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Namgial T, Singh AK, Singh NP, Francis A, Chattopadhyay D, Voloudakis A, Chakraborty S. Correction to: Differential expression of genes during recovery of Nicotiana tabacum from tomato leaf curl Gujarat virus infection. PLANTA 2023; 258:51. [PMID: 37490148 PMCID: PMC10368538 DOI: 10.1007/s00425-023-04206-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
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Namgial T, Singh AK, Singh NP, Francis A, Chattopadhyay D, Voloudakis A, Chakraborty S. Differential expression of genes during recovery of Nicotiana tabacum from tomato leaf curl Gujarat virus infection. PLANTA 2023; 258:37. [PMID: 37405593 PMCID: PMC10322791 DOI: 10.1007/s00425-023-04182-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/10/2023] [Indexed: 07/06/2023]
Abstract
MAIN CONCLUSION Nicotiana tabacum exhibits recovery response towards tomato leaf curl Gujarat virus. Transcriptome analysis revealed the differential expression of defense-related genes. Genes encoding for cysteine protease inhibitor, hormonal- and stress-related to DNA repair mechanism are found to be involved in the recovery process. Elucidating the role of host factors in response to viral infection is crucial in understanding the plant host-virus interaction. Begomovirus, a genus in the family Geminiviridae, is reported throughout the globe and is known to cause serious crop diseases. Tomato leaf curl Gujarat virus (ToLCGV) infection in Nicotiana tabacum resulted in initial symptom expression followed by a quick recovery in the systemic leaves. Transcriptome analysis using next-generation sequencing (NGS) revealed a large number of differentially expressed genes both in symptomatic as well as recovered leaves when compared to mock-inoculated plants. The virus infected N. tabacum results in alteration of various metabolic pathways, phytohormone signaling pathway, defense related protein, protease inhibitor, and DNA repair pathway. RT-qPCR results indicated that Germin-like protein subfamily T member 2 (NtGLPST), Cysteine protease inhibitor 1-like (NtCPI), Thaumatin-like protein (NtTLP), Kirola-like (NtKL), and Ethylene-responsive transcription factor ERF109-like (NtERTFL) were down-regulated in symptomatic leaves when compared to recovered leaves of ToLCGV-infected plants. In contrast, the Auxin-responsive protein SAUR71-like (NtARPSL) was found to be differentially down-regulated in recovered leaves when compared to symptomatic leaves and the mock-inoculated plants. Lastly, Histone 2X protein like (NtHH2L) gene was found to be down-regulated, whereas Uncharacterized (NtUNCD) was up-regulated in both symptomatic as well as recovered leaves compared to the mock-inoculated plants. Taken together, the present study suggests potential roles of the differentially expressed genes that might govern tobacco's susceptibility and/or recovery response towards ToLCGV infection.
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Wong M, Nakhoul G, Calice-Silva V, Tannor E, Kumar V, Abdul Hafidz M, Chanchlani R, Chen T, Ekrikpo U, Francis A, Kalyesubula R, Karam S, Pereira-Kamath N, Wijewickrama E, Jha V. WCN23-0776 BARRIERS TO ACCESSING ESSENTIAL MEDICINES IN NEPHROLOGY AND RELATED NON-COMMUNICABLE DISEASES: A SCOPING REVIEW. Kidney Int Rep 2023. [DOI: 10.1016/j.ekir.2023.02.539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023] Open
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Williams JAE, Chester-Jones M, Francis A, Marian I, Goff M, Brewer G, Gulati M, Eldridge L, Julier P, Minns Lowe C, Barber V, Glover V, Mackworth-Young C, Vincent T, Lamb SE, Vincent K, Dutton SJ, Watt FE. AB0980 Hand Osteoarthritis: investigating Pain Effects in a randomised placebo-controlled feasibility study of estrogen-containing therapy (HOPE-e): report on the primary feasibility outcomes. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.2437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundThere is an unmet need for new treatments for hand osteoarthritis (OA). Symptomatic hand OA is more common in women and its incidence increases round the age of menopause. Pre-clinical, epidemiological and post hoc studies in Hormone Replacement Therapy (HRT) trials implicate estrogen deficiency as of likely importance in OA aetiopathogenesis. No clinical trials of HRT have been carried out in hand OA to date. The licensed HRT Duavive (conjugated estrogens + SERM bazedoxifene) was selected on its potential for efficacy and tolerability.ObjectivesWe set out to determine the feasibility and acceptability of this form of HRT in post-menopausal women with hand OA, to generate proof of concept data and refine methods for a full study.MethodsISRCTN12196200. Females aged 40-65 yrs and 1-10yrs after final menstrual period with hand OA fulfilling ACR criteria and 2+ painful hand joints were recruited. Eligibility incorporated best practice for HRT prescription but did not require menopausal symptoms. Recruitment was at 3 sites in primary/secondary care, including directly from the community. Design was parallel group, double-blind 1:1 randomisation of Duavive or placebo, orally once daily for 24 weeks, then weaning for 4 weeks before stopping. Routes and rates of recruitment and the acceptability of randomisation, medication (compliance, retention), and proposed outcomes were measured, and the likelihood of unblinding. Measures related to hand pain and function, menopause symptoms and joint appearance. Patient and Public Involvement actively informed study rationale, design and materials. An end of study questionnaire and 2 participant focus groups provided further acceptability data.ResultsRecruitment was for 12/possible 18 months, interrupted due to COVID-19. Some study procedures were modified to allow reopening whilst collecting all primary outcomes. 