32 results on '"Donaldson SL"'
Search Results
2. Detection of Covid-19 Outbreaks Using Built Environment Testing for SARS-CoV-2.
- Author
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Fralick M, Nott C, Moggridge J, Castellani L, Raudanskis A, Guttman DS, Hinz A, Thampi N, Wong A, Manuel D, McGeer A, Doukhanine E, Mejbel H, Zanichelli V, Burella M, Donaldson SL, Wang PW, Kassen R, and MacFadden DR
- Subjects
- Humans, SARS-CoV-2, COVID-19 Testing, Long-Term Care, Disease Outbreaks, COVID-19
- Abstract
BACKGROUND: Environmental surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through wastewater has become a useful tool for population-level surveillance. Built environment sampling may provide a more spatially refined approach for surveillance in congregate living settings. METHODS: We conducted a prospective study in 10 long-term care homes (LTCHs) between September 2021 and November 2022. Floor surfaces were sampled weekly at multiple locations within each building and analyzed for the presence of SARS-CoV-2 using quantitative reverse transcriptase polymerase chain reaction. The primary outcome was the presence of a coronavirus disease 2019 (Covid-19) outbreak in the week that floor sampling was performed. RESULTS: Over the 14-month study period, we collected 4895 swabs at 10 LTCHs. During the study period, 23 Covid-19 outbreaks occurred with 119 cumulative weeks under outbreak. During outbreak periods, the proportion of floor swabs that were positive for SARS-CoV-2 was 54.3% (95% confidence interval [CI], 52 to 56.6), and during non-outbreak periods it was 22.3% (95% CI, 20.9 to 23.8). Using the proportion of floor swabs positive for SARS-CoV-2 to predict Covid-19 outbreak status in a given week, the area under the receiver-operating characteristic curve was 0.84 (95% CI, 0.78 to 0.9). Among 10 LTCHs with an outbreak and swabs performed in the prior week, eight had positive floor swabs exceeding 10% at least 5 days before outbreak identification. For seven of these eight LTCHs, positivity of floor swabs exceeded 10% more than 10 days before the outbreak was identified. CONCLUSIONS: Detection of SARS-CoV-2 on floors is strongly associated with Covid-19 outbreaks in LTCHs. These data suggest a potential role for floor sampling in improving early outbreak identification.
- Published
- 2023
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3. Effect of in-bed cycling on acute muscle wasting in critically ill adults: A randomised clinical trial.
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Nickels MR, Aitken LM, Barnett AG, Walsham J, King S, Gale NE, Bowen AC, Peel BM, Donaldson SL, Mealing STJ, and McPhail SM
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- Adult, Aged, Critical Illness, Female, Hand Strength, Humans, Intensive Care Units, Male, Middle Aged, Muscle Strength, Quadriceps Muscle physiopathology, Quality of Life, Exercise Therapy methods, Muscular Atrophy prevention & control
- Abstract
Purpose: To examine whether in-bed cycling assists critically ill adults to reduce acute muscle wasting, improve function and improve quality of life following a period of critical illness., Materials and Methods: A single-centre, two-group, randomised controlled trial with blinded assessment of the primary outcome was conducted in a tertiary ICU. Critically ill patients expected to be mechanically ventilated for at least 48 h were randomised to 30 min daily in-bed cycling in addition to usual-care physiotherapy (n = 37) or usual-care physiotherapy (n = 37). The primary outcome was muscle atrophy of rectus femoris cross-sectional area (RF
CSA ) measured by ultrasound at Day 10 following study enrolment. Secondary outcomes included manual muscle strength, handgrip strength, ICU mobility score, six-minute walk test distance and health-related quality of life up to six-months following hospital admission., Results: Analysis included the 72 participants (mean age, 56-years; male, 68%) who completed the study. There were no significant between-group differences in muscle atrophy of RFCSA at Day 10 (mean difference 3.4, 95% CI -6.9% to 13.6%; p = .52), or for secondary outcomes (p-values ranged p = .11 to p = .95)., Conclusions and Relevance: In-bed cycling did not reduce muscle wasting in critically ill adults, but this study provides useful effect estimates for large-scale clinical trials., Trial Registration: anzctr.org.au Identifier: ACTRN12616000948493., Competing Interests: Declaration of Competing Interest None to declare., (Copyright © 2020 Elsevier Inc. All rights reserved.)- Published
- 2020
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4. Penicillin-binding protein 3 is a common adaptive target among Pseudomonas aeruginosa isolates from adult cystic fibrosis patients treated with β-lactams.
