The development of generative Bayesian models for classification of cell images

A generative model for shape recognition of biological cells in images is developed. The model is designed for analysing high throughput screens, and is tested on a genome wide morphology screen. The genome wide morphology screen contains order of 104 images of fluorescently stained cells with order of 102 cells per image. It was generated using automated techniques through knockdown of almost all putative genes in Drosphila melanogaster. A major step in the analysis of such a dataset is to classify cells into distinct classes: both phenotypic classes and cell cycle classes. However, the quantity of data produced presents a major time bottleneck for human analysis. Human analysis is also known to be subjective and variable. The development of a generalisable computational analysis tool is an important challenge for the field. Previously cell morphology has been characterized by automated measurement of user-defined biological features, often specific to one dataset. These methods are surveyed and discussed. Here a more ambitious approach is pursued. A novel generalisable classification method, applicable to our images, is developed and implemented. The algorithm decomposes training images into constituent patches to build Bayesian models of cell classes. The model contains probability distributions which are learnt via the Expectation Maximization algorithm. This provides a mechanism for comparing the similarity of the appearance of cell phenotypes. The method is evaluated by comparison with results of Support Vector Machines at the task of performing binary classification. This work provides the basis for clustering large sets of cell images into biologically meaningful classes

Impact of Nurses’ Work Patterns on Nurses and Patients in Critical Care and Toxicology Care Units of Alexandria University Hospitals

Background: Nowadays, there are difficulties in recruiting and retaining nursing staff with increasing pressures and demands on nurses working in critical care areas. The role of nursing care in patients' safety and healthcare outcomes has led to increased interest in measuring and reporting nurses’ work patterns and their consequences on nurses and patients. Objectives:  Describe nurses’ work patterns and their impacts on nurses and patient outcomes. Methods: Self-report forms were used to collect data regarding nurses’ time spent on direct and indirect nursing activities, non- nursing care and personal activities as well as care left undone. Questionnaires were used to measure stress, tension, conflict, nurses’ intent to leave, nurses' satisfaction and  patient satisfaction  Results: nurses spent their working time on direct nursing care (36.64 %); indirect nursing care (28.18 %), non-nursing care (30.64 %) and personal activities ( 4.7%). Profile of direct and indirect patient care and personal activities increased in night shifts, while the profile of non-nursing tasks increased in morning shifts.  There was a positive correlation between care left undone and three non-nursing tasks. Besides, there was a positive correlation between left care undone, non-nursing duties and four nursing job outcomes. There also was a negative correlation between care left undone, non-nursing tasks and nurses' and patients' satisfaction.  Conclusion:  the study focused on the importance of direct patient care on improving quality of care and patient safety. Reducing the performance of non-nursing duties by nurses and decreasing care left undone will most likely result in greater nurses’ and patients’  satisfaction, reduced stress, tension, and conflict and decreased numbers of  nurses’ leaving their jobs. Keywords: work, patterns, nurses, patients, outcome

Consensus evidence-based recommendations for treat-to-target management of immunoglobulin A vasculitis

IgA vasculitis (IgAV), formerly known as Henoch-Schönlein purpura, is the most common cause of systemic vasculitis in childhood. Given its potential life-threatening systemic complications, early and accurate diagnosis as well as management of IgAV represent a major challenge for health care professionals. This study was carried out to attain an evidence-based expert consensus on a treat-to-target management approach for IgAV using Delphi technique. The preliminary scientific committee identified a total of 16 key clinical questions according to the patient, intervention, comparison, and outcomes (PICO) approach. An evidence-based, systematic, literature review was conducted to compile evidence for the IgAV management. The core leadership team identified researchers and clinicians with expertise in IgAV management in Egypt upon which experts were gathered from different governorates and health centers across Egypt. Delphi process was implemented (two rounds) to reach a consensus. An online questionnaire was sent to expert panel (n = 26) who participated in the two rounds. After completing round 2, a total of 20 recommendation items, categorized into two sections were obtained. Agreement with the recommendations (rank 7–9) ranged from 91.7–100%. Consensus was reached (i.e. ⩾75% of respondents strongly agreed or agreed) on the wording of all the 20 clinical standards identified by the scientific committee. Algorithms for the diagnosis and management have been suggested. This was an expert, consensus recommendations for the diagnosis and treatment of IgAV and IgA vasculitic nephritis, based on best available evidence and expert opinion. The guideline presented a strategy of care with a pathway to achieve a state of remission as early as possible

