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Cluver CA, Alexander R, Pistorius L. Maternal propranolol treatment for fetal pleural effusion. Ultrasound Obstet Gynecol 2024. [PMID: 38477157 DOI: 10.1002/uog.27639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Affiliation(s)
- C A Cluver
- Department of Obstetrics and Gynaecology, Stellenbosch University, Cape Town, South Africa
- Panorama Perinatology, Cape Town, South Africa
- Mercy Perinatal, University of Melbourne, Melbourne, Australia
| | - R Alexander
- Panorama Mediclinic, Cape Town, South Africa
| | - L Pistorius
- Department of Obstetrics and Gynaecology, Stellenbosch University, Cape Town, South Africa
- Panorama Perinatology, Cape Town, South Africa
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Douthwaite JA, Lesage B, Gleirscher M, Calinescu R, Aitken JM, Alexander R, Law J. A Modular Digital Twinning Framework for Safety Assurance of Collaborative Robotics. Front Robot AI 2022; 8:758099. [PMID: 34977162 PMCID: PMC8719333 DOI: 10.3389/frobt.2021.758099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Digital twins offer a unique opportunity to design, test, deploy, monitor, and control real-world robotic processes. In this paper we present a novel, modular digital twinning framework developed for the investigation of safety within collaborative robotic manufacturing processes. The modular architecture supports scalable representations of user-defined cyber-physical environments, and tools for safety analysis and control. This versatile research tool facilitates the creation of mixed environments of Digital Models, Digital Shadows, and Digital Twins, whilst standardising communication and physical system representation across different hardware platforms. The framework is demonstrated as applied to an industrial case-study focused on the safety assurance of a collaborative robotic manufacturing process. We describe the creation of a digital twin scenario, consisting of individual digital twins of entities in the manufacturing case study, and the application of a synthesised safety controller from our wider work. We show how the framework is able to provide adequate evidence to virtually assess safety claims made against the safety controller using a supporting validation module and testing strategy. The implementation, evidence and safety investigation is presented and discussed, raising exciting possibilities for the use of digital twins in robotic safety assurance.
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Affiliation(s)
- J A Douthwaite
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield, United Kingdom
| | - B Lesage
- Department of Computer Science, University of York, York, United Kingdom
| | - M Gleirscher
- Mathematics and Computer Science, University of Bremen, Bremen, Germany
| | - R Calinescu
- Department of Computer Science, University of York, York, United Kingdom
| | - J M Aitken
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield, United Kingdom
| | - R Alexander
- Department of Computer Science, University of York, York, United Kingdom
| | - J Law
- Department of Computer Science and the Advanced Manufacturing Research Centre, University of Sheffield, Sheffield, United Kingdom
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Schneider LS, Bennett DA, Farlow MR, Peskind ER, Raskind MA, Sano M, Stern Y, Haneline S, Welsh-Bohmer KA, O'Neil J, Walter R, Maresca S, Culp M, Alexander R, Saunders AM, Burns DK, Chiang C. Adjudicating Mild Cognitive Impairment Due to Alzheimer's Disease as a Novel Endpoint Event in the TOMMORROW Prevention Clinical Trial. J Prev Alzheimers Dis 2022; 9:625-634. [PMID: 36281666 DOI: 10.14283/jpad.2022.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
BACKGROUND The onset of mild cognitive impairment (MCI) is an essential outcome in Alzheimer's disease (AD) prevention trials and a compelling milestone for clinically meaningful change. Determining MCI, however, may be variable and subject to disagreement. Adjudication procedures may improve the reliability of these determinations. We report the performance of an adjudication committee for an AD prevention trial. METHODS The TOMMORROW prevention trial selected cognitively normal participants at increased genetic risk for AD and randomized them to low-dose pioglitazone or placebo treatment. When adjudication criteria were triggered, a participant's clinical information was randomly assigned to a three-member panel of a six-member independent adjudication committee. Determination of whether or not a participant reached MCI due to AD or AD dementia proceeded through up to three review stages - independent review, collaborative review, and full committee review - requiring a unanimous decision and ratification by the chair. RESULTS Of 3494 participants randomized, the committee adjudicated on 648 cases from 386 participants, resulting in 96 primary endpoint events. Most participants had cases that were adjudicated once (n = 235, 60.9%); the rest had cases that were adjudicated multiple times. Cases were evenly distributed among the eight possible three-member panels. Most adjudicated cases (485/648, 74.8%) were decided within the independent review (stage 1); 14.0% required broader collaborative review (stage 2), and 11.1% needed full committee discussion (stage 3). The primary endpoint event decision rate was 39/485 (8.0%) for stage 1, 29/91 (31.9%) for stage 2, and 28/72 (38.9%) for stage 3. Agreement between the primary event outcomes supported by investigators' clinical diagnoses and the decisions of the adjudication committee increased from 50% to approximately 93% (after around 100 cases) before settling at 80-90% for the remainder of the study. CONCLUSIONS The adjudication process was designed to provide independent, consistent determinations of the trial endpoints. These outcomes demonstrated the extent of uncertainty among trial investigators and agreement between adjudicators when the transition to MCI due to AD was prospectively assessed. These methods may inform clinical endpoint determination in future AD secondary prevention studies. Reliable, accurate assessment of clinical events is critical for prevention trials and may mean the difference between success and failure.