- Author
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Clark ST, Sinha U, Zhang Y, Wang PW, Donaldson SL, Coburn B, Waters VJ, Yau YCW, Tullis DE, Guttman DS, and Hwang DM
- Subjects
- Adaptation, Biological, Adult, Amino Acid Substitution, Female, Humans, Longitudinal Studies, Male, Microbial Sensitivity Tests, Mutation, Missense, Penicillin-Binding Proteins metabolism, Polymerase Chain Reaction, Pseudomonas Infections microbiology, Pseudomonas aeruginosa drug effects, Pseudomonas aeruginosa genetics, Pseudomonas aeruginosa isolation & purification, Sequence Analysis, DNA, Sputum microbiology, Anti-Bacterial Agents therapeutic use, Cystic Fibrosis complications, Penicillin-Binding Proteins genetics, Pseudomonas Infections drug therapy, Pseudomonas aeruginosa enzymology, beta-Lactam Resistance, beta-Lactams therapeutic use
- Abstract
Objective: Determining the mechanisms that modulate β-lactam resistance in clinical Pseudomonas aeruginosa (P. aeruginosa) isolates can be challenging, as the molecular profiles identified in mutation-based or expression-based resistance determinant screens may not correlate with in vitro phenotypes. One of the lesser studied resistance mechanisms in P. aeruginosa is the modification of penicillin-binding protein 3 (pbpB/ftsI). This study reported that nonsynonymous polymorphisms within pbpB frequently occur among β-lactam resistant sputum isolates, and are associated with unique antibiotic susceptibility patterns., Methods: Longitudinally collected isolates (n = 126) from cystic fibrosis (CF) patients with or without recent β-lactam therapy or of non-clinical origin were tested for susceptibility to six β-lactams (aztreonam, ceftazidime, cefsulodin, cefepime, meropenem, and piperacillin). Known β-lactam resistance mechanisms were characterised by polymerase chain reaction (PCR)-based methods, and polymorphisms in the transpeptidase-encoding domain of pbpB identified by sequencing., Results: Twelve nonsynonymous polymorphisms were detected among 86 isolates (67%) from five CF patients with a history of β-lactam therapy, compared with one polymorphism in 30 (3.3%) from three patients who had not received β-lactam treatments. No nonsynonymous polymorphisms were found in ten environmental isolates. Multiple pbpB alleles, often with different combinations of polymorphisms, were detected within the population of strains from each CF patient for up to 2.6 years. Traditional patterns of ampC or mexA de-repression reduced expression of oprD or the presence of extended-spectrum β-lactamases were not observed in resistant isolates with nonsynonymous polymorphisms in pbpB., Conclusion: This study's findings suggest that pbpB is a common adaptive target, and may contribute to the development of β-lactam resistance in P. aeruginosa., (Copyright © 2019 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.)
- Published
- 2019
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5. Quality improvement priorities for safer out-of-hours palliative care: Lessons from a mixed-methods analysis of a national incident-reporting database.
- Author
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Williams H, Donaldson SL, Noble S, Hibbert P, Watson R, Kenkre J, Edwards A, and Carson-Stevens A
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- After-Hours Care statistics & numerical data, Databases, Factual, Hospice and Palliative Care Nursing statistics & numerical data, Humans, Palliative Care statistics & numerical data, Patient Safety statistics & numerical data, Primary Health Care statistics & numerical data, Quality Improvement statistics & numerical data, Risk Management statistics & numerical data, United Kingdom, After-Hours Care standards, Hospice and Palliative Care Nursing standards, Medical Errors statistics & numerical data, Palliative Care standards, Patient Safety standards, Primary Health Care standards, Quality Improvement organization & administration
- Published
- 2019
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6. Epidermodysplasia verruciformis in a young adult with activated PI3Kδ syndrome.
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Donaldson SL, Purnell JC, Pavlidakey PG, Atkinson TP, and Kissel R
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- 2019
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7. Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations.
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Layeghifard M, Li H, Wang PW, Donaldson SL, Coburn B, Clark ST, Caballero JD, Zhang Y, Tullis DE, Yau YCW, Waters V, Hwang DM, and Guttman DS
- Subjects
- Bacteria genetics, Canada, Child, Humans, Longitudinal Studies, Metagenomics, Bacteria classification, Cystic Fibrosis complications, Microbiota, Pneumonia microbiology, Sputum microbiology
- Abstract
Over 90% of cystic fibrosis (CF) patients die due to chronic lung infections leading to respiratory failure. The decline in CF lung function is greatly accelerated by intermittent and progressively severe acute pulmonary exacerbations (PEs). Despite their clinical impact, surprisingly few microbiological signals associated with PEs have been identified. Here we introduce an unsupervised, systems-oriented approach to identify key members of the microbiota. We used two CF sputum microbiome data sets that were longitudinally collected through periods spanning baseline health and PEs. Key taxa were defined based on three strategies: overall relative abundance, prevalence, and co-occurrence network interconnectedness. We measured the association between changes in the abundance of the key taxa and changes in patient clinical status over time via change-point detection, and found that taxa with the highest level of network interconnectedness tracked changes in patient health significantly better than taxa with the highest abundance or prevalence. We also cross-sectionally stratified all samples into the clinical states and identified key taxa associated with each state. We found that network interconnectedness most strongly delineated the taxa among clinical states, and that anaerobic bacteria were over-represented during PEs. Many of these anaerobes are oropharyngeal bacteria that have been previously isolated from the respiratory tract, and/or have been studied for their role in CF. The observed shift in community structure, and the association of anaerobic taxa and PEs lends further support to the growing consensus that anoxic conditions and the subsequent growth of anaerobic microbes are important predictors of PEs., Competing Interests: The authors declare no competing interests.
