Detection of foot-and-mouth disease viruses from the A/AFRICA/G-I genotype in the Sultanate of Oman.

Rapid identification and characterization of circulating foot-and-mouth disease virus (FMDV) strains is crucial for effective disease control. In Oman, a few serological and molecular studies have been conducted to identify the strains of FMDV responsible for the outbreaks that have been occurring within the country. In this study, 13 oral epithelial tissue samples from cattle were collected from suspected cases of FMD in Ash Sharqiyah North, Al Batinah North, Dhofar and Ad Dhakhyilia governorates of Oman between 2018 and 2021. FMDV RNA was detected in all samples by real-time RT-PCR and viruses were isolated after one- or two-blind passages in the porcine Instituto Biologico-Rim Suino-2 cell line. Antigen capture ELISA characterized all isolates as serotype A and VP1 phylogenetic analysis placed all sequences within a single clade of the G-I genotype within the A/AFRICA topotype. These sequences shared the closest nucleotide identities to viruses circulating in Bahrain in 2021 (93.5% to 99.5%) and Kenya in 2017 (93.4% to 99.1%). To the best of our knowledge, this is the first time that A/AFRICA/G-I viruses have been detected in Oman. Together with the closely related viruses detected recently in Bahrain, these findings reinforce the importance of deploying effective quarantine control measures to minimize the risks of transboundary transmission of FMD associated with the importation of cattle from East Africa.

Machine Learning Approach for Predicting Systemic Lupus Erythematosus in an Oman-Based Cohort.

Objectives: This study aimed to design a machine learning-based prediction framework to predict the presence or absence of systemic lupus erythematosus (SLE) in a cohort of Omani patients. Methods: Data of 219 patients from 2006 to 2019 were extracted from Sultan Qaboos University Hospital's electronic records. Among these, 138 patients had SLE, while the remaining 81 had other rheumatologic diseases. Clinical and demographic features were analysed to focus on the early stages of the disease. Recursive feature selection was implemented to choose the most informative features. The CatBoost classification algorithm was utilised to predict SLE, and the SHAP explainer algorithm was applied on top of the CatBoost model to provide individual prediction reasoning, which was then validated by rheumatologists. Results: CatBoost achieved an area under the receiver operating characteristic curve score of 0.95 and a sensitivity of 92%. The SHAP algorithm identified four clinical features (alopecia, renal disorders, acute cutaneous lupus and haemolytic anaemia) and the patient's age as having the greatest contribution to the prediction. Conclusion: An explainable framework to predict SLE in patients and provide reasoning for its prediction was designed and validated. This framework enables clinicians to implement early interventions that will lead to positive healthcare outcomes.

The Association of Human Leukocyte Antigens Complex with Type 1 Diabetes in the Omani Population.

Objectives: Identification of the high risk alleles, genotypes and haplotypes of the human leukocyte antigens (HLA) in different populations is beneficial for understanding their roles in type 1 diabetes (T1D) pathogenesis and intervention practices. This study aimed to identify T1D-associated HLA gene alleles in the Omani population. Methods: The present case-control study included 73 diabetic seropositive children (mean age 9.08 ± 3.27 years) attending the paediatric clinic at Sultan Qaboos University Hospital in Muscat, Oman, and 110 healthy controls. HLA-A, -B, -C, -DRB1 and -DQB1 genes were genotyped using a sequence-specific primer polymerase chain reaction (SSP-PCR). Results: Two HLA class I alleles (B*08, B*58) and three class II alleles (DQB1*02, DRB1*03 and DRB1*04) were associated with T1D susceptibility, while one class I (B*51) and three class II (DQB1*05, DQB1*06 and DRB1*16) alleles were associated with T1D protection. HLA-DRB1*03 and DQB1*02 alleles showed the strongest risk association among all alleles. Six DRB1 residues (E9, S11, S13, Y30, V70 and K71) were significantly associated with T1D susceptibility. Heterozygous genotypes, HLA-DRB1*03/*04 and DQB1*02/*03 were significantly associated with T1D susceptibility (P <0.0001, odds ratio [OR] = 63.21 and P = 0.02, OR = 3.63, respectively). Furthermore, a significant combined action of DRB1*03-DQB1*02 haplotype in T1D risk (P = 0.000176, OR = 15) and DRB1*16-DQB1*05 haplotype in protection (P = 0.0312, OR = 0.48) was detected. Conclusion: Known HLA class II gene alleles are associated with T1D in Omani children.

