276 results on '"Fitzpatrick, David"'
Search Results
102. Visual Physiology: Perceived Size Looms Large
- Author
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MacEvoy, Sean P. and Fitzpatrick, David
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SIZE perception , *SIZE judgment , *VISUAL cortex , *OCCIPITAL lobe - Abstract
Visual illusions tell us that size perception depends heavily upon complex contextual cues, often thought to be extracted by brain areas high in the visual hierarchy. Now, a new study shows that perceived size is reflected in activity as early as the primary visual cortex. [Copyright &y& Elsevier]
- Published
- 2006
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- View/download PDF
103. OR.3. Coexpression of CD103 and CD25 Identifies Human Regulatory CD4+ T-Cells
- Author
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Allakhverdi, Zoulfia, Fitzpatrick, David, Sarfati, Marika, and Delespesse, Guy
- Published
- 2006
- Full Text
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104. Easter 1916: The Irish Rebellion.
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Fitzpatrick, David
- Subjects
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NONFICTION ,EASTER Rising, Ireland, 1916 - Abstract
The article reviews the book "Easter 1916: The Irish Rebellion," by Charles Townshend.
- Published
- 2009
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105. Nationalism and the Irish Party: Provincial Ireland, 1910-1916.
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Fitzpatrick, David
- Subjects
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NATIONALISM , *NONFICTION - Abstract
Reviews the book "Nationalism and the Irish Party: Provincial Ireland, 1910-1916," by Michael Wheatley.
- Published
- 2006
- Full Text
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106. Sending out Ireland's Poor: Assisted Emigration to North America in the Nineteenth Century.
- Author
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Fitzpatrick, David
- Subjects
- *
EMIGRATION & immigration , *NONFICTION - Abstract
Reviews the book "Sending Out Ireland's Poor: Assisted Emigration to North America in the Nineteenth Century," by Gerald Moran.
- Published
- 2006
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- View/download PDF
107. Ireland and the British Empire.
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Fitzpatrick, David
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COLONIES , *NONFICTION - Abstract
Reviews the book "Ireland and the British Empire," edited by Kevin Kenny.
- Published
- 2006
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108. The Irish Regiments in the Great War: Discipline and Morale/Ireland, the Great War and the Geography of Remembrance/Irelands's Unknown Soldiers: The 16th (Irish) Division in the Great War (Book).
- Author
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Fitzpatrick, David
- Subjects
- IRISH Regiments in the Great War: Discipline & morale (Book), IRELAND, the Great War & the Geography of Remembrance (Book), IRELAND'S Unknown Soldiers: The 16th (Irish) Division in the Great War (Book), BOWMAN, Timothy, JOHNSON, Nuala C., DENMAN, Terence
- Abstract
Reviews three books about the history of Ireland. "The Irish Regiments in the Great War: Discipline and Morale," by Timothy Bowman; "Ireland, the Great War and the Geography of Remembrance," by Nuala C. Johnson; "Ireland's Unknown Soldiers: The 16th (Irish) Division in the Great War," by Terence Denman.
- Published
- 2004
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109. Ireland's Holy Wars: The Struggle for a Nation's Soul, 1500-2000 (Book).
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Fitzpatrick, David
- Subjects
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JIHAD , *NONFICTION - Abstract
Reviews the book "Ireland's Holy Wars: The Struggle for a Nation's Soul, 1500-2000," by Marcus Tanner.
- Published
- 2003
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110. Melancholy Accidents: The Meaning of Violence in Post-Famine Ireland (Book).
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Fitzpatrick, David
- Subjects
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VIOLENCE , *NONFICTION - Abstract
Reviews the book 'Melancholy Accidents: The Meaning of Violence in Post-Famine Ireland,' by Carolyn A. Conley.
- Published
- 2003
- Full Text
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111. They Shall Not Grow Old (Book Review).
- Author
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Fitzpatrick, David
- Subjects
- THEY Shall Not Grow Old (Book)
- Abstract
Reviews the book `They Shall Not Grow Old: Irish Soldiers and the Great War,' by Myles Dungan.
