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Resta RG, Sullivan J, McConkie-Rosell A. INTRODUCTION TO EXPLORING THE EXOME SPECIAL ISSUE. J Genet Couns 2019; 28:181. [PMID: 30964587 DOI: 10.1002/jgc4.1113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 11/10/2022]
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Buncha V, Cherezova A, Gillis E, Covington K, McDonough A, Brands M, Sullivan J, Mamenko M. Spironolactone Effectively Reduces Renal ENaC Activity and Hypertension in Ang II‐Infused Female Rats in a Sex‐Specific Manner. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.751.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Belanger KM, Gillis E, Musall J, Sullivan J. A Decrease in Tregs Exacerbates DOCA‐Salt Hypertension and Renal Injury in Female Rats. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.573.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Castro HE, Malpica-Llanos T, Musila R, Konduri N, Amaris A, Sullivan J, Gilmartin C. Sharing knowledge for policy action in low- and middle-income countries: A literature review of managed entry agreements. MEDICINE ACCESS @ POINT OF CARE 2019. [DOI: 10.1177/2399202619834246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Managed entry agreements (MEAs)—a type of formal institutional arrangement between pharmaceutical companies and payers for sharing the risk with respect to the introduction of new pharmaceutical technologies—may expand access to new pharmaceutical technologies for non-communicable diseases (NCDs). Although common in highincome countries (HICs), there is limited evidence of their use in low- and middle-income countries (LMICs). This article aims to document international experiences of countries implementing MEAs and potential barriers and facilitators for their use in LMICs. We reviewed published literature sources on MEAs over the past 10 years considering peer-reviewed publications and gray literature data. We took into consideration the MEAs taxonomy presented by Kanavos and Ferrario et al. to categorize our findings, and extract information on factors for their implementation. We retrieved 285 MEAs documented in the literature, mostly from HICs and for a broad spectrum of NCDs. Financial schemes were slightly more prominent than performance-based agreements. Identified factors that could potentially facilitate or hinder the implementation of MEAs included the presence of quality administrative and information systems to track their implementation; availability of quality data and evidence of positive outcomes; uncertainty of drug efficacy/effectiveness, safety, and financial impact; and cultural factors, namely country’s preference for certain type of agreement and trust among payers and manufacturers. The increased availability of publications in recent years suggests a growing interest among policy-makers and researchers in the implementation of MEAs. While the use of MEAs in LMICs is very limited, this could be the result of limited empirical evidence on its use and possibly due to the use of a different taxonomy for describing MEAs in these settings. As any other policy option, the implementation and use of MEAs come with advantages and challenges. Since there is limited evidence on their use in LMICs, the identified cases of implementation in HICs may serve to inform the interest on MEAs in resource limited settings. Therefore, further research in this field especially in the context of LMICs may be of value for the global community as all countries are embarking into fairer and sustainable Universal Health Coverage (UHC).
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Wallace C, Sullivan J, Supan E. QIM19-146: A Multidisciplinary Approach to Conquer Central-Line Associated Blood Stream Infections: Establishing the Continuum of Prevention. J Natl Compr Canc Netw 2019. [DOI: 10.6004/jnccn.2018.7121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background: Central line associated blood stream infection (CLABSI) rates have been above the benchmark for our academic medical center that includes a comprehensive cancer center. In response, a 20% CLABSI reduction rate was set by the hospital Chief Medical and Associate Chief Nursing Officers. A multidisciplinary group convened to standardize central line insertion and maintenance practices. Product review showed 20 different central line insertion kits and 6 different dressing kits throughout the system. Hospital central line policy focused solely on nursing practice and there was not a policy including provider practice regarding central line insertion. A gap analysis determined dressing and insertion site integrity was compromised in 53% of our patients, including visible blood under 38% of the dressings, with oncology patients having some of our highest rates of bleeding. Objective: The purpose of this quality improvement project was to collaborate amongst disciplines to review practice, products, and policy for central line insertion and maintenance. We aimed to systematically improve practice across the central line continuum of prevention. Methods: A multidisciplinary team evaluated and defined current and best practice for policy and product changes. Implementation of best practice checklists included a team checklist to be used during insertion of every central line in the intensive care units and checklists that detailed practice steps in accordance with the updated central line policy. Central line dressing change prototypes were designed, products were compared, and approval for a standardized kit to support practice occurred. A new antimicrobial and hemostatic dressing was selected for line care to improve site integrity. The number of central line insertion kits was reduce by half and dressing kits were reduced to just one standard kit for the hospital system. Results: CLABSI rates have decreased from 7.43 cases/month to 3.6 cases/month following. Trends post-product rollout and repeat gap analysis data will be included at time of presentation. Conclusion: Reduction of CLABSI requires a multidisciplinary approach focusing simultaneously on best practices for central line insertion and maintenance. Best evidence for provider and nursing practice needs to be bundled in a comprehensive policy with checklist and products to support the standardization. Clinician evaluation and input on choosing products is critical to positive patient outcomes.
