Application of Machine Learning to Predict COVID-19 Spread via an Optimized BPSO Model.

During the pandemic of the coronavirus disease (COVID-19), statistics showed that the number of affected cases differed from one country to another and also from one city to another. Therefore, in this paper, we provide an enhanced model for predicting COVID-19 samples in different regions of Saudi Arabia (high-altitude and sea-level areas). The model is developed using several stages and was successfully trained and tested using two datasets that were collected from Taif city (high-altitude area) and Jeddah city (sea-level area) in Saudi Arabia. Binary particle swarm optimization (BPSO) is used in this study for making feature selections using three different machine learning models, i.e., the random forest model, gradient boosting model, and naive Bayes model. A number of predicting evaluation metrics including accuracy, training score, testing score, F-measure, recall, precision, and receiver operating characteristic (ROC) curve were calculated to verify the performance of the three machine learning models on these datasets. The experimental results demonstrated that the gradient boosting model gives better results than the random forest and naive Bayes models with an accuracy of 94.6% using the Taif city dataset. For the dataset of Jeddah city, the results demonstrated that the random forest model outperforms the gradient boosting and naive Bayes models with an accuracy of 95.5%. The dataset of Jeddah city achieved better results than the dataset of Taif city in Saudi Arabia using the enhanced model for the term of accuracy.

Post COVID-19 Vaccination-Associated Neurological Complications.

PURPOSE: Neurological sequelae after COVID-19 vaccination are rare. We investigated the possible pathogenesis behind the development of neurological complications within a short period after Saudi residents received a COVID-19 vaccine. PATIENTS AND METHODS: We evaluated 18 patients who recently received a COVID-19 vaccine (Comirnaty and Vaxzevria vaccines) and presented with neurological complications to the Saudi German Hospitals in Jeddah, Saudi Arabia. Neurologists assessed the patients' clinical presentation, radiological investigations, and laboratory findings. RESULTS: Three patients who received the first dose of the Vaxzevria vaccine experienced severe cerebral venous thrombosis, two of them were complicated by intracranial hemorrhage. Their laboratory investigations showed very high d-dimers and severe thrombocytopenia, which have been linked to higher mortality and poor outcome. Ischemic stroke occurred in eight cases (44.4%) with a predominance in older male patients. Three patients presented with seizures, two had optic neuritis. Guillain-Barré syndrome (GBS) and Miller Fisher syndrome (MFS) occurred in two male patients following vaccination with Comirnaty. CONCLUSION: Neurological complications after COVID-19 vaccinations are very rare, and only a few cases have been reported worldwide. The shared pathophysiological basis between COVID-19 viral infection and COVID-19 vaccines stands behind the very rare neurological complications resulting from the hypercoagulable state triggered by the general inflammatory condition. We suspect some differences in the pathogenesis of ischemic stroke caused by COVID-19 infection and COVID-19 vaccines, which render COVID-19 vaccine-associated ischemic stroke more responsive to treatment. To date, no definitive association between the vaccine and GBS has been proven by any strong evidence, but it has recently been added as a very rare side effect of the Janssen COVID-19 vaccine. No possible links of Miller Fisher syndrome to COVID-19 vaccines have been reported before the one reported in this study.

Clinical and Laboratory Findings of COVID-19 in High-Altitude Inhabitants of Saudi Arabia.

Background: SARS-CoV-2, the causative agent of COVID-19, continues to cause a worldwide pandemic, with more than 147 million being affected globally as of this writing. People's responses to COVID-19 range from asymptomatic to severe, and the disease is sometimes fatal. Its severity is affected by different factors and comorbidities of the infected patients. Living at a high altitude could be another factor that affects the severity of the disease in infected patients. Methods: In the present study, we have analyzed the clinical, laboratory, and radiological findings of COVID-19-infected patients in Taif, a high-altitude region of Saudi Arabia. In addition, we compared matched diseased subjects to those living at sea level. We hypothesized that people living in high-altitude locations are prone to develop a more severe form of COVID-19 than those living at sea level. Results: Age and a high Charlson comorbidity score were associated with increased numbers of intensive care unit (ICU) admissions and mortality among COVID-19 patients. These ICU admissions and fatalities were found mainly in patients with comorbidities. Rates of leukocytosis, neutrophilia, higher D-dimer, ferritin, and highly sensitive C-reactive protein (CRP) were significantly higher in ICU patients. CRP was the most independent of the laboratory biomarkers found to be potential predictors of death. COVID-19 patients who live at higher altitude developed a less severe form of the disease and had a lower mortality rate, in comparison to matched subjects living at sea level. Conclusion: CRP and Charlson comorbidity scores can be considered predictive of disease severity. People living at higher altitudes developed less severe forms of COVID-19 disease than those living at sea level, due to a not-yet-known mechanism.

