RAt-CapsNet: A Deep Learning Network Utilizing Attention and Regional Information for Abnormality Detection in Wireless Capsule Endoscopy.

Background: The emergence of wireless capsule endoscopy (WCE) has presented a viable non-invasive mean of identifying gastrointestinal diseases in the field of clinical gastroenterology. However, to overcome its extended time of manual inspection, a computer aided automatic detection system is getting vast popularity. In this case, major challenges are low resolution and lack of regional context in images extracted from WCE videos. Methods: For tackling these challenges, in this paper a convolution neural network (CNN) based architecture, namely RAt-CapsNet, is proposed that reliably employs regional information and attention mechanism to classify abnormalities from WCE video data. The proposed RAt-CapsNet consists of two major pipelines: Compression Pipeline and Regional Correlative Pipeline. In the compression pipeline, an encoder module is designed using a Volumetric Attention Mechanism which provides 3D enhancement to feature maps using spatial domain condensation as well as channel-wise filtering for preserving relevant structural information of images. On the other hand, the regional correlative pipeline consists of Pyramid Feature Extractor which operates on image driven feature vectors to generalize and propagate local relationships of pixels from WCE abnormalities with respect to the normal healthy surrounding. The feature vectors generated by the pipelines are then accumulated to formulate a classification standpoint. Results: Promising computational accuracy of mean 98.51% in binary class and over 95.65% in multi-class are obtained through extensive experimentation on a highly unbalanced public dataset with over 47 thousand labelled. Conclusion: This outcome in turn supports the efficacy of the proposed methodology as a noteworthy WCE abnormality detection as well as diagnostic system.

Aspergillus fumigatus allergen expression is coordinately regulated in response to hydrogen peroxide and cyclic AMP.

BACKGROUND: A. fumigatus has been associated with a wide spectrum of allergic disorders such as ABPA or SAFS. It is poorly understood what allergens in particular are being expressed during fungal invasion and which are responsible for stimulation of immune responses. Study of the dynamics of allergen production by fungi may lead to insights into how allergens are presented to the immune system. METHODS: Expression of 17 A. fumigatus allergen genes was examined in response to various culture conditions and stimuli as well as in the presence of macrophages in order to mimic conditions encountered in the lung. RESULTS: Expression of 14/17 allergen genes was strongly induced by oxidative stress caused by hydrogen peroxide (Asp f 1, -2, -4, -5, -6, -7, -8, -10, -13, -17 and -18, all >10-fold and Asp f 11, -12, and -22, 5-10-fold) and 16/17 allergen genes were repressed in the presence of cAMP. The 4 protease allergen genes (Asp f -5, -10, -13 and -18) were expressed at very low levels compared to the comparator (ß-tubulin) under all other conditions examined. Mild heat shock, anoxia, lipid and presence of macrophages did not result in coordinated changes in allergen gene expression. Growth on lipid as sole carbon source contributed to the moderate induction of most of the allergen genes. Heat shock (37°C > 42°C) caused moderate repression in 11/17 genes (Asp f 1, -2, -4, -5, -6, -9, -10, -13, -17, -18 and -23) (2- to 9-fold), which was mostly evident for Asp f 1 and -9 (~9-fold). Anaerobic stress led to moderate induction of 13/17 genes (1.1 to 4-fold) with one, Asp f 8 induced over 10-fold when grown under mineral oil. Complex changes were seen in gene expression during co-culture of A. fumigatus with macrophages. CONCLUSIONS: Remarkable coordination of allergen gene expression in response to a specific condition (oxidative stress or the presence of cAMP) has been observed, implying that a single biological stimulus may play a role in allergen gene regulation. Interdiction of a putative allergen expression induction signalling pathway might provide a novel therapy for treatment of fungal allergy.

Retinopathy and microalbuminuria are common microvascular complications in cystic fibrosis-related diabetes.

AIMS: To study the prevalence of microvascular complications and renal changes associated with cystic fibrosis-related diabetes (CFRD). METHODS: This retrospective cohort study was conducted at the West Midlands Adult Cystic Fibrosis centre, United Kingdom. Data regarding age, sex, microalbuminuria, retinopathy neuropathy, and biochemical results were collected for all people with CFRD who had an annual review from 1 January 2018 to 31 December 2018 at the centre. Descriptive statistics were analysed using STATAv15.1. RESULTS: A total of 189 patients were included, of which 56.6% were male and median age (interquartile range) was 33 (27-39) years; 79.4% (150/189) had their annual review in 2018. Those with a biochemically impaired renal function numbered 7.2% (13/180) and 22.7% (32/141) had microalbuminuria; 17.2% (10/58) had diabetes related retinopathy. No one in our cohort had diabetic ulcers; however, 10.3% (13/126) had absent foot pulses. CONCLUSION: We found a higher prevalence of microalbuminuria compared with retinopathy in a large cohort of cystic fibrosis adults. This study demonstrates the need for regular specialist follow-up to facilitate early identification of such complications and a long-term prospective cohort to understand underlying mechanisms.