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Cogné B, Ehresmann S, Beauregard-Lacroix E, Rousseau J, Besnard T, Garcia T, Petrovski S, Avni S, McWalter K, Blackburn PR, Sanders SJ, Uguen K, Harris J, Cohen JS, Blyth M, Lehman A, Berg J, Li MH, Kini U, Joss S, von der Lippe C, Gordon CT, Humberson JB, Robak L, Scott DA, Sutton VR, Skraban CM, Johnston JJ, Poduri A, Nordenskjöld M, Shashi V, Gerkes EH, Bongers EM, Gilissen C, Zarate YA, Kvarnung M, Lally KP, Kulch PA, Daniels B, Hernandez-Garcia A, Stong N, McGaughran J, Retterer K, Tveten K, Sullivan J, Geisheker MR, Stray-Pedersen A, Tarpinian JM, Klee EW, Sapp JC, Zyskind J, Holla ØL, Bedoukian E, Filippini F, Guimier A, Picard A, Busk ØL, Punetha J, Pfundt R, Lindstrand A, Nordgren A, Kalb F, Desai M, Ebanks AH, Jhangiani SN, Dewan T, Coban Akdemir ZH, Telegrafi A, Zackai EH, Begtrup A, Song X, Toutain A, Wentzensen IM, Odent S, Bonneau D, Latypova X, Deb W, Redon S, Bilan F, Legendre M, Troyer C, Whitlock K, Caluseriu O, Murphree MI, Pichurin PN, Agre K, Gavrilova R, Rinne T, Park M, Shain C, Heinzen EL, Xiao R, Amiel J, Lyonnet S, Isidor B, Biesecker LG, Lowenstein D, Posey JE, Denommé-Pichon AS, Férec C, Yang XJ, Rosenfeld JA, Gilbert-Dussardier B, Audebert-Bellanger S, Redon R, Stessman HA, Nellaker C, Yang Y, Lupski JR, Goldstein DB, Eichler EE, Bolduc F, Bézieau S, Küry S, Campeau PM, Küry S, Campeau PM. Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability. Am J Hum Genet 2019; 104:530-541. [PMID: 30827496 DOI: 10.1016/j.ajhg.2019.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.