Successful Use of Virtual Microscopy in the Assessment of Practical Histology during Pandemic COVID-19: A Descriptive Study.

BACKGROUND: Practical knowledge and skills of microscopy has classically been delivered for medical students using conventional microscopes (CMs). Using virtual microscopy (VM) in teaching practical histology was established during distance learning for Taif medical students during COVID 19 pandemic period. However, the suitable assessment methods for student performance during distance learning are still debatable. We focused on how to ensure the learner's achievement of course practical outcomes and learning domain. AIMS AND OBJECTIVES: This study aimed to ascertain whether using VM to evaluate student learning in practical Histology during distance education programs and if moving to VM affecting students' scores. MATERIALS AND METHODS: For the first time, we used VM during online objective structural practical examination (OSPE) of 3rd year medical students. Different sets of virtual slides were given for students at the time of assessment, then different tasks were described and each student was asked to finalize his/her task during the designed time. A specific rubric was designed for the evaluation of student work. Moreover, student perceptions of VM as teaching and assessment method were assessed using online survey. Post examination psychometric analysis of VM OSPE was done and compared with previous OSPE results of the same batch of students. RESULTS: The average student score was 4.63 ± 0.51 with no significant difference from previous student's scores. The net students' feedback was positive. Their average satisfaction on all items ranged from 3.7 to 4.25 on Likert scale. Students recorded the easy image access at any time and place with VM as the most distinctive feature. CONCLUSION: Our results indicated that VM is not only an effective method in teaching histology but also it is an assessment method for measuring student performance during online assessment.

Association between cytokine genes polymorphisms and type 1 diabetes: a case-control study on Saudi population.

BACKGROUND: Association studies of genes encoding cytokines that play an important role in inflammatory response represent one approach to finding type 1 diabetes (T1D) disease genes. The aim of this study was to investigate the association of single nucleotide polymorphisms (SNPs) within cytokine genes with T1D in a cohort of Saudi subjects. METHODS: A total of 300 well-characterized type 1 diabetic patients and 300 T1D-free control subjects were enrolled in this investigation. Cytokine SNPs were genotyped by using Polymerase chain reaction (PCR) with sequence-specific primers. RESULTS: Our data revealed that IFN-γ +874T allele carriers [odds ratio (OR) = 1.87, p < 0.001] and TT homozygotes (OR = 1.28, p < 0.001) were significantly more susceptible to developing T1D than the A allele carriers. In addition, TNF-α -308A allele carriers (OR = 1.73, p < 0.001) and AA homozygotes (OR = 1.74, p < 0.001) were also overrepresented among the diabetics than G allele carriers. IL-4 -590C/T TT homozygotes (OR = 2.23, p < 0.001) were significantly more susceptible to develop T1D than CC genotypes, whereas CT heterozygotes were not significantly associated (OR = 1.43, p = 0.78) with T1D. Furthermore, IL-4 T allele was statistically associated with T1D patients compared to control group (OR = 2.24, p < 0.001). Similarly, IL-1ß -511C/T TT homozygotes (OR = 1.85, p = 0.012) and the T allele (OR = 1.85, p < 0.001) were significantly more susceptible to T1D than CC genotypes, whereas TC heterozygotes (OR = 1.04, p = 0.86) were not significantly associated with T1D. CONCLUSION: Our data concluded that IFN-γ +874T allele, TNF-α -308A allele, IL-1ß -511T allele, and IL-4 -590T allele could be considered risk factors for T1D development in Saudi subjects.

