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Ruth Clark

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https://www.readbyqxmd.com/read/27884822/a-framework-for-remission-in-sle-consensus-findings-from-a-large-international-task-force-on-definitions-of-remission-in-sle-doris
#1
Ronald van Vollenhoven, Alexandre Voskuyl, George Bertsias, Cynthia Aranow, Martin Aringer, Laurent Arnaud, Anca Askanase, Petra Balážová, Eloisa Bonfa, Hendrika Bootsma, Dimitrios Boumpas, Ian Bruce, Ricard Cervera, Ann Clarke, Cindy Coney, Nathalie Costedoat-Chalumeau, László Czirják, Ronald Derksen, Andrea Doria, Thomas Dörner, Rebecca Fischer-Betz, Ruth Fritsch-Stork, Caroline Gordon, Winfried Graninger, Noémi Györi, Frédéric Houssiau, David Isenberg, Soren Jacobsen, David Jayne, Annegret Kuhn, Veronique Le Guern, Kirsten Lerstrøm, Roger Levy, Francinne Machado-Ribeiro, Xavier Mariette, Jamil Missaykeh, Eric Morand, Marta Mosca, Murat Inanc, Sandra Navarra, Irmgard Neumann, Marzena Olesinska, Michelle Petri, Anisur Rahman, Ole Petter Rekvig, Jozef Rovensky, Yehuda Shoenfeld, Josef Smolen, Angela Tincani, Murray Urowitz, Bernadette van Leeuw, Carlos Vasconcelos, Anne Voss, Victoria P Werth, Helena Zakharova, Asad Zoma, Matthias Schneider, Michael Ward
OBJECTIVES: Treat-to-target recommendations have identified 'remission' as a target in systemic lupus erythematosus (SLE), but recognise that there is no universally accepted definition for this. Therefore, we initiated a process to achieve consensus on potential definitions for remission in SLE. METHODS: An international task force of 60 specialists and patient representatives participated in preparatory exercises, a face-to-face meeting and follow-up electronic voting...
November 24, 2016: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/27884193/reorganising-specialist-cancer-surgery-for-the-twenty-first-century-a-mixed-methods-evaluation-respect-21
#2
Naomi J Fulop, Angus I G Ramsay, Cecilia Vindrola-Padros, Michael Aitchison, Ruth J Boaden, Veronica Brinton, Caroline S Clarke, John Hines, Rachael M Hunter, Claire Levermore, Satish B Maddineni, Mariya Melnychuk, Caroline M Moore, Muntzer M Mughal, Catherine Perry, Kathy Pritchard-Jones, David C Shackley, Jonathan Vickers, Stephen Morris
BACKGROUND: There are longstanding recommendations to centralise specialist healthcare services, citing the potential to reduce variations in care and improve patient outcomes. Current activity to centralise specialist cancer surgical services in two areas of England provides an opportunity to study the planning, implementation and outcomes of such changes. London Cancer and Manchester Cancer are centralising specialist surgical pathways for prostate, bladder, renal, and oesophago-gastric cancers, so that these services are provided in fewer hospitals...
November 25, 2016: Implementation Science: IS
https://www.readbyqxmd.com/read/27871240/abo-antigen-and-secretor-statuses-are-not-associated-with-gut-microbiota-composition-in-1-500-twins
#3
Emily R Davenport, Julia K Goodrich, Jordana T Bell, Tim D Spector, Ruth E Ley, Andrew G Clark
BACKGROUND: Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in host factors secreted into the gut lumen may lead to variation in microbiome composition. One such factor is the ABO antigen. This molecule is not only expressed on the surface of red blood cells, but is also secreted from mucosal surfaces in individuals containing an intact FUT2 gene (secretors)...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27802289/has-metal-on-metal-resurfacing-been-a-cost-effective-intervention-for-health-care-providers-a-registry-based-study
#4
Ruth Pulikottil-Jacob, Martin Connock, Ngianga-Bakwin Kandala, Hema Mistry, Amy Grove, Karoline Freeman, Matthew Costa, Paul Sutcliffe, Aileen Clarke
BACKGROUND: Total hip replacement for end stage arthritis of the hip is currently the most common elective surgical procedure. In 2007 about 7.5% of UK implants were metal-on-metal joint resurfacing (MoM RS) procedures. Due to poor revision performance and concerns about metal debris, the use of RS had declined by 2012 to about a 1% share of UK hip procedures. This study estimated the lifetime cost-effectiveness of metal-on-metal resurfacing (RS) procedures versus commonly employed total hip replacement (THR) methods...
