1
|
Fletcher K, Wydera S, Thorpe N, Radford K, das Nair R, Booth V. A rapid realist review of clinical neuropsychology rehabilitation programmes to improve psychological wellbeing and quality of life for people with acquired brain injuries. Neuropsychol Rehabil 2023:1-36. [PMID: 37975854 DOI: 10.1080/09602011.2023.2273580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023]
Abstract
Approximately 20% of acquired brain injury (ABI) survivors experience reduced psychological wellbeing (PWB). Neuropsychological rehabilitation (NPR) is one approach supporting people with ABI to participate meaningfully in activities despite challenges. Although literature supports NPR effectiveness, little is known about change mechanisms. This systematic realist review identifies what NPR programmes have been designed, delivered, and evaluated for people with ABI to improve PWB and/or quality of life (QOL), as well as providing a context-relevant understanding of what NPR includes and how NPR might lead to positive outcomes. A rapid realist review was conducted in three phases: (1) structured retrieval and evidence extraction; (2) stakeholder consultation; (3) analysis and synthesis. Searches were completed, and findings from 35 publications and one stakeholder consultation were synthesized into a refined logic model. Six context-mechanism-outcome chains (CMOCs) were identified. Participants' relationships to internal experiences, and feelings of self-worth, mastery, and connection appeared to be mechanisms that led to improved PWB and QOL. Adaptation and individualized programmes were also key mechanisms to explain successful NPR. Embedding CMOCs into NPR could improve PWB and/or QOL for people with ABI. The logic model will inform ongoing development of a new online, group-based, NPR programme.
Collapse
Affiliation(s)
- K Fletcher
- Division of Rehabilitation & Ageing, University of Nottingham, Nottingham, UK
- Midlands Partnership NHS Foundation Trust, Stafford, UK
| | | | - N Thorpe
- Nottinghamshire Healthcare NHS Foundation Trust, Nottingham, UK
| | - K Radford
- Division of Rehabilitation & Ageing, University of Nottingham, Nottingham, UK
| | - R das Nair
- Nottinghamshire Healthcare NHS Foundation Trust, Nottingham, UK
- SINTEF, Trondheim, Norway
- Institute of Mental Health, University of Nottingham, Nottingham, UK
| | - V Booth
- Division of Rehabilitation & Ageing, University of Nottingham, Nottingham, UK
| |
Collapse
|
2
|
Fletcher K, Michelmore R. Genome-Enabled Insights into Downy Mildew Biology and Evolution. Annu Rev Phytopathol 2023; 61:165-183. [PMID: 37268005 DOI: 10.1146/annurev-phyto-021622-103440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Oomycetes that cause downy mildew diseases are highly specialized, obligately biotrophic phytopathogens that can have major impacts on agriculture and natural ecosystems. Deciphering the genome sequence of these organisms provides foundational tools to study and deploy control strategies against downy mildew pathogens (DMPs). The recent telomere-to-telomere genome assembly of the DMP Peronospora effusa revealed high levels of synteny with distantly related DMPs, higher than expected repeat content, and previously undescribed architectures. This provides a road map for generating similar high-quality genome assemblies for other oomycetes. This review discusses biological insights made using this and other assemblies, including ancestral chromosome architecture, modes of sexual and asexual variation, the occurrence of heterokaryosis, candidate gene identification, functional validation, and population dynamics. We also discuss future avenues of research likely to be fruitful in studies of DMPs and highlight resources necessary for advancing our understanding and ability to forecast and control disease outbreaks.
Collapse
Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, California, USA
| | - Richard Michelmore
- The Genome Center, University of California, Davis, California, USA
- Department of Plant Sciences; Department of Molecular and Cellular Biology; Department of Medical Microbiology and Immunology, University of California, Davis, California, USA;
| |
Collapse
|
3
|
Fletcher K, Martin F, Isakeit T, Cavanaugh K, Magill C, Michelmore R. The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes. G3 (Bethesda) 2023; 13:jkac340. [PMID: 36592124 PMCID: PMC9997571 DOI: 10.1093/g3journal/jkac340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/14/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023]
Abstract
Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.
Collapse
Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, CA 95616, USA
| | - Frank Martin
- U.S. Department of Agriculture–Agriculture Research Service, Salinas, CA, 93905, USA
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Keri Cavanaugh
- The Genome Center, University of California, Davis, CA 95616, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Richard Michelmore
- The Genome Center, University of California, Davis, CA 95616, USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA 95616, USA
| |
Collapse
|
4
|
Abstract
BACKGROUND Systemic racism and inequity are embedded in higher education, especially in nursing. By disregarding health disparities and inequities, a hidden curriculum is endorsed, implicitly letting both instructors and students know that not addressing these subjects is acceptable. METHOD Needs assessments were performed to assess faculty and student attitudes about the needs for justice, equity, diversity, and inclusion (JEDI) concepts. Using the Plan-Do-Study-Act model, the School of Nursing leadership, faculty, and students created taskforces to implement anti-oppression curricula throughout prelicensure courses. RESULTS Anti-oppression curricula and workshops were piloted successfully in the first semester of prelicensure nursing. Student feedback was positive with constructive suggestions. JEDI curriculum mapping was completed across the prelicensure nursing curriculum. CONCLUSION JEDI concepts must be integrated across nursing curricula to identify gaps. Forming a collaboration between leadership, faculty, and students is an optimal way to proceed as they all are invested and accountable for change. [J Nurs Educ. 2022;61(8):447-454.].
Collapse
|
5
|
Fletcher K, Shin OH, Clark KJ, Feng C, Putman AI, Correll JC, Klosterman SJ, Van Deynze A, Michelmore RW. Ancestral Chromosomes for Family Peronosporaceae Inferred from a Telomere-to-Telomere Genome Assembly of Peronospora effusa. Mol Plant Microbe Interact 2022; 35:450-463. [PMID: 35226812 DOI: 10.1094/mpmi-09-21-0227-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Downy mildew disease of spinach, caused by the oomycete Peronospora effusa, causes major losses to spinach production. In this study, the 17 chromosomes of P. effusa were assembled telomere-to-telomere, using Pacific Biosciences high-fidelity reads. Of these, 16 chromosomes are complete and gapless; chromosome 15 contains one gap bridging the nucleolus organizer region. This is the first telomere-to-telomere genome assembly for an oomycete. Putative centromeric regions were identified on all chromosomes. This new assembly enables a reevaluation of the genomic composition of Peronospora spp.; the assembly was almost double the size and contained more repeat sequences than previously reported for any Peronospora species. Genome fragments consistently underrepresented in six previously reported assemblies of P. effusa typically encoded repeats. Some genes annotated as encoding effectors were organized into multigene clusters on several chromosomes. Putative effectors were annotated on 16 of the 17 chromosomes. The intergenic distances between annotated genes were consistent with compartmentalization of the genome into gene-dense and gene-sparse regions. Genes encoding putative effectors were enriched in gene-sparse regions. The near-gapless assembly revealed apparent horizontal gene transfer from Ascomycete fungi. Gene order was highly conserved between P. effusa and the genetically oriented assembly of the oomycete Bremia lactucae; high levels of synteny were also detected with Phytophthora sojae. Extensive synteny between phylogenetically distant species suggests that many other oomycete species may have similar chromosome organization. Therefore, this assembly provides the foundation for genomic analyses of diverse oomycetes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, CA, U.S.A
| | - Oon-Ha Shin
- Seed Biotechnology Center, Department of Plant Sciences, University of California, Davis, CA, U.S.A
| | - Kelley J Clark
- United States Department of Agriculture-Agricultural Research Station, 1636 East Alisal Street, Salinas, CA, U.S.A
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AR, U.S.A
| | - Chunda Feng
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AR, U.S.A
| | - Alexander I Putman
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, U.S.A
| | - James C Correll
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AR, U.S.A
| | - Steven J Klosterman
- United States Department of Agriculture-Agricultural Research Station, 1636 East Alisal Street, Salinas, CA, U.S.A
| | - Allen Van Deynze
- Seed Biotechnology Center, Department of Plant Sciences, University of California, Davis, CA, U.S.A
| | - Richard W Michelmore
- The Genome Center, University of California, Davis, CA, U.S.A
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA, U.S.A
| |
Collapse
|
6
|
Fletcher K, Han R, Smilde D, Michelmore R. Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state. BMC Bioinformatics 2022; 23:150. [PMID: 35468720 PMCID: PMC9040317 DOI: 10.1186/s12859-022-04685-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/10/2022] [Indexed: 11/28/2022] Open
Abstract
Background Polyploidy and heterokaryosis are common and consequential genetic phenomena that increase the number of haplotypes in an organism and complicate whole-genome sequence analysis. Allele balance has been used to infer polyploidy and heterokaryosis in diverse organisms using read sets sequenced to greater than 50× whole-genome coverage. However, sequencing to adequate depth is costly if applied to multiple individuals or large genomes. Results We developed VCFvariance.pl to utilize the variance of allele balance to infer polyploidy and/or heterokaryosis at low sequence coverage. This analysis requires as little as 10× whole-genome coverage and reduces the allele balance profile down to a single value, which can be used to determine if an individual has two or more haplotypes. This approach was validated using simulated, synthetic, and authentic read sets from the oomycete species Bremia lactucae and Phytophthora infestans, the fungal species Saccharomyces cerevisiae, and the plant species Arabidopsis arenosa. This approach was deployed to determine that nine of 21 genotyped European race-type isolates of Bremia lactucae were inconsistent with diploidy and therefore likely heterokaryotic. Conclusions Variance of allele balance is a reliable metric to detect departures from a diploid state, including polyploidy, heterokaryosis, a mixed sample, or chromosomal copy number variation. Deploying this strategy is computationally inexpensive, can reduce the cost of sequencing by up to 80%, and used to test any organism. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04685-z.
