Search results for: Iman I. Salama

Authors: Behrang Ekrami, Amin Tamadon, Iman Razeghian Jahromi, Darioush Moghadas, Mehdi Ghahremani-Seno, Mostafa Ghaderi-Zefrehei, Ahmad Sodagar Amiri, Taheri Reza

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Persian fallow deer (Dama dama mesopotamica) is belonging to the family Cervidae and is only found in a few protected areas in the northwest, north, and southwest of Iran. The aims of this study were analysis of inbreeding and morphometric parameters of semen in male Persian fallow deer to investigate the cause of reduced fertility of this endangered species in Dasht-e-Naz National Refuge, Sari, Iran. The Persian fallow deer semen was collected from four adult bucks randomly during the breeding and non-breeding season from five dehorned and horned deer's by an artificial vagina. Twelve blood samples was taken from Persian fallow deer and mitochondrial DNA was extracted, amplified, extracted, sequenced and then were considered for genetic analysis. The Persian fallow deer semen, both with normal and abnormal spermatozoa, is similar to that of domestic ruminants but very smaller and difficult to observe at the primary observation. The post-mating season collected ejaculates contained abnormal spermatozoa, debris and secretion of accessory glands in horned bucks and accessory glands secretion free of any spermatozoa in dehorned or early velvet budding bucks. Microscopic evaluation in all four bucks during the mating season showed the mean concentration of 9×106 spermatozoa/ml. The mean ± SD of age, testes length and testes width was 4.60 ± 1.52 years, 3.58 ± 0.32 and 1.86 ± 0.09 cm, respectively. The results identified 1120 loci (assuming each nucleotide as locus) in which 377 were polymorphic. In conclusion, reduced fertility of male Persian fallow deer may be caused by inbreeding of the protected herd in a limited area of Dasht-e-Naz National Refuge.

Keywords: Persian fallow deer, genetic analysis, spermatozoa, reproductive characteristics

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Authors: Heba Salama, Barry Gibson, Jennifer Burr

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Introduction: It is often argued that better oral health leads to better wellbeing, and the goal of dental care is to improve wellbeing. Notwithstanding, to our best knowledge, there is a lack of evidence to support the relationship between oral health and wellbeing. Aim: The scoping review aims to examine current definitions of health and wellbeing as well as map the evidence to examine the relationship between oral health and wellbeing. Methods: The scoping review followed the Preferred Reporting Items for Systematic Reviews Extension for Scoping Review (PRISMA-ScR). A two-phase search strategy was followed because of the unmanageable number of hits returned. The first phase was to identify how well-being was conceptualised in oral health literacy, and the second phase was to search for extracted keywords. The extracted keywords were searched in four databases: PubMed, CINAHL, PsycINFO, and Web of Science. To limit the number of studies to a manageable amount, the search was limited to the open-access studies that have been published in the last five years (from 2018 to 2022). Results: Only eight studies (0.1%) of the 5455 results met the review inclusion criteria. Most of the included studies defined wellbeing based on the hedonic theory. And the Satisfaction with Life Scale is the most used. Although the research results are inconsistent, it has generally been shown that there is a weak or no association between oral health and wellbeing. Interpretation: The review revealed a very important point about how oral health literature uses loose definitions that have significant implications for empirical research. That results in misleading evidence-based conclusions. According to the review results, improving oral health is not a key factor in improving wellbeing. It appears that investing in oral health care to improve wellbeing is not a top priority to tell policymakers about. This does not imply that there should be no investment in oral health care to improve oral health. That could have an indirect link to wellbeing by eliminating the potential oral health-related barriers to quality of life that could represent the foundation of wellbeing. Limitation: Only the most recent five years (2018–2022), peer-reviewed English-language literature, and four electronic databases were included in the search. These restrictions were put in place to keep the volume of literature at a manageable level. This suggests that some significant studies might have been omitted. Furthermore, the study used a definition of wellbeing that is currently being evolved and might not everyone agrees with it. Conclusion: Whilst it is a ubiquitous argument that oral health is related to wellbeing, and this seems logical, there is little empirical evidence to support this claim. This question, therefore, requires much more detailed consideration. Funding: This project was funded by the Ministry of Higher Education and Scientific Research in Libya and Tripoli University.

Keywords: oral health, wellbeing, satisfaction, emotion, quality of life, oral health related quality of life

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Authors: R. A. Abdel Rahman, A. E. Abdel Wahab, E. A. Goghneimy, H. F. Mohamed, E. M. Salama

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Infectious diseases are a major cause of death worldwide. The treatment of infections continues to be problematic in modern time because of the severe side effects of some drugs and the growing resistance to antimicrobial agents. Hence, the search for newer, safer and more potent antimicrobials is a pressing need. Herbal medicines have received much attention as a source of new antibacterial drugs since they are considered time-tested and comparatively safe both for human use and the environment. In the present study, the antimicrobial activity of marjoram (Origanum majorana L.) essential oil on some gram positive and gram negative reference bacteria, as well as some hospital resistant microbes, was tested. Marjoram oil was extracted and the oil chemical constituents were identified using GC/MS analysis. Staphylococcus aureas ATCC 6923, Pseudomonus auregonosa ATCC 9027, Bacillus subtilis ATCC 6633, E. coli ATCC 8736 and two hospital resistant microbes isolates 16 and 21 were used. The two isolates were identified by biochemical tests and 16s rRNA as proteus spp. and Enterococcus facielus. The effect of different concentrations of essential oils on bacterial growth was tested using agar disk diffusion assay method to determine the minimum inhibitory concentrations and using micro dilution method to determine the minimum bactericidal concentrations. Marjoram oil was found to be effective against both reference and hospital resistance strains. Hospital strains were more resistant to marjoram oil than reference strains. P. auregonosa growth was completely inhibited at a low concentration of oil (4µl/ml). The other reference strains showed sensitivity to marjoram oil at concentrations ranged from 5 to 7µl/ml. The two hospital strains showed sensitivity at media containing 10 and 15µl/ml oil. The major components of oil were terpineol, cis-beta (23.5%), 1,6 – octadien –3-ol,3,7-dimethyl, 2 aminobenzoate (10.9%), alpha terpieol (8.6%) and linalool (6.3%). Scanning electron microscope (SEM) and transmission electron microscope (TEM) analysis were used to determine the difference between treated and untreated hospital strains. SEM results showed that treated cells were smaller in size than control cells. TEM data showed that cell lysis has occurred to treated cells. Treated cells have ruptured cell wall and appeared empty of cytoplasm compared to control cells which shown to be intact with normal volume of cytoplasm. The results indicated that marjoram oil has a positive antimicrobial effect on hospital resistance microbes. Natural crude extracts can be perfect resources for new antimicrobial drugs.