- Published
- 2000
- Full Text
- View/download PDF
112. Robust Genetic Analysis of the X-Linked Anophthalmic (Ie) Mouse.
- Author
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Hernandez-Moran, Brianda A., Papanastasiou, Andrew S., Parry, David, Meynert, Alison, Gautier, Philippe, Grimes, Graeme, Adams, Ian R., Trejo-Reveles, Violeta, Bengani, Hemant, Keighren, Margaret, Jackson, Ian J., Adams, David J., FitzPatrick, David R., and Rainger, Joe
- Subjects
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GENETIC variation , *GENE expression , *TRANSCRIPTION factors , *CIS-regulatory elements (Genetics) , *MOLECULAR diagnosis , *MICE , *PHENOTYPES , *X chromosome - Abstract
Anophthalmia (missing eye) describes a failure of early embryonic ocular development. Mutations in a relatively small set of genes account for 75% of bilateral anophthalmia cases, yet 25% of families currently are left without a molecular diagnosis. Here, we report our experimental work that aimed to uncover the developmental and genetic basis of the anophthalmia characterising the X-linked Ie (eye-ear reduction) X-ray-induced allele in mouse that was first identified in 1947. Histological analysis of the embryonic phenotype showed failure of normal eye development after the optic vesicle stage with particularly severe malformation of the ventral retina. Linkage analysis mapped this mutation to a ~6 Mb region on the X chromosome. Short- and long-read whole-genome sequencing (WGS) of affected and unaffected male littermates confirmed the Ie linkage but identified no plausible causative variants or structural rearrangements. These analyses did reduce the critical candidate interval and revealed evidence of multiple variants within the ancestral DNA, although none were found that altered coding sequences or that were unique to Ie. To investigate early embryonic events at a genetic level, we then generated mouse ES cells derived from male Ie embryos and wild type littermates. RNA-seq and accessible chromatin sequencing (ATAC-seq) data generated from cultured optic vesicle organoids did not reveal any large differences in gene expression or accessibility of putative cis-regulatory elements between Ie and wild type. However, an unbiased TF-footprinting analysis of accessible chromatin regions did provide evidence of a genome-wide reduction in binding of transcription factors associated with ventral eye development in Ie, and evidence of an increase in binding of the Zic-family of transcription factors, including Zic3, which is located within the Ie-refined critical interval. We conclude that the refined Ie critical region at chrX: 56,145,000–58,385,000 contains multiple genetic variants that may be linked to altered cis regulation but does not contain a convincing causative mutation. Changes in the binding of key transcription factors to chromatin causing altered gene expression during development, possibly through a subtle mis-regulation of Zic3, presents a plausible cause for the anophthalmia phenotype observed in Ie, but further work is required to determine the precise causative allele and its genetic mechanism. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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113. A Single Aspergillus fumigatus Gene Enables Ergothioneine Biosynthesis and Secretion by Saccharomyces cerevisiae.
- Author
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Doyle, Sean, Cuskelly, Daragh D., Conlon, Niall, Fitzpatrick, David A., Gilmartin, Ciara B., Dix, Sophia H., and Jones, Gary W.
- Subjects
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ASPERGILLUS fumigatus , *SACCHAROMYCES cerevisiae , *HIGH performance liquid chromatography , *BIOSYNTHESIS , *YEAST culture - Abstract
The naturally occurring sulphur-containing histidine derivative, ergothioneine (EGT), exhibits potent antioxidant properties and has been proposed to confer human health benefits. Although it is only produced by select fungi and prokaryotes, likely to protect against environmental stress, the GRAS organism Saccharomyces cerevisiae does not produce EGT naturally. Herein, it is demonstrated that the recombinant expression of a single gene, Aspergillus fumigatus egtA, in S. cerevisiae results in EgtA protein presence which unexpectedly confers complete EGT biosynthetic capacity. Both High Performance Liquid Chromatography (HPLC) and LC–mass spectrometry (MS) analysis were deployed to detect and confirm EGT production in S. cerevisiae. The localisation and quantification of the resultant EGT revealed a significantly (p < 0.0001) larger quantity of EGT was extracellularly present in culture supernatants than intracellularly accumulated in 96 h yeast cultures. Methionine addition to cultures improved EGT production. The additional expression of two candidate cysteine desulfurases from A. fumigatus was thought to be required to complete EGT biosynthesis, namely AFUA_2G13295 and AFUA_3G14240, termed egt2a and egt2b in this study. However, the co-expression of egtA and egt2a in S. cerevisiae resulted in a significant decrease in the observed EGT levels (p < 0.05). The AlphaFold prediction of A. fumigatus EgtA 3-Dimensional structure illuminates the bidomain structure of the enzyme and the opposing locations of both active sites. Overall, we clearly show that recombinant S. cerevisiae can biosynthesise and secrete EGT in an EgtA-dependent manner which presents a facile means of producing EGT for biotechnological and biomedical use. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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114. Modular Representation of Luminance Polarity in the Superficial Layers of Primary Visual Cortex.
- Author
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Smith, Gordon B., Whitney, David E., and Fitzpatrick, David
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VISUAL cortex , *SPATIAL arrangement , *NEURAL physiology , *BRAIN imaging , *TWO-photon-spectroscopy - Abstract
Summary The spatial arrangement of luminance increments (ON) and decrements (OFF) falling on the retina provides a wealth of information used by central visual pathways to construct coherent representations of visual scenes. But how the polarity of luminance change is represented in the activity of cortical circuits remains unclear. Using wide-field epifluorescence and two-photon imaging we demonstrate a robust modular representation of luminance polarity (ON or OFF) in the superficial layers of ferret primary visual cortex. Polarity-specific domains are found with both uniform changes in luminance and single light/dark edges, and include neurons selective for orientation and direction of motion. The integration of orientation and polarity preference is evident in the selectivity and discrimination capabilities of most layer 2/3 neurons. We conclude that polarity selectivity is an integral feature of layer 2/3 neurons, ensuring that the distinction between light and dark stimuli is available for further processing in downstream extrastriate areas. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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115. The Molecular Basis of Malonyl-CoA Decarboxylase Deficiency.
- Author
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FitzPatrick, David R., Hill, Alison, Tolmie, John L., Thorburn, David R., and Christodoulou, John
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COENZYMES , *DECARBOXYLASES - Abstract
Examines the molecular basis of malonyl-coenzyme A decarboxylase (MCD) deficiency. Characterization of a 2.1-kb human cDNA with a 454-amino acid open reading frame showing 70.3% amino acid identity; Homozygous mutations in human MCD; Result of an intronic mutation generating a splice acceptor sequence.
- Published
- 1999
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116. The Irish in the Great War.
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FITZPATRICK, DAVID and LEITH, IAN
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LETTERS to the editor , *IRISH athletes , *WORLD War I , *SOCCER - Abstract
Two letters to the editor are presented in response to Keith Jeffery's essay on Irish drama and World War I from the November 7, 2008 issue.