Complexity of case mix in a regional allergy service

<p>Abstract</p> <p>Background</p> <p>Currently in the United Kingdom (UK), there is a mismatch between limited financial resources and the large proportion of patients with suspected allergies actually being referred to specialist allergy clinics. To better understand the case mix of patients being referred, we audited referrals to a regional allergy service over an 8 year period.</p> <p>The main source of data was consultant letters to General Practitioners (GP) summarising the diagnosis of patients, archived from January 2002 to September 2009. Letters were reviewed, extracting the clinic date, doctor seen, gender, date of birth, postcode, GP, and diagnoses. Diagnoses were classified into seven groups and illustrative cases for each group noted.</p> <p>Findings</p> <p>Data from 2,028 new referrals with suspected allergy were analysed. The largest group of patients (43%) were diagnosed with a type I hypersensitivity. The other diagnostic groups were chronic idiopathic (spontaneous) urticaria (35%), suspected type I hypersensitivity but no allergen identified (8%), idiopathic (spontaneous) angioedema (8%), physical urticaria (2.5%), non-allergic symptoms (1.6%), type IV hypersensitivity (0.8%) and ACE inhibitor sensitivity (0.5%). Two thirds of patients seen were female with a higher percentage of female patients in the non type-I hypersensitivity group (71%) than the type 1 hypersensitivity (66%) (χ²= 5.1, 1df, <it>p = 0.024</it>). The type 1 hypersensitivity patients were younger than other patients (38 Vs 46 years, t = -10.8, <it>p < 0.001</it>)</p> <p>Conclusions</p> <p>This study highlights the complexity of specialist allergy practice and the large proportion of patients referred with non-type I hypersensitivities, chronic idiopathic (spontaneous) urticaria being by far the largest group. Such information is critical to inform commissioning decisions, define referral pathways and in primary care education.</p

Chronic urticaria in the real‐life clinical practice setting in the UK: results from the non‐interventional multicentre AWARE study

Abstract Background Chronic urticaria (CU) is a skin condition characterised by repeated occurrence of itchy wheals and/or angioedema for >6 weeks. Aim To provide data demonstrating the real‐life burden of CU in the UK. Methods This UK subset of the worldwide, prospective, non‐interventional AWARE study included patients aged 18–75 years diagnosed with H1‐antihistamine (H1‐AH)‐refractory chronic spontaneous urticaria (CSU) for >2 months. Baseline characteristics, disease activity, treatments, comorbidities and healthcare resource use were documented. Quality of life, work productivity and activity impairment were assessed. Results Baseline analysis included 252 UK patients. Mean age and body mass index were 45.0 years and 29.0 kg/m2, respectively. Most patients were female (77.8%) and had moderate/severe disease activity (mean Urticaria Activity Score over 7 days, 18.4) and a ‘spontaneous’ component to their CU (73.4% CSU; 24.6% CSU and chronic inducible urticaria). Common comorbidities included depression/anxiety (24.6%), asthma (23.8%) and allergic rhinitis (12.7%). A previous treatment was recorded for 57.9% of patients. Mean Dermatology Life Quality Index score was 9.5 and patients reported impairments in work productivity and activity. Healthcare resource use was high. Severity of CSU was associated with gender, obesity, anxiety and diagnosis. Only 28.5% of patients completed all nine study visits, limiting analysis of long‐term treatment patterns and disease impact. Conclusions Adult H1‐AH‐refractory CU patients in the UK reported high rates of healthcare resource use and impairment in quality of life, work productivity and activity at baseline. The differing structures of UK healthcare may explain the high study discontinuation rates versus other countries

In Vitro and In Silico Antioxidant Efficiency of Bio-Potent Secondary Metabolites From Different Taxa of Black Seed-Producing Plants and Their Derived Mycoendophytes