- Published
- 2019
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8. A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans.
- Author
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Diaz Caballero J, Clark ST, Wang PW, Donaldson SL, Coburn B, Tullis DE, Yau YCW, Waters VJ, Hwang DM, and Guttman DS
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- Genes, Bacterial genetics, Genetic Variation drug effects, Genome-Wide Association Study, Humans, Recombination, Genetic, Burkholderia Infections genetics, Burkholderia cepacia complex genetics, Drug Resistance, Bacterial genetics, Evolution, Molecular
- Abstract
Cystic fibrosis (CF) lung infections caused by members of the Burkholderia cepacia complex, such as Burkholderia multivorans, are associated with high rates of mortality and morbidity. We performed a population genomics study of 111 B. multivorans sputum isolates from one CF patient through three stages of infection including an early incident isolate, deep sampling of a one-year period of chronic infection occurring weeks before a lung transplant, and deep sampling of a post-transplant infection. We reconstructed the evolutionary history of the population and used a lineage-controlled genome-wide association study (GWAS) approach to identify genetic variants associated with antibiotic resistance. We found the incident isolate was basally related to the rest of the strains and more susceptible to antibiotics from three classes (β-lactams, aminoglycosides, quinolones). The chronic infection isolates diversified into multiple, distinct genetic lineages and showed reduced antimicrobial susceptibility to the same antibiotics. The post-transplant reinfection isolates derived from the same source as the incident isolate and were genetically distinct from the chronic isolates. They also had a level of susceptibility in between that of the incident and chronic isolates. We identified numerous examples of potential parallel pathoadaptation, in which multiple mutations were found in the same locus or even codon. The set of parallel pathoadaptive loci was enriched for functions associated with virulence and resistance. Our GWAS analysis identified statistical associations between a polymorphism in the ampD locus with resistance to β-lactams, and polymorphisms in an araC transcriptional regulator and an outer membrane porin with resistance to both aminoglycosides and quinolones. Additionally, these three loci were independently mutated four, three and two times, respectively, providing further support for parallel pathoadaptation. Finally, we identified a minimum of 14 recombination events, and observed that loci carrying putative parallel pathoadaptations and polymorphisms statistically associated with β-lactam resistance were over-represented in these recombinogenic regions., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2018
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9. Red-brown macules in a linear distribution on the arm.
- Author
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Donaldson SL, Hunt KM, and Theos A
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- 2018
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10. Image Gallery: Molluscum contagiosum-like facial lesions in a patient with a renal transplant: deep dermatophytosis due to Trichophyton rubrum.
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Ergen EN, Donaldson SL, Stratton MS, Pavlidakey PG, and Elewski BE
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- Administration, Oral, Antifungal Agents administration & dosage, Facial Dermatoses drug therapy, Humans, Male, Middle Aged, Molluscum Contagiosum drug therapy, Terbinafine administration & dosage, Tinea drug therapy, Facial Dermatoses diagnosis, Kidney Transplantation, Molluscum Contagiosum diagnosis, Tinea diagnosis
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- 2018
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11. Anionic Bismuth-Oxido Carboxylate Clusters with Transition Metal Countercations.
- Author
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Loera Fernandez II, Donaldson SL, Schipper DE, Andleeb S, and Whitmire KH
- Abstract
Six new anionic bismuth-oxido clusters containing trifluoroacetate ligands were prepared. These include two new Bi
6 O8 clusters: [M(NCMe)2 (H2 O)4 ]3 [Bi6 (μ3 -O)4 (μ3 -OH)4 (CF3 CO2 )12 ] with an octahedral Bi6 O4 (OH)4 core (M = Ni, 1a; Co, 1b) and four Bi4 O2 clusters, {[Co(NCMe)6 ][Bi4 (μ3 -O)2 (CF3 CO2 )10 ]}n (2a), {[Co{HC(MeCO)2 (MeCNH)}2 ][Bi4 (μ3 -O)2 (CF3 CO2 )10 ]·2[CF3 CO2 ]·2[CF3 CO2 H]·2[H2 O]}n (2b), {[Cu(NCMe)4 ]2 [Bi4 (μ3 -O)2 (CF3 CO2 )10 ]·2[CF3 CO2 H]}n (2c), and {[Me4 N]2 [Bi4 (μ3 -O)2 (CF3 CO2 )10 ]·2[CF3 CO2 H]}n (2d). These are among the first bismuth-oxido anionic clusters synthesized, and the first to have transition metal countercations. The Bi6 O8 anion in 1a and 1b is a high-symmetry octahedron. Additionally, two of the new Bi4 O2 clusters are arranged in 1D polymeric structures via bridging carboxylate ligands. The cation in compound 2c had not been previously characterized and was also observed in the synthesis of [Co{HC(MeCO)2 (MeCNH)}2 ][Bi(NO3 )6 ] (3). The new compounds were characterized using single crystal X-ray crystallography and elemental analysis.- Published
- 2016
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12. Experimental and Finite Element Investigations of Damage Resistance in Biomimetic Composite Sandwich T-Joints.