Cilia Ultrastructure Associated with Primary Ciliary Dyskinesia in Omani Patients.

Objectives: Primary ciliary dyskinesia (PCD) is a disorder affecting the structure and function of the motile cilia of the respiratory system. Transmission electron microscopy is one method that can be used to examine ciliary ultrastructure in airway biopsies. Although the role of ultrastructural findings in PCD has been described in the literature, this role has not been well-studied in the Middle East or, specifically, Oman. This study aimed to describe ultrastructural features in Omani patients with high suspicion of PCD. Methods: This retrospective cross-sectional study included 129 adequate airway biopsies obtained from Omani patients attending pulmonary clinics at Sultan Qaboos University Hospital and the Royal Hospital, Muscat, Oman, from 2010 to 2020 who were suspected of having PCD. Results: Ciliary ultrastructural abnormalities in the current study population were outer dynein arm (ODA) associated with inner dynein arm (IDA) defects (8%), microtubular disorganisation associated with IDA defect (5%) and isolated ODA defect (2%). Most of the biopsies showed normal ultrastructure (82%). Conclusion: In Omani patients suspected to have PCD, normal ultrastructure was the most common feature.

Impact of delay in adjuvant therapy for gallbladder adenocarcinoma.

BACKGROUND: Receipt of adjuvant therapy for gallbladder adenocarcinoma (GBAC) is associated with a survival benefit. This study sought to identify whether delays in initiation of adjuvant therapy among patients with resected GBAC impacts long-term survival. METHODS: Patients with stage II and III GBAC who underwent a curative-intent resection followed by adjuvant chemotherapy or chemoradiation between 2004 and 2017 were queried from the National Cancer Data Base. Descriptive statistics and multivariate models were constructed to determine the relationship between timely (<12 weeks) and delayed (>12 weeks) adjuvant therapy and overall survival (OS). RESULTS: A total of 871 patients with GBAC were identified. The median time to receipt of adjuvant chemotherapy was 67 days and the median time to receipt of adjuvant chemoradiation was 69 days. After controlling for all factors, treatment at an Academic/Research center was the only variable associated with timely receipt of adjuvant therapy. However, after controlling for clinically relevant factors, the timing of adjuvant therapy did not impact OS (delayed: HR 0.93, 95% CI: 0.46-1.85; P = .83). CONCLUSION: Current guidelines support the use of adjuvant therapy following resection of GBAC. This national cohort study demonstrates that delays in adjuvant therapy >12 weeks did not impact long-term survival.

Two unique BAP1 pathogenic variants identified in the same family by panel cascade testing.

