resonance of conventional plasmonic materials lie. This is because conventional materials tend to suffer from low confinement in the mid-infrared region, and are rendered inconvenient for applications that require high confinement such as sensing and on-chip communications. For this reason and for its CMOS compatibility, doped silicon plasmonics seems to be a viable solution. We demonstrate that plasma resonance tunability can be achieved through controlling the doping level. Moreover, the dispersion characteristics of doped silicon devices were analyzed for different applications at the mid-infrared region, and displayed valuable phenomenon such as negative dispersion, which can be utilized for slow light and metamaterial applications, and epsilon-near-zero characteristics, that can be used for extraordinary transmission. The mid-infrared dispersion was studied thoroughly for multiple structures, including the slot structure and the rectangular shell structure. The potential for biological and environmental sensing for the aforementioned structures, as well as for a doped silicon nanoparticle was investigated and very high sensitivity was achieved. In addition, the performance of the slot structure in the negative dispersion region was established through using the waveguide as a slow light medium. Moreover, plasmonic structures that can be used for on-chip light-guiding, such as bends and junctions were evaluated. FDTD simulations showed superior performance through successful lightsplitting in gaps as wide as 1μm

Antibody responses to acute COVID-19 infection; assessment via multiplex LABScreen COVID Plus Assay

Background: Understanding the profile of antibody responses following acute COVID-19 infection is required. Aim: to describe the pattern of IgG anti-COVID-19 antibody production in patients with acute infection using the LABScreen COVID Plus assay. Results: The overall seropositivity was 69/73(94.5%). Anti-Spike, Spike 1 and spike S2 subunits were positive in 78.1%, while anti spike receptor binding domain  (RBD) was detected in 68.4% and anti nucleocapsid protein in 61.6%. The overall positivity of the assay reached 100.0% during the second week post symptoms. The mean fluorescent intensities (MFI) of anti-Spike S1 was higher in the second week than the first week, p < /em>=0.03. MFI of anti-Spike S2 was significantly higher in PCR positive patients in comparison with the negative ones, p < /em>=0.006. When compared to the RT-PCR results; the overall antibodies positivity, anti-Spike, and anti-Spike2 antibodies had sensitivities (100% and 84.7%) and specificities (28.6% and 50.0%) and accuracies (86.3% and 78.1%).  Patients' outcome correlated significantly with the time of hospital admission, p < /em>=0.001. Conclusion: COVID-19 IgG antibodies are detectable with considerable frequencies during the first two weeks post infection. Anti S2 antibodies correlates well with the RT-PCR results. The LABScreen COVID Plus is a sensitive assay for the detection of post-acute COVID-19 infection antibody responses.Background: Understanding the profile of antibody responses following acute COVID-19 infection is required. Aim: to describe the pattern of IgG anti-COVID-19 antibody production in patients with acute infection using the LABScreen COVID Plus assay. Results: The overall seropositivity was 69/73(94.5%). Anti-Spike, Spike 1 and spike S2 subunits were positive in 78.1%, while anti spike receptor binding domain  (RBD) was detected in 68.4% and anti nucleocapsid protein in 61.6%. The overall positivity of the assay reached 100.0% during the second week post symptoms. The mean fluorescent intensities (MFI) of anti-Spike S1 was higher in the second week than the first week, p < /em>=0.03. MFI of anti-Spike S2 was significantly higher in PCR positive patients in comparison with the negative ones, p < /em>=0.006. When compared to the RT-PCR results; the overall antibodies positivity, anti-Spike, and anti-Spike2 antibodies had sensitivities (100% and 84.7%) and specificities (28.6% and 50.0%) and accuracies (86.3% and 78.1%).  Patients' outcome correlated significantly with the time of hospital admission, p < /em>=0.001. Conclusion: COVID-19 IgG antibodies are detectable with considerable frequencies during the first two weeks post infection. Anti S2 antibodies correlates well with the RT-PCR results. The LABScreen COVID Plus is a sensitive assay for the detection of post-acute COVID-19 infection antibody responses

Impact of maternal gestational diabetes on neutrophil functions of full term neonates