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Saeid AA and Donaldson SL
- Abstract
Composite sandwich structural joints, such as T-joints, are used in many different composite applications to transfers the load orthogonally between two sandwich elements. However, these joints connecting the sections can represent the weakest link in sandwich composite structures due to the lack of reinforcement in the out-of-plane direction. Therefore, this paper presents a new methodology for the design and analysis of composite sandwich T-joints using new biomimetic fabrication methods. The fabricated idea comes from biological fixed joints as an evolutionary alteration processes of trunk-branches of trees. It offers unique attributes to optimize the continuous fiber paths for minimum stress concentrations and multi-sandwich layers to increase the bending stiffness and strength. The focus is on how the biomimetic technique can improve sandwich T-joint structures by increasing their strength and load carrying capability without adding a significant weight penalty. The major attention is to investigate the comprehensive failure modes in the joint numerically and verified by experiments. Investigations were conducted on three different designs of biomimetic composite sandwich T-joints under tension and bending loads. The results show significant improvements to the ultimate load up to 68% in the case of bending load and 40% in the case of pull-off load in the biomimetic sandwich T-joints compared to the reference conventional T-joint design. The final failure was significantly deferred in both load status. The FE models provided important insights into the core failure and delamination of multi-interface biomimetic T-joints.
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- 2016
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13. Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung.
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Diaz Caballero J, Clark ST, Coburn B, Zhang Y, Wang PW, Donaldson SL, Tullis DE, Yau YC, Waters VJ, Hwang DM, and Guttman DS
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- Adaptation, Biological, Biota, Cluster Analysis, DNA, Bacterial chemistry, DNA, Bacterial genetics, Genetics, Population, Genome, Bacterial, Genotype, Humans, Pseudomonas aeruginosa genetics, Pseudomonas aeruginosa isolation & purification, Selection, Genetic, Sequence Analysis, DNA, Sequence Homology, Sputum microbiology, Cystic Fibrosis complications, Evolution, Molecular, Genetic Variation, Lung microbiology, Pseudomonas Infections microbiology, Pseudomonas aeruginosa classification, Pseudomonas aeruginosa physiology
- Abstract
Unlabelled: Pulmonary infections caused by Pseudomonas aeruginosa are a recalcitrant problem in cystic fibrosis (CF) patients. While the clinical implications and long-term evolutionary patterns of these infections are well studied, we know little about the short-term population dynamics that enable this pathogen to persist despite aggressive antimicrobial therapy. Here, we describe a short-term population genomic analysis of 233 P. aeruginosa isolates collected from 12 sputum specimens obtained over a 1-year period from a single patient. Whole-genome sequencing and antimicrobial susceptibility profiling identified the expansion of two clonal lineages. The first lineage originated from the coalescence of the entire sample less than 3 years before the end of the study and gave rise to a high-diversity ancestral population. The second expansion occurred 2 years later and gave rise to a derived population with a strong signal of positive selection. These events show characteristics consistent with recurrent selective sweeps. While we cannot identify the specific mutations responsible for the origins of the clonal lineages, we find that the majority of mutations occur in loci previously associated with virulence and resistance. Additionally, approximately one-third of all mutations occur in loci that are mutated multiple times, highlighting the importance of parallel pathoadaptation. One such locus is the gene encoding penicillin-binding protein 3, which received three independent mutations. Our functional analysis of these alleles shows that they provide differential fitness benefits dependent on the antibiotic under selection. These data reveal that bacterial populations can undergo extensive and dramatic changes that are not revealed by lower-resolution analyses., Importance: Pseudomonas aeruginosa is a bacterial opportunistic pathogen responsible for significant morbidity and mortality in cystic fibrosis (CF) patients. Once it has colonized the lung in CF, it is highly resilient and rarely eradicated. This study presents a deep sampling examination of the fine-scale evolutionary dynamics of P. aeruginosa in the lungs of a chronically infected CF patient. We show that diversity of P. aeruginosa is driven by recurrent clonal emergence and expansion within this patient and identify potential adaptive variants associated with these events. This high-resolution sequencing strategy thus reveals important intraspecies dynamics that explain a clinically important phenomenon not evident at a lower-resolution analysis of community structure., (Copyright © 2015 Diaz Caballero et al.)
- Published
- 2015
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14. Phenotypic diversity within a Pseudomonas aeruginosa population infecting an adult with cystic fibrosis.
