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Article ; Online: Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers

Gennady Verkhivker / Mohammed Alshahrani / Grace Gupta

International Journal of Molecular Sciences, Vol 24, Iss 6642, p

Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants

2023 Volume 6642

Abstract: Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. ... ...

Abstract	Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable among these variants. A systematic mutational scanning of the inter-protomer interfaces in the spike trimers revealed a group of conserved structural stability hotspots that play a key role in the modulation of functional dynamics and are also involved in the inter-protomer couplings through local contacts and interaction networks with the Omicron mutational sites. The results of mutational scanning provided evidence that BA.2.75 trimers are more stable than BA.2 and comparable in stability to the BA.1 variant. Using dynamic network modeling of the S Omicron BA.1, BA.2, and BA.2.75 trimers, we showed that the key network mediators of allosteric interactions are associated with the major stability hotspots that are interconnected along potential communication pathways. The network analysis of the BA.1, BA.2, and BA.2.75 trimers suggested that the increased thermodynamic stability of the BA.2.75 variant may be linked with the organization and modularity of the residue interaction network that allows for allosteric communications between structural stability hotspots and Omicron mutational sites. This study provided a plausible rationale for a mechanism in which Omicron mutations may evolve by targeting vulnerable sites of conformational adaptability to elicit immune escape ...
Keywords	SARS-CoV-2 spike protein ; Omicron subvariants ; ACE2 host receptor ; molecular dynamics ; protein stability ; network analysis ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	612
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Histopathological Analysis for Detecting Lung and Colon Cancer Malignancies Using Hybrid Systems with Fused Features

Mohammed Al-Jabbar / Mohammed Alshahrani / Ebrahim Mohammed Senan / Ibrahim Abdulrab Ahmed

Bioengineering, Vol 10, Iss 383, p

2023 Volume 383

Abstract: Lung and colon cancer are among humanity’s most common and deadly cancers. In 2020, there were 4.19 million people diagnosed with lung and colon cancer, and more than 2.7 million died worldwide. Some people develop lung and colon cancer simultaneously ... ...

Abstract	Lung and colon cancer are among humanity’s most common and deadly cancers. In 2020, there were 4.19 million people diagnosed with lung and colon cancer, and more than 2.7 million died worldwide. Some people develop lung and colon cancer simultaneously due to smoking which causes lung cancer, leading to an abnormal diet, which also causes colon cancer. There are many techniques for diagnosing lung and colon cancer, most notably the biopsy technique and its analysis in laboratories. Due to the scarcity of health centers and medical staff, especially in developing countries. Moreover, manual diagnosis takes a long time and is subject to differing opinions of doctors. Thus, artificial intelligence techniques solve these challenges. In this study, three strategies were developed, each with two systems for early diagnosis of histological images of the LC25000 dataset. Histological images have been improved, and the contrast of affected areas has been increased. The GoogLeNet and VGG-19 models of all systems produced high dimensional features, so redundant and unnecessary features were removed to reduce high dimensionality and retain essential features by the PCA method. The first strategy for diagnosing the histological images of the LC25000 dataset by ANN uses crucial features of GoogLeNet and VGG-19 models separately. The second strategy uses ANN with the combined features of GoogLeNet and VGG-19. One system reduced dimensions and combined, while the other combined high features and then reduced high dimensions. The third strategy uses ANN with fusion features of CNN models (GoogLeNet and VGG-19) and handcrafted features. With the fusion features of VGG-19 and handcrafted features, the ANN reached a sensitivity of 99.85%, a precision of 100%, an accuracy of 99.64%, a specificity of 100%, and an AUC of 99.86%.
Keywords	VGG-19 ; GoogLeNet ; lung and colon cancer ; FCH ; ANN ; GLCM ; Technology ; T ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Prevalence of multidrug-resistant in a critical care setting

Thabit Alotaibi / Abdulrhman Abuhaimed / Mohammed Alshahrani / Ahmed Albdelhady / Yousef Almubarak / Osama Almasari

SAGE Open Medicine, Vol

A tertiary teaching hospital experience

2021 Volume 9

Abstract: Background: The management of Acinetobacter baumannii infection is considered a challenge especially in an intensive care setting. The resistance rate makes it difficult to manage and is believed to lead to higher mortality. We aim to investigate the ... ...

Abstract	Background: The management of Acinetobacter baumannii infection is considered a challenge especially in an intensive care setting. The resistance rate makes it difficult to manage and is believed to lead to higher mortality. We aim to investigate the prevalence of Acinetobacter baumannii and explore how different antibiotic regimens could impact patient outcomes as there are no available published data to reflect our population in our region. Methods: We conducted a retrospective review of all infected adult patients admitted to the intensive care unit at King Fahad University Hospital with a confirmed laboratory diagnosis of Acinetobacter baumannii from 1 January 2013 until 31 December 2017. Positive cultures were obtained from the microbiology department and those meeting the inclusive criteria were selected. Variables were analyzed using descriptive analysis and cross-tabulation. Results were further reviewed and audited by blinded co-authors. Results: A comprehensive review of data identified 198 patients with Acinetobacter baumannii . The prevalence of Acinetobacter baumannii is 3.37%, and the overall mortality rate is 40.81%. Our sample consisted mainly of male patients, that is, 68.7%, with a mean age of 49 years, and the mean age of female patients was 56 years. The mean age of survivors was less than that of non-survivors, that is, 44.95 years of age. We observed that prior antibiotic use was higher in non-survivors compared to survivors. From the review of treatment provided for patients infected with Acinetobacter baumannii , 65 were treated with colistin alone, 18 were treated with carbapenems, and 22 were treated with a combination of both carbapenems and colistin. The mean length of stay of Acinetobacter baumannii– infected patients was 20.25 days. We found that the survival rates among patients who received carbapenems were higher compared to those who received colistin. Conclusion: We believe that multidrug-resistant Acinetobacter baumannii is prevalent and associated with a higher mortality rate ...
Keywords	Medicine (General) ; R5-920
Subject code	616
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Nano-treatment of HEPA filters in COVID-19 isolation rooms in an academic medical center in Saudi Arabia

Khaled F. Salama / Amani Alnimr / Aisha Alamri / Mahmoud Radi / Bashayer Alshehri / Ali A. Rabaan / Mohammed Alshahrani

Journal of Infection and Public Health, Vol 15, Iss 9, Pp 937-

2022 Volume 941

Abstract: Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread globally. The major reservoir for SARS-CoV-2 transmission remains controversial, with the airborne route remaining a ... ...

Abstract	Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread globally. The major reservoir for SARS-CoV-2 transmission remains controversial, with the airborne route remaining a possible transmission vehicle for carrying the virus within indoor environments. This study aimed to detect contamination of SARS-CoV-2 in high-efficiency particulate air (HEPA) filters within hospital isolation rooms of confirmed COVID-19 patients, exploring the role of nano-treatment of these filters with silver and titanium dioxide nanoparticles (Ag/TiO2 NPs). Materials and methods: We investigated the effectiveness of Ag-NPs/TiO2-treated HEPA filters in the air of rooms occupied by patients with confirmed COVID-19 in a university teaching hospital in the Eastern province of Saudi Arabia during the first wave of the pandemic. Ag/TiO2 NPs were designed and coated on HEPA filters to examine the filtration efficiency and antiviral ability in the presence of aerosolized virus particles. A total of 20 viral swab samples were collected from five patients’ rooms before and after treatment with nanoparticle-prepared solutions into the sterile virus-transporting media. Samples were evaluated for SARS-CoV-2 with a reverse transcription-polymerase chain reaction. Results: Two samples taken from the HEPA filter air exhaust outlets prior to nano-treatment tested positive for SARS-CoV-2 RNA in the intensive care unit, which has stringent aerosolization control procedures, suggesting that small virus-laden droplets may be displaced by airflow. All air samples collected from the HEPA filters from the rooms of patients with confirmed COVID-19 following nano-treatment were negative. Conclusion: We recommend further experimental exploration using a larger number of HEPA filters in areas with aerosol-generating procedures, along with viability studies on the HEPA filters to facilitate decision-making in high-risk facilities regarding the replacement, storage, and disposal of HEPA ...
Keywords	SARS-CoV-2 ; Outbreak ; Airborne ; Silver-titanium nanoparticles ; Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
Subject code	600
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Selection of top-K influential users based on radius-neighborhood degree, multi-hops distance and selection threshold

Mohammed Alshahrani / Fuxi Zhu / Lin Zheng / Soufiana Mekouar / Sheng Huang

Journal of Big Data, Vol 5, Iss 1, Pp 1-

2018 Volume 20

Abstract: Abstract Influence maximization in the social network becomes increasingly important due to its various benefit and application in diverse areas. In this paper, we propose DERND D-hops that adapt the radius-neighborhood degree to a directed graph which ... ...

Abstract	Abstract Influence maximization in the social network becomes increasingly important due to its various benefit and application in diverse areas. In this paper, we propose DERND D-hops that adapt the radius-neighborhood degree to a directed graph which is an improvement of our previous algorithm RND d-hops. Then, we propose UERND D-hops algorithm for the undirected graph which is based on radius-neighborhood degree metric for selection of top-K influential users by improving the selection process of our previous algorithm RND d-hops. We set up in the two algorithms a selection threshold value that depends on structural properties of each graph data and thus improves significantly the selection process of seed set, and use a multi-hops distance to select most influential users with a distinct range of influence. We then, determine a multi-hops distance in which each consecutive seed set should be chosen. Thus, we measure the influence spread of selected seed set performed by our algorithms and existing approaches on two diffusion models. We, therefore, propose an analysis of time complexity of the proposed algorithms and show its worst time complexity. Experimental results on large scale data of our proposed algorithms demonstrate its performance against existing algorithms in term of influence spread within a less time compared with our previous algorithm RND d-hops thanks to a selection threshold value.
Keywords	Influence maximization ; Multi-hops distance ; Selection threshold ; Top-K influential users ; DERND D-hops ; UERND D-hops ; Computer engineering. Computer hardware ; TK7885-7895 ; Information technology ; T58.5-58.64 ; Electronic computers. Computer science ; QA75.5-76.95
Subject code	006
Language	English
Publishing date	2018-08-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The prevalence of celiac disease in Saudi patients with type 1 diabetes mellitus

Mohammed Zaid Aljulifi / Moeber Mahzari / Lujain Alkhalifa / Esra Hassan / Abdullah Mohammed Alshahrani / Abdulwahed Abdulaziz Alotay

Annals of Saudi Medicine, Vol 41, Iss 2, Pp 71-

2021 Volume 77

Abstract: BACKGROUND: Celiac disease (CD) is an autoimmune disease that is highly associated with type 1 diabetes mellitus (T1DM). The reported prevalence of CD in patients with T1DM in Saudi Arabia varies and the number of studies is limited. OBJECTIVES: ... ...

Abstract	BACKGROUND: Celiac disease (CD) is an autoimmune disease that is highly associated with type 1 diabetes mellitus (T1DM). The reported prevalence of CD in patients with T1DM in Saudi Arabia varies and the number of studies is limited. OBJECTIVES: Determine the prevalence of CD diagnosed with anti-tissue transglutaminase (anti-tTG) antibodies or by endoscopic biopsy in adolescents and adults with T1DM. DESIGN: Cross-sectional, retrospective medical record review. SETTING: Tertiary care center. PATIENTS AND METHODS: The study population included adolescents and adults with T1DM who were screened for CD between 2010 and 2019. The study variables included age, sex, age at diagnosis of T1DM, age of positive celiac screening, glycated hemoglobin (HbA1c), total daily insulin dose, frequency of diabetic ketoacidosis (DKA) and other autoimmune diseases. MAIN OUTCOME MEASURES: The prevalence of celiac disease in adolescents and adults with T1DM. SAMPLE SIZE: 539 patients. RESULTS: The prevalence of positive celiac test results was 11.5% (n=62). A small proportion (n=5, 8%) of the positive CD group was diagnosed with T1DM after they tested positive with the celiac screening test. Ten (16%) were diagnosed with T1DM and CD in the same year. The rest of the sample had a positive screening test after being diagnosed with T1DM. There was no statistically significant difference between the CD positive and negative groups for HbA1C, DKA frequency, microvascular complications of diabetes or thyroid disorder. For histopathological confirmation of CD, only 37% (n=23) of the group with a positive screening test underwent endoscopy. In this group, 43% (n=10) had normal endoscopic biopsy findings, 21.7% (n=5) had partial villous atrophy and 34.7% (n=8) had total villous atrophy. CONCLUSIONS: This study highlights the importance of screening for CD in T1DM patients. CD prevalence is high in patients with T1DM, despite the high likelihood of underdiagnosis. Additional studies of different age groups and the use of different study methods ...
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	King Faisal Specialist Hospital and Research Centre
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Association of demographic characteristics to depression, anxiety, and stress among diabetics

Vigneshwaran Easwaran / Sai Varun Kudumula Mulammagari / Chaitanyakumar Lakkepogu / Rajarajeshwari Byram / Sultan Mohammed Alshahrani / Sirajudeen Shaik Alavudeen / Noohu Abdulla Khan

CHRISMED Journal of Health and Research, Vol 8, Iss 2, Pp 89-

A cross-sectional report from resource-limited settings of South India

2021 Volume 94

Abstract: Background: In India, there is a scarcity of epidemiological data related to risk factors and prevalence of depression, anxiety, and stress (DAS) among diabetics. Therefore, their estimation may provide data for an effective management of these disorders ...

Abstract	Background: In India, there is a scarcity of epidemiological data related to risk factors and prevalence of depression, anxiety, and stress (DAS) among diabetics. Therefore, their estimation may provide data for an effective management of these disorders in diabetic patients. Aim: The current study was undertaken to analyze the effect of sociodemographic characteristics toward DAS symptoms and to estimate the prevalence of DAS among diabetics. Materials and Methods: It was a cross-sectional study conducted among diabetics at the resource-limited settings of South India. Non probabilistic convenient sampling was used for recruitment fo study subjects. DAS scale 21 questionnaire is a validated self-report questionnaire designed to measure the severity of a range of symptoms for DAS. The patients with established psychiatric disorders were excluded from the study. Results: Overall, the prevalence of DAS symptoms was 57.5%, 55.9%, and 44.9%, respectively, and which ranges from mild to extremely severe. Gender plays a major role in increasing the prevalence of depressive and stress symptoms. The elderly age group was found to have more prevalence of all these three symptoms than younger age. Conclusions: The study showed that the prevalence of DAS symptoms was high. However, in our study, these symptoms are poorly associated to demographic characteristics. We recommend to screen all the diabetic patients for DAS symptoms.
Keywords	anxiety ; depression ; diabetics ; stress ; Medicine ; R ; Nursing ; RT1-120
Subject code	150
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Sensitivity and Specificity of Rapid SARS-CoV-2 Antigen Detection Using Different Sampling Methods

Faisal Alonaizan / Jehan AlHumaid / Reem AlJindan / Sumit Bedi / Heba Dardas / Dalia Abdulfattah / Hanadi Ashour / Mohammed AlShahrani / Omar Omar

International Journal of Environmental Research and Public Health, Vol 19, Iss 6836, p

A Clinical Unicentral Study

2022 Volume 6836

Abstract: Rapid antigen detection of SARS-CoV-2 has been widely used. However, there is no consensus on the best sampling method. This study aimed to determine the level of agreement between SARS-CoV-2 fluorescent detection and a real-time reverse-transcriptase ... ...

Abstract	Rapid antigen detection of SARS-CoV-2 has been widely used. However, there is no consensus on the best sampling method. This study aimed to determine the level of agreement between SARS-CoV-2 fluorescent detection and a real-time reverse-transcriptase polymerase chain reaction (rRT-PCR), using different swab methods. Fifty COVID-19 and twenty-six healthy patients were confirmed via rRT-PCR, and each patient was sampled via four swab methods: oropharyngeal (O), nasal (N), spit saliva (S), and combined O/N/S swabs. Each swab was analyzed using an immunofluorescent Quidel system. The combined O/N/S swab provided the highest sensitivity (86%; Kappa = 0.8), followed by nasal (76%; Kappa = 0.68), whereas the saliva revealed the lowest sensitivity (66%; kappa = 0.57). Further, when considering positive detection in any of the O, N, and S samples, excellent agreements with rRT-PCR were achieved (Kappa = 0.91 and 0.97, respectively). Finally, among multiple factors, only patient age revealed a significant negative association with antigenic detection in the saliva. It is concluded that immunofluorescent detection of SARS-CoV-2 antigen is a reliable method for rapid diagnosis under circumstances where at least two swabs, one nasal and one oropharyngeal, are analyzed. Alternatively, a single combined O/N/S swab would improve the sensitivity in contrast to each site swabbed alone.
Keywords	coronavirus/SARS-CoV-2 ; diagnostic systems ; fluorescent immunoassay ; oropharyngeal swab ; nasal swab ; saliva swab ; Medicine ; R
Subject code	610
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Pharmacokinetics after subcutaneous administration of a single dose of cefovecin sodium in African lions (Panthera leo)

Flaminio, Kelly P / John Mark Christensen / Sultan Mohammed Alshahrani / Sumeia Mohammed Mohammed

American journal of veterinary research. 2019 Mar., v. 80, no. 3

2019

Abstract: OBJECTIVE To determine the pharmacokinetics of cefovecin sodium after SC administration of a single dose to African lions (Panthera leo). ANIMALS 3 adult (9 to 10 years old; 1 male and 2 females) and 3 juvenile (2 years old; 1 male and 2 females) African ...

Abstract	OBJECTIVE To determine the pharmacokinetics of cefovecin sodium after SC administration of a single dose to African lions (Panthera leo). ANIMALS 3 adult (9 to 10 years old; 1 male and 2 females) and 3 juvenile (2 years old; 1 male and 2 females) African lions. PROCEDURES A crossover study was conducted. A single dose of cefovecin was administered SC at 4 mg/kg (half dose) and 8 mg/kg (full dose) to African lions. Blood samples were collected daily for 14 days after cefovecin injection. Plasma drug concentrations were determined by use of high-performance liquid chromatography with UV detection. RESULTS Cefovecin had first-order elimination kinetics for doses of 4 and 8 mg/kg. Mean ± SD maximum plasma concentration was 9.73 ± 1.01 μg/mL and 18.35 ± 0.94 μg/mL after doses of 4 and 8 mg/kg, respectively. Time to maximum plasma concentration was approximately 4 hours for both doses. Mean elimination half-life was approximately 111 and 115 hours after doses of 4 and 8 mg/kg, respectively. CONCLUSIONS AND CLINICAL RELEVANCE Cefovecin was detected in lion plasma for 336 hours after administration at both 4 and 8 mg/kg at concentrations greater than the reported minimum inhibitory concentration (0.06 μg/mL) for common bacterial organisms in domestic cats. These results indicated that cefovecin administered at 4 mg/kg SC reached therapeutic concentrations for an extended period in African lions.
Keywords	Panthera leo ; adults ; blood sampling ; cats ; cefovecin ; cross-over studies ; drugs ; females ; half life ; high performance liquid chromatography ; juveniles ; males ; minimum inhibitory concentration ; pharmacokinetics ; subcutaneous injection ; therapeutics
Language	English
Dates of publication	2019-03
Size	p. 230-234.
Publishing place	American Veterinary Medical Association
Document type	Article
ZDB-ID	390796-x
ISSN	1943-5681 ; 0002-9645
ISSN (online)	1943-5681
ISSN	0002-9645
DOI	10.2460/ajvr.80.3.230
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Mammography uptake among the female staff of King Saud University

Sulaiman Abdullah Alshammari / Ali Mohsen Alhazmi / Hanan Awad Alenazi / Hotoon Sulaiman Alshammari / Abdullah Mohammed Alshahrani

Journal of Family Medicine and Primary Care, Vol 9, Iss 1, Pp 221-

2020 Volume 228

Abstract: Background: Breast cancer is having a major impact on women's health worldwide. Early detection is the best defense against the associated morbidity and mortality of the disease. Objectives: To assess the level of mammography uptake among working Saudi ... ...

Abstract	Background: Breast cancer is having a major impact on women's health worldwide. Early detection is the best defense against the associated morbidity and mortality of the disease. Objectives: To assess the level of mammography uptake among working Saudi women and identify the obstacles and barriers that negatively affect it. In addition, to identify the most effective sources of breast-cancer-related information and early detection screening. Method: We conducted a cross-sectional study of women employees of King Saud University aged 40 years and above on March–May 2015 using a self-report questionnaire. Results: A total of 229 participants were recruited from the female staff of King Saud University. Of the participants, 34% were aged 41 years or above, approximately 66% were married, 53.3% had a bachelor's degree, and 61.1% worked as administrators; further, 64.6% had a history of breastfeeding. The rate of mammography uptake was 51.5%. Univariate logistic regression indicated that age, education, and being single predict the rate of mammography uptake. However, multivariate logistic regression indicated that earlier age significantly predicts a higher risk of a low rate of mammography uptake. The main obstacle negatively affecting mammography uptake was ineligible criteria (21.8%). The main sources of information regarding breast cancer were awareness campaigns and television and radio (45.4% and 43.7%, respectively). Conclusion: The participants' rate of mammography uptake, awareness of mammograms, the risk factors, and signs of breast cancer were low. To improve breast-cancer mortality rates in Saudi Arabia, earlier detection of breast cancer through increasing awareness of mammograms is of paramount importance.
Keywords	female university staff ; mammography ; saudi arabia ; Medicine ; R
Subject code	610
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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