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Affiliation(s)
- L S Schneider
- Lon S. Schneider, Keck School of Medicine of USC, 1540 Alcazar St, CHP216, Los Angeles CA, 90033, USA, Phone no: +1 323 442 7600,
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Beggs M, Young K, Pan W, O'Neill D, Saurette M, Cordat E, Dimke H, Alexander R. Claudin‐2 or Claudin ‐12 Is Required to Maintain Calcium Homeostasis. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.02192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Megen W, Tan R, Alexander R, Dimke H. Differential activation of parathyroid and renal Ca
2+
‐sensing receptors underlies the renal phenotype in autosomal dominant hypocalcemia 1. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.05335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Evans R, Tanaka S, Tanaka S, Touno S, Shimizu K, Sakui S, Wu J, Faessel H, Hang Y, Alexander R, Rosen L, Hartman D. A Phase 1 single ascending dose study of a novel orexin 2 receptor agonist, TAK-925, in healthy volunteers (HV) and subjects with narcolepsy type 1 (NT1) to assess safety, tolerability, pharmacokinetics, and pharmacodynamic outcomes. Sleep Med 2019. [DOI: 10.1016/j.sleep.2019.11.290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Byggmästar J, Granberg F, Sand AE, Pirttikoski A, Alexander R, Marinica MC, Nordlund K. Collision cascades overlapping with self-interstitial defect clusters in Fe and W. J Phys Condens Matter 2019; 31:245402. [PMID: 30754035 DOI: 10.1088/1361-648x/ab0682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Overlap of collision cascades with previously formed defect clusters become increasingly likely at radiation doses typical for materials in nuclear reactors. Using molecular dynamics, we systematically investigate the effects of different pre-existing self-interstitial clusters on the damage produced by an overlapping cascade in bcc iron and tungsten. We find that the number of new Frenkel pairs created in direct overlap with an interstitial cluster is reduced to essentially zero, when the size of the defect cluster is comparable to that of the disordered cascade volume. We develop an analytical model for this reduced defect production as a function of the spatial overlap between a cascade and a defect cluster of a given size. Furthermore, we discuss cascade-induced changes in the morphology of self-interstitial clusters, including transformations between [Formula: see text] and [Formula: see text] dislocation loops in iron and tungsten, and between C15 clusters and dislocation loops in iron. Our results provide crucial new cascade-overlap effects to be taken into account in multi-scale modelling of radiation damage in bcc metals.
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Affiliation(s)
- J Byggmästar
- Department of Physics, University of Helsinki, Helsinki, PO Box 43, FIN-00014, Finland
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Tanase A, Badenoch T, Alexander R. Retrospective analysis of fistula in-ano rates and antibiotic use after perianal abscess drainage. Int J Surg 2018. [DOI: 10.1016/j.ijsu.2018.05.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Perry BI, Cooray SE, Mendis J, Purandare K, Wijeratne A, Manjubhashini S, Dasari M, Esan F, Gunaratna I, Naseem RA, Hoare S, Chester V, Roy A, Devapriam J, Alexander R, Kwok HF. Problem behaviours and psychotropic medication use in intellectual disability: a multinational cross-sectional survey. J Intellect Disabil Res 2018; 62:140-149. [PMID: 29349928 DOI: 10.1111/jir.12471] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/06/2017] [Accepted: 12/15/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Problem behaviours (PBs) are a common cause for clinician contact in people with disorders of intellectual development and may be a common cause for the prescription of psychotropic medication. We aimed to use a large, multinational sample to define the prevalence of PBs, the associations with psychotropic medication use, and to assess for any potential 'diagnostic overshadowing' by the label of PBs in a population of people with disorders of intellectual development. METHOD A multinational, multi-setting, cross-sectional service evaluation and baseline audit was completed. Data were collected from UK hospitals, UK community settings, Sri Lanka and Hong Kong. A semi-structured questionnaire was completed by treating clinicians, capturing demographic details, prevalence rates of intellectual disability and psychotropic medication use, alongside psychiatric co-morbidity. RESULTS A sample size of 358 was obtained, with 65% of included participants treated in an inpatient setting. Psychotropic use was prevalent (90%) in our sample, particularly antipsychotics (74%). The prevalence of PB was high (83%). There was no statistically significant association between psychotropic prescription and recorded psychiatric co-morbidity, suggesting prevalent 'off-label' use for PBs, or poor recording of psychiatric co-morbidity. There was some evidence of possible diagnostic overshadowing due to the PB classification. A higher dose of psychotropic medication was associated with aggression toward others (P = 0.03). CONCLUSIONS We found evidence of prevalent potential 'off-label' use for psychotropic medication, which may be due to PBs. We also found evidence of potential diagnostic-overshadowing, where symptoms of psychiatric co-morbidity may have been attributed to PBs. Our findings provide renewed importance, across borders and health systems, for clinicians to consider a holistic approach to treating PBs, and attempting to best understand the precipitants and predisposing factors before psychotropic prescribing.
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Affiliation(s)
- B I Perry
- Division of Mental Health and Wellbeing, University of Warwick, Coventry, UK
- Coventry and Warwickshire Partnership NHS Trust, Coventry, UK
| | | | - J Mendis
- National Institute of Mental Health, Angoda, Sri Lanka
| | - K Purandare
- Central and North West London NHS Foundation Trust, London, UK
| | - A Wijeratne
- Central and North West London NHS Foundation Trust, London, UK
| | - S Manjubhashini
- South West London and St Georges Mental Health Foundation NHS Trust, London, UK
| | - M Dasari
- Humber NHS Foundation Trust, Driffield, UK
| | - F Esan
- Partnerships in Care, Diss, Diss, UK
| | | | | | - S Hoare
- Partnerships in Care, Diss, Diss, UK
| | - V Chester
- Partnerships in Care, Diss, Diss, UK
| | - A Roy
- Coventry and Warwickshire Partnership NHS Trust, Coventry, UK
| | - J Devapriam
- Leicestershire Partnership NHS Trust, Leicester, UK
| | | | - H F Kwok
- Faculty of Health Sciences, University of Macau, Zhuhai Shi, China
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Abstract
Aims and MethodA postal survey was sent to all consultants in the psychiatry of learning disability from four English regions. Their views on job satisfaction, their core roles and the management re-structuring of services were elicited.ResultsThe proportion agreeing or strongly agreeing with each management option was 79% for integrated mental health–learning disability trusts, 61% for specialist learning disability trusts, 47% for care trusts, 10% for primary care trusts and 5% for social services. Only 34% felt consulted or able to influence the process of change and only 33% were satisfied with the current management changes within their trust but 67% were satisfied overall with their jobs.Clinical ImplicationsManagement from integrated mental health–learning disability trusts is the most preferred option for psychiatrists in learning disability. A large number of consultants, though otherwise satisfied with their jobs, feel excluded or unable to influence the current changes in management structures. A model of integrated service provision in line with the government's learning disability strategy is presented.
