DeepLab V3+ Based Semantic Segmentation of COVID -19 Lesions in Computed Tomography Images

Abstract- Coronavirus 2019 spreads rapidly worldwide causing a global epidemic. Early detection and diagnosis of COVID-19 is critical for treatment as it causes respiratory syndrome appears in the chest medical images, such as computed tomography (CT) images, and X-ray images. The CT images are more sensitive and have more details compared to the X-ray images. Thus, automated segmentation plays an imperative role in detecting, diagnosing, and determining the spreading of COVID-19. In this paper, the DeepLabV3+ combined with MobileNet-V2 model was implemented. To validate this combination, we conducted a comparative study between the DeepLabV3+ variants by its combination with MobileNet-V2 against DeepLabV3+ combined with different CNN, namely ResNet-18, and ResNet50. Also, a comparative study with the basic traditional U-Net and modified Alex for segmentation was carried out. The experimental results showed the superiority of the using DeepLabV3+ combined with MobileNet-V2 for COVID-19 segmentation by achieving 97.5% mean accuracy, 95.2% sensitivity, 99.7% specificity, 99.7% precision, 99.3 % weighted Jaccard coefficient, and 97.5% weighted dice coefficient

Sero-prevalence and risk factors associated with toxoplasma gondii infection among pregnant women in Alexandria, Egypt

Background: Toxoplasma gondii infection during pregnancy can result in fetal death, neonatal death or various congenital defects. This study aimed to estimate the seroprevalence of toxoplasma gondii infection using two different diagnostic tests, Enzyme-Linked Immunosorbent Assay (ELISA) versus Immunochromatographic assay (ICA) and to study the potential risk factors for acquiring infection in pregnant women attending antenatal care clinics in Alexandria, Egypt.Methods: A cross sectional study, conducted between May 2015 and June 2016. The study was done in antenatal care centers of most districts of Alexandria Governorate, Egypt. 382 pregnant women, of a gestational age between 8-40 weeks were included in the study and were given pretested structured questionnaire to assess risk factors, which included: demographic, socio-economic data, kitchen hygiene and behavioral variables. Blood samples were taken and sera were divided into two parts; the first part was examined for anti-T.gondii IgG and IgM antibodies using rapid diagnostic test RDT kit, the other part tested by ELISA.Results: The overall seroprevalence of T.gondii infection was (11.3%) detected by RDT, significantly increased to (57.9%) by ELISA test (X2= 5.3; p=0.001). RDT had the sensitivity of (15.8%), the specificity of (95%), PPV of (81.4%), NPV of (45.1%), with overall diagnostic efficiency of (49.2%). The association between T.gondii infection and the age of the pregnant women was found to be statistically significant (OR=2.84, 95%CI=1.251-6.455).Conclusions: The present study has documented a bad diagnostic performance of RDT in detection T.gondii in serum samples of infected pregnant women as compared to ELISA technique. Age is the only risk factor to be associated statistically with toxoplasma gondii infection

Care Bundle Application Decreases The Frequency and Severity of Intraventricular Hemorrhage in Preterm Neonates: Single Center Study

Background: Intraventricular hemorrhage (IVH) is a severe complication in preterm babies admitted to Neonatal Intensive Care Units (NICU). Advanced stages of IVH predispose to neurological deficits such as cerebral palsy and hydrocephalus. There are numerous strategies and policies implemented in NICUs around the world to decrease the incidence of IVH in preterm babies and prevent its ensuing neurodevelopmental complications. Aim of the Work: To study the effect of implementing a bundle of care on incidence and severity of IVH among preterm neonates. Materials and Methods: Retrospective analysis of patient records for incidence and severity of IVH between May and August 2018 was done. This was followed by an educational interim period where NICU staff received training of pre-natal, natal, and postnatal care bundle guidelines to reduce IVH. The guidelines were then implemented on all preterm babies (28-34 weeks gestational age (GA)) born and admitted to Kasr Al Ainy Teaching Hospital NICU, Cairo University between October 2018 and January 2019 (n=58). Cranial ultrasonography was performed at week 1 and week 2-3 of life. Frequency and severity of IVH were compared among studied groups. Risk factors for IVH were analyzed and recorded. Results: The frequency of IVH was significantly lower in the post-bundle group (44-46% pre-bundle, and 27% post-bundle) especially evidenced by the ultrasonography in week two of life. Severity of IVH also improved post bundle since there were no grade III IVH patients in that group. Exposure to hypocapnia, blood pressure fluctuations, IV fluid boluses and administration of sodium bicarbonate were significantly correlated with development of IVH in preterm babies (p = 0.001). Conclusion: Implementation of an IVH care bundle that includes perinatal measures can positively affect the neurological outcome by decreasing incidence and severity of IVH in preterm babies

