26 results on '"Browne DJ"'
Search Results
2. Technical pitfalls when collecting, cryopreserving, thawing, and stimulating human T-cells.
- Author
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Browne DJ, Miller CM, and Doolan DL
- Subjects
- Humans, Cell Survival, HIV Infections immunology, Cryopreservation methods, T-Lymphocytes immunology, Leukocytes, Mononuclear immunology
- Abstract
The collection, cryopreservation, thawing, and culture of peripheral blood mononuclear cells (PBMCs) can profoundly influence T cell viability and immunogenicity. Gold-standard PBMC processing protocols have been developed by the Office of HIV/AIDS Network Coordination (HANC); however, these protocols are not universally observed. Herein, we have explored the current literature assessing how technical variation during PBMC processing can influence cellular viability and T cell immunogenicity, noting inconsistent findings between many of these studies. Amid the mounting concerns over scientific replicability, there is growing acknowledgement that improved methodological rigour and transparent reporting is required to facilitate independent reproducibility. This review highlights that in human T cell studies, this entails adopting stringent standardised operating procedures (SOPs) for PBMC processing. We specifically propose the use of HANC's Cross-Network PBMC Processing SOP , when collecting and cryopreserving PBMCs, and the HANC member network International Maternal Pediatric Adolescent AIDS Clinical Trials (IMPAACT) PBMC Thawing SOP when thawing PBMCs. These stringent and detailed protocols include comprehensive reporting procedures to document unavoidable technical variations, such as delayed processing times. Additionally, we make further standardisation and reporting recommendations to minimise and document variability during this critical experimental period. This review provides a detailed overview of the challenges inherent to a procedure often considered routine, highlighting the importance of carefully considering each aspect of SOPs for PBMC collection, cryopreservation, thawing, and culture to ensure accurate interpretation and comparison between studies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Browne, Miller and Doolan.)
- Published
- 2024
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3. Evaluating the stability of host-reference gene expression and simultaneously quantifying parasite burden and host immune responses in murine malaria.
- Author
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Browne DJ, Kelly AM, Brady J, Proietti C, Sarathkumara YD, Pattinson DJ, and Doolan DL
- Subjects
- Animals, Mice, Immunity, Cytokines genetics, Gene Expression, Sporozoites genetics, Mice, Inbred BALB C, Parasites genetics, Malaria parasitology, Malaria Vaccines genetics, Plasmodium yoelii genetics
- Abstract
The efficacy of pre-erythrocytic stage malaria antigens or vaccine platforms is routinely assessed in murine models challenged with Plasmodium sporozoites. Relative liver-stage parasite burden is quantified using reverse transcription quantitative PCR (RTqPCR), which relies on constitutively expressed endogenous control reference genes. However, the stability of host-reference gene expression for RTqPCR analysis following Plasmodium challenge and immunization has not been systematically evaluated. Herein, we evaluated the stability of expression of twelve common RTqPCR reference genes in a murine model of Plasmodium yoelii sporozoite challenge and DNA-adenovirus IV 'Prime-Target' immunization. Significant changes in expression for six of twelve reference genes were shown by one-way ANOVA, when comparing gene expression levels among challenge, immunized, and naïve mice groups. These changes were attributed to parasite challenge or immunization when comparing group means using post-hoc Bonferroni corrected multiple comparison testing. Succinate dehydrogenase (SDHA) and TATA-binding protein (TBP) were identified as stable host-reference genes suitable for relative RTqPCR data normalisation, using the RefFinder package. We defined a robust threshold of 'partial-protection' with these genes and developed a strategy to simultaneously quantify matched host parasite burden and cytokine responses following immunisation or challenge. This is the first report systematically identifying reliable host reference genes for RTqPCR analysis following Plasmodium sporozoite challenge. A robust RTqPCR protocol incorporating reliable reference genes which enables simultaneous analysis of host whole-liver cytokine responses and parasite burden will significantly standardise and enhance results between international malaria vaccine efficacy studies., (© 2023. The Author(s).)
- Published
- 2023
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4. In-situ X-ray monitoring of solidification and related processes of metal alloys.
- Author
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Reinhart G, Browne DJ, Kargl F, García-Moreno F, Becker M, Sondermann E, Binder K, Mullen JS, Zimmermann G, Mathiesen RH, Sillekens WH, and Nguyen-Thi H
- Abstract
X-ray radioscopy enables the in-situ monitoring of metal alloy processes and then gives access to crucial information on the dynamics of the underlying phenomena. In the last decade, the utilisation of this powerful imaging technique has been adapted to microgravity platforms such as sounding rockets and parabolic flights. The combination of microgravity experimentation with X-ray radioscopy has resulted in a leap in the understanding of fundamental science and has opened new paths in the fields of materials science. The present review focuses on the short history of this research, which includes facility developments, microgravity experiments and results obtained by partners of the XRMON (In-situ X-Ray MONitoring of advanced metallurgical processes under microgravity and terrestrial conditions) research project in the framework of the MAP (Microgravity Application Promotion) programme of the European Space Agency. Three illustrative research topics that were advanced significantly through the use of X-ray radioscopy will be detailed: solidification of metal alloys, metallic foam formation and diffusion in melts., (© 2023. Springer Nature Limited.)
- Published
- 2023
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5. The influence of a large build area on the microstructure and mechanical properties of PBF-LB Ti-6Al-4 V alloy.