2016: PloS One
https://www.readbyqxmd.com/read/27746295/turkish-and-japanese-mycobacterium-tuberculosis-sublineages-share-a-remote-common-ancestor
#5
Guislaine Refrégier, Edgar Abadia, Tomoshige Matsumoto, Hiromi Ano, Tetsuya Takashima, Izuo Tsuyuguchi, Elif Aktas, Füsun Cömert, Michel Kireopori Gomgnimbou, Stefan Panaiotov, Jody Phelan, Francesc Coll, Ruth McNerney, Arnab Pain, Taane G Clark, Christophe Sola
Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity...
October 14, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27731410/no-association-of-coronary-artery-disease-with-x-chromosomal-variants-in-comprehensive-international-meta-analysis
#6
Christina Loley, Maris Alver, Themistocles L Assimes, Andrew Bjonnes, Anuj Goel, Stefan Gustafsson, Jussi Hernesniemi, Jemma C Hopewell, Stavroula Kanoni, Marcus E Kleber, King Wai Lau, Yingchang Lu, Leo-Pekka Lyytikäinen, Christopher P Nelson, Majid Nikpay, Liming Qu, Elias Salfati, Markus Scholz, Taru Tukiainen, Christina Willenborg, Hong-Hee Won, Lingyao Zeng, Weihua Zhang, Sonia S Anand, Frank Beutner, Erwin P Bottinger, Robert Clarke, George Dedoussis, Ron Do, Tõnu Esko, Markku Eskola, Martin Farrall, Dominique Gauguier, Vilmantas Giedraitis, Christopher B Granger, Alistair S Hall, Anders Hamsten, Stanley L Hazen, Jie Huang, Mika Kähönen, Theodosios Kyriakou, Reijo Laaksonen, Lars Lind, Cecilia Lindgren, Patrik K E Magnusson, Eirini Marouli, Evelin Mihailov, Andrew P Morris, Kjell Nikus, Nancy Pedersen, Loukianos Rallidis, Veikko Salomaa, Svati H Shah, Alexandre F R Stewart, John R Thompson, Pierre A Zalloua, John C Chambers, Rory Collins, Erik Ingelsson, Carlos Iribarren, Pekka J Karhunen, Jaspal S Kooner, Terho Lehtimäki, Ruth J F Loos, Winfried März, Ruth McPherson, Andres Metspalu, Muredach P Reilly, Samuli Ripatti, Dharambir K Sanghera, Joachim Thiery, Hugh Watkins, Panos Deloukas, Sekar Kathiresan, Nilesh J Samani, Heribert Schunkert, Jeanette Erdmann, Inke R König
In recent years, genome-wide association studies have identified 58 independent risk loci for coronary artery disease (CAD) on the autosome. However, due to the sex-specific data structure of the X chromosome, it has been excluded from most of these analyses. While females have 2 copies of chromosome X, males have only one. Also, one of the female X chromosomes may be inactivated. Therefore, special test statistics and quality control procedures are required. Thus, little is known about the role of X-chromosomal variants in CAD...