Keywords: antimicrobial activity, essential oil, hospital resistance microbes, marjoram

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Authors: I. M. Salama, R. N. Miftahof

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A functional element of the myenteric nervous plexus is a morphologically distinct ganglion. Composed of sensory, inter- and motor neurons and arranged via synapses in neuronal circuits, their task is to decipher and integrate spike coded information within the plexus into regulatory output signals. The stability of signal processing in response to a wide range of internal/external perturbations depends on the plasticity of individual neurons. Any aberrations in this inherent property may lead to instability with the development of a dynamics chaos and can be manifested as pathological conditions, such as intestinal dysrhythmia, irritable bowel syndrome. The aim of this study is to investigate patterns of signal transduction within a two-neuronal chain - a ganglion - under normal physiological and structurally altered states. The ganglion contains the primary sensory (AH-type) and motor (S-type) neurons linked through a cholinergic dendro somatic synapse. The neurons have distinguished electrophysiological characteristics including levels of the resting and threshold membrane potentials and spiking activity. These are results of ionic channel dynamics namely: Na+, K+, Ca++- activated K+, Ca++ and Cl-. Mechanical stretches of various intensities and frequencies are applied at the receptive field of the AH-neuron generate a cascade of electrochemical events along the chain. At low frequencies, ν < 0.3 Hz, neurons demonstrate strong connectivity and coherent firing. The AH-neuron shows phasic bursting with spike frequency adaptation while the S-neuron responds with tonic bursts. At high frequency, ν > 0.5 Hz, the pattern of electrical activity changes to rebound and mixed mode bursting, respectively, indicating ganglionic loss of plasticity and adaptability. A simultaneous increase in neuronal conductivity for Na+, K+ and Ca++ ions results in tonic mixed spiking of the sensory neuron and class 2 excitability of the motor neuron. Although the signal transduction along the chain remains stable the synchrony in firing pattern is not maintained and the number of discharges of the S-type neuron is significantly reduced. A concomitant increase in Ca++- activated K+ and a decrease in K+ in conductivities re-establishes weak connectivity between the two neurons and converts their firing pattern to a bistable mode. It is thus demonstrated that neuronal plasticity and adaptability have a stabilizing effect on the dynamics of signal processing in the ganglion. Functional modulations of neuronal ion channel permeability, achieved in vivo and in vitro pharmacologically, can improve connectivity between neurons. These findings are consistent with experimental electrophysiological recordings from myenteric ganglia in intestinal dysrhythmia and suggest possible pathophysiological mechanisms.

Keywords: neuronal chain, signal transduction, plasticity, stability

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Authors: Iram Zahair, Tanith Rose, Oyinlola Oyebode, Stephen Clayton, Iman Ghosh, Michelle Maden, Ben Barr

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Background: Gastrointestinal infections exert a significant public health burden on UK healthcare services and the community. However, there are conflicting findings on where ethnic inequalities are likely to persist. This systematic review aimed to identify studies that ascertain differences in the incidence and prevalence of gastrointestinal infections within and between UK ethnic groups and explore possible explanations for heterogeneity observed within the literature. Methods: Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidance, a systematic review methodology was used. Medline, Web of Science, CINAHL Plus, and grey literature were searched from 1980 to 2021 for studies reporting an association between ethnicity and gastrointestinal infections in UK population samples. Two reviewers independently screened the articles and conducted quality appraisals; data extraction was undertaken by one reviewer and verified by two reviewers (PROSPERO CRD 42021240714). A narrative synthesis was undertaken to synthesise the study findings. Results: The searches identified 8134 studies; 13 met the inclusion criteria. 12 out of 13 studies found a difference in the prevalence of gastrointestinal infections between different ethnic groups. UK ethnic minorities, predominantly men and children of Asian ethnicity, had an increased risk of infection than the white British majority in 12 studies; the Pakistani ethnic group had a higher risk of infection in three out of 13 studies. Studies reported that age and sex confounded the relationship between ethnicity and gastrointestinal infections. At the same time, the country of birth, socioeconomic status, and geographical location of ethnic groups mediated this association and significantly explained the heterogeneity observed across the studies. Harvest plots supported the textual synthesis. Conclusion: This systematic review elucidates the lack of extensive UK quantitative evidence examining the association between ethnicity and gastrointestinal infections. Insights into gastrointestinal infections and ethnicity's association can help address policy actions to mitigate the inequalities identified within and between UK ethnic groups.

Keywords: ethnic and racial populations, public health, public health policy, systematic review

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Authors: Nur Iman Subono, Meidi Kosandi

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This paper examines the role of regional cooperation in the Association of Southeast Asian Nations (ASEAN) in the fight against human trafficking for Indonesia. Many among scholars suggest that regional cooperation is necessary for combating human trafficking for its transnational and organized character as a crime against humanity. ASEAN members have been collectively active in responding transnational security issues with series of talks and collaboration agreement since early 2000s. Lately in 2015, ASEAN agreed on ASEAN Convention against Trafficking in Persons, particularly Women and Children (ACTIP) that requires each member to collaborate in information sharing and providing effective safeguard and protection of victims. Yet, the frequency of human trafficking crime occurrence remains high and tend to increase in Indonesian in 2017-2018. The objective of this paper is to examine the effectiveness and success of ACTIP implementation in the fight against human trafficking in Indonesia. Based on two years of research (2017-2018) in three provinces with the largest number of victims in Indonesia, this paper shows the tendency of persisting crime despite the implementation of regional and national anti-trafficking policies. The research was conducted by archive study, literature study, discourse analysis, and depth interviews with local government officials, police, prosecutors, victims, and traffickers. This paper argues that the relative success of ASEAN in establishing convention at the high-level meetings has not been followed with the success in its implementation in the society. Three main factors have contributed to the ineffectiveness of the agreements, i.e. (1) ASEAN institutional arrangement as a collection of sovereign states instead of supranational organization with binding authority; (2) the lack of commitment of ASEAN sovereign member-states to the agreements; and (3) the complexity and variety of the nature of the crime in each member-state. In effect, these factors have contributed to generating the regionalism paradox in ASEAN where states tend to revert to national policies instead of seeking regional collective solution.