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Abstract
Understanding the role of extracellular RNA (exRNA) has emerged as an exciting avenue for biomarker, therapeutic, as well as basic cell-cell communication applications and discoveries. Multiple protocols, kits, and procedures have been developed in the last decade to allow fractionation as well as isolation of subpopulations of macromolecules of interest found in biofluids. Here, we introduce the protocols decision tree developed by the Extracellular RNA Communication Consortium and available on their website (exRNA portal), and compare all methods currently available to the exRNA field and report pros and cons for each platform.
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Affiliation(s)
- Julia Small
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sabrina Roy
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA.,Human Biology Department, University of Toronto, ON, Canada
| | - Roger Alexander
- Pacific Northwest Diabetes Research Institute, Seattle, WA, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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Chester V, Alexander R. Head banging as a form of self-harm among inpatients within forensic mental health and intellectual disability services. Eur Psychiatry 2017. [DOI: 10.1016/j.eurpsy.2017.01.883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Introduction“Head banging” is a common form of self-harm, linked to numerous negative outcomes including significant brain damage. However, little research has investigated the prevalence and correlates of head banging behaviour in clinical populations.MethodHead banging episodes were identified from the incident records (n = 5417) of two inpatient forensic services (one intellectual disability and one mental health), using relevant search terms. Rates were compared between individual patients, by gender, diagnosis and level of security. Incident accounts were analysed qualitatively using thematic analysis.ResultsTwo hundred and twenty nine incidents of head banging were recorded, occurring approximately every three days in each service. The prevalence of the behaviour between individual patients varied widely, ranging from one to 38 incidents within one year. Women and patients with intellectual disability appeared more likely to engage in head banging. Qualitative incident reports indicated that head banging was associated with mental distress, anger, and psychotic experiences.DiscussionHead banging occurs frequently in forensic services, and has documented associations with traumatic brain injury in affected individuals, thus negatively impacting progress through the care pathway and treatment outcomes. Further research should investigate short and long term management strategies and treatment approaches, in order to minimise harm.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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Alexander R, Chester V, Langdon P. A Systematic Review and Synthesis of Outcome Domains for use Within Forensic Services for People with Intellectual Disabilities. Eur Psychiatry 2017. [DOI: 10.1016/j.eurpsy.2017.01.2008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
AimsIn response to the Winterbourne scandal, and the large number of people with intellectual disabilities (IDs) and offending behavior being treated in psychiatric hospitals, this study identified the domains that should be used to measure treatment outcomes of this group.MethodsA systematic search of relevant databases was undertaken to identify domains. Sixty studies met the eligibility criteria, and findings were synthesized using content analysis. The findings were refined within a consultation and consensus exercises with carers, service users, and experts.ResultsThe final framework encompassed three a priori super-ordinate domains (a) effectiveness, (b) patient safety, and (c) patient and carer experience. Within each of these, further sub-domains emerged from our systematic review and consultation exercises. These included severity of clinical symptoms, offending behaviors, reactive and restrictive interventions, quality of life and patient satisfaction.ConclusionsTo index recovery, services need to measure outcome using this framework.
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Denman R, Chester V, Watson J, Nyakunuwa C, Alexander R. The prevalence of obesity among forensic intellectual disability inpatients. Eur Psychiatry 2017. [DOI: 10.1016/j.eurpsy.2017.01.884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BackgroundInpatient mental health settings have been described as “obesogenic” environments, due to factors including psychotropic medication, high calorie food, restricted physical activity and sedentary lifestyles. No research has investigated obesity among forensic intellectual disability inpatients, despite this populations’ increased risk. Therefore, this paper aims to evaluate the prevalence and correlates of overweight and obesity on, and during admission.MethodThe weight and body mass index data of 46 inpatients (15 women and 31 men) within a specialist intellectual disability forensic service was examined for the study.ResultsOnly six patients (13%) were a normal weight at admission, whereas 40 (87%) were overweight or obese. During their admission, 28 (61%) gained weight (average 11.8 kg), and one (2%) maintained. However, 17 patients (37%) lost weight (average 6.2 kg), though 16 remained in overweight/obese categories. There was no correlation between length of stay and weight/BMI.ConclusionsThe majority of patients were overweight or obese on admission, and approximately 60% gained weight during their admission. Women appeared at greater risk of obesity. There was no relationship between length of stay and weight. This is potentially due to the high prevalence of obesity on admission and the impact of previous admissions on weight. The results highlight the need for effective weight management interventions with this population.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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Upton D, Upton P, Alexander R. Well-being in wounds inventory (WOWI): development of a valid and reliable measure of well-being in patients with wounds. J Wound Care 2016; 25:114, 116-20. [PMID: 26947691 DOI: 10.12968/jowc.2016.25.3.114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Physical and psychosocial deficits have been reported in people living with chronic wounds. While the negative impact of these factors on an individual's quality of life (QoL) is well documented, there has been little research into the well-being of those living with chronic wounds, despite recent calls for increased attention to this related, yet distinct construct. This paper introduces the Well-being in Wounds Inventory (WOWI) and provides support for the WOWI as a valid and reliable measure of well-being in patients living with chronic wounds. METHOD A draft questionnaire was administered to a convenience sample of individuals with chronic wounds (n=85) and the resulting data subject to factor analysis in order to refine the structure of the questionnaire. The reliability, validity and responsiveness of the resulting questionnaire were then tested by administration to a second sample of individuals with wounds (n=49). Socio-demographic data, issues affecting patient well-being and well-being factors, such as, emotions; perceived coping skills; social support; personal control; hope for the future, were measured. RESULTS Results confirmed the WOWI as a reliable and valid measure of well-being. Items loaded onto two subscales, 'personal resources' and 'wound worries'. Analysis revealed the WOWI to be highly feasible measure of well-being, with good test-retest reliability and responsiveness to changes in health status. CONCLUSION The current study highlights the importance of assessing well-being factors in individuals living with chronic wounds. It introduces the WOWI as a valid and reliable measure of well-being in chronic wound patients. The authors recommend health-care practitioners take account of well-being as part of a holistic treatment plan in order to maximise patient outcomes. DECLARATION OF INTEREST This project was funded by Urgo Medical. The authors have no conflict of interest to declare.