- Published
- 2008
117. What are the signs of mild cystic fibrosis?
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Fitzpatrick, David
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CYSTIC fibrosis , *GENETIC disorders , *LUNG diseases , *GENETICS , *FAMILIAL diseases , *GENETIC disorder diagnosis - Abstract
Discusses the early indications of mild cystic fibrosis. Likelihood of the occurrence of the disease in adults with a lesser phenotype; Details of the main clinical presentations.
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- 2004
118. Reviews of books: Modern Europe.
- Author
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Fitzpatrick, David
- Subjects
- LAND & Popular Politics in Ireland: County Mayo From the Plantation to the Land War (Book)
- Abstract
Reviews the book `Land and Popular Politics in Ireland: County Mayo From the Plantation to the Land War,' by Donald E. Jordan Jr.
- Published
- 1995
119. Reviews.
- Author
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Fitzpatrick, David
- Subjects
- SEA Changes: British Emigration & American Literature (Book)
- Abstract
Reviews the book `Sea Changes: British Emigration and American Literature,' by Stephen Fender. Analysis of British emigrants' letters and their relationship to the shaping of the American literature.
- Published
- 1993
120. Shorter notices.
- Author
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Fitzpatrick, David
- Subjects
- LARGEST Amount of Good, The (Book), RICHARD Davis Webb (Book)
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Reviews the books `The Largest Amount of Good. Quaker Relief in Ireland, 1654-1921,' by Helen E. Hatton and `Richard Davis Webb. Dublin Quaker Printer,' by Richard S. Harrison.
- Published
- 1996
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121. Shorter notices.
- Author
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Fitzpatrick, David
- Subjects
- INDUSTRIAL Development & Irish National Identity 1922-1939 (Book), DEVELOPMENT of Industrial Society in Ireland, The (Book)
- Abstract
Reviews the books `Industrial Development and Irish National Identity, 1922-1939,' by Mary E. Daly and `The Development of Industrial Society in Ireland,' edited by J.H. Goldthorpe and C.T. Whelan.
- Published
- 1996
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122. The Invisible Irish: Finding Protestants in the Nineteenth-Century Migrations to America.
- Author
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FITZPATRICK, DAVID
- Subjects
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PRESBYTERIANS , *IRISH people , *NONFICTION , *HISTORY - Published
- 2017
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123. Éamon de Valera: A Will to Power.
- Author
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FITZPATRICK, DAVID
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NONFICTION - Published
- 2017
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124. The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine.
- Author
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Jones, Gary W., Doyle, Sean, and Fitzpatrick, David A.
- Subjects
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BIOSYNTHESIS , *ANTIOXIDANTS , *BETAINES , *HISTIDINE , *NEUROSPORA crassa , *ACTINOBACTERIA , *PROKARYOTES - Abstract
Ergothioneine (EGT) is a histidine betaine derivative that exhibits antioxidant action in humans. EGT is primarily synthesized by fungal species and a number of bacterial species. A five-gene cluster (egtA, egtB, egtC, egtD &egtE) responsible for EGT production in Mycobacteria smegmatis has recently been identified. The first fungal biosynthetic EGT gene (NcEgt-1) has also been identified in Neurospora crassa. NcEgt-1 contains domains similar to those found in M. smegmatis egtB and egtD. EGT is biomembrane impermeable. Here we inferred the evolutionary history of the EGT cluster in prokaryotes as well as examining the phyletic distribution of Egt-1 in the fungal kingdom. A genomic survey of 2509 prokaryotes showed that the five-gene EGT cluster is only found in the Actinobacteria. Our survey identified more than 400 diverse prokaryotes that contain genetically linked orthologs of egtB and egtD. Phylogenetic analyses of Egt proteins show a complex evolutionary history and multiple incidences of horizontal gene transfer. Our analysis also identified two independent incidences of a fusion event of egtB and egtD in bacterial species. A genomic survey of over 100 fungal genomes shows that Egt-1 is found in all fungal phyla, except species that belong to the Saccharomycotina subphylum. This analysis provides a comprehensive analysis of the distribution of the key genes involved in the synthesis of EGT in prokaryotes and fungi. Our phylogenetic inferences illuminate the complex evolutionary history of the genes involved in EGT synthesis in prokaryotes. The potential to synthesize EGT is a fungal trait except for species belonging to the Saccharomycotina subphylum. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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125. Variant detection sensitivity and biases in whole genome and exome sequencing.
- Author
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Meynert, Alison M., Ansari, Morad, FitzPatrick, David R., and Taylor, Martin S.
- Abstract
Background: Less than two percent of the human genome is protein coding, yet that small fraction harbours the majority of known disease causing mutations. Despite rapidly falling whole genome sequencing (WGS) costs, much research and increasingly the clinical use of sequence data is likely to remain focused on the protein coding exome. We set out to quantify and understand how WGS compares with the targeted capture and sequencing of the exome (exome-seq), for the specific purpose of identifying single nucleotide polymorphisms (SNPs) in exome targeted regions. Results: We have compared polymorphism detection sensitivity and systematic biases using a set of tissue samples that have been subject to both deep exome and whole genome sequencing. The scoring of detection sensitivity was based on sequence down sampling and reference to a set of gold-standard SNP calls for each sample. Despite evidence of incremental improvements in exome capture technology over time, whole genome sequencing has greater uniformity of sequence read coverage and reduced biases in the detection of non-reference alleles than exome-seq. Exome-seq achieves 95% SNP detection sensitivity at a mean on-target depth of 40 reads, whereas WGS only requires a mean of 14 reads. Known disease causing mutations are not biased towards easy or hard to sequence areas of the genome for either exome-seq or WGS. Conclusions: From an economic perspective, WGS is at parity with exome-seq for variant detection in the targeted coding regions. WGS offers benefits in uniformity of read coverage and more balanced allele ratio calls, both of which can in most cases be offset by deeper exome-seq, with the caveat that some exome-seq targets will never achieve sufficient mapped read depth for variant detection due to technical difficulties or probe failures. As WGS is intrinsically richer data that can provide insight into polymorphisms outside coding regions and reveal genomic rearrangements, it is likely to progressively replace exome-seq for many applications. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
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126. Endobronchial cryotherapy facilitates end-stage treatment options in patients with bronchial stenosis: A case series.