434 enquiries/referrals were received, leading to 96 telephone pre-screens, of which 33 gave written informed consent and attended face to face screening. 28/33 screened (85%) were eligible and randomised. The highest number of randomisations was from study web presence (n=7) followed by SMS text from GP surgeries (n=5). Of 401 not proceeding, 250 (62%) were ineligible, most commonly due to contraindicated medication, followed by medical contraindication, whilst 55 (14%) decided not to take part, for reasons including not wanting to take a hormone-based drug or difficulty attending study visits. Retention and compliance were excellent. All 28 participants completed all study follow ups, with only 3 withdrawals from treatment due to AEs, 2 of these at week 24 and all in the placebo arm. There were no serious AEs. High levels of completeness of all study outcome measures were achieved. Bang’s blinding index suggested that participants/investigators were well blinded. There were overall high/good levels of satisfaction with taking part in the study. 26/28 (92%) would recommend taking part to others with hand OA (irrespective of study arm). Many found the flexibility offered by a combination of remote and face to face visits (due to the pandemic) attractive. Additional insights from focus groups were to include hand stiffness as well as pain measures but to reduce the overall number of questions.ConclusionDespite COVID-19 and a reduced recruitment period, this study recruited sufficient numbers to assess feasibility outcomes. Randomisation of eligible people and retention rates were high. A mixture of remote and face to face visits due to COVID-19 probably improved recruitment and retention and was supported by participants, who were generally satisfied with the study design and medication. The study provided useful insight and improvements that would be incorporated into a future study. Overall, this feasibility study showed that with clear messaging on eligibility and a defined recruitment strategy, recruitment and retention to a study testing this treatment is possible.AcknowledgementsThis research was funded by the National Institute for Health Research (NIHR) under its Research for Patient Benefit (RfPB) Programme (Grant Reference Number PB-PG-0416-20023). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. The study team thank the sites and the participants who made this research possible.Disclosure of InterestsJennifer A.E. Williams: None declared, Mae Chester-Jones: None declared, Anne Francis: None declared, Ioana Marian: None declared, Megan Goff: None declared, Gretchen Brewer: None declared, Malvika Gulati: None declared, Lucy Eldridge: None declared, Patrick Julier: None declared, Catherine Minns Lowe: None declared, Vicki Barber: None declared, Victoria Glover: None declared, Charles Mackworth-Young: None declared, Tonia Vincent Consultant of: Pfizer, Grant/research support from: Grant support from Fidia, Biosplice, Novartis, Pfizer as part of their contribution to an international consortium., Sarah E Lamb: None declared, Katy Vincent: None declared, Susan J Dutton: None declared, Fiona E Watt Consultant of: Pfizer, Grant/research support from: Pfizer and from Astellas Pharma (> 3 years ago)
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LALJI R, Francis A, Blazek K, Teixeira-Pinto A, Wong G, Johnson D. POS-777 SEX DIFFERENCES IN ACCESS TO AND OUTCOMES AFTER PAEDIATRIC KIDNEY TRANSPLANTATION. Kidney Int Rep 2022. [DOI: 10.1016/j.ekir.2022.01.813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Molodyk A, Samoilenkov S, Markelov A, Degtyarenko P, Lee S, Petrykin V, Gaifullin M, Mankevich A, Vavilov A, Sorbom B, Cheng J, Garberg S, Kesler L, Hartwig Z, Gavrilkin S, Tsvetkov A, Okada T, Awaji S, Abraimov D, Francis A, Bradford G, Larbalestier D, Senatore C, Bonura M, Pantoja AE, Wimbush SC, Strickland NM, Vasiliev A. Development and large volume production of extremely high current density YBa 2Cu 3O 7 superconducting wires for fusion. Sci Rep 2021; 11:2084. [PMID: 33483553 PMCID: PMC7822827 DOI: 10.1038/s41598-021-81559-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/05/2021] [Indexed: 01/30/2023] Open
Abstract
The fusion power density produced in a tokamak is proportional to its magnetic field strength to the fourth power. Second-generation high temperature superconductor (2G HTS) wires demonstrate remarkable engineering current density (averaged over the full wire), JE, at very high magnetic fields, driving progress in fusion and other applications. The key challenge for HTS wires has been to offer an acceptable combination of high and consistent superconducting performance in high magnetic fields, high volume supply, and low price. Here we report a very high and reproducible JE in practical HTS wires based on a simple YBa2Cu3O7 (YBCO) superconductor formulation with Y2O3 nanoparticles, which have been delivered in just nine months to a commercial fusion customer in the largest-volume order the HTS industry has seen to date. We demonstrate a novel YBCO superconductor formulation without the c-axis correlated nano-columnar defects that are widely believed to be prerequisite for high in-field performance. The simplicity of this new formulation allows robust and scalable manufacturing, providing, for the first time, large volumes of consistently high performance wire, and the economies of scale necessary to lower HTS wire prices to a level acceptable for fusion and ultimately for the widespread commercial adoption of HTS.