- Author
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Bagasol AJI, Kaschel FR, Ramachandran S, Mirihanage W, Browne DJ, and Dowling DP
- Abstract
This study investigated the print homogeneity of Ti-6Al-4 V alloy parts, when printed over a large build area of 250 × 250 × 170 mm
3 , using a production scale laser powder bed additive manufacturing system. The effect of part location across this large build area was investigated based on printed part porosity, microstructure, hardness, and tensile properties. In addition, a Hot Isostatic Pressing (HIP) treatment was carried out on the as-built parts, to evaluate its impact on the material properties. A small increase in part porosity from 0.01 to 0.09%, was observed with increasing distance from the argon gas flow inlet, which was located on one side of the build plate, during printing. This effect, which was found to be independent of height from the build plate, is likely to be associated with enhanced levels of condensate or spatter residue, being deposited at distances, further from the gas flow. Despite small differences in porosity, no significant differences were obtained for microstructural features such as prior β grain, α lath thickness, and phase fraction, over the entire build area. Due to this, mechanical performances such as hardness and tensile strengths were also found to be homogenous across the build area. Additionally, it was also observed based on the lattice constants that partial in-situ decomposition of α ' → α + β phases occurred during printing. Post HIP treatment result showed a decrease of 7 and 6%, in the yield strength (YS) and ultimate tensile strength (UTS), respectively, which was associated with a coarsening of α lath widths. The potential of the laser powder bed system for large area printing was successfully demonstrated based on the homogenous microstructure and mechanical properties of the Ti-6Al-4 V alloy parts., Competing Interests: Competing interestsThe authors declare no competing interests., (© The Author(s) 2023.)- Published
- 2023
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6. The Effect of Tropical Temperatures on the Quality of RNA Extracted from Stabilized Whole-Blood Samples.
- Author
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Sarathkumara YD, Browne DJ, Kelly AM, Pattinson DJ, Rush CM, Warner J, Proietti C, and Doolan DL
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- Biomarkers, Blood Specimen Collection methods, Gene Expression Profiling methods, RNA, Messenger genetics, RNA, Ribosomal, 18S genetics, TATA-Box Binding Protein genetics, Temperature, RNA genetics, Succinate Dehydrogenase genetics
- Abstract
Whole-blood-derived transcriptional profiling is widely used in biomarker discovery, immunological research, and therapeutic development. Traditional molecular and high-throughput transcriptomic platforms, including molecular assays with quantitative PCR (qPCR) and RNA-sequencing (RNA-seq), are dependent upon high-quality and intact RNA. However, collecting high-quality RNA from field studies in remote tropical locations can be challenging due to resource restrictions and logistics of post-collection processing. The current study tested the relative performance of the two most widely used whole-blood RNA collection systems, PAXgene
® and Tempus™, in optimal laboratory conditions as well as suboptimal conditions in tropical field sites, including the effects of extended storage times and high storage temperatures. We found that Tempus™ tubes maintained a slightly higher RNA quantity and integrity relative to PAXgene® tubes at suboptimal tropical conditions. Both PAXgene® and Tempus™ tubes gave similar RNA purity (A260/A280). Additionally, Tempus™ tubes preferentially maintained the stability of mRNA transcripts for two reference genes tested, Succinate dehydrogenase complex, subunit A ( SDHA ) and TATA-box-binding protein ( TBP ), even when RNA quality decreased with storage length and temperature. Both tube types preserved the rRNA transcript 18S ribosomal RNA ( 18S ) equally. Our results suggest that Tempus™ blood RNA collection tubes are preferable to PAXgene® for whole-blood collection in suboptimal tropical conditions for RNA-based studies in resource-limited settings.- Published
- 2022
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7. Novel antiinflammatory biologics shaped by parasite-host coevolution.
- Author
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Ryan SM, Ruscher R, Johnston WA, Pickering DA, Kennedy MW, Smith BO, Jones L, Buitrago G, Field MA, Esterman AJ, McHugh CP, Browne DJ, Cooper MM, Ryan RYM, Doolan DL, Engwerda CR, Miles K, Mitreva M, Croese J, Rahman T, Alexandrov K, Giacomin PR, and Loukas A
- Subjects
- Animals, Helminths, Humans, Mice, Anti-Inflammatory Agents pharmacology, Biological Products pharmacology, Colitis drug therapy, Helminth Proteins genetics, Helminth Proteins pharmacology, Inflammatory Bowel Diseases drug therapy, Inflammatory Bowel Diseases parasitology
- Abstract
Parasitic helminth infections, while a major cause of neglected tropical disease burden, negatively correlate with the incidence of immune-mediated inflammatory diseases such as inflammatory bowel diseases (IBD). To evade expulsion, helminths have developed sophisticated mechanisms to regulate their host's immune responses. Controlled experimental human helminth infections have been assessed clinically for treating inflammatory conditions; however, such a radical therapeutic modality has challenges. An alternative approach is to harness the immunomodulatory properties within the worm's excretory-secretory (ES) complement, its secretome. Here, we report a biologics discovery and validation pipeline to generate and screen in vivo a recombinant cell-free secretome library of helminth-derived immunomodulatory proteins. We successfully expressed 78 recombinant ES proteins from gastrointestinal hookworms and screened the crude in vitro translation reactions for anti-IBD properties in a mouse model of acute colitis. After statistical filtering and ranking, 20 proteins conferred significant protection against various parameters of colitis. Lead candidates from distinct protein families, including annexins, transthyretins, nematode-specific retinol-binding proteins, and SCP/TAPS were identified. Representative proteins were produced in mammalian cells and further validated, including ex vivo suppression of inflammatory cytokine secretion by T cells from IBD patient colon biopsies. Proteins identified herein offer promise as novel, safe, and mechanistically differentiated biologics for treating the globally increasing burden of inflammatory diseases.
- Published
- 2022
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8. Multiplex Microsphere PCR (mmPCR) Allows Simultaneous Gram Typing, Detection of Fungal DNA, and Antibiotic Resistance Genes.