Collapse
Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, USA
| | - Rongkui Han
- The Genome Center, University of California, Davis, USA.,The Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA
| | - Diederik Smilde
- Naktuinbouw, Postbus 40, Sotaweg 22, 2370 AA, Roelofarendsveen, The Netherlands
| | - Richard Michelmore
- The Genome Center, University of California, Davis, USA. .,Departments of Plant Sciences, Molecular and Cellular Biology, Medical Microbiology and Immunology, University of California, Davis, USA.
| |
Collapse
|
7
|
Fletcher K, Zhang L, Gil J, Han R, Cavanaugh K, Michelmore R. AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data. Genome Biol 2021; 22:115. [PMID: 33883006 PMCID: PMC8061198 DOI: 10.1186/s13059-021-02326-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/25/2021] [Indexed: 11/20/2022] Open
Abstract
Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.
Collapse
Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, USA
| | - Lin Zhang
- The Genome Center, University of California, Davis, USA
| | - Juliana Gil
- The Genome Center, University of California, Davis, USA
| | - Rongkui Han
- The Genome Center, University of California, Davis, USA
| | | | - Richard Michelmore
- The Genome Center, University of California, Davis, USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, USA
| |
Collapse
|
8
|
Wood KJ, Nur M, Gil J, Fletcher K, Lakeman K, Gann D, Gothberg A, Khuu T, Kopetzky J, Naqvi S, Pandya A, Zhang C, Maisonneuve B, Pel M, Michelmore R. Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif. PLoS Pathog 2020; 16:e1009012. [PMID: 33104763 PMCID: PMC7644090 DOI: 10.1371/journal.ppat.1009012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/05/2020] [Accepted: 09/29/2020] [Indexed: 12/11/2022] Open
Abstract
Pathogens that infect plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen Bremia lactucae by searching the predicted proteome for the WY domain, a structural fold found in effectors that has been implicated in immune suppression as well as effector recognition by host resistance proteins. We predicted 55 WY domain containing proteins in the genome of B. lactucae and found substantial variation in both sequence and domain architecture. These candidate effectors exhibit several characteristics of pathogen effectors, including an N-terminal signal peptide, lineage specificity, and expression during infection. Unexpectedly, only a minority of B. lactucae WY effectors contain the canonical N-terminal RXLR motif, which is a conserved feature in the majority of cytoplasmic effectors reported in Phytophthora spp. Functional analysis of 21 effectors containing WY domains revealed 11 that elicited cell death on wild accessions and domesticated lettuce lines containing resistance genes, indicative of recognition of these effectors by the host immune system. Only two of the 11 recognized effectors contained the canonical RXLR motif, suggesting that there has been an evolutionary divergence in sequence motifs between genera; this has major consequences for robust effector prediction in oomycete pathogens.
Collapse
Affiliation(s)
- Kelsey J. Wood
- The Genome Center, University of California, Davis, Davis, California, United States of America
- Integrative Genetics & Genomics Graduate Group, University of California, Davis, Davis, California, United States of America
| | - Munir Nur
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Juliana Gil
- The Genome Center, University of California, Davis, Davis, California, United States of America
- Plant Pathology Graduate Group, University of California, Davis, Davis, California, United States of America
| | - Kyle Fletcher
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | | | - Dasan Gann
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Ayumi Gothberg
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Tina Khuu
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Jennifer Kopetzky
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Sanye Naqvi
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Archana Pandya
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Chi Zhang
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | | | | | - Richard Michelmore
- The Genome Center, University of California, Davis, Davis, California, United States of America
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, Davis, California, United States of America
| |
Collapse
|
9
|
Fletcher K, Gil J, Bertier LD, Kenefick A, Wood KJ, Zhang L, Reyes-Chin-Wo S, Cavanaugh K, Tsuchida C, Wong J, Michelmore R. Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae. Nat Commun 2019; 10:2645. [PMID: 31201315 PMCID: PMC6570648 DOI: 10.1038/s41467-019-10550-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce globally. This oomycete is highly variable and rapidly overcomes resistance genes and fungicides. The use of multiple read types results in a high-quality, near-chromosome-scale, consensus assembly. Flow cytometry plus resequencing of 30 field isolates, 37 sexual offspring, and 19 asexual derivatives from single multinucleate sporangia demonstrates a high incidence of heterokaryosis in B. lactucae. Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence. Therefore, selection should be considered as acting on a population of nuclei within coenocytic mycelia. This provides evolutionary flexibility to the pathogen enabling rapid adaptation to different repertoires of host resistance genes and other challenges. The advantages of asexual persistence of heterokaryons may have been one of the drivers of selection that resulted in the loss of uninucleate zoospores in multiple downy mildews.
Collapse
Affiliation(s)
- Kyle Fletcher
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Juliana Gil
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, 95616, USA
| | - Lien D Bertier
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Aubrey Kenefick
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Kelsey J Wood
- Genome Center, University of California, Davis, CA, 95616, USA
- Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616, USA
| | - Lin Zhang
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Sebastian Reyes-Chin-Wo
- Genome Center, University of California, Davis, CA, 95616, USA
- Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616, USA
- Bayer Crop Science, 37437 CA-16, Woodland, CA, 95695, USA
| | - Keri Cavanaugh
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Cayla Tsuchida
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, 95616, USA
- Arcadia Biosciences, Davis, CA, 95616, USA
| | - Joan Wong
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA
- Pacific Biosciences of California, Inc., Menlo Park, CA, 94025, USA
| | - Richard Michelmore
- Genome Center, University of California, Davis, CA, 95616, USA.
- Departments of Plant Sciences, Molecular and Cellular Biology, Medical Microbiology and Immunology, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
10
|
Fletcher K, Klosterman SJ, Derevnina L, Martin F, Bertier LD, Koike S, Reyes-Chin-Wo S, Mou B, Michelmore R. Comparative genomics of downy mildews reveals potential adaptations to biotrophy. BMC Genomics 2018; 19:851. [PMID: 30486780 PMCID: PMC6264045 DOI: 10.1186/s12864-018-5214-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/31/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. RESULTS We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp. CONCLUSIONS We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
Collapse
Affiliation(s)
- Kyle Fletcher
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven J. Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lida Derevnina
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Present Address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Frank Martin
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lien D. Bertier
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven Koike
- UC Davis Cooperative Extension Monterey County, Salinas, CA 93901 USA
- Present Address: TriCal Diagnostics, Hollister, CA 95023 USA
| | - Sebastian Reyes-Chin-Wo
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Beiquan Mou
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Richard Michelmore
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, 95616 USA
| |
Collapse
|
11
|
Fletcher K, Baines D. The effects of acaricide treatment of sheep on red grouse Lagopus lagopus scotica tick burdens and productivity in a multi-host system. Med Vet Entomol 2018; 32:235-243. [PMID: 29194726 DOI: 10.1111/mve.12282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/14/2017] [Accepted: 10/07/2017] [Indexed: 06/07/2023]
Abstract
Ixodes ricinus (Ixodida: Ixodidae) ticks are of economic and pathogenic importance across Europe. Within the uplands of the U.K., management to reduce ticks is undertaken to benefit red grouse Lagopus lagopus scotica (Galliformes: Phasianidae). Management strategies focus on the acaricide treatment of domestic sheep Ovis aries (Artiodactyla: Bovidae), but the effectiveness of this is less certain in the presence of wild hosts, particularly red deer Cervus elaphus (Artiodactyla: Cervidae) and mountain hare Lepus timidus (Lagomorpha: Leporidae). This study examines the effects of sheep management on grouse tick burdens and productivity using sites with a range of wild host densities. Sites at which applications of acaricide were more frequent had lower tick burdens; this relationship was similar on sites with a range of deer densities. However, no direct link was detected between acaricide treatment interval and grouse productivity. Sites with higher deer densities had higher grouse tick burdens and lower productivity [mean ± standard error (SE) young : adult ratio: 1.2 ± 0.2] compared with sites with lower deer densities (mean ± SE young : adult ratio: 1.8 ± 0.1). Sites with higher grouse brood sizes and higher proportions of hens with broods were also those with higher mountain hare abundance indices. This study highlights the importance of the frequent treatment of sheep with acaricide to reduce tick burdens on grouse, even in the presence of wild hosts.
Collapse
Affiliation(s)
- K Fletcher
- Game and Wildlife Conservation Trust, Perth, U.K
| | - D Baines
- Game and Wildlife Conservation Trust, Eggleston, U.K
| |
Collapse
|
12
|
Abstract
A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.