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Francis A, Firth J, Islam N, Gorelik J, MacLeod K. The effect of oestrogen withdrawal on cardiac Ca2+ regulation and the influence of GPER1. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Post-menopausal women have an enhanced risk of developing heart failure, attributed to declining oestrogen levels during menopause. However, the signalling mechanisms remain undetermined.
Purpose
We aim to determine the role of G-protein coupled oestrogenic receptor 1 (GPER1) in intracellular Ca2+ regulation and the consequences of hormonal changes that may exacerbate the pathophysiology of heart failure.
Methods
Ovariectomy (OVx) (mimics menopausal hormone changes) or sham surgeries were conducted on female guinea pigs. Left ventricular cardiomyocytes were isolated 150-days post-operatively for experimental use. Cellular t-tubule network and structural integrity was measured using fluorescent di-8-ANEPPs staining and scanning ion conductance microscopy. GPER1 expression and localisation was measured by Western blot and immunostaining. The role of GPER1 activation was measured using selective agonist G-1 in electrophysiological and Ca2+-sensitive dye fluorescence experiments.
Results
Following oestrogen withdrawal, the t-tubule network density decreased by 13% and z-groove index reduced by 15%. GPER1 predominantly localised to the peri-nuclear endoplasmic reticulum and its expression increased by 32% in OVx. Action potential duration (APD) prolonged in OVx and following GPER1 activation, APD90 shortened by 11% and 25% in sham and OVx respectively. OVx cells had larger peak inward Ca2+ current (ICaL) (by 22%) and sarcoplasmic reticulum (SR) Ca2+ content (by 13%), compared with sham. While GPER1 activation had little effect on peak ICaL or SR content, it reduced Ca2+ transient amplitude (by 20%), SR fractional release (by 11%) in OVx cells. The frequency of occurrence of spontaneous Ca2+ waves evoked by periods of rapid stimulation reduced by 40% and wave-free survival time prolonged in OVx cells following GPER1 activation.
Conclusions
In the hearts of an animal species whose electrophysiology and intracellular Ca2+ regulation is akin to humans, we show that following oestrogen deficiency, the t-tubule network is down-regulated and becomes disorganised, GPER1 expression is increased and its activation induces negative inotropic responses in cardiomyocytes. This may limit the adverse changes to Ca2+ signalling reported in OVx that could be pro-arrhythmic and exacerbate the progression to heart failure.
Funding Acknowledgement
Type of funding source: Foundation. Main funding source(s): British Heart Foundation
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Gardosi J, Turner S, Williams M, Buller S, Hugh O, Francis A. The Growth Assessment Protocol: a major cause of declining stillbirth rates in the UK. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2020; 56:117-119. [PMID: 32506617 DOI: 10.1002/uog.22100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
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Nasri K, Hantoushzadeh S, Hugh O, Heidarzadeh M, Habibelahi A, Shariat M, Tara F, Kashanian M, Radmehr M, Yekaninejad MS, Homeira VC, Francis A, Gardosi J. Customized birthweight standard for an Iranian population. J Matern Fetal Neonatal Med 2019; 34:3651-3656. [PMID: 31766924 DOI: 10.1080/14767058.2019.1689557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Objective: To produce a customized birthweight standard for Iran.Method: Retrospective study of a pregnancy database collected from five hospitals across Iran. The cohort consisted of 4994 consecutive term births with complete data, delivered between July 2013 and November 2014. Coefficients were derived using a backwards stepwise multiple regression technique.Results: Maternal height, weight in early pregnancy and parity as well as the baby's sex were identified as significant physiological variables affecting birthweight. Paternal height and weight were also significant although weaker factors. The expected 280-day birthweight, free from pathological influences, of a standard size mother (height 163 cm, weight 64 kg) in her first pregnancy was 3390 g. Pathological factors found to affect birthweight in this cohort included village housing, anemia, preexisting and gestational diabetes and preeclampsia.Conclusion: The analysis confirmed the main physiological variables that affect birthweight in other countries and shows paternal factors also to be significant variables. Development of a country-specific customized birthweight standard will aid clinicians in Iran to distinguish between fetuses that are either constitutionally or pathologically small, thereby avoiding unnecessary interventions, and improving identification of at-risk pregnancies and perinatal outcome.
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Parker CN, Francis A, Finlayson KJ. Methods for chronic wound research — A scoping systematic review of the recommendations, guidelines and standards. WOUND PRACTICE AND RESEARCH 2019. [DOI: 10.33235/wpr.27.2.62-73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Background This scoping systematic review aimed to investigate the existing literature for recommendations, guidelines and standards for research on chronic wound diagnosis, assessment, management and prevention; to identify gaps in this literature; and produce recommendations to support future wound management research.