- Author
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Browne DJ, Liang F, Gartlan KH, Harris PNA, Hill GR, Corrie SR, and Markey KA
- Subjects
- DNA Primers genetics, DNA, Fungal genetics, Drug Resistance, Microbial, Humans, Microspheres, Sensitivity and Specificity, Anti-Bacterial Agents, Multiplex Polymerase Chain Reaction methods
- Abstract
Objective: To show the high analytical specificity of our multiplex microsphere polymerase chain reaction (mmPCR) method, which offers the simultaneous detection of both general (eg, Gram type) and specific (eg, Pseudomonas species) clinically relevant genetic targets in a single modular multiplex reaction., Materials and Methods: Isolated gDNA of 16S/rRNA Sanger-sequenced and Basic Local Alignment Tool-identified bacterial and fungal isolates were selectively amplified in a custom 10-plex Luminex MagPlex-TAG microsphere-based mmPCR assay. The signal/noise ratio for each reaction was calculated from flow cytometry standard data collected on a BD LSR Fortessa II flow cytometer. Data were normalized to the no-template negative control and the signal maximum. The analytical specificity of the assay was compared to single-plex SYBR chemistry quantitative PCR., Results: Both general and specific primer sets were functional in the 10-plex mmPCR. The general Gram typing and pan-fungal primers correctly identified all bacterial and fungal isolates, respectively. The species-specific and antibiotic resistance-specific primers correctly identified the species- and resistance-carrying isolates, respectively. Low-level cross-reactive signals were present in some reactions with high signal/noise primer ratios., Conclusion: We found that mmPCR can simultaneously detect specific and general clinically relevant genetic targets in multiplex. These results serve as a proof-of-concept advance that highlights the potential of high multiplex mmPCR diagnostics in clinical practice. Further development of specimen-specific DNA extraction techniques is required for sensitivity testing., (© The Author(s) 2022. Published by Oxford University Press on behalf of American Society for Clinical Pathology.)
- Published
- 2022
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9. A high-throughput screening RT-qPCR assay for quantifying surrogate markers of immunity from PBMCs.
- Author
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Browne DJ, Kelly AM, Brady JL, and Doolan DL
- Subjects
- Biomarkers, Cytokines, Epitopes, High-Throughput Screening Assays, Immunosorbents, Leukocytes, Mononuclear, Reverse Transcription
- Abstract
Immunoassays that quantitate cytokines and other surrogate markers of immunity from peripheral blood mononuclear cells (PBMCs), such as flow cytometry or Enzyme-Linked Immunosorbent Spot (ELIspot), allow highly sensitive measurements of immune effector function. However, those assays consume relatively high numbers of cells and expensive reagents, precluding comprehensive analyses and high-throughput screening (HTS). To address this issue, we developed a sensitive and specific reverse transcription-quantitative PCR (RT-qPCR)-based HTS assay, specifically designed to quantify surrogate markers of immunity from very low numbers of PBMCs. We systematically evaluated the volumes and concentrations of critical reagents within the RT-qPCR protocol, miniaturizing the assay and ultimately reducing the cost by almost 90% compared to current standard practice. We assessed the suitability of this cost-optimized RT-qPCR protocol as an HTS tool and determined the assay exceeds HTS uniformity and signal variance testing standards. Furthermore, we demonstrate this technique can effectively delineate a hierarchy of responses from as little as 50,000 PBMCs stimulated with CD4
+ or CD8+ T cell peptide epitopes. Finally, we establish that this HTS-optimized protocol has single-cell analytical sensitivity and a diagnostic sensitivity equivalent to detecting 1:10,000 responding cells ( i.e. , 100 Spot Forming Cells/106 PBMCs by ELIspot) with over 90% accuracy. We anticipate this assay will have widespread applicability in preclinical and clinical studies, especially when samples are limited, and cost is an important consideration., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Browne, Kelly, Brady and Doolan.)- Published
- 2022
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10. Nitrogen fertilizer rate but not form affects the severity of Fusarium wilt in banana.
- Author
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Orr R, Dennis PG, Wong Y, Browne DJ, Cooper M, Birt HWG, Lapis-Gaza HR, Pattison AB, and Nelson PN
- Abstract
Nitrogen (N) fertilizers are routinely applied to bananas ( Musa spp.) to increase production but may exacerbate plant diseases like Fusarium wilt of banana (FWB), which is the most economically important disease. Here, we characterized the effects of N rate and form on banana plant growth, root proteome, bacterial and fungal diversity in the rhizosphere, the concentration of Fusarium oxysporum f.sp. cubense (Foc) in the soil, and the FWB severity. Banana plants ( Musa subgroup ABB) were grown under greenhouse conditions in soil with ammonium or nitrate supplemented at five N rates, and with or without inoculation with Foc. The growth of non-inoculated plants was positively correlated with the N rate. In bananas inoculated with Foc, disease severity increased with the N rate, resulting in the Foc-inoculated plant growth being greatest at intermediate N rates. The abundance of Foc in the soil was weakly related to the treatment conditions and was a poor predictor of disease severity. Fungal diversity was consistently affected by Foc inoculation, while bacterial diversity was associated with changes in soil pH resulting from N addition, in particular ammonium. N rate altered the expression of host metabolic pathways associated with carbon fixation, energy usage, amino acid metabolism, and importantly stress response signaling, irrespective of inoculation or N form. Furthermore, in diseased plants, Pathogenesis-related protein 1, a key endpoint for biotic stress response and the salicylic acid defense response to biotrophic pathogens, was negatively correlated with the rate of ammonium fertilizer but not nitrate. As expected, inoculation with Foc altered the expression of a wide range of processes in the banana plant including those of defense and growth. In summary, our results indicate that the severity of FWB was negatively associated with host defenses, which was influenced by N application (particularly ammonium), and shifts in microbial communities associated with ammonium-induced acidification., (Copyright © 2022 Orr, Dennis, Wong, Browne, Cooper, Birt, Lapis-Gaza, Pattison and Nelson.)
- Published
- 2022
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11. Maternal choline supplementation in a rat model of periconceptional alcohol exposure: Impacts on the fetus and placenta.
