hazem awad

Spina bifida (SB) is the second most common nonlethal congenital malformation. The existence of monogenic SB mouse models and human monogenic syndromes with SB features indicate that human SB may be caused by monogenic genes. We hypothesized that whole exome sequencing (WES) allows identification of potential candidate genes by (i) generating a list of 136 candidate genes for SB, and (ii) by unbiased exome‐wide analysis. We generated a list of 136 potential candidate genes from three categories and evaluated WES data of 50 unrelated SB cases for likely deleterious variants in 136 potential candidate genes, and for potential SB candidate genes exome‐wide. We identified 6 likely deleterious variants in 6 of the 136 potential SB candidate genes in 6 of the 50 SB cases, whereof 4 genes were derived from mouse models, 1 gene was derived from human nonsyndromic SB, and 1 gene was derived from candidate genes known to cause human syndromic SB. In addition, by unbiased exome‐wide analysis, we identified 12 genes as potential candidates for SB. Identification of these 18 potential candidate genes in larger SB cohorts will help decide which ones can be considered as novel monogenic causes of human SB.

This thesis details the simulation and experimental validation of several all-optical signal-processing configurations that utilise competitive optics principles. Competitive optics refers to any number of optical systems where different optical modes or wavelengths compete for a limited system resource, such as the optical gain of some common gain medium, in order to receive amplification. The gain medium can utilise different materials including photorefractive materials (e.g. BaTO3 crystals) and saturated gain material (e.g. semiconductor optical amplifiers). Competitive optics configurations are capable of sophisticated all-optical signal processing functions ranging from all-optical wavelength conversion to optical logic and storage. This thesis will present a series of simulated competitive optics configurations that utilise a semiconductor ring laser a basic competitive optics structure. These simulations will prove the viability and validity of competitive optics configurations that utilise saturated gain material, specifically the Semiconductor Optical Amplifier. The thesis will demonstrate the application of the Lotka-Volterra mathematical model of competitive interactions to the modelling of some of aforementioned configurations. Finally, experimental investigations of different semiconductor ring lasers configurations are presented and analysed from a competitive optics point of view.

Moderate or intense low-oxygen dilution (MILD) combustion is a novel combustion technique that can simultaneously improve thermal efficiency and reduce emissions. This paper focuses on the differences in statistical behaviours of the surface density function (SDF = magnitude of the reaction progress variable gradient) between conventional premixed flames and exhaust gas recirculation (EGR) type homogeneous-mixture combustion under MILD conditions using direct numerical simulations (DNS) data. The mean values of the SDF in the MILD combustion cases were found to be significantly smaller than those in the corresponding premixed flame cases. Moreover, the mean behaviour of the SDF in response to the variations of turbulence intensity were compared between MILD and premixed flame cases, and the differences are explained in terms of the strain rates induced by fluid motion and the ones arising from flame displacement speed. It was found that the effects of dilatation rate were much weake...

Congenital anomalies of the kidneys and urinary tract (CAKUT) constitute the most common cause of early‐onset chronic kidney disease. In a previous study, we identified a heterozygous truncating variant in nuclear receptor‐interacting protein 1 (NRIP1) as CAKUT causing via dysregulation of retinoic acid signaling. This large family remains the only family with NRIP1 variant reported so far. Here, we describe one additional CAKUT family with a truncating variant in NRIP1. By whole‐exome sequencing, we identified one heterozygous frameshift variant (p.Asn676Lysfs*27) in an isolated CAKUT patient with bilateral hydroureteronephrosis and right grade V vesicoureteral reflux (VUR) and in the affected father with left renal hypoplasia. The variant is present twice in a heterozygous state in the gnomAD database of 125,000 control individuals. We report the second CAKUT family with a truncating variant in NRIP1, confirming that loss‐of‐function mutations in NRIP1 are a novel monogenic cause of human autosomal dominant CAKUT.

ABSTRACT We describe the design and fabrication of a lambda/4 phase-shifted laterally-coupled distributed-feedback laser. The third-order grating for distributed-feedback is fabricated without regrowth using stepper lithography, a process that is amenable to high-yield, low-cost manufacturing.

We introduce a novel gas sensor based on photonic crystal (PhC) waveguides where the gas sensing is based on the interaction between the slow light mode and the gas. Specifically, when the refractive index of the photonic crystal waveguide changes (due to a change in gas), the slow light regime of the photonic crystal waveguide is affected and shifts in wavelength. We have performed experiments with Helium and Argon gases to confirm the operation of the sensor, with Air being used as reference gas. Results show that the slow light regime typically shifts by 0.6 nm for Helium and 0.05nm for Argon.