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Bauer MS, Miller CJ, Kim B, Lew R, Stolzmann K, Sullivan J, Riendeau R, Pitcock J, Williamson A, Connolly S, Elwy AR, Weaver K. Effectiveness of Implementing a Collaborative Chronic Care Model for Clinician Teams on Patient Outcomes and Health Status in Mental Health: A Randomized Clinical Trial. JAMA Netw Open 2019; 2:e190230. [PMID: 30821830 PMCID: PMC6484628 DOI: 10.1001/jamanetworkopen.2019.0230] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
IMPORTANCE Collaborative chronic care models (CCMs) have extensive randomized clinical trial evidence for effectiveness in serious mental illnesses, but little evidence exists regarding their feasibility or effect in typical practice conditions. OBJECTIVE To determine the effectiveness of implementation facilitation in establishing the CCM in mental health teams and the impact on health outcomes of team-treated individuals. DESIGN, SETTING, AND PARTICIPANTS This quasi-experimental, randomized stepped-wedge implementation trial was conducted from February 2016 through February 2018, in partnership with the US Department of Veterans Affairs (VA) Office of Mental Health and Suicide Prevention. Nine facilities were enrolled from all VA facilities in the United States to receive CCM implementation support. All veterans (n = 5596) treated by designated outpatient general mental health teams were included for hospitalization analyses, and a randomly selected sample (n = 1050) was identified for health status interviews. Individuals with dementia were excluded. Clinicians (n = 62) at the facilities were surveyed, and site process summaries were rated for concordance with the CCM process. The CCM implementation start time was randomly assigned across 3 waves. Data analysis of this evaluable population was performed from June to September 2018. INTERVENTIONS Internal-external facilitation, combining a study-funded external facilitator and a facility-funded internal facilitator working with a designated team for 1 year. MAIN OUTCOMES AND MEASURES Facilitation was hypothesized to be associated with improvements in both implementation and intervention outcomes (hybrid type II trial). Implementation outcomes included the clinician Team Development Measure (TDM) and proportion of CCM-concordant team care processes. The study was powered for the primary health outcome, mental component score (MCS). Hospitalization rate was derived from administrative data. RESULTS The veteran population (n = 5596) included 881 women (15.7%), and the mean (SD) age was 52.2 (14.5) years. The interviewed sample (n = 1050) was similar but was oversampled for women (n = 210 [20.0%]). Facilitation was associated with improvements in TDM subscales for role clarity (53.4%-68.6%; δ = 15.3; 95% CI, 4.4-26.2; P = .01) and team primacy (50.0%-68.6%; δ = 18.6; 95% CI, 8.3-28.9; P = .001). The percentage of CCM-concordant processes achieved varied, ranging from 44% to 89%. No improvement was seen in veteran self-ratings, including the primary outcome. In post hoc analyses, MCS improved in veterans with 3 or more treated mental health diagnoses compared with others (β = 5.03; 95% CI, 2.24-7.82; P < .001). Mental health hospitalizations demonstrated a robust decrease during facilitation (β = -0.12; 95% CI, -0.16 to -0.07; P < .001); this finding withstood 4 internal validity tests. CONCLUSIONS AND RELEVANCE Implementation facilitation that engages clinicians under typical practice conditions can enhance evidence-based team processes; its effect on self-reported overall population health status was negligible, although health status improved for individuals with complex conditions and hospitalization rate declined. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02543840.
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Barman SA, Li X, Haigh S, Kondrikov D, Mahboubi K, Bordan Z, Stepp DW, Zhou J, Wang Y, Weintraub DS, Traber P, Snider W, Jonigk D, Sullivan J, Crislip GR, Butcher JT, Thompson J, Su Y, Chen F, Fulton DJR. Galectin-3 is expressed in vascular smooth muscle cells and promotes pulmonary hypertension through changes in proliferation, apoptosis, and fibrosis. Am J Physiol Lung Cell Mol Physiol 2019; 316:L784-L797. [PMID: 30724100 DOI: 10.1152/ajplung.00186.2018] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A defining characteristic of pulmonary hypertension (PH) is the extensive remodeling of pulmonary arteries (PAs), which results in progressive increases in vascular resistance and stiffness and eventual failure of the right ventricle. There is no cure for PH and identification of novel molecular mechanisms that underlie increased proliferation, reduced apoptosis, and excessive extracellular matrix production in pulmonary artery smooth muscle cells (PASMCs) is a vital objective. Galectin-3 (Gal-3) is a chimeric lectin and potent driver of many aspects of fibrosis, but its role in regulating PASMC behavior in PH remains poorly understood. Herein, we evaluated the importance of increased Gal-3 expression and signaling on PA vascular remodeling and cardiopulmonary function in experimental models of PH. Gal-3 expression was quantified by qRT-PCR, immunoblotting, and immunofluorescence imaging, and its functional role was assessed by specific Gal-3 inhibitors and CRISPR/Cas9-mediated knockout of Gal-3 in the rat. In rat models of PH, we observed increased Gal-3 expression in PASMCs, which stimulated migration and resistance to apoptosis, whereas silencing or genetic deletion reduced cellular migration and PA fibrosis and increased apoptosis. Gal-3 inhibitors attenuated and reversed PA remodeling and fibrosis, as well as hemodynamic indices in monocrotaline (MCT)-treated rats in vivo. These results were supported by genetic deletion of Gal-3 in both MCT and Sugen Hypoxia rat models. In conclusion, our results suggest that elevated Gal-3 levels contribute to inappropriate PA remodeling in PH by enhancing multiple profibrotic mechanisms. Therapeutic strategies targeting Gal-3 may be of benefit in the treatment of PH.