- Author
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Steane SE, Fielding AM, Kent NL, Andersen I, Browne DJ, Tejo EN, Gårdebjer EM, Kalisch-Smith JI, Sullivan MA, Moritz KM, and Akison LK
- Subjects
- Animals, Brain embryology, Choline blood, DNA Methylation, Dietary Supplements, Female, Fetal Development drug effects, Fetal Growth Retardation chemically induced, Glycogen analysis, Liver embryology, Organ Size drug effects, Placenta chemistry, Placenta metabolism, Pregnancy, Rats, Rats, Sprague-Dawley, Choline administration & dosage, Ethanol adverse effects, Fertilization, Fetal Growth Retardation prevention & control, Fetus drug effects, Placenta drug effects
- Abstract
Background: Maternal choline supplementation in rats can ameliorate specific neurological and behavioral abnormalities caused by alcohol exposure during pregnancy. We tested whether choline supplementation ameliorates fetal growth restriction and molecular changes in the placenta associated with periconceptional ethanol exposure (PCE) in the rat., Methods: Sprague Dawley dams were given either 12.5% ethanol (PCE) or 0% ethanol (Con) in a liquid diet from 4 days prior to 4 days after conception. At day 5 of pregnancy, dams were either placed on a standard chow (1.6 g choline/kg chow) or an intermediate chow (2.6 g choline/kg chow). On day 10 of pregnancy, a subset of the intermediate dams were placed on a chow further supplemented with choline (7.2 g choline/kg chow), resulting in 6 groups. Fetuses and placentas were collected on day 20 of pregnancy for analysis., Results: Choline supplementation resulted in increased fetal weight at late gestation, ameliorating the deficits due to PCE. This was most pronounced in litters on a standard chow during pregnancy. Choline also increased fetal liver weight and decreased fetal brain:liver ratio, independent of alcohol exposure. Placental weight was reduced as choline levels in the chow increased, particularly in female placentas. This resulted in a greater ratio of fetal:placental weight, suggesting increased placental efficiency. Global DNA methylation in the placenta was altered in a sex-specific manner by both PCE and choline. However, the increased glycogen deposition in female placentas, previously reported in this PCE model, was not prevented by choline supplementation., Conclusions: Our results suggest that choline has the potential to ameliorate fetal growth restriction associated with PCE and improve placental efficiency following prenatal alcohol exposure. Our study highlights the importance of maternal nutrition in moderating the severity of adverse fetal and placental outcomes that may arise from prenatal alcohol exposure around the time of conception., (© 2021 Research Society on Alcoholism.)
- Published
- 2021
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12. Systematic comparison of duration of untreated illness versus duration of untreated psychosis in relation to psychopathology and dysfunction in the Cavan-Monaghan first episode psychosis study (CAMFEPS).
- Author
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Nkire N, Scully PJ, Browne DJ, Baldwin PA, Kingston T, Owoeye O, Kinsella A, O'Callaghan E, Russell V, and Waddington JL
- Subjects
- Humans, Psychopathology, Quality of Life, Time Factors, Psychotic Disorders psychology, Schizophrenia complications
- Abstract
This study systematically compared duration of untreated illness (DUI) with duration of untreated psychosis (DUP) in prediction of impairment at first-episode psychosis and investigated the extent to which these relationships are influenced by premorbid features. The Cavan-Monaghan First Episode Psychosis Study ascertained cases of first-episode psychosis in rural Ireland via all routes to care with limited variations in socioeconomic milieu. Cases were evaluated for DUI and DUP and assessed clinically for psychopathology, neuropsychology, neurology, insight and quality of life, together with premorbid features. Analyses then determined prediction of clinical assessments by DUI versus DUP. The study population consisted of 163 cases of first episode psychosis, among which 74 had a schizophrenia spectrum disorder. Shorter DUI but not DUP predicted less severe positive and general symptoms, while shorter DUP and particularly DUI predicted less severe negative symptoms; neither shorter DUP nor shorter DUI predicted less severe cognitive impairment or fewer neurological soft signs; shorter DUP and DUI predicted increased quality of life; shorter DUI but not DUP predicted greater insight. Only prediction of quality of life was weakened by consideration of premorbid features. Results were generally similar across the two diagnostic groupings. The present findings systematically delineate associations with DUI versus DUP across domains of impairment in first episode psychosis. They suggest that DUI may reflect a more insidious process than DUP and that reduction in DUI may be associated with more consistent and broader diminutions in impairment than for DUP., Competing Interests: Declaration of Competing Interest All authors declare that they have no conflict of interest., (Copyright © 2021. Published by Elsevier B.V.)
- Published
- 2021
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13. Systematic epidemiological and clinical comparisons across all 12 DSM-IV psychotic diagnoses in the Cavan-Monaghan First Episode Psychosis Study (CAMFEPS).
- Author
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Nkire N, Scully PJ, Browne DJ, Baldwin PA, Kingston T, Owoeye O, Kinsella A, O'Callaghan E, Russell V, and Waddington JL
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Female, Humans, Incidence, Ireland epidemiology, Male, Middle Aged, Quality of Life, Young Adult, Diagnostic and Statistical Manual of Mental Disorders, Psychotic Disorders epidemiology
- Abstract
Background: Research on psychotic illness is loosening emphasis on diagnostic stringency in favour of including a more dimensionally based conceptualization of psychopathology and pathobiology. However, to clarify these notions requires investigation of the full scope of psychotic diagnoses., Methods: The Cavan-Monaghan First Episode Psychosis Study ascertained cases of first episode psychosis across all 12 DSM-IV psychotic diagnoses via all routes to care: public, private or forensic; home-based, outpatient or inpatient. There was no arbitrary upper age cut-off and minimal impact of factors associated with variations in social milieu, ethnicity or urbanicity. Cases were evaluated epidemiologically and assessed for psychopathology, neuropsychology, neurology, antecedent factors, insight and quality of life., Results: Among 432 cases, the annual incidence of any DSM-IV psychotic diagnosis was 34.1/100 000 of population and encompassed functional psychotic diagnoses, substance-induced psychopathology and psychopathology due to general medical conditions, through to psychotic illness that defied contemporary diagnostic algorithms. These 12 DSM-IV diagnostic categories, including psychotic disorder not otherwise specified, showed clinical profiles that were consistently more similar than distinct., Conclusions: There are considerable similarities and overlaps across a broad range of diagnostic categories in the absence of robust discontinuities between them. Thus, psychotic illness may be of such continuity that it cannot be fully captured by operational diagnostic algorithms that, at least in part, assume discontinuities. This may reflect the impact of diverse factors each of which acts on one or more overlapping components of a common, dysfunctional neuronal network implicated in the pathobiology of psychotic illness.