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Clark ST, Diaz Caballero J, Cheang M, Coburn B, Wang PW, Donaldson SL, Zhang Y, Liu M, Keshavjee S, Yau YC, Waters VJ, Elizabeth Tullis D, Guttman DS, and Hwang DM
- Subjects
- Adult, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Female, Humans, Phenotype, Pseudomonas Infections drug therapy, Pseudomonas aeruginosa isolation & purification, Respiratory Tract Infections drug therapy, beta-Lactam Resistance, Cystic Fibrosis microbiology, Pseudomonas Infections microbiology, Pseudomonas aeruginosa genetics, Respiratory Tract Infections microbiology
- Abstract
Chronic airway infections caused by Pseudomonas aeruginosa contribute to the progression of pulmonary disease in individuals with cystic fibrosis (CF). In the setting of CF, within-patient adaptation of a P. aeruginosa strain generates phenotypic diversity that can complicate microbiological analysis of patient samples. We investigated within- and between- sample diversity of 34 phenotypes among 235 P. aeruginosa isolates cultured from sputum samples collected from a single CF patient over the span of one year, and assessed colony morphology as a screening tool for predicting phenotypes, including antimicrobial susceptibilities. We identified 15 distinct colony morphotypes that varied significantly in abundance both within and between sputum samples. Substantial within sample phenotypic heterogeneity was also noted in other phenotypes, with morphotypes being unreliable predictors of antimicrobial susceptibility and other phenotypes. Emergence of isolates with reduced susceptibility to β-lactams was observed during periods of clinical therapy with aztreonam. Our findings confirm that the P. aeruginosa population in chronic CF lung infections is highly dynamic, and that intra-sample phenotypic diversity is underestimated if only one or few colonies are analyzed per sample.
- Published
- 2015
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15. Safety incidents in the primary care office setting.
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Rees P, Edwards A, Panesar S, Powell C, Carter B, Williams H, Hibbert P, Luff D, Parry G, Mayor S, Avery A, Sheikh A, Donaldson SL, and Carson-Stevens A
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- Child, Cross-Sectional Studies, Humans, Retrospective Studies, United Kingdom, Family Practice, Medical Errors statistics & numerical data, Office Visits, Patient Safety, Primary Health Care
- Abstract
Background: In the United Kingdom, 26% of child deaths have identifiable failures in care. Although children account for 40% of family physicians' workload, little is known about the safety of care in the community setting. Using data from a national patient safety incident reporting system, this study aimed to characterize the pediatric safety incidents occurring in family practice., Methods: We undertook a retrospective, cross-sectional, mixed methods study of pediatric reports submitted to the UK National Reporting and Learning System from family practice. Analysis involved detailed data coding using multiaxial frameworks, descriptive statistical analysis, and thematic analysis of a special-case sample of reports. Using frequency distributions and cross-tabulations, the relationships between incident types and contributory factors were explored., Results: Of 1788 reports identified, 763 (42.7%) described harm to children. Three crosscutting priority areas were identified: medication management, assessment and referral, and treatment. The 4 incident types associated with the most harmful outcomes are errors associated with diagnosis and assessment, delivery of treatment and procedures, referrals, and medication provision. Poor referral and treatment decisions in severely unwell or vulnerable children, along with delayed diagnosis and insufficient assessment of such children, featured prominently in incidents resulting in severe harm or death., Conclusion: This is the first analysis of nationally collected, family practice-related pediatric safety incident reports. Recommendations to mitigate harm in these priority areas include mandatory pediatric training for all family physicians; use of electronic tools to support diagnosis, management, and referral decision-making; and use of technological adjuncts such as barcode scanning to reduce medication errors., (Copyright © 2015 by the American Academy of Pediatrics.)
- Published
- 2015
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16. Curry-assisted diagnosis in the rheumatology clinic.
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Donaldson SL, Cobine-Davies M, Morgan AW, Gough A, and Mackie SL
- Abstract
We report five cases of glucocorticoid-responsive mouth symptoms in polymyalgia rheumatica/giant cell arteritis (GCA); three cases of tongue pain exacerbated by hot/spicy food, a case of scalp pain made worse by eating hot/spicy food and a case of sore tongue as a presenting feature of GCA. These cases emphasize the importance of asking about mouth symptoms and changes in taste when evaluating patients with suspected GCA.
- Published
- 2015
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17. Prolonged remission of marginal zone lymphoma in a patient with rheumatoid arthritis treated with anti-tumor necrosis factor agents.
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Donaldson SL, Owen RG, and McGonagle DG
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- Antibodies, Monoclonal, Murine-Derived administration & dosage, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Cyclophosphamide administration & dosage, Etanercept, Female, Humans, Infliximab, Middle Aged, Remission Induction, Rituximab, Treatment Outcome, Vidarabine administration & dosage, Vidarabine analogs & derivatives, Antibodies, Monoclonal therapeutic use, Arthritis, Rheumatoid drug therapy, Immunoglobulin G therapeutic use, Lymphoma, B-Cell, Marginal Zone drug therapy, Receptors, Tumor Necrosis Factor therapeutic use, Tumor Necrosis Factor-alpha antagonists & inhibitors
- Published
- 2014
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18. Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions.