Collapse
Affiliation(s)
- Kyle Fletcher
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA
| | - Richard Michelmore
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA.
| |
Collapse
|
13
|
Roper DR, De la Salle B, Soni V, Fletcher K, Green JA. Abrogation of red blood cell G6PD enzyme activity through Heat treatment: development of survey material for the UK NEQAS G6PD scheme. Int J Lab Hematol 2017; 39:308-316. [PMID: 28318100 DOI: 10.1111/ijlh.12627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/28/2016] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Participation in external quality assessment (EQA) is central to the maintenance of high-quality laboratory results in patient diagnosis and clinical trials. Laboratories in the TAF112582 DETECTIVE study (ClinicalTrials.gov identifier: NCT01376167) are enrolled in the United Kingdom National Quality Assessment Scheme (UK NEQAS) for glucose-6-phosphate dehydrogenase (G6PD) quantitative assay, which utilizes ovine (sheep) blood as a readily available source of apparently G6PD-deficient survey material. A substitute for sheep blood was sought because some non-UK sites in the study encountered participation difficulties due to the strict regulations on the import of sheep blood into their countries. METHODS G6PD activity in normal human donor blood was abrogated by the action of heat under controlled conditions. Residual G6PD activity in the heated samples was measured by UK NEQAS using the Trinity Biotech 345 kit (Trinity Biotech) and a Jenway 6715 UV/Vis spectrophotometer with external temperature control to monitor enzyme kinetics and linearity over a set time. Heat-treated material was also assayed for G6PD activity and assessed for its acceptability as EQA survey material by selected UK laboratories. RESULTS Blood heated at 45 °C for 15 h showed a reduction in G6PD activity of 76.3 ± 4.6% (n = 6) and was considered acceptable as EQA material in terms of appearance and behaviour by the majority of UK sites in the trial. CONCLUSIONS We have developed a simple heat-treatment procedure to produce EQA survey material with low/intermediate G6PD activity, similar to that found in females heterozygous for G6PD deficiency.
Collapse
Affiliation(s)
- D R Roper
- GlaxoSmithKline, Uxbridge, UK.,UK NEQAS Haematology, Watford, UK
| | | | - V Soni
- UK NEQAS Haematology, Watford, UK
| | | | | |
Collapse
|
14
|
Salih Z, Conway A, Papaxoinis G, Patrao A, Fletcher K, Noble R, Owen-Holt V, Mansoor W. Prognostic significance of neutrophil to lymphocyte ratio (NLR) in patients (pts) with resectable gastric/gastroesophageal junction (GOJ) adenocarcinoma undergoing perioperative chemotherapy. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw371.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
15
|
Bayes AJ, McClure G, Fletcher K, Román Ruiz Del Moral YE, Hadzi-Pavlovic D, Stevenson JL, Manicavasagar VL, Parker GB. Differentiating the bipolar disorders from borderline personality disorder. Acta Psychiatr Scand 2016; 133:187-95. [PMID: 26432099 DOI: 10.1111/acps.12509] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/08/2015] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To identify features differentiating bipolar disorder (BP) from borderline personality disorder (BPD) and with each condition variably defined. METHOD Participants were assigned a BP or BPD diagnosis on the basis of DSM criteria and, separately, by clinical judgment, and undertook a diagnostic interview and completed self-report measures. RESULTS Predictors of BPD status varied according to diagnostic decisions, but with the most consistent items being childhood sexual abuse, childhood depersonalization, personality variables relating to relationship difficulties and sensitivity to criticism, and the absence of any BP family history. Across diagnostic groups, personality measure items alone predicted diagnostic allocation with an accuracy of 81-84%, the refined study variables other than hypo/manic features improved the classification rates to 88%, and when the presence or absence of hypo/manic features was added, classification rates increased to 92-95%. CONCLUSION Study findings indicate that BPD can be differentiated from BP with a high degree of accuracy.
Collapse
Affiliation(s)
- A J Bayes
- School of Psychiatry, The University of New South Wales, Sydney, NSW, Australia
| | - G McClure
- School of Psychiatry, The University of New South Wales, Sydney, NSW, Australia.,The Black Dog Institute, Sydney, NSW, Australia
| | - K Fletcher
- School of Psychiatry, The University of New South Wales, Sydney, NSW, Australia.,The Black Dog Institute, Sydney, NSW, Australia
| | | | - D Hadzi-Pavlovic
- School of Psychiatry, The University of New South Wales, Sydney, NSW, Australia.,The Black Dog Institute, Sydney, NSW, Australia
| | | | | | - G B Parker
- School of Psychiatry, The University of New South Wales, Sydney, NSW, Australia.,The Black Dog Institute, Sydney, NSW, Australia
| |
Collapse
|
16
|
Fletcher K, Uljević A, Tsirigoti A, Antolić B, Katsaros C, Nikolić V, van West P, Küpper FC. New record and phylogenetic affinities of the oomycete Olpidiopsis feldmanni infecting Asparagopsis sp. (Rhodophyta). Dis Aquat Organ 2015; 117:45-57. [PMID: 26575155 DOI: 10.3354/dao02930] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A new geographic record of the oomycete Olpidiopsis feldmanni infecting the tetrasporophytic stage of the red alga Asparagopsis sp. from the Adriatic Sea, confirmed through morphological identification, allowed us to expand previous observations of this organism. Ultrastructural investigations of environmental material showed a large central vacuole and a cell wall thicker than previously reported from other basal oomycete pathogens of algae. Phylogenetic analysis closely associates O. feldmanni to O. bostrychiae concurrent with structural observations. This constitutes the first genetic characterisation of an Olpidiopsis species that was initially described before 1960, adding to the genetic data of 3 other marine Olpidiopsis species established and genetically characterised in the last 2 decades. The paper discusses concurrences of the ultrastructural observations made here and in previous studies of the marine Olpidiopsis species with those made on the freshwater species.
Collapse
Affiliation(s)
- Kyle Fletcher
- Oceanlab, University of Aberdeen, Newburgh, AB41 6AA, UK
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Fletcher K. Very Low Cost Intensive Therapeutic Support and Long Term Monitoring for Patients with Alcohol Dependence Using New Technology. Eur Psychiatry 2015. [DOI: 10.1016/s0924-9338(15)31902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
18
|
|
19
|
Parker G, Fletcher K, Blanch B, Greenfield L. The 'real world' utility of a web-based bipolar disorder screening measure. Acta Psychiatr Scand 2013; 127:373-80. [PMID: 23039131 DOI: 10.1111/acps.12017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/03/2012] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To determine whether those completing a self-report bipolar self-test measure and identified as having a likely bipolar disorder judged the self-test as useful and had a subsequent superior illness course. METHOD We invited those completing the web-based Mood Swings Questionnaire (or MSQ) to provide contact details and contribute to a 3-month study evaluating their responses to being identified as having a likely bipolar disorder, any subsequent action taken and the impact of such actions on their illness trajectory. RESULTS We analysed data received from 665 participants screening 'positive' on the MSQ and completing baseline and 3-month follow-up data. High rates of satisfaction with the MSQ were quantified, with respondents viewing the measure as informative, validating and/or motivating. Of those receiving a confirmed bipolar diagnosis, such clarification occurred on average 12 years after their first depressive episode. Most implemented self-management strategies irrespective of whether seeking formal diagnostic clarification or not. Participants improved on depressive, quality of life and overall functioning measures over the study period, but with results indicating (via analysis of three sample subsets differing by the degree of 'actions taken') that those who took assertive action and had the diagnosis confirmed had the most superior outcome. CONCLUSION This is the first study to formally evaluate the clinical impact of a self-report bipolar disorder screening measure. High acceptance and superior outcomes quantified for those acting assertively in response to such a new diagnosis argue for its 'real world' utility.
Collapse
Affiliation(s)
- G Parker
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia.
| | | | | | | |
Collapse
|
20
|
Casey DT, Frenje JA, Johnson MG, Séguin FH, Li CK, Petrasso RD, Glebov VY, Katz J, Magoon J, Meyerhofer DD, Sangster TC, Shoup M, Ulreich J, Ashabranner RC, Bionta RM, Carpenter AC, Felker B, Khater HY, LePape S, MacKinnon A, McKernan MA, Moran M, Rygg JR, Yeoman MF, Zacharias R, Leeper RJ, Fletcher K, Farrell M, Jasion D, Kilkenny J, Paguio R. The magnetic recoil spectrometer for measurements of the absolute neutron spectrum at OMEGA and the NIF. Rev Sci Instrum 2013; 84:043506. [PMID: 23635195 DOI: 10.1063/1.4796042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The neutron spectrum produced by deuterium-tritium (DT) inertial confinement fusion implosions contains a wealth of information about implosion performance including the DT yield, ion-temperature, and areal-density. The Magnetic Recoil Spectrometer (MRS) has been used at both the OMEGA laser facility and the National Ignition Facility (NIF) to measure the absolute neutron spectrum from 3 to 30 MeV at OMEGA and 3 to 36 MeV at the NIF. These measurements have been used to diagnose the performance of cryogenic target implosions to unprecedented accuracy. Interpretation of MRS data requires a detailed understanding of the MRS response and background. This paper describes ab initio characterization of the system involving Monte Carlo simulations of the MRS response in addition to the commission experiments for in situ calibration of the systems on OMEGA and the NIF.