Improving the care of patients with cystic fibrosis (CF).

BACKGROUND: The West Midlands Adult Cystic Fibrosis (CF) Centre based at Birmingham Heartlands Hospital provides care for adults with CF in the West Midlands. People with CF are prone to pulmonary exacerbations, which often require inpatient admission for intravenous antibiotics. We observed that the admission process was efficient during working hours (9:00-17:00, Monday-Friday) when the CF team are routinely available, but out-of-working hours, there were delays in these patients being clerked and receiving their first antibiotic dose. We were concerned that this was resulting in quality and potential safety issues by causing delays in starting treatment and prolonging hospital inpatient stays. We therefore undertook a quality improvement project (QIP) aimed at addressing these issues. An initial survey showed median time to clerk of 5 hours, with 60% of patients missing their first dose of antibiotics and mean length of stay of 16 days. METHODS: We applied the Plan-Do-Study-Act (PDSA) cycle approach, with the first PDSA cycle involving raising awareness of the issue through education to doctors, nurses and patients. RESULTS: This led to a reduction of median time to clerk from 5 to 2 hours with 23% of patients missing their first antibiotic dose and mean length of stay reducing to 14 days. The second cycle involved introducing an admissions checklist and displaying education posters around the hospital, resulting in median time to clerk remaining at 2 hours but only 20% of patients missing their first antibiotic dose and the mean length of stay remaining at 14 days. CONCLUSION: This QIP has improved the out-of-hours admissions process for adults with CF in our centre. We plan to review the longer term effects of the project including sustainability, effects on clinical outcomes and patient satisfaction.

Physical activity in adults with cystic fibrosis receiving intravenous antibiotics in hospital and in the community.

INTRODUCTION: Intravenous antibiotic therapy (IVAT) for CF acute pulmonary exacerbations (APE) can be delivered in hospital or in the community. This study aimed to compare physical activity in CF patients receiving hospital and community-delivered IVAT, as well as other health outcomes. MATERIALS AND METHODS: This was a non-randomised parallel group prospective observational study. Hospitalised and community-treated CF adults receiving IVAT for APE were asked to wear ActiGraph® activity monitors, complete the habitual activity estimation scale (HAES), food diary, modified shuttle test (MST) and CFQ-R at the start and end of therapy. Nutritional and clinical outcomes were also compared between the cohorts. The primary outcomes was physical activity measured by the ActiGraph® activity monitors at the beginning and end of treatment in both cohorts. RESULTS: Physical activity (measured and self-reported) was no different between the cohorts, with both hospitalised and community-treated subjects being generally sedentary. Body weight increased significantly in the hospitalised cohort, whereas no difference was seen in the community-treated cohort. FEV1 % predicted and FVC % predicted increased in community-treated subjects, whereas only FVC % predicted increased in hospitalised subjects. CFQ-R respiratory domain increased to a greater extent in community-treated subjects. CONCLUSION: CF adults receiving IVAT for APE, both in hospital and in the community, are generally sedentary and we found no difference in physical activity between the two groups. These findings suggests the need to further promote physical activity in suitable patients during APE where considered appropriate.

Invasive pulmonary aspergillosis 10 years post bone marrow transplantation: a case report.

INTRODUCTION: Invasive pulmonary aspergillosis is a leading cause of mortality and morbidity in bone marrow transplant recipients. Establishing the diagnosis remains a challenge for clinicians working in acute care setting. However, prompt diagnosis and treatment can lead to favourable outcomes CASE PRESENTATION: We report a case of invasive aspergillosis occurring in a 39-year-old Caucasian female 10 years after an allogeneic haematopoietic bone marrow transplant, and 5 years after stopping all immunosuppression. Possible risk factors include bronchiolitis obliterans and exposure to building dust (for example, handling her husband's dusty overalls). There are no similar case reports in the literature at this time. CONCLUSION: High clinical suspicion, especially in the setting of failure to respond to broad-spectrum antibiotics, should alert clinicians to the possibility of invasive pulmonary aspergillosis, which, in this case, responded to antifungal therapy.

A case of spotted fever group rickettsiosis imported into the United Kingdom and treated with ciprofloxacin: a case report.

INTRODUCTION: Spotted fever group rickettsioses are an interesting group of infections, which are increasing in incidence worldwide. CASE PRESENTATION: Here we describe an imported case to the United Kingdom occurring in a patient who had recently visited Kruger National Park in South Africa - a highly endemic area for Rickettsia infections. Initial treatment with doxycycline failed but the patient made a prompt recovery after commencement of ciprofloxacin. CONCLUSION: This finding raises the possibility that there are resistant strains of Rickettsia present.