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Maughan H, Wang PW, Diaz Caballero J, Fung P, Gong Y, Donaldson SL, Yuan L, Keshavjee S, Zhang Y, Yau YC, Waters VJ, Tullis DE, Hwang DM, and Guttman DS
- Subjects
- Bacteria classification, Computer Simulation, DNA, Bacterial chemistry, DNA, Bacterial genetics, Genetic Variation, Humans, Lung microbiology, Lung pathology, Phylogeny, Polymerase Chain Reaction, Sputum microbiology, Bacteria genetics, Cystic Fibrosis microbiology, Metagenome genetics, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA methods
- Abstract
The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients.
- Published
- 2012
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19. Laparoscopic cholecystectomy: device-related errors revealed through a national database.
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Panesar SS, Salvilla SA, Patel B, and Donaldson SL
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- Equipment and Supplies, Gallbladder surgery, Humans, Patient Safety, Patient Satisfaction, Postoperative Complications, Risk, United Kingdom, Cholecystectomy, Laparoscopic adverse effects, Cholecystectomy, Laparoscopic methods, Databases, Factual, Medical Errors statistics & numerical data
- Abstract
Laparoscopic techniques represent a key milestone in the development of modern surgery, offering a step change in quality of care, patient satisfaction and efficiency in use of health service resources. Laparoscopy is most widely used for gall bladder surgery. As would be expected with the introduction of any new technology, the early phase of development was accompanied by complications in its use. Arguably some of these should have been anticipated, but nevertheless standards and training programs were subsequently put in place to secure a more consistent standard of care across the UK. Now that this early learning curve has largely been negotiated, we wanted to examine the nature of the errors associated with laparoscopic gall bladder surgery, particularly in relation to equipment. We used data from the largest error-reporting system in the world to examine the problem of equipment-related incidents amongst patients who had laparoscopic cholecystectomy. Over the 6-year period 2004-2010, the number of such reports increased 15-fold, whilst the growth in use of the procedure itself increased 1.3-fold. The majority of the increase was in device-related errors. User-related errors constituted a smaller proportion of errors. Whilst most surgeons appear to carry out laparoscopic surgery with a low level of harm to their patients, problems with their equipment remains a risk for many procedures. In some ways, this is an easier problem to address than one associated with competency. A risk associated with faulty, substandard or misused equipment is one that should be minimized in a 21st Century surgical service.
- Published
- 2011
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20. GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.
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Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, and Bader GD
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- Algorithms, Databases, Factual, Gene Regulatory Networks, Genes, Computational Biology methods, Software
- Abstract
Unlabelled: The GeneMANIA Cytoscape plugin brings fast gene function prediction capabilities to the desktop. GeneMANIA identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses over 800 networks from six organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data., Availability and Implementation: The GeneMANIA Cytoscape plugin is implemented in Java and is freely available at http://www.genemania.org/plugin/.
- Published
- 2010
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21. Cytoscape Web: an interactive web-based network browser.
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Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, and Bader GD
- Subjects
- Internet, Software
- Abstract
Unlabelled: Cytoscape Web is a web-based network visualization tool-modeled after Cytoscape-which is open source, interactive, customizable and easily integrated into web sites. Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF., Availability and Implementation: Cytoscape Web is implemented in Flex/ActionScript with a JavaScript API and is freely available at http://cytoscapeweb.cytoscape.org/.
- Published
- 2010
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22. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
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Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, and Morris Q
- Subjects
- Algorithms, Animals, Gene Regulatory Networks, Genomics, Humans, Internet, Mice, Genes physiology, Software
- Abstract
GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist.
- Published
- 2010
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23. Life support.
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Donaldson SL
- Subjects
- Health Status Disparities, Humans, Program Evaluation, Smoking adverse effects, Smoking economics, Smoking epidemiology, Smoking Cessation economics, State Medicine, United Kingdom epidemiology, Health Policy, Smoking Cessation methods, Smoking Prevention
- Published
- 2009
24. An international language for patient safety: Global progress in patient safety requires classification of key concepts.
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Donaldson SL
- Subjects
- Humans, Medical Errors prevention & control, Concept Formation classification, International Cooperation, Language, Safety Management
- Published
- 2009
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25. Championing patient safety: going global.
- Author
-
Donaldson SL
- Subjects
- Diffusion of Innovation, Evidence-Based Medicine, Humans, United Kingdom, Global Health, International Cooperation, Medical Errors prevention & control, Safety Management legislation & jurisprudence
- Published
- 2002
- Full Text
- View/download PDF
26. Blastogenic responses by lymphocytes from periodontally healthy populations induced by periodontitis-associated bacteria.