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Affiliation(s)
- D Upton
- Deputy Dean, Faculty of Health, University of Canberra, ACT
| | - P Upton
- Senior Research Fellow, Centre for Research and Action in Public Health, University of Canberra, ACT
| | - R Alexander
- Research Assistant, School of Applied Psychology, University of Canberra, ACT
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White TS, Alexander R, Callow G, Cooke A, Harris S, Sargent J. A Mobile Climbing Robot for High Precision Manufacture and Inspection of Aerostructures. Int J Rob Res 2016. [DOI: 10.1177/0278364905055701] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this paper we describe the design, development, and experimental trials of a climbing robot for manufacturing and inspection applications within the aerospace industry. We describe the mechanical platform, which utilizes vacuum for attachment to vertical and overhanging surfaces, and a traction system that enables rapid movement of the robot over planar and curved surfaces of any orientation. The main applications considered during the research were the manufacturing processes for large external surface structures such as wings and the post-manufacturing and in-service inspection of such structures. The design of suitable tool packages for manufacturing and non-destructive testing is considered in the paper. The first tool package to be implemented and tested was a five-axis high precision drill, which is described. The control system is described within this paper along with the software architecture. The software architecture for the robot was generalized, allowing different robot configurations to be described and implemented rapidly through structured configuration files. Particular attention is paid to the robot’s localization and navigation system, which provides tool point precision to aircraft manufacturing tolerances. The localization system uses data from several different types of sensors and combines these with information provided by a surface model to derive six-degrees-of-freedom position and orientation using an extended Kalman filter to fuse the state information from the different sources. Tool point position is calculated through direct kinematic transformations. Improvements to this work are described, which utilize one of the initial releases of Lieca’s new six-degrees-of-freedom precision measurement instruments, the Lieca LTD-800. We also summarize the experimental trials and the initial performance in terms of tool point precision and climbing performance. The concept of application of the robot and details of the technologies included in the robot that are outlined in this paper are the subject of separate pending patent applications filed by BAE SYSTEMS plc.
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Affiliation(s)
- T. S. White
- Advanced Information Processing Department, BAE SYSTEMS Advanced Technology Centre, Bristol, UK,
| | - R. Alexander
- Advanced Information Processing Department, BAE SYSTEMS Advanced Technology Centre, Bristol, UK
| | - G. Callow
- Advanced Information Processing Department, BAE SYSTEMS Advanced Technology Centre, Bristol, UK
| | - A. Cooke
- Advanced Information Processing Department, BAE SYSTEMS Advanced Technology Centre, Bristol, UK
| | - S. Harris
- Advanced Information Processing Department, BAE SYSTEMS Advanced Technology Centre, Bristol, UK
| | - J. Sargent
- Advanced Information Processing Department, BAE SYSTEMS Advanced Technology Centre, Bristol, UK
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Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MHM, Mathivanan S, Milosavljevic A, Laurent LC. Extending gene ontology in the context of extracellular RNA and vesicle communication. J Biomed Semantics 2016; 7:19. [PMID: 27076901 PMCID: PMC4830068 DOI: 10.1186/s13326-016-0061-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/04/2016] [Indexed: 12/31/2022] Open
Abstract
Background To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. Methods By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO. In addition, we have initiated an ongoing process of extractions of gene product annotations associated with these terms from Vesiclepedia and ExoCarta, conversion of the extracted annotations to Gene Association File (GAF) format for batch submission to GO, and curation of the submitted annotations by the GO Consortium. As a use case, we have incorporated some of the GO terms into annotations of samples from the exRNA Atlas and implemented a faceted search interface based on such annotations. Results We have added 7 new terms and modified 9 existing terms (along with their synonyms and relationships) to GO. Additionally, 18,695 unique coding gene products (mRNAs and proteins) and 963 unique non-coding gene products (ncRNAs) which are associated with the terms: “extracellular vesicle”, “extracellular exosome”, “apoptotic body”, and “microvesicle” were extracted from ExoCarta and Vesiclepedia. These annotations are currently being processed for submission to GO. Conclusions As an inter-community effort, we have made a substantial update to GO in the exRNA context. We have also demonstrated the utility of some of the new GO terms for sample annotation and metadata search.
