13 results on '"Samuel S. Bailey"'
Search Results
2. Heterologous production, reconstitution and EPR spectroscopic analysis of prFMN dependent enzymes
- Author
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Huan-Ming Huang, David J. Procter, Godwin A. Aleku, Arune Balaikaite, Annica Saaret, Stephen E. J. Rigby, Irina Gostimskaya, Karl A. P. Payne, David Leys, Karl Fisher, Samuel S. Bailey, Stephen A. Marshall, and Deepankar Gahloth
- Subjects
chemistry.chemical_classification ,Enzyme ,Biochemistry ,biology ,Decarboxylation ,Chemistry ,Prenyltransferase ,biology.protein ,Heterologous ,Phosphorylation ,Flavin group ,Oxidative phosphorylation ,Cofactor - Abstract
The recent discovery of the prenylated FMN (prFMN) cofactor has led to a renewed interest in the prFMN-dependent UbiD family of enzymes. The latter catalyses the reversible decarboxylation of alpha-beta unsaturated carboxylic acids and features widely in microbial metabolism. The flavin prenyltransferase UbiX synthesizes prFMN from reduced FMN and phosphorylated dimethylallyl precursors. Oxidative maturation of the resulting prFMNreduced species to the active prFMNiminium form is required for UbiD activity. Heterologous production of active holo-UbiD requires co-expression of UbiX, but the levels of prFMN incorporation and oxidative maturation appear variable. Detailed protocols and strategies for in vitro reconstitution and oxidative maturation of UbiD are presented that can yield an alternative source of active holo-UbiD for biochemical studies.
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- 2019
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3. The challenge of comprehensive and consistent sequence variant interpretation between clinical laboratories
- Author
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Dru Leistritz-Kessler, Ulrike Schwarze, Samuel S. Bailey, Mitzi L. Murray, Melanie Pepin, and Peter H. Byers
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0301 basic medicine ,Protein structure and function ,Genetics ,medicine.diagnostic_test ,Interpretation (philosophy) ,Concordance ,Genetic Variation ,Reproducibility of Results ,Sequence Analysis, DNA ,Computational biology ,Biology ,03 medical and health sciences ,030104 developmental biology ,Gene Frequency ,Data Interpretation, Statistical ,Clinical information ,medicine ,Humans ,Genetic Testing ,Diagnostic laboratory ,Allele frequency ,Genetic Association Studies ,Genetics (clinical) ,Sequence (medicine) ,Genetic testing - Abstract
Genetic testing has shifted from academic laboratories with expertise in specific genes to commercial laboratories that offer tests of a diverse array of genes. The purpose of this comparative study was to determine whether one academic laboratory’s model of variant interpretation is similar to that of several commercial laboratories. The Collagen Diagnostic Laboratory (CDL) received, over a 14-month period, 38 requests to interpret variants originally identified by an outside laboratory (OL). The interpretations by the OL and CDL were compared and discrepancies were assessed. Interpretations from the OL and CDL were concordant in 11 inquiries (29%); discrepancies were moderate in 11 instances (29%) and significant in 16 (42%). Factors that caused discrepancies included the following: (i) private data were not shared in a public database (n = 9); (ii) publicly available allele frequency data were not referenced and used as evidence (n = 5); and (iii) important aspects of protein structure and function were not taken into account (n = 13). Comprehensive interpretation of sequence variants depends on good functional tests and well-curated variant databases. Provision of clinical information to the clinical laboratory, mandatory submission of identified variants with phenotype data to common resources, and collaboration between clinical laboratories and recognized experts is likely to improve consistency in variant interpretation among clinical laboratories. Genet Med 18 1, 20–24.