Background: Maternal gestational diabetes is associated with an inflammatory environment that may contribute to fetal and placental inflammatory profile changes. Few studies investigated the effect of maternal gestational diabetes on neonatal innate immunity.Objectives: Our objective was to study neutrophil number and function in neonates born to mothers with gestational diabetes.Methods: Neutrophil number (complete blood count) and functions [CD11b, CD62L and Dihydrorhodamine 123 (DHR) by flow cytometry] were assessed in the cord blood of 30 full term neonates born to gestational diabetic mothers on insulin during pregnancy and another 15 born to healthy mothers as controls.Results: The mean total leucocytic and absolute neutrophil count were significantly lower in neonates of diabetics than in normal neonates (13.55± 2.51 and 17.89± 3.66 p> 0.001; 9.01±1.59 and 14.18±3.44 p>0.001 respectively). Mean CD11b, CD62L and DHR were lower among neonates of diabetic mothers than normal neonates (82.48± 8.09 & 87.85± 4.87 p < 0.05; 8.63±4.41 and 24.98±10.47 p <0.001; 68.71± 10.24 and 79.57±8.64 p< 0.001 respectively). Unlike the control neonates, neonates of gestational diabetic mothers had positive correlation between the functional neutrophil parameters (r0.39 p<0.05).Conclusion: Gestational diabetes affects cord blood neutrophil count and functions leading to high susceptibility to infection.Keywords: Gestational, diabetes mellitus, neutrophil

Optic nerve head perfusion changes in eyes with proliferative diabetic retinopathy treated with intravitreal ranibizumab or photocoagulation: a randomized controlled trial

Background: Proliferative diabetic retinopathy (PDR) is a serious sight-threatening disease, and half of the patients with high-risk PDR can develop legal blindness within 5 years, if left untreated. This study was aimed at comparing panretinal photocoagulation (PRP) and intravitreal ranibizumab injections in terms of radial peripapillary capillary (RPC) density on optical coherence tomography angiography (OCTA) in patients with treatment-naive PDR.  Methods: This open-label, prospective, randomized clinical trial included 50 patients with treatment-naive PDR with optic disc neovascularization and randomized them into two groups: group 1, with patients undergoing two sessions of PRP 2 weeks apart, and group 2, with patients received three intravitreal ranibizumab injections (0.5 mg) 1 month apart for 3 consecutive months. Patients underwent a full ophthalmological examination, including best-corrected distance visual acuity (BCDVA) measurement in the logarithm of minimal angle of resolution (logMAR) notation and OCTA before intervention and monthly after the last laser session or the first intravitreal ranibizumab injection for 3 months of follow-up. Visual field (VF) was tested at the beginning and end of 3 months.   Results: Forty-two (84%) eyes completed the 3-month follow-up, including 22 eyes in the PRP group (88%) and 20 (80%) eyes in the ranibizumab group. The two groups were comparable in terms of demographic characteristics, diabetes duration, baseline BCDVA, glycated hemoglobin level, OCTA parameters, VF indices, and intraocular pressure (all P > 0.05). The RPC density change from baseline to the 3-month follow-up was significantly lower in the PRP group than in the ranibizumab group (mean difference in RPC density change: - 3.61%; 95% confidence interval: - 5.57% to - 1.60%; P = 0.001). The median (interquartile range) logMAR change from baseline to the 3-month follow-up (0.0 [0.2]) was significantly higher in the PRP group than in the ranibizumab group (- 0.15 [0.3]; P < 0.05). The median changes in central foveal thickness from baseline to the 3-month follow-up differed significantly between the two groups (P = 0.001). Conclusions: In eyes with PDR and neovascularization of the disc RPC density on OCTA increased in the ranibizumab group and decreased in the PRP group. Visual acuity gain was higher in the ranibizumab group than in the PRP group. Future multicenter trials addressing our limitations are required to verify the findings of this study

Facile conversion of the quinone-semicarbazone chromophore of Naftazone into a fluorescent quinol-semicarbazide: kinetic study and analysis of naftazone in pharmaceuticals and human serum

Naftazone is a quinone-semi carbazone drug that possesses a strong orange color, and hence it was usually analyzed colorimetrically or by HPLC-UV. However, these methods are not sensitive enough to determine naftazone in biological samples. Naftazone lacks intrinsic fluorescence and does not possess easily derivatizable functional groups. In this contribution, we introduced the first spectrofluorimetric method for naftazone assay through reduction-elicited fluorogenic derivatization through the reduction of its quinone-semicarbazone moiety to the corresponding quinol-semicarbazide derivative by potassium borohydride as a reduction probe. The solvent-dependent fluorescence of the reaction product was studied in various protic and aprotic solvents. Eventually, the fluorescence of the reduced naftazone was measured in 2-propanol at λemission of 350 nm after excitation at λecxitation of 295 nm. The relative fluorescence intensity was linearly correlated to the drug concentration (r = 0.9995) from 10.0 to 500 ng/mL with high sensitivity, where the lower detection limit was 2.9 ng/mL. Hence, the method was effectively applied for naftazone tablets quality control with a mean %recovery of 100.3 ± 1.5, and the results agreed with those of the comparison HPLC-UV method. Furthermore, a new salting-out assisted liquid-liquid extraction (SALLE) method was established for naftazone extraction from human serum, followed by its determination using the developed reduction-based fluorogenic method. The developed SALLE method showed excellent recovery for naftazone from human serum (92.3−106.5%) with good precision (RSD ≤ 6.8%). Additionally, the reaction of naftazone with potassium borohydride was kinetically monitored, and it was found to follow pseudo-first-order kinetics with an activation energy of 43.8 kcal/mol. The developed method’s greenness was approved using three green analytical chemistry metrics