Germline pathogenic variants in the tumor suppressor gene BAP1 are associated with the hereditary tumor predisposition syndrome with susceptibility to uveal melanoma, mesothelioma, cutaneous melanoma, renal cell carcinoma, and other cancers. Germline BAP1 pathogenic variants are rare in the non-cancer general population with an estimated carrier frequency of 1:19,898 but more common in cancer patients with a carrier frequency of 1:1299. In the following we present the first report of a family with two unique BAP1 pathogenic variants. Retrospective case report of a family with two unique pathogenic variants in BAP1. A male (proband) was referred to our ocular oncology clinic for second opinion for his multiple independent uveal melanomas at ages 65, 68 and 71. Given his personal history of squamous cell carcinoma at age 61, renal cell carcinoma at age 63, and family history of atypical meningioma, basal cell carcinoma, pancreatic and prostate cancers he was assessed for germline pathogenic variants in BAP1 through our ongoing research study. Sanger sequencing identified the American founder pathogenic variant, c.1717delC, pL573Wfs*3, that was confirmed in a clinical laboratory. Both the proband's brother and nephew tested negative for the familial variant through single site cascade genetic testing. However, based on the personal history of multiple basal cell carcinoma in the nephew and family history of pancreatic and laryngeal cancers (both not known to be associated with BAP1-TPDS), a large cancer panel testing was recommended for the nephew. His panel testing revealed a different BAP1 pathogenic variant, c.605G>A, p. Trp202*. This variant was not detected in the proband or the proband's brother. Based on the frequency of germline BAP1 variants in the cancer population, the chance of occurrence of two different BAP1 variants in a family with cancer history is 5.9 × 10-7. This case report provides support for the importance of offering large panel cascade genetic testing, rather than single site testing for only the family pathogenic variant, for all at risk family members especially when the family variant cannot explain all the cancers in the family.

Detection of Trypanosoma Infection in Dromedary Camels by Using Different Diagnostic Techniques in Northern Oman.

Camel trypanosomoses is considered a devastating disease with severe health consequences that can be caused by different hemoprotozoan parasites. Camel samples (388) from the five regions in Northern Oman were assessed using a thin blood film. In addition, 95 seropositive samples were analyzed using various primers of mechanically transmitted trypanosomes. Out of the 388 blood smears examined, 0.8% (CI 95%, 2/388) were found to be positive for Trypanosoma sp. using a microscope. The parasitologically positive cases were detected in samples from females. The overall molecular prevalences were as follows: TBR was 78/95, 77% (CI 73.1-89.2%); ITS was 30/95, 31.6% (CI 73.1-89.2%); and T. evansi type A (RoTat 1.2) was 8/95, 8.4% (CI 4.0-16.0%). There were two species of trypanosomes that were observed in the camels.

Short- and long-term outcomes following robotic and open resection for intrahepatic cholangiocarcinoma: A national cohort study.

BACKGROUND: Curative-intent liver resection with porta hepatis lymphadenectomy provides the best chance for long-term survival for patients with intrahepatic cholangiocarcinoma (ICC). While the robotic approach has been increasingly utilized, its impact on perioperative and long-term outcomes of patients with ICC are largely unknown. METHODS: Patients with stages I-III ICC who underwent surgical resection between 2004 and 2017 were identified from the National Cancer Database. Descriptive statistics and multivariate models were constructed to examine the association between surgical approach and surgical and oncological outcomes. RESULTS: A total of 1876 patients with ICC who underwent open (n = 1804, 96.2%) and robotic-assisted (n = 72, 3.8%) resection were identified. Following surgery, patients who underwent a robotic-assisted resection had a shorter length of hospital stay yet there was no difference in 30-day readmission or 90-day mortality. Older age, disease stage, and higher comorbidity were associated with worse OS. Patients undergoing robotic-assisted surgery had no difference in long-term risk of death compared with patients who underwent an open procedure. CONCLUSION: This national cohort study demonstrated that the robotic approach for patients undergoing resection for ICC resulted in a shorter hospitalization while not compromising oncological outcomes such as negative margins, postoperative mortality, and long-term survival.

Surgical treatment of hepatic oligometastatic pancreatic ductal adenocarcinoma: An analysis of the National Cancer Database.

