The Cystic Fibrosis Airway Microbiome and Pathogens

Cystic fibrosis (CF) is an autosomal recessive genetic disorder resulting from genetic defects in the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR) protein. CFTR dysfunction in patients with CF leads to a number of pleiotropic manifestations with the prime pathology being mucus plugging in the airways and paranasal sinuses. Patients with CF are prone to polymicrobial infections and the airway microbiome in such patients changes continuously and evolves over time. The composition of the airway microbiome in CF patients is dependent on a number of factors including geographic variation, type of genetic mutation (e.g., ΔF508), antibiotic exposures, and chronic infection with certain pathogenic bacteria (e.g., Pseudomonas aeruginosa). Proteomic and genomic approaches to understanding the microbiome of patients with CF have provided new insights into the pathogenesis of this disease. High‐throughput pyrosequencing, Sanger sequencing, and phylogenetic microarray analysis have enabled the recognition of multiple lineages and clonal populations of a single bacterial species within the same patient. This provides a unique opportunity to explore novel therapeutic approaches to this disease (for instance, use of probiotics and environmental manipulation) and potentially translate them into bedside clinical interventions

Prospective Cohort Studies in Medical Research

Cohort studies are the analytical design of observational studies that are epidemiologically used to identify and quantify the relationship between exposure and outcome. Due to the longitudinal design, cohort studies have several advantages over other types of observational studies. The purpose of this chapter is to cover the various characteristics of prospective cohort studies. This chapter is divided into three main sections. In the first we introduce the concept and ranking of cohort studies, as well as the advantages and disadvantages. In the second we focus on the design of cohort studies, mainly its prospective aspect, and the distinguishing features from the retrospective type. The section also covers the essential characteristics of a cohort study design and its varied applications in medical research. In the third we go over examples of prospective studies in the medical field. For each, an overview of the study design is given, along with a random selection of study findings/impact, strengths and weaknesses

Corticosteroids and Their Use in Respiratory Disorders

Corticosteroids are adrenal hormones that play important physiologic roles including modulation of glucose metabolism, protein catabolism, alteration of calcium metabolism, regulation of bone turnover, suppression of immune system, and down-regulation of the inflammatory cascade. Because of their diverse effects, corticosteroids have been used therapeutically for treating a wide variety of auto-immune, rheumatologic, inflammatory, neoplastic and infectious diseases. In the field of pulmonology, corticosteroids have been used for the treatment of reactive airway diseases (such as asthma and allergic bronchopulmonary aspergillosis), chronic obstructive pulmonary disease, sarcoidosis, collagen vascular diseases (such as vasculitic disorders), eosinophilic pneumonitis, idiopathic interstitial pneumonias and infectious disorders (such as laryngotracheobronchitis). Different formulations of corticosteroids are commercially available including tablets, intravenous injections, intramuscular formulations and inhaled preparations. Long-term use of corticosteroids is often limited by their adverse effects, which include abnormal fat deposition, weight gain, diabetes mellitus, cataracts, glaucoma, osteoporosis, osteonecrosis, elevated risk of fractures, increased susceptibility to infections, proximal myopathy, depression, psychosis, adrenal atrophy with risk of Addisonian crisis, abdominal striae, acne vulgaris, delayed wound healing, easy bruising, electrolyte abnormalities and increased risk of peptic ulcer disease. As our understanding of corticosteroids advances, we may be able to identify individuals at higher risk of experiencing adverse effects

The Effect of Using Applied Mathematics Lessons On 7th Grade Students’ Attitudes Towards Mathematics

This study aims to explore the effect of using applied mathematics lessons on 7th grade students’ attitudes towards mathematics in Qatari preparatory governmental schools. It investigates the change in students’ attitudes after being exposed to a series of applied math media content, customized based on the students’ environment. A quantitative research design approach was used by implementing an attitude towards mathematics measurement inventory (ATMI) before and after experiment for an experimental group and controlled group. The ATMI covers four dimensions which represent different aspects of the attitude. Eighty eight participants responded to the assessment surveys and provided their responses to the forty items in the questionnaire. The results showed a significant difference between the experimental group and the controlled group data in the dimensions of value and motivation. However, the analysis didn’t provide evidence of a significant change in participants’ enjoyment and confidence. This can be a result of the limited time of the experiment and the short duration of the media content compared to the length of the math classes. Therefore, a list of further investigation areas were provided, such as studying the proper media duration and the type of content that links mathematics more to daily life experiences

Pet ownership and associated respiratory diseases

Background Studies have shown that pets are very important sensitizing agents in patients with asthma. Respiratory disorders and allergic diseases are common in the State of Qatar