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Affiliation(s)
- Kei-Hoi Cheung
- Department of Emergency Medicine, Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT USA ; VA Connecticut Healthcare System, West Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Paola Roncaglia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; Gene Ontology Consortium (GOC), ᅟ, ᅟ
| | - Sai Lakshmi Subramanian
- Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Matthew E Roth
- Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Monisha Samuel
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Sushma Anand
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Lahiru Gangoda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Stephen Gould
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ ; American Society for Exosomes and Microvesicles (ASEMV), ᅟ, ᅟ
| | - Roger Alexander
- Pacific Northwest Diabetes Research Institute, Seattle, WA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - David Galas
- Pacific Northwest Diabetes Research Institute, Seattle, WA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Mark B Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA ; Department of Computer Science, Yale University, New Haven, CT USA ; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Andrew F Hill
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
| | - Robert R Kitchen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Jan Lötvall
- University of Gothenburg, Gothenburg, Sweden ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
| | - Tushar Patel
- Mayo Clinic, Jacksonville, FL USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Dena C Procaccini
- Division of Neuroscience and Behavior, National Institute on Drug Abuse (NIDA), Rockville, MD USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Peter Quesenberry
- University Medicine Comprehensive Cancer Center, Providence, RI USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA ; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Robert L Raffai
- Department of Surgery, University of California San Francisco and VA Medical Center, San Francisco, CA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Aleksandra Shypitsyna
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; Gene Ontology Consortium (GOC), ᅟ, ᅟ
| | - Andrew I Su
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Clotilde Théry
- Institut Curie, PSL Research University, INSERM U932, Paris, France ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
| | - Kasey Vickers
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Marca H M Wauben
- Department of Biochemistry & Cell Biology, Utrecht University, Utrecht, Netherlands ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
| | - Aleksandar Milosavljevic
- Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
| | - Louise C Laurent
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
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Coyle MJ, Main B, Hughes C, Craven R, Alexander R, Porter G, Thomas S. Enhanced recovery after surgery (ERAS) for head and neck oncology patients. Clin Otolaryngol 2016; 41:118-26. [PMID: 26083896 DOI: 10.1111/coa.12482] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2015] [Indexed: 01/08/2023]
Abstract
OBJECTIVES To describe the development of an enhanced recovery after surgery (ERAS) protocol for people undergoing surgery for head and neck cancer. DESIGN Service improvement project. PARTICIPANTS Head and neck oncology patients. METHODS The programme was developed in a series of structured meetings over a 6-month period. Stakeholders included oral and maxillofacial surgeons, otolaryngologists, anaesthetists, dieticians, physiotherapists, speech and language therapists (SALT) and nursing staff. Based on evidence within current literature and a consensus among the group, an ERAS programme for head and neck surgery patients was formulated. A 12-month study of compliance with the ERAS programme was undertaken from February 2014 to January 2015. RESULTS The process has resulted in the realisation of a head and neck ERAS programme. Key elements include a patient diary, nutritional optimisation, avoiding tracheostomy when possible, goal-directed fluid therapy intra-operatively and a specific head and neck postoperative pain management protocol. Overall compliance was high. Important areas showed lower levels of compliance - only 55% of people were given an explanation of the ERAS programme preoperatively, 75% took preoperative carbohydrate drinks, 10% had individualised goal-directed fluid therapy, and 7% were mobilised in the first 24 h after surgery. The mean length of hospital stay was 14.55 days (sd 7.48). CONCLUSIONS The ERAS programme developed is now embedded in the care pathway for people undergoing head and neck cancer surgery in our unit. The mean length of hospital stay has reduced since the introduction of the programme.
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Affiliation(s)
- M J Coyle
- Department of Oral and Maxillofacial Surgery, University Hospitals Bristol, Bristol, UK
| | - B Main
- Department of Oral and Maxillofacial Surgery, University Hospitals Bristol, Bristol, UK
| | - C Hughes
- Department of Oral and Maxillofacial Surgery, University Hospitals Bristol, Bristol, UK
| | - R Craven
- Department of Anaesthetics, University Hospitals Bristol, Bristol, UK
| | - R Alexander
- Department of Anaesthetics, University Hospitals Bristol, Bristol, UK
| | - G Porter
- Department of Otolaryngology, University Hospitals Bristol, Bristol, UK
| | - S Thomas
- Department of Oral and Maxillofacial Surgery, University Hospitals Bristol, Bristol, UK
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Abstract
OBJECTIVE Social support impacts well-being. Higher levels of social support encourage treatment adherence and aid healing in people living with chronic wounds. The Leg Club model of care harnesses social support mechanisms to improve patient outcomes. This study investigated whether social support mechanisms available through a Leg Club environment influenced well-being. METHOD Participants were community Leg Club members. Socio-demographic data was collected, and the Well-being in Wounds Inventory (WOWI) administered to assess 'wound worries,' 'personal resources,' and 'well-being'. Participants' perceived social situation, length of time attending a Leg Club, wound duration, and feelings about their physical appearance were also measured. RESULTS The subjects recruited (n=49) were aged between 50 and 94 years (mean=75.34, standard deviation=10.31). Membership of a Leg Club did impact well-being factors. Time spent at a Leg Club improved 'personal resources' over time. 'Perceived social situation' predicted key aspects of well-being, as did 'time spent attending a Leg Club' and 'feelings about physical appearance.' Social support and relief from social isolation were important aspects of Leg Club membership for participants. CONCLUSION Attending a Leg Club enhances well-being in people living with a chronic wound; social support has an important role to play in this relationship. Future research should consider the specific interplay of social support mechanisms of Leg Club, and other relevant wound-related variables to optimise patient well-being and treatment outcomes. DECLARATION OF INTEREST The Urgo Foundation funded this project. The authors have no conflicts of interest to declare.