- Author
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Fitzmaurice, Gerard J., Redmond, Karen C., Fitzpatrick, David A., and Bartosik, Waldemar
- Subjects
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COLD therapy , *BRONCHIAL diseases , *TREATMENT of lung tumors , *ENDOSCOPY , *PALLIATIVE treatment , *TOMOGRAPHY , *BRONCHOCONSTRICTION , *THERAPEUTICS - Abstract
In keeping with international trends, lung cancer incidence and mortality are increasing among the Irish population with many patients presenting with advanced disease that excludes the potential for curative management. Consequently palliative treatment options for this patient group are being increasingly explored with various degrees of success. Endobronchial stenosis represents a particularly challenging area of management among these patients and a number of techniques have been described without the identification of a single gold standard. We report our experience of the first time use of endobronchial cryotherapy in Ireland with reference to a case series, including an example of its use in the management of benign disease, in order to support patients with borderline lung function and enable definitive palliative treatment. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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127. Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature.
- Author
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Rawlings, Anna, O'Connor, Eoin, Moody, Suzy C., Dudley, Ed, Boddy, Lynne, Fowler, Mike S., Fitzpatrick, David A., Doyle, Sean, and Eastwood, Dan C.
- Subjects
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WOOD-decaying fungi , *WOOD decay , *BIOTIC communities , *KREBS cycle , *PENTOSE phosphate pathway , *PROTEIN synthesis - Abstract
Decomposition of lignin‐rich wood by fungi drives nutrient recycling in woodland ecosystems. Fluctuating abiotic conditions are known to promote the functioning of ecological communities and ecosystems. In the context of wood decay, fluctuating temperature increases decomposition rates. Metabolomics, in tandem with other 'omics tools, can highlight the metabolic processes affected by experimental treatments, even in the absence of genome sequences and annotations. Globally, natural wood decay communities are dominated by the phylum Basidiomycota. We examined the metabolic responses of Mucidula mucida, a dominant constituent of pioneer communities in beech branches in British woodlands, and Exidia glandulosa, a stress‐selected constituent of the same communities, in response to constant and diurnally cycling temperature.We applied untargeted metabolomics and proteomics to beech wood blocks, colonised by M. mucida or E. glandulosa and exposed to either diurnally cycling (mean 15 ± 10°C) or constant (15°C) temperature, in a fully factorial design.Metabolites and proteins linked to lignin breakdown, the citric acid cycle, pentose phosphate pathway, carbohydrate metabolism, fatty acid metabolism and protein biosynthesis and turnover were under‐enriched in fluctuating, compared to stable temperatures, in the generalist M. mucida. Conversely, E. glandulosa showed little differential response to the experimental treatments.Synthesis. By demonstrating temperature‐dependant metabolic signatures related to nutrient acquisition in a generalist wood decay fungus, we provide new insights into how abiotic conditions can affect community‐mediated decomposition and carbon turnover in forests. We show that mechanisms underpinning important biogeochemical processes can be highlighted using untargeted metabolomics and proteomics in the absence of well‐annotated genomes. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
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128. Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders.
- Author
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Gardner, Eugene J., Sifrim, Alejandro, Lindsay, Sarah J., Prigmore, Elena, Rajan, Diana, Danecek, Petr, Gallone, Giuseppe, Eberhardt, Ruth Y., Martin, Hilary C., Wright, Caroline F., FitzPatrick, David R., Firth, Helen V., and Hurles, Matthew E.
- Subjects
- *
GENETIC variation , *GENETIC disorders , *DIAGNOSIS methods - Abstract
Structural variation (SV) describes a broad class of genetic variation greater than 50 bp in size. SVs can cause a wide range of genetic diseases and are prevalent in rare developmental disorders (DDs). Individuals presenting with DDs are often referred for diagnostic testing with chromosomal microarrays (CMAs) to identify large copy-number variants (CNVs) and/or with single-gene, gene-panel, or exome sequencing (ES) to identify single-nucleotide variants, small insertions/deletions, and CNVs. However, individuals with pathogenic SVs undetectable by conventional analysis often remain undiagnosed. Consequently, we have developed the tool InDelible, which interrogates short-read sequencing data for split-read clusters characteristic of SV breakpoints. We applied InDelible to 13,438 probands with severe DDs recruited as part of the Deciphering Developmental Disorders (DDD) study and discovered 63 rare, damaging variants in genes previously associated with DDs missed by standard SNV, indel, or CNV discovery approaches. Clinical review of these 63 variants determined that about half (30/63) were plausibly pathogenic. InDelible was particularly effective at ascertaining variants between 21 and 500 bp in size and increased the total number of potentially pathogenic variants identified by DDD in this size range by 42.9%. Of particular interest were seven confirmed de novo variants in MECP2 , which represent 35.0% of all de novo protein-truncating variants in MECP2 among DDD study participants. InDelible provides a framework for the discovery of pathogenic SVs that are most likely missed by standard analytical workflows and has the potential to improve the diagnostic yield of ES across a broad range of genetic diseases. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
129. Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom.