October 12, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27717381/critical-evaluation-of-the-illumina-methylationepic-beadchip-microarray-for-whole-genome-dna-methylation-profiling
#7
Ruth Pidsley, Elena Zotenko, Timothy J Peters, Mitchell G Lawrence, Gail P Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker, Susan J Clark
BACKGROUND: In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements. Illumina have now released the MethylationEPIC (EPIC) BeadChip, with new content specifically designed to target these regions. We have used HM450 and whole-genome bisulphite sequencing (WGBS) to perform a critical evaluation of the new EPIC array platform. RESULTS: EPIC covers over 850,000 CpG sites, including >90 % of the CpGs from the HM450 and an additional 413,743 CpGs...
October 7, 2016: Genome Biology
https://www.readbyqxmd.com/read/27704009/penicillin-use-in-meningococcal-disease-management-active-bacterial-core-surveillance-sites-2009
#8
Amy E Blain, Sema Mandal, Henry Wu, Jessica R MacNeil, Lee H Harrison, Monica M Farley, Ruth Lynfield, Lisa Miller, Megin Nichols, Sue Petit, Arthur Reingold, William Schaffner, Ann Thomas, Shelley M Zansky, Raydel Anderson, Brian H Harcourt, Leonard W Mayer, Thomas A Clark, Amanda C Cohn
In 2009, in the Active Bacterial Core surveillance sites, penicillin was not commonly used to treat meningococcal disease. This is likely because of inconsistent availability of antimicrobial susceptibility testing and ease of use of third-generation cephalosporins. Consideration of current practices may inform future meningococcal disease management guidelines.
September 2016: Open Forum Infectious Diseases
https://www.readbyqxmd.com/read/27666579/heritable-components-of-the-human-fecal-microbiome-are-associated-with-visceral-fat
#9
Michelle Beaumont, Julia K Goodrich, Matthew A Jackson, Idil Yet, Emily R Davenport, Sara Vieira-Silva, Justine Debelius, Tess Pallister, Massimo Mangino, Jeroen Raes, Rob Knight, Andrew G Clark, Ruth E Ley, Tim D Spector, Jordana T Bell
BACKGROUND: Variation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-metabolic disease risk factor. Here, we explore links between the fecal microbiota and abdominal adiposity using body composition as measured by dual-energy X-ray absorptiometry in a large sample of twins from the TwinsUK cohort, comparing fecal 16S rRNA diversity profiles with six adiposity measures...
September 26, 2016: Genome Biology
https://www.readbyqxmd.com/read/27649868/the-draft-genome-of-mycobacterium-aurum-a-potential-model-organism-for-investigating-drugs-against-mycobacterium-tuberculosis-and-mycobacterium-leprae
#10
Jody Phelan, Arundhati Maitra, Ruth McNerney, Mridul Nair, Antima Gupta, Francesc Coll, Arnab Pain, Sanjib Bhakta, Taane G Clark
Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria...
September 2015: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27628565/22-years-of-predictive-testing-for-huntington-s-disease-the-experience-of-the-uk-huntington-s-prediction-consortium
#11
Sheharyar S Baig, Mark Strong, Elisabeth Rosser, Nicola V Taverner, Ruth Glew, Zosia Miedzybrodzka, Angus Clarke, David Craufurd, Uk Huntington's Disease Prediction Consortium, Oliver W Quarrell
No abstract text is available yet for this article.