- Published
- 2021
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14. An Analytically and Diagnostically Sensitive RNA Extraction and RT-qPCR Protocol for Peripheral Blood Mononuclear Cells.
- Author
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Browne DJ, Brady JL, Waardenberg AJ, Loiseau C, and Doolan DL
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- Amino Acid Sequence, Antigens, Viral immunology, Epitopes immunology, Histocompatibility Testing, Humans, Immunoassay, Lymphocyte Activation, Microspheres, Peptide Fragments immunology, RNA genetics, Reagent Kits, Diagnostic, Sensitivity and Specificity, Single-Cell Analysis, Leukocytes, Mononuclear chemistry, RNA isolation & purification, Real-Time Polymerase Chain Reaction methods
- Abstract
Reliable extraction and sensitive detection of RNA from human peripheral blood mononuclear cells (PBMCs) is critical for a broad spectrum of immunology research and clinical diagnostics. RNA analysis platforms are dependent upon high-quality and high-quantity RNA; however, sensitive detection of specific responses associated with high-quality RNA extractions from human samples with limited PBMCs can be challenging. Furthermore, the comparative sensitivity between RNA quantification and best-practice protein quantification is poorly defined. Therefore, we provide herein a critical evaluation of the wide variety of current generation of RNA-based kits for PBMCs, representative of several strategies designed to maximize sensitivity. We assess these kits with a reverse transcription quantitative PCR (RT-qPCR) assay optimized for both analytically and diagnostically sensitive cell-based RNA-based applications. Specifically, three RNA extraction kits, one post-extraction RNA purification/concentration kit, four SYBR master-mix kits, and four reverse transcription kits were tested. RNA extraction and RT-qPCR reaction efficiency were evaluated with commonly used reference and cytokine genes. Significant variation in RNA expression of reference genes was apparent, and absolute quantification based on cell number was established as an effective RT-qPCR normalization strategy. We defined an optimized RNA extraction and RT-qPCR protocol with an analytical sensitivity capable of single cell RNA detection. The diagnostic sensitivity of this assay was sufficient to show a CD8
+ T cell peptide epitope hierarchy with as few as 1 × 104 cells. Finally, we compared our optimized RNA extraction and RT-qPCR protocol with current best-practice immune assays and demonstrated that our assay is a sensitive alternative to protein-based assays for peptide-specific responses, especially with limited PBMCs number. This protocol with high analytical and diagnostic sensitivity has broad applicability for both primary research and clinical practice., (Copyright © 2020 Browne, Brady, Waardenberg, Loiseau and Doolan.)- Published
- 2020
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15. Revealing internal flow behaviour in arc welding and additive manufacturing of metals.
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Aucott L, Dong H, Mirihanage W, Atwood R, Kidess A, Gao S, Wen S, Marsden J, Feng S, Tong M, Connolley T, Drakopoulos M, Kleijn CR, Richardson IM, Browne DJ, Mathiesen RH, and Atkinson HV
- Abstract
Internal flow behaviour during melt-pool-based metal manufacturing remains unclear and hinders progression to process optimisation. In this contribution, we present direct time-resolved imaging of melt pool flow dynamics from a high-energy synchrotron radiation experiment. We track internal flow streams during arc welding of steel and measure instantaneous flow velocities ranging from 0.1 m s
-1 to 0.5 m s-1 . When the temperature-dependent surface tension coefficient is negative, bulk turbulence is the main flow mechanism and the critical velocity for surface turbulence is below the limits identified in previous theoretical studies. When the alloy exhibits a positive temperature-dependent surface tension coefficient, surface turbulence occurs and derisory oxides can be entrapped within the subsequent solid as result of higher flow velocities. The widely used arc welding and the emerging arc additive manufacturing routes can be optimised by controlling internal melt flow through adjusting surface active elements.- Published
- 2018
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16. Functional outcome and service engagement in major depressive disorder with psychotic features: comparisons with schizophrenia, schizoaffective disorder and bipolar disorder in a 6-year follow-up of the Cavan-Monaghan First Episode Psychosis Study (CAMFEPS).
- Author
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Kingston T, Scully PJ, Browne DJ, Baldwin PA, Kinsella A, O'Callaghan E, Russell V, and Waddington JL
- Subjects
- Adult, Aged, Female, Humans, Ireland epidemiology, Longitudinal Studies, Male, Middle Aged, Psychotic Disorders diagnosis, Psychotic Disorders epidemiology, Psychotic Disorders psychology, Quality of Life psychology, Rural Population, Bipolar Disorder diagnosis, Bipolar Disorder epidemiology, Bipolar Disorder psychology, Disease Management, Schizophrenia diagnosis, Schizophrenia epidemiology, Schizophrenic Psychology
- Abstract
Objective: While long-term outcome following a first psychotic episode is well studied in schizophrenia (SZ), schizoaffective disorder (SA), and bipolar disorder (BD), major depressive disorder with psychotic features (MDDP) has received less investigation. This study compares MDDP with SZ, SA, and BD at 6-year follow-up., Methods: At 6 years after a first psychotic episode, follow-up data on psychopathology, functioning, quality of life, and service engagement were obtained for 27 cases of MDDP in comparison to 60 SZ, 27 SA, and 35 BD., Results: Positive psychotic symptoms were less prominent in MDDP and BD than in SZ and SA. Negative symptoms, impaired functioning, and reduction in objectively determined quality of life were less prominent in MDDP and BD, intermediate in SA and most prominent in SZ. However, subjectively determined quality of life was indistinguishable across diagnoses. Service engagement was highest for MDDP, intermediate for SA and BD, and lowest for SZ., Conclusions: At 6-year follow-up, these diagnoses are characterized by quantitative rather than qualitative differences in psychopathology, functionality, quality of life, and service engagement, with considerable overlap between them. These findings suggest that MDDP should join SZ, SA, and BD in a milieu of psychosis that transcends arbitrary boundaries., (© 2018 John Wiley & Sons Ltd.)