Introduction to Arabic: Egyptian Arabic for first-year students

422 page pdf and alternative eBook version.This textbook was written to accompany ARB 101 at University of Oregon.This book presents materials for mastering the Arabic alphabet and the student's first steps in Egyptian Arabic. This book contains interactive activities that can only be accessed through the web version of this book which can be found at: https://opentext.uoregon.edu/introarabic/ (clickable link above).Open Oregon Educational Resource

Nucleotide Oligomerization Domain-like receptor 4 (NLR4) Gene Expression and Interleukin 1-β (IL 1-β) Level in Urine Samples Before and After Intravesical BCG Therapy For Treatment of Bladder Cancer

Bladder cancer is the 7th most commonly diagnosed cancer in males worldwide and the 11th when both genders are considered. Seventy five per cent of bladder cancer cases are non-muscle invasive bladder cancer (NMIBC). Bacillus Calmette–Gu rin (BCG) immunotherapy remains the standard intravesical agent for NMIBC. The exact mechanism by which BCG prevents recurrence is unknown. The aim of this study was to evaluate NLR4 gene expression and IL-1β as possible prognostic indicators for NMIBC recurrence and BCG treatment failure, and to detect the difference in their levels among muscle invasive bladder cancer (MIBC) and NMIBC that may aid in primary differentiation between cases. This study was conducted in 30 patients who had NMIBC and 17 patients who had MIBC. Urine samples were obtained in sterile cups before operation. From NMIBC cases, four more samples were obtained as mentioned below. Evaluation of NLR4 gene expression was performed in pre-surgical sample for MIBC and in 4 samples for NMIBC: pre-surgical sample, sample collected 4 hours after the 3rd dose of BCG instillation, and samples collected during follow up (3 and 6 months post-surgically). There was statistical significant increase in NLRP4 expression levels in NMIBC (CT=0.87±1.48) compared to MIBC (CT=2.82±2.07). As far as we searched, no published results were found regarding comparative gene expression levels between NMIBC and MIBC cases. Gene expression in recurrent cases was higher in pre-surgical urine samples than in non-recurrent cases. The expression level further increased up to 21 fold than the pre-surgical level in the sample taken after injection of the 3rd dose of BCG. This level decreased distinctly to become 1-fold increase over pre-surgical level at the 3rd month follow up then to only 0.9-fold at the 6th month. In non- recurrent cases, gene expression level started pre-surgically in much lower levels than those encountered in recurrent cases. There were 11-fold increase in expression level after 3rd dose of BCG instillation and then decreased to be 5.6 folds higher in the sample taken at 3rd month follow up than in presurgical samples. Gene expression further decreased to become 4.1 fold higher in samples taken at 6 month follow up than the pre-surgical levels. IL-1β levels were estimated for NMIBC and MIBC cases in urine samples pre-surgically and during BCG therapy in case of NMIBC before and 4 hours after the 3rd dose and during 3rd month follow-up of those cases for searching its possible use of for primary differentiation between NMIBC and MIBC, and also as a prognostic factor for possible recurrence in case of NMIBC cases. The level of IL-1β was generally higher in pre-surgical samples (0.62±0.12 pg/ml) when compared to its level before the 3rd dose of BCG induction therapy (0.53±0.13 pg/ml). Its level was distinctly higher four hours after administration of the 3rd dose BCG (1.96±0.62 pg/ml) than both previous levels. Levels decreased bellow pre-surgical level at 3rd month follow up (0.57±0.099 pg/ml). The levels of IL-1β estimated in samples collected four hours after the 3rd dose BCG was higher in cases that showed recurrence later on than non-recurrent cases. The levels decreased in both cases and became higher in non-recurrent cases (0.64±0.05 pg/ml) than in cases already developed recurrence at the 3rd month diagnosed during follow-up (0.45±0.05 pg/ml). To conclude, on following NLRP4 gene expression and IL-1β levels during BCG administration among recurrent and non-recurrent cases of thirty NMIBC cases, there was a significant statistical difference in both levels for the samples collected after the third dose BCG, being higher in patients who showed subsequent recurrence at the 3rd and 6th month of follow-up. If these preliminary reported findings will be confirmed in upcoming larger cohort’s studies, it could be promising in prognosis of such cases, with the possibility of early manipulation of individualized treatment schedule, keeping patients most probably prone to encounter recurrence safe from possible side effects of BCG therapy. The assessment of NLRP4 expression and IL-1β levels could help predict failure of BCG therapy, playing an appreciable role in early deciding radical surgery. When comparing NLRP4 expression and IL-1β levels between MIBC and NMIBC cases, increased values were noted among non-invasive ones. This finding may serve as a possible diagnostic tool, which represents a challenging issue. Hence, cut-off values for gene expression and cytokine level are to be specified