- Author
-
Donaldson SL, Ranney RR, Burmeister JA, and Tew JG
- Subjects
- Adolescent, Adult, Female, Humans, Lymphocytes immunology, Male, Middle Aged, Periodontitis immunology, Periodontium immunology, Periodontium microbiology, Time Factors, Bacteria immunology, Lymphocyte Activation, Periodontitis microbiology
- Abstract
Studies of blastogenic responsiveness induced in peripheral blood lymphocytes (PBL) from periodontally healthy subjects by periodontal bacteria have conflicted. This study was undertaken to examine the blastogenic response of periodontally healthy subjects under experimental conditions which provide improved control of laboratory variables. By using cryopreserved PBL the responses of all subjects in an experiment were determined on the same day under identical conditions. The periodontally healthy populations consisted of subjects of the same age range and sex matched to three distinct groups of periodontally diseased subjects (i.e., juvenile (JP), severe (SP), and moderate (MP) periodontitis). The bacterial stimulants tested were chosen on the basis of known association with and isolation from persons fitting the disease classifications. If PBL response differences between periodontally healthy and diseased subjects exist they should be most obvious in response to predominant organisms associated with the disease states. PBL cultures were harvested after a 4 hour pulse with 3H-thymidine on days 4 and 6 of culture. Three separate experiments were conducted comparing one healthy group and one diseased group. In all three experiments subjects in the healthy group responded as frequently as did those in the diseased group, the dose-response distribution was indistinguishable, and the magnitude of the responses was not substantially different between groups. These results suggest nonspecific activation as the major determinant in the blastogenic response, rather than specific sensitization occurring during initiation or progression of periodontitis.
- Published
- 1982
- Full Text
- View/download PDF
27. Polyclonal B-cell activating capacities of gram-positive bacteria frequently isolated from periodontally diseased sites.
- Author
-
Donaldson SL, Bick PH, Moore WE, Ranney RR, Burmeister JA, and Tew JG
- Subjects
- Actinomyces immunology, Adult, Eubacterium immunology, Humans, Peptostreptococcus immunology, Pokeweed Mitogens immunology, Streptococcus immunology, B-Lymphocytes immunology, Bacteria immunology, Lymphocyte Activation, Periodontal Diseases microbiology
- Published
- 1982
- Full Text
- View/download PDF
28. The maintenance of B-cell and T-cell function in frozen and stored human lymphocytes.
- Author
-
Donaldson SL, Miller GA, Rice PL, Ranney RR, and Tew JG
- Subjects
- Antibody-Producing Cells immunology, B-Lymphocytes immunology, Cell Survival, Freezing, Hemolytic Plaque Technique, Humans, Lymphocyte Activation, Pokeweed Mitogens pharmacology, T-Lymphocytes immunology, B-Lymphocytes physiology, Blood Preservation, T-Lymphocytes physiology
- Abstract
The objective of this study was to identify and test a convenient means for long-term storage of lymphocytes taken from clinically characterized patients without losing B- or T-cell function. Accordingly, peripheral blood lymphocytes were frozen and stored, and portions of each sample were subsequently assayed for T-cell blastogenic response and B-cell Jerne plaquing at various time intervals after freezing. A comparison of the cell counts of fresh and frozen cultures indicated that cell were recovered after freezing. Furthermore, these cells showed no significant differences in (i) cell viability; (ii) blastogenic response to antigens of Actinomyces maeslandii, Bacteroides melaninogenicus, Fusobacterium nucleatum, and tetanus toxoid; (iii) blastogenic response to phytohemagglutinin and pokeweed mitogen; and (iv) polyclonal B-cell response to pokeweed mitogen as measured by the direct Jerne plaque assay. The retained blastogenic and plaquing responses seen in frozen cultures indicated the maintenance of both T-cell and B-cell function, respectively. This is the first reported demonstration of Jerne plaquing of normal human lymphocytes after freezing. It appears that freezing techniques provide a means for repeating and extending both T- and B-cell assays using frozen stored portions of the same cell samples.
- Published
- 1981
- Full Text
- View/download PDF
29. Evidence of mitogenic activity in periodontitis-associated bacteria.
- Author
-
Donaldson SL, Ranney RR, and Tew JG
- Subjects
- Animals, B-Lymphocytes immunology, Female, Fetal Blood, Germ-Free Life, Humans, Mice, Mice, Inbred C3H, Periodontitis immunology, Pregnancy, Spleen immunology, Bacteria immunology, Lymphocyte Activation, Lymphocytes immunology, Periodontitis microbiology
- Abstract
This study examines several periodontitis-associated bacterial isolates for the presence of mitogenic activity, as indicated by their capacity to stimulate unsensitized lymphocytes to undergo blastogenesis. Germfree mouse spleen cells responded vigorously to all of the bacterial sonic extracts tested. The kinetics and dose responses to these activators in germfree mouse spleen cell cultures paralleled those seen with the standard murine B-cell mitogen, Escherichia coli lipopolysaccharide. In contrast, Streptokinase-Streptodornase (Varidase; Lederle Laboratories) antigen elicited no response. Human cord blood lymphocytes also responded upon stimulation with these same bacterial isolates but failed to respond to Streptokinase-Streptodornase. The frequency, magnitude, and kinetics of these cord blood lymphocyte responses were remarkably similar to those seen with adult peripheral blood lymphocytes. However, in this and previous studies, individuals with unresponsive peripheral blood lymphocytes have been observed. Studies were initiated to determine whether these unresponsive leukocyte preparations truly lacked the capacity to respond to these bacteria or whether unresponsiveness reflected the presence of a regulatory cell population in these cultures. After the removal of the adherent cells from unresponsive peripheral blood lymphocyte cultures, the nonadherent cells were found to be responsive. Therefore, peripheral blood lymphocyte responsiveness appears to be regulated via an adherent cell population. The removal of adherent cells from unresponsive cord blood lymphocyte preparations resulted in a less consistent alteration to responsiveness. However, cord blood lymphocyte preparations unresponsive at a standard cell density were shown to be responsive at altered cell densities.