- Published
- 2016
- Full Text
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4. Terminal Alkenes from Acrylic Acid Derivatives via Non-Oxidative Enzymatic Decarboxylation by Ferulic Acid Decarboxylases
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Godwin A. Aleku, Silvia M. Glueck, Karl A. P. Payne, Ruth T. Bradshaw-Allen, David A. Parker, Katharina Plasch, Samuel S. Bailey, Kurt Faber, Christoph Prause, and David Leys
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Stereochemistry ,Decarboxylation ,Prenyltransferase ,Flavin group ,010402 general chemistry ,01 natural sciences ,Catalysis ,Cofactor ,Cinnamic acid ,Inorganic Chemistry ,Ferulic acid ,chemistry.chemical_compound ,Manchester Institute of Biotechnology ,Terminal alkenes ,Physical and Theoretical Chemistry ,biology ,Full Paper ,Ferulic acid decarboxylase ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Full Papers ,ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology ,0104 chemical sciences ,Carboxylation ,Biocatalysis ,biology.protein ,Prenylated flavin - Abstract
Fungal ferulic acid decarboxylases (FDCs) belong to the UbiD-family of enzymes and catalyse the reversible (de)carboxylation of cinnamic acid derivatives through the use of a prenylated flavin cofactor. The latter is synthesised by the flavin prenyltransferase UbiX. Herein, we demonstrate the applicability of FDC/UbiX expressing cells for both isolated enzyme and whole-cell biocatalysis. FDCs exhibit high activity with total turnover numbers (TTN) of up to 55000 and turnover frequency (TOF) of up to 370 min−1. Co-solvent compatibility studies revealed FDC's tolerance to some organic solvents up 20 % v/v. Using the in-vitro (de)carboxylase activity of holo-FDC as well as whole-cell biocatalysts, we performed a substrate profiling study of three FDCs, providing insights into structural determinants of activity. FDCs display broad substrate tolerance towards a wide range of acrylic acid derivatives bearing (hetero)cyclic or olefinic substituents at C3 affording conversions of up to >99 %. The synthetic utility of FDCs was demonstrated by a preparative-scale decarboxylation.
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- 2018
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5. Molecular Outcome, Prediction, and Clinical Consequences of Splice Variants inCOL1A1, Which Encodes the proα1(I) Chains of Type I Procollagen
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Susan Stowers, Thao Tran, Samuel S. Bailey, Jennifer Schleit, Diana Chen, Ulrike Schwarze, and Peter H. Byers
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Adult ,Adolescent ,Sequence analysis ,RNA Splicing ,Biology ,Collagen Type I ,Cohort Studies ,Young Adult ,Exon ,Pregnancy ,Genetics ,Humans ,Protein Isoforms ,Computer Simulation ,splice ,Child ,Gene ,Genetics (clinical) ,Splice site mutation ,Alternative splicing ,Infant, Newborn ,Infant ,Fibroblasts ,Middle Aged ,Osteogenesis Imperfecta ,Phenotype ,Molecular biology ,Collagen Type I, alpha 1 Chain ,Child, Preschool ,RNA splicing ,Female ,Software - Abstract
Approximately 10%-20% of germline pathogenic variants alter mRNA splicing, with phenotypes often dependent on the stability of the mRNA produced by the mutant allele. To better understand the relationships between genotype, mRNA splicing, and phenotype, we examined clinical and molecular data from 243 probands with osteogenesis imperfecta (OI) representing 145 unique splicing variants within the type I procollagen gene, COL1A1. All individuals with IVSX-1G>A mutations had OI type I because the substitution shifted the splice acceptor site 1 nt downstream and destabilized the mRNA. OI phenotypes were not consistent for any other splice variant identified. We sequenced all cDNA species from cultured dermal fibroblasts from 40 individuals to identify splice outcome and compared those results to splice predictions from Human Splice Finder (HSF), Spliceport (SP), and Automatic Splice Site and Exon Definition Analyses (ASSEDA). Software-based splice predictions were correct in 42%, 55%, and 74% instances for HSF, SP, and ASSEDA, respectively. As molecular diagnostics move increasingly to DNA sequence analysis, the need to understand the effects of splice site variants will increase. These data demonstrate that caution must be exercised when using splice prediction software to predict splice outcome.
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- 2015
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6. New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition
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Basile Khara, Sam Hay, Drupad K. Trivedi, Karl A. P. Payne, David Leys, Stephen E. J. Rigby, Perdita E. Barran, Mark D. White, Nigel S. Scrutton, Royston Goodacre, Rebecca Beveridge, David A. Parker, Samuel S. Bailey, Nicholas J. W. Rattray, and Karl Fisher
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Multidisciplinary ,biology ,Stereochemistry ,Chemistry ,Decarboxylation ,Aryl ,Azomethine ylide ,Flavin group ,Cofactor ,Cycloaddition ,chemistry.chemical_compound ,Carboxylation ,1,3-Dipolar cycloaddition ,biology.protein - Abstract
The bacterial ubiD and ubiX or the homologous fungal fdc1 and pad1 genes have been implicated in the non-oxidative reversible decarboxylation of aromatic substrates, and play a pivotal role in bacterial ubiquinone (also known as coenzyme Q) biosynthesis or microbial biodegradation of aromatic compounds, respectively. Despite biochemical studies on individual gene products, the composition and cofactor requirement of the enzyme responsible for in vivo decarboxylase activity remained unclear. Here we show that Fdc1 is solely responsible for the reversible decarboxylase activity, and that it requires a new type of cofactor: a prenylated flavin synthesized by the associated UbiX/Pad1. Atomic resolution crystal structures reveal that two distinct isomers of the oxidized cofactor can be observed, an isoalloxazine N5-iminium adduct and a N5 secondary ketimine species with markedly altered ring structure, both having azomethine ylide character. Substrate binding positions the dipolarophile enoic acid group directly above the azomethine ylide group. The structure of a covalent inhibitor-cofactor adduct suggests that 1,3-dipolar cycloaddition chemistry supports reversible decarboxylation in these enzymes. Although 1,3-dipolar cycloaddition is commonly used in organic chemistry, we propose that this presents the first example, to our knowledge, of an enzymatic 1,3-dipolar cycloaddition reaction. Our model for Fdc1/UbiD catalysis offers new routes in alkene hydrocarbon production or aryl (de)carboxylation.