- Author
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Medina, Edgar, Jones, Gary, and Fitzpatrick, David
- Subjects
- *
YEAST , *FUNGI , *GENES , *GENOMES , *PROTEINS - Abstract
We have used three independent phylogenomic approaches (concatenated alignments, single-, and multi-gene supertrees) to reconstruct the fungal tree of life (FTOL) using publicly available fungal genomes. This is the first time multi-gene families have been used in fungal supertree reconstruction and permits us to use up to 66% of the 1,001,217 genes in our fungal database. Our analyses show that different phylogenomic datasets derived from varying clustering criteria and alignment orientation do not have a major effect on phylogenomic supertree reconstruction. Overall the resultant phylogenomic trees are relatively congruent with one another and successfully recover the major fungal phyla, subphyla and classes. We find that where incongruences do occur, the inferences are usually poorly supported. Within the Ascomycota phylum, our phylogenies reconstruct monophyletic Saccharomycotina and Pezizomycotina subphyla clades and infer a sister group relationship between these to the exclusion of the Taphrinomycotina. Within the Pezizomycotina subphylum, all three phylogenies infer a sister group relationship between the Leotiomycetes and Sordariomycetes classes. However, there is conflict regarding the relationships with the Dothideomycetes and Eurotiomycetes classes. Within the Basidiomycota phylum, supertrees derived from single- and multi-gene families infer a sister group relationship between the Pucciniomycotina and Agaricomycotina subphyla while the concatenated phylogeny infers a poorly supported relationship between the Agaricomycotina and Ustilagomycotina. The reconstruction of a robust FTOL is important for future fungal comparative analyses. We illustrate this point by performing a preliminary investigation into the phyletic distribution of yeast prion-like proteins in the fungal kingdom. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
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130. Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer.
- Author
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Creevey, Christopher J., Doerks, Tobias, Fitzpatrick, David A., Raes, Jeroen, and Bork, Peer
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GENETIC transformation , *GENETIC translation , *GENES , *BIOLOGICAL evolution , *STATISTICS , *GENOMES , *CLADISTIC analysis , *BIOLOGICAL classification - Abstract
Single copy genes, universally distributed across the three domains of life and encoding mostly ancient parts of the translation machinery, are thought to be only rarely subjected to horizontal gene transfer (HGT). Indeed it has been proposed to have occurred in only a few genes and implies a rare, probably not advantageous event in which an ortholog displaces the original gene and has to function in a foreign context (orthologous gene displacement, OGD). Here, we have utilised an automatic method to identify HGT based on a conservative statistical approach capable of robustly assigning both donors and acceptors. Applied to 40 universally single copy genes we found that as many as 68 HGTs (implying OGDs) have occurred in these genes with a rate of 1.7 per family since the last universal common ancestor (LUCA). We examined a number of factors that have been claimed to be fundamental to HGT in general and tested their validity in the subset of universally distributed single copy genes. We found that differing functional constraints impact rates of OGD and the more evolutionarily distant the donor and acceptor, the less likely an OGD is to occur. Furthermore, species with larger genomes are more likely to be subjected to OGD. Most importantly, regardless of the trends above, the number of OGDs increases linearly with time, indicating a neutral, constant rate. This suggests that levels of HGT above this rate may be indicative of positively selected transfers that may allow niche adaptation or bestow other benefits to the recipient organism. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
131. The Representation of S-Cone Signals in Primary Visual Cortex.
- Author
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Johnson, Elizabeth N., Van Hooser, Stephen D., and Fitzpatrick, David
- Subjects
- *
VISUAL cortex , *WAVELENGTHS , *NEURONS , *OCCIPITAL lobe , *NERVOUS system - Abstract
Recent studies of middle-wavelength-sensitive and long-wavelength-sensitive cone responses in primate primary visual cortex (V1) have challenged the view that color and form are represented by distinct neuronal populations. Individual V1 neurons exhibit hallmarks of both color and form processing (cone opponency and orientation selectivity), and many display cone interactions that do not fit classic chromatic/achromatic classifications. Comparable analysis of short-wavelength-sensitive (S) cone responses has yet to be achieved and is of considerable interest because S-cones are the basis for the primordial mammalian chromatic pathway. Using intrinsic and two-photon imaging techniques in the tree shrew, we assessed the properties of V1 layer 2/3 neurons responsive to S-cone stimulation. These responses were orientation selective, exhibited distinct spatiotemporal properties, and reflected integration of S-cone inputs via opponent, summing, and intermediate configurations. Our observations support a common framework for the representation of cone signals in V1, one that endows orientation-selective neurons with a range of chromatic, achromatic, and mixed response properties. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
132. A precise form of divisive suppression supports population coding in the primary visual cortex.
- Author
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MacEvoy, Sean P., Tucker, Thomas R., and Fitzpatrick, David
- Subjects
- *
VISUAL cortex physiology , *NEURONS , *NEUROSCIENCES , *NORTHERN tree shrew , *NEUROBIOLOGY - Abstract
The responses of neurons in the primary visual cortex (V1) to an optimally oriented grating are suppressed when a non-optimal grating is superimposed. Although cross-orientation suppression is thought to reflect mechanisms that maintain a distributed code for orientation, the effect of superimposed gratings on V1 population responses is unknown. Using intrinsic signal optical imaging, we found that patterns of tree shrew V1 activity evoked by superimposed equal-contrast gratings were predicted by the averages of patterns evoked by individual component gratings. This prediction held across contrasts, for summed sinusoidal gratings or nonsumming square-wave gratings, and was evident in single-unit extracellular recordings. Intracellular recordings revealed consistent levels of suppression throughout the time course of subthreshold responses. These results indicate that divisive suppression powerfully governs population responses to multiple orientations. Moreover, the specific form of suppression that we observed appears to support independent population codes for stimulus orientation and strength and calls for a reassessment of mechanisms that underlie cross-orientation suppression. [ABSTRACT FROM AUTHOR]
- Published
- 2009
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133. Rear-impact neck protection devices for adult wheelchair users.