Keywords: human trafficking, transnational security, regionalism, anti trafficking policy

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Authors: Badawia Ibrahim, Iman Hussein, Samar El Sheikh, Fatma Abou Elkasem, Hazem Abo Ismael

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Background: Response of breast carcinoma to neoadjuvant chemotherapy (NAC) varies regarding many factors including hormonal receptor status. Breast cancer is a heterogenous disease with different outcomes, hence a need arises for new markers predicting the outcome of NAC especially for the triple negative group when estrogen, progesterone receptors and Her2/neu are negative. FOXP3 is a promising target with unclear role. Aim: To examine the value of FOXP3 expression in locally advanced triple negative breast cancer tumoral cells as well as tumor infiltrating lymphocytes (TILs) and to elucidate its relation to the extent of NAC response. Material and Methods: Forty five cases of immunohistochemically confirmed to be triple negative breast carcinoma were evaluated for NAC (Doxorubicin, Cyclophosphamide AC x 4 cycles + Paclitaxel x 12 weeks, patients with ejection fraction less than 60% received Taxotere or Cyclophosphamide, Methotrexate, Fluorouracil CMF) response in both tumour and lymph nodes status according to Miller & Payne's and Sataloff's systems. FOXP3 expression in tumor as well as TILs evaluated in the pretherapy biopsies was correlated with NAC response in breast tumor and lymph nodes as well as other clinicopathological factors. Results: Breast tumour cells showed FOXP3 positive cytoplasmic expression in (42%) of cases. High FOXP3 expression percentage was detected in (47%) of cases. High infiltration by FOXP3+TILs was detected in (49%) of cases. Positive FOXP3 expression was associated with negative lymph node metastasis. High FOXP3 expression percentage and high infiltration by FOXP3+TILs were significantly associated with complete therapy response in axillary lymph nodes. High FOXP3 expression in tumour cells was associated with high infiltration by FOXP3+TILs. Conclusion: This result may provide evidence that FOXP3 marker is a good prognostic and predictive marker for triple negative breast cancer (TNBC) indicated for neoadjuvant chemotherapy and can be used for stratifications of TNBC cases indicated for NAC. As well, this study confirmed the fact that the tumour cells and the surrounding microenvironment interact with each other and the tumour microenvironment can influence the treatment outcomes of TNBC.

Keywords: breast cancer, FOXP3 expression, prediction of neoadjuvant chemotherapy effect, triple negative

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Authors: Ayda Youssef, Tarek Rafaat, Iman zaky

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Purpose: Langerhans’ cell histiocytosis (LCH) is not uncommon pathology that implies aberrant proliferation of a specific dendritic (Langerhans) cell. These atypical but mature cells of monoclonal origin can infiltrate many sites of the body and may occur as localized lesions or as widespread systemic disease. Liver is one of the uncommon sites of affection. The twofold objective of this study is to illustrate the radiological presentation of this disease, and to compare these results with previously reported series. Methods and Materials: Between 2007 and 2012, 150 patients with biopsy-proven LCH were treated in our hospital, a paediatric cancer tertiary care center. A retrospective review of radiographic images and reports was performed. There were 33 patients with liver affection are stratified. All patients underwent imaging studies, mostly US and CT. A chart review was performed to obtain demographic, clinical and radiological data. They were analyzed and compared to other published series. Results: Retrospective assessment of 150 patients with LCH was performed, among them 33 patients were identified who had liver involvement. All these patients developed multisystemic disease; They were 12 females and 21 males with (n= 32), seven of them had marked hepatomegaly. Diffuse hypodense liver parenchyma was encountered in five cases, the periportal location has a certain predilection in cases of focal affection where three cases has a hypodense periportal soft tissue sheets, one of them associated with dilated biliary radicals, only one case has multiple focal lesions unrelated to portal tracts. On follow up of the patients, two cases show abnormal morphology of liver with bossy outline. Conclusion: LCH is a not infrequent disease. A high-index suspicion should be raised in the context of diagnosis of liver affection. A biopsy is recommended in the presence of radiological suspicion. Chemotherapy is the preferred therapeutic modality. Liver histiocytosis are not disease specific features but should be interpreted in conjunction with the clinical history and the results of biopsy. Clinical Relevance/Application: Radiologist should be aware of different patterns of hepatobiliary histiocytosis, Thus early diagnosis and proper management of patient can be conducted.

Keywords: langerhans’ cell histiocytosis, liver, medical and health sciences, radiology

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Authors: Iman Farasat, Howard M. Salis

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The CRISPR/Cas9 system has revolutionized genome engineering by enabling site-directed and high-throughput genome editing, genome insertion, and gene knockdowns in several species, including bacteria, yeast, flies, worms, and human cell lines. This technology has the potential to enable human gene therapy to treat genetic diseases and cancer at the molecular level; however, the current CRISPR/Cas9 system suffers from seemingly sporadic off-target genome mutagenesis that prevents its use in gene therapy. A comprehensive mechanistic model that explains how the CRISPR/Cas9 functions would enable the rational design of the guide-RNAs responsible for target site selection while minimizing unexpected genome mutagenesis. Here, we present the first quantitative model of the CRISPR/Cas9 genome mutagenesis system that predicts how guide-RNA sequences (crRNAs) control target site selection and cleavage activity. We used statistical thermodynamics and law of mass action to develop a five-step biophysical model of cas9 cleavage, and examined it in vivo and in vitro. To predict a crRNA's binding specificities and cleavage rates, we then compiled a nearest neighbor (NN) energy model that accounts for all possible base pairings and mismatches between the crRNA and the possible genomic DNA sites. These calculations correctly predicted crRNA specificity across 5518 sites. Our analysis reveals that cas9 activity and specificity are anti-correlated, and, the trade-off between them is the determining factor in performing an RNA-mediated cleavage with minimal off-targets. To find an optimal solution, we first created a scheme of safe-design criteria for Cas9 target selection by systematic analysis of available high throughput measurements. We then used our biophysical model to determine the optimal Cas9 expression levels and timing that maximizes on-target cleavage and minimizes off-target activity. We successfully applied this approach in bacterial and mammalian cell lines to reduce off-target activity to near background mutagenesis level while maintaining high on-target cleavage rate.