Methods A scoping systematic literature review was undertaken in 2017–2018, which aligned with PRISMA guidelines and searched academic databases and grey literature published between 2007 and 2017.
Results Eighty-nine documents included recommendations or outcomes on research methods for studies on chronic wound diagnosis, assessment, management and/or prevention; covering the areas of research design, sampling, randomisation and blinding, independent and outcome measures and interventions for research in chronic wounds. Common themes regarding research gaps and flaws were identified.
Conclusion This review identified existing evidence, guidelines, recommendations and standards regarding the conduct of chronic wound research internationally. Recommendations include the need for standardised vocabulary, standardised checklists for wound research, development of core outcome datasets and an agreed and standardised set of economic parameters and methodology for cost-effectiveness. Establishment of a centralised national methodology service for wound research to assist with methodology design would be beneficial.
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Francis A, Nusbaum J, Melendez Torres A, Spruill T, Buyon J, Mehta-Lee S. Breastfeeding in the systemic lupus erythematosus patient. Lupus 2019; 28:914-915. [PMID: 31046571 DOI: 10.1177/0961203319846651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kshrisagar S, Francis A, J. Yee J, Natarajan S, K. Lee C. Implementing the Node Based Smoothed Finite Element Method as User Element in Abaqus for Linear and Nonlinear Elasticity. ACTA ACUST UNITED AC 2019. [DOI: 10.32604/cmc.2019.07967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Francis A, Huber KT, Moulton V. Correction to: Tree-Based Unrooted Phylogenetic Networks. Bull Math Biol 2018; 81:936-937. [PMID: 30446916 DOI: 10.1007/s11538-018-0530-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 11/24/2022]
Abstract
The level-5 example of a network presented in Fig. 4 of Francis et al. (2018) is tree-based even though it states in the caption and in the text that this is not the case.
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Fucci E, Abdoun O, Caclin A, Francis A, Dunne JD, Ricard M, Davidson RJ, Lutz A. Differential effects of non-dual and focused attention meditations on the formation of automatic perceptual habits in expert practitioners. Neuropsychologia 2018; 119:92-100. [PMID: 30040956 DOI: 10.1016/j.neuropsychologia.2018.07.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 07/15/2018] [Accepted: 07/20/2018] [Indexed: 10/28/2022]
Abstract
Non-dual meditation aims to undo maladaptive cognitive and affective patterns by recognizing their constructed and transient nature. We previously found high-amplitude spontaneous gamma (25-40 Hz) oscillatory activity during such practice. Nonetheless, it is unclear how this meditation state differs from other practices, in terms of perceptual information processing. Here, we hypothesized that non-dual meditation can downregulate the automatic formation of perceptual habits. To investigate this hypothesis, we recorded EEG from expert Buddhist meditation practitioners and matched novices to measure two components of the auditory evoked response: the Mismatch Negativity (MMN) and the Late Frontal Negativity (LFN), a potential observed at a latency sensitive to attentional engagement to the auditory environment, during the practices of Open Presence (OP) and Focused Attention (FA), as well as during a control state, in the context of a passive oddball paradigm. We found an increase in gamma oscillatory power during both meditation states in expert practitioners and an interaction between states and groups in the amplitude of the MMN. A further investigation identified the specific interplay between the MMN and the LFN as a possible marker to differentiate the two meditation states as a function of expertise. In experts, the MMN increased during FA, compared to OP, while the opposite pattern was observed at the LFN latency. We propose that the state of OP in experts is characterized by increased sensory monitoring and reduced perceptual inferences compared to FA. This study represents a first attempt to describe the impact of non-dual meditation states on the regulation of automatic brain predictive processes.
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Francis A, Jasani S, Bachmann G. Contraceptive challenges and the transgender individual. Womens Midlife Health 2018; 4:12. [PMID: 30766722 PMCID: PMC6297942 DOI: 10.1186/s40695-018-0042-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/02/2018] [Indexed: 11/21/2022] Open
Abstract
In recent years public awareness of healthcare disparities experienced by transgender individuals throughout the world have garnered increasing attention within the media and from health advocates. Despite this increasing awareness, a paucity of research data and clinical protocols of care for clinicians continues to exist, especially in regard to the transgender individual’s family planning needs. Clinicians should be on the forefront of promoting strategies that forge a meaningful and collaborative relationship with the transgender man, including as he transitions through to the menopause and his sexual and reproductive healthcare needs. Unfortunately, despite best efforts to address the health concerns of transgender men in midlife, including their contraceptive needs and pregnancy desires, there is currently a paucity of research. Although hormonal contraceptives are not an option for this group of individuals, especially those on masculinizing hormones, IUD’s, both copper containing and progestin containing, should be considered for those with intact pelvic organs. For this group of transgender men with potential for pregnancy who have either completed their family or choose not to give birth, sterilization can be offered. Regardless of where they identify along the gender spectrum, these midlife individuals with potential reproductive potential should have equitable access to and up to date counseling on their contraceptive options. This commentary addresses the contraceptive challenges of the midlife transgender man. (Note: Pronouns used in this article are he/him for cis and transgender men and she/her for cis and transgender women).