Collapse
Affiliation(s)
- D T Casey
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Casey DT, Frenje JA, Gatu Johnson M, Séguin FH, Li CK, Petrasso RD, Glebov VY, Katz J, Knauer JP, Meyerhofer DD, Sangster TC, Bionta RM, Bleuel DL, Döppner T, Glenzer S, Hartouni E, Hatchett SP, Le Pape S, Ma T, MacKinnon A, McKernan MA, Moran M, Moses E, Park HS, Ralph J, Remington BA, Smalyuk V, Yeamans CB, Kline J, Kyrala G, Chandler GA, Leeper RJ, Ruiz CL, Cooper GW, Nelson AJ, Fletcher K, Kilkenny J, Farrell M, Jasion D, Paguio R. Measuring the absolute deuterium-tritium neutron yield using the magnetic recoil spectrometer at OMEGA and the NIF. Rev Sci Instrum 2012; 83:10D912. [PMID: 23126915 DOI: 10.1063/1.4738657] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A magnetic recoil spectrometer (MRS) has been installed and extensively used on OMEGA and the National Ignition Facility (NIF) for measurements of the absolute neutron spectrum from inertial confinement fusion implosions. From the neutron spectrum measured with the MRS, many critical implosion parameters are determined including the primary DT neutron yield, the ion temperature, and the down-scattered neutron yield. As the MRS detection efficiency is determined from first principles, the absolute DT neutron yield is obtained without cross-calibration to other techniques. The MRS primary DT neutron measurements at OMEGA and the NIF are shown to be in excellent agreement with previously established yield diagnostics on OMEGA, and with the newly commissioned nuclear activation diagnostics on the NIF.
Collapse
Affiliation(s)
- D T Casey
- Plasma Science and Fusion Center, MIT, Cambridge, Massachusetts 02139, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Sheppard JP, Singh S, Fletcher K, McManus RJ, Mant J. Impact of age and sex on primary preventive treatment for cardiovascular disease in the West Midlands, UK: cross sectional study. BMJ 2012; 345:e4535. [PMID: 22791787 PMCID: PMC3395734 DOI: 10.1136/bmj.e4535] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/23/2012] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To establish the impact of age and sex on primary preventive treatment for cardiovascular disease in a typical primary care population. DESIGN Cross sectional study of anonymised patient records. PARTICIPANTS All 41,250 records of patients aged ≥ 40 registered at 19 general practices in the West Midlands, United Kingdom, were extracted and analysed. MAIN OUTCOME MEASURES Patients' demographics, risk factors for cardiovascular disease (blood pressure, total cholesterol concentration), and prescriptions for primary preventive drugs were extracted from patients' records. Patients were subdivided into five year age bands up to 85 (patients aged ≥ 85 were analysed as one group) and prescribing trends across the population were assessed by estimating the proportion of patients prescribed with antihypertensive drug or statin drug, or both, in each group. RESULTS Of the 41,250 records screened in this study, 36,679 (89%) patients did not have a history of cardiovascular disease and therefore could be considered for primary preventive treatment. The proportion receiving antihypertensive drugs increased with age (from 5% (378/6978) aged 40-44 to 57% (621/1092) aged ≥ 85) as did the proportion taking statins up to the age of 74 (from 3% (201/6978) aged 40-44 to 29% (675/2367) aged 70-74). In those aged 75 and above, the odds of a receiving prescription for a statin (relative to the 40-44 age group) decreased with every five year increment in age (odds ratio 12.9 (95% confidence interval 10.8 to 15.3) at age 75-79 to 5.7 (4.6 to 7.2) at age ≥ 85; P<0.001). There were no consistent differences in prescribing trends by sex. CONCLUSIONS Previously described undertreatment of women in secondary prevention of cardiovascular disease was not observed for primary prevention. Low use of statins in older people highlights the need for a stronger evidence base and clearer guidelines for people aged over 75.
Collapse
Affiliation(s)
- J P Sheppard
- Primary Care Clinical Sciences, NIHR School for Primary Care Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - S Singh
- Primary Care Clinical Sciences, NIHR School for Primary Care Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - K Fletcher
- Primary Care Clinical Sciences, NIHR School for Primary Care Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - R J McManus
- Primary Care Health Sciences, NIHR School for Primary Care Research, University of Oxford, Oxford OX33 6GG, UK
| | - J Mant
- Primary Care Unit, University of Cambridge, Cambridge CB2 0SR, UK
| |
Collapse
|
23
|
Roalfe AK, Bryant TL, Davies MH, Hackett TG, Saba S, Fletcher K, Lip GYH, Hobbs FDR, Mant J. A cross-sectional study of quality of life in an elderly population (75 years and over) with atrial fibrillation: secondary analysis of data from the Birmingham Atrial Fibrillation Treatment of the Aged study. Europace 2012; 14:1420-7. [DOI: 10.1093/europace/eus102] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
24
|
Parker G, Fletcher K, Hadzi-Pavlovic D. Is context everything to the definition of clinical depression? A test of the Horwitz and Wakefield postulate. J Affect Disord 2012; 136:1034-8. [PMID: 21183224 DOI: 10.1016/j.jad.2010.11.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 11/23/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
Abstract
BACKGROUND In arguing for the need to distinguish clinical depression from sadness, Horwitz and Wakefield argued for weighting consideration to nuances of life event stressors. Their definition of clinical depression corresponds to the concept of endogenous depression or melancholia, while their model would position reactive (or context specific) non-melancholic depressive disorders more as manifestations of 'sadness' rather than as clinical depression. METHOD We test their postulate by examining the extent to which 141 clinically diagnosed melancholic and non-melancholic depressed patients reported episodes as being preceded by a life event stressor or not--and the salience of any life stressor to episode onset and severity. RESULTS While melancholic patients were more likely than non-melancholic patients to report episodes coming 'out of the blue' and to be more severe than might be expected from the severity of antecedent stressors, differences were more ones of degree and not absolute. Such context variables appeared, however, to differentiate melancholic and non-melancholic patients more consistently than depression symptom variables. As depression severity and impairment levels did not differ across the melancholic and non-melancholic patients, findings were unlikely to be artefacts of such factors. CONCLUSIONS The study finds some support for the Horwitz and Wakefield hypothesis of clinical (or, at least melancholic) depression requiring independence of context or an antecedent stressor, but with precision likely to be compromised by nuances intrinsic to assessment of life event stressors and their contribution to depression onset, difficulties in defining valid 'melancholic' and 'non-melancholic' depressive sub-groups and the parsimony of the hypothesis.
Collapse
Affiliation(s)
- G Parker
- School of Psychiatry, University of New South Wales, Sydney, Australia.
| | | | | |
Collapse
|
25
|
|
26
|
Ammoun S, Zhou L, Barczyk M, Hilton D, Hafizi S, Hanemann C, Lehnus KS, Donovan LK, Pilkington GJ, An Q, Anderson IA, Thomson S, Bailey M, Lekka E, Law J, Davis C, Banfill K, Loughrey C, Hatfield P, Bax D, Elliott R, Bishop R, Taylor K, Marshall L, Gaspar N, Viana-Pereira M, Reis R, Renshaw J, Ashworth A, Lord C, Jones C, Bellamy C, Shaw L, Alder J, Shorrocks A, Lea R, Birks S, Burnet M, Pilkington G, Bruch JD, Ho J, Watts C, Price SJ, Camp S, Apostolopoulos V, Mehta A, Roncaroli F, Nandi D, Clark B, Mackinnon M, MacLeod N, Stewart W, Chalmers A, Cole A, Hanna G, Bailie K, Conkey D, Harney J, Darlow C, Chapman S, Mohsen L, Price S, Donovan L, Birks S, Pilkington G, Dyer H, Lord H, Fletcher K, das Nair R, MacNiven J, Basu S, Byrne P, Glancz L, Critchley G, Grech-Sollars M, Saunders D, Phipps K, Clayden J, Clark C, Greco A, Acquati S, Marino S, Hammouche S, Wilkins SP, Smith T, Brodbelt A, Hammouche S, Clark S, Wong AHL, Eldridge P, Farah JO, Ho J, Bruch J, Watts C, Price S, Lamb G, Smith S, James A, Glegg M, Jeffcote T, Boulos S, Robbins P, Knuckey N, Banigo A, Brodbelt AR, Jenkinson MD, Jeyapalan JN, Mumin MA, Forshew T, Lawson AR, Tatevossian RG, Jacques TS, Sheer D, Kilday J, Wright K, Leavy S, Lowe J, Schwalbe E, Clifford S, Gilbertson R, Coyle B, Grundy R, Kinsella P, Clynes M, Amberger-Murphy V, Barron N, Lambert SR, Jones D, Pearson D, Ichimura I, Collins V, Steele L, Sinha P, Chumas P, Tyler J, Ogawa D, Chiocca E, DeLay M, Bronisz A, Nowicki M, Godlewski J, Lawler S, Lee MK, Javadpour M, Jenkinson MD, Lekka E, Abel P, Dawson T, Lea B, Davis C, Lim CSK, Grundy PL, Pendleton M, Lord H, Mackinnon M, Williamson A, James A, Stewart W, Clark B, Chalmers A, Merve A, Zhang X, Marino S, Miller S, Rogers HA, Lyon P, Rand V, Adamowicz-Brice M, Clifford SC, Hayden JT, Dyer S, Pfister S, Korshunov A, Brundler MA, Lowe J, Coyle B, Grundy RG, Nankivell M, Mulvenna P, Barton R, Wilson P, Faivre-Finn C, Pugh C, Langley R, Ngoga D, Tennant D, Williams A, Moss P, Cruickshank G, Owusu-Agyemang K, Bell S, Stewart W, St.George J, Piccirillo SG, Watts C, Qadri S, Pirola E, Jenkinson M, Brodbelt A, Rahman R, Rahman C, Smith S, MacArthur D, Rose F, Shakesheff K, Grundy R, Carroll C, Watson P, Hawkins M, Spoudeas H, Walker D, Holland T, Ring H, Rooney A, McNamara S, Mackinnon M, Fraser M, Rampling R, Carson A, Grant R, Royds J, Al Nadaf S, Ahn A, Chen YJ, Wiles A, Jellinek D, Braithwaite A, Baguley B, MacFarlane M, Hung N, Slatter T, Rusbridge S, Walmsley N, Griffiths S, Wilford P, Rees J, Ryan D, Watts C, Liu P, Galavotti S, Shaked-Rabi M, Tulchinsky E, Brandner S, Jones C, Salomoni P, Schulte A, Gunther HS, Zapf S, Riethdorf S, Westphal M, Lamszus K, Selvanathan SK, Hammouche S, Salminen HJ, Jenkinson MD, Setua S, Watts C, Welland ME, Shevtsov M, Khachatryan W, Kim A, Samochernych K, Pozdnyakov A, Guzhova IV, Romanova IV, Margulis B, Smith S, Rahman R, Rahman C, Barrow J, Macarthur D, Rose F, Grundy R, Smith S, Long A, Barrow J, Macarthur D, Coyle B, Grundy R, Maherally Z, Smith JR, Dickson L, Pilkington GJ, Prabhu S, Harris F, Lea R, Snape TJ, Sussman M, Wilne S, Whitehouse W, Chow G, Liu JF, Walker D, Snape T, Karakoula A, Rowther F, Warr T, Williamson A, Mackinnon M, Zisakis A, Varsos V, Panteli A, Karypidou O, Zampethanis A, Fotovati A, Abu-Ali S, Wang PS, Deleyrolle L, Lee C, Triscott J, Chen JY, Franciosi S, Nakamura Y, Sugita Y, Uchiumi T, Kuwano M, Leavitt BR, Singh SK, Jury A, Jones C, Wakimoto H, Reynolds BA, Pallen CJ, Dunn SE, Shepherd S, Scott S, Bowyer D, Wallace L, Hacking B, Mohsen L, Jena R, Gillard J, Price S, Lee C, Fotovati A, Verraeult M, Wakimoto H, Reynolds B, Dunham C, Bally M, Hukin J, Singhal S, Singh S, Dunn S. Abstracts from the 2011 BNOS Conference, June 29 - July 1, 2011, Homerton College, Cambridge. Neuro Oncol 2011. [DOI: 10.1093/neuonc/nor144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