Influenza can cause severe infection in hematology/oncology patients. The occurrence of the 2009 pandemic represented an opportunity to study the impact of influenza on such patients in pandemic and post-pandemic seasons. We retrospectively reviewed medical records of hematology/oncology patients who had laboratory-confirmed influenza infection during the 2009 pandemic and the first post-pandemic seasons. We assessed influenza-related outcomes in both seasons with emphasis on the development of pneumonia and mortality. We also analyzed factors associated with poor outcomes. We included 350 patients; 207 were diagnosed in the pandemic and 143 in the post-pandemic seasons. Influenza severity was similar in both seasons with no significant differences in the development of pneumonia or death. Infection with the pH1N1 virus was associated with the development of pneumonia (24.7% vs 14.9%, p = 0.029) but did not affect mortality. A multivariate analysis showed that initiation of antiviral treatment after > 48 h, healthcare acquisition of influenza, and low albumin were independent risk factors for the development of pneumonia (p values 0.022, 0.003, and < 0.0001, respectively). A log-rank test showed increased mortality in patients who received therapy > 48 h after onset of symptoms (p = 0.001). In hematology/oncology patients, influenza was as severe in the post-pandemic as in the pandemic season. Pneumonia developed more commonly in patients infected with pH1N1 virus. Healthcare acquisition of infection and low albumin were associated with the development of pneumonia. Delayed initiation of antiviral treatment was associated with both pneumonia and mortality.

Stability and linewidth (FWHM & 20-dB) measurements of a tuneable, high power, narrow linewidth multiwavelength Hybrid Cavity Semiconductor Fibre Ring Laser (HC-SFRL) are presented. The laser incorporates a SOA, a polarization controller (PC), and a tuneable optical filter. The ring cavity itself is composed of Single Mode Fibre (SMF) and a 1-m long Polarization Maintaining Fibre (PMF). The laser is

ABSTRACT A novel SOA based fibre ring laser is presented. An S-band optimized SOA is added to the cavity of a C-band SOA fibre ring laser resulting in significant improvements in the ring laser characteristics. Three main linewidth control parameters are identified: 1) Bias current of C-band SOA, 2) Bias current of S-band SOA, and 3) SOP of lasing light in ring's cavity. Experimental measurements suggest the SOP of the lasing light to be the dominant control parameter for reduction or enhancement of the laser's linewidth. An output power level of 5.27 dBm (corresponding to 10.54 dBm cavity power) and less than 20 kHz FWHM (limited by equipment resolution) and 190 kHz 20-dB linewidth at 1558 nm is demonstrated. The measured 20-dB linewidths displayed stronger variations to changes in the bias currents of the ring lasers compared to variations in the FWHM. This suggests that the optical spectrum of the ring lasers becomes asymmetric at high bias currents and is no longer pure Lorentzian.

In this paper we introduce a multi gas sensor system based on refractive index changes in a 2D slab photonic crystal. The sensor is formed by a L3 resonant cavity sandwiched between two W1.06 waveguides in the photonic crystal. The sensor configuration is similar to an ...

ABSTRACT An innovative technique to tune the slow light propagated through photonic crystal cavity filled with E7 type nematic crystal has been simulated and presented. Observed propagating modes in the previously fabricated photonic crystal indicate that both slow and fast modes propagate in the waveguide. Design efforts were made to adjust the propagating modes as well as their group velocities. Numerical studies show that by inserting nematic liquid crystal, designer can achieve additional degree of freedom to tune the device by using external perturbation such as applying heat or electric field. Comparative studies have also been done to see the performance of the devices fabricated in two deferent material platforms (silicon and InP) with an objective to develop economic and efficient functional material systems for building robust integrated photonic devices that have the ability to slow, store, and process light pulses.

Abstract. Slow light propagated through a photonic crystal with a nematic liquid crystal-filled cavity has been simulated and presented. Both slow and fast modes propagate in the waveguide. Design efforts were made to adjust the group velocities of the propagating modes. Numerical studies show that the nematic liquid crystal provides designers an additional degree of freedom to tune the device by using external perturbations such as applying heat or electric field. Comparative studies have also been done to see the performance of the devices built in two different material platforms (silicon and InP). The device can be used as an economic and efficient functional materials system for building robust integrated photonic devices that have the ability to slow, store, and process light pulses.