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Della Morte M, Francis A, Gérardin A, Gülpers V, Herdoíza G, von Hippel G, Horch H, Jäger B, Meyer H, Nyffeler A, Wittig H. A lattice calculation of the hadronic vacuum polarization contribution to (g – 2)µ. EPJ WEB OF CONFERENCES 2018. [DOI: 10.1051/epjconf/201817506031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present results of calculations of the hadronic vacuum polarisation contribution to the muon anomalous magnetic moment. Specifically, we focus on controlling the infrared regime of the vacuum polarisation function. Our results are corrected for finite-size effects by combining the Gounaris-Sakurai parameterisation of the timelike pion form factor with the Lüscher formalism. The impact of quark-disconnected diagrams and the precision of the scale determination is discussed and included in our final result in two-flavour QCD, which carries an overall uncertainty of 6%. We present preliminary results computed on ensembles with Nf = 2 + 1 dynamical flavours and discuss how the long-distance contribution can be accurately constrained by a dedicated spectrum calculation in the iso-vector channel.
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Fallowfield LJ, Matthews L, Jenkins VA, May SF, Francis A, Rae D, Wallis M. Abstract OT3-08-01: Interview data from women contemplating LORIS trial entry during the feasibility study. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-ot3-08-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: LORIS is a multi-centre, randomised (1:1) controlled trial of Surgery v Active Monitoring with annual mammography in patients with low risk ductal carcinoma in situ (DCIS). During a 2 year Feasibility Study potential patients were invited to complete the Clinical Trials Questionnaire (CTQ)1 and participate in a semi structured telephone interview about the verbal, written and DVD based trial information. The DVD was produced to complement the patient information sheet (PIS) and incorporates simple graphics and a Q&A session with women asking the Chief Investigator questions about the trial.
Aims:To examine the reasons for trial participation/rejection and obtain feedback about the clarity, timing and usefulness of the PIS and DVD in order to identify potential communication drivers and barriers to trial recruitment.
Methods: Participants completed the CTQ1 prior to randomisation and with their consent were contacted following randomisation for an interview. Women declining the trial were issued with an optional pack containing the CTQ1 and the researchers' contact details if they wanted an interview. The CTQ1 comprises16 reasons that might influence a decision to either accept or decline a trial. For each statement participants register their agreement or disagreement on a scale of 1 (strongly agree) to 5 (strongly disagree) and indicate the most important reason for their decision. Interviews explored factors such as, attitudes about randomisation, and usefulness of the trial information provided.
Results: 41 patients were randomised during feasibility; 20 surgery, 21 active monitoring, 16 patients declined the trial. 40/41(98%) acceptors and 9/16 (56%) decliners completed the CTQ1. The main reason for joining LORIS was:- “I thought the trial offered the best treatment available” 13/40 (32%) and for decling the trial was “The idea of randomisation worried me” (4/9; 44%).
35 interviews were conducted (31/41 (76%) accepted and 4/16 (25%) declined LORIS). At interview acceptors commented that the PIS was very useful and clear (84%; 26/31 & 90%; 28/31, respectively). 74% (23/31) of women who joined LORIS watched the DVD and the majority (19/23; 83%) found it “very useful” and 22 (22/23; 96%) “very easy to understand”. A third of women (10/31) said the PIS and the DVD helped them decide to participate in LORIS. Women who declined the trial had clear treatment preferences; 2/4 did not watch the DVD. Three quarters of women interviewed (19/25) watched the DVD with family members/friends and found it reassuring. One commented it was “Put in words you can understand and not be baffled by”. The most popular aspect was the Q&A session (13/25; 52%).
Conclusions:The LORIS DVD was a useful, easy to understand recruitment tool, complementing the PIS. Many women felt reassured that the content was consistent with, and added to that provided by healthcare professionals. Opinions of family and friends, worries about randomisation and personal preferences exert an influence of those declining these types of trial.
Fallowfield LJ, Jenkins V, et al. (1998) Attitudes of patients to randomised clinical trials of cancer therapy. Eur J Cancer 34(10):1554–1559.
Citation Format: Fallowfield LJ, Matthews L, Jenkins VA, May SF, Francis A, Rae D, Wallis M. Interview data from women contemplating LORIS trial entry during the feasibility study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT3-08-01.
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Francis A, Huber KT, Moulton V. Tree-Based Unrooted Phylogenetic Networks. Bull Math Biol 2018; 80:404-416. [PMID: 29238909 PMCID: PMC5790869 DOI: 10.1007/s11538-017-0381-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 12/05/2017] [Indexed: 11/30/2022]
Abstract
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.