27
|
Hobbs FDR, Roalfe AK, Lip GYH, Fletcher K, Fitzmaurice DA, Mant J. Performance of stroke risk scores in older people with atrial fibrillation not taking warfarin: comparative cohort study from BAFTA trial. BMJ 2011; 342:d3653. [PMID: 21700651 PMCID: PMC3121229 DOI: 10.1136/bmj.d3653] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/24/2011] [Indexed: 01/20/2023]
Abstract
OBJECTIVE To compare the predictive power of the main existing and recently proposed schemes for stratification of risk of stroke in older patients with atrial fibrillation. DESIGN Comparative cohort study of eight risk stratification scores. SETTING Trial of thromboprophylaxis in stroke, the Birmingham Atrial Fibrillation in the Aged (BAFTA) trial. PARTICIPANTS 665 patients aged 75 or over with atrial fibrillation based in the community who were randomised to the BAFTA trial and were not taking warfarin throughout or for part of the study period. MAIN OUTCOME MEASURES Events rates of stroke and thromboembolism. RESULTS 54 (8%) patients had an ischaemic stroke, four (0.6%) had a systemic embolism, and 13 (2%) had a transient ischaemic attack. The distribution of patients classified into the three risk categories (low, moderate, high) was similar across three of the risk stratification scores (revised CHADS(2), NICE, ACC/AHA/ESC), with most patients categorised as high risk (65-69%, n = 460-457) and the remaining classified as moderate risk. The original CHADS(2) (Congestive heart failure, Hypertension, Age ≥ 75 years, Diabetes, previous Stroke) score identified the lowest number as high risk (27%, n = 180). The incremental risk scores of CHADS(2), Rietbrock modified CHADS(2), and CHA(2)DS(2)-VASc (CHA(2)DS(2)-Vascular disease, Age 65-74 years, Sex) failed to show an increase in risk at the upper range of scores. The predictive accuracy was similar across the tested schemes with C statistic ranging from 0.55 (original CHADS(2)) to 0.62 (Rietbrock modified CHADS(2)), with all except the original CHADS(2) predicting better than chance. Bootstrapped paired comparisons provided no evidence of significant differences between the discriminatory ability of the schemes. CONCLUSIONS Based on this single trial population, current risk stratification schemes in older people with atrial fibrillation have only limited ability to predict the risk of stroke. Given the systematic undertreatment of older people with anticoagulation, and the relative safety of warfarin versus aspirin in those aged over 70, there could be a pragmatic rationale for classifying all patients over 75 as "high risk" until better tools are available.
Collapse
Affiliation(s)
- F D R Hobbs
- Department of Primary Care Health Sciences, University of Oxford, Oxford OX1 2ET, United Kingdom.
| | | | | | | | | | | |
Collapse
|
28
|
Parker G, Fletcher K, Barrett M, Breakspear M, Rees AM. Evaluating the first 1000 patients referred to a specialist depression clinic: a case for tertiary referral facilities. J Affect Disord 2011; 131:52-8. [PMID: 21130500 DOI: 10.1016/j.jad.2010.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 11/10/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
Abstract
BACKGROUND We report on the assessment and outcome of the first 1000 patients referred to a tertiary referral depression clinic established to assess the utility of diagnostic sub-typing on clinical course of illness. METHODS Diagnostic, treatment recommendations, prognostic judgments and 12-week outcome data were examined. RESULTS Nearly 40% of those with a primary mood disorder were diagnosed with bipolar disorder, of whom three-quarters received such a diagnosis for the first time. Alternative diagnoses or formulations were provided for 68% of the total sample, with the therapeutic paradigm altered for the majority (86%) of patients. Improvement rates were indicative of a higher level of improvement in those diagnosed with bipolar disorder (some 70%) compared to those with unipolar disorders (some 60%). Overall, however, rates of 'full remission' were low, being 2% and up to 12% for bipolar and unipolar patients respectively and perhaps reflecting the tertiary nature of the assessing clinical facility. Baseline clinician predictions were in the order of 60% accuracy in predicting outcome, irrespective of diagnostic grouping. LIMITATIONS Anticipation factors (e.g. attending a specialist tertiary referral service) may have contributed non-specifically to outcome. Use of clinician-derived diagnoses rather than strict DSM-IV criteria limits comparisons to other studies. CONCLUSIONS The high rates of a first-time bipolar diagnosis suggest that detection and diagnosis of this condition continues to be problematic. Low remission rates underline the chronic nature of many mood disorders, and the need for ongoing management given the high risk of relapse. Our findings offer support for the importance of identifying bipolar disorder and distinguishing depressive sub-types in order to shape more targeted treatments, a task that might be advanced by the establishment of more tertiary referral services.
Collapse
Affiliation(s)
- G Parker
- School of Psychiatry, University of New South Wales, Sydney, Australia.
| | | | | | | | | |
Collapse
|
29
|
Fletcher K, Mant J, Roalfe A, Hobbs FDR. Impact of study design on recruitment of patients to a primary care trial: an observational time series analysis of the Birmingham Atrial Fibrillation Treatment of the Aged (BAFTA) study. Fam Pract 2010; 27:691-7. [PMID: 20610490 DOI: 10.1093/fampra/cmq050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND recruitment targets to randomized controlled trials (RCTs) are often not met. Many interventions are used to improve recruitment but there is little empirical evidence on whether these approaches work. OBJECTIVE to examine whether changes to the design and conduct of a primary care-based RCT were associated with changes in patient recruitment. METHODS an observational time series analysis of recruitment to a primary care-based multi-centre RCT of aspirin versus warfarin for stroke prevention, which involved 330 practices. Several changes to the trial protocol and procedures were made over the 4 years of patient recruitment. For each quarter throughout the recruitment period, the recruitment rate per 1000 total population in active practices was calculated. RESULTS the recruitment target of 930 patients was exceeded. Fluctuations in recruitment rate occurred during the recruitment period. Following protocol changes aimed to reduce clinical workload, there was a significant increase in recruitment during the final 6 months of the study, during a period when there was not a similarly large increase in the total population available. CONCLUSIONS these findings suggest that the conduct of a trial is an important consideration if studies are to recruit successfully. Expanding the number of centres may not be the most effective way to improve recruitment.
Collapse
Affiliation(s)
- K Fletcher
- Department of Primary Care and General Practice, Clinical Sciences Building, University of Birmingham, Birmingham B15 2TT, UK.
| | | | | | | |
Collapse
|
30
|
Abstract
OBJECTIVE We examine the depressive symptom profile of bipolar II disorder patients compared with a comparator (composite) group of those with unipolar depression, with stratification by melancholic and non-melancholic subtypes. METHOD Out-patients (n = 394) attending a specialist depression clinic comprised the sample. Data on severity and prototypic status of depressive symptoms were analysed. RESULTS Age-matched analyses revealed minimal differentiation between bipolar II and composite unipolar groups. Stratified analyses suggested that 'bipolar II depression' more closely approximated melancholic depression in terms of psychomotor and cognitive slowing. Severity-based analyses and prototypic symptom patterns yielded differing results, suggesting that definition of bipolar II depression is influenced by rating strategies, and age. CONCLUSION We found limited differentiation of bipolar II depression from unipolar, melancholic and non-melancholic depression. Differences suggested previously may reflect age, gender and severity differences, highlighting the need for appropriately matched groups in defining bipolar II depression.