Keywords: biophysical model, CRISPR, Cas9, genome editing

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Authors: Iman Jabbar

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Within the scope of professionalism and in order to compete with the modern world, teachers, are expected to develop their teaching skills and activities in addition to their professional knowledge. At the college level, the teacher should be able to face classroom challenges through his engagement with the learning situation to understand the students and their needs. In our field of TESOL, the role of the English teacher is no longer restricted to teaching English texts, but rather he should endeavor to enhance the students’ skills such as communication and critical analysis. Within the literature of professionalism, there are certain strategies and tools that an English teacher should adopt to develop his competence and performance. Reflective practice, which is an exploratory process, is one of these strategies. Another strategy contributing to classroom development is motivation. It is crucial in students’ learning as it affects the quality of learning English in the classroom in addition to determining success or failure as well as language achievement. This is a qualitative study grounded on interpretive perspectives of teachers and students regarding the process of professional development. This study aims at (a) understanding how teachers at the college level conceptualize reflective practice and motivation inside EFL classroom, and (b) exploring the methods and strategies that they implement to practice reflection and motivation. This study and is based on two questions: 1. How do EFL teachers perceive and view reflection and motivation in relation to their teaching and professional development? 2. How can reflective practice and motivation be developed into practical strategies and actions in EFL teachers’ professional context? The study is organized into two parts, theoretical and practical. The theoretical part reviews the literature on the concept of reflective practice and motivation in relation to professional development through providing certain definitions, theoretical models, and strategies. The practical part draws on the theoretical one, however; it is the core of the study since it deals with two issues. It involves the research design, methodology, and methods of data collection, sampling, and data analysis. It ends up with an overall discussion of findings and the researcher's reflections on the investigated topic. In terms of significance, the study is intended to contribute to the field of TESOL at the academic level through the selection of the topic and investigating it from theoretical and practical perspectives. Professional development is the path that leads to enhancing the quality of teaching English as a foreign or second language in a way that suits the modern trends of globalization and advanced technology.

Keywords: professional development, motivation, reflection, learning

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Authors: Iman Shabanzadeh

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Earthquake is known as one of the most frequent natural hazards in Iran. Therefore, policy making to improve the strengthening of structures is one of the requirements of the approach to prevent and reduce the risk of the destructive effects of earthquakes. In order to choose the optimal policy in the face of earthquakes, this article tries to examine the cost of financial damages caused by earthquakes in the building sector and compare it with the costs of retrofitting. In this study, the results of adopting the scenario of "action after the earthquake" and the policy scenario of "strengthening structures before the earthquake" have been collected, calculated and finally analyzed by putting them together. Methodologically, data received from governorates and building retrofitting engineering companies have been used. The scope of the study is earthquakes occurred in the geographical area of Iran, and among them, eight earthquakes have been specifically studied: Miane, Ahar and Haris, Qator, Momor, Khorasan, Damghan and Shahroud, Gohran, Hormozgan and Ezgole. The main basis of the calculations is the data obtained from retrofitting companies regarding the cost per square meter of building retrofitting and the data of the governorate regarding the power of earthquake destruction, the realized costs for the reconstruction and construction of residential units. The estimated costs have been converted to the value of 2021 using the time value of money method to enable comparison and aggregation. The cost-benefit comparison of the two policies of action after the earthquake and retrofitting before the earthquake in the eight earthquakes investigated shows that the country has suffered five thousand billion Tomans of losses due to the lack of retrofitting of buildings against earthquakes. Based on the data of the Budget Law's of Iran, this figure was approximately twice the budget of the Ministry of Roads and Urban Development and five times the budget of the Islamic Revolution Housing Foundation in 2021. The results show that the policy of retrofitting structures before an earthquake is significantly more optimal than the competing scenario. The comparison of the two policy scenarios examined in this study shows that the policy of retrofitting buildings before an earthquake, on the one hand, prevents huge losses, and on the other hand, by increasing the number of earthquake-resistant houses, it reduces the amount of earthquake destruction. In addition to other positive effects of retrofitting, such as the reduction of mortality due to earthquake resistance of buildings and the reduction of other economic and social effects caused by earthquakes. These are things that can prove the cost-effectiveness of the policy scenario of "strengthening structures before earthquakes" in Iran.

Keywords: disaster economy, earthquake economy, cost-benefit analysis, resilience

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Authors: A. Odoom, A. Salama, H. Ibrahim

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Hydrogen is a clean source of energy for power production and transportation. The main source of hydrogen in this research is biodiesel. Glycerol also called glycerine is a by-product of biodiesel production by transesterification of vegetable oils and methanol. This is a reliable and environmentally-friendly source of hydrogen production than fossil fuels. A typical composition of crude glycerol comprises of glycerol, water, organic and inorganic salts, soap, methanol and small amounts of glycerides. Crude glycerol has limited industrial application due to its low purity thus, the usage of crude glycerol can significantly enhance the sustainability and production of biodiesel. Reforming techniques is an approach for hydrogen production mainly Steam Reforming (SR), Autothermal Reforming (ATR) and Partial Oxidation Reforming (POR). SR produces high hydrogen conversions and yield but is highly endothermic whereas POR is exothermic. On the downside, PO yields lower hydrogen as well as large amount of side reactions. ATR which is a fusion of partial oxidation reforming and steam reforming is thermally neutral because net reactor heat duty is zero. It has relatively high hydrogen yield, selectivity as well as limits coke formation. The complex chemical processes that take place during the production phases makes it relatively difficult to construct a reliable and robust numerical model. Numerical model is a tool to mimic reality and provide insight into the influence of the parameters. In this work, we introduce a finite volume numerical study for an 'in-house' lab-scale experiment of ATR. Previous numerical studies on this process have considered either using Comsol or nodal finite difference analysis. Since Comsol is a commercial package which is not readily available everywhere and lab-scale experiment can be considered well mixed in the radial direction. One spatial dimension suffices to capture the essential feature of ATR, in this work, we consider developing our own numerical approach using MATLAB. A continuum fixed bed reactor is modelled using MATLAB with both pseudo homogeneous and heterogeneous models. The drawback of nodal finite difference formulation is that it is not locally conservative which means that materials and momenta can be generated inside the domain as an artifact of the discretization. Control volume, on the other hand, is locally conservative and suites very well problems where materials are generated and consumed inside the domain. In this work, species mass balance, Darcy’s equation and energy equations are solved using operator splitting technique. Therefore, diffusion-like terms are discretized implicitly while advection-like terms are discretized explicitly. An upwind scheme is adapted for the advection term to ensure accuracy and positivity. Comparisons with the experimental data show very good agreements which build confidence in our modeling approach. The models obtained were validated and optimized for better results.