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Francis A, Johnson DW, Craig JC, Wong G. Incidence and Predictors of Cancer Following Kidney Transplantation in Childhood. Am J Transplant 2017; 17:2650-2658. [PMID: 28371054 DOI: 10.1111/ajt.14289] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/10/2017] [Accepted: 03/18/2017] [Indexed: 01/25/2023]
Abstract
Cancer risk is increased substantially in adult kidney transplant recipients, but the long-term risk of cancer in childhood recipients is unclear. Using the Australian and New Zealand Dialysis and Transplant Registry, the authors compared overall and site-specific incidences of cancer after transplantation in childhood recipients with population-based data by using standardized incidence ratios (SIRs). Among 1734 childhood recipients (median age 14 years, 57% male, 85% white), 289 (16.7%) developed cancer (196 nonmelanoma skin cancers, 143 nonskin cancers) over a median follow-up of 13.4 years. The 25-year cumulative incidences of any cancer were 27% (95% confidence intervals 24-30%), 20% (17-23%) for nonmelanoma skin cancer, and 14% (12-17%) for nonskin cancer (including melanoma). The SIR for nonskin cancer was 8.23 (95% CI 6.92-9.73), with the highest risk for posttransplant lymphoproliferative disease (SIR 45.80, 95% CI 32.71-62.44) and cervical cancer (29.4, 95% CI 17.5-46.5). Increasing age at transplantation (adjusted hazard ratio [aHR] per year 1.10, 95% CI 1.06-1.14), white race (aHR 3.36, 95% CI 1.61-6.79), and having a functioning transplant (aHR 2.27, 95% CI 1.47-3.71) were risk factors for cancer. Cancer risk, particularly for virus-related cancers, is increased substantially after kidney transplantation during childhood.
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Francis A, Hudspith RJ, Lewis R, Maltman K. Lattice Prediction for Deeply Bound Doubly Heavy Tetraquarks. PHYSICAL REVIEW LETTERS 2017; 118:142001. [PMID: 28430484 DOI: 10.1103/physrevlett.118.142001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Indexed: 06/07/2023]
Abstract
We investigate the possibility of qq^{'}b[over ¯]b[over ¯] tetraquark bound states using n_{f}=2+1 lattice QCD ensembles with pion masses ≃164, 299, and 415 MeV. Motivated by observations from heavy baryon phenomenology, we consider two lattice interpolating operators, both of which are expected to couple efficiently to tetraquark states: one with a diquark-antidiquark and one with a meson-meson structure. Using nonrelativistic QCD to simulate the bottom quarks, we study the udb[over ¯]b[over ¯], ℓsb[over ¯]b[over ¯] channels with ℓ=u, d, and find unambiguous signals for strong-interaction-stable J^{P}=1^{+} tetraquarks. These states are found to lie 189(10) and 98(7) MeV below the corresponding free two-meson thresholds.
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Godeke A, Abraimov DV, Arroyo E, Barret N, Bird MD, Francis A, Jaroszynski J, Kurteva DV, Markiewicz WD, Marks EL, Marshall WS, McRae DM, Noyes PD, Pereira RCP, Viouchkov YL, Walsh RP, White JM. A Feasibility Study of High-Strength Bi-2223 Conductor for High-Field Solenoids. SUPERCONDUCTOR SCIENCE & TECHNOLOGY 2017; 30:035011. [PMID: 28360455 PMCID: PMC5367628 DOI: 10.1088/1361-6668/aa5582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We performed a feasibility study on a high-strength Bi2-x Pb x Sr2Ca2Cu3O10-x (Bi-2223) tape conductor for high-field solenoid applications. The investigated conductor, DI-BSCCO Type HT-XX, is a pre-production version of Type HT-NX, which has recently become available from Sumitomo Electric Industries (SEI). It is based on their DI-BSCCO Type H tape, but laminated with a high-strength Ni-alloy. We used stress-strain characterizations, single- and double-bend tests, easy- and hard-way bent coil-turns at various radii, straight and helical samples in up to 31.2 T background field, and small 20-turn coils in up to 17 T background field to systematically determine the electro-mechanical limits in magnet-relevant conditions. In longitudinal tensile tests at 77 K, we found critical stress- and strain-levels of 516 MPa and 0.57%, respectively. In three decidedly different experiments we detected an amplification of the allowable strain with a combination of pure bending and Lorentz loading to ≥ 0.92% (calculated elastically at the outer tape edge). This significant strain level, and the fact that it is multi-filamentary conductor and available in the reacted and insulated state, makes DI-BSCCO HT-NX highly suitable for very high-field solenoids, for which high current densities and therefore high loads are required to retain manageable magnet dimensions.
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Thomas J, Hanby A, Pinder S, Pirrie S, Rea D, Gaunt C, Young J, Francis A. Abstract P3-17-06: LORIS trial of active monitoring for DCIS: How does the online pathology eligibility review process work? Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p3-17-06] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction
The LORIS Trial is a UK randomized clinical trial comparing active monitoring with surgery for low risk ductal carcinoma in situ (DCIS), defined as low or low-intermediate grade DCIS without comedo necrosis, as diagnosed on vacuum-assisted (wide bore) core needle samples. Because of the inconsistency of grading DCIS, we have underpinned this trial with a Central Histopathology Review (CHR) before randomisation. The process of the CHR for the first 22 months of a two year pilot study between July 2014 and May 2016 is reported here.