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Affiliation(s)
- D Upton
- Associate Dean, Education, University of Canberra, ACT, 2601
| | - P Upton
- Senior Research Fellow, University of Canberra, ACT, 2601
| | - R Alexander
- Research Assistant, University of Canberra, ACT, 2601
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Orchard P, Mustafa R, Thorn C, Alexander R. The yield of pathology from diagnostic flexible sigmoidoscopy in patients under 40 years. Int J Surg 2015. [DOI: 10.1016/j.ijsu.2015.07.646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. J Extracell Vesicles 2015; 4:27497. [PMID: 26320941 PMCID: PMC4553261 DOI: 10.3402/jev.v4.27497] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/26/2015] [Accepted: 07/24/2015] [Indexed: 12/27/2022] Open
Abstract
The large diversity and volume of extracellular RNA (exRNA) data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNA profiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a) selection of samples from a virtual biorepository for exRNA profiling and for inclusion in the exRNA Atlas; (b) retrieval of a data slice from the exRNA Atlas for integrative analysis and (c) interpretation of exRNA analysis results in the context of pathways and networks. As exRNA profiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data.
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Affiliation(s)
- Sai Lakshmi Subramanian
- Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Robert R Kitchen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Division of Molecular Psychiatry, Abraham Ribicoff Research Facilities, Connecticut Mental Health Center, Yale University School of Medicine, New Haven, CT, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Roger Alexander
- Pacific Northwest Diabetes Research Institute, Seattle, WA, USA
| | - Bob S Carter
- Division of Neurosurgery, UC San Diego School of Medicine, UC San Diego Health System, La Jolla, CA, USA
| | - Kei-Hoi Cheung
- Department of Emergency Medicine, Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA
| | - Louise C Laurent
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Matthew E Roth
- Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joel S Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Andrew I Su
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Mark B Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.,Department of Computer Science, Yale University, New Haven, CT, USA
| | - Aleksandar Milosavljevic
- Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA;
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Affiliation(s)
- Emmanuelle Cordat
- Department of Physiology and Membrane Protein Disease Research Group University of AlbertaEdmontonABCanada
| | - Ensaf Almomani
- Department of Physiology and Membrane Protein Disease Research Group University of AlbertaEdmontonABCanada
| | - Martin Jung
- Medical Biochemistry and Molecular Biology Saarland UniversityHomburgGermany
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology Saarland UniversityHomburgGermany
| | - R. Alexander
- Department of Physiology and Membrane Protein Disease Research Group University of AlbertaEdmontonABCanada
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Bryant C, Wharton N, Alexander R. Psychogenic paresis following neuraxial anaesthesia in a complex obstetric case. Int J Obstet Anesth 2015; 24:200-1. [PMID: 25797239 DOI: 10.1016/j.ijoa.2015.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
Affiliation(s)
- C Bryant
- Department of Anaesthetics, Gloucester Royal Hospital, Gloucester, UK
| | - N Wharton
- Department of Anaesthetics, Bristol Royal Infirmary, Bristol, UK
| | - R Alexander
- Department of Anaesthetics, Bristol Royal Infirmary, Bristol, UK
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Alexander R, Rizer M, Beasley R. Endoleak Outcomes of Suprarenal vs. Infrarenal Endovascular Aneurysm Repairs Outside Instructions for Use Standards. J Vasc Interv Radiol 2015. [DOI: 10.1016/j.jvir.2014.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Bignan G, Alexander R, Bischoff J, Connolly P, Cummings M, de Breucker S, Esser N, Fraiponts E, Gilissen R, Grasberger B, Janssens B, Lu T, Ludovici D, Meerpoel L, Meyer C, Parker M, Peeters D, Rocaboy C, Schubert C, Smans K. 430 Design and structure–activity relationships of highly potent and bioavailable imidazolinone FASN KR domain inhibitors. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)70556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Alexander R, Zelinsky G. The dominance of color in guiding visual search: Evidence from mismatch effects. J Vis 2014. [DOI: 10.1167/14.10.218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Alexander R, Kerby A, Aubdool AA, Power AR, Grover S, Gentry C, Grant AD. 4α-phorbol 12,13-didecanoate activates cultured mouse dorsal root ganglia neurons independently of TRPV4. Br J Pharmacol 2013; 168:761-72. [PMID: 22928864 DOI: 10.1111/j.1476-5381.2012.02186.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 07/22/2012] [Accepted: 08/15/2012] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND PURPOSE The Ca(2+) -permeable cation channel TRPV4 is activated by mechanical disturbance of the cell membrane and is implicated in mechanical hyperalgesia. Nerve growth factor (NGF) is increased during inflammation and causes mechanical hyperalgesia. 4α-phorbol 12,13-didecanoate (4αPDD) has been described as a selective TRPV4 agonist. We investigated NGF-induced hyperalgesia in TRPV4 wild-type (+/+) and knockout (-/-) mice, and the increases in [Ca(2+) ](i) produced by 4αPDD in cultured mouse dorsal root ganglia neurons following exposure to NGF. EXPERIMENTAL APPROACH Withdrawal thresholds to heat, von Frey hairs and pressure were measured in mice before and after systemic administration of NGF. Changes in intracellular Ca(2+) concentration were measured by ratiometric imaging with Fura-2 in cultured DRG and trigeminal ganglia (TG) neurons during perfusion of TRPV4 agonists. KEY RESULTS Administration of NGF caused a significant sensitization to heat and von Frey stimuli in TRPV4 +/+ and -/- mice, but only TRPV4 +/+ mice showed sensitization to noxious pressure. 4αPDD stimulated a dose-dependent increase in [Ca(2+) ](i) in neurons from +/+ and -/- mice, with the proportion of responding neurons and magnitude of increase unaffected by the genotype. In contrast, the selective TRPV4 agonist GSK1016790A failed to stimulate an increase in intracellular Ca(2+) in cultured neurons. Responses to 4αPDD were unaffected by pretreatment with NGF. CONCLUSIONS AND IMPLICATIONS TRPV4 contributes to mechanosensation in vivo, but there is little evidence for functional TRPV4 in cultured DRG and TG neurons. We conclude that 4αPDD activates these neurons independently of TRPV4, so it is not appropriate to refer to 4αPDD as a selective TRPV4 agonist.