- Author
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Simms, Ciaran K., Madden, Brian, FitzPatrick, David, and Tiernan, John
- Subjects
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WHEELCHAIR design & construction , *NECK injuries , *MEDICAL rehabilitation , *SAFETY , *PREVENTION , *EQUIPMENT & supplies - Abstract
Many wheelchair users remain in their wheelchairs during transit. Safety research for wheelchair users has focused mainly on frontal impact. However, although they are generally less severe, rear-impact injuries are expensive and difficult to treat and whiplash injury protection for adult wheelchair users remains poorly understood. In this article, 10 g (16 km/h) rear-impact sled tests conducted with the Biofidelic Rear Impact Dummy II or BioRID-II (Denton ATD Inc and Chalmers University of Technology; Gothenburg, Sweden) seated in a rigid wheelchair with no head restraint showed that Abbreviated Injury Scale-score 1 neck injury risk evaluated with the neck injury criterion (NIC) and Nkm criterion is substantially above proposed threshold levels. A prototype wheelchair head restraint was developed and tested together with an existing commercial head restraint (Rolko; Borgholzhausen, Germany) in the same 10 g (16 km/h) rear impact. Both head restraints reduced the injury scores substantially. NIC test scores for the head restraints with no gap ranged from 18 to 24 (approximately 20%-30% chance of neck injury symptoms of duration >1 month) compared with test scores for no head restraints that ranged from 34 to 37 (approximately 95% chance of neck injury). The corresponding extension-posterior Nkm scores with no gap ranged from 0.30 to 0.35 (approximately 5% chance of neck injury) compared with no head restraint of 1.16 (approximately 45% chance of neck injury symptoms). However, the number of sled tests performed was small (three with no head restraint and six with a head restraint), and these results should be considered mainly trends. Preliminary results also showed that the horizontal gap between the head and the wheelchair head-restraint cushion should be as small possible. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
134. Effect of elbow joint angle on force–EMG relationships in human elbow flexor and extensor muscles
- Author
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Doheny, Emer P., Lowery, Madeleine M., FitzPatrick, David P., and O’Malley, Mark J.
- Subjects
- *
ELECTROMYOGRAPHY , *ELBOW , *MUSCLES , *ISOMETRIC exercise , *MUSCLE contraction , *BICEPS brachii - Abstract
Abstract: The purpose of this study was to examine the effect of joint angle on the relationship between force and electromyogram (EMG) amplitude and median frequency, in the biceps, brachioradialis and triceps muscles. Surface EMG were measured at eight elbow angles, during isometric flexion and extension at force levels from 10% to 100% of maximum voluntary contraction (MVC). Joint angle had a significant effect on MVC force, but not on MVC EMG amplitude in all of the muscles examined. The median frequency of the biceps and triceps EMG decreased with increasing muscle length, possibly due to relative changes in electrode position or a decrease in muscle fibre diameter. The relationship between EMG amplitude and force, normalised with respect to its maximum force at each angle, did not vary with joint angle in the biceps or brachioradialis muscles over all angles, or in the triceps between 45° and 120° of flexion. These results suggest that the neural excitation level to each muscle is determined by the required percentage of available force rather than the absolute force required. It is, therefore, recommended that when using surface EMG to estimate muscle excitation, force should be normalised with respect to its maximum value at each angle. [Copyright &y& Elsevier]
- Published
- 2008
- Full Text
- View/download PDF
135. A morphological basis for orientation tuning in primary visual cortex.
- Author
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Mooser, François, Bosking, William H., and Fitzpatrick, David
- Subjects
- *
MENTAL orientation , *VISUAL cortex , *OCCIPITAL lobe , *NEURONS , *NERVOUS system - Abstract
Feedforward connections are thought to be important in the generation of orientation-selective responses in visual cortex by establishing a bias in the sampling of information from regions of visual space that lie along a neuron's axis of preferred orientation. It remains unclear, however, which structural elements-dendrites or axons-are ultimately responsible for conveying this sampling bias. To explore this question, we have examined the spatial arrangement of feedforward axonal connections that link non-oriented neurons in layer 4 and orientation-selective neurons in layer 2/3 of visual cortex in the tree shrew. Target sites of labeled boutons in layer 2/3 resulting from focal injections of biocytin in layer 4 show an orientation-specific axial bias that is sufficient to confer orientation tuning to layer 2/3 neurons. We conclude that the anisotropic arrangement of axon terminals is the principal source of the orientation bias contributed by feedforward connections. [ABSTRACT FROM AUTHOR]
- Published
- 2004
- Full Text
- View/download PDF
136. Transmission of mushroom virus X and the impact of virus infection on the transcriptomes and proteomes of different strains of Agaricus bisporus.
- Author
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O'Connor, Eoin, Doyle, Sean, Amini, Aniça, Grogan, Helen, and Fitzpatrick, David A.