Keywords: autothermal reforming, crude glycerol, hydrogen, numerical model

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Authors: Abdullah S. Alghamdi, Khaled Alghamdi, Richard O. Jenkins, Parvez I. Haris

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Background: Physical activity is an important factor in the treatment and prevention of type 2 diabetes mellitus (T2DM). Reduction in HbA1c level, an important diabetes biomarker, was reported in patients who increased their daily physical activity. Although the ambient temperature was reported to be positively correlated to a negative impact on health and increase the incidences of diabetes, the exposure to bright sunlight was recently found to be associated with enhanced insulin sensitivity and improved beta-cell function. How Ramadan alters physical activity, and especially sunlight exposure, has not been adequately investigated. Aim: This study aimed to assess the physical activity and sun exposure of Saudis with T2DM over different periods (before, during, and after Ramadan) and related this to HbA1c levels. Methods: This study recruited 82 Saudis with T2DM, who chose to fast during Ramadan, from the Endocrine and Diabetic Centre of Al Iman General Hospital, Riyadh, Saudi Arabia. Ethical approvals for this study were obtained from De Montfort University and Saudi Ministry of Health. Physical activity and sun exposure were assessed by a self-administered questionnaire. Physical activity was estimated using the International Physical Activity Questionnaire (IPAQ), while the sun exposure was assessed by asking the patients about their hours per week of direct exposure to the sun, and daily hours spent outdoors. Blood samples were collected in each period for measuring HbA1c. Results: Low physical activity was observed in more than 60% of the patients, with no significant changes between periods. There were no significant variances between periods in the daily hours spent outdoors and the total number of weekly hours of direct exposure to the sun. The majority of patients reported only few hours of exposure to the sun (1h or less per week) and time spent outdoors (1h or less per day). The mean HbA1c significantly changed between periods (P = 0.001), with lowest level during Ramadan. There were significant differences in the mean HbA1c between the groups for the level of physical activity (P < 0.001), with significant lower mean HbA1c in the higher-level group. There were no significant variances in the mean of HbA1c between the groups for the daily hours spent outdoors. The mean HbA1c of the patients, who reported never in their total weekly hours of exposure to the sun, was significantly lower than the mean HbA1c of those who reported 1 hour or less (P = 0.001). Conclusion: Physical inactivity was prevalent among the study population with very little exposure to the sun or time spent outdoors. Higher level of physical activity was associated with lower mean HbA1c levels. Encouraging T2DM patients to achieve the recommended levels of physical activity may help them to obtain greater benefits of Ramadan fasting, such as reducing their HbA1c levels. The impact of low direct exposure to the sun and the time spent outdoors needs to be further investigated in both healthy and diabetic patients.

Keywords: diabetes, fasting, physical activity, sunlight, Ramadan

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Authors: Maryam Hasanali, Syed Mohammad Mojtabaei, Iman Hajirasouliha, G. Charles Clifton, James B. P. Lim

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Cold-formed steel (CFS) elements are increasingly being used as main load-bearing components in the modern construction industry, including low- to mid-rise buildings. In typical multi-storey buildings, CFS structural members act as beam-column elements since they are exposed to combined axial compression and bending actions, both in moment-resisting frames and stud wall systems. Current design specifications, including the American Iron and Steel Institute (AISI S100) and the Australian/New Zealand Standard (AS/NZS 4600), neglect the beneficial effects of warping-restrained boundary conditions in the design of beam-column elements. Furthermore, while a non-linear relationship governs the interaction of axial compression and bending, the combined effect of these actions is taken into account through a simplified linear expression combining pure axial and flexural strengths. This paper aims to evaluate the reliability of the well-known Direct Strength Method (DSM) as well as design proposals found in the literature to provide a better understanding of the efficiency of the code-prescribed linear interaction equation in the strength predictions of CFS beam columns and the effects of warping-restrained boundary conditions on their behavior. To this end, the experimentally validated finite element (FE) models of CFS elements under compression and bending were developed in ABAQUS software, which accounts for both non-linear material properties and geometric imperfections. The validated models were then used for a comprehensive parametric study containing 270 FE models, covering a wide range of key design parameters, such as length (i.e., 0.5, 1.5, and 3 m), thickness (i.e., 1, 2, and 4 mm) and cross-sectional dimensions under ten different load eccentricity levels. The results of this parametric study demonstrated that using the DSM led to the most conservative strength predictions for beam-column members by up to 55%, depending on the element’s length and thickness. This can be sourced by the errors associated with (i) the absence of warping-restrained boundary condition effects, (ii) equations for the calculations of buckling loads, and (iii) the linear interaction equation. While the influence of warping restraint is generally less than 6%, the code suggested interaction equation led to an average error of 4% to 22%, based on the element lengths. This paper highlights the need to provide more reliable design solutions for CFS beam-column elements for practical design purposes.

Keywords: beam-columns, cold-formed steel, finite element model, interaction equation, warping-restrained boundary conditions

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Authors: Afnan Al-Romi, Iman Al-Momani

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The urge of applying the Software Engineering (SE) processes is both of vital importance and a key feature in critical, complex large-scale systems, for example, safety systems, security service systems, and network systems. Inevitably, associated with this are risks, such as system vulnerabilities and security threats. The probability of those risks increases in unsecured environments, such as wireless networks in general and in Wireless Sensor Networks (WSNs) in particular. WSN is a self-organizing network of sensor nodes connected by wireless links. WSNs consist of hundreds to thousands of low-power, low-cost, multi-function sensor nodes that are small in size and communicate over short-ranges. The distribution of sensor nodes in an open environment that could be unattended in addition to the resource constraints in terms of processing, storage and power, make such networks in stringent limitations such as lifetime (i.e. period of operation) and security. The importance of WSN applications that could be found in many militaries and civilian aspects has drawn the attention of many researchers to consider its security. To address this important issue and overcome one of the main challenges of WSNs, security solution systems have been developed by researchers. Those solutions are software-based network Intrusion Detection Systems (IDSs). However, it has been witnessed, that those developed IDSs are neither secure enough nor accurate to detect all malicious behaviours of attacks. Thus, the problem is the lack of coverage of all malicious behaviours in proposed IDSs, leading to unpleasant results, such as delays in the detection process, low detection accuracy, or even worse, leading to detection failure, as illustrated in the previous studies. Also, another problem is energy consumption in WSNs caused by IDS. So, in other words, not all requirements are implemented then traced. Moreover, neither all requirements are identified nor satisfied, as for some requirements have been compromised. The drawbacks in the current IDS are due to not following structured software development processes by researches and developers when developing IDS. Consequently, they resulted in inadequate requirement management, process, validation, and verification of requirements quality. Unfortunately, WSN and SE research communities have been mostly impermeable to each other. Integrating SE and WSNs is a real subject that will be expanded as technology evolves and spreads in industrial applications. Therefore, this paper will study the importance of Requirement Engineering when developing IDSs. Also, it will study a set of existed IDSs and illustrate the absence of Requirement Engineering and its effect. Then conclusions are drawn in regard of applying requirement engineering to systems to deliver the required functionalities, with respect to operational constraints, within an acceptable level of performance, accuracy and reliability.