Allergic bronchopulmonary aspergillosis in patients with cystic fibrosis

Allergic bronchopulmonary aspergillosis (ABPA) is a pulmonary disorder that often occurs in patients with asthma or cystic fibrosis (CF) and is characterized by a hypersensitivity response to the allergens of the fungus Aspergillus fumigatus. In patients with CF, growth of A. fumigatus hyphae within the bronchial lumen triggers an immunoglobulin E (IgE)-mediated hypersensitivity response that results in airway inflammation, bronchospasm, and bronchiectasis. In most published studies, the prevalence of ABPA is about 8.9% in patients with CF. Since the clinical features of this condition overlap significantly with that of CF, ABPA is challenging to diagnose and remains underdiagnosed in many patients. Diagnosis of ABPA in CF patients should be sought in those with evidence of clinical and radiologic deterioration that is not attributable to another etiology, a markedly elevated total serum IgE level (while off steroid therapy) and evidence of A. fumigatus sensitization. Management of ABPA involves the use of systemic steroids to reduce inflammation and modulate the immune response. In patients who do not respond to steroids or cannot tolerate them, antifungal agents should be used to reduce the burden of A. fumigatus allergens. Recent studies suggest that omalizumab may be an effective option to reduce the frequency of ABPA exacerbations in patients with CF. Further randomized controlled trials are needed to better establish the efficacy of omalizumab in managing patients with CF and ABPA

Sensitization to common food and inhalant allergens in children attending Allergy and Asthma Pediatric Clinic in Doha, Qatar

The prevalence of allergic diseases such as asthma, allergic rhinitis and atopic dermatitis have risen at an alarming rate throughout the world in the past 50 years. Sensitization to food (FA) and inhalant allergens (IA) have been associated with an increase of allergic diseases. The objective of this study was to estimate the prevalence of sensitization to FA and IA among children attending Allergy and Asthma Pediatric Clinic in Doha, Qatar. A total of 134 children with age between 1 month and 10 years were recruited. Sensitization to common FA and IA was determined by allergy screen test for in vitro diagnostics (R-Biopharm). Allergic disorders (asthma, eczema or wheezing) were present in 56.7, 14.4 and 61.9%, respectively, and 29.9 and 19.4% were sensitized to FA and IA, respectively. Cheese was the most often identified FA followed by milk, casein, peanut, nut, fish, banana and egg yolk. Among IA, sensitization to pets (cat and dog) and dust were the most prevalent among children. Boys were more sensitized to FA than girls (35.9% vs. 27.4%). The same pattern was observed for IA where 20.5% of boys were sensitized compared to 18.9% for girls. The prevalence of sensitization to FA decreased as age increases (35% at 0-2 years vs. 32.5% at the age 6-10 years). Rate of sensitization to IA, however, increased with age (from 7.7% in the youngest group to 69.2% in the oldest group). Sensitization to FA and IA was associated with age (P<0.05). Of children with FA, 37.5% were sensitized to IA. A statistically significant association between FA and IA was observed (OR:1.82; 95% CI: 1.15-2.88; P = 0.001), 76.9 and 75% sensitized to IA and FA, respectively, reported family history of allergy. The prevalence of asthma and eczema was higher among girls,while wheezing was higher among boys. This study is the first in Qatar, which has used two specific panels: panel2DOHA for inhalant allergens and panel3DOHA for food allergens. The results suggest that food and inhalant allergens sensitization is highly prevalent among the studied populationQatarFoundation, UREP program under fund grant No 3-3-3

Interpreting patient-Specific risk prediction using contextual decomposition of BiLSTMs: application to children with asthma

Background Predictive modeling with longitudinal electronic health record (EHR) data offers great promise for accelerating personalized medicine and better informs clinical decision-making. Recently, deep learning models have achieved state-of-the-art performance for many healthcare prediction tasks. However, deep models lack interpretability, which is integral to successful decision-making and can lead to better patient care. In this paper, we build upon the contextual decomposition (CD) method, an algorithm for producing importance scores from long short-term memory networks (LSTMs). We extend the method to bidirectional LSTMs (BiLSTMs) and use it in the context of predicting future clinical outcomes using patients’ EHR historical visits. Methods We use a real EHR dataset comprising 11071 patients, to evaluate and compare CD interpretations from LSTM and BiLSTM models. First, we train LSTM and BiLSTM models for the task of predicting which pre-school children with respiratory system-related complications will have asthma at school-age. After that, we conduct quantitative and qualitative analysis to evaluate the CD interpretations produced by the contextual decomposition of the trained models. In addition, we develop an interactive visualization to demonstrate the utility of CD scores in explaining predicted outcomes. Results Our experimental evaluation demonstrate that whenever a clear visit-level pattern exists, the models learn that pattern and the contextual decomposition can appropriately attribute the prediction to the correct pattern. In addition, the results confirm that the CD scores agree to a large extent with the importance scores generated using logistic regression coefficients. Our main insight was that rather than interpreting the attribution of individual visits to the predicted outcome, we could instead attribute a model’s prediction to a group of visits. Conclusion We presented a quantitative and qualitative evidence that CD interpretations can explain patient-specific predictions using CD attributions of individual visits or a group of visits.Other Information Published in: BMC Medical Informatics and Decision Making License: https://creativecommons.org/licenses/by/4.0See article on publisher's website: http://dx.doi.org/10.1186/s12911-019-0951-4</p