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Reich K, Sullivan J, Arenberger P, Mrowietz U, Jazayeri S, Augustin M, Parneix A, Regnault P, You R, Milutinovic M. Effect of secukinumab on the clinical activity and disease burden of nail psoriasis: 32‐week results from the randomized placebo‐controlled
TRANSFIGURE
trial. Br J Dermatol 2019; 181:954-966. [DOI: 10.1111/bjd.17351] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2018] [Indexed: 12/14/2022]
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Kube E, Hicken B, Moye J, Harris G, Sullivan J. MENTAL HEALTH INTEGRATION IN GERI PACT. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Sullivan J, Adjognon O, Shay K, Harvey K, Yaksic E, Intrator O, Moye J, Solimeo S. GERIATRIC PATIENT-ALIGNED CARE TEAMS IN THE VETERANS HEALTH ADMINISTRATION: HOW ARE THEY STRUCTURED? Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ryan C, Menter A, Guenther L, Blauvelt A, Bissonnette R, Meeuwis K, Sullivan J, Cather J, Yosipovitch G, Gottlieb A, Merola J, Callis Duffin K, Fretzin S, Osuntokun O, Burge R, Naegeli A, Yang F, Lin CY, Todd K, Potts Bleakman A. Ixekizumab efficacy and safety in moderate-to-severe genital psoriasis. Br J Dermatol 2018. [DOI: 10.1111/bjd.17168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ryan C, Menter A, Guenther L, Blauvelt A, Bissonnette R, Meeuwis K, Sullivan J, Cather J, Yosipovitch G, Gottlieb A, Merola J, Callis Duffin K, Fretzin S, Osuntokun O, Burge R, Naegeli A, Yang F, Lin CY, Todd K, Potts Bleakman A. 伊赛珠单抗在中度至重度生殖器银屑病中的疗效和安全性. Br J Dermatol 2018. [DOI: 10.1111/bjd.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lange R, Lippa S, French L, Gartner R, Driscoll A, Wright M, Bailie J, Nora D, Sullivan J, Varbedian N, Camelo-Lopez V, Cheselka J, Bellini P, Holzinger J, Walker H, Brandler B, Freud J, Schaper A, Reese M, Barnhart E, Casey K, Ndege V, Ramin D, Eshera Y, Robinson G, Brickell T. A - 60Ten Year Neurobehavioral Outcome Following Mild, Moderate, Severe, and Penetrating Traumatic Brain Injury in U.S. Military Service Members. Arch Clin Neuropsychol 2018. [DOI: 10.1093/arclin/acy061.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Brickell T, Lippa S, French L, Gartner R, Driscoll A, Wright M, Bailie J, Nora D, Sullivan J, Varbedian N, Camelo-Lopez V, Cheselka J, Bellini P, Holzinger J, Walker H, Brandler B, Freud J, Schaper A, Reese M, Barnhart E, Casey K, Ndege V, Ramin D, Eshera Y, Robinson G, Lange R. A - 46Post-Concussion Symptom Reporting within the First 5-Years of the Recovery Trajectory Following Uncomplicated Mild Traumatic Brain Injury: A Cross-Sectional Perspective. Arch Clin Neuropsychol 2018. [DOI: 10.1093/arclin/acy061.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ryan C, Menter A, Guenther L, Blauvelt A, Bissonnette R, Meeuwis K, Sullivan J, Cather J, Yosipovitch G, Gottlieb A, Merola J, Callis Duffin K, Fretzin S, Osuntokun O, Burge R, Naegeli A, Yang F, Lin CY, Todd K, Potts Bleakman A. Efficacy and safety of ixekizumab in a randomized, double-blinded, placebo-controlled phase IIIb study of patients with moderate-to-severe genital psoriasis. Br J Dermatol 2018; 179:844-852. [DOI: 10.1111/bjd.16736] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2018] [Indexed: 11/27/2022]