- Published
- 1983
- Full Text
- View/download PDF
30. Localization of antibody-forming cells in draining lymphoid organs during long-term maintenance of the antibody response.
- Author
-
Donaldson SL, Kosco MH, Szakal AK, and Tew JG
- Subjects
- Animals, Female, Horseradish Peroxidase immunology, Immunologic Memory, Lymph Nodes immunology, Mice, Spleen cytology, Spleen immunology, Time Factors, Antibody Formation, Antibody-Producing Cells cytology, Lymph Nodes cytology
- Abstract
Previous studies on the "spontaneous antibody response" have included in vitro steps and it is possible that the response is an in vitro artifact. The objective of the present study was to induce a spontaneous antibody response entirely in vivo and determine if the response is localized and if the magnitude of the response is related to the location of persisting antigen. Antigen was injected into the right hind footpads of mice, and lymph nodes on the right side were draining and lymph nodes on the left side were controls. Antibody-forming cells (AFCs) were enumerated in both draining and nondraining nodes 2 weeks, 2 months, and 1 year after secondary immunization. Four days prior to determining AFC number, the mice were severely bled to stimulate AFC production. Thousands of AFCs were found in the draining lymph nodes and the numbers were dramatic in nodes closest to the injection site that retain the most antigen. In contrast, the vast majority of nondraining nodes lacked any AFCs. One year after immunization, the response was almost exclusively in the popliteal node, draining the foot where antigen was administered a year earlier. These results are consistent with previous data on the spontaneous response and support the hypothesis that antigen retained on FDCs is essential in the maintenance of serum antibody levels.
- Published
- 1986
- Full Text
- View/download PDF
31. Blastogenic responsiveness in periodontally healthy subjects. Evidence for mitogenic activity in oral bacteria.
- Author
-
Tew JG, Ranney RR, and Donaldson SL
- Subjects
- Animals, Female, Humans, Lymphocytes immunology, Mice, Mice, Inbred C3H, Mitogens, Bacteria immunology, Lymphocyte Activation, Mouth microbiology
- Published
- 1982
- Full Text
- View/download PDF
32. B-lymphocyte blastogenesis in response to periodontitis-associated bacteria. Kinetics and proportion of total response.
- Author
-
Donaldson SL, Ranney RR, and Tew JG
- Subjects
- Actinomyces immunology, Adult, B-Lymphocytes cytology, Cell Division, Fetal Blood immunology, Fusobacterium immunology, Humans, Kinetics, Leukocyte Count, Peptostreptococcus immunology, T-Lymphocytes cytology, T-Lymphocytes immunology, B-Lymphocytes immunology, Bacteria immunology, Lymphocyte Activation, Periodontitis microbiology
- Abstract
A role for activated B-lymphocytes in mediating the initiation and/or progression of periodontal diseases has been proposed in previous work. The present study was conducted to: (1) assess the proportion of total lymphocyte blastogenic response to selected oral bacteria which is composed of T-cell and B-cell activation, respectively, and (2) to determine whether different kinetic patterns exist for the T-cell vs. the B-cell responses to these bacteria. Using lymphocyte rosetting and culturing techniques, rosette-positive and rosette-negative lymphocyte preparations were examined for blastogenic responsiveness following stimulation with a variety of both Gram-positive and Gram-negative periodontitis-associated bacteria. Results of these studies indicated that both peripheral blood lymphocytes (PBL) from healthy adults and cord blood lymphocytes (CBL) from placental afterbirths responded to these bacteria with similar kinetic patterns. The net PBL blastogenic response appeared to consist of an early B-cell response, which peaked at Days 2 or 3 of culture, followed by a later T-cell response, which peaked at Days 5 to 6 of culture. The B-cell response appeared to be T-cell-dependent in that B-cells cultured alone showed minimal thymidine uptake over the entire 6-day period, but the addition of irradiated T-cells to these B-cell cultures resulted in a greatly enhanced B-cell response.
- Published
- 1984
- Full Text
- View/download PDF
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