Collapse
Affiliation(s)
- G B Parker
- School of Psychiatry, University of New South Wales and Black Dog Institute, Prince of Wales Hospital, Randwick 2031, Sydney, Australia.
| | | |
Collapse
|
31
|
Mant J, Doust J, Roalfe A, Barton P, Cowie MR, Glasziou P, Mant D, McManus RJ, Holder R, Deeks J, Fletcher K, Qume M, Sohanpal S, Sanders S, Hobbs FDR. Systematic review and individual patient data meta-analysis of diagnosis of heart failure, with modelling of implications of different diagnostic strategies in primary care. Health Technol Assess 2009; 13:1-207, iii. [PMID: 19586584 DOI: 10.3310/hta13320] [Citation(s) in RCA: 236] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES To assess the accuracy in diagnosing heart failure of clinical features and potential primary care investigations, and to perform a decision analysis to test the impact of plausible diagnostic strategies on costs and diagnostic yield in the UK health-care setting. DATA SOURCES MEDLINE and CINAHL were searched from inception to 7 July 2006. 'Grey literature' databases and conference proceedings were searched and authors of relevant studies contacted for data that could not be extracted from the published papers. REVIEW METHODS A systematic review of the clinical evidence was carried out according to standard methods. Individual patient data (IPD) analysis was performed on nine studies, and a logistic regression model to predict heart failure was developed on one of the data sets and validated on the other data sets. Cost-effectiveness modelling was based on a decision tree that compared different plausible investigation strategies. RESULTS Dyspnoea was the only symptom or sign with high sensitivity (89%), but it had poor specificity (51%). Clinical features with relatively high specificity included history of myocardial infarction (89%), orthopnoea (89%), oedema (72%), elevated jugular venous pressure (70%), cardiomegaly (85%), added heart sounds (99%), lung crepitations (81%) and hepatomegaly (97%). However, the sensitivity of these features was low, ranging from 11% (added heart sounds) to 53% (oedema). Electrocardiography (ECG), B-type natriuretic peptides (BNP) and N-terminal pro-B-type natriuretic peptides (NT-proBNP) all had high sensitivities (89%, 93% and 93% respectively). Chest X-ray was moderately specific (76-83%) but insensitive (67-68%). BNP was more accurate than ECG, with a relative diagnostic odds ratio of ECG/BNP of 0.32 (95% CI 0.12-0.87). There was no difference between the diagnostic accuracy of BNP and NT-proBNP. A model based upon simple clinical features and BNP derived from one data set was found to have good validity when applied to other data sets. A model substituting ECG for BNP was less predictive. From this a simple clinical rule was developed: in a patient presenting with symptoms such as breathlessness in whom heart failure is suspected, refer directly to echocardiography if the patient has a history of myocardial infarction or basal crepitations or is a male with ankle oedema; otherwise, carry out a BNP test and refer for echocardiography depending on the results of the test. On the basis of the cost-effectiveness analysis carried out, such a decision rule is likely to be considered cost-effective to the NHS in terms of cost per additional case detected. The cost-effectiveness analysis further suggested that, if likely benefit to the patient in terms of improved life expectancy is taken into account, the optimum strategy would be to refer all patients with symptoms suggestive of heart failure directly for echocardiography. CONCLUSIONS The analysis suggests the need for important changes to the NICE recommendations. First, BNP (or NT-proBNP) should be recommended over ECG and, second, some patients should be referred straight for echocardiography without undergoing any preliminary investigation. Future work should include evaluation of the clinical rule described above in clinical practice.
Collapse
Affiliation(s)
- J Mant
- Primary Care Clinical Sciences, University of Birmingham, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Abstract
BACKGROUND Melancholia has long resisted classification, with many of its suggested markers lacking specificity. The imprecision of depressive symptoms, in addition to self-report biases, has limited the capacity of existing measures to delineate melancholic depression as a distinct subtype. Our aim was to develop a self-report measure differentiating melancholic and non-melancholic depression, weighting differentiation by prototypic symptoms and determining its comparative classification success with a severity-based strategy. METHOD Consecutively recruited depressed out-patients (n=228) rated 32 symptoms by prototypic or 'characteristic' relevance (using the Q-sort strategy) and severity [using the Severity-based Depression Rating System (SDRS) strategy]. Clinician diagnosis of melancholic/non-melancholic depression was the criterion measure, but two other formal measures of melancholia (Newcastle and DSM-IV criteria) were also tested. RESULTS The prevalence of 'melancholia' ranged from 20.9% to 54.2% across the subtyping measures. The Q-sort measure had the highest overall correct classification rate in differentiating melancholic and non-melancholic depression (81.6%), with such decisions supported by validation analyses. CONCLUSIONS In differentiating a melancholic subtype or syndrome, prototypic symptoms should be considered as a potential alternative to severity-based ratings.
Collapse
Affiliation(s)
- G Parker
- School of Psychiatry, University of New South Wales, Sydney, Australia.
| | | | | | | | | | | |
Collapse
|
33
|
Abstract
BACKGROUND Case management of vulnerable older people by Community Matrons has been introduced into the UK. A locally designed case management approach, The Specialist Workers for Older People (SWOP) Service, was implemented by a Central England Primary Care Trust. Here we report an evaluation of this service. METHODS Before and after study of 418 people (207 before; 211 after) aged > or =75 at high risk of emergency hospital admission. SWOPs carry out assessments of social and medical needs, produce individual care plans, coordinate care and refer to appropriate agencies. Univariable analysis was used to determine the association of SWOPs on changes in hospital admission rates and primary care workload. RESULTS There was a non-significant reduction in hospital admissions from 0.91 to 0.67 per patient. There was a significant increase in routine GP surgery visits, from an average 1.3 to 2.6 per patient. The number of emergency home visits decreased from an average 2.8 to 1.1 per patient (P < 0.001). CONCLUSIONS Case management might reduce hospital admissions and is potentially a cost-effective service. However, not all case management schemes are successful. With the introduction of Community Matrons, it is important to understand what elements of the SWOP service contributed to its success.
Collapse
Affiliation(s)
- K Fletcher
- Stroke Prevention Programme Manager, Professor of Primary Care Stroke Research, Department of Primary Care and General Practice, Clinical Sciences Building, University of Birmingham, Edgbaston, Birmingham, UK.
| | | |
Collapse
|
34
|
Abstract
BACKGROUND Case management of vulnerable older people by Community Matrons has been introduced into the UK. A locally designed case management approach, the Specialist Workers for Older People (SWOP) Service, was implemented by a Central England Primary Care Trust. Here, we report an evaluation of this service. METHODS Before and after study of 418 people (207 before; 211 after) aged >or=75 at high risk of emergency hospital admission. SWOPs carry out assessments of social and medical needs, produce individual care plans, co-ordinate care and refer to appropriate agencies. Univariable analysis was used to determine the association of SWOPs on changes in hospital admission rates and primary care workload. RESULTS There was a non-significant reduction in hospital admissions from 0.91 to 0.67 per patient. There was a significant increase in routine general practitioner surgery visits, from an average 1.3 to 2.6 per patient. The number of emergency home visits decreased from an average 2.8 to 1.1 per patient (P < 0.001). CONCLUSIONS Case management might reduce hospital admissions and is potentially a cost-effective service. However, not all case management schemes are successful. With the introduction of Community Matrons, it is important to understand what elements of the SWOP service contributed to its success.
Collapse
Affiliation(s)
- K Fletcher
- Department of Primary Care and General Practice, University of Birmingham, Edgbaston, Birmingham, UK.
| | | |
Collapse
|
35
|
|
36
|
Fletcher K. Taking the waters in Banff, Alberta. CMAJ 2008. [DOI: 10.1503/cmaj.080044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
|
37
|
Alexander D, Clarkson J, Buchanan R, Chadwick G, Chesters R, Drisko CL, Douglass CW, Farrell L, Fletcher K, Makoni F, Monaco M, Nordquist B, Park NI, Riggs S, Schou L, Smales FC, Stamm JW, Toh CG, Volpe T, Ward P, Warren P. Exploring opportunities for collaboration between the corporate sector and the dental education community. Eur J Dent Educ 2008; 12 Suppl 1:64-73. [PMID: 18289269 DOI: 10.1111/j.1600-0579.2007.00481.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The ultimate purpose of both dental industry and dental education is to improve the oral health of the public. This report provides background information on the different roles and objectives of the dental industry and dental education communities, the different operating environment of each sector and also areas of common interest where collaboration will be of mutual benefit. The report addresses five areas for potential collaboration between the dental industry and the dental education communities: 1. Contribution to joint activities. 2. Effectiveness and efficiency. 3. Workforce needs. 4. Middle- and low-income countries. 5. The future of International Federation of Dental Educators and Associations (IFDEA). The traditional areas of support and their limitations that have been provided by industry are outlined in the report and some new approaches for collaboration are considered. Industry-based research has been an important factor in developing new products and technologies and in promoting oral health. However there is a need to facilitate the introduction of these developments at an early stage in the education process. Industry has to operate in an efficient manner to remain competitive and maximise its returns and therefore survive. The academic sector operates in a different environment and under different governance structures; although some trends are noted towards adoption of greater efficiency and financial accountability similar to industry. Opportunities to jointly develop best business practices should be explored. Industry has responded well to the oral health needs of the public through the development of new products and technologies. The education community needs to respond in a similar way by examining different healthcare delivery models worldwide and developing programmes to train members of the dental team to cater for future needs and demands of communities in different regions of the world. The reputation of industry-based scientists and clinicians is high, and their role in contributing to the dental education process in practical ways needs to be explored and further developed. Closer relationships between industry scientists and faculty and students could assist industrys need and desire to develop new technologies for the broader dental care system. The corporate sector can play a key role in the future success of IFDEA by providing support and expertise in developing areas such as regional leadership institutes, a Global Faculty and Network and in collaborating in developing continuing education programmes as well as involvement in its governance. Thirteen recommendations are made in the report. These are considered to be important initial steps in developing the already strong relationship between the education and corporate sectors. Partnership and collaborating more effectively along the lines suggested should, almost certainly, generate mutually beneficial outcomes, whilst serving over the long term to elevate the publics oral health status on a global basis.