BACKGROUND: Patients with liver-only metastatic pancreatic adenocarcinoma have traditionally been offered palliative chemotherapy alone. Recent studies have explored the role of surgical resection among patients with limited metastatic disease. National practice patterns and the impact of surgery among these patients remains unknown. METHODS: The National Cancer Database was queried for all patients with pancreatic adenocarcinoma between 2010 and 2015. The primary outcome was overall survival from the time of diagnosis. Patients with liver-only metastatic disease were included. Univariable and multivariable logistic regression models were constructed to determine the association of patient, hospital, and regional factors with receipt of surgical resection. A propensity score-matched cohort (1:1) was generated by matching patient- and tumor-related factors (age, sex, race, comorbidity burden, primary tumor site, primary tumor size) among patients with liver-only stage IV pancreatic adenocarcinoma who received chemotherapy alone compared to those who received chemotherapy and underwent pancreatectomy and liver metastatectomy. RESULTS: Among 312,426 patients who met the study criteria, one half (n = 140,043, 50.4%) had stage IV disease; metastatic sites included bone (n = 5493, 3.1%), brain (n = 620, 0.4%), lung (n = 16,580, 9.5%), and liver (n = 62,444, 35.7%). Patients with stage IV disease were more likely to be younger (odds ratio: 1.10, 95% confidence interval: 1.0-1.2; P = .03) and have poorly (odds ratio: 2.1, 95% confidence interval: 1.8-2.5; P < .001) or undifferentiated (odds ratio: 3.1, 95% confidence interval: 2.3-4.1; P < .001) tumors. Among stage IV patients with liver-only disease (n = 47,785, 14.9%), 891 patients (1.9%) underwent pancreatic resection. Patients who underwent resection were more likely to be younger (odds ratio 1.4, 95% confidence interval: 1.0-1.8; P = .03) and treated at an academic/research center (odds ratio 2.1, 95% confidence interval: 1.2-3.5; P = .006). Median overall survival among patients who underwent resection was 10.74 months versus 3.4 months among patients who did not undergo resection. After controlling for patient and disease-related factors, patients who underwent surgical resection had a lower risk of death versus patients who did not undergo surgery (hazard ratio: 0.5, 95% confidence interval: 0.4-0.6; P < .001). After propensity score matching, patients who received multimodality treatment for liver-only metastatic pancreatic adenocarcinoma (surgery, chemotherapy) had a longer median overall survival (15.6 months vs 8.1 months) compared to those who received chemotherapy alone (P < .001). CONCLUSION: This study suggests that pancreatic resection in patients with liver metastases, in combination with chemotherapy and/or chemoradiation, may be associated with improved survival in well-selected patients. However, attempts at an aggressive surgical approach for patients with liver-only stage IV pancreatic adenocarcinoma patients should only be performed only under a well-designed prospective clinical trial.

Estimate of the HOMA-IR Cut-off Value for Identifying Subjects at Risk of Insulin Resistance Using a Machine Learning Approach.

OBJECTIVES: This study describes an unsupervised machine learning approach used to estimate the homeostatic model assessment-insulin resistance (HOMA-IR) cut-off for identifying subjects at risk of IR in a given ethnic group based on the clinical data of a representative sample. METHODS: The approach was applied to analyse the clinical data of individuals with Arab ancestors, which was obtained from a family study conducted in Nizwa, Oman, between January 2000 and December 2004. First, HOMA-IR-correlated variables were identified to which a clustering algorithm was applied. Two clusters having the smallest overlap in their HOMA-IR values were retrieved. These clusters represented the samples of two populations, which are insulin-sensitive subjects and individuals at risk of IR. The cut-off value was estimated from intersections of the Gaussian functions, thereby modelling the HOMA-IR distributions of these populations. RESULTS: A HOMA-IR cut-off value of 1.62 ± 0.06 was identified. The validity of this cut-off was demonstrated by showing the following: 1) that the clinical characteristics of the identified groups matched the published research findings regarding IR; 2) that a strong relationship exists between the segmentations resulting from the proposed cut-off and those resulting from the two-hour glucose cut-off recommended by the World Health Organization for detecting prediabetes. Finally, the method was also able to identify the cut-off values for similar problems (e.g. fasting sugar cut-off for prediabetes). CONCLUSION: The proposed method defines a HOMA-IR cut-off value for detecting individuals at risk of IR. Such methods can identify high-risk individuals at an early stage, which may prevent or delay the onset of chronic diseases such as type 2 diabetes.

Bioremediation of copper by active cells of Pseudomonas stutzeri LA3 isolated from an abandoned copper mine soil.

