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Pai VJ, Lau CJ, Garcia-Ruiz A, Donaldson C, Vaughan JM, Miller B, De Souza EV, Pinto AM, Diedrich J, Gavva NR, Yu S, DeBoever C, Horman SR, Saghatelian A. Microprotein-encoding RNA regulation in cells treated with pro-inflammatory and pro-fibrotic stimuli. BMC Genomics 2024; 25:1034. [PMID: 39497054 PMCID: PMC11536906 DOI: 10.1186/s12864-024-10948-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 10/24/2024] [Indexed: 11/06/2024] Open
Abstract
BACKGROUND Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins. RESULTS We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates. CONCLUSION This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest.
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Morgado-Palacin L, Brown JA, Martinez TF, Garcia-Pedrero JM, Forouhar F, Quinn SA, Reglero C, Vaughan J, Heydary YH, Donaldson C, Rodriguez-Perales S, Allonca E, Granda-Diaz R, Fernandez AF, Fraga MF, Kim AL, Santos-Juanes J, Owens DM, Rodrigo JP, Saghatelian A, Ferrando AA. The TINCR ubiquitin-like microprotein is a tumor suppressor in squamous cell carcinoma. Nat Commun 2023; 14:1328. [PMID: 36899004 PMCID: PMC10006087 DOI: 10.1038/s41467-023-36713-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023] Open
Abstract
The TINCR (Terminal differentiation-Induced Non-Coding RNA) gene is selectively expressed in epithelium tissues and is involved in the control of human epidermal differentiation and wound healing. Despite its initial report as a long non-coding RNA, the TINCR locus codes for a highly conserved ubiquitin-like microprotein associated with keratinocyte differentiation. Here we report the identification of TINCR as a tumor suppressor in squamous cell carcinoma (SCC). TINCR is upregulated by UV-induced DNA damage in a TP53-dependent manner in human keratinocytes. Decreased TINCR protein expression is prevalently found in skin and head and neck squamous cell tumors and TINCR expression suppresses the growth of SCC cells in vitro and in vivo. Consistently, Tincr knockout mice show accelerated tumor development following UVB skin carcinogenesis and increased penetrance of invasive SCCs. Finally, genetic analyses identify loss-of-function mutations and deletions encompassing the TINCR gene in SCC clinical samples supporting a tumor suppressor role in human cancer. Altogether, these results demonstrate a role for TINCR as protein coding tumor suppressor gene recurrently lost in squamous cell carcinomas.
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Littlecott HJ, Moore GF, Evans RE, Melendez-Torres GJ, McCann M, Reed H, Mann M, Dobbie F, Jennings S, Donaldson C, Hawkins J. Perceptions of friendship, peers and influence on adolescent smoking according to tobacco control context: a systematic review and meta-ethnography of qualitative research. BMC Public Health 2023; 23:424. [PMID: 36869343 PMCID: PMC9983235 DOI: 10.1186/s12889-022-14727-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/25/2022] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND A relationship between smoking and interpersonal influences has been well established within the literature. There have been cultural shifts in denormalisation and a reduction in tobacco smoking in many countries. Hence there is a need to understand social influences on adolescents' smoking across smoking normalisation contexts. METHODS The search was conducted in July 2019 and updated in March 2022 within 11 databases and secondary sources. Search terms included schools, adolescents, smoking, peers, social norms and qualitative research. Screening was conducted by two researchers independently and in duplicate. Study quality was assessed using the eight-item Evidence for Policy and Practice Information and Co-ordinating Centre (EPPI-centre) tool for the appraisal of qualitative studies. Results were synthesised using a meta-narrative lens for meta-ethnography and compared across smoking normalisation contexts. RESULTS Forty one studies were included and five themes were developed, mapping onto the socio ecological model. The social processes by which adolescents take up smoking differed according to a mixture of school type, peer group structure and the smoking culture within the school, as well as the wider cultural context. Data available from smoking denormalised contexts, described changes in social interactions around smoking to cope with its stigmatisation. This was manifested through i) direct peer influence, whereby subtle techniques were employed, ii) group belonging whereby smoking was less likely to be seen as a key determinant of group membership and smoking was less commonly reported to be used as a social tool, and iii) popularity and identity construction, whereby smoking was perceived more negatively in a denormalised context, compared with a normalised context. CONCLUSIONS This meta-ethnography is the first study to demonstrate, drawing on international data, that peer processes in adolescent smoking may undergo changes as smoking norms within society change. Future research should focus on understanding differences across socioeconomic contexts, to inform the adaptation of interventions.