- Subjects
- *
CULTIVATED mushroom , *FRUITING bodies (Fungi) , *TRANSCRIPTOMES , *INOCULATION of crops , *MUSHROOMS , *VIRUS diseases - Abstract
Cultivation of Agaricus bisporus is a large horticultural industry for many countries worldwide, where a single variety is almost grown exclusively. Mushroom virus X (MVX), a complex of multiple positive-sense single stranded RNA (ss(+)RNA) viruses, is a major pathogen of typical A. bisporus crops. MVX can manifest a variety of symptoms in crops and is highly infective and difficult to eradicate once established in host mycelium. Currently our knowledge regarding the molecular response of A. bisporus fruit bodies to MVX infection is limited. In order to study the response of different A. bisporus strains with different susceptibilities to MVX, we designed a model system to evaluate the in-vitro transmission of viruses in A. bisporus hyphae over a time-course, at two crucial phases in the crop cycle. The symptom expression of MVX in these varieties and the transcriptomic and proteomic response of fruit bodies to MVX-infection were examined. Transmission studies revealed the high potential of MVX to spread to uninfected mycelium yet not into the fruit bodies of certain strains in a crop. MVX affected colour and quality of multiple fruit bodies. Gene expression is significantly altered in all strains and between times of inoculation in the crop. Genes related to stress responses displayed differential expression. Proteomic responses revealed restriction of cellular signalling and vesicle transport in infected fruit bodies. This in-depth analysis examining many factors relevant to MVX infection in different A. bisporus strains, will provide key insights into host responses for this commercially important food crop. • MVX affected colour and quality of multiple fruit bodies. • MVX significantly alters gene expression in all strains. • Transcription factors and stress response genes expression were altered. • Proteomic revealed restriction of cellular signalling and vesicle transport. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
137. Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex.
- Author
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Hanson, Sara J., Cinnéide, Eoin O., Salzberg, Letal I., Wolfe, Kenneth H., McGowan, Jamie, Fitzpatrick, David A., and Matlin, Kate
- Subjects
- *
CHROMOSOMAL rearrangement , *PROTEIN expression , *SPECIES hybridization , *PLANT hybridization , *SPECIES , *NUCLEOTIDE sequence - Abstract
The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the O. polymorpha species complex, including representatives of the species O. polymorpha, Ogataea parapolymorpha, Ogataea haglerorum, and Ogataea angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
138. Mapping multiple features in the population response of visual cortex.
- Author
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Basole, Amit, White, Leonard E., and Fitzpatrick, David
- Subjects
- *
VISUAL cortex , *NEURONS , *FERRET , *MAPS , *RESEARCH - Abstract
Stimulus features such as edge orientation, motion direction and spatial frequency are thought to be encoded in the primary visual cortex by overlapping feature maps arranged so that the location of neurons activated by a particular combination of stimulus features can be predicted from the intersections of these maps. This view is based on the use of grating stimuli, which limit the range of stimulus combinations that can be examined. We used optical imaging of intrinsic signals in ferrets to assess patterns of population activity evoked by the motion of a texture (a field of iso-oriented bars). Here we show that the same neural population can be activated by multiple combinations of orientation, length, motion axis and speed. Rather than reflecting the intersection of multiple maps, our results indicate that population activity in primary visual cortex is better described as a single map of spatiotemporal energy. [ABSTRACT FROM AUTHOR]
- Published
- 2003
- Full Text
- View/download PDF
139. Emergent Properties of Layer 2/3 Neurons Reflect the Collinear Arrangement of Horizontal Connections in Tree Shrew Visual Cortex.
- Author
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Chisum, Heather J., Mooser, Francois, and Fitzpatrick, David
- Subjects
- *
NEURONS , *CELLS , *NERVOUS system , *TUPAIIDAE , *SCANDENTIA , *VISUAL cortex , *OCCIPITAL lobe , *ELECTROPHYSIOLOGY , *PHYSIOLOGY , *NEUROLOGY - Abstract
Provides information on a study that compared the receptive field properties of layers 2/3 and 4 neurons in tree shrew primary visual cortex with electrophysiological recordings. Methodology of the study; Results and discussion on the study.
- Published
- 2003
- Full Text
- View/download PDF
140. Single-cell perforin and granzyme expression reveals the anatomical localization of effector CD8[sup +] T cells in influenza virus-infected mice.
- Author
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Johnson, Barbara J., Costelloe, Elaine O., Fitzpatrick, David R., Haanen, John B.A.G., Schumacher, Ton N.M., Brown, Lorena E., and Kelso, Anne
- Subjects
- *
INFLUENZA viruses , *T cells - Abstract
Influenza virus infection activates cytolytic T lymphocytes (CTL) that contribute to viral clearance by releasing perforin and granzymes from cytoplasmic granules. Virus-specific, perforindependent CD8[sup +] CTL were detected in freshly isolated cells from the mouse lung parenchyma but not from the mediastinal lymph nodes (MLN), where they are primed, or from the spleen during primary influenza virus infection. To determine whether this difference was due to the low frequency or incomplete maturation of effector CTL in MLN, we measured expression of perforin, granzymes A, B, and C, and IFN-γ, mRNAs in CD8[sup +] populations and single cells immediately after isolation from virus-infected mice. Quantitative PCR revealed significant expression of perforin, granzyme A, granzyme B, and IFN-γ in activated CD8[sup +] cells from MLN, spleen, and lung parenchyma. Granzyme C expression was not detected. Individual activated or nucleoprotein peptide/class I tetramerbinding CD8[sup +] cells from the three tissues expressed diverse combinations of perforin, granzyme, and IFN-γ mRNAs. Although cells from lung expressed granzymes A and B at higher frequency, each of the tissues contained cells that coexpressed perforin with granzymes A and/or B. The main difference between MLN and lung was the elevated frequency of activated CD8[sup +] T cells in the lung, rather than their perforin/granzyme expression profile. The data suggest that some CTL mature into perforin/granzyme-expressing effector cells in MLN but reach detectable frequencies only when they accumulate in the infected lung. [ABSTRACT FROM AUTHOR]