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Affiliation(s)
- R Alexander
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK
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Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res 2013; 22:1658-67. [PMID: 22955978 PMCID: PMC3431483 DOI: 10.1101/gr.136838.111] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Statistical models have been used to quantify the relationship between gene expression and transcription factor (TF) binding signals. Here we apply the models to the large-scale data generated by the ENCODE project to study transcriptional regulation by TFs. Our results reveal a notable difference in the prediction accuracy of expression levels of transcription start sites (TSSs) captured by different technologies and RNA extraction protocols. In general, the expression levels of TSSs with high CpG content are more predictable than those with low CpG content. For genes with alternative TSSs, the expression levels of downstream TSSs are more predictable than those of the upstream ones. Different TF categories and specific TFs vary substantially in their contributions to predicting expression. Between two cell lines, the differential expression of TSS can be precisely reflected by the difference of TF-binding signals in a quantitative manner, arguing against the conventional on-and-off model of TF binding. Finally, we explore the relationships between TF-binding signals and other chromatin features such as histone modifications and DNase hypersensitivity for determining expression. The models imply that these features regulate transcription in a highly coordinated manner.
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Affiliation(s)
- Chao Cheng
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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Smoktunowicz N, Alexander R, Franklin L, Williams AE, Jarai G, Scotton CJ, Mercer PF, Chambers RC. S128 The Extrinsic Coagulation Pathway is Locally Upregulated in an Experimental Model of Viral Exacerbation of Pulmonary Fibrosis. Thorax 2012. [DOI: 10.1136/thoraxjnl-2012-202678.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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McNulty K, Sage EK, Alexander R, Scotton CJ, Janes SM. S130 Exogenous Macrophages Are Retained in Mouse Lungs After Injury and Target Therapeutic Transgenes to the Injured Lung Parenchyma. Thorax 2012. [DOI: 10.1136/thoraxjnl-2012-202678.135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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32
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Alexander R, Zelinsky G. Hide and Seek: Amodal Completion During Visual Search. J Vis 2012. [DOI: 10.1167/12.9.736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Murthy NV, Mahncke H, Wexler BE, Maruff P, Inamdar A, Zucchetto M, Lund J, Shabbir S, Shergill S, Keshavan M, Kapur S, Laruelle M, Alexander R. Computerized cognitive remediation training for schizophrenia: an open label, multi-site, multinational methodology study. Schizophr Res 2012; 139:87-91. [PMID: 22342330 DOI: 10.1016/j.schres.2012.01.042] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 01/19/2012] [Accepted: 01/30/2012] [Indexed: 10/28/2022]
Abstract
A recent single-site study (Fisher et al., 2009. Am J Psychiatry. 166 (7) 805-11) showed that repeated training with the Brain Fitness Program (BFP) improved performance on a battery of neuropsychological tasks. If replicated these data suggest an important non-pharmacological method for ameliorating cognitive impairment in schizophrenia. Our study evaluated the BFP training effects in an open-label, multi-site, multinational clinical trial. Fifty-five stable adult patients with schizophrenia on regular antipsychotic medication completed ≥ 32 BFP training sessions over 8-10 weeks. Training effects on cognitive performance and functional capacity outcome measures were measured using CogState® schizophrenia battery, UCSD Performance based Skills Assessment (UPSA-2) and Cognitive Assessment Interview (CAI). BFP training showed a large and significant treatment effect on a training exercise task (auditory processing speed), however this effect did not generalize to improved performance on independent CogState® assessment. There were no significant effects on UPSA-2 or CAI scores. Our study demonstrated the feasibility of implementing BFP training in a multi-site study. However, BFP training did not show significant treatment effects on cognitive performance or functional capacity outcome measures despite showing large and significant effects on a training exercise.
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Affiliation(s)
- N V Murthy
- Neurosciences CEDD, GlaxoSmithKline R&D, New Frontier Science Park, Harlow, UK.
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Le Y, Alexander R, Armour E, Song D. OC-34 A NOVEL METHOD TO QUANTIFY PROSTATE SEED IMPLANT PLAN QUALITY BY PERFORMING INDIVIDUAL SEED DISPLACEMENT ANALYSIS. Radiother Oncol 2012. [DOI: 10.1016/s0167-8140(12)72001-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Dortch R, Alexander R, Li J, Gore J, Smith S. Assessment of Dysmyelination in Charcot-Marie-Tooth Disease Type 1A Via Magnetization Transfer Ratio MRI (S07.005). Neurology 2012. [DOI: 10.1212/wnl.78.1_meetingabstracts.s07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Lindsey P, Alexander R, Balme G, Midlane N, Craig J. Possible Relationships between the South African Captive-Bred Lion Hunting Industry and the Hunting and Conservation of Lions Elsewhere in Africa. ACTA ACUST UNITED AC 2012. [DOI: 10.3957/056.042.0103] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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37
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Alexander R, Zelinsky G. Searching for target parts. J Vis 2011. [DOI: 10.1167/11.11.1321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Van Kets V, Liebenberg L, Wainwright H, Martin L, Gunston G, Alexander R. Atherosclerotic lesions in the thoracic aorta: a South African anatomical and histological mortuary study. S Afr Med J 2011; 101:409-412. [PMID: 21920077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 03/11/2011] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Worldwide, the prevalence of cardiovascular diseases such as atherosclerosis is on the increase. Younger people may be especially vulnerable owing to their exposure to risk factors such as drug abuse and HIV. METHODS The thoracic aortas of 149 South Africans under the age of 50 years were collected at the Salt River Mortuary, Cape Town, and examined macroscopically and microscopically for evidence of anomalies. The sample comprised predominantly males, and included black, coloured and white individuals. RESULTS A significantly higher level of macroscopic pathology was found in coloured males, although overall prevalence of pathology in this sample was lower than expected. A positive association was also found between body mass index and vascular pathology in the black and coloured population groups. Microscopic anomalies were common and present at high levels, irrespective of age and racial grouping. CONCLUSIONS The widespread prevalence of microscopic anomalies in all groups suggests that these are normal variations that result from haemodynamic forces. The higher prevalence of atherosclerotic lesions in coloured males, however, probably results from specific genetic conditions such as hypercholesterolaemia or lifestyle factors such as diet or tik abuse. The findings suggest that coloured individuals may be at increased risk of developing cardiovascular disease.
