Publications by authors named "Majed Alghamdi"

24 Publications

  • Page 1 of 1

A retrospective evaluation of the value of COVID-19 screening and testing in patients with cancer: Aiming at a moving target.

J Infect Public Health 2021 Jul 26;14(7):949-953. Epub 2021 May 26.

Department of Oncology, King Abdulaziz Medical City, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia.

Background: Diagnosis of COVID-19 infection in cancer patients is critical to co-manage their underlying disease and infection appropriately. Our study aimed at evaluating the sensitivity and specificity of screening patients with cancer for COVID-19 infection.

Methods: All oncology patients receiving care at Department of Oncology at King Abdulaziz Medical City in Riyadh were screened using the acute respiratory infection (ARI) survey. Nasopharyngeal and throat swap for polymerase chain reaction (PCR) testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was performed on patients who have high ARI score (i.e. ≥ 4), or any patient requiring elective/emergency hospitalization, undergoing a procedure as well as screening asymptomatic patients receiving chemotherapy between April 1st and July 30, 2020. Institutional Review Board approval was obtained. Descriptive and inferential analyses were done and sensitivity, specificity, positive and negative predictive values (PPV and NPV) were calculated considering the COVID-19 PCR as the gold standard.

Results: During the study period, a total of 473 patients were included with a median age was 56 years (14-104), 51% were female, 73% had solid tumors, and 66% received treatment within the last 3 months. These patients underwent 688 PCR tests along with ARI survey screening. Testing was done in the outpatient, inpatient, and emergency department setting in 41%, 40% and 19% of the patients, respectively. Majority of tests were screening of asymptomatic patients and only 23% were tested for suspected infections with ARI ≥ 4. A total of 54 patients (8%) had positive PCR for COVID-19 infection. The prevalence of infection varied from month to month ranging from 1.09% in April up to 19.70% in June and correlated with the average daily and active case load at a national level. The diagnostic yield of the ARI score also correlated with infection burden nationally. The PPV and NPV of the ARI as a screening tool was 18.24% (0-31.8) and 95.6% (86.36-98.86%) with the PPN fluctuating considerably in parallel with the prevalence of COVID-19 result. Similarly, the sensitivity and specificity of the ARI were 55.77% (0-70.59) and 79.4 (69.19-92), respectively.

Conclusion: The yield of screening asymptomatic patients with cancer varies based on the community burden of COVID-19 infection. As universal screening can cause delays to patient care, it should be tailored based on the individual patient risks and infection burden in the region.
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http://dx.doi.org/10.1016/j.jiph.2021.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8152208PMC
July 2021

Scholarly Activity of Radiation Oncologists in High-Income Developing Countries: Saudi Arabia as an Example.

JCO Glob Oncol 2021 Mar;7:378-383

Radiation Oncology, Comprehensive Cancer Center, King Fahad Medical City, Riyadh, Saudi Arabia.

Purpose: To examine the trends and quality metrics of publications by radiation oncologists in Saudi Arabia.

Methods: PubMed was searched using names of all Saudi radiation oncologists to retrieve published articles between January 2010 and December 2019. International collaboration, journal impact factor and country of origin, and number of citations were collected. Each article was assessed for epidemiologic type and independently assigned a level of evidence (LOE) by two authors. The trend in publications was examined and compared in the first and second 5-year periods (2010-2014 and 2015-2019) using relevant parameters.

Results: A total of 186 publications were found and included. The most common type of research was cohort studies followed by case reports and case series in 24%, 14%, and 13% of all publications, respectively. Dosimetry, clinical, and preclinical studies formed 7%, 8.6%, and 7.5% of the total publications, respectively. The LOE was I, II, III, IV, and not applicable in 8.6%, 22%, 25.8%, 29%, and 14.5% of the included publications, respectively. Comparing the first and second 5-year periods, there was an increase in international collaboration ( < .001) in the second period. The number of citations ( < .001) and journal impact factor ( = .028) were lower in the second period. LOE and publications in international journals were not statistically different between the two periods.

Conclusion: Although radiation oncology research activity in Saudi Arabia has gained momentum in terms of volume and international collaboration over time, the LOE has not improved. This calls for a national effort to make the contribution to the literature a priority, allocate adequate resources, and apply appropriate measures to enhance research productivity and quality.
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http://dx.doi.org/10.1200/GO.20.00449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081503PMC
March 2021

Management guidelines for stage III non-small cell lung cancer.

Crit Rev Oncol Hematol 2021 Jan 7;157:103144. Epub 2020 Nov 7.

College of Medicine, Thoracic Surgery, Alfaisal University, Riyadh, Saudi Arabia.