Competency assessment in laboratory medicine: Standardization and utility for technical staff assessment and recertification in Saudi Arabia.

PURPOSE: The assessment of technical staff members' competency has been a challenge for laboratory workers, to ensure patient safety and high quality services. The aim of this study was to (1) investigate awareness on best ways to assess lab competencies; (2) identify existing institutional methods of competency assessment and how staff perceptions; and (3) gather opinions of respondents about a proposed program for competency assessment in laboratory medicine. METHODS: A cross-sectional survey was conducted, followed by an interview and discussion with laboratory stakeholders about a proposed competency assessment program that included all the six procedural elements of laboratory personnel competency assessment. An online questionnaire was sent via email to different hospitals in Saudi Arabia through survey monkey. A proposed competency assessment program was circulated via email to laboratory stakeholders who agreed to be enrolled in structured interviews. RESULTS: A total of 47 out of the 168 (25.3%) laboratory workers responded to the emailed survey administered via survey monkey. Among the survey respondents, 16 out of the 47 (34%) participated in the structured interview and the discussion and formed the community of practice group that provided insight and opinion about the proposed competency program. Among stakeholders, 87.2% practiced in accredited laboratories. Over half (52%) of respondents positively rated the proposed program. Results of interviews and discussions revealed suggestions about continuous ongoing assessment, such as the inclusion of laboratory quality management and safety as separate items to be unified for all sections. CONCLUSIONS: The proposed competency assessment program overcomes challenges noted in competency assessment and has been positively received by stakeholders. This program will be validated by a group of experts then implemented as part of a core curriculum for laboratory staff, in their assessment, certification, recertification, registration, evaluation and licensure in sample laboratories in Saudi Arabia. The program will be monitored and evaluated during and after implementation for processes and outcomes. Conclusions will be utilized for national competency program. This study represents an important step towards the implementation of a standardized laboratory competence assessment program at a national level.

Vitamin D receptor gene polymorphisms and steroid receptor status among Saudi women with breast cancer.

The vitamin D receptor (VDR) is a mediator for the cellular effects of vitamin D and interacts with other cell signaling pathways that influence cancer development. We evaluated the associations of the FOK1 and Taq1 VDR polymorphisms and breast cancer risk and possible effect modification by steroid receptor status of the tumor. This case-control study includes 95 breast cancer patients and 100 age-matched controls. Genotyping for VDR FOK1 and Taq1 polymorphisms was performed using polymerase chain reaction-based restriction fragment length polymorphism. Level of 25(OH)D in serum was determined using ELISA. Immunohistochemical studies were performed for estrogen receptors (ER) and progesterone receptors (PR). The frequencies of ff genotype were significantly increased in the breast cancer group compared to the control group. Carriers of the f allele were significantly more likely to develop BC. We observed a statistically significant interaction for the Fok1 polymorphism and ER status. Our results demonstrated that FOK1 f. genotype and f allele have an important role in breast cancer risk in Saudi patients.

Ovarian angiosarcoma: a case report and review of the literature.

INTRODUCTION: Sarcomas of the ovary can either be histologically pure or can represent components of a more complex tumor. Ovarian angiosarcomas are rare, and probably arise from carcinosarcomas, teratomas or the rich ovarian vasculature. To date, only two small case series have been published, one with four cases and the other with seven. CASE PRESENTATION: A 41-year-old Saudi woman presented to our gynecological clinic with abnormal vaginal bleeding. The initial clinical diagnosis was left ovarian cyst. The results of the remainder of her abdominopelvic examination were normal. Peri-operatively, the left ovarian mass resembled a hemorrhagic solid tumor. It was sent for frozen sectioning, which revealed it was an undifferentiated neoplasm. The final histopathological examination showed a vascular neoplasm showing vasoformative arborizing channels of variable sizes and shapes lined by atypical endothelial cells with intact capsule. Areas of necrosis were seen, along with fused anastomosing solid vascular area. She was diagnosed as having an angiosarcoma of intermediate grade, International Federation of Gynecology and Obstetrics stage IA. CONCLUSIONS: Patients with ovarian angiosarcomas most commonly present with abdominal pain, however some patients present with distant metastases, often in the lungs. Spread beyond the ovary is present at the time of diagnosis in most reported cases, with disease progression within less than a year after diagnosis. Cases of advanced stage disease behave aggressively and demonstrate poor response to surgery and chemotherapy, with an overall poor prognosis. They have a tendency for local recurrence and metastases, and prognosis is hence poor; the reported five-year survival rate is 10 percent to 35 percent, however, cases confined to the ovary have survived up to nine years.