Patients and methods
Patients were eligible for CHR if they satisfied all of the eligibility criteria and had locally reported low or intermediate grade DCIS. Patients were identified at 28 pilot sites and were registered for potential trial entry following written informed consent before being subjected to CHR. CHR comprised online examination of digitally scanned histology slides of all material from all diagnostic biopsies and was performed by at least two of the three LORIS specialist breast pathologists. Histology slides were submitted using Royal Mail Safebox® to the University of Birmingham where they were digitally scanned and made available for review via the Leica digital image hub. The outcome of the review was reported in a separate secure online database by completion of a Central Pathology Review Form. Access to both online systems is password protected. Eligibility was confirmed if two pathologists agreed that there was low or low to intermediate grade DCIS and no comedo necrosis. A maximum of 7 calendar days from receipt of the diagnostic material was allowed for the central review process.
The digital images of the histology slides are stored by the Leica system for future reference.
Results
100 patients were registered and their slides reviewed. 55 of these were deemed eligible by CHR; of these 38 have been randomised. 45 patients were deemed ineligible, most commonly due to grade being in the upper half of the intermediate category and/or comedo necrosis. In addition, 9 patients were deemed not to have DCIS and 1 patient had invasive disease.
Grouping the grade categories as low and low to intermediate grade (low risk and eligible for randomisation) Vs intermediate to high and high cytonuclear grade (ineligible for randomisation) showed 91% agreement on grade category amongst the reviewing pathologists.
Results of the central review were made available to sites within 7 days for 97% of cases submitted. On average, central review was completed within 4 days. Average time between registration and randomisation was 3 weeks. The LORIS central review pathologists found online viewing and reporting of sections acceptable.
Conclusions
Central Histopathology Review using online viewing of digital slides provides timely and efficient pathology Quality Assurance in this clinical trial setting, with acceptable turnaround times and good agreement between reviewing specialist breast pathologists. This process will be continued in the main phase of the trial.
Citation Format: Thomas J, Hanby A, Pinder S, Pirrie S, Rea D, Gaunt C, Young J, Francis A. LORIS trial of active monitoring for DCIS: How does the online pathology eligibility review process work? [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-17-06.
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Singh JK, McEvoy K, Marla S, Wilcox M, Rea D, Hallissey MT, Francis A. Abstract P3-13-05: Multicentre observational study evaluating why mastectomies are advised by UK multi-disciplinary teams. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p3-13-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Marked variation in mastectomy rates exists across the UK. Identification of variation in practice is a key step towards standardisation of service. The rationale for advising mastectomy by multi-disciplinary teams (MDTs) has not been previously explored in the UK. The main aim of this multicentre observational study was to describe current practice in MDT decision-making for patients undergoing mastectomy. A secondary aim was to determine utilisation of neoadjuvant therapies.
Methods: A multicentre, protocol-driven, prospective cohort study, led by trainees of the West Midlands Research Collaborative was performed during July and September 2015. Data was collected securely using Research Electronic Data Capture. Inclusion criteria were: women >18 years undergoing mastectomy for in situ/invasive disease; presenting with symptomatic or screen detected disease; performed as a primary procedure or following failure of breast conserving surgery (BCS); with or without immediate breast reconstruction (IR).
Results: A total of 1776 patients (1823 mastectomies; 47 bilateral procedures) from 68 units were included. Median age was 63 years (range 20-99). In total 481 (26%) IRs were performed; median IR rate was 22% (range 0-67%).
Mastectomy was advised by the MDT in 1402 (77%) cases. Reasons for advising mastectomy are shown in Table 1.
Table 1. MDT rationale for advising mastectomyRationaleNumber of mastectomiesProportion (%)Large tumour to breast size ratio making BCS unsuitable53029.1Multi-centric disease on imaging37220.4Extensive malignant microcalcification1799.8Previous radiotherapy (Breast/Mantle)1638.9Requiring further surgery for positive margins following BCS1588.7Central tumour1136.2Large primary tumour, patient not suitable for neoadjuvant endocrine or chemotherapy treatment1126.1Neoadjuvant therapy failed to downsize tumour to allow BCS884.8Neoadjuvant therapy apparently successful but mastectomy advised anyway794.3Family History-High Risk512.8
In total 153 patients with oestrogen receptor positive (ER+) tumours were offered neoadjuvant endocrine treatment (NET); 131 (86%) received treatment. A total of 293 post-menopausal women with uni-focal, ER+ tumours, >20mm were not offered NET; mastectomy was advised by MDTs in 202 patients and the rationale for advising mastectomy in 173 patients (86%) was large tumour to breast size ratio.
In total 104 patients with Human Epidermal Growth Factor Receptor 2 over-expressing (HER2+) tumours were offered neoadjuvant chemotherapy and trastuzumab (NACT); 89 (86%) received treatment. A total of 88 women <70 years old with HER2+ tumours, >20mm were not offered NACT; mastectomy was advised by MDTs in 75 patients and rationale for advising mastectomy in 45 women (60%) was large tumour to breast size ratio.