Management of stage III non- small cell lung cancer (NSCLC) is very challenging due to being a group of widely heterogeneous diseases that require multidisciplinary approaches with timely and coordinated care. The standards of care had significant changes over the last couple of years because of the introduction of consolidation therapy with checkpoint inhibitor following concurrent chemo-radiotherapy and the evolving new role of tyrosine kinase inhibitors in the adjuvant setting. The manuscript presents evidence-based recommendations for the workup, staging, treatment and follow up of the various subtypes of stage III NSCLC. The guidelines were developed by experts in various fields of thoracic oncology and guidelines development. The guidelines consider the sequence of interventions and the role of each discipline in the management of the disease taking into account the recent development and included required resources to help physicians provide better care.
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http://dx.doi.org/10.1016/j.critrevonc.2020.103144DOI Listing
January 2021

Contribution of Pathologists in Leading Clinical Cancer Research Through Interdisciplinary Collaboration in Saudi Arabia.

Cureus 2020 Sep 17;12(9):e10513. Epub 2020 Sep 17.

Department of Internal Medicine/Oncology, Al Baha University, Jeddah, SAU.

Background Interdisciplinary collaboration is often the key to advance cancer research. This research collaboration is frequently observed between oncologists and pathologists. While clinical cancer research is often led by oncologists, the leading role of pathologists is likely limited to laboratory-based and preclinical research. Therefore, the magnitude and characteristics of clinical studies led by pathologists is largely unknown. Objectives The objective of our study was to assess the quantity and quality of clinical cancer-related publications led by Saudi pathologists over a 10-year period. Methods A PubMed search was conducted between January 2008 and December 2017 to extract all published clinical articles regarding cancer by at least one Saudi pathologist with the collaboration of other cancer specialists. Information about articles and authors were collected. The level of evidence (LOE) was independently assessed by two authors. Two five-year periods (2008 - 2012 and 2013 - 2017) were compared using the relevant parameters. Results A total of 127 publications met our inclusion criteria and were included. Review articles (27%) were the most common type of publication. There were no experimental studies. The LOE was III and IV in 59.1% and 40.9% of the included publications, respectively. Comparing the two five-year periods, the number of publications (p < 0.001), publications in international journals (p = 0.004), and international collaborations (p < 0.001) increased in the second period. The LOE and journal impact factor were the same in the two periods. Conclusions The pathologist-led clinical cancer research in Saudi Arabia increased over time. Despite the observed increase in international collaboration and publications in international journals, the LOE was low (III/IV) and did not change over time.
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http://dx.doi.org/10.7759/cureus.10513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7571775PMC
September 2020

Locally Advanced Oral Cavity Cancers: What Is The Optimal Care?

Cancer Control 2020 Jan-Dec;27(1):1073274820920727

Radiation Oncology Section, King Abdulaziz Medical City, Ministry of National Guard, Jeddah, Saudi Arabia.

Patients with oral cavity cancers often present late to seek medical care. Surgery is usually the preferred upfront treatment. However, surgical resection cannot be achieved in many cases with advanced disease without major impact on patient's quality of life. On the other hand, radiotherapy (RT) and chemotherapy (CT) have not been employed routinely to replace surgery as curative treatment or to facilitate surgery as neoadjuvant therapy. The optimal care of these patients is challenging when surgical treatment is not feasible. In this review, we aimed to summarize the best available evidence-based treatment approaches for patients with locally advanced oral cavity cancer. Surgery followed by RT with or without CT is the standard of care for locally advanced oral cavity squamous cell carcinoma. In the case of unresectable disease, induction CT prior to surgery or chemoradiotherapy (CRT) can be attempted with curative intent. For inoperable patients or when surgery is expected to result in poor functional outcome, patients may be candidates for possibly curative CRT or palliative RT with a focus on quality of life.
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http://dx.doi.org/10.1177/1073274820920727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218312PMC
December 2020

Oncology research in Saudi Arabia over a 10-year period. A synopsis.

Saudi Med J 2020 Mar;41(3):261-266

Department of Internal Medicine, Faculty of Medicine, Al-Baha University, Al-Baha, Kingdom of Saudi Arabia. E-mail.

Objectives: To assess the quality and quantity of Saudi publications in oncology over a 10-year period.

Methods: A systematic PubMed search was conducted between January 2008 and December 2017 to retrieve all Saudi oncology publications. Data about the articles was collected. The level of evidence (LOE) was independently assessed by 2 authors. Two 5-year periods (2008-2012 and 2013-2017) were compared using the relevant parameters. Clinicaltrials.gov was also searched for all oncology trials registered in Saudi Arabia.

Results: A total of 839 publications met our inclusion criteria. The most common type of research was case series, totaling 32% of all publications. Clinical trials formed less than 2% of the total. The LOE was I, II, III, and IV in 0.3%, 2.1%, 58.4%, and 39.3% of the included publications, respectively. The LOE was the same in the 2 periods. There were more publications in international journals (p=0.004), more international collaborations (p=0.001), and higher journal impact factors (p=0.037) in 2013-2017 than in 2008-2012. Only 76 registered clinical trials were found in the Clinicaltrials.gov registry.