Efficacy of pentoxifylline as an antifibrotic drug in experimental murine schistosomal hepatic fibrosis.

This study evaluated the possible antifibrotic effect of pentoxifylline on experimentally induced schistosomal hepatic fibrosis and its effect on serum leptin and transforming growth factor-ß1 levels as possible antifibrotic mechanisms in correlation with the hepatic fibrosis indices. A total of ninety clean laboratories bred, males Swiss, albino mice were included, of which ten mice served as a control non-infected, non-treated group and sacrificed at one time. Eighty mice, each was subcutaneously infected with 50 Schistosoma mansoni cercariae and classified into groups: GI (infected & non-treated), GII (infected & treated with Mirazid), GIII (infected & treated with Pentoxifylline) and GIV (infected & treated with a combination of Mirazid and Pentoxifylline). Each group was further subdivided into 2 subgroups; subgroup 'a' which started treatment at 6th week post-infection (P.I.) and sacrificed at the end of 9th week P.I and subgroup 'b' which started treatment at 14th week P.I and sacrificed at the end of 17th week P.I. The efficacy of the treatment was assessed by histopathological examination of the liver with measurement of granuloma sizes, estimation of hydroxyproline content in the liver, and assessment of serum levels of leptin and transforming growth factor- ß1 (TGF-ß1).Mirazid (MZD) caused significant reductions in granuloma sizes and hepatic hydroxyproline content and caused non-significant reductions in serum levels of leptinand transforming growth factor- ß1 t 9th & 17t hweeks P.II(GIII. Pentoxifylline (PTX) caused significant reductions in granuloma sizes, hepatic hydroxyproline, and serum levels of leptin and transforming growth factor- ß1 t the 9"th& 17kt weeks P.II (GIII. While combined therapy of both MZD & PTX in GIIVcaused more reductions in granuloma sizes, hepatic hydroxyproline, and serum levels of leptin and TGF- ß1 t the 9th & 17th weeks P.IIwhen compared to the other groups.

Histopathological features of an incidental case of cytomegalovirus salpingitis in a patient with inflammatory bowel disease.

Ovarian and fallopian tube cytomegalovirus (CMV) infection is a rare finding, reported mostly in autopsy studies of immunocompromised patients. We report here a case of CMV salpingitis in a 22-year-old female, with Crohn's disease and on immunosuppressive drugs. The fallopian tube involvement by CMV infection was an incidental finding during resection of a large, matted mass involving the appendix, right ovary and right fallopian tube with bowel perforation and abscess formation. Review of literature revealed that most cases of CMV involving the fallopian tube have concurrent CMV oophoritis in pre- and postmenopausal women having pelvic inflammatory disease (PID). We concluded that fallopian tube can be involved by CMV infection in an immunocompromised patient.

Antiproliferative properties of methanolic extract of Nigella sativa against the MDA-MB-231 cancer cell line.

Breast cancer is the most commonly diagnosed cancer in women in the world and is one of the leading causes of death due to cancer. Health benefits have been linked to additive and synergistic combinations of phytochemicals in fruits and vegetables. Nigella sativa has been shown to possess anti-carcinogenic activity, inhibiting growth of several cancer cell lines in vitro. However, the molecular mechanisms of the anti-cancer properties of Nigella sativa phytochemical extracts have not been completely understood. Our data showed that Nigella sativa extracts significantly inhibited human breast cancer MDA-MB-231 cell proliferation at doses of 2.5-5 µg/mL (P<0.05). Apoptotic induction in MDA-MB-231 cells was observed in a dose-dependent manner after exposure to Nigella sativa extracts for 48 h. Real time PCR and flow cytometry analyses suggested that Nigella sativa extracts possess the ability to suppress the proliferation of human breast cancer cells through induction of apoptosis.