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Martinez TF, Lyons-Abbott S, Bookout AL, De Souza EV, Donaldson C, Vaughan JM, Lau C, Abramov A, Baquero AF, Baquero K, Friedrich D, Huard J, Davis R, Kim B, Koch T, Mercer AJ, Misquith A, Murray SA, Perry S, Pino LK, Sanford C, Simon A, Zhang Y, Zipp G, Bizarro CV, Shokhirev MN, Whittle AJ, Searle BC, MacCoss MJ, Saghatelian A, Barnes CA. Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins. Cell Metab 2023; 35:166-183.e11. [PMID: 36599300 PMCID: PMC9889109 DOI: 10.1016/j.cmet.2022.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/19/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023]
Abstract
Microproteins (MPs) are a potentially rich source of uncharacterized metabolic regulators. Here, we use ribosome profiling (Ribo-seq) to curate 3,877 unannotated MP-encoding small ORFs (smORFs) in primary brown, white, and beige mouse adipocytes. Of these, we validated 85 MPs by proteomics, including 33 circulating MPs in mouse plasma. Analyses of MP-encoding mRNAs under different physiological conditions (high-fat diet) revealed that numerous MPs are regulated in adipose tissue in vivo and are co-expressed with established metabolic genes. Furthermore, Ribo-seq provided evidence for the translation of Gm8773, which encodes a secreted MP that is homologous to human and chicken FAM237B. Gm8773 is highly expressed in the arcuate nucleus of the hypothalamus, and intracerebroventricular administration of recombinant mFAM237B showed orexigenic activity in obese mice. Together, these data highlight the value of this adipocyte MP database in identifying MPs with roles in fundamental metabolic and physiological processes such as feeding.
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Vernazza C, Carr K, Holmes R, Wildman J, Gray J, Exley C, Smith R, Donaldson C. Resource Allocation in a National Dental Service Using Program Budgeting Marginal Analysis. JDR Clin Trans Res 2021; 8:23800844211056241. [PMID: 34844457 PMCID: PMC9772892 DOI: 10.1177/23800844211056241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION In any health system, choices must be made about the allocation of resources (budget), which are often scarce. Economics has defined frameworks to aid resource allocation, and program budgeting marginal analysis (PBMA) is one such framework. In principle, patient and public values can be incorporated into these frameworks, using techniques such as willingness to pay (WTP). However, this has not been done before, and few formal resource allocation processes have been undertaken in dentistry. This study aimed to undertake a PBMA with embedded WTP values in a national dental setting. METHODS The PBMA process was undertaken by a panel of participant-researchers representing commissioners, dentists, dental public health staff, and academics. The panel reviewed current allocations and generated a set of weighted criteria to evaluate services against. Services to be considered for removal and investment were determined by the panel and wider discussion and then scored against the criteria. Values from a nationally representative WTP survey of the public contributed to the scores for interventions. Final decisions on removal and investment were taken after panel discussion using individual anonymous electronic voting. RESULTS The PBMA process resulted in recommendations to invest in new program components to improve access to general dentists, care home dentistry, and extra support for dental public health input into local government decisions. Disinvestments were recommended in orthodontics and to remove routine scaling and polishing of teeth. DISCUSSION The PBMA process was successful in raising awareness of resource allocation issues. Implementation of findings will depend on the ability of decision makers to find ways of operationalizing the decisions. The process illustrates practical aspects of the process that future dental PBMAs could learn from. KNOWLEDGE TRANSFER STATEMENT This study illustrates a framework for resource allocation in dental health services and will aid decision makers in implementing their own resource allocation systems.