Conclusion: Despite an increase in the number of Saudi publications in the field of oncology over time, the LOE did not change. There were, however, some improvements in the international collaboration and journal impact factor, as well as an increase in the number of studies published in international journals. These observations call for a national strategy to improve oncology research in Saudi Arabia.
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http://dx.doi.org/10.15537/smj.2020.3.24912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841566PMC
March 2020

Postoperative Stereotactic Body Radiotherapy for Spinal Metastases and the Impact of Epidural Disease Grade.

Neurosurgery 2019 12;85(6):E1111-E1118

Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada.

Background: Postoperative stereotactic body radiotherapy (pSBRT) is an emerging indication for spinal metastases (SM).

Objective: To report our experience with pSBRT for SM.

Methods: A retrospective chart review was performed for prospectively collected data of patients treated between September 2008 to December 2015 with pSBRT and followed with serial spinal MRIs every 2 to 3 mo until death or last follow-up. Univariate and multivariable analyses were performed to identify predictive factors.

Results: A total of 83 spinal segments in 47 patients treated with a median dose of 24 Gy in 2 fractions were included, with mostly lung and breast primaries. A total of 59.3% had preoperative high-grade epidural disease (ED) and 39.7% were unstable. The 12-mo cumulative incidence of local failure was 17% for all segments, and 33.3%, 21.8%, and 0% in segments with postoperative high-grade, low-grade, and no ED, respectively. Downgrading preoperative ED was predictive of better local control (P = .03). The grade of postoperative ED was also predictive for local control (P < .0001), as was a longer interval between prior radiotherapy and pSBRT in those previously irradiated (P = .004). The 12-mo overall survival rate was 55%. One case of radiculopathy, 3 vertebral compression fractures, and no cases of myelopathy, hardware failure, or skin breakdown were observed.

Conclusion: pSBRT is an effective and safe treatment. The association between downgrading preoperative ED and better local control following pSBRT is confirmed and supports the concept of separation surgery.
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http://dx.doi.org/10.1093/neuros/nyz349DOI Listing
December 2019

Synthesis and evaluation of N-allylthiourea-modified chitosan for adsorptive removal of arsenazo III dye from aqueous solutions.

Int J Biol Macromol 2019 Sep 26;137:107-118. Epub 2019 Jun 26.

Chemistry Department, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.

N-allylthiourea chitosan (ATUCS), a chelating material, was prepared, characterized, and studied for the removal of arsenazo III (As (III)) dye from aqueous solution. Scanning electron microscopy (SEM), energy-dispersive X-ray (EDX), Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), and H- and C-nuclear magnetic resonance (NMR) were used to characterize the prepared adsorbent and to investigate the adsorption mechanism. Furthermore, the adsorption behavior of chitosan (CS) and ATUCS were studied under various conditions. The equilibrium adsorbed amount of As (III) onto ATUCS was found to be 116.3 mg/g, compared to 87.3 mg/g with respect to CS. The regeneration of the loaded CS and ATUCS were studied using 1:1 solution of HO-HSO and reused with certain change in efficiency after the third cycle. The adsorption process was found to fit well with pseudo-second-order kinetic model. The equilibrium data were better described with the Freundlich isotherm. The monolayer adsorption capacity was found to be 204.08 and 90.90 mg/g for the As (III)/ATUCS and As (III)/CS systems, respectively, at 25 °C. The pH of the higher uptake of As (III) onto ATUCS and CS was 4-5 and 8.0, respectively. The results demonstrated improved adsorption of As (III) using ATUCS as compared to the CS.
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http://dx.doi.org/10.1016/j.ijbiomac.2019.06.193DOI Listing
September 2019

Comprehensive and esthetic rehabilitation for phobic patient "case report".

Saudi Dent J 2019 29;31(Suppl):S85-S88. Epub 2019 Jan 29.

Head of Dental Department in King Salman Bin Abdulaziz Hospital, Riyadh, Saudi Arabia.

Background: One of the main reasons for a patient to be referred for sedation in order to receive dental treatment is dental fear. Minimal Invasive Dentistry is caused by the ceramic material improvement along with luting composites ceramic and well secured to teeth. Modern society considers a lovely smile being the perfect image for beauty and great health.

Case Details: A 24-year old phobic patient Male presented to the clinic, with a chief complaint of an unaesthetic smile. We end up by excellent management of phobic patient and complete comprehensive and esthetic treatment and the patient was highly satisfied with the results.

Conclusion: Successful management of a fearful patient during the first visit build good patient dentist relationship thus completing comprehensive dental treatment.
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http://dx.doi.org/10.1016/j.sdentj.2019.01.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6488716PMC
January 2019

Pretruncal Nonaneurysmal Subarachnoid Hemorrhage with Underlying Hemophilia C.

World Neurosurg 2019 Jul 4;127:109-112. Epub 2019 Apr 4.