Neonatal meningitis caused by Elizabethkingia meningoseptica in Saudi Arabia.

Elizabethkingia meningoseptica is a multi-drug resistant organism that can cause meningitis in premature neonates. We report a case of Elizabethkingia meningoseptica meningitis that was detected early in an extremely premature low birth weight infant. He was successfully treated with a combination of ciprofloxacin and piperacillin-tazobactam. The spread of infection was controlled with no other reported cases.

Leiomyosarcoma metastatic to the thyroid diagnosed by fine needle aspiration cytology.

The thyroid gland is a known but an unusual site for metastatic tumours from various primary sites. Primary smooth muscle tumours of thyroid are rare. Leiomyosarcoma of the thyroid gland whether of primary or metastatic origin should be distinguished from anaplastic carcinoma. Few cases of leiomyosarcoma metastatic to thyroid, diagnosed by fine needle aspiration cytology (FNAC) have been documented. We are reporting this case to highlight the importance of FNAC as a tool for diagnosing sarcomas and to plan further management accordingly. Ancillary techniques can be applied on FNAC and give comparative results to tissue sections.

Dermatofibrosarcoma protuberance of the oral cavity: does it exist?

Dermatofibrosarcoma protuberance (DFSP) is a low grade spindle cell malignant tumour that is locally aggressive especially it incompletely excised. A 64-year-old man presented with intra-oral buccal mass of 34 year duration with accelerated increase in size in the last two years. CT scan showed well-circumscribed tumour with no relation to the overlying skin. Fine needle aspiration cytology revealed a highly cellular mitotically active spindle cell neoplasm with recommendation of excision with safety margins. Histological examination of the excised mass showed typical dermatofibrosarcoma protuberance with cytoplasmic positivity for Vimentin and CD34. Intra-oral sarcomas are rare and to the best of our knowledge only a single case of DFSP has been described in literature. We present another case for its unusual site, presentation, duration and surgical approach.

Gastrointestinal basidiobolomycosis: an unusual fungal infection mimicking colon cancer.

CONTEXT: -Basidiobolomycosis is a rare disease caused by the fungus Basidiobolus ranarum, an environmental saprophyte found worldwide. Patients with B ranarum infection may present with subcutaneous, gastrointestinal, or systemic lesions. Gastrointestinal basidiobolomycosis poses diagnostic difficulties, as its clinical presentation is nonspecific, with no identifiable risk factors. OBJECTIVE: -To discuss and compare the clinical features and histopathologic findings and other ancillary techniques that could be helpful in identifying gastrointestinal basidiobolomycosis. DESIGN: -We report 3 cases of gastrointestinal basidiobolomycosis and describe the clinical and morphologic findings while emphasizing the importance of identifying this unusual entity on endoscopic biopsies, thus avoiding unnecessary major surgeries. Fungal cultures were also performed, which are of diagnostic significance. Our first patient was lost to follow-up; however, patients 2 and 3 were followed up for 4 and 2 years, respectively. RESULTS: -In all 3 cases, patients presented with a clinical profile suggestive of malignancy. None of the patients gave any specific history. There was widespread abdominal disease with peritoneal involvement and colonic masses. Colonoscopic biopsy specimens showed nonspecific inflammation in 1 case; however, they showed only granulomatous inflammation in a second case and granulomas associated with fungal hyphae in a third. Typical morphology included hyphae, irregularly branched, thin-walled, occasionally septated and surrounded by a thick eosinophilic cuff (Splendore-Hoeppli phenomenon). CONCLUSION: -Gastrointestinal basidiobolomycosis can be detected on small endoscopic biopsy. The unequivocal diagnosis requires microbiologic cultivation of the fungus obtained from tissues. The prognosis for this disease is usually favorable as seen in 3 of our cases; however, cases with fatal outcome are on record.

Fine needle aspiration cytology of granulomatous mastitis with special emphasis on microbiologic correlation.