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Hayes AG, Corlies P, Tate C, Barrington M, Bell JF, Maki JN, Caplinger M, Ravine M, Kinch KM, Herkenhoff K, Horgan B, Johnson J, Lemmon M, Paar G, Rice MS, Jensen E, Kubacki TM, Cloutis E, Deen R, Ehlmann BL, Lakdawalla E, Sullivan R, Winhold A, Parkinson A, Bailey Z, van Beek J, Caballo-Perucha P, Cisneros E, Dixon D, Donaldson C, Jensen OB, Kuik J, Lapo K, Magee A, Merusi M, Mollerup J, Scudder N, Seeger C, Stanish E, Starr M, Thompson M, Turenne N, Winchell K. Pre-Flight Calibration of the Mars 2020 Rover Mastcam Zoom (Mastcam-Z) Multispectral, Stereoscopic Imager. SPACE SCIENCE REVIEWS 2021; 217:29. [PMID: 33678912 PMCID: PMC7892537 DOI: 10.1007/s11214-021-00795-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 01/12/2021] [Indexed: 05/28/2023]
Abstract
UNLABELLED The NASA Perseverance rover Mast Camera Zoom (Mastcam-Z) system is a pair of zoomable, focusable, multi-spectral, and color charge-coupled device (CCD) cameras mounted on top of a 1.7 m Remote Sensing Mast, along with associated electronics and two calibration targets. The cameras contain identical optical assemblies that can range in focal length from 26 mm ( 25.5 ∘ × 19.1 ∘ FOV ) to 110 mm ( 6.2 ∘ × 4.2 ∘ FOV ) and will acquire data at pixel scales of 148-540 μm at a range of 2 m and 7.4-27 cm at 1 km. The cameras are mounted on the rover's mast with a stereo baseline of 24.3 ± 0.1 cm and a toe-in angle of 1.17 ± 0.03 ∘ (per camera). Each camera uses a Kodak KAI-2020 CCD with 1600 × 1200 active pixels and an 8 position filter wheel that contains an IR-cutoff filter for color imaging through the detectors' Bayer-pattern filters, a neutral density (ND) solar filter for imaging the sun, and 6 narrow-band geology filters (16 total filters). An associated Digital Electronics Assembly provides command data interfaces to the rover, 11-to-8 bit companding, and JPEG compression capabilities. Herein, we describe pre-flight calibration of the Mastcam-Z instrument and characterize its radiometric and geometric behavior. Between April 26 t h and May 9 t h , 2019, ∼45,000 images were acquired during stand-alone calibration at Malin Space Science Systems (MSSS) in San Diego, CA. Additional data were acquired during Assembly Test and Launch Operations (ATLO) at the Jet Propulsion Laboratory and Kennedy Space Center. Results of the radiometric calibration validate a 5% absolute radiometric accuracy when using camera state parameters investigated during testing. When observing using camera state parameters not interrogated during calibration (e.g., non-canonical zoom positions), we conservatively estimate the absolute uncertainty to be < 10 % . Image quality, measured via the amplitude of the Modulation Transfer Function (MTF) at Nyquist sampling (0.35 line pairs per pixel), shows MTF Nyquist = 0.26 - 0.50 across all zoom, focus, and filter positions, exceeding the > 0.2 design requirement. We discuss lessons learned from calibration and suggest tactical strategies that will optimize the quality of science data acquired during operation at Mars. While most results matched expectations, some surprises were discovered, such as a strong wavelength and temperature dependence on the radiometric coefficients and a scene-dependent dynamic component to the zero-exposure bias frames. Calibration results and derived accuracies were validated using a Geoboard target consisting of well-characterized geologic samples. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11214-021-00795-x.