National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia. Electronic address:

Background: Pretruncal nonaneurysmal subarachnoid hemorrhage (PNSAH) accounts for 15%-12% of all case of subarachnoid hemorrhage. Its precise etiology is not yet established. Multiple theories and risk factors have been investigated to address the possible cause of this type of hemorrhage including basilar tip dissecting aneurysms, high spinal arteriovenous fistula, venous stenosis/hypertension or venous bleeding. Hereditary coagulopathies and hemophilias have rarely been reported in the literature as a potential cause of PNSAH.

Case Description: Here, we reported a rare case of PNSAH with negative angiogram and magnetic resonance imaging who was also found to have hemophilia C (factor XI deficiency) confirmed by laboratory investigation. We also included a literature review of hereditary coagulopathies and their role as a possible cause of PNSAH.

Conclusions: Detailed medical history and physical examination of patients with PNSAH may lead to further hematologic evaluation for this group of patients, as in this case, and may reveal more cases of mild coagulopathy that require treatment.
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http://dx.doi.org/10.1016/j.wneu.2019.03.278DOI Listing
July 2019

Survey of flexible bronchoscopy practice in adults in Saudi Arabia.

Saudi Med J 2019 Mar;40(3):238-245

Department of Internal Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia. E-mail.

Objectives: To assess current adherence to international guidelines for practitioners of bronchoscopy in the Kingdom of Saudi Arabia. Methods: A cross-sectional survey was conducted in Saudi Arabia between December 2016 and March 2017. Pulmonologists, thoracic surgeons, and intensivists were invited to answer an emailed self-administered questionnaire survey seeking information on how they performed flexible bronchoscopy in adults. The data collected were compared between the 3 specialties. Results: Eighty-two (18%) of 456 invited practitioners completed the survey. Fifty-eight (72%) of the 82 respondents were pulmonologists. Forty (53%) of 76 respondents (93%) who had received bronchoscopy training received it abroad. Twenty-seven respondents (33%) had also received training in endobronchial ultrasound, electrocautery, brachytherapy, stent insertion, and laser procedures. Fifty-eight respondents (70%) preferred patients to undergo fasting for at least 4 hours before the procedure. Lidocaine was used for topical anesthesia, mainly by aerosol spray or nebulization. Midazolam was used by 62%, fentanyl by 50%, and propofol by 12% of respondents. Ninety percent of pulmonologists reported requesting a chest radiograph after transbronchial lung biopsy. Safety procedures for bronchoscopists, for example, wearing masks and eye protection, and for patients, for example, availability of anesthetic reversal agents, were not universally applied. Conclusion: Bronchoscopy is not standardized in Saudi Arabia. National guidelines for the indications and practice of bronchoscopy are required.
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http://dx.doi.org/10.15537/smj.2019.3.23964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6468201PMC
March 2019

Saudi lung cancer prevention and screening guidelines.

Ann Thorac Med 2018 Oct-Dec;13(4):198-204

Department of Medicine, Pulmonary, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.

Background: While lung cancer is the leading cancer cause of death, it is largely preventable. Furthermore, early diagnosis enhances the chance of cure. Therefore, we developed guidelines for lung cancer prevention and early detection.

Methods: A multidisciplinary team of experts in lung cancer representing different health-care sectors was assembled based on the National Cancer Center request and in coordination with the Saudi Lung Cancer Association of Saudi Thoracic Society. The team reviewed various reliable international guidelines and the data and experience in the Kingdom and formulated guidelines that address the primary and secondary prevention approaches in lung cancer, including tobacco control, early diagnosis, and lung cancer screening.

Results: The team developed guidelines to assist healthcare professionals in the Kingdom manage the different aspects of lung cancer prevention. Primary prevention through tobacco control: the recommendations encourage all healthcare professionals in all practice settings to screen their patients for smoking and to provide counseling and if needed referral to smoking cessation programs for current smokers. For early diagnosis of patients with symptoms suspicions of lung cancer, it is expected standard of care to investigate, work up, and refer the patients appropriately. Mass screening of patients at high risk for developing lung cancer: the recommendations listed the program requirements, eligible patients, and algorithm to manage findings. However, the team does not recommend that national screening program be mandated or implemented for lung cancer at this stage until more data and studies provide stronger evidence to justify adopting a national program.

Conclusions: Physicians can play an important role in preventing lung cancer by tobacco control and also detect lung cancer at earlier presentation. However, national mass screening programs require further study.
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http://dx.doi.org/10.4103/atm.ATM_147_18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6196665PMC
November 2018

Stereotactic radiosurgery for resected brain metastasis: Cavity dynamics and factors affecting its evolution.

J Radiosurg SBRT 2018 ;5(3):191-200

Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada.

Objective: To determine changes in post-surgical cavity volume for metastases based on time from surgery, pre-operative tumor dimensions and other predictors, in patients planned for post-operative stereotactic radiosurgery (SRS).