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- 2015
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7. Enzymatic control of cycloadduct conformation ensures reversible 1,3-dipolar cycloaddition in a prFMN-dependent decarboxylase
- Author
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David Leys, Annica Saaret, Karl A. P. Payne, Samuel S. Bailey, Iaroslav Kosov, Stephen A. Marshall, Sam Hay, Irina Gostimskaya, and Karl Fisher
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Models, Molecular ,Stereochemistry ,Carboxy-Lyases ,General Chemical Engineering ,Molecular Conformation ,Flavin mononucleotide ,010402 general chemistry ,01 natural sciences ,Reversible reaction ,Cinnamic acid ,Cofactor ,Article ,chemistry.chemical_compound ,Density Functional Theory ,biology ,Cycloaddition Reaction ,010405 organic chemistry ,Chemistry ,Active site ,General Chemistry ,Cycloaddition ,0104 chemical sciences ,Carboxylation ,Alkynes ,1,3-Dipolar cycloaddition ,biology.protein ,Biocatalysis ,Propionates - Abstract
The UbiD enzyme plays an important role in bacterial ubiquinone (coenzyme Q) biosynthesis. It belongs to a family of reversible decarboxylases that interconvert propenoic or aromatic acids with the corresponding alkenes or aromatic compounds using a prenylated flavin mononucleotide cofactor. This cofactor is suggested to support (de)carboxylation through a reversible 1,3-dipolar cycloaddition process. Here, we report an atomic-level description of the reaction of the UbiD-related ferulic acid decarboxylase with substituted propenoic and propiolic acids (data ranging from 1.01–1.39 A). The enzyme is only able to couple (de)carboxylation of cinnamic acid-type compounds to reversible 1,3-dipolar cycloaddition, while the formation of dead-end prenylated flavin mononucleotide cycloadducts occurs with distinct propenoic and propiolic acids. The active site imposes considerable strain on covalent intermediates formed with cinnamic and phenylpropiolic acids. Strain reduction through mutagenesis negatively affects catalytic rates with cinnamic acid, indicating a direct link between enzyme-induced strain and catalysis that is supported by computational studies. The UbiD family of reversible decarboxylases interconvert propenoic or aromatic acids with the corresponding alkenes or aromatic compounds, using a transient 1,3-dipolar cycloaddition between the substrate and the prenylated flavin mononucleotide cofactor. Atomic-resolution crystallography shows targeted destabilization of the intermediate covalent adducts, allowing the enzyme to harness 1,3-dipolar cycloaddition as a readily reversible reaction.
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8. MelRisk: Using neutrophil-to-lymphocyte ratio to improve risk prediction models for metastatic cutaneous melanoma in the sentinel lymph node.