Characterization of greater middle eastern genetic variation for enhanced disease gene discovery

The Greater Middle East (GME) has been a central hub of human migration and population admixture. The tradition of consanguinity, variably practiced in the Persian Gulf region, North Africa, and Central Asia1-3, has resulted in an elevated burden of recessive disease4. Here we generated a whole-exome GME variome from 1,111 unrelated subjects. We detected substantial diversity and admixture in continental and subregional populations, corresponding to several ancient founder populations with little evidence of bottlenecks. Measured consanguinity rates were an order of magnitude above those in other sampled populations, and the GME population exhibited an increased burden of runs of homozygosity (ROHs) but showed no evidence for reduced burden of deleterious variation due to classically theorized ‘genetic purging’. Applying this database to unsolved recessive conditions in the GME population reduced the number of potential disease-causing variants by four- to sevenfold. These results show variegated genetic architecture in GME populations and support future human genetic discoveries in Mendelian and population genetics

Geochemical and Isotopic Evidence of Groundwater Salinization Processes in El Dabaa Area, Northwestern Coast, Egypt

El Dabaa city is located along the northwestern coast ridge zone of Egypt, where the groundwater is the major water source for drinking, domestic, and agricultural purposes. The groundwater salinity increased over the last decades, therefore, geochemical techniques and environmental isotopes have been utilized to identify the main groundwater recharge and salinization sources. The study area comprises two main groundwater aquifers: the porous oolitic Pleistocene and the fractured limestone Miocene aquifers. The groundwater salinity of the Pleistocene aquifer ranges from 751 to 27,870 mg/L, with an average value of 6006 mg/L. The salinity of the Miocene aquifer ranges from 3645 to 41,357 mg/L, with an average value of 11,897 mg/L. Fresh and brackish groundwater have been recorded in the shallow hand-dug wells, while saline groundwater has been found in deeper wells close to the shoreline. Groundwater samples have been categorized into two distinct groups according to the salinity ranges, hydrochemical ion ratios, and stable isotopic content. Group I is composed of groundwater with salinity less than 10,000 mg/L, and depleted stable isotopic content (−5.64 < δ18O < −2.45; −23.5 < δ2H < −0.02), while Group II contains groundwater with salinity values above 10,000 mg/L and relatively enriched stable isotopic content (−1.86 < δ18O < −0.48; −10.3 < δ2H < −2.0). The weight mass balance mixing model shows that Group I falls close to the rain and/or water extract samples, indicating meteoric water origin that has evolved due to leaching and dissolution processes. Group II is mostly located between the rainwater and the seawater samples, revealing mixing with water of marine origin due to groundwater overexploitation. The estimated seawater mixing index (SMI) of groundwater samples of Group II is greater than one, which confirms mixing with seawater. The water-rock reaction NETPATH (geochemical groundwater reaction and mixing code) model scenarios representing Group I suggests that gypsum, dolomite, and halite are dissolved, while calcite is formed with a slight influence from evaporation processes. Six mixing models representing Group II are used to investigate seawater mixing scenarios. The models suggest that illite and dolomite are dissolved, while calcite and gypsum are precipitated with a seawater mixing ratios ranging from 28% to 98%. In conclusion, due to the scarcity of annual groundwater recharge in the El Dabaa area, groundwater withdrawal should be well managed to avoid groundwater salinization and further seawater intrusion

Sero-prevalence and risk factors associated with toxoplasma gondii infection among pregnant women in Alexandria, Egypt