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Affiliation(s)
- V Van Kets
- Department of Human Biology, University of Cape Town
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Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M. A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol 2011; 12:R15. [PMID: 21324173 PMCID: PMC3188797 DOI: 10.1186/gb-2011-12-2-r15] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 01/26/2011] [Accepted: 02/16/2011] [Indexed: 12/16/2022] Open
Abstract
We develop a statistical framework to study the relationship between chromatin features and gene expression. This can be used to predict gene expression of protein coding genes, as well as microRNAs. We demonstrate the prediction in a variety of contexts, focusing particularly on the modENCODE worm datasets. Moreover, our framework reveals the positional contribution around genes (upstream or downstream) of distinct chromatin features to the overall prediction of expression levels.
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Affiliation(s)
- Chao Cheng
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA
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Maidment B, Yovino S, Herman J, Goloubeva O, Wolfgang C, Schulick R, Laheru D, Hanna N, Alexander R, Regine W. Analysis of Local Control in Patients Receiving IMRT for Resected Pancreas Cancer. Int J Radiat Oncol Biol Phys 2010. [DOI: 10.1016/j.ijrobp.2010.07.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Alexander R, Zelinsky G. Visual Similarity Predicts Categorical Search Guidance. J Vis 2010. [DOI: 10.1167/10.7.1316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Abstract
Sera from sheep which were infected with heartwater fever from 39 to 110 days before the serum was withdrawn failed to fix complement in the presence of lymphogranuloma venereum antigen.
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Alexander R, Zelinsky G. The Frankenbear experiment: Looking for part-based similarity effects on search guidance with complex objects. J Vis 2010. [DOI: 10.1167/9.8.1184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Alexander R, Chinery J, Swales H, Sutton D. “Mouth to mouth ventilation”: A comparison of the laryngeal mask airway with the Laerdal Pocket Facemask. Resuscitation 2009; 80:1240-3. [DOI: 10.1016/j.resuscitation.2009.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 07/10/2009] [Accepted: 07/20/2009] [Indexed: 12/01/2022]
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Odofin O, Alexander R, Bowers H, Chave H, Branagan G. Do patients require outpatient follow-up after rapid referral double contrast barium enema? Colorectal Dis 2009; 11:729-32. [PMID: 18624822 DOI: 10.1111/j.1463-1318.2008.01605.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION In our hospital, patients above the age of 40 years referred with a change in bowel habit without rectal bleeding undergo a double contrast barium enema (DCBE) ideally within 2 weeks. Results of benign studies are sent to a consultant colorectal surgeon and a routine clinic visit arranged. The aim of this study was to identify whether, following DCBE, patients (i) presented at a later date with colorectal cancer and (ii) needed assessment in clinic. METHOD This is a review looking at all patients who underwent DCBE prior to routine clinic visit between January 2004 and December 2005. Hospital databases were cross-referenced to identify any patients presenting with a new diagnosis of colorectal malignancy between DCBE and April 2007. Clinic letters were reviewed to identify the number of outpatient visits prior to discharge and reasons for continued follow-up. RESULTS During the study period, 521 patients (age range 31-93 years, 316 female) had DCBE prior to assessment in clinic. Diagnoses: cancer 48 (9.2%), polyps 13 (2.5%), colitis 3 (0.6%), no significant pathology 457 (87.7%). Of this latter cohort, 387 (84.7%) were discharged after one clinic visit; 54 (11.9%) attended twice and 11 (2.4%) were seen more than twice. Reasons for multiple attendances were management of haemorrhoids/anal fissure or investigations of unrelated symptoms. No new cancers were identified in this cohort between January 2004 and April 2007. CONCLUSION Double contrast barium enema is a safe screening tool following a '2-week rule' referral with CIBH. Following a report of no significant pathology, there is no need to arrange routine follow-up.
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Affiliation(s)
- O Odofin
- Department of General Surgery, Salisbury NHS Foundation Trust, Odstock, Salisbury, Wiltshire, UK
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Yovino S, Garofalo M, David V, Poppe M, Jabbour S, Hanna N, Alexander R, Pandya N, Regine W. IMRT Significantly Improves Acute Gastrointestinal Toxicity in Pancreatic and Ampullary Cancers: A Multi-institutional Experience. Int J Radiat Oncol Biol Phys 2008. [DOI: 10.1016/j.ijrobp.2008.06.653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Robin J, Alexander R. Remifentanil obtunds intraocular pressure rises associated with suxamethonium. Br J Anaesth 2008; 101:432; author reply 432-3. [DOI: 10.1093/bja/aen226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cook T, Alexander R. Major complications during anaesthesia for elective laryngeal surgery in the UK: a national survey of the use of high-pressure source ventilation. Br J Anaesth 2008; 101:266-72. [DOI: 10.1093/bja/aen139] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Alexander R, Volpe NG, Catchpole C, Allen R, Cope S. Are lanyards a risk for nosocomial transmission of potentially pathogenic bacteria? J Hosp Infect 2008; 70:92-3. [PMID: 18621435 DOI: 10.1016/j.jhin.2008.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 05/30/2008] [Indexed: 11/17/2022]
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