Oxidative stress is involved in the pathophysiology of multiple health complications, and it has become a major focus in targeted research fields. As known, black seeds are rich sources of bio-active compounds and widely used to promote human health due to their excellent medicinal and pharmaceutical properties. The present study investigated the antioxidant potency of various black seeds from plants and their derived mycoendophytes, and determined the total phenolic and flavonoid contents in different extracts, followed by characterization of major constituents by HPLC analysis. Finally, in silico docking determined their binding affinities to target myeloperoxidase enzymes. Ten dominant mycoendophytes were isolated from different black seed plants. Three isolates were then selected based on high antiradical potency and further identified by ITS ribosomal gene sequencing. Those isolated were Aspergillus niger TU 62, Chaetomium madrasense AUMC14830, and Rhizopus oryzae AUMC14823. Nigella sativa seeds and their corresponding endophyte A. niger had the highest content of phenolics in their n-butanol extracts (28.50 and 24.43 mg/g), flavonoids (15.02 and 11.45 mg/g), and antioxidant activities (90.48 and 81.48%), respectively, followed by Dodonaea viscosa and Portulaca oleracea along with their mycoendophytic R. oryzae and C. madrasense. Significant positive correlations were found between total phenolics, flavonoids, and the antioxidant activities of different tested extracts. The n-butanol extracts of both black seeds and their derived mycoendophytes showed reasonable IC50 values (0.81–1.44 mg/ml) compared to the control with significant correlations among their phytochemical contents. Overall, seventeen standard phenolics and flavonoids were used, and the compounds were detected in different degrees of existence and concentration in the examined extracts through HPLC analysis. Moreover, the investigation of the molecular simulation results of detected compounds against the myeloperoxidase enzyme revealed that, as a targeted antioxidant, rutin possessed a high affinity (−15.3184 kcal/mol) as an inhibitor. Taken together, the black seeds and their derived mycoendophytes are promising bio-prospects for the broad industrial sector of antioxidants with several valuable potential pharmaceutical and nutritional applications

CD4(+)CD25(+)FOXP3(+) Regulatory T Cells Suppress Anti-Tumor Immune Responses in Patients with Colorectal Cancer

BACKGROUND: A wealth of evidence obtained using mouse models indicates that CD4(+)CD25(+)FOXP3(+) regulatory T cells (Treg) maintain peripheral tolerance to self-antigens and also inhibit anti-tumor immune responses. To date there is limited information about CD4(+) T cell responses in patients with colorectal cancer (CRC). We set out to measure T cell responses to a tumor-associated antigen and examine whether Treg impinge on those anti-tumor immune responses in CRC patients. METHODOLOGY AND PRINCIPAL FINDINGS: Treg were identified and characterized as CD4(+)CD25(+)FOXP3(+) using flow cytometry. An increased frequency of Treg was demonstrated in both peripheral blood and mesenteric lymph nodes of patients with colorectal cancer (CRC) compared with either healthy controls or patients with inflammatory bowel disease (IBD). Depletion of Treg from peripheral blood mononuclear cells (PBMC) of CRC patients unmasked CD4(+) T cell responses, as observed by IFNγ release, to the tumor associated antigen 5T4, whereas no effect was observed in a healthy age-matched control group. CONCLUSIONS/SIGNIFICANCE: Collectively, these data demonstrate that Treg capable of inhibiting tumor associated antigen-specific immune responses are enriched in patients with CRC. These results support a rationale for manipulating Treg to enhance cancer immunotherapy

Loss of function NFKB1 variants are the most common monogenic cause of CVID in Europeans.

BACKGROUND: The genetic etiology of primary immunodeficiency disease (PID) carries prognostic information. OBJECTIVE: We conducted a whole-genome sequencing study assessing a large proportion of the NIHR-BioResource - Rare Disease cohort. METHODS: In the predominantly European study population of principally sporadic unrelated PID cases (n=846), a novel Bayesian method identified NFKB1 as one most strongly associated with PID, and the association was explained by 16 novel heterozygous truncating, missense and gene deletion variants. This accounted for 4% of common variable immunodeficiency (CVID) cases (n=390) in the cohort. Amino-acid substitutions predicted to be pathogenic were assessed by analysis of structural protein data. Immunophenotyping, immunoblotting and ex vivo stimulation of lymphocytes determined the functional effects of these variants. Detailed clinical and pedigree information was collected for genotype-phenotype co-segregation analyses. RESULTS: Both sporadic and familial cases demonstrated evidence of the non-infective complications of CVID, including massive lymphadenopathy (24%), unexplained splenomegaly (48%) and autoimmune disease (48%), features prior studies correlate with worse clinical prognosis. Although partial penetrance of clinical symptoms was noted in certain pedigrees, all carriers have a deficiency in B lymphocyte differentiation. Detailed assessment of B lymphocyte numbers, phenotype and function identifies the presence of a raised CD21lowB cell population: combined with identification of the disease-causing variant, this distinguishes between healthy individuals, asymptomatic carriers and clinically affected cases. CONCLUSION: We show that heterozygous loss-of-function variants in NFKB1 are the most common known monogenic cause of CVID that results in a temporally progressive defect in the formation of immunoglobulin-producing B cells.This study was supported by The National Institute for Health Research England (grant number RG65966), and by the Center of Immunodeficiencies Amsterdam (CIDA). JET is supported by an MRC Clinician Scientist Fellowship (MR/L006197/1). AJT is supported by both the Wellcome Trust (104807/Z/14/Z) and by the National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London. EO receives personal fees from CSL Behring and MSD