- Published
- 2018
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17. Development of a Multiplexed Microsphere PCR for Culture-Free Detection and Gram-Typing of Bacteria in Human Blood Samples.
- Author
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Liang F, Browne DJ, Gray MJ, Gartlan KH, Smith DD, Barnard RT, Hill GR, Corrie SR, and Markey KA
- Subjects
- Gram-Negative Bacteria classification, Gram-Negative Bacteria genetics, Gram-Positive Bacteria classification, Gram-Positive Bacteria genetics, Humans, Microspheres, Multiplex Polymerase Chain Reaction, Bacteremia diagnosis, Bacteremia microbiology, Bacteria classification, Bacteria genetics, Molecular Typing methods, Polymerase Chain Reaction methods
- Abstract
Bloodstream infection is a significant clinical problem, particularly in vulnerable patient groups such as those undergoing chemotherapy and bone marrow transplantation. Clinical diagnostics for suspected bloodstream infection remain centered around blood culture (highly variable timing, in the order of hours to days to become positive), and empiric use of broad-spectrum antibiotics is therefore employed for patients presenting with febrile neutropenia. Gram-typing provides the first opportunity to target therapy (e.g., combinations containing vancomycin or teicoplanin for Gram-positives; piperacillin-tazobactam or a carbapenem for Gram-negatives); however, current approaches require blood culture. In this study, we describe a multiplexed microsphere-PCR assay with flow cytometry readout, which can distinguish Gram-positive from Gram-negative bacterial DNA in a 3.5 h time period. The combination of a simple assay design (amplicon-dependent release of Gram-type specific Cy3-labeled oligonucleotides) and the Luminex-based readout (for quantifying each specific Cy3-labeled sequence) opens opportunities for further multiplexing. We demonstrate the feasibility of detecting common Gram-positive and Gram-negative organisms after spiking whole bacteria into healthy human blood prior to DNA extraction. Further development of DNA extraction methods is required to reach detection limits comparable to blood culture.
- Published
- 2018
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18. Flt-3L Expansion of Recipient CD8α + Dendritic Cells Deletes Alloreactive Donor T Cells and Represents an Alternative to Posttransplant Cyclophosphamide for the Prevention of GVHD.
- Author
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Markey KA, Kuns RD, Browne DJ, Gartlan KH, Robb RJ, Martins JP, Henden AS, Minnie SA, Cheong M, Koyama M, Smyth MJ, Steptoe RJ, Belz GT, Brocker T, Degli-Esposti MA, Lane SW, and Hill GR
- Subjects
- Animals, Bone Marrow Transplantation methods, Dendritic Cells drug effects, Female, Graft vs Host Disease prevention & control, Graft vs Leukemia Effect drug effects, Leukemia immunology, Mice, Mice, Inbred C57BL, T-Lymphocytes drug effects, Tissue Donors, Transplantation, Homologous methods, CD8 Antigens immunology, Cyclophosphamide pharmacology, Dendritic Cells immunology, Graft vs Host Disease immunology, Graft vs Leukemia Effect immunology, Membrane Proteins immunology, T-Lymphocytes immunology
- Abstract
Purpose: Allogeneic bone marrow transplantation (BMT) provides curative therapy for leukemia via immunologic graft-versus-leukemia (GVL) effects. In practice, this must be balanced against life threatening pathology induced by graft-versus-host disease (GVHD). Recipient dendritic cells (DC) are thought to be important in the induction of GVL and GVHD. Experimental Design: We have utilized preclinical models of allogeneic BMT to dissect the role and modulation of recipient DCs in controlling donor T-cell-mediated GVHD and GVL. Results: We demonstrate that recipient CD8α
+ DCs promote activation-induced clonal deletion of allospecific donor T cells after BMT. We compared pretransplant fms-like tyrosine kinase-3 ligand (Flt-3L) treatment to the current clinical strategy of posttransplant cyclophosphamide (PT-Cy) therapy. Our results demonstrate superior protection from GVHD with the immunomodulatory Flt-3L approach, and similar attenuation of GVL responses with both strategies. Strikingly, Flt-3L treatment permitted maintenance of the donor polyclonal T-cell pool, where PT-Cy did not. Conclusions: These data highlight pre-transplant Flt-3L therapy as a potent new therapeutic strategy to delete alloreactive T cells and prevent GVHD, which appears particularly well suited to haploidentical BMT where the control of infection and the prevention of GVHD are paramount. Clin Cancer Res; 24(7); 1604-16. ©2018 AACR ., (©2018 American Association for Cancer Research.)- Published
- 2018
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19. Bulk Metallic Glasses for Implantable Medical Devices and Surgical Tools.
- Author
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Meagher P, O'Cearbhaill ED, Byrne JH, and Browne DJ
- Subjects
- Alloys, Biocompatible Materials, Corrosion, Glass, Prostheses and Implants
- Abstract
With increasing knowledge of the materials science of bulk metallic glasses (BMGs) and improvements in their properties and processing, they have started to become candidate materials for biomedical devices. A dichotomy in the types of medical applications has also emerged, in which some families of BMGs are being developed for permanent devices whilst another family - of Mg-based alloys - is showing promise in bioabsorbable implants. The current status of these metallurgical and technological developments is summarized., (© 2016 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2016
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20. Diagnostic trajectory, interplay and convergence/divergence across all 12 DSM-IV psychotic diagnoses: 6-year follow-up of the Cavan-Monaghan First Episode Psychosis Study (CAMFEPS).