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Naidoo J, Stanek LM, Ohno K, Trewman S, Samaranch L, Hadaczek P, O'Riordan C, Sullivan J, San Sebastian W, Bringas JR, Snieckus C, Mahmoodi A, Mahmoodi A, Forsayeth J, Bankiewicz KS, Shihabuddin LS. Extensive Transduction and Enhanced Spread of a Modified AAV2 Capsid in the Non-human Primate CNS. Mol Ther 2018; 26:2418-2430. [PMID: 30057240 DOI: 10.1016/j.ymthe.2018.07.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 11/17/2022] Open
Abstract
The present study was designed to characterize transduction of non-human primate brain and spinal cord with a modified adeno-associated virus serotype 2, incapable of binding to the heparan sulfate proteoglycan receptor, referred to as AAV2-HBKO. AAV2-HBKO was infused into the thalamus, intracerebroventricularly or via a combination of both intracerebroventricular and thalamic delivery. Thalamic injection of this modified vector encoding GFP resulted in widespread CNS transduction that included neurons in deep cortical layers, deep cerebellar nuclei, several subcortical regions, and motor neuron transduction in the spinal cord indicative of robust bidirectional axonal transport. Intracerebroventricular delivery similarly resulted in widespread cortical transduction, with one striking distinction that oligodendrocytes within superficial layers of the cortex were the primary cell type transduced. Robust motor neuron transduction was also observed in all levels of the spinal cord. The combination of thalamic and intracerebroventricular delivery resulted in transduction of oligodendrocytes in superficial cortical layers and neurons in deeper cortical layers. Several subcortical regions were also transduced. Our data demonstrate that AAV2-HBKO is a powerful vector for the potential treatment of a wide number of neurological disorders, and highlight that delivery route can significantly impact cellular tropism and pattern of CNS transduction.
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Sullivan J, Bernie H, Ortega Y, Mulhall J. 615 Comparative analysis of the natural history of de novo Peyronie’s Disease versus post-radical prostatectomy Peyronie’s Disease. J Sex Med 2018. [DOI: 10.1016/j.jsxm.2018.04.522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics 2018; 19:134. [PMID: 29642841 PMCID: PMC5896046 DOI: 10.1186/s12859-018-2118-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/20/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. RESULTS The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. CONCLUSIONS PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.
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Sivade Dumousseau M, Koch M, Shrivastava A, Alonso-López D, De Las Rivas J, Del-Toro N, Combe CW, Meldal BHM, Heimbach J, Rappsilber J, Sullivan J, Yehudi Y, Orchard S. JAMI: a Java library for molecular interactions and data interoperability. BMC Bioinformatics 2018; 19:133. [PMID: 29642846 PMCID: PMC5896107 DOI: 10.1186/s12859-018-2119-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/20/2018] [Indexed: 11/22/2022] Open
Abstract
Background A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. Results A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Conclusion Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI’s model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.