Keywords: software engineering, requirement engineering, Intrusion Detection System, IDS, Wireless Sensor Networks, WSN

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Authors: Abdullah S. Alghamdi, Khaled Alghamdi, Richard O. Jenkins, Parvez I. Haris

Abstract:

Background: Unhealthy diet is one of the modifiable risk factors for developing type 2 diabetes mellitus (T2DM). Improvement in diet can be beneficial for countering diabetes. For example, HbA1c, an important biomarker for diabetes, can be reduced by 1.1% through only alteration in diet. Ramadan fasting has been reported to provide positive health benefits. However, optimal benefits are not achieved, often due to poor dietary habits and lifestyle. There is a need to better understand the dietary habits of people fasting during Ramadan, so that necessary improvements can be made to develop this form of fasting as a non-pharmacological strategy for management and prevention of T2DM. Aim: This study aimed to assess the dietary patterns of Saudi adult patients with T2DM over three different periods (before, during, and after Ramadan) and relate this to HbA1c levels. Methods: This study recruited 82 Saudi with T2DM, who chose to fast during Ramadan, from the Endocrine and Diabetic Centre of Al Iman General Hospital, Riyadh, Saudi Arabia. Ethical approvals for the study were obtained from De Montfort University and Saudi Ministry of Health. Dietary patterns were assessed by a self-administered questionnaire in each period. This assessment included the diet type and frequency. Blood samples were collected in each period for determination of HbA1c. Results: The number of meals per day for the participants significantly decreased during Ramadan (P < 0.001). The consumption of fruit and vegetables significantly increased during Ramadan (P = 0.017). However, the consumption of sugary drinks significantly increased during and after Ramadan (P = 0.005). Approximately 60% of the patients indicated that they ate sugary foods at least once per week. The consumption of bread and rice was reported to be at least two times per week. The consumption of rice significantly reduced during Ramadan (P = 0.002). The mean HbA1c significantly varied between periods (P = 0.001), with lowest level during Ramadan compared to before and after Ramadan. The increase in the consumption of fruits and vegetables had a medium effect size on the reduction in HbA1c during Ramadan. There was a variance of 7.7% in the mean difference in HbA1c levels between groups (who changed their fruit and vegetable consumption) which can be accounted for by the increase in the consumption of fruits and vegetables. Likewise, 9.3% of the variance in the mean HbA1c difference between the groups was accounted for by a decrease in the consumption of rice. Conclusion: The increase in the frequency of fruit and vegetables intake, and especially the reduction in the frequency of rice consumption, during Ramadan produce beneficial effects in reducing HbA1c level. Therefore, further improving the dietary habits of patients with T2DM, such as reducing their sugary drinks intake, may help them to obtain greater benefits from Ramadan fasting in the management of their diabetes. It is recommended that dietary guidance is provided to the public to maximise health benefits through Ramadan fasting.

Keywords: Diabetes, Diet, Fasting, HbA1c, Ramadan

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Authors: Iman Janghorban Esfahani

Abstract:

Due to the increased use of irrigation in agriculture, the importance and need for highly reliable water pumping systems have significantly increased. The pumping of the groundwater is essential to provide water for both drip and furrow irrigation to increase the agricultural yield, especially in arid regions that suffer from scarcities of surface water. The most common irrigation pumping systems (IPS) consume conventional energies through the use of electric motors and generators or connecting to the electricity grid. Due to the shortage and transportation difficulties of fossil fuels, and unreliable access to the electricity grid, especially in the rural areas, and the adverse environmental impacts of fossil fuel usage, such as greenhouse gas (GHG) emissions, the need for renewable energy sources such as photovoltaic systems (PVS) as an alternative way of powering irrigation pumping systems is urgent. Integration of the photovoltaic systems with irrigation pumping systems as the Photovoltaic Powered-Irrigation Pumping System (PVP-IPS) can avoid fossil fuel dependency and the subsequent greenhouse gas emissions, as well as ultimately lower energy costs and improve efficiency, which made PVP-IPS systems as an environmentally and economically efficient solution for agriculture irrigation in every region. The greatest problem faced by integration of PVP with IPS systems is matching the intermittence of the energy supply with the dynamic water demand. The best solution to overcome the intermittence is to incorporate a storage system into the PVP-IPS to provide water-on-demand as a highly reliable stand-alone irrigation pumping system. The water storage tank (WST) is the most common storage device for PVP-IPS systems. In the integrated PVP-IPS with a water storage tank (PVP-IPS-WST), a water storage tank stores the water pumped by the IPS in excess of the water demand and then delivers it when demands are high. The Freshwater pinch analysis (FWaPA) as an alternative to mathematical modeling was used by other researchers for retrofitting the off-grid battery less photovoltaic-powered reverse osmosis system. However, the Freshwater pinch analysis has not been used to integrate the photovoltaic systems with irrigation pumping system with water storage tanks. In this study, FWaPA graphical and numerical tools were used for retrofitting an existing PVP-IPS system located in Salahadin, Republic of Iraq. The plant includes a 5 kW submersible water pump and 7.5 kW solar PV system. The Freshwater Composite Curve as the graphical tool and Freashwater Storage Cascade Table as the numerical tool were constructed to determine the minimum required outsourced water during operation, optimal amount of delivered electricity to the water pump, and optimal size of the water storage tank for one-year operation data. The results of implementing the FWaPA on the case study show that the PVP-IPS system with a WST as the reliable system can reduce outsourced water by 95.41% compare to the PVP-IPS system without storage tank.