- Author
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Kingston T, Scully PJ, Browne DJ, Baldwin PA, Kinsella A, Russell V, O'Callaghan E, and Waddington JL
- Subjects
- Adult, Depression diagnosis, Depression epidemiology, Depression mortality, Diagnostic and Statistical Manual of Mental Disorders, Disease Progression, Female, Follow-Up Studies, Humans, Ireland epidemiology, Male, Middle Aged, Prospective Studies, Psychotic Disorders epidemiology, Psychotic Disorders mortality, Psychotic Disorders classification
- Abstract
Background: The boundaries of psychotic illness and the extent to which operational diagnostic categories are distinct in the long term remain poorly understood. Clarification of these issues requires prospective evaluation of diagnostic trajectory, interplay and convergence/divergence across psychotic illness, without a priori diagnostic or other restrictions., Method: The Cavan-Monaghan First Episode Psychosis Study (CAMFEPS), conducted using methods to attain the closest approximation to epidemiological completeness, incepts all 12 DSM-IV psychotic diagnoses. In this study we applied methodologies to achieve diagnostic reassessments on follow-up, at a mean of 6.4 years after first presentation, for 196 (97%) of the first 202 cases, with quantification of prospective and retrospective consistency., Results: Over 6 years, the 12 initial psychotic diagnoses were characterized by numerous transitions but only limited convergence towards a smaller number of more stable diagnostic nodes. In particular, for initial brief psychotic disorder (BrP), in 85% of cases this was the harbinger of long-term evolution to serious psychotic illness of diagnostic diversity; for initial major depressive disorder with psychotic features (MDDP), in 18% of cases this was associated with mortality of diverse causality; and for initial psychotic disorder not otherwise specified (PNOS), 31% of cases continued to defy DSM-IV criteria., Conclusions: CAMFEPS methodology revealed, on an individual case basis, a diversity of stabilities in, and transitions between, all 12 DSM-IV psychotic diagnoses over 6 years; thus, psychotic illness showed longitudinal disrespect to current nosology and may be better accommodated by a dimensional model. In particular, a first episode of BrP or MDDP may benefit from more vigorous, sustained interventions.
- Published
- 2013
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21. The influence of cooling conditions on grain size, secondary phase precipitates and mechanical properties of biomedical alloy specimens produced by investment casting.
- Author
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Kaiser R, Williamson K, O'Brien C, Ramirez-Garcia S, and Browne DJ
- Subjects
- Elastic Modulus, Metals, Heavy chemistry, Particle Size, Alloys chemistry, Biocompatible Materials chemistry, Chemical Precipitation, Cold Temperature, Mechanical Phenomena
- Abstract
The objective of this work was to investigate and evaluate the effect of the cooling environment on the microstructure, secondary phase precipitates and mechanical properties of an as-cast cobalt alloy. The microstructure of castings has a large bearing on the mechanical properties, grain size, porosity and the morphology of carbide precipitates are thought to influence hardness, tensile strength and ductility. It is postulated that a greater understanding of microstructure and secondary phase precipitate response to casting parameters could lead to the optimisation of casting parameters and serve to reduce the requirement of thermo-mechanical treatments currently applied to refine as-cast structures and achieve adequate mechanical properties. Thermal analysis was performed to determine the critical stages of cooling. Ten millimetre diameter cylindrical specimens which could be machined into tension test specimens were cast and cooled under different conditions to impose different cooling rates. Analytical techniques such as optical microscopy (OM), scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDX), tensile testing and micro-hardness testing were used to study the specimens. Parameters studied include grain size, secondary dendrite arm spacing, secondary phase precipitates, porosity, hardness, ultimate tensile strength, yield strength and elongation. The microstructure of as-cast Co-28Cr-6Mo was found to consist of a dendritic matrix with secondary phases precipitated at grain boundaries and interdendritic zones. These secondary phase precipitates consist of carbides, rich in chromium and molybdenum. The size and area fraction of carbides was found to decrease significantly with increasing cooling rate while the micro-porosity was only marginally affected. The as-cast grains are illustrated for the first time showing a significant difference in size between insulated and naturally cooled specimens. The secondary dendrite arm spacing was determined to be significantly affected by the various cooling environments and the mechanical properties of hardness, ultimate tensile strength and yield strength all increased with increasing cooling rate while the ductility decreased. Correlations between microstructural features and mechanical properties are proposed., (Copyright © 2013 Elsevier Ltd. All rights reserved.)
- Published
- 2013
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22. CE with a boron-doped diamond electrode for trace detection of endocrine disruptors in water samples.
- Author
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Browne DJ, Zhou L, Luong JH, and Glennon JD
- Subjects
- Electrodes, Limit of Detection, Boron chemistry, Diamond chemistry, Drinking Water analysis, Electrophoresis, Capillary methods, Endocrine Disruptors analysis, Water Pollutants, Chemical analysis
- Abstract
Off-line SPE and CE coupled with electrochemical detection have been used for the determination of bisphenol A (BPA), bisphenol F, 4-ethylphenol, and bisphenol A diglycidyl ether in bottled drinking water. The use of boron-doped diamond electrode as an electrochemical detector in amperometric mode that provides a favorable analytical performance for detecting these endocrine-disrupting compounds, such as lower noise levels, higher peak resolution with enhanced sensitivity, and improved resistance against electrode passivation. The oxidative electrochemical detection of the endocrine-disrupting compounds was accomplished by boron-doped diamond electrode poised at +1.4 V versus Ag/AgCl without electrode pretreatment. An off-line SPE procedure (Bond Elut® C18 SPE cartridge) was utilized to extract and preconcentrate the compounds prior to separation and detection. The minimum concentration detectable for all four compounds ranged from 0.01 to 0.06 μM, having S/N equal to three. After exposing the plastic bottle water container under sunlight for 7 days, the estimated concentration of BPA in the bottled drinking water was estimated to be 0.03 μM. This proposed approach has great potential for rapid and effective determination of BPA content present in water packaging of plastic bottles that have been exposed to sunlight for an extended period of time., (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2013
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23. Employment services as an early intervention for young people with mental illness.