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Lucid M, Rankin A, Espíndola A, Chichester L, Ehlers S, Robinson L, Sullivan J. Taxonomy and biogeography of Hemphillia (Gastropoda: Pulmonata: Arionidae) in North American rainforests, with description of a new species (Skade’s jumping-slug, Hemphillia skadei sp. nov.). CAN J ZOOL 2018. [DOI: 10.1139/cjz-2017-0260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Species diversity of the genus Hemphillia Bland and W.G. Binney, 1872 (jumping-slugs) was studied across its range in western North America’s inland temperate rainforests. The taxonomic relationships among jumping-slug populations were clarified by integrating morphological, molecular, and biogeographic approaches. A new species, Skade’s jumping-slug (Hemphillia skadei sp. nov.), was discovered in this process and is described herein. We base this taxonomic decision on molecular comparison of representatives from other Hemphillia species and four morphological characters that distinguish H. skadei from its sister species, the pale jumping-slug (Hemphillia camelus Pilsbry and Vanatta, 1897). The distribution of H. skadei and H. camelus is described along with the notable lack of detection of the marbled jumping-slug (Hemphillia danielsi Vanatta, 1914) within the primary survey area.
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Eaton KA, Lloyd HA, Wheeler M, Sullivan J, Klass C, Allen Y, Lambert-Humble S. Looking after the mouth - Evaluation of a pilot for a new approach to training care home carers in Kent, Surrey and Sussex. Br Dent J 2018; 221:31-6. [PMID: 27388088 DOI: 10.1038/sj.bdj.2016.497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 11/09/2022]
Abstract
Objective This pilot study aimed to produce and evaluate training resources and training in oral health care, including oral hygiene, for carers in care homes in Surrey and Medway.Methods During two training days, for carers from these homes, short, interactive presentations were given on a range of topics relevant to oral health care and oral hygiene of older people, followed by practical training. Prior to any training all attendees completed a 39 question questionnaire to establish their baseline knowledge of oral health and hygiene. At the end of the training day they completed an evaluation form. Fourteen weeks later, they were visited at their place of work and completed the same questionnaire again. Differences in responses between baseline and after 14 weeks were statistically tested using the chi-squared test.Results Sixty-six carers attended the training sessions and 44 were followed up 14 weeks later. The results showed an improvement in carer knowledge at follow up. The majority of carers (36/44) spoke English as their first language. They had a mean age of 41 years, 37 were female and 7 male. They had worked as carers for a mean of 10.9 years (range 4 months-34 years). Over 90% stated that the training day fully met or exceeded their requirements and expectations.Conclusions The results indicated improvements in carer knowledge. However, the carers were atypical of carers in general, as they were self-selected and well-motivated. Nevertheless the content of the training day and the questionnaire should inform future work in this area.
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MacEwan JP, Gill TM, Johnson K, Doctor J, Sullivan J, Shim J, Goldman DP. Measuring Sarcopenia Severity in Older Adults and the Value of Effective Interventions. J Nutr Health Aging 2018; 22:1253-1258. [PMID: 30498834 PMCID: PMC6302764 DOI: 10.1007/s12603-018-1104-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Little is known about the severity and long-term health and economic consequences of sarcopenia. We developed a sarcopenia index to measure severity in older Americans and estimated the long-term societal benefits generated by effective interventions to mitigate severity. DESIGN Using a micro-simulation model, we quantified the potential societal value generated in the US in 2010-2040 by reductions in sarcopenia severity in older adults. All analyses were performed in Stata and SAS. SETTING AND PARTICIPANTS Secondary data from the National Health and Nutrition Examination Survey (NHANES) (N = 1634) and Health and Retirement Study (HRS) (N = 952) were used to develop a sarcopenia severity index in older adults. MEASUREMENTS Multi-trait multi-method and factor analyses were used to validate and calibrate the sarcopenia severity index, which was modeled as a function of gait speed, walking without an assistive device, and moderate physical activity. RESULTS In representative elderly populations, reducing sarcopenia severity by improving gait speed by 0.1 m/s in those with gait speed under 0.8 m/s generated a cumulative benefit of $65B by 2040 (2015 dollars). Improving walking ability in those with walking difficulty generated cumulative social benefit of $787B by 2040. CONCLUSIONS Reducing sarcopenia severity would generate significant health and economic benefits to society-almost $800B in the most optimistic scenarios.