Keywords: irrigation, photovoltaic, pinch analysis, pumping, solar energy

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Authors: Iman Zafarparandeh, Muzammil Mumtaz, Paniz Taherzadeh, Deniz Erbulut

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The instability in the atlantoaxial joint may occur due to cervical surgery, congenital anomalies, and trauma. There are different types of fixation techniques proposed for restoring the stability and preventing harmful neurological deterioration. Application of the screw constructs has become a popular alternative to the older techniques for stabilizing the joint. The main difference between the various screw constructs is the type of the screw which can be lateral mass screw, pedicle screw, transarticular screw, and translaminar screw. The aim of this paper is to study the effect of three popular screw constructs fixation techniques on the biomechanics of the atlantoaxial joint using the finite element (FE) method. A three-dimensional FE model of the upper cervical spine including the skull, C1 and C2 vertebrae, and groups of the existing ligaments were developed. The accurate geometry of the model was obtained from the CT data of a 35-year old male. Three screw constructs were designed to compare; Magerl transarticular screw (TA-Screw), Goel-Harms lateral mass screw and pedicle screw (LM-Screw and Pedicle-Screw), and Wright lateral mass screw and translaminar screw (LM-Screw and TL-Screw). Pure moments were applied to the model in the three main planes; flexion (Flex), extension (Ext), axial rotation (AR) and lateral bending (LB). The range of motion (ROM) of C0-C1 and C1-C2 segments for the implanted FE models are compared to the intact FE model and the in vitro study of Panjabi (1988). The Magerl technique showed less effect on the ROM of C0-C1 than the other two techniques in sagittal plane. In lateral bending and axial rotation, the Goel-Harms and Wright techniques showed less effect on the ROM of C0-C1 than the Magerl technique. The Magerl technique has the highest fusion rate as 99% in all loading directions for the C1-C2 segment. The Wright technique has the lowest fusion rate in LB as 79%. The three techniques resulted in the same fusion rate in extension loading as 99%. The maximum stress for the Magerl technique is the lowest in all load direction compared to other two techniques. The maximum stress in all direction was 234 Mpa and occurred in flexion with the Wright technique. The maximum stress for the Goel-Harms and Wright techniques occurred in lateral mass screw. The ROM obtained from the FE results support this idea that the fusion rate of the Magerl is more than 99%. Moreover, the maximum stress occurred in each screw constructs proves the less failure possibility for the Magerl technique. Another advantage of the Magerl technique is the less number of components compared to other techniques using screw constructs. Despite the benefits of the Magerl technique, there are drawbacks to using this method such as reduction of the C1 and C2 before screw placement. Therefore, other fixation methods such as Goel-Harms and Wright techniques find the solution for the drawbacks of the Magerl technique by adding screws separately to C1 and C2. The FE model implanted with the Wright technique showed the highest maximum stress almost in all load direction.

Keywords: cervical spine, finite element model, atlantoaxial, fixation technique

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Authors: Mohammad Ehsani, Iman Zarei, Soudabeh Moazemigoudarzi

Abstract:

The aim of this study is to determine Pro-Environmental Behavioral Intention of Mountain Hikers to the Theory of Planned Behavior. According to many researchers nature-based recreation activities play a significant role in the tourism industry and have provided myriad opportunities for the protection of natural areas. It is essential to investigate individuals' behavior during such activities to avoid further damage to precious and dwindling natural resources. This study develops a robust model that provides a comprehensive understanding of the formation of pro-environmental behavioral intentions among climbers of Mount Damavand National Park in Iran. To this end, we combined the theory of planned behavior (TPB), value-belief-norm theory (VBN), and a hierarchical model of leisure constraints to predict individuals’ pro-environmental hiking behavior during outdoor recreation. It was used structural equation modeling to test the theoretical framework. A sample of 787 climbers was analyzed. Among the theory of planned behavior variables, perceived behavioral control showed the strongest association with behavioral intention (β = .57). This relationship indicates that if people feel they can have fewer negative impacts on national resources while hiking, it will result in more environmentally acceptable behavior. Subjective norms had a moderate positive impact on behavioral intention, indicating the importance of other people on the individual's behavior. Attitude had a small positive effect on intention. Ecological worldview positively influenced attitude and personal belief. Personal belief (awareness of consequences and ascribed responsibility) showed a positive association with TPB variables. Although the data showed a high average score in awareness of consequences (mean = 4.219 out of 5), evidence from Damavand Mount shows that there are many environmental issues that need addressing (e.g., vast amounts of garbage). National park managers need to make sure that their solutions result in awareness about proenvironmental behavior (PEB). Findings showed that negative relationship between constraints and all TPB predictors. Providing proper restrooms and parking spaces in campgrounds, strategies controlling limiting capacity and solutions for removing waste from high altitudes are helpful to decrease the negative impact of structural constraints. In order to address intrapersonal constraints, managers should provide opportunities to interest individuals in environmental activities, such as environmental celebrations or making documentaries about environmental issues. Moreover, promoting a culture of environmental protection in the Damavand Mount area would reduce interpersonal constraints. Overall, the proposed model improved the explanatory power of the TPB by predicting 64.7% of intention compared to the original TPB that accounted for 63.8% of the variance in intention.

Keywords: theory of planned behavior, pro-environmental behavior, national park, constraints

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Authors: Kareem Abdelwahed, Ahmed Salama, Ahmed Rabie, Ahmed Hamdy, Waleed Abdelfattah, Ahmed Abd El-Rahman

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Conventional vapor-compression refrigeration systems rely on typical refrigerants, such as CFC, HCFC and ammonia. Despite of their suitable thermodynamic properties and their stability in the atmosphere, their corresponding global warming potential and ozone depletion potential raise concerns about their usage. Thus, the need for new refrigeration systems, which are environment-friendly, inexpensive and simple in construction, has strongly motivated the development of thermoacoustic energy conversion systems. A thermoacoustic refrigerator (TAR) is a device that is mainly consisting of a resonator, a stack and two heat exchangers. Typically, the resonator is a long circular tube, made of copper or steel and filled with Helium as a the working gas, while the stack has short and relatively low thermal conductivity ceramic parallel plates aligned with the direction of the prevailing resonant wave. Typically, the resonator of a standing-wave refrigerator has one end closed and is bounded by the acoustic driver at the other end enabling the propagation of half-wavelength acoustic excitation. The hot and cold heat exchangers are made of copper to allow for efficient heat transfer between the working gas and the external heat source and sink respectively. TARs are interesting because they have no moving parts, unlike conventional refrigerators, and almost no environmental impact exists as they rely on the conversion of acoustic and heat energies. Their fabrication process is rather simpler and sizes span wide variety of length scales. The viscous and thermal interactions between the stack plates, heat exchangers' plates and the working gas significantly affect the flow field within the plates' channels, and the energy flux density at the plates' surfaces, respectively. Here, the design, the manufacture and the testing of a compact refrigeration system that is based on the thermoacoustic energy-conversion technology is reported. A 1-D linear acoustic model is carefully and specifically developed, which is followed by building the hardware and testing procedures. The system consists of two harmonically-oscillating pistons driven by a simple 1-HP rotary drive mechanism operating at a frequency of 42Hz -hereby, replacing typical expensive linear motors and loudspeakers-, and a thermoacoustic stack within which the energy conversion of sound into heat is taken place. Air at ambient conditions is used as the working gas while the amplitude of the driver's displacement reaches 19 mm. The 30-cm-long stack is a simple porous ceramic material having 100 square channels per square inch. During operation, both oscillating-gas pressure and solid-stack temperature are recorded for further analysis. Measurements show a maximum temperature difference of about 27 degrees between the stack hot and cold ends with a Carnot coefficient of performance of 11 and estimated cooling capacity of five Watts, when operating at ambient conditions. A dynamic pressure of 7-kPa-amplitude is recorded, yielding a drive ratio of 7% approximately, and found in a good agreement with theoretical prediction. The system behavior is clearly non-linear and significant non-linear loss mechanisms are evident. This work helps understanding the operation principles of thermoacoustic refrigerators and presents a keystone towards developing commercial thermoacoustic refrigerator units.

Keywords: refrigeration system, rotary drive mechanism, standing-wave, thermoacoustic refrigerator

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Authors: Abdullah S. Alghamdi, Khaled Alghamdi, Richard O. Jenkins, Parvez I. Haris

Abstract:

Background: Quantity and quality of sleep have been reported to be significant risk factors for obesity and development of metabolic disorders such as type 2 diabetes mellitus (T2DM). The relationship between diabetes and sleep quantity was reported to be U-shaped, which means increased or decreased sleeping hours can increase the risk of diabetes. The plasma glucagon levels were found to continuously decrease during night-time sleep in healthy individuals, independently of blood glucose and insulin levels. The disturbance of the circadian rhythm is also important and has been linked with an increased the chance of diabetes incidence. There is a lack of research on sleep patterns on Saudis with T2DM and how this is affected by Ramadan fasting. Aim: To assess the sleeping patterns of Saudis with T2DM (before, during, and after Ramadan), using two different techniques and relate this to their HbA1c levels. Method: This study recruited 82 Saudi with T2DM, who chose to fast during Ramadan, from the Endocrine and Diabetic Centre of Al Iman General Hospital, Riyadh, Saudi Arabia. Ethical approvals for the study were obtained from De Montfort University and Saudi Ministry of Health. Their sleeping patterns were assessed by a self-administered questionnaire (before, during, and after Ramadan). The assessment included the daily total sleeping hours (DTSH), and total night-time sleeping hours (TNTSH) of the participants. In addition, sleeping patterns of 36 patients, randomly selected from the 82 participants, were further tracked during and after Ramadan by using Fitbit Flex 2™ accelerometer. Blood samples were collected in each period for measuring HbA1c. Results: Questionnaire analysis revealed that the sleeping patterns significantly changed between the periods, with shorter hours during Ramadan (P < 0.001 for DTSH, and P < 0.001 for TNTSH). These findings were confirmed by the Fitbit data, which also indicated significant shorter sleeping hours for the DTSH, and the TNTSH during Ramadan (P < 0.001 and P < 0.001, respectively). Although there were no significant correlations between the questionnaire and Fitbit data, the TNTSH were shorter among the participants in all periods by both techniques. The mean HbA1c significantly varied between periods, with lowest level during Ramadan. Although the statistical tests did not show significant variances in the mean HbA1c between the groups of participants regarding their hours of sleeping, the lowest mean HbA1c was observed in the group of participants who slept for 6-8 hours and had longer night-time sleeping hours. Conclusion: A short sleep duration, and absence of night-time sleep were significantly observed among the majority of the study population during Ramadan, which could suppress the full benefits of Ramadan fasting for diabetic patients. This study showed that there is a good agreement between the findings of the questionnaire and the Fitbit device for evaluating sleeping patterns in a Saudi population. A larger study is needed in the future to investigate the impact of Ramadan fasting on sleep quality and quantity and its relationship with health and disease.

Keywords: Diabetes, Fasting, Fitbit, HbA1c, IPAQ, Ramadan, Sleep

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Authors: Iman Farasat, Howard M. Salis

Abstract:

Engineered genetic circuits reprogram cellular behavior to act as living computers with applications in detecting cancer, creating self-controlling artificial tissues, and dynamically regulating metabolic pathways. Phenemenological models are often used to simulate and design genetic circuit behavior towards a desired behavior. While such models assume that each circuit component’s function is modular and independent, even small changes in a circuit (e.g. a new promoter, a change in transcription factor expression level, or even a new media) can have significant effects on the circuit’s function. Here, we use statistical thermodynamics to account for the several factors that control transcriptional regulation in bacteria, and experimentally demonstrate the model’s accuracy across 825 measurements in several genetic contexts and hosts. We then employ our first principles model to design, experimentally construct, and characterize a family of signal amplifying genetic circuits (genetic OpAmps) that expand the dynamic range of cell sensors. To develop these models, we needed a new approach to measuring the in vivo binding free energies of transcription factors (TFs), a key ingredient of statistical thermodynamic models of gene regulation. We developed a new high-throughput assay to measure RNA polymerase and TF binding free energies, requiring the construction and characterization of only a few constructs and data analysis (Figure 1A). We experimentally verified the assay on 6 TetR-homolog repressors and a CRISPR/dCas9 guide RNA. We found that our binding free energy measurements quantitatively explains why changing TF expression levels alters circuit function. Altogether, by combining these measurements with our biophysical model of translation (the RBS Calculator) as well as other measurements (Figure 1B), our model can account for changes in TF binding sites, TF expression levels, circuit copy number, host genome size, and host growth rate (Figure 1C). Model predictions correctly accounted for how these 8 factors control a promoter’s transcription rate (Figure 1D). Using the model, we developed a design framework for engineering multi-promoter genetic circuits that greatly reduces the number of degrees of freedom (8 factors per promoter) to a single dimensionless unit. We propose the Ptashne (Pt) number to encapsulate the 8 co-dependent factors that control transcriptional regulation into a single number. Therefore, a single number controls a promoter’s output rather than these 8 co-dependent factors, and designing a genetic circuit with N promoters requires specification of only N Pt numbers. We demonstrate how to design genetic circuits in Pt number space by constructing and characterizing 15 2-repressor OpAmp circuits that act as signal amplifiers when within an optimal Pt region. We experimentally show that OpAmp circuits using different TFs and TF expression levels will only amplify the dynamic range of input signals when their corresponding Pt numbers are within the optimal region. Thus, the use of the Pt number greatly simplifies the genetic circuit design, particularly important as circuits employ more TFs to perform increasingly complex functions.

Keywords: transcription factor, synthetic biology, genetic circuit, biophysical model, binding energy measurement

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