- Author
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Browne DJ and Waghorn G
- Subjects
- Adolescent, Adult, Evidence-Based Practice statistics & numerical data, Female, Humans, Male, New Zealand, Outcome Assessment, Health Care methods, Employment, Supported statistics & numerical data, Mental Disorders rehabilitation, Outcome Assessment, Health Care statistics & numerical data, Rehabilitation, Vocational methods
- Abstract
Aim: To examine the service characteristics and effectiveness of a segregated employment service assisting young clients with mental illness in New Zealand., Methods: The service assisted both youth and adults with severe mental illness to find and keep competitive employment. A retrospective case study method was used to examine service effectiveness with respect to employment outcomes attained by 49 clients aged 16–25 years over a 2-year period (2005–2007). These results were compared with recent national and international benchmarks., Results: As a service segregated from public mental health services, there were no formal arrangements with local mental health teams, limiting coordination of services and reducing fidelity to evidence-based practices in supported employment. Despite an inability to collaborate closely with local community mental health services and a contract not specifically targeting youth, the service was high performing on a range of employment outcome variables., Conclusions: Subject to some study design and benchmarking limitations, these results support the continuing use of evidence-based practices in supported employment and supported education as important early interventions for young people with mental illnesses.
- Published
- 2010
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24. Frontonasal dysmorphology in bipolar disorder by 3D laser surface imaging and geometric morphometrics: comparisons with schizophrenia.
- Author
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Hennessy RJ, Baldwin PA, Browne DJ, Kinsella A, and Waddington JL
- Subjects
- Adult, Analysis of Variance, Female, Humans, Imaging, Three-Dimensional methods, Lasers, Male, Middle Aged, Principal Component Analysis, Young Adult, Bipolar Disorder pathology, Cephalometry methods, Diagnostic Imaging methods, Face pathology, Forehead pathology, Nose pathology, Schizophrenia pathology
- Abstract
Any developmental relationship between bipolar disorder and schizophrenia engenders continuing debate. As the brain and face emerge in embryological intimacy, brain dysmorphogenesis is accompanied by facial dysmorphogenesis. 3D laser surface imaging was used to capture the facial surface of 13 male and 14 female patients with bipolar disorder in comparison with 61 male and 75 female control subjects and with 37 male and 32 female patients with schizophrenia. Surface images were analysed using geometric morphometrics and 3D visualisations to identify domains of facial shape that distinguish bipolar patients from controls and bipolar patients from those with schizophrenia. Both male and female bipolar patients evidenced significant facial dysmorphology: common to male and female patients was overall facial widening, increased width of nose, narrowing of mouth and upward displacement of the chin; dysmorphology differed between male and female patients for nose length, lip thickness and tragion height. There were few morphological differences in comparison with schizophrenia patients. That dysmorphology of the frontonasal prominences and related facial regions in bipolar disorder is more similar to than different from that found in schizophrenia indicates some common dysmorphogenesis. Bipolar disorder and schizophrenia might reflect similar insult(s) acting over slightly differing time-frames or slightly differing insult(s) acting over a similar time-frame., ((c) 2010 Elsevier B.V. All rights reserved.)
- Published
- 2010
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25. A 'silent' political protest by an asylum seeker presenting to an Irish psychiatric service.
- Author
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Browne DJ, Rohllia H, and Gannon M
- Abstract
We report a case of a male asylum seeker, protesting politically, who stitched his lips together, presenting to a psychiatric service for assessment. We review the literature in this area. Funding of psychiatric services to meet the complex needs of immigrants should be an integral part of service development.
- Published
- 2008
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26. Three-dimensional laser surface imaging and geometric morphometrics resolve frontonasal dysmorphology in schizophrenia.
- Author
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Hennessy RJ, Baldwin PA, Browne DJ, Kinsella A, and Waddington JL
- Subjects
- Adult, Cephalometry, Female, Humans, Male, Middle Aged, Nose abnormalities, Reference Values, Sex Factors, Craniofacial Abnormalities diagnosis, Diagnostic Imaging, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Lasers, Schizophrenia diagnosis
- Abstract
Background: Although a role for early developmental disturbance(s) in schizophrenia is postulated, it has proved difficult to identify hard, biological evidence. The brain and face emerge in embryologic intimacy, such that in neurodevelopmental disorders, brain dysmorphogenesis is accompanied by facial dysmorphogenesis., Methods: Three-dimensional (3D) laser surface imaging was used to capture the facial surface of patients and control subjects in 37 male and 32 female patients who satisfied DSM-IV criteria for schizophrenia in comparison with 58 male and 34 female control subjects. Surface images were analyzed using geometric morphometrics and 3D visualizations to identify domains of facial shape that distinguish patients from control subjects., Results: Both male and, particularly, female patients evidenced significant facial dysmorphology. There was narrowing and reduction of the mid to lower face and frontonasal prominences, including reduced width and posterior displacement of the mouth, lips, and chin; increased width of the upper face, mandible, and skull base, with lateral displacement of the cheeks, eyes, and orbits; and anterior displacement of the superior margins of the orbits., Conclusions: The frontonasal prominence, which enjoys the most intimate embryologic relationship with the anterior brain and also orchestrates aspects of development in maxillary and mandibular domains, evidences a characteristic topography of dysmorphogenesis in schizophrenia.
- Published
- 2007
- Full Text
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