- Author
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Wade RG, Bailey S, Robinson AV, Lo MCI, Peach H, Moncrieff MDS, and Martin J
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- Adult, Cohort Studies, Humans, Lymph Nodes pathology, Lymphocytes, Neutrophils pathology, Prognosis, Sentinel Lymph Node Biopsy, Melanoma, Cutaneous Malignant, Melanoma pathology, Sentinel Lymph Node pathology, Skin Neoplasms surgery
- Abstract
Background: Identifying metastatic melanoma in the sentinel lymph node (SLN) is important because 80% of SLN biopsies are negative and 11% of patients develop complications. The neutrophil-to-lymphocyte ratio (NLR), a biomarker of micrometastatic disease, could improve prediction models for SLN status. We externally validated existing models and developed 'MelRisk' prognostic score to better predict SLN metastasis., Methods: The models were externally validated using data from a multicenter cohort study of 1,251 adults. Additionally, we developed and internally validated a new prognostic score `MelRisk', using candidate predictors derived from the extant literature., Results: The Karakousis model had a C-statistic of 0.58 (95% CI, 0.54-0.62). The Sondak model had a C-statistic of 0.57 (95% CI 0.53-0.61). The MIA model had a C-statistic of 0.60 (95% CI. 0.56-0.64). Our 'MelRisk' model (which used Breslow thickness, ulceration, age, anatomical site, and the NLR) showed an adjusted C-statistic of 0.63 (95% CI, 0.56-0.64)., Conclusion: Our prediction tool is freely available in the Google Play Store and Apple App Store, and we invite colleagues to externally validate its performance ., (Copyright © 2021 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2022
- Full Text
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9. Hepatitis B Virus Reactivation Following Treatment of HNSCC With Cisplatin.
- Author
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Crosby J, Smith F, Ganti SS, Moka N, and Bailey S
- Subjects
- Antiviral Agents adverse effects, Cisplatin adverse effects, Hepatitis B virus genetics, Humans, Male, Middle Aged, Squamous Cell Carcinoma of Head and Neck drug therapy, Head and Neck Neoplasms drug therapy, Hepatitis B drug therapy, Hepatitis B prevention & control
- Abstract
Hepatitis B Virus (HBV) reactivation is a known complication of intense immunosuppression with B-cell depleting monoclonal antibody therapy and transplantation immunosuppression. HBV reactivation has occurred following treatment with chemotherapy regimens for hematologic malignancies and solid tumors. There are 2 prior case reports of HBV reactivation following cisplatin monotherapy for head and neck squamous cell carcinoma (HNSCC). Here, we present a case of a 49-year-old Caucasian male with a past medical history of laryngeal squamous cell carcinoma (SCC). There are no consensus guidelines on how to define hepatitis B reactivation. There are guidelines on when to initiate prophylaxis with Entecavir while on immunosuppressive therapy with risk according to medication category and hepatitis B surface antigen/hepatitis B core antibody IgG serology. CDC recommends screening everyone. American Society of Clinical Oncology (ASCO) now with a recent update in 2020 recommends screening everyone. There is a definite role of immunosuppression in HBV reactivation, however, there is also direct enhancement by cisplatin of viral replication by creating endoplasmic reticulum stress which increases HBV DNA indirectly. Finally, cytotoxicity enhances HBV reactivation and immune reconstitution post withdrawing immunosuppressive treatment. Because of the effects of chemotherapy, aka cisplatin goes beyond immunosuppression-related reactivation of HBV, our recommendations are in line with CDC and ASCO to screen all patients for HBV before onset of chemotherapy and start Entecavir/Tenofovir Disoproxil Fumarate before the onset of chemotherapy for HBV-positive patients.
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- 2022
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10. The challenge of comprehensive and consistent sequence variant interpretation between clinical laboratories.
- Author
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Pepin MG, Murray ML, Bailey S, Leistritz-Kessler D, Schwarze U, and Byers PH
- Subjects
- Data Interpretation, Statistical, Gene Frequency, Genetic Association Studies, Genetic Testing methods, Genetic Variation, Humans, Reproducibility of Results, Sequence Analysis, DNA methods
- Abstract
Purpose: Genetic testing has shifted from academic laboratories with expertise in specific genes to commercial laboratories that offer tests of a diverse array of genes. The purpose of this comparative study was to determine whether one academic laboratory's model of variant interpretation is similar to that of several commercial laboratories., Methods: The Collagen Diagnostic Laboratory (CDL) received, over a 14-month period, 38 requests to interpret variants originally identified by an outside laboratory (OL). The interpretations by the OL and CDL were compared and discrepancies were assessed., Results: Interpretations from the OL and CDL were concordant in 11 inquiries (29%); discrepancies were moderate in 11 instances (29%) and significant in 16 (42%). Factors that caused discrepancies included the following: (i) private data were not shared in a public database (n = 9); (ii) publicly available allele frequency data were not referenced and used as evidence (n = 5); and (iii) important aspects of protein structure and function were not taken into account (n = 13)., Conclusion: Comprehensive interpretation of sequence variants depends on good functional tests and well-curated variant databases. Provision of clinical information to the clinical laboratory, mandatory submission of identified variants with phenotype data to common resources, and collaboration between clinical laboratories and recognized experts is likely to improve consistency in variant interpretation among clinical laboratories.Genet Med 18 1, 20-24.