Conclusions: Although most mastectomies are advised for large tumour to breast size ratio, there is inconsistency in the utilisation of neoadjuvant therapies with many potentially eligible patients with large tumours not being given the opportunity to be downsized. Application of standardised recommendations for neoadjuvant treatment resulting in increased and appropriate use of neoadjuvant therapies could reduce the number of mastectomies advised by MDTs.
Citation Format: Singh JK, McEvoy K, Marla S, Wilcox M, Rea D, Hallissey MT, Francis A, West Midlands Research Collaborative. Multicentre observational study evaluating why mastectomies are advised by UK multi-disciplinary teams [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-13-05.
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Francis A, Bartlett J, Billingham L, Bowden S, Brookes C, Dodwell D, Evans A, Fairbrother P, Fallowfield L, Gaunt C, Hanby A, Jenkins V, Matthews L, Pinder S, Pirrie S, Rea D, Reed M, Roberts T, Thomas J, Wallis M, Wilcox M, Young J. Abstract OT1-03-01: The UK LORIS trial: Randomizing patients with low or low intermediate grade ductal carcinoma in situ (DCIS) to surgery or active monitoring. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-ot1-03-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The independent review of the UK National Health Service Breast Screening Programme reported (The Lancet, Volume 380, Issue 9855, Page 1778, 17 Nov 2012) on the benefits and harms of breast screening. It concluded that breast screening saves lives and acknowledged the existence of overtreatment. It encouraged randomized trials to elucidate the appropriate treatment of screen-detected DCIS to gain a better understanding of its natural history. The LORIS trial addresses the possible overtreatment of low and low/intermediate grade screen-detected (low risk) DCIS by randomizing patients to standard surgical treatment or active monitoring, each with long term follow up.
Trial Design: LORIS is a phase III, multicentre, 2 arm study, with a built in 2 year Feasibility Phase, in patients confirmed to have low risk DCIS defined by strict criteria and determined by central pathology review. Patients will be randomized between standard surgery and active monitoring with annual mammography. Patients will be followed up for a minimum of 10 years.
Eligibility Criteria:
1) Female, age ≥ 46 years
2) Screen-detected or incidental microcalcification (with no mass lesion clinically or on imaging)
3) Low risk DCIS on large volume vacuum-assisted biopsy, confirmed by central pathology review
4) Patient fit to undergo surgery
5) No previous breast cancer or ipsilateral DCIS diagnosis
6) Written informed consent
Specific Aims: The LORIS Trial aims to establish whether patients with newly diagnosed low risk DCIS can safely avoid surgery without detriment to their wellbeing (psychological and physical) and whether those patients that do require surgery can be identified by pathological and radiological means.
Primary endpoint: Ipsilateral invasive breast cancer free survival time
Secondary endpoints: Overall survival; mastectomy rate; time to mastectomy; time to surgery; patient reported outcomes; health resource utilisation and assessment of predictive biomarkers.
A digital image data repository and tissue bank will provide a prospective resource for both translational and imaging studies.
Statistical Methods: A total of 932 patients will be randomized to a non-inferiority design to test the null hypothesis that active monitoring of women diagnosed with low risk DCIS is not non-inferior in terms of ipsilateral invasive breast cancer free survival (iiBCFS) time compared to treatment with surgery. The iiBCFS time will be compared across the two arms on a per protocol and intent-to-treat basis, using a 1-sided (α=0.05) log-rank test for non-inferiority. The iiBCFS rate is assumed to be 97.5% in the surgery arm at 5 years, utilizing 80% power to exclude a difference of more than 2.5% in the active monitoring arm.
Present Accrual and Target Accrual: 32 UK centres are open for the Feasibility Phase of the trial which is nearing completion. The web-based central pathology review process is functioning efficiently, with a one week maximum turn around. Registrations and sites randomizing patients are on or above target. Randomizations are currently approximately 70% of target. A total of 60 centres will open in the main trial.
Contact Information: For further information, please email the LORIS Trial Office LORIS@trials.bham.ac.uk.
Citation Format: Francis A, Bartlett J, Billingham L, Bowden S, Brookes C, Dodwell D, Evans A, Fairbrother P, Fallowfield L, Gaunt C, Hanby A, Jenkins V, Matthews L, Pinder S, Pirrie S, Rea D, Reed M, Roberts T, Thomas J, Wallis M, Wilcox M, Young J. The UK LORIS trial: Randomizing patients with low or low intermediate grade ductal carcinoma in situ (DCIS) to surgery or active monitoring [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT1-03-01.
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Francis A, Bosio E, Stone SF, Fatovich DM, Arendts G, Nagree Y, Macdonald SPJ, Mitenko H, Rajee M, Burrows S, Brown SGA. Neutrophil activation during acute human anaphylaxis: analysis of MPO and sCD62L. Clin Exp Allergy 2017; 47:361-370. [DOI: 10.1111/cea.12868] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/14/2016] [Accepted: 11/18/2016] [Indexed: 12/01/2022]
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