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Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A. Accurate Annotation of Protein‐coding Small Open Reading Frames in the Human Genome. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03051] [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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Chapman SJ, Blanco-Colino R, Pérez-Ajates S, Bautista OA, Hodson J, Blanco-Colino R, Chapman SJ, Glasbey JC, Pata F, Pellino G, Soares ASA, van Elst T, Van Straten S, Nepogodiev D, Hodson J, Borakati A, Bath MF, Yasin IH, Mclean K, Arthur T, Kovacevic M, Delibegovic S, Karamanliev M, Swamad M, Žebrák R, Paramasivam R, Martensen A, Larsen HM, Rãdeker L, Frey PE, Kechagias A, Venara A, Duchalais E, Ioannidis A, Pata F, Pellino G, Pasquali S, Simioni ASA, Farina V, Podda M, Lorenzon L, ItSURG, Schaeff V, Otto A, Jakubauskas M, van Elst TR, Chu M, Fagan PVB, Wells CI, João AA, Soares A, Juloski J, Blanco-Colino R, Pérez-Ajates S, Bautista OA, El Kasmi YEK, Espin-Basany E, Clerc D, Ciubotaru C, Popescu S, Yanishev A, Lee S, Ozkan BB, Sen AY, Aktas MK, Baki BE, Yüksek B, Glasbey JC, Kamarajah S, Mclean K, Borakati A, Yasin IH, Khaw RA, Mills E, Goodson R, Thakral N, Ablett AD, Adra M, Kwek I, Khan SM, Quinn P, Manley LR, Badran A, Ramjeeawon A, Campbell A, Tan HL, Rye DS, Rajaraman N, Norman JG, Vutipongsatorn K, Solomou G, Akhbari M, Ali A, Brandao BD, Stainer B, Thavayogan R, Jones D, Onafowokan OO, Gharooni A, Dabab N, Carlton-Carew S, Kungwengwe G, Gabriel M, Sewart E, Shortland TC, Lawday S, Pockney P, Dawson A, Stewart P, Ng B, Luong JK, Delibegovic S, Ivanov V, Borisova A, Neykov V, Žebrák MFR, Harbjerg JL, Brandsborg S, Mark-Christensen A, Unbehaun KP, Dalsgaard P, Lycke KD, Kechagias A, LeNaoures P, Duchalais E, Brigand C, Dumange E, Gout M, Moehwald C, Prem M, Alhalabi O, Sliwinski S, Krupp J, Gablenz E, Schmitzer L, Kopp A, Steinle J, Gsenger J, Pohl LJ, Riccardi M, Christodoulou IM, Konstantinidis M, Machairas N, Zoikas A, Balalis D, Manatakis DK, Aguilera ML, Simioni ASA, Marano L, Fleres F, Lovisetto F, Sasia D, Segalini E, Pata G, Lucchi A, Sagnotta A, Campagnaro T, Petrelli F, Gallo G, Papandrea M, Testa V, Sinibaldi G, Di Candido F, Colombo F, Perrone G, Aresu S, Biancafarina A, Canonico G, Pagnanelli M, Curletti G, Bini R, de Manzoni Garberini A, Impellizzeri H, Cillara N, Tutino R, Picciariello A, Coletta D, Savino G, Ferrara F, Tamini N, Talamo G, Parini D, Giamundo P, Pagano G, Ripetti V, Pesce A, Menduni N, Pellino G, Giudicissi R, Podda M, Goldin E, Rega D, Belli A, Andriola V, Gordini L, Pata F, Foppa C, Piccolo G, Birindelli A, Ferrari C, Ballarini Z, Tirelli F, Milone M, De Rosa M, Federico NSP, Molteni B, Tilocca PL, Sancini G, Piozzi GN, Lauretta A, Mulas S, Schaeff V, Otto A, Jakubauskas M, Simcikas D, Portelli L, van Wijnbergen JWM, Dinger TL, ten Doesschate SFH, van Dalen ASHM, van den Bos DD, Hansmann M, Feliz JM, Kuiper SZ, Abdulrahman Z, Pruijssers SR, Geneta VP, Chu M, Wilton S, Kandelaki H, Peng SL, Campbell S, Lim YK, Yassaie SS, Murray M, Fagan PVB, Haran C, Tan J, Castro J, Laranjeira A, Catarino S, Neves-Marques C, Correia JG, Vieira BN, Quintela AC, Serra ML, Maciel J, Cunha M, Aparício DJ, Neves J, Azevedo J, Romano M, Eiró F, Romano J, Monteiro C, Claro M, Almeida, Peyroteo M, Machado ND, Capote H, Ferreira M, Sousa X, Devesa H, Cavadas D, Guerreiro I, Costa M, Rosete M, Salman M, English C, Mohammed N, Popescu S, Yanishev A, Litvin A, Ćuk VV, Mészárosová K, Van Straten S, Jaich R, De Lima H, Brooks S, Marx M, Salvation MN, Cardo JG, Mora-Guzmán I, Muriel JS, de Andres Olabarria U, Muriel