Methods: Patients with resected brain metastases from a primary solid tumor, treated with post-operative surgical cavity SRS from 2008 to 2014 were identified from an institutional prospective database. The segmented three-dimensional (3D) volume of the pre-operative tumor and post-operative surgical cavity were determined based on MRI and percent volume change was calculated. Patients were grouped according to early (<21 days), intermediate (22-42 days), and late (>42 days) intervals based on the number of days between the date of surgery and the treatment planning MRI. Potential predictive factors including tumor size, location, age, dural involvement, and degree of surgical resection were also analyzed.

Results: Sixty-one cavities in 59 patients were evaluated. Overall, a significant volume reduction (4cm, p=0.03) was observed comparing tumor and cavity volumes. For larger tumors, an average volume reduction of 11.6% (p=0.01) was observed compared to an increase of 34.4% in smaller tumors (p=0.69). For both large and small tumors, cavities were larger in the early interval especially for smaller tumors. During the intermediate interval, a significant volume reduction was observed for larger tumors (28%, p=0.0007). Tumor size, dural involvement, age and time from surgery were significant predictors for volume change on univariate analysis. On multivariate analysis, tumor size, dural involvement and time from surgery were significant.

Conclusion: Tumor size (>3cm), dural involvement and longer time from surgery were significant predictors of cavity volume reduction. Caution must be taken when treating cavities in the early (<21 days) interval after surgery as it may lead to irradiating more normal tissue especially in small tumors.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018046PMC
January 2018

Clinical implementation of AXB from AAA for breast: Plan quality and subvolume analysis.

J Appl Clin Med Phys 2018 May 25;19(3):243-250. Epub 2018 Apr 25.

Department of Physics and Astronomy, University of Calgary, Calgary, AB, Canada.

Purpose: Two dose calculation algorithms are available in Varian Eclipse software: Anisotropic Analytical Algorithm (AAA) and Acuros External Beam (AXB). Many Varian Eclipse-based centers have access to AXB; however, a thorough understanding of how it will affect plan characteristics and, subsequently, clinical practice is necessary prior to implementation. We characterized the difference in breast plan quality between AXB and AAA for dissemination to clinicians during implementation.

Methods: Locoregional irradiation plans were created with AAA for 30 breast cancer patients with a prescription dose of 50 Gy to the breast and 45 Gy to the regional node, in 25 fractions. The internal mammary chain (IMC ) nodes were covered by 80% of the breast dose. AXB, both dose-to-water and dose-to-medium reporting, was used to recalculate plans while maintaining constant monitor units. Target coverage and organ-at-risk doses were compared between the two algorithms using dose-volume parameters. An analysis to assess location-specific changes was performed by dividing the breast into nine subvolumes in the superior-inferior and left-right directions.

Results: There were minimal differences found between the AXB and AAA calculated plans. The median difference between AXB and AAA for breast V , was <2.5%. For IMC , the median differences V , and V were <5% and 0%, respectively; indicating IMC coverage only decreased when marginally covered. Mean superficial dose increased by a median of 3.2 Gy. In the subvolume analysis, the medial subvolumes were "hotter" when recalculated with AXB and the lateral subvolumes "cooler" with AXB; however, all differences were within 2 Gy.

Conclusion: We observed minimal difference in magnitude and spatial distribution of dose when comparing the two algorithms. The largest observable differences occurred in superficial dose regions. Therefore, clinical implementation of AXB from AAA for breast radiotherapy is not expected to result in changes in clinical practice for prescribing or planning breast radiotherapy.
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http://dx.doi.org/10.1002/acm2.12329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5978944PMC
May 2018

PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media.

BMC Microbiol 2018 01 24;18(1). Epub 2018 Jan 24.

Department of Genetics & Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.

Background: Microbial arrays, with a large number of different strains on a single plate printed with robotic precision, underpin an increasing number of genetic and genomic approaches. These include Synthetic Genetic Array analysis, high-throughput Quantitative Trait Loci (QTL) analysis and 2-hybrid techniques. Measuring the growth of individual colonies within these arrays is an essential part of many of these techniques but is useful for any work with arrays. Measurement is typically done using intermittent imagery fed into complex image analysis software, which is not especially accurate and is challenging to use effectively. We have developed a simple and fast alternative technique that uses a pinning robot and a commonplace microplate reader to continuously measure the thickness of colonies growing on solid agar, complemented by a technique for normalizing the amount of cells initially printed to each spot of the array in the first place. We have developed software to automate the process of combining multiple sets of readings, subtracting agar absorbance, and visualizing colony thickness changes in a number of informative ways.

Results: The "PHENOS" pipeline (PHENotyping On Solid media), optimized for Saccharomyces yeasts, produces highly reproducible growth curves and is particularly sensitive to low-level growth. We have empirically determined a formula to estimate colony cell count from an absorbance measurement, and shown this to be comparable with estimates from measurements in liquid. We have also validated the technique by reproducing the results of an earlier QTL study done with conventional liquid phenotyping, and found PHENOS to be considerably more sensitive.

Conclusions: "PHENOS" is a cost effective and reliable high-throughput technique for quantifying growth of yeast arrays, and is likely to be equally very useful for a range of other types of microbial arrays. A detailed guide to the pipeline and software is provided with the installation files at https://github.com/gact/phenos .
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http://dx.doi.org/10.1186/s12866-017-1143-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5784713PMC
January 2018

Vertebral Compression Fracture After Spine Stereotactic Body Radiation Therapy: A Review of the Pathophysiology and Risk Factors.

Neurosurgery 2018 09;83(3):314-322

Department of Radiation Oncology, Sunnybrook Odette Cancer Centre, University of Toronto, Toronto, Ontario, Canada.

Background: Vertebral compression fracture (VCF) is a challenging and not infrequent complication observed following spine stereotactic body radiation therapy (SBRT).

Objective: To summarize the data from the multiple studies that have been published, addressing the risk and predictive factors for VCF post-SBRT.

Methods: A systematic literature review was conducted. Studies were selected if they specifically addressed risk factors for post-SBRT VCF in their analyses.

Results: A total of 11 studies were identified, reporting both the risk of VCF post-SBRT and an analysis of risk factors based on univariate and multivariate analysis. A total of 2911 spinal segments were treated with a crude VCF rate of 13.9%. The most frequently identified risk factors on multivariate analysis were: lytic disease (hazard ratio [HR] range, 2.76-12.2), baseline VCF prior to SBRT (HR range, 1.69-9.25), higher dose per fraction SBRT (HR range, 5.03-6.82), spinal deformity (HR range, 2.99-11.1), older age (HR range, 2.15-5.67), and more than 40% to 50% of vertebral body involved by tumor (HR range, 3.9-4.46). In the 9 studies that specifically reported on the use of post-SBRT surgical procedures, 37% of VCF had undergone an intervention (range, 11%-60%).

Conclusion: VCF is an important adverse effect following SBRT. Risk factors have been identified to guide the selection of high-risk patients. Evidence-based algorithms with respect to patient selection and intervention are needed.
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http://dx.doi.org/10.1093/neuros/nyx493DOI Listing
September 2018

Hepatitis C virus infection in Jeddah city, Saudi Arabia: Seroprevalence and knowledge.

J Med Virol 2018 03 9;90(3):526-531. Epub 2017 Nov 9.

College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.

The infection rate of the hepatitis C virus (HCV) in Saudi Arabia is among the lowest in the world. However, it is likely that poor knowledge and awareness of HCV infection could minimize the effectiveness of prevention and control programs in the kingdom. Thus, the study objective was to estimate the prevalence of HCV infection, and to assess current knowledge about it, in the targeted population. Data on 5482 Saudi people attending primary healthcare centers in Jeddah City in 2014/2015 were analyzed in this cross-sectional study. Questions that covered the natural history, risk behavior, and prevention, and treatment of HCV were collected using a predesigned questionnaire. HCV seroprevalence was assessed using an enzyme-linked immunosorbent assay. HCV prevalence of 0.38% (95% confidence interval: 0.22-0.54) was found. The level of knowledge of the natural history, risk behavior, and prevention and treatment of HCV was poor among the participants. The lowest level of knowledge for all participants pertained to its prevention and treatment. The prevalence of HCV was low in Saudi Arabia (0.38%). However, adequate knowledge of HCV was lacking. Thus, the need to increase knowledge and awareness of HCV in the Saudi population is warranted.
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http://dx.doi.org/10.1002/jmv.24973DOI Listing
March 2018

Postoperative stereotactic body radiotherapy for spinal metastases.

Chin Clin Oncol 2017 Sep;6(Suppl 2):S18

Department of Radiation Oncology, Sunnybrook Odette Cancer Centre, University of Toronto, Toronto, ON, Canada.

Spine is a common site of metastases in cancer patients. Spine surgery is indicated for select patients, typically those with mechanical instability and/or malignant epidural spinal cord (or cauda equina) compression. Although post-operative conventional palliative external beam radiation therapy has been the standard of care, technical improvements in radiation planning and image-guided radiotherapy have allowed for the application of stereotactic body radiotherapy (SBRT) to the spine. Spine SBRT is intended to ablate residual tumor and optimize local control by delivering several fold greater biologically effective doses. Early clinical experience of postoperative spinal SBRT report encouraging results in terms of safety and efficacy. In this review, we summarize the clinical and technical aspects pertinent to a safe and effective practice of postoperative SBRT for spinal metastases.
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http://dx.doi.org/10.21037/cco.2017.06.27DOI Listing
September 2017

Reactivation pulmonary tuberculosis in two patients treated with pirfenidone.

Int J Mycobacteriol 2017 Apr-Jun;6(2):193-195

Department of Medicine, Division of Pulmonary, King Saud bin Abdulaziz University for Health Sciences; King Abdulaziz Medical City, Riyadh, Saudi Arabia.