October 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27604469/an-expanded-evaluation-of-protein-function-prediction-methods-shows-an-improvement-in-accuracy
#12
Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark, Asma R Bankapur, Daniel D'Andrea, Rosalba Lepore, Christopher S Funk, Indika Kahanda, Karin M Verspoor, Asa Ben-Hur, Da Chen Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra Lin, Sayed M E Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio, Renzhi Cao, Zhaolong Zhong, Jianlin Cheng, Adrian Altenhoff, Nives Skunca, Christophe Dessimoz, Tunca Dogan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching-Tai Chen, Wen-Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T Jones, Samuel Chapman, Dukka Bkc, Ishita K Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrian-Uhalte, Paul Denny, Rebecca E Foulger, Reija Hieta, Duncan Legge, Ruth C Lovering, Michele Magrane, Anna N Melidoni, Prudence Mutowo-Meullenet, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon-Charles Tranchevent, Sayoni Das, Natalie L Dawson, David Lee, Jonathan G Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, Jesse Gillis, Adriana E Sedeño-Cortés, Paul Pavlidis, Shou Feng, Juan M Cejuela, Tatyana Goldberg, Tobias Hamp, Lothar Richter, Asaf Salamov, Toni Gabaldon, Marina Marcet-Houben, Fran Supek, Qingtian Gong, Wei Ning, Yuanpeng Zhou, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Stefano Toppo, Carlo Ferrari, Manuel Giollo, Damiano Piovesan, Silvio C E Tosatto, Angela Del Pozo, José M Fernández, Paolo Maietta, Alfonso Valencia, Michael L Tress, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino, Hafeez Ur Rehman, Matteo Re, Marco Mesiti, Giorgio Valentini, Joachim W Bargsten, Aalt D J van Dijk, Branislava Gemovic, Sanja Glisic, Vladmir Perovic, Veljko Veljkovic, Nevena Veljkovic, Danillo C Almeida-E-Silva, Ricardo Z N Vencio, Malvika Sharan, Jörg Vogel, Lakesh Kansakar, Shanshan Zhang, Slobodan Vucetic, Zheng Wang, Michael J E Sternberg, Mark N Wass, Rachael P Huntley, Maria J Martin, Claire O'Donovan, Peter N Robinson, Yves Moreau, Anna Tramontano, Patricia C Babbitt, Steven E Brenner, Michal Linial, Christine A Orengo, Burkhard Rost, Casey S Greene, Sean D Mooney, Iddo Friedberg, Predrag Radivojac
BACKGROUND: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. RESULTS: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function...
2016: Genome Biology
https://www.readbyqxmd.com/read/27557630/strategies-for-assessing-renal-function-prior-to-outpatient-contrast-enhanced-ct-a-uk-survey
#13
Martine Ann Harris, Beverly Snaith, Ruth Clarke
OBJECTIVES: To identify current UK screening practices prior to contrast-enhanced computerised tomography (CT). To determine the patient management strategies to minimise the risk of contrast induced acute kidney injury risk (CI-AKI) in outpatients. METHODS: An invitation to complete an electronic survey was distributed to the CT managers of 174 UK adult NHS hospital trusts. The survey included questions related to local protocols and national guidance on which these are based...
August 25, 2016: British Journal of Radiology
https://www.readbyqxmd.com/read/27433284/genome-scale-methylation-assessment-did-not-identify-prognostic-biomarkers-in-oral-tongue-carcinomas
#14
Annette M Lim, Nicholas C Wong, Ruth Pidsley, Elena Zotenko, June Corry, Alexander Dobrovic, Susan J Clark, Danny Rischin, Benjamin Solomon
BACKGROUND: DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 109 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27325572/rb-regulates-the-production-and-the-survival-of-newborn-neurons-in-the-embryonic-and-adult-dentate-gyrus
#15
Renaud Vandenbosch, Alysen Clark, Bensun C Fong, Saad Omais, Carine Jaafar, Delphie Dugal-Tessier, Jagroop Dhaliwal, Diane C Lagace, David S Park, Noël Ghanem, Ruth S Slack
In mammals, hippocampal dentate gyrus granule cells (DGCs) constitute a particular neuronal population produced both during embryogenesis and adult life, and play key roles in neural plasticity and memory. However, the molecular mechanisms regulating neurogenesis in the dentate lineage throughout development and adulthood are still not well understood. The retinoblastoma protein (RB), a transcriptional repressor primarily involved in cell cycle control and cell death, plays crucial roles during cortical development but its function in the formation and maintenance of DGCs remains unknown...
June 20, 2016: Hippocampus
https://www.readbyqxmd.com/read/27237737/mitochondrial-dynamics-impacts-stem-cell-identity-and-fate-decisions-by-regulating-a-nuclear-transcriptional-program
#16
Mireille Khacho, Alysen Clark, Devon S Svoboda, Joelle Azzi, Jason G MacLaurin, Cynthia Meghaizel, Hiromi Sesaki, Diane C Lagace, Marc Germain, Mary-Ellen Harper, David S Park, Ruth S Slack
Regulated mechanisms of stem cell maintenance are key to preventing stem cell depletion and aging. While mitochondrial morphology plays a fundamental role in tissue development and homeostasis, its role in stem cells remains unknown. Here, we uncover that mitochondrial dynamics regulates stem cell identity, self-renewal, and fate decisions by orchestrating a transcriptional program. Manipulation of mitochondrial structure, through OPA1 or MFN1/2 deletion, impaired neural stem cell (NSC) self-renewal, with consequent age-dependent depletion, neurogenesis defects, and cognitive impairments...
August 4, 2016: Cell Stem Cell
https://www.readbyqxmd.com/read/27173935/genetic-determinants-of-the-gut-microbiome-in-uk-twins
#17
Julia K Goodrich, Emily R Davenport, Michelle Beaumont, Matthew A Jackson, Rob Knight, Carole Ober, Tim D Spector, Jordana T Bell, Andrew G Clark, Ruth E Ley
Studies in mice and humans have revealed intriguing associations between host genetics and the microbiome. Here we report a 16S rRNA-based analysis of the gut microbiome in 1,126 twin pairs, a subset of which was previously reported. Tripling the sample narrowed the confidence intervals around heritability estimates and uncovered additional heritable taxa, some of which are validated in other studies. Repeat sampling of subjects showed heritable taxa to be temporally stable. A candidate gene approach uncovered associations between heritable taxa and genes related to diet, metabolism, and olfaction...
May 11, 2016: Cell Host & Microbe
https://www.readbyqxmd.com/read/27165004/22-years-of-predictive-testing-for-huntington-s-disease-the-experience-of-the-uk-huntington-s-prediction-consortium
#18
Sheharyar S Baig, Mark Strong, Elisabeth Rosser, Nicola V Taverner, Ruth Glew, Zosia Miedzybrodzka, Angus Clarke, David Craufurd, Oliver W Quarrell
Huntington's disease (HD) is a progressive neurodegenerative condition. At-risk individuals have accessed predictive testing via direct mutation testing since 1993. The UK Huntington's Prediction Consortium has collected anonymised data on UK predictive tests, annually, from 1993 to 2014: 9407 predictive tests were performed across 23 UK centres. Where gender was recorded, 4077 participants were male (44.3%) and 5122 were female (55.7%). The median age of participants was 37 years. The most common reason for predictive testing was to reduce uncertainty (70...
October 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27126034/cross-species-comparisons-of-host-genetic-associations-with-the-microbiome
#19
REVIEW
Julia K Goodrich, Emily R Davenport, Jillian L Waters, Andrew G Clark, Ruth E Ley
Recent studies in human populations and mouse models reveal notable congruences in gut microbial taxa whose abundances are partly regulated by host genotype. Host genes associating with these taxa are related to diet sensing, metabolism, and immunity. These broad patterns are further validated in similar studies of nonmammalian microbiomes. The next generation of genome-wide association studies will expand the size of the data sets and refine the microbial phenotypes to fully capture these intriguing signatures of host-microbiome coevolution...
April 29, 2016: Science
https://www.readbyqxmd.com/read/27063700/what-do-speech-language-pathologists-think-parents-expect-when-treating-their-children-with-autism-spectrum-disorder
#20
David Trembath, Ruth Hawtree, Joanne Arciuli, Teena Caithness
PURPOSE: Despite the importance of Speech-Language Pathologists (SLPs) collaborating with parents in the treatment of children with Autism Spectrum Disorder (ASD), few studies have examined the nature of this working relationship and how best to facilitate collaboration. To explore what SLPs think parents of children with ASD expect of them when it comes to the delivery of evidence-based interventions. METHOD: The participants were 22 SLPs from Australia who specialised in ASD and who each participated in a semi-structured interview...
June 2016: International Journal of Speech-language Pathology
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