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Aboumatar H, Naqibuddin M, Chung S, Adebowale H, Bone L, Brown T, Cooper LA, Gurses AP, Knowlton A, Kurtz D, Piet L, Putcha N, Rand C, Roter D, Shattuck E, Sylvester C, Urteaga-Fuentes A, Wise R, Wolff JL, Yang T, Hibbard J, Howell E, Myers M, Shea K, Sullivan J, Syron L, Wang NY, Pronovost P. Better Respiratory Education and Treatment Help Empower (BREATHE) study: Methodology and baseline characteristics of a randomized controlled trial testing a transitional care program to improve patient-centered care delivery among chronic obstructive pulmonary disease patients. Contemp Clin Trials 2017; 62:159-167. [PMID: 28887069 DOI: 10.1016/j.cct.2017.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 11/15/2022]
Abstract
BACKGROUND Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of hospitalizations. Interventional studies focusing on the hospital-to-home transition for COPD patients are few. In the BREATHE (Better Respiratory Education and Treatment Help Empower) study, we developed and tested a patient and family-centered transitional care program that helps prepare hospitalized COPD patients and their family caregivers to manage COPD at home. METHODS In the study's initial phase, we co-developed the BREATHE transitional care program with COPD patients, family-caregivers, and stakeholders. The program offers tailored services to address individual patients' needs and priorities at the hospital and for 3months post discharge. We tested the program in a single-blinded RCT with 240 COPD patients who were randomized to receive the program or 'usual care'. Program participants were offered the opportunity to invite a family caregiver, if available, to enroll with them into the study. The primary outcomes were the combined number of COPD-related hospitalizations and Emergency Department (ED) visits per participant at 6months post discharge, and the change in health-related quality of life over the 6months study period. Other measures include 'all cause' hospitalizations and ED visits; patient activation; self-efficacy; and, self-care behaviors. DISCUSSION Unlike 1month transitional care programs that focus on patients' post-acute care needs, the BREATHE program helps hospitalized COPD patients manage the post discharge period as well as prepare them for long term self-management of COPD. If proven effective, this program may offer a timely solution for hospitals in their attempts to reduce COPD rehospitalizations.
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McIntosh P, Austin S, Sullivan J, Bailey L, Bailey C, Viskochil D, Kishnani PS. Three cases of multi-generational Pompe disease: Are current practices missing diagnostic and treatment opportunities? Am J Med Genet A 2017; 173:2628-2634. [PMID: 28763149 DOI: 10.1002/ajmg.a.38369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/08/2017] [Accepted: 06/25/2017] [Indexed: 11/07/2022]
Abstract
Pompe disease (Glycogen storage disease type II, GSDII, or acid maltase deficiency) is an autosomal recessive metabolic myopathy with a broad clinical spectrum, ranging from infantile to late-onset presentations. In 2015, Pompe disease was added as a core condition to the Recommended Uniform Screening Panel for state newborn screening (NBS). The clinical importance of Pompe disease is evolving with the use of NBS, increasing awareness of the disease, and higher than previously reported disease prevalence; however, current practices miss additional diagnostic and potential treatment opportunities in close relatives of the family proband. In this report, we describe three families with multiple individuals in multiple generations affected by both infantile and late-onset clinical presentations of Pompe disease. The presence of multi-generational disease within these families highlights the importance of subsequent risk assessment through medical history and physical examination, with a low threshold for the screening of a proband's family members. We recommend enzymology (GAA activity assay) as the first screening method, as opposed to targeted mutation analysis, for at-risk family members. Given that the initial symptoms of the slowly progressive late-onset presentation of Pompe disease may be mild or non-specific, enzymatic testing of all parents of affected infants should be considered.
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