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Article
Real Time PCR as a Diagnostic Tool for HBV Infection in Iraq

Author: Mohammed Ghanim
Journal: Iraqi Academic Scientific Journal المجلة العراقية للاختصاصات الطبية ISSN: 16088360 Year: 2012 Volume: 11 Issue: 2 Pages: 146-150
Publisher: The Iraqi Borad for Medical Specialization المجلس العراقي للاختصاصات الطبية

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ABSTRACT :BACKGROUND:HBV infection is a worldwide infectious disease that acutely infects 2 billion yearly, thus finding a precise, accurate and sensitive diagnostic test for this infection is highly advisable. Real Time PCR has been introduced to achieve that mission.OBJECTIVE:Confirm the role of Real Time PCR as a precise tool for diagnosis of HBV infection in Iraq.PATIENTS AND METHODS:In this study, 40 patients of HBV with HBs Antigen positive serological test and 20 individuals with HBs Antigen negative were selected to be the material of the study and they were tested by Real Time PCR to estimate the exact amount of HBV genome in their blood.RESULTS:All the cases with HBs Antigen positive have had viral load with different values and no case with HBs Antigen negative have been found to have any viral element.CONCLUSION:Real Time PCR is useful and precise tool for the diagnosis and monitoring of patients with HBV infection and further studies are required to find a useful classification of the viral load and a correlation need to be found between viral load and the serological panel and especially HBe Antigen and HBe Antibody

Keywords

real time pcr --- hbv --- diagnosis


Article
Real-Time PCR For Detection CP1 & CP5 Virulence Factors Of Entamoeba Histolytica In Patients Stool Samples In Al - Najaf Al- Ashraf Province
التحري عن عوامل الضراوة CP5,CP1 للاميبا الحالة للنسيج في محافظة النجف الاشرف بتقنية التفاعل التسلسلي لإنزيم البلمرة.

Authors: Zainab Ali Hussein --- Haiytham Mohamed Hamady
Journal: kufa Journal for Nursing sciences مجلة الكوفة لعلوم التمريض ISSN: 22234055 Year: 2013 Volume: 3 Issue: 3 Pages: 190-196
Publisher: University of Kufa جامعة الكوفة

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Objective: It aims to determine the genes characterization of CP1 and CP5 pathogenic factors of E.histolytica parasitic in stool samples of patients in AL- Najaf Al Ashraf Province Methodology: This study was carried out for 6 months from the first of December 2012 till the end of June 2013The samples collected from Al-Sadar teaching hospital, AL-Zahra maternity and children hospital, AL-abasia hospital, AL-Forat hospital ,AL-Hakime hospital ,AL-Manathera hospital and private clinic in Al- Najaf governorate.Results: To detect the major virulence factors (V.F.) cysteine proteinase1(Cp1), cysteine proteinase5(CP5) of E.histolytica, Real -Time PCR technique was conducted, by using specific primers for E.histolytica, the results showed that 40 samples out of 162 were positive, out of these positive samples, there were 16 samples positive for C P1, 24 samples were positive for CP5. Conclusion: CP1 & CP5 is one of the most important virulence factors in E.histolytica such as toxin like activity. Recommendation: further study development of molecular diagnosis such as real time PCR for other non-pathogenic Entamoeba species which found in human, such as E.moskoviskii in comparison with E.histolytica, because the RT-PCR quantitative and qualitative improved method for the specific diagnosis of E.histolytica infection.

الهدف: اجريت هذه الدراسة للكشف عن عوامل الفوعة الرئيسية , CP1 CP5 لطفيلي الاميبا الحالة للنسيج المعوي Entamoeba histolytica وتشخيصها باستخدام تقنية التفاعل السلسلي لانزيم البلمرة Real-Time- PCR)).المنهجية: اجريت هذه الدراسة على 678 من المرضى الوافدين وثلاثين من الافراد الاصحاء كمجموعة سيطرة الذين زاروا مستشفى مدينة الصدر الطبية ،مستشفى الزهراء التعليمي ،مستشفى السجاد، مستشفى الفرات ،مستشفى الحكيم ومستشفى المناذرة وكذللك المختبرات الاهلية في محافظة النجف الاشرف خلال الفترة من كانون الاول 2012 ولغاية نهاية شهر حزيران 2013.النتائج: أظهرت نتائج الكشف عن العوامل الممرضة الرئيسية وهي السيستين بروتينيز1 (CP1) السيستين بروتينيز5 (CP5) لطفيلي الاميبا الحالة للنسيج بأجراء تقنية التفاعل السلسلي لانزيم البلمرة Real-Time- PCR)) وباستخدام بادئات محددة لطفيلي الاميبا الحالة للنسيج واظهرت النتائج ان 40 عينة من اصل 162 عينة كانت ايجابية الفحص ومن هذه العينات الايجابية الفحص كانت 16 عينة ايجابية الفحص للسيستين بروتينيز1 (CP1) و 24 عينة كانت ايجابية الفحص للسيستين بروتينيز5 (CP5) . الاستنتاجات : من اهم عوامل الفوعة الرئيسية لطفيلي الاميبا الحالة للنسيج المعوي هي السيستين بروتينيز1 (CP1) السيستين بروتينيز5 (CP5).التوصيات: اجراء دراسات اضافية للتشخيص الجزيئي بواسطة تقنية التفاعل السلسلي لانزيم البلمرة Real-Time- PCR)) لانواع الاميبا الغير ممرضة في الانسان .


Article
Evaluation of Commercial Real Time PCR and Immunochromatography Techniques in Laboratory Diagnosis of Tuberculosis
تقييم تقنيات Real Time PCR و الكروماتوكرافيا المناعية في التشخيص المختبري للتدرن

Authors: Ammar Abbas Shalan عما عباس شعلان --- Habeeb S. Naher حبيب صاحب نهر --- Mohammed A.K. Al-Saadi محمد عبد كاظم
Journal: Medical Journal of Babylon مجلة بابل الطبية ISSN: 1812156X 23126760 Year: 2014 Volume: 11 Issue: 1 Pages: 58-69
Publisher: Babylon University جامعة بابل

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Abstract

This study is a diagnostic evaluation study to real time PCR and Immunochromatography compared to conventional microbiological techniques (represented by Acid fast smear and culture) in laboratory diagnosis of tuberculosis. Whole blood and sputum samples were collected from 136 tuberculosis patients, 124 of them were pulmonary tuberculosis and 12 of them were extrapolmonary tuberculosis in addition to 102 healthy control subjects at consultant clinic for respiratory diseases in Hilla – Babil province-Iraq, during the period from May 2010 to June 2011. Real-time PCR kits, Immunochromatography rapid test in addition to acid fast smear and Lowenstein-Jensen culture were used to diagnose the tuberculosis cases. The results show that the sensitivities of the AFB smear, culture, RT-PCR and ICG were 74%, 43% 88% and 24%, respectively. The sensitivity of 99% was obtained by using RT-PCR and/or AFB smear as a diagnostic criteria. The specificity of AFB smear, culture, RT-PCR was 100%, while the specificity of ICG was 98%. The using of both AFB smear and RT-PCR as diagnostic tests raised the sensitivity to 99% compared with the using of the AFB smear, culture and ICG as a single test

هذه الدراسة هي دراسة تقييم تشخيصي لطرق (Real time PCR) و الكروماتوكرافيا المناعية (Immunochromatography) مقارنة بالتقنيات المجهرية التقليدية المتمثلة بالصبغة الصامدة للحامض و الزرع في التشخيص المختبري للتدرن. تم خلال الدراسة جمع عينات الدم والبلغم من 136 حالة تدرن 124 حالة تدرن رئوي و 12 حالة تدرن خارج الرئة بالاضافة 102 شخص من الملامسين كمجموعة سيطرة، وذلك في العيادة الاستشارية للامراض الصدرية في الحلة - محافظة بابل خلال الفترة ما بين شهر ايار 2010 الى حزيران 2011. تم استخدام التقنيات التشخيصية للـ (Real time PCR ) و (Immunochromatography) بالاضافة الى الصبغة الصامدة للحامض و الزرع على وسط لونشتن-جنسن في التشخيص المختبري لحالات التدرن. أظهرت نتائج الدراسة ان الحساسية التشخيصية للصبغة الصامدة للحامض، الزرع البكتيري، RT-PCR و الكروماتوكرافيا المناعية كانت 74%، 43% ، 88% و 24% على التوالي. تم الحصول على درجة حساسية تشخيصية بلغت 99% باستخدام كلا تقنيتي الصبغة الصامدة للحامض و RT-PCR. بلغ التخصص التشخيصي 100% لكل من الصبغة الصامدة للحامض و RT-PCR بينما كلن التخصص التشخيصي للكروماتوكرافيا المناعية 98%. تبين من النتائج ان استخدام كلا تقنيتي الصبغة الصامدة للحامض و RT-PCR مما ادى الى ارتفاع قيمة الحساسية التشخيصية الى 99% وذلك مقارنة بالحساسية التشخيصية لاستخدام تقنيات الصبغة الصامدة للحامض، الرزع البكتيري، RT-PCR و الكروماتوكرافيا المناعية كفحص تشخيصي منفرد.


Article
comparison of the combination of recomline and ELISA with real- time polymerase chain reaction on the final diagnosis of toxoplasmosis

Authors: Maysoon M.jabir ميسون محمد جابر --- Jassim T. ALkhafaji جاسم الخفاجي --- Sami Y. Guirges سامي يوسف --- Suha A. ALfakhar سهى احمد
Journal: Journal of the Faculty of Medicine مجلة كلية الطب ISSN: 00419419 Year: 2011 Volume: 53 Issue: 1 Pages: 72-76
Publisher: Baghdad University جامعة بغداد

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Article
Quantitative detection and correlation of Epstein - Barr Virus in plasma with gingivitis and severity of chronic periodontitis by using real-time polymerase chain reaction technique

Authors: Nada K. Imran ندى كاظم عمران --- Basima Gh. Ali --- Duraid Q. Jassim
Journal: Journal of baghdad college of dentistry مجلة كلية طب الاسنان بغداد ISSN: 16800087 Year: 2014 Volume: 26 Issue: 4 Pages: 133-140
Publisher: Baghdad University جامعة بغداد

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Abstract

Background: This study aimed to detect EBV quantitatively in plasma using real-time polymerase chain reactiontechnique in chronic periodontitis and gingivitis patients and to compare the finding with control subjects (healthyperiodontium) and to investigate the relationship between the presence of EBV & the severity of periodontaldiseases using the clinical periodontal parameters (PLI ,GI , BOP ,PPD and CAL) between each of (chronicperiodontitis and gingivitis) patients and compare with control (healthy periodontium) subjects .Materials and methods: The study sample consisted of (101) individual of both genders, (61) chronic periodontitispatients which were subdivided into (mild, moderate & severe) depending on the scores of clinical attachmentlevel, (20) gingivitis patients and (20) control subjects (healthy periodontium) with age ranged from (30-50) years. Allthe groups were without any history of systemic diseases. Clinical periodontal parameters used in this study were (PLI,GI , BOP ,PPD and CAL) .Blood samples were collected from all individuals and examined by Real-Time PCRtechnique for the detection of EBV.Results: The result of comparison for the occurrence of EBV among study and control groups according to sequentialresponding of EBV appears to be highly significant at negative level of EBV, significant in (100 - 500 copy/105 cells)level and the results of leftover levels appear non significant difference. The result of correlation between the actualoccurrence of EBV and PPD scores in severe chronic periodontitis subgroup appears to be significant at PPD score(1) and non significant at scores (2&3). The correlations between EBV and PPD scores in moderate and mild chronicperiodontitis subgroups appear to be non significant with all scores. The results of correlation between EBV and CALparameter appear to be non significant among all scores of chronic periodontitis subgroup. Concerning plaqueindex, the correlation appears to be significant in mild chronic periodonttis subgroup and highly significant in controlgroup. In case of gingival index, the correlation appears to be significant in severe chronic periodontitis subgroupand control group .The result of correlation with (B.O.P. score 1) appears to be highly significant in severe subgroup ofchronic periodontitis group and significant in gingivitis group, while in case of (B.O.P. score 0), the correlationappears to be significant only in severe chronic periodonttis subgroup.Conclusions: The present findings revealed that there may be an association between EBV infection and the severityof periodontal diseases and thus coinfection with EBV may play a role in increase destruction of periodontal tissues


Article
Role of HEF1 Gene Expression in Prognosis of Urinary Bladder Transitional Cell Carcinoma

Authors: Athraa Falah Hasan --- Alaa Salah Jumaah
Journal: Medical Journal of Babylon مجلة بابل الطبية ISSN: 1812156X 23126760 Year: 2016 Volume: 13 Issue: 2 Pages: 354 -365
Publisher: Babylon University جامعة بابل

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Abstract

Urinary bladder carcinoma is a common malignant tumor of the urogenital system worldwide. In 2015 ; it is the fourth most common cancer in men in the United State, while in Iraq it is one of the ten most common cancers in 2011. Human enhancer of filamentation 1 (HEF1) is a multidomain scaffolding protein of the Cas family; it is also an integral player in normal and pathological cell biology. The HEF1 protein has been implicated in the regulation of cell polarity, adhesion, motility, and invasion in multiple cell types. The main objective of the current study is to analyze HEF1 gene expression levels in urothelial carcinoma specimens and to study the impacts of HEF1 gene as genetic factors that contribute to development and prognosis of bladder cancer. Sixty samples of malignant bladder tumors as well as 60 samples of non-tumorous bladder tissues were investigated. Ages of patients were (62.95±12.839 s.d.) year. Total mRNA was extracted from FFPE blocks by using a specific kit. HEF1 gene expressions were estimated by using real-time PCR. Results were normalized to GAPDA gene as housekeeping gene. The gene expression data were analyzed in relevance to the patient's information obtained. Several statistical analyses were applied to analyze the data and found that the expression folds of HEF1 gene were found to be 11.219 folds in malignant bladder tumors in relation to non-tumorous bladder tissue. HEF1 genes were observed to be expressed excessively in high grade and advanced stage tumors which indicate that HEF1 gene may represent a novel bladder tumor marker with prognostic significance that could be introduced in plans of bladder cancer management.


Article
Real-Time PCR for direct detection of Clostridium perfringens from horse with enterocolitis infection

Authors: Jabbar A. Alwan --- Ali A. Al-zaidy --- Kadhim H. Abbas
Journal: Kufa Journal For Veterinary Medical Sciences مجلة الكوفة للعلوم الطبية البيطرية ISSN: 20779798 Year: 2016 Volume: 7 Issue: 1 Pages: 74-80
Publisher: University of Kufa جامعة الكوفة

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Abstract

Clostridium perfringens is one of the most important causative agents of enterocolitis infection in horses. This bacterium capable to produce potential enterotoxin that cause diarrhea in horses. This study was aimed to molecular identification of Clostridium perfringens from horses infected by diarrhea by using Real-Time PCR technique. The Clostridium perfringens type C was identified by using specific primers for enterotoxin (CPE) gene that designed in this study using NCBI-Genbank data base (Genbank code: GQ225719.1) and primer3 plus for primer design. The results show that prevalence of infection by Clostridium perfringens type C was (40%) of 12 positive samples out of 30 fecal samples. This study demonstrated that the direct Real-Time PCR technique is a highly specific and rapid tool for the detection Clostridium perfringens.

تعد بكتريا Clostridium perfringens واحدة من اهم مسببات الاضطرابات المعوية في الخيول وذلك لقدرة هذه البكتريا على انتاج الذيفانات الداخلية القوية المفعول والذي يحدث الاسهال في الخيول . هدفت هذه الدراسة تشخيص بكتريا Clostridium perfringens نوع C باستخدام تقانة Reat time PCR . بكتريا Clostridium perfringens نوع C شخصت باستعمال باديء خاص بالذيفان الداخلي الجين (CPE)والذي تم تصميميه لغرض الدراسة بالاعتماد على NCBI-Genbank data base (Genbank code: GQ225719.1) and primer3 plus لتصمصم البادئ و اضهرت النتائج ان نسبة الاصابة كانت 40% أي بواقع 12 عينة موجبة من أصل 30 عينة براز التي تم جمعها من الخيول المصابة .أعتمدت هذه الدراسة استخدام تقانة Real time PCR والذي يعد فائق التخصصية والسرعة في تشخيص بكتريا Clostridium perfringens نوع C .


Article
Determination of Human Sapovirus Genotypes Causing Gastroenteritis in Children under Five Years in Baghdad

Authors: Nadira Salman Mohamed --- Mohammed Nadher Maaroof --- Haider Kadhem Hussein
Journal: Al-Nahrain Journal of Science مجلة النهرين للعلوم ISSN: (print)26635453,(online)26635461 Year: 2017 Volume: 20 Issue: 3 Pages: 121-126
Publisher: Al-Nahrain University جامعة النهرين

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Sapoviruses (SaVs) may cause acute gastroenteritis (AGE) in young children. To prove the presences of Sapovirus infection in Iraq AGE patients, a total of 200 stool samples from children patients under five years with AGE were collected and screened by reverse transcription real time PCR using specific primers was performed for partial sequencing SaVs capsid and probes cover all Sapovirus genogroups, this was followed by revers transcription PCR and nested PCR using the specific primers. The SaVs partial capsid gene amplicons were sequenced. Partial capsid sequences were blasted with National Center of Information Technology (NCBI) and phylogenetic analysis was conducted using MEGA 6.0 program. Out of the 200 samples tested, 18 (9%) were found SaVs positive. Amplicons were sequenced and only 7 samples were genotyped, 5(5/7) were belonged to the genotype GI.1, 1(1/7) were belonged to the GI.4, and 1(1/7) were belong to the GII.8 .The GI.1 was the dominant strain in Baghdad and the more infected age stage was the children 4 ≤5 years. SaVs was diagnosed in Baghdad in the current study for the first time. These results need more extensive surveillance study to determine the distribution and burden of virus in Iraq community.


Article
Gene Expression Bcl-2 Gene in Cancer of Brest in Iraqi population

Author: H. M. Al-Khafaji
Journal: Engineering and Technology Journal مجلة الهندسة والتكنولوجيا ISSN: 16816900 24120758 Year: 2017 Volume: 35 Issue: 2 Part (B) Scientific Pages: 119-125
Publisher: University of Technology الجامعة التكنولوجية

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Abstract

The breast cancer is dangerous disease in the world . Molecular methods are important and necessary to diagnose breast cancer. Many of the genes with expression change like Bcl-2 gene is specifically, coding an anti-apoptotic protein and and therefore classified as an oncogene. Determine the damage of Bcl- 2 gene as a cause of some types of cancer, such as breast cancer, leukemia, prostate cancer and lung cancer .In this study, we examined Bcl-2 expression levels in (malignant, benign and healthy) tissues of the breast .They were fifty Laboratory samples (18 cancer tumor , 12 benign and 20 marginal (non-cancer) breast tissue that diagnosed based on their information were obtained from their files and records in all patients in this study , to extract the DNA and measure the level of expression of gene under study by molecular technique of ( r –t PCR ). Expression of gene under study is higher levels in malignant group and the fold of expression was 10.00 time higher than the control group and also in the benign group the fold of expression was 2.18 that higher than the control group.The results showed the expressed gene Bcl-2 is significantly higher in the third grade of breast tumor samples with Ct (22.14) of the first grade with CT (25.63) and the second with CT (24.07). According to the results of the study that the use of molecular methods in measuring the expression of Bcl-2 gene may help to diagnose the disease and may be considered that the Bcl2 gene is molecular tool for the early detection of breast cancer


Article
Phylogenetic Analysis of MERSCoV in Human and Camels in Iraq
التحليل الوراثي لل MERSCoV في الإنسان والجمال في العراق

Authors: Mohsen A. Alrodhan محسن نعمة الروضان --- Saba F. Al salihi صبا فلاح الصالحي
Journal: Al-Qadisiyah Medical Journal مجلة القادسية الطبية ISSN: 18170153 Year: 2017 Volume: 13 Issue: 23 Pages: 151-159
Publisher: Al-Qadisiyah University جامعة القادسية

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The present study was conducted to evaluate the genetic relationship among Middle East respiratory syndrome coronavirus (MERSCoV) of human and camels origin at the period from October 2015 to February 2016.One hundred samples were collected from camel and 100 from human. Nighty four from nasal swabs and six from oropharyngeal swabs Camel samples secerned by immunochromatographic assay (ICA) for detection of viral antigen. The total percentage of ICA positivity was 28%. Human and camel samples subjected to Revers transcription real time- PCR and carried out by RNA extraction by using specific primers and Taq- Man-Probe for detection of nucleocapsid gene 113 bp. The total positive result in camels were 15% ,there was no significant difference between sex and type of samples, in relation to the age group the results showed that age group more than ten years of camel was the heights percent. With significant difference at P<0.05. According to the months of the year October recorded the highest infection rate with significant difference at p<0.05. the result of RT-qPCR according to the regions of study showed that Al-shinafyah in western borders of Iraq-Saudi was the highest infection rate 35% .On the other hand ,100 human 81 nasal swabs and 19 bronchial lavage samples were collected from pilgrims and non-pilgrims. The total positive result was 5%. The pilgrims recorded the highest infection rate. The results of conventional PCR by using specific primers for detection of Nucleocapsid gene (217 bp) of MERSCoV. The results were confirmative. Three human and 11 camel positive samples were used in further sequencing and phylogenetic analysis by extraction and purification of the PCR products. Our clones sequence submitted in GenBank-NCBI for accession number. The phylogenetic tree construction and analysis results showed that most of Iraqi variants of camel and human were located in clade-B in which Saudi Arabia strains were clustered. One of our clones (MERS-Iq.2Huh) of accession number KX150500.1 was located in clade-A in the same branch of Jordanian strain while bat corona virus, SARS corona and neoromica corona virus was out group clustered in separated branch.

أجريت هذه الدراسة لتقييم العلاقة الوراثية بين فيروس كورونا المتلازمة التنفسية في الشرق الأوسط (MERSCoV) من أصل إنسان وجمال في الفترة من أكتوبر 2015 إلى فبراير 2016. تم جمع مائة عينة من الإبل و 100 من الإنسان. أربعة من كل ليلة من مسحات الأنف وستة من مسحات الفم والبلعوم عينات من الإبل المخلل بواسطة الفحص المناعي (ICA) للكشف عن المستضد الفيروسي. وكانت النسبة المئوية لإيجابية ICA 28 ٪. عينات من البشر والجمال تخضع لنسخ Revers في الوقت الحقيقي- PCR ونفذت بواسطة استخراج الحمض النووي الريبي باستخدام بادئات محددة و Taq- Man-Probe للكشف عن الجين النووي النواة 113 bp. بلغت النتيجة الإيجابية الكلية للإبل 15٪ ، ولم يكن هناك فرق كبير بين الجنس ونوع العينات ، فيما يتعلق بالفئة العمرية ، أظهرت النتائج أن الفئة العمرية لأكثر من عشر سنوات من الإبل هي النسبة المئوية المرتفعة. مع اختلاف كبير في P <0.05. وفقًا لأشهر العام ، سجل شهر أكتوبر أعلى معدل إصابة بفارق كبير عند P <0.05. أظهرت نتيجة RT-qPCR وفقًا لمناطق الدراسة أن الشنافية في الحدود الغربية للعراق-السعودية كانت أعلى نسبة إصابة بنسبة 35٪. ومن ناحية أخرى ، تم جمع 100 قطعة بشرية من 81 مسحة للأنف و 19 عينة لغسل الشعب الهوائية من الحجاج وغير الحجاج. وكانت النتيجة الإيجابية الإجمالية 5 ٪. سجل الحجاج أعلى نسبة إصابة. نتائج PCR التقليدية باستخدام الاشعال محددة للكشف عن الجين Nucleocapsid (217 سنة مضت) من MERSCoV. وكانت النتائج مؤكدة. تم استخدام ثلاث عينات إنسانية و 11 عينة من الإبل في تحليل التسلسل والنشوء عن طريق استخلاص وتنقية منتجات PCR. تم إرسال تسلسل النسخ لدينا في GenBank-NCBI لرقم الانضمام.أوضحت نتائج تحليل شجرة التكاثر وتحليلها أن معظم المتغيرات العراقية من الإبل والبشر كانت موجودة في clade-B حيث تم تجميع سلالات المملكة العربية السعودية. يوجد واحد من الحيوانات المستنسخة (MERS-Iq.2Huh) من رقم المدخل KX150500.1 في clade-A في نفس الفرع من السلالة الأردنية بينما كان فيروس الخفافيش corona و SARS corona وفيروس neoromica corona خارج المجموعة في فرع منفصل.

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