Copper bioremoval efficiency and bioaccumulation capacity of Pseudomonas stutzeri LA3 isolated from copper contaminated soil were investigated. P. stutzeri LA3 removed about 50% of Cu (II) at 50 mg l-1 of concentration and accumulated a maximum of 1.62 mg of Cu g-1 biomass dry weight. Bioremediation by P. stutzeri LA3 partially depended on the production of extracellular polymeric substances, composed of proteins and carbohydrates. Cell surface alterations were observed on the Cu (II) treated biomass through a scanning electron microscope (SEM). Energy dispersive spectrometer (EDX) investigation of Cu (II) treated biomass showed clear signals of Cu, confirming the presence of copper ions on the cell surface. Fourier transform infrared spectroscopy (FTIR) showed the contribution of functional groups such as hydroxyl (-OH), carboxyl (-COOH), amide and amine (-NH2) in the remediation process. Based on the results, the isolated strain P. stutzeri LA3 could serve as a potential candidate for copper due to its significant copper removal effeciency.

Computed Tomography-Assessed Skeletal Muscle Mass as a Predictor of Outcomes in Lung Cancer Surgery.

BACKGROUND: Sarcopenia is characterized by loss of skeletal muscle and strength, associated with aging, poor nutrition, sedentary lifestyle, and long-term illness. We sought to evaluate the current evidence on the prevalence of sarcopenia assessed by computed tomography (CT) imaging in patients undergoing lung cancer resection and its predictive value for perioperative and long-term outcomes. METHODS: We performed a systematic literature search of the PubMed/MEDLINE database to identify studies that examined CT-assessed muscle mass and outcomes of patients undergoing lung resection. Pooled odds ratio for complications and hazard ratio for survival with 95% confidence intervals (CI) were generated using the Mantel-Haenszel or inverse variance methods with random effects models. RESULTS: Nine observational studies met the inclusion criteria. Four studies measured skeletal muscle at the thoracic level (T5, T12, T8) and 5 studies at the lumbar level (L3). The prevalence of sarcopenia by CT skeletal muscle measurements ranged from 22.4% to 55.8%, with an average of 42.8% in 1010 patients. Four of 6 studies that reported perioperative outcomes were included in the meta-analysis, which showed higher risk of perioperative complications for patients with sarcopenia (odds ratio 2.51, 95% CI: 1.55-4.08, P < .001). Sarcopenia was associated with worse survival in 6 of 7 studies that evaluated long-term outcomes after lung cancer resection (hazard ratio 2.31, 95% CI: 1.26-4.24, P = .007). CONCLUSIONS: Sarcopenia can be frequently detected in patients undergoing lung cancer resection with the use of CT-based muscle measurements. Sarcopenia was associated with greater risk of perioperative complications and worse long-term prognosis.

Family planning in Pakistan: applying what we have learned.

Despite six decades of government and private sector programs, CPR in Pakistan is among the lowest in the region. This article reviews published and grey literature to understand why despite sufficient time and usually sufficient funding, CPR remains low in Pakistan. This paper looks beyond the usual factors of quality of services, coverage and supplies and management issues to examine how family planning may be improved in Pakistan. Based on analysis of the Pakistan Demographic Health Survey 2006-7, the public sector provides around a third of FP services, while NGOs and private providers another 15%. More than half of all family planning users buy their methods directly from stores. Within the government, the services cost 5-8 fold more than the private sector. Nearly a fifth of pregnancies end in an abortion suggesting the role of abortions as a key FP method. This together with a high unmet need pose the question: why is there such low uptake of FP services in the country. To explain this lack of uptake, we explore the limitations of the public sector in providing services, the lack of effect of religious beliefs, of abundant, yet misdirected funding and gaps in demand creation. The increasing role of NGOs and donors in filling the void left by the public sector is discussed. Suggestions are provided about improving public and private sector services including better information gathering and use in defining needs, measuring results and creating demand for FP.