OBJECTIVE: To describe the cytomorphology of granulomatous mastitis (GM) and to evaluate the causative agents involved, proven on the basis of microbiologic culture results and polymerase chain reaction (PCR) studies. STUDY DESIGN: We retrospectively reviewed the inflammatory breast aspirates reported at King Abdul Aziz Specialist Hospital and Al Hada Armed Forces Hospital, Taif, Kingdom of Saudi Arabia, from January 2000 until March 2008. The pathology reports, clinical information, slides, microbiologic culture results and tuberculosis (TB)/PCR were reviewed. Cases of inflammatory carcinoma or duct ectasia were excluded. RESULTS: A total of 49 cases of inflammatory breast aspirates were identified, of which 15 cases were GM. The microbiologic cultures of all 15 cases were available. Six of 15 cases had positive culture for Brucella melitenses, and 2 cases were positive for TB, which was further confirmed by TB/PCR. The fungal cultures were negative in all the cases. Seven of 15 cases were classified as idiopathic GM. CONCLUSION: Fine needle aspiration cytology was found to be a useful tool in the early diagnosis of GM and its classification if performed by a pathologist as the material can be submitted for culture. The definitive diagnosis can be established by a combination of the cytomorphologic features and microbiologic studies.

Breast brucellosis in Taif, Saudi Arabia: cluster of six cases with emphasis on FNA evaluation.

BACKGROUND: Brucellosis is an endemic zoonosis seen in a variety of geographical locations such as the Middle East and Latin American and Mediterranean countries. Brucellosis is hyper-endemic in Saudi Arabia with an incidence of 5.4 per 1000 per year. Breast involvement very rarely occurs as a focal complication of brucellosis. METHODOLOGY: We report six cases of breast brucellosis retrieved from the files of the patients. Fine needle aspiration (FNA) was performed on all patients. In all cases direct smears were made at the patient's side for assessment of sample quality. Cytospin and cell block preparation was done and Gram, periodic acid-Schiff and Ziel-Nelson stains were done on all samples. Microbiological analysis included routine fungal and bacterial culture for tuberculosis. RESULTS: Age range was 20 to 48 years with a median of 22 years. Two patients gave history of raw milk ingestion, one was lactating, and one patient was pregnant. Cytomorphologic features of brucellosis in the breast include an abscess-like background with granulomatous inflammation. Cytology of the patients presented with breast abscess showed predominant neutrophilic infiltrate compatible with acute pyogenic inflammation. Culture was positive for B. melitensis in all cases. CONCLUSION: Brucellosis should be kept in mind in the differential diagnosis of breast abscess in endemic areas where ingestion of unpasteurized milk and milk products is common. Needle aspiration establishes a preliminary diagnosis and has the advantage of material submission for microbiologic cultures and provides focal treatment along with long-term combined antibacterial treatment for the control of systemic infection.

Fine needle aspiration cytology of inflammatory breast lesions.

OBJECTIVE: To study the characteristics of inflammatory breast aspirate by Fine Needle Aspiration, performed by pathologist. METHODS: Inflammatory breast aspirates reported at two hospitals in Taif area (King Abdul Aziz Specialist Hospital and Al Hada Armed Forces Hospital, Taif, Kingdom of Saudi Arabia (KSA) from January 2000 till September 2007 were reviewed. The cytopathology reports, slides, clinical information, microbiology culture results, Tuberculosis; Polymerase Chain Reaction (TB; PCR) and histology were reviewed. The aspirates were identified as inflammatory based on presence of inflammatory cells and/or granulomas with occasional benign ductal epithelial cells. Cases of inflammatory carcinoma or duct ectasia were excluded. RESULTS: Forty-nine cases of inflammatory breast aspirates were included in the study. The aspirates were categorized into: Acute mastitis/Abscess 13 (26.5%), Granulomatous Mastitis 15 (30.6%), Fat Necrosis / Organized Haematoma 8 (16.4%) and Inflammation, not otherwise specified (NOS) 13 (26.5%), based on morphologic criteria combined with clinical impression. The Granulomatous Mastitis cases were subcategorized into Idiopathic and Infection related which included Brucellosis, Tuberculosis, and fungal mastitis. CONCLUSION: FNA of inflammatory breast lesions is a useful tool if performed by a pathologist and combined with further workup including microbiologic culture correlation. It helps in management and treatment of the patient and avoiding unnecessary surgery.