We report two cases of patients with biopsy-proven idiopathic pulmonary fibrosis (IPF) who were treated with new antifibrotic agent for pirfenidone for more than 12 months. Both cases developed cavitary pulmonary tuberculosis (TB) proven by positive sputum TB culture. Both cases were treated with standard anti-TB drugs for 9 months and had complete clinical and radiological resolution. To our knowledge, these are the first reported human cases of patients with IPF who have been on pirfenidone and developed cavitary pulmonary TB.
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http://dx.doi.org/10.4103/ijmy.ijmy_64_17DOI Listing
February 2018

Atypical Meningioma: Referral Patterns, Treatment and Adherence to Guidelines.

Can J Neurol Sci 2017 May;44(3):283-287

1Division of Radiation Oncology,Department of Oncology,Calgary,Alberta,Canada.

Objective: To determine the referral rate to radiation oncologist (RO), use of postoperative radiotherapy (PORT) and the impact of a clinical practice guideline (CPG) on patients with atypical meningioma (AM).

Methods: A retrospective review of meningioma patients (n=526) treated between 2003 and 2013 was undertaken. Patients' characteristics, extent of surgical resection (EOR), RO referral, PORT, date and treatment of first recurrence were collected for all patients >18 years with a new diagnosis of AM after surgical resection (n=83). Progression free survival (PFS) and overall survival (OS) according to EOR were assessed by the Log-Rank test of Kaplan-Meier survival.

Results: Median age was 57 years. EOR was gross total (GTR) in 44 patients, subtotal (STR) in 36 patients and 3 patients had unknown EOR. RO referral rate was 26.5% (n=22); 5 patients initially had GTR and 17 had STR. Only 7 patients received PORT. At a median follow up time of 29 months, recurrences occurred in 28 patients, 4 had GTR, 21 had STR and 3 had an unknown EOR. With PORT, 2 patients developed recurrence. 5-year PFS was 62% after GTR and 33% after STR (P=0.002). 5-year OS was 92% after GTR and 83% after STR (P=0.45).

Conclusion: In this cohort with AM, RO referral rate was low and was not influenced by the CPG. Use of PORT was also low. Given the lack of conclusive evidence supporting PORT in such patients, a multidisciplinary approach, including RO consultation, is needed to provide patients with optimal and individualised care.
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http://dx.doi.org/10.1017/cjn.2016.449DOI Listing
May 2017

An audit of referral and treatment patterns of high-risk prostate cancer patients in Alberta.

Can Urol Assoc J 2016 Nov-Dec;10(11-12):410-415

Division of Radiation Oncology, University of Calgary and Tom Baker Cancer Centre, Calgary, AB, Canada.

Introduction: We aimed to determine the impact of clinical practice guidelines (CPG) on rates of radiation oncologist (RO) referral, androgen-deprivation therapy (ADT), radiation therapy (RT), and radical prostatectomy (RP) in patients with high-risk prostate cancer (HR-PCa).

Methods: All men >18 years, diagnosed with PCa in 2005 and 2012 were identified from the Alberta Cancer Registry. Patient age, aggregated clinical risk group (ACRG) score, Gleason score (GS), pre-treatment prostate-specific antigen (PSA), RO referral, and treatment received were extracted from electronic medical records. Logistic regression modelling was used to examine associations between RO referral rates and relevant factors.

Results: HR-PCa was diagnosed in 261 of 1792 patients in 2005 and 435 of 2148 in 2012. Median age and ACRG scores were similar in both years (p>0.05). The rate of patients with PSA >20 were 67% and 57% in 2005 and 2012, respectively (p=0.004). GS ≤6 was found in 13% vs. 5% of patients, GS 7 in 27% vs. 24%, and GS ≥8 in 59% vs. 71% in 2005 and 2012, respectively (p<0.001). In 2005, RO referral rate was 68% compared to 56% in 2012 (p=0.001), use of RT + ADT was 53% compared to 32% (p<0.001), and RP rate was 9% vs. 17% (p=0.002). On regression analysis, older age, 2012 year of diagnosis and higher PSA were associated with decreased RO referral rates (odds ratios [OR] 0.49, 95% confidence interval [CI] 0.39-0.61; OR 0.51, 95% CI 0.34-0.76; and OR 0.64, 95% CI 0.39-0.61), respectively [p<0.001]).

Conclusions: Since CPG creation in 2005, RO referral rates and ADT + RT use declined and RP rates increased, which demonstrates a need to improve adherence to CPG in the HR-PCa population.
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http://dx.doi.org/10.5489/cuaj.3910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167598PMC
January 2017

Prevalence and predictors of hepatitis B in Jeddah City, Saudi Arabia: a population-based seroprevalence study.

J Infect Dev Ctries 2016 Oct 31;10(10):1116-1123. Epub 2016 Oct 31.

Ministry of Health, Jeddah, Saudi Arabia.

Introduction: Despite solid preventive strategies to reduce the risk of hepatitis B virus (HBV) infection, recent reports about its prevalence and predictors are lacking in several Saudi cities at the community level. This study aimed to assess the seroprevalence of HBV and to identify the most important predictors among the Saudi population in Jeddah city, Saudi Arabia.