Collapse
|
38
|
Charlot L, Deutsch C, Hunt A, Fletcher K, McLlvane W. Validation of the mood and anxiety semi-structured (MASS) interview for patients with intellectual disabilities. J Intellect Disabil Res 2007; 51:821-34. [PMID: 17803500 DOI: 10.1111/j.1365-2788.2007.00972.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
BACKGROUND When assessing people with intellectual disabilities (ID), using the DSM-IV-TR can be challenging. Frequently, significant clinical data must be obtained from interviews with key informants. A new semi-structured interview tool was developed including behavioural descriptions of each DSM-IV-TR symptom criterion for a number of mood and anxiety disorders. A goal was to provide mental health clinicians with an instrument easy to use in clinical practice that would increase reliable identification of diagnostically important mood and anxiety symptoms. This is especially important given the fact that many experts believe these 'internalizing' clinical syndromes may often be missed in this population, because of characteristic limitations in expressive language skills. METHOD To establish validity, the Mood and Anxiety Semi-structured (MASS) Interview-derived diagnoses were compared with clinical DSM-IV diagnoses derived from an extensive inpatient evaluation and classifications based on the Hamilton Depression Rating Scale for 93 psychiatric inpatients served on a specialized unit for people with ID and major mental health disorders. RESULTS Agreement with the MASS Interview was high yielding significant kappa coefficients ranging from 0.42 to 0.78. CONCLUSIONS The MASS Interview, a semi-structured interview containing behavioural descriptions of DSM-IV symptom criteria, shows promise as a potentially helpful tool in the psychiatric diagnostic evaluation of persons with ID and limited expressive language skills, in the detection of mood and anxiety disorders. The tool also yields a wide breadth of clinical information and is easy for mental health clinicians to use.
Collapse
Affiliation(s)
- L Charlot
- Department of Psychiatry, University of Massachusetts Medical School (UMMS), Worcester, MA 01655, USA.
| | | | | | | | | |
Collapse
|
39
|
Abstract
The confined fluid-filled labyrinth of the human inner ear presents an opportunity for introduction of gene therapy reagents designed to treat hearing and balance dysfunction. Here we present a novel model system derived from the sensory epithelia of human vestibular organs and show that the tissue can survive up to 5 days in vitro. We generated organotypic cultures from 26 human sensory epithelia excised at the time of labyrinthectomy for intractable Meniere's disease or vestibular schwannoma. We applied multiply deleted adenoviral vectors at titers between 10(5) and 10(8) viral particles/ml directly to the cultures for 4-24 h and examined the tissue 12-96 h post-transfection. We noted robust expression of the exogenous transgene, green fluorescent protein (GFP), in hair cells and supporting cells suggesting both were targets of adenoviral transfection. We also transfected cultures with a vector that carried the genes for GFP and KCNQ4, a potassium channel subunit that causes dominant-progressive hearing loss when mutated. We noted a positive correlation between GFP fluorescence and KCNQ4 immunolocalization. We conclude that our in vitro model system presents a novel and effective experimental paradigm for evaluation of gene therapy reagents designed to restore cellular function in patients who suffer from inner ear disorders.
Collapse
Affiliation(s)
- BW Kesser
- Department of Otolaryngology – Head and Neck Surgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - GT Hashisaki
- Department of Otolaryngology – Head and Neck Surgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - K Fletcher
- Department of Otolaryngology – Head and Neck Surgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - H Eppard
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - JR Holt
- Department of Otolaryngology – Head and Neck Surgery, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| |
Collapse
|
40
|
Abstract
OBJECTIVE While Cognitive Behaviour Therapy (CBT) and Interpersonal Therapy (IPT) have been positioned as first-line evidence-based treatments for depression, we suggest that limitations to the 'evidence' deserve wider appreciation. METHOD A systematic literature search was undertaken, and limitations to the evidence base discussed. RESULTS The review suggests that the specificity of CBT and IPT treatments for depression has yet to be demonstrated and details likely reasons. CONCLUSION The superiority of CBT and IPT may well be able to be demonstrated across defined rather than universal circumstances. To achieve this aim, outcome research should move away from testing treatments as if they have universal application for heterogeneous disorder categories. Findings have distinct implications for the clinical management of depressive disorders, and particularly in relation to the utility of psychotherapy.
Collapse
Affiliation(s)
- G Parker
- School of Psychiatry, University of New South Wales, and Black Dog Institute, Prince of Wales Hospital, Sydney, Australia.
| | | |
Collapse
|
41
|
Catchpole O, Tallon S, Grey J, Fenton K, Fletcher K, Fletcher A. Extraction of Lipids from Aqueous Protein-Rich Streams using Near-Critical Dimethylether. Chem Eng Technol 2007. [DOI: 10.1002/ceat.200600351] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
42
|
Elger CE, Moskau S, Scholz A, Fletcher K, Stoffel-Wagner B, Widman G, Klockgether T, Helmstaedter C, Linnebank M. Die Einnahme von Antiepileptika ist ein Risiko für das Auftreten eines Folsäuremangels. Akt Neurol 2007. [DOI: 10.1055/s-2007-987705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
43
|
Abstract
A systematic review of the literature has been conducted and studies reporting investigations of genotoxicity biomarkers in pesticide workers have been assessed with view to establishing whether there was evidence for any risk to those using pesticides approved in the United Kingdom. Each of the studies was evaluated using a set of criteria drawn up by members of the UK Committee of Mutagenicity based upon the guidelines proposed by the International Programme on Chemical Safety (IPCS) working group [R. J. Albertini, D. Anderson, G. R. Douglas, L. Hagmar, K. Hemminki, F. Merlo, A. T. Natarajan, H. Norppa, D. E. Shuker, R. Tice, M. D. Waters and A. Aitio (2000) Mutat. Res., 463, 111-172]; 24 out of 70 studies met the criteria for inclusion in the substantive evaluation. Positive findings were compared with occupational practices and evidence of exposure to specific pesticides with view to developing hypotheses for further consideration. Seventeen of the 24 studies reported positive findings, although in the majority of these the magnitude of increase was small. There was some limited evidence that the use of benzimidazoles was more consistently associated with positive findings. However, limitations in the data, particularly evidence of exposure, did not allow definitive conclusions to be drawn. Also, it was noted that the use (or not) of personal protective equipment (PPE) was not well documented and in the few studies in which its use was reported, the findings were more likely to be positive in the absence of PPE usage. An independent epidemiological review concluded that all studies were of limited design, particularly with regards to study size, the assessment of subject selection and potential recruitment bias. Variance in genotoxicity indices in the control population and a lack of understanding of the factors influencing this variability complicate attempts to characterize positive responses. More substantive data are needed in this respect so that the significance of relatively small increases in biomonitoring indices can be accurately assessed. Once these data are available, a study in workers using benzimidazoles would be appropriate.
Collapse
Affiliation(s)
- S Bull
- DH Toxicology Unit, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
| | | | | | | |
Collapse
|
44
|
Abstract
BACKGROUND Diagnosis of chlamydia, gonorrhea, and vaginitis is now possible in adolescents using urine testing and vaginal swabs obtained by care provider or patient. However, a complete pelvic examination is necessary to diagnose pelvic inflammatory disease (PID). It is thus important to identify patients who might have pelvic inflammatory disease to assure complete gynecologic assessment of genitourinary symptoms. PURPOSE To determine whether adolescent patients with pelvic inflammatory disease report predictable symptoms during the medical interview and to determine what proportion of patients diagnosed with PID report at least one predictor symptom. DESIGN Observational study. SETTINGS Hospital-based adolescent clinic and Job Corps health service. PATIENTS A convenience sample (n = 193) of adolescent and young adult women who had a pelvic examination performed to evaluate a wide range of genitourinary symptoms. MAIN OUTCOME MEASURE Clinical diagnosis of pelvic inflammatory disease. ANALYSIS Sensitivity, specificity, and positive and negative predictive value of predictor symptoms for identifying patients given a diagnosis of pelvic inflammatory disease. RESULTS Twenty (10.4%) patients received a clinical diagnosis of PID. Lower abdominal pain was the most common symptom (90.0%) reported by these patients. All of the patients with PID reported either lower abdominal pain or dyspareunia in the medical history compared with 97 (56.1%) of those without PID. The presence of lower abdominal pain and/or dyspareunia in the clinical history yielded a sensitivity of 100%, specificity of 44%, and positive and negative predictive value of 17% and 100%, respectively, for identifying patients given a diagnosis of PID. CONCLUSION This study identified two symptoms reported in the medical history (lower abdominal pain and dyspareunia) that were associated with a clinical diagnosis of pelvic inflammatory disease. If lack of these two symptoms was used as a criterion for omitting a pelvic examination, more than one third of the patients in this study could have been evaluated for cervical and vaginal infections with urine and directly obtained vaginal swabs. Although some of these patients might have required a pelvic examination to exclude other causes of abnormal vaginal bleeding, at least 30% of the total sample could have been evaluated without a speculum and bimanual examination. If further studies support these findings, patients with symptoms suggestive of uncomplicated genitourinary infection (e.g., vaginal discharge, vaginal pruritus, or dysuria) who deny lower abdominal pain and dyspareunia can be evaluated with urine and vaginal samples in place of a speculum and bimanual examination.