The School Environment in Egypt. A Situation Analysis of Public Preparatory Schools [Arabic]

Very little research exists in Egypt on contemporary education outcomes and their relationship to an array of education inputs. Also, few datasets are available on the acquisition and retention of basic skills from education. This research aims at filling that gap in our knowledge by drawing a profile of the situation of public preparatory schools, investigating the distinct dimensions of the environment in these schools, and examining the links among these dimensions and specific education outcomes. As noted in this report, this study focuses on the preparatory stage of the general education system. Students in this stage comprise one-quarter of all pre-university students in Egypt

Molecular insights into human transmembrane protease serine-2 (TMPS2) inhibitors against SARS-CoV2: homology modelling, molecular dynamics, and docking studies

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), which caused novel corona virus disease-2019 (COVID-19) pandemic, necessitated a global demand for studies related to genes and enzymes of SARS-CoV2. SARS-CoV2 infection depends on the host cell Angiotensin-Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease-2 (TMPRSS2), where the virus uses ACE2 for entry and TMPRSS2 for S protein priming. The TMPRSS2 gene encodes a Transmembrane Protease Serine-2 protein (TMPS2) that belongs to the serine protease family. There is no crystal structure available for TMPS2, therefore, a homology model was required to establish a putative 3D structure for the enzyme. A homology model was constructed using SWISS-MODEL and evaluations were performed through Ramachandran plots, Verify 3D and Protein Statistical Analysis (ProSA). Molecular dynamics simulations were employed to investigate the stability of the constructed model. Docking of TMPS2 inhibitors, camostat, nafamostat, gabexate, and sivelestat, using Molecular Operating Environment (MOE) software, into the constructed model was performed and the protein-ligand complexes were subjected to MD simulations and computational binding affinity calculations. These in silico studies determined the tertiary structure of TMPS2 amino acid sequence and predicted how ligands bind to the model, which is important for drug development for the prevention and treatment of COVID-19

Factors affecting time to pain relief in patients with osteoid osteoma treated by computed tomography (CT)-guided percutaneous radiofrequency ablation (RFA)

Background: Osteoid osteoma (OO) is a readily treatable, painful benign bone tumor that preferentially afflicts young patients. Computed tomography (CT)-guided percutaneous radiofrequency ablation (RFA) treatment has been accepted since 1992 as a noticeably safe and minimally invasive treatment option for OO. Objective: To prospectively analyze the factors that may affect time to pain relief post CT-guided percutaneous RFA treatment of OO. These factors include patient’s age, sex, amount of sclerosis surrounding the nidus, the relation to nearby joint and the number of muscles that have to be traversed. Materials and methods: This study was conducted on 30 patients diagnosed to have OO on the basis of clinical and radiological criteria. All patients were treated by CT-guided percutaneous RFA. Pain was evaluated after the procedure daily for one week using a visual analogue scale (VAS) with 0 denoting no pain and 10 the worst pain imaginable. Moreover, time to pain relief was analyzed in relation to patient’s age and sex, the amount of sclerosis surrounding the nidus, the relation to nearby joint and the number of muscles that have to be traversed to reach the lesion. Results: There was a highly significant statistical difference (p = 0.001) between the mean time to pain relief in OOs with variable amount of sclerosis surrounding the nidus. On the contrary, there was no significant statistical difference considering patient’s sex (p = 0.654), relation to nearby joint (p = 1.0) or number of muscles that have to be traversed (p = 0.108) in relation to time to pain relief. Considering patient’s age, there was a significant positive correlation (p = 0.013) and (r = 0.446) between patient’s age and time to pain relief. In addition, there was a highly significant positive correlation (p = 0.0001) and (r = 0.636) between the amount of sclerosis surrounding the nidus and time to pain relief. Eventually, the amount of sclerosis surrounding the nidus was shown to be a highly significant independent factor affecting time to pain relief. Conclusion: The amount of sclerosis surrounding the nidus of osteoid osteoma is the most effectual factor for time to pain relief post CT-guided percutaneous radiofrequency ablation treatment

Optical biosensor based on silicon nanowire ridge waveguide

[abstract not available