Methodology: A cross-sectional study was conducted among 5,584 Saudi people attending primary health-care centers in Jeddah city during 2012/2013. Sociodemographic and hepatitis-related data were collected. HBV was diagnosed by ELISA test. The seroprevalence of HBV was estimated, and appropriate statistical analyses were performed, including univariate and multivariable regression analyses.

Results: The seroprevalence of HBV was 2.2% (95% CI = 1.82-2.58) in the studied participants. The prevalence was higher among non-governmental workers (3.5%), male participants (3.4%) and those aged ≥ 25 years (2.4%). The most important predictors for increasing the risk of HBV in this study were HBV contacts, male sex, history of dental procedures and blood transfusion. The significant positive risks associated with these predictors were 3.3, 2.5, 2.0 and 1.65, respectively. HBV vaccination, on the other hand, was associated with a significant risk reduction of 88% (OR = 0.12; 95% CI = 0.03-0.51).

Conclusions: The seroprevalence of HBV was relatively low among the Saudi population in Jeddah city reflecting the actions taken by health authorities to control HBV infection. However, more efforts, particularly in relation to health education programmes, strict control of blood banks and dental clinics, are still needed.
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http://dx.doi.org/10.3855/jidc.7880DOI Listing
October 2016

Assessing guideline impact on referral patterns of post-prostatectomy patients to radiation oncologists.

Can Urol Assoc J 2016 Sep-Oct;10(9-10):314-318

Department of Oncology, Division of Radiation Oncology, University of Calgary, Tom Baker Cancer Centre, Calgary, AB, Canada.

Introduction: Adjuvant radiotherapy (aRT) can improve biochemical progression-free survival in patients with high-risk features (HRF) after radical prostatectomy (RP). Guidelines from Alberta and the Genitourinary Radiation Oncologists of Canada (GUROC) recommend that patients with HRF be referred to radiation oncologists (RO) based on the findings from three randomized, controlled trials (RCT). Our study examines the impact of these recommendations both pre- (2005) and post- (2012) publication of RCT and GUROC guideline establishment.

Methods: Patients undergoing RP during 2005 and 2012 were identified from the provincial cancer registry. Charts were retrospectively reviewed and variables of interest were linked to the registry data. RO referral patterns for each year were determined and variables influencing referral (extracapsular extension, positive margin, seminal vesicle invasion, and post-RP prostate-specific antigen [PSA]) were compared.

Results: Median time to referral was 26.4 months in 2005 compared to 3.7 months 2012 (p<0.001). Among patients referred post-RP, a higher proportion was referred within six months in 2012 (21%) as compared to 2005 (13%) (p=0.003). Among eligible patients in 2012, 30% were referred for discussion of aRT compared to 24% in 2005 (p=0.003). There was a marked drop in patients referred for salvage radiation therapy beyond six months and a rise in the number of patients who are never referred.

Conclusions: Despite an increase in referral rates to RO post-RP from 2005-2012, more than 50% of those patients with HRF did not receive a referral. Initiatives aimed at improving multidisciplinary care and guideline adherence should be undertaken.
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http://dx.doi.org/10.5489/cuaj.3539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5085909PMC
November 2016

Derivation and validation of clinical phenotypes for COPD: a systematic review.

Respir Res 2015 Apr 18;16:50. Epub 2015 Apr 18.

Respiratory Division, McGill University Health Centre, Montreal, Quebec, Canada.

Background: The traditional classification of COPD, which relies solely on spirometry, fails to account for the complexity and heterogeneity of the disease. Phenotyping is a method that attempts to derive a single or combination of disease attributes that are associated with clinically meaningful outcomes. Deriving phenotypes entails the use of cluster analyses, and helps individualize patient management by identifying groups of individuals with similar characteristics. We aimed to systematically review the literature for studies that had derived such phenotypes using unsupervised methods.

Methods: Two independent reviewers systematically searched multiple databases for studies that performed validated statistical analyses, free of definitive pre-determined hypotheses, to derive phenotypes among patients with COPD. Data were extracted independently.

Results: 9156 citations were retrieved, of which, 8 studies were included. The number of subjects ranged from 213 to 1543. Most studies appeared to be biased: patients were more likely males, with severe disease, and recruited in tertiary care settings. Statistical methods used to derive phenotypes varied by study. The number of phenotypes identified ranged from 2 to 5. Two phenotypes, with poor longitudinal health outcomes, were common across multiple studies: young patients with severe respiratory disease, few cardiovascular co-morbidities, poor nutritional status and poor health status, and a phenotype of older patients with moderate respiratory disease, obesity, cardiovascular and metabolic co-morbidities.

Conclusions: The recognition that two phenotypes of COPD were often reported may have clinical implications for altering the course of the disease. This review also provided important information on limitations of phenotype studies in COPD and the need for improvement in future studies.
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http://dx.doi.org/10.1186/s12931-015-0208-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460884PMC
April 2015