Background: Toxoplasma gondii infection during pregnancy can result in fetal death, neonatal death or various congenital defects. This study aimed to estimate the seroprevalence of toxoplasma gondii infection using two different diagnostic tests, Enzyme-Linked Immunosorbent Assay (ELISA) versus Immunochromatographic assay (ICA) and to study the potential risk factors for acquiring infection in pregnant women attending antenatal care clinics in Alexandria, Egypt.Methods: A cross sectional study, conducted between May 2015 and June 2016. The study was done in antenatal care centers of most districts of Alexandria Governorate, Egypt. 382 pregnant women, of a gestational age between 8-40 weeks were included in the study and were given pretested structured questionnaire to assess risk factors, which included: demographic, socio-economic data, kitchen hygiene and behavioral variables. Blood samples were taken and sera were divided into two parts; the first part was examined for anti-T.gondii IgG and IgM antibodies using rapid diagnostic test RDT kit, the other part tested by ELISA.Results: The overall seroprevalence of T.gondii infection was (11.3%) detected by RDT, significantly increased to (57.9%) by ELISA test (X2= 5.3; p=0.001). RDT had the sensitivity of (15.8%), the specificity of (95%), PPV of (81.4%), NPV of (45.1%), with overall diagnostic efficiency of (49.2%). The association between T.gondii infection and the age of the pregnant women was found to be statistically significant (OR=2.84, 95%CI=1.251-6.455).Conclusions: The present study has documented a bad diagnostic performance of RDT in detection T.gondii in serum samples of infected pregnant women as compared to ELISA technique. Age is the only risk factor to be associated statistically with toxoplasma gondii infection

A New Design Identification and Control Based on GA Optimization for An Autonomous Wheelchair

The daily lifestyle of an average human has changed drastically. Robotics and AI systems are applied to many fields, including the medical field. An autonomous wheelchair that improves the degree of independence that a wheelchair user has can be a very useful contribution to society. This paper presents the design and implementation of an autonomous wheelchair that uses LIDAR to navigate and perform SLAM. It uses the ROS framework and allows the user to choose a goal position through a touchscreen or using deep learning-based voice recognition. It also presents a practical implementation of system identification and optimization of PID control gains, which are applied to the autonomous wheelchair robot. Input/output data were collected using Arduino, consisting of linear and angular speeds and wheel PWM signal commands, and several black-box models were developed to simulate the actual wheelchair setup. The best-identified model was the NLARX model, which had the highest square error (0.1259) among the other candidate models. In addition, using MATLAB, Optimal PID gains were obtained from the genetic algorithm. Performance on real hardware was evaluated and compared to the identified model response. The two responses were identical, except for some of the noise due to the encoder measurement errors and wheelchair vibration

Polysaccharide extracts of the brown alga <i>Sargassum</i><i>asperifolium</i> possess <i>in vitro</i> cancer chemopreventive properties

<div><p>The cancer chemopreventive activity of the polysaccharide extracts (<b>E1</b>–<b>E4</b>) of <i>Sargassum asperifolium</i>, a brown alga in Red Sea shores in Egypt, was investigated. Tumour anti-initiation activity (the modulation of carcinogen metabolism) indicated that <b>E3</b> and <b>E4</b> were potent anti-initiators by inhibiting the carcinogen activator cytochrome P450-1A, and enhancing carcinogen detoxification enzymes glutathione-<i>S</i>-transferase. Only <b>E4</b> significantly enhanced quinone reductase activity. All polysaccharide extracts possessed anti-promotion property by their anti-inflammatory activity. <b>E3</b> and <b>E4</b> dramatically induced the growth of spleen macrophages. <b>E2</b>, <b>E3</b> and <b>E4</b> significantly inhibited nitric oxide generation from lipopolysaccharide (LPS)-stimulated spleen macrophages, while <b>E1</b>, <b>E3</b> and <b>E4</b> led to significant inhibition of LPS-induced tumour necrosis factor-α. The extracts <b>E1</b>, <b>E2</b> and <b>E4</b> showed cytotoxicity against HepG2 cells, where <b>E2</b> and <b>E4</b> induced cell death due to apoptosis. In conclusion, <b>E3</b> and <b>E4</b> are promising cancer chemopreventive extracts, since they had tumour anti-initiating activity via their protective modulation of carcinogen metabolism.</p></div