Collapse
Affiliation(s)
- D R Blake
- Department of Pediatrics, University of Massachusetts Medical School, Worcester 01655, USA.
| | | | | | | |
Collapse
|
45
|
DiFranza JR, Savageau JA, Rigotti NA, Fletcher K, Ockene JK, McNeill AD, Coleman M, Wood C. Development of symptoms of tobacco dependence in youths: 30 month follow up data from the DANDY study. Tob Control 2002; 11:228-35. [PMID: 12198274 PMCID: PMC1759001 DOI: 10.1136/tc.11.3.228] [Citation(s) in RCA: 322] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To determine if there is a minimum duration, frequency or quantity of tobacco use required to develop symptoms of dependence. DESIGN AND SETTING A retrospective/prospective longitudinal study of the natural history of tobacco dependence employing individual interviews conducted three times annually in two urban school systems over 30 months. Detailed histories of tobacco use were obtained including dates, duration, frequency, quantity, patterns of use, types of tobacco, and symptoms of dependence. PARTICIPANTS A cohort of 679 seventh grade students (age 12-13 years). MAIN OUTCOME MEASURES The report of any of 11 symptoms of dependence. RESULTS Among 332 subjects who had used tobacco, 40% reported symptoms, with a median latency from the onset of monthly smoking of 21 days for girls and 183 days for boys. The median frequency of use at the onset of symptoms was two cigarettes, one day per week. The report of one or more symptoms predicted continued smoking through the end of follow up (odds ratio (OR) 44, 95% confidence interval (CI) 17 to 114, p < 0.001). CONCLUSIONS Symptoms of tobacco dependence commonly develop rapidly after the onset of intermittent smoking, although individuals differ widely in this regard. Girls tend to develop symptoms faster. There does not appear to be a minimum nicotine dose or duration of use as a prerequisite for symptoms to appear. The development of a single symptom strongly predicted continued use, supporting the theory that the loss of autonomy over tobacco use begins with the first symptom of dependence.
Collapse
Affiliation(s)
- J R DiFranza
- University of Massachusetts Medical School, Worcester, Massachusetts, USA Harvard Medical School, Massachusetts, USA University of London, London, UK.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Fletcher K, Painter V. Building a dream: creating an oncology day/evening hospital. Can J Nurs Leadersh 2002; 15:10-3. [PMID: 12102237 DOI: 10.12927/cjnl.2002.19147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The demand for inpatient beds has reached and often exceeds capacity producing waiting lists for cancer care. There is a need to explore alternative approaches to oncology treatment. The Oncology Day/Evening Hospital (ODEH), originally envisioned in 1995 as a joint project between an ambulatory cancer centre and a large teaching hospital, is an important cancer treatment initiative offering extended hours of ambulatory oncology treatment on days, evenings, weekends and statutory holidays. A review of current inpatient treatment modalities revealed that many patients receiving inpatient therapy could be safely and effectively managed in the ambulatory setting if treatment regimens were modified and if ambulatory hours of operation were extended. Healthcare improvements expected were: appropriate movement of inpatient activity to the ambulatory setting; more opportunities for patient choice in treatment time thereby allowing for maintenance of normal living; better quality of life for patients through prevention of hospitalization; decrease in treatment waiting times; consolidation of patients into an ambulatory oncology treatment setting as opposed to utilization of adult medicine units; and more rational inpatient bed utilization with reduction of admissions and intra-treatment transfers. This article describes our experience in building a dream, the challenges and lessons learned in implementing a better way to deliver oncology care in an environment of rapid change and staff shortages.
Collapse
|
47
|
Fletcher K, Butcher PN. Solution of the Boltzmann equation in ellipsoidal valleys with application to the <100> valleys of GaAs and gaP. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0022-3719/6/6/013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
48
|
Barkley RA, Edwards G, Laneri M, Fletcher K, Metevia L. The efficacy of problem-solving communication training alone, behavior management training alone, and their combination for parent-adolescent conflict in teenagers with ADHD and ODD. J Consult Clin Psychol 2001; 69:926-41. [PMID: 11777120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Two family therapies were compared using teens with attention-deficit/hyperactivity disorder. Ninety-seven families were assigned to either 18 sessions of problem-solving communication training (PSCT) alone or behavior management training (BMT) for 9 sessions followed by PSCT for 9 sessions (BMT/PSCT). Both treatments demonstrated significant improvement in ratings of parent-teen conflicts at the midpoint but did not differ. By posttreatment, both produced improvement on ratings and observations but did not differ. Significantly more families dropped out of PSCT alone than out of BMT/PSCT. At most, 23% of families showed reliable change either by midpoint or by posttreatment, with no differences between therapies. Yet 31%-70% of families were normalized. Group-level change and normalization rates support treatment efficacy, whereas indices of reliable change are less impressive.
Collapse
Affiliation(s)
- R A Barkley
- Department of Psychiatry, University of Massachusetts Medical School, Worcester 01655, USA.
| | | | | | | | | |
Collapse
|
49
|
Barkley RA, Edwards G, Laneri M, Fletcher K, Metevia L. Executive functioning, temporal discounting, and sense of time in adolescents with attention deficit hyperactivity disorder (ADHD) and oppositional defiant disorder (ODD). J Abnorm Child Psychol 2001; 29:541-56. [PMID: 11761287 DOI: 10.1023/a:1012233310098] [Citation(s) in RCA: 366] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Clinic-referred teens (ages 12-19) with ADHD and ODD (N = 101) were compared to community control (CC) teens, equated for age and sex, (N = 39) on a variety of psychological tasks assessing executive functioning (EF), temporal reward discounting, and time estimation and reproduction. A factor analysis reduced the EF measures to three dimensions, representing CPF Inattention, Working Memory, and CPT Inhibition. Results indicated that the ADHD group had significantly more CPT Inattention than the CC group. No differences were found for Working Memory or CPT Inhibition. The ADHD group displayed significantly greater temporal discounting of delayed hypothetical monetary rewards relative to immediate ones and manifested more impaired time reproduction, but not time estimation, than did the CC group. Main effects for level of IQ were found only on the Working Memory factor and largely did not interact with the group factor otherwise. The group differences in CPT Inattention, temporal discounting, and time reproduction were not a function of level of comorbid oppositional defiant disorder, delinquency, or anxiety-depression. Results are reasonably consistent with past research on EF and sense of time in children with ADHD and extend these findings to the adolescent age group. Problems with working memory and CPT inhibition found in prior studies of children with ADHD, however, were not evident here, perhaps owing to age-related improvements or insufficient task difficulty.
Collapse
Affiliation(s)
- R A Barkley
- Department of Psychiatry, University of Massachusetts Medical School, Worcester 01655, USA.
| | | | | | | | | |
Collapse
|
50
|
Abstract
Eighty-seven male teens (ages 12-18 years) with ADHD/ODD and their parents were compared to 32 male teens and their parents in a community control (CC) group on mother, father, and teen ratings of parent-teen conflict and communication quality, parental self-reports of psychological adjustment, and direct observations of parent-teen problem-solving interactions during a neutral and conflict discussion. Parents and teens in the ADHD/ODD group rated themselves as having significantly more issues involving parent-teen conflict, more anger during these conflict discussions, and more negative communication generally, and used more aggressive conflict tactics with each other than did parents and teens in the CC group. During a neutral discussion, only the ADHD/ODD teens demonstrated more negative behavior. During the conflict discussion, however, the mothers, fathers, and teens in the ADHD/ODD group displayed more negative behavior, and the mothers and teens showed less positive behavior than did participants in the CC group. Differences in conflicts related to sex of parent were evident on only a few measures. Both mother and father self-rated hostility contributed to the level of mother-teen conflict whereas father self-rated hostility and anxiety contributed to father-teen conflict beyond the contribution made by level of teen ODD and ADHD symptoms. Results replicated past studies of mother-child interactions in ADHD/ODD children, extended these results to teens with these disorders, showed that greater conflict also occurs in father-teen interactions, and found that degree of parental hostility, but not ADHD symptoms, further contributed to levels of parent-teen conflict beyond the contribution made by severity of teen ADHD and ODD symptoms.
Collapse
Affiliation(s)
- G Edwards
- Department of Psychiatry, University of Massachusetts Medical School, Worcester 01655, USA
| | | | | | | | | |
Collapse
|