- Published
- 2003
- Full Text
- View/download PDF
141. Spatial coding of position and orientation in primary visual cortex.
- Author
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Bosking, William H., Crowley, Justin C., and Fitzpatrick, David
- Subjects
- *
VISUAL cortex , *TUPAIIDAE , *OPTICAL images , *ELECTROPHYSIOLOGY - Abstract
We examined the spatial distribution of population activity in primary visual cortex (V1) of tree shrews with optical imaging and electrophysiology. A line stimulus, thinner than the average V1 receptive field, evoked a broad strip of neural activity of nearly constant size for all stimulus locations tested within the central 10° of visual space. Stimuli in adjacent positions activated highly overlapping populations of neurons; nevertheless, small changes in stimulus position produced orderly changes in the location of the peak of the population response. Statistically significant shifts in the population response were found for stimulus displacements an order of magnitude smaller than receptive field width, down to the limit of optical imaging resolution. Based on the pattern of population activity, we conclude that the map of visual space in V1 is orderly at a fine scale and has uniform coverage of position and orientation without local relationships in the mapping of these features. [ABSTRACT FROM AUTHOR]
- Published
- 2002
- Full Text
- View/download PDF
142. The contribution of sensory experience to the maturation of orientation selectivity in ferret visual cortex.
- Author
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White, Leonard E., Coppola, David M., and Fitzpatrick, David
- Subjects
- *
SENSORY stimulation , *MENTAL orientation , *BRAIN , *NEUROPHYSIOLOGY - Abstract
Provides information on a study which examined the role of visual experience in the maturation of orientation and underlying cortical circuits. Results; Discussion; Methods.
- Published
- 2001
- Full Text
- View/download PDF
143. Guidelines and care pathways for genetic diseases: the Scottish collaborative project on tuberous sclerosis.
- Author
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Bradshaw, Nicola, Brewer, Carole, FitzPatrick, David, Murray, George, Rodgers, Frances, Porteous, Mary, and Campbell, Harry
- Subjects
- *
TUBEROUS sclerosis , *DISEASE management - Abstract
In Scotland a national audit project has been undertaken to devise evidence-based guidelines for the clinical management of patients with tuberous sclerosis (TS), a dominantly inherited multisystem disorder. In order to facilitate the audit and use of these guidelines a ‘Care Pathway’ was devised to form the patient records. We describe the process of guideline development for TS and our TS Care Pathway. [ABSTRACT FROM AUTHOR]
- Published
- 1998
- Full Text
- View/download PDF
144. HERCVLES FVRENS.
- Author
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Fitzpatrick, David
- Subjects
- *
CLASSICAL drama (Tragedy) , *NONFICTION - Abstract
The article reviews the book "Euripides: Heracles," by Emma Griffiths.
- Published
- 2007
- Full Text
- View/download PDF
145. Land and Revolution: Nationalist Politics in the West of Ireland, 1891-1921.
- Author
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Fitzpatrick, David
- Subjects
- *
NONFICTION ,IRISH history - Abstract
The article reviews the book "Land and Revolution: Nationalist Politics in the West of Ireland, 1891-1921," by Fergus Campbell.
- Published
- 2007
- Full Text
- View/download PDF
146. U.S. Intelligence and the Nazis.
- Author
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Fitzpatrick, David and Citino, Robert
- Subjects
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INTELLIGENCE service , *NONFICTION - Abstract
This article reviews the book "U.S. Intelligence and the Nazis," by Richard Breitman, Norman J. W. Goda, Timothy Naftali and Robert Wolfe.
- Published
- 2006
147. To and From Ireland: Planned Migration Schemes, c.1600-2000.
- Author
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Fitzpatrick, David
- Subjects
- *
EMIGRATION & immigration , *NONFICTION - Abstract
Reviews the book "To and From Ireland: Planned Migration Schemes, c.1600-2000," edited by Patrick J. Duffy.
- Published
- 2006
- Full Text
- View/download PDF
148. Conceiving Revolution: Irish Nationalist Propaganda during the First World War (Book).
- Author
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Fitzpatrick, David
- Subjects
- *
WORLD War I , *NONFICTION - Abstract
Reviews the book "Conceiving Revolution: Irish Nationalist Propaganda During the First World War," by Ben Novick.
- Published
- 2003
- Full Text
- View/download PDF
149. Making Citizen Soldiers: ROTC and the Ideology of American Military Service (Book).
- Author
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Fitzpatrick, David J.
- Subjects
- *
MILITARY reserve forces , *NONFICTION - Abstract
Reviews the non-fiction book 'Making Citizen Soldiers: ROTC and the Ideology of American Military Service,' by Michael S. Neiberg.
- Published
- 2002
150. Reviews of Books: Comparative/World.
- Author
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Fitzpatrick, David
- Subjects
- *
EMIGRATION & immigration , *NONFICTION - Abstract
Reviews the book 'The Irish Diaspora,' edited by Andy Bielenberg.
- Published
- 2001
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