- Published
- 2016
- Full Text
- View/download PDF
11. Hepatitis C polymerase chain reaction testing by GPs.
- Author
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Bailey S, Scalley B, and Gilles M
- Subjects
- Hepatitis C Antibodies analysis, Humans, Physicians, Primary Care, Pilot Projects, Surveys and Questionnaires, Hepatitis C diagnosis, Polymerase Chain Reaction methods, Primary Health Care methods
- Abstract
Background: Approximately 75% of patients exposed to the hepatitis C virus will become chronically infected. Polymerase chain reaction (PCR) testing more than 6 months after exposure is necessary to identify this group. This pilot study assessed the practical ap-plication of PCR testing in the general practice context., Methods: General practitioners of patients newly notified as positive for hepatitis C antibody between 1 August 2007 and 1 August 2012 were invited to participate. They completed a self-administered survey, recording details on the use of hepatitis C PCR testing in their patients., Results: The survey found that 16 patients (46%) did not undergo any PCR testing for hepatitis C. Of those who underwent PCR testing, 11 (58%) were positive on PCR testing but only six (55%) of those with a positive PCR test were retested 6 months later., Discussion: Appropriate use of PCR is necessary to identify patients with chronic hepatitis C and offer appropriate referral and treatment.
- Published
- 2015
12. The effectiveness of therapeutic exercise for joint hypermobility syndrome: a systematic review.
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Palmer S, Bailey S, Barker L, Barney L, and Elliott A
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- Ehlers-Danlos Syndrome physiopathology, Humans, Joint Instability congenital, Ehlers-Danlos Syndrome rehabilitation, Exercise Therapy methods
- Abstract
Background: Joint hypermobility syndrome (JHS) is a heritable connective tissue disorder characterised by excessive range of movement at multiple joints accompanied by pain. Exercise is the mainstay of management yet its effectiveness is unclear., Objectives: To establish the effectiveness of therapeutic exercise for JHS., Design: Systematic literature review., Data Sources: A search of nine online databases, supplemented by a hand search and snowballing., Study Eligibility Criteria (participants and Interventions): People diagnosed with JHS (rather than asymptomatic generalised joint laxity); therapeutic exercise (of any type) used as an intervention; primary data reported; English language; published research., Study Appraisal and Synthesis Methods: Methodological quality was appraised by each reviewer using Critical Appraisal Skills Programme checklists. Articles were then discussed collectively and disagreements resolved through debate., Results: 2001 titles were identified. Four articles met the inclusion criteria, comprising one controlled trial, one comparative trial and two cohort studies. All studies found clinical improvements over time. However there was no convincing evidence that exercise was better than control or that joint-specific and generalised exercise differed in effectiveness., Limitations: The studies used heterogeneous outcome measures, preventing pooling of results. Only one study was a true controlled trial which failed to report between-group statistical analyses post-treatment., Conclusions and Implications of Key Findings: There is some evidence that people with JHS improve with exercise but there is no convincing evidence for specific types of exercise or that exercise is better than control. Further high quality research is required to establish the effectiveness of exercise for JHS., (Copyright © 2013 Chartered Society of Physiotherapy. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2014
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13. Food allergy training event for restaurant staff; a pilot evaluation.
- Author
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Bailey S, Billmeier Kindratt T, Smith H, and Reading D
- Abstract
A previous cross-sectional survey highlighted that restaurant staff in Brighton had gaps in their knowledge of food allergy, which could lead to the provision of unsafe meals to food-allergic customers. A food allergy training event was developed by a multi-disciplinary team (health service researcher, clinician, teacher and patient group representative) to equip restaurant staff with the knowledge and skills necessary to safely serve food-allergic customers. This evaluation summarises the training event's impact on participants' knowledge of food allergy and their satisfaction with the event. No attendee had previously attended any formal training on food allergy. The percentage of participants who answered all true-false questions correctly increased from 82% before the training event to 91% afterwards. The percentage of participants who were able to name at least three common allergens increased from 9% to 64%. Both quantitative and qualitative feedback was positive. Restaurant staff require a good understanding of food allergy to ensure that food-allergic customers are kept safe, and their restaurants operate within the law. This food allergy training event improved participants' absolute knowledge of food allergy, and attendees changed practice. Recommendations are made which could improve the impact and uptake of future food allergy training events.
- Published
- 2014
- Full Text
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