P, Viñas CJ, Alconchel F, Sinovas OE, El Kasmi YEK, Oro CF, Pérez-Ajates S, Otero ML, Jiménez SF, Bellmunt OC, Caballero JM, Rubio-Pérez I, Aguilar-Martínez MM, Segura-Sampedro JJ, Moreno CO, Parra DN, Diz AME, Martín-Balbuena R, Recuenco CB, Bolaños REL, Fernández P, Padillo AD, Forero-Torres A, Román IAS, Rosés HS, Campos PV, Moreira CCL, Peralta PU, Navidad MS, Ripollés-Melchor J, Garcea A, Facundo HG, Bautista OA, Pereira PT, Guarinos CVP, Clerc D, Blaser B, Piazza G, Gagliardi B, Serin H, Sen AY, Yurdaor SS, Aktas MK, Arslan E, Kopac O, Uyanik A, Ozmen BB, Tiftik E, Aksoy B, Yalcinkaya A, Bilicen G, Cinar EN, Uslu Ö, Kaya Y, Wong J, Farhan-Alanie MMH, Suresh G, Asif A, Finch BJ, Bhahirathan Y, Herron J, Tew ZY, Obukofe R, Russell C, Suchett-Kay I, Netke T, Williams L, Kisiel A, Liu FY, Claireaux H, James P, Mondal A, Kalderon R, Nadama HH, Al-Saraff Z, Tam JPH, Powell-Chandler A, Wood F, Campbell A, Gorgievska R, Ragavoodoo A, Thakrar C, Rojoa D, Palmer C, Davidson K, Giacci L, Hale J, Gan FW, Makin-Taylor R, Hey CY, Toh C, Findlay JM, Griffiths N, Ganesananthan S, Jasionowska S, Poustie M, Wong C, Turner T, Pyc W, Sloper W, Warner C, Coey J, Mason D, Sait S, Kowal M, Shortland TC, Owen M, Saiyed A, Ashworth I, Akbari K, Curran M, Martin P, Parker D, Dawson A, Kwok K, Lye C, Pockney P, Ghaly M, Sammour T, Lewis D, Mundasad R, Wilkes A, Ctercteko G, Stewart P, Delibegovic S, Maslyankov S, Dimov R, Iliev S, Dimitrov D, Marek F, Örhalmi J, Skalický P, Skalický T, Chrz K, Christensen P, Worsøe J, Kristensen ES, Emmertsen KJ, Loeve US, Duchalais E, Mihaljevic AL, Herrle F, Konstantinidis KM, Manatakis DK, Korkolis D, Karanikas I, Aguilera ML, Vincenti L, Anania G, Borghi F, Agresta F, Maretto I, Parisi A, Bucci L, De Palma G, Guglielmi A, Cucinotta E, La Torre F, Cianchi F, Guerrieri M, Lauretta A, Trompetto M, Persiani R, Micheletto G, Delrio P, Belli A, Cantafio S, Lovisetto F, Ronconi M, Bisagni PAG, De Prizio M, Tamini N, Sinibaldi G, Franceschi A, Galleano R, Cavallini M, Brescia A, D'Ambra L, Benevento A, Niolu P, Calgaro M, Colangelo E, Grottola T, Altomare DF, Puleo S, Salamone G, Pietrabissa A, Poggioli G, Ripetti V, Erdas E, Ottonello R, Canonico G, Tonini V, Selvaggi F, Sammarco G, Ceccarelli G, De Nisco C, Surgo D, Taglietti L, Ozolins A, Sivinš A, Poskus T, Psaila J, Bemelman WA, Graat LJ, Langenhoff B, Wijnhoven BPL, van de Ven AHW, Poelman M, Stassen LPS, Slooter G, Acherman YIZ, Hoff C, Gerhards MF, Stommel MWJ, Hazebroek EJ, van Geloven AAW, Schasfoort RA, van Leeuwen BL, Tuynman JB, van Tilburg MWA, Boerma EG, Sharma P, Jenkins B, Bissett IP, Peng SL, Herd A, Gordon A, Vernon D, Omundsen M, Ly J, Reddy A, Bonnet G, Harmston C, Morales M, Francisco V, Costa S, Manso A, Amorim E, Pereira J, Cardoso J, Ourô S, Caratão M, Nascimento C, da Silva BR, Taranu V, Dias R, Devesa H, Mendes J, Allen M, Silva A, Carlos S, Barbosa E, Carneiro C, Ramos L, Maciel J, Lencastre L, Martins R, Silva-Vaz P, Cahill R, Hogan A, Larkin J, Negoi I, Abelevich A, Ćuk VM, Vician M, Ede C, Sardiwalla I, Mulira S, Montwedi D, Oyomno M, Sabia D, Porras VP, Vigorita V, Ortega GS, García J, Macías AE, Antona FB, Mompeán JAL, Ruiz SS, Villarejo-Campos P, Simó MR, Sánchez-Guillén L, Jiménez-Gómez LM, López AS, Golda T, Bergkvist DJ, Nevado C, Aguilar JFN, Felipe BR, Septiem J, Sánchez AR, Cañete-Gómez J, Montesinos IR, Ripollés-Melchor J, Millán-Scheiding M, Prieto-Nieto I, Segura-Sampedro JJ, Espin-Basany E, Frasson M, Román IAS, Olmo DG, Hübner M, Petermann D, Sauvain MO, Ozben V, Geçim IE, Disçi E, Rencuzogullari A, Kurt A, Bisgin T, Pehlivan M, Isik A, Onur E, Leventoglu S, Keskin M, Guner A, Sahin ST, Ozbalci GS, Pergel A, Albayrak D, Bruce D, Fearnhead N, Arthur J, Harron M, Beattie G, Titu L, Ali A, Saunders M, Phillips J, Dindyal S, Cresswell B, Gercek Y, Lee J, Linn T, Faulkner G, Lockwood S, Rees J, Charalabopoulos A, Campbell B, Kontovounisios C, Amarnath T, Johnson M, Epanomeritakis E, Vigs S, Nastro P, Gilliam A, Smolarek S, Wilson T, Orbell J, McIntyre R, Agarwal T, Hainsworth P, Patel P, Vijay J, Liu B, Rao PD, Roxburgh C, Vipond M, Youssef H, Thorn C, Schizas A, Denley S, Bowley D, Das K, Cuming T, Saha A, Chung L, Pitt J, Davis P, Jones O, Taylor M, Bhargava A, Haji A, Watson N, Bloom I, Singh B, Norwood M, Gurjar S, Stylianides N, Mirza S, Evans M, Williams G, Patil P, Hernon J, Finch G, Green S, Chapple K, Fafemi O, Warusavitarne J, Samee A, Carden C, Ong L, Verma K, Joseph A, Rawat N, Pinkney T, Oke O, Glen P, Maxwell-Armstrong C, Oliphant R, Garner J, Moug SJ, Middleton S, Lund JN, Smart NJ, Osborn G, Moore T, Raymond T, Knowles CH, Hany TS, Clarke R, Khera G, Brady R, Sellahewa C, Mason C, Torrance A, Lasithiotakis K, Knight J, Pullybank A, Ainsworth P, Reid F, Ramwell A, Maslekar S, George R, Skull A, Holtham S, Muhammad K, Lal R, Varcada M, Smith FM, Howlader M, Defriend D, Kirk S, Richards T, Evans C, Borg CM, Telford K, Sarfraz N, Busby K, Hollingshead J, Speake D, Pawa N, West D, Chadwick M, Komolafe O, Richardson S, Thornton M, Goede A, Osborne C, Bandyopadhyay D, Foong J, Lee YJ, Liebenberg P, Mijalkov D, Wells A, Bull N, Ajmera A, Warburton T, Morgan S, Mahmoud A, Schachtel M, Mikhail B, Fomin I, Mekaeil B, Taylor N, Stevenson C, Drane A, Pahalawatta U, Lai LT, Debiasio A, Chrimes A, Agarwal A, Zhao J, Williams S, Jayalath JMSN, Liebenberg P, Khor S, Muddasani T, Childs S, Ridgway S, Blefari NDA, Tam H, Puchalski N, Ngai C, Horne D, Borrow JL, Campbell C, Cousins G, Jackson L, Maheepala K, Zhao S, Holden E, Tutt L, Thompson B, Collins H, Louie F, Buckland B, Smith D, Chong C, Chua TH, Nayak C, Redmond J, Tan RR, Gramlick M, Teh JS, Ng SY, Britten-Jones P, Rosli RM, Pham HDV, Jegathees T, Coulter-Nile SMCJ, Gosselink MP, Luong JK, Wang YL, Maciaszek M, Chrapko PS, Nair A, Thirugnanasundralingam V, Muir K, Salibasic M, Pavlov V, Paycheva T, Borisova A, Lyulenina E, Kolev N, Ivanov V, Nguen D, Mitkov Y, Mitkov E, Vladova P, Dimitrov V, Hussain M, Gabarski A, Ivanov T, Yotsov T, Ilieva I, Karamanliev M, Akisheva A, Shoshkova M, Nawaz E, Feradova H, Mladenov T, Neykov V, Jozaf V, Klail MFT, Pös M, Adel A, Sotona O, Bartoš M, Amjad T, Malý O, Berec S, Hurný MHM, Chodora S, Houdek O, Novický R, Antonova T, Cha KSS, Kimle KŠ, Jirankova K, Bujda M, Paclík A, Trap A, Jürgens-Lahnstein J, Storm M, Dalsgaard P, Damgaard I, Olawi F, Ehlern F, Raos M, Kristensen FP, Lycke KD, Bønnerup K, Unbehaun KP, Brandsborg S, Amiri S, Enevoldsen M, Harbjerg JL, Pedersen JH, Jepsen BN, Hillgaard TK, Erichsen SB, Nielsen CV, Madsen CP, Bjerke J, Skejø CD, Aabling RR, Sørensen JS, Mark-Christensen A, Kechagias A, Turunen A, Katunin J, Niskakangas M, Vignaud T, Frey S, Ricolleau C, 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Brandsma AM, Davids J, Rottier SJ, de Roy van Zuidewijn D, Hawkins R, Ong HI, Li Y, Desmond B, Winstanley J, Martins M, Rosete M, Americano M, Santos M, Frade S, Senhorinho R, Peixoto R, João AA, Alves-Vale C, Lamas M, O'Connor DB, Hoo M, Gopaul A, Scanlon K, O'Dwyer N, Negoi I, Jovanović M, Panyko A, De Lima H, Van Vuuren S, Centeno A, Bernado IR, Señorans MPG, Amor LG, Ramírez AC, Abrisqueta J, Gomez ME, Arroyo A, Cerdán C, Romeu NG, Forero-Torres A, Enriquez-Navascues JM, Collado-Roura F, Curchod P, Gaspar S, Imadalou L, Mutlu D, Akyol C, Uygur FA, Eray IC, Biyiklioglu O, Çetin MF, Isik AE, Karip B, Dogan H, Sarıgül L, Tunc E, Aydin T, Bodur S, Karabulut K, Francis AA, Al-hadithi A, Lau ISF, Smith E, Mahapatra S, McAuliffe O, Francis AA, Imam L, Akram B, Hossaini S, Davies R, Ko M, Collins J, Pandya A, Reilly S, Archer J, Livie J, Chaudhry FA, Ntakomyti E, Diallo R, Bylinski T, Wright J, Lawday S, Masiha E, Tung J, Shirazi B, Neilson A, Epton S, Patel N, Trussell S, Couldrey A, Donnelly C, Eftychiou S. Safety of hospital discharge before return of bowel function after elective colorectal surgery. Br J Surg 2020; 107:552-559. [PMID: 31976560 DOI: 10.1002/bjs.11422] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/06/2019] [Accepted: 10/08/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Ileus is common after colorectal surgery and is associated with an increased risk of postoperative complications. Identifying features of normal bowel recovery and the appropriateness for hospital discharge is challenging. This study explored the safety of hospital discharge before the return of bowel function. METHODS A prospective, multicentre cohort study was undertaken across an international collaborative network. Adult patients undergoing elective colorectal resection between January and April 2018 were included. The main outcome of interest was readmission to hospital within 30 days of surgery. The impact of discharge timing according to the return of bowel function was explored using multivariable regression analysis. Other outcomes were postoperative complications within 30 days of surgery, measured using the Clavien-Dindo classification system. RESULTS A total of 3288 patients were included in the analysis, of whom 301 (9·2 per cent) were discharged before the return of bowel function. The median duration of hospital stay for patients discharged before and after return of bowel function was 5 (i.q.r. 4-7) and 7 (6-8) days respectively (P < 0·001). There were no significant differences in rates of readmission between these groups (6·6 versus 8·0 per cent; P = 0·499), and this remained the case after multivariable adjustment for baseline differences (odds ratio 0·90, 95 per cent c.i. 0·55 to 1·46; P = 0·659). Rates of postoperative complications were also similar in those discharged before versus after return of bowel function (minor: 34·7 versus 39·5 per cent; major 3·3 versus 3·4 per cent; P = 0·110). CONCLUSION Discharge before return of bowel function after elective colorectal surgery appears to be safe in appropriately selected patients.
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Illahi M, Hale J, Xuan Tan Z, Edwards S, Stahl R, Stahl J, Hickman A, Collett D, Goolam-Mahomed Z, Allen B, Atiyah A, Ahmad H, Jones J, McGregor O, Ogundiya E, Gan FW, Boulbadaoui A, Kirnon-Jackman O, Lim QX, Peckham H, Yeoh T, Yong SQ, Chen JY, Siva S, Sam ZH, Gilani M, Goh YN, Muthukumar MG, Phillips S, Makin-Taylor R, Tjoakarfa J, Giri A, Suresan S, Thavayogan R, Hey CY, Thomas P, Johnson TA, Williams RI, Rashid A, Kushairi A, Rais A, James A, Bugelli M, Chechelnitskaya Y, Sandhu N, Toh C, Tandon R, Gray M, Kumar A, Ciurleo C, Nyamali I, Hiremath S, Sinha S, Chowdhary M, Bradley E, McTiernan M, Macdonald S, Sharkey S, McLaughlin N, Amey C, Kraria L, Skan O, Kind C, Findlay JM, Tupper P, Van Rhee C, Honeyman SI, Menon G, Ahmed M, Jegatheeswaran L, Griffiths N, Madhavan A, Warne M, Malcolm FL, Lessware T, Wilkerson HT, Chatterjee-Woolman S, Yoong A, Ahmed WUR, Longshaw A, Flannery O, Green R, Leaning M, Cragg J, Sharriff H, Doherty C, Ganesananthan S, Kwan KWL, Sanders-Crook L, Bhatia S, Eames S, Lewis F, Kirupananthan P, Boh ZY, Dass S, Soma A, Newton A, Hill M, Shafiq Y, Brkljac M, Boyce L, Jasionowska S, English WJ, Lam S, Chipeta C, Yilmaz D, Jain C, Garofalidou T, Novotny SA, Locke S, Bowman C, Begaj A, Murphy C, Radcliffe K, Chong JT, Poustie M, Jeffrey E, Chaudhury N, Rajendran K, Akbar Z, Walters B, Kulendrarajah B, Tran N, Shrestha S, Parmar S, Gallagher C, Hennessy L, Pentti E, Badhrinarayanan S, Fung A, Mansoor M, Kenny R, Kan P, Lee DE, Khosla S, Samake M, Shaban F, Aftab R, Gough M, Woodburn B, Vayalapra S, McMurrugh K, Wong C, Jimulia D, Deol S, Pike S, Embury-Young Y, Turner T, Patel M, Kilgallon E, Keating R, Walsh A, Khan H, Logue G, Orekoya M, Alasmar M, Charalambides M, Clavé Llavall A, Williamson E, Bharwada Y, Zearmal S, Evans H, Panikkar M, Cruz G, Caplan J, Ruparelia A, Tanvir T, Soare C, Pang YL, Trotter J, Zaidi A, Thakrar V, Pulickal P, Ahmed H, Parnell J, Khan H, Lennock S, Ford V, Pyc W, Brignall R, O'Neill D, Hanna R, Kane R, Nicola M, Rajput K, Xiao Y, Warner C, Michael S, Wright E, Juniper S, Thompson E, Hoskyns L, Kanitkar A, Ross C, Unsworth A, Rshaidat H, Demarre K, Chiang A, Bareh A, Dellen J, Faqihinejad C, Gadhvi A, Grant R, Lewsey J, Morris A, Martin H, McClarty C, Sanyal S, Alsaif A, Palkhi A, Bhopal S, Vishnu K S, Papanikolaou A, Mitra A, Nur A, Ali F, Burford C, Huq T, Sloper W, Irwin E, Matthews L, Ngu WS, Hosfield T, Muneeb F, Page O, Zeb E, Coey J, Al-Azzawi A, McIntosh J, Vucicevic A, Hughes M, Brooks L, Fanibi B, Dixon M, Njoku P, Morris D, Jobson J, Chowdhury H, Alawode DOT, Wynell-Mayow W, Udayachandran V, Alsoof D, Ekert J, Joseph N, Zulkefley N, Hunt G, Christodoulou T, Wright O, Soman S, Jamal M, Beqiri S, Borgas P, Christie S, Pereira F, Browne S, Yiu J, Dworkin A, Brayley J, Palmer A, Charalambos M, Jones CJ, Toner S, Cowden R, Lee L, Nicol P, Holman O, Imtiaz M, Albert V, Leung SP, Erotocritou M, Wong J, Stroud R, Mason D, Wilkin R, Thomson W, Mackee L, G N, Bei Y, Sait S, Mckenna Favier S, Ibrahim A, Kler A, Reynolds L, Mohamed SH, Majeed Y, Fakim B, Jones A, Kowal M, Liversedge G, Carrington Z, Windebank J, Izzarina A, Akbani U, Craven J, Aldarragi A, Harding S, Millward A, Shortland TC, Bedford M, Stroud R, Obukofe R, Mackenzie E, Gopalan V, Midgen A, Khadka P, Cheng O, Taneja S, Manobharath N, Kok JY, Lim DWE, Buick T, Boland M, Piya S, Devlin R, Fairfield CJ, George RJ, Rahi M, Zaman S, Hajiev S, Ross T, Owen M, Crisp E, Thompson C, Charalambous A, Hollywood JL, Saiyed A, Hammond RFL, Matthews J, Mendonca V, Spinty J, Khan K, Cheng J, Glynn N, Muhammad U, Khan M, Anderson L, Mccormack K, Mak J, Patrawala S, Milinkovic N, Schofield R, Chauhan M, Hartley L, Hind J, Ashworth I, Nelson L, Ratnasingham D, Akbari K, Whitehead T, Dimitriadis S, Marshall K, Flint EJ, Curran M, Horner C, Heybourne A, Morgan H, Wickstone C, Panagiotou D, O'Connell E, Dean K, Iqbal R, Walsh L, Yu N, Rana N, Massie E, Ng J, Jung M, Lee YD, Harris M, White S, Delibegovic S, Boev B, Tonchev P, Prochazka V, Örhalmi J, Riško J, Skalický A, Chrz K, Ravn S, Ojakäär A, Duchalais E, Dörr-Harim C, Herrle F, Koutserimpas C, Giraudo G, Armellini A, Ruzzenente A, Mazzeo C, De Padua C, Realis Luc A, Maroli A, Giani I, Cufari ME, Vitali M, Ceccarelli G, Gusai GP, Quattromani R, Virgilio E, Berti S, Mulas S, Di Mola FF, Papagni V, Tuminello F, Magnoli M, Vittori L, Longheu A, Loche GA, Braccio B, De Luca E, Resta G, Ancans G, Tamosiunas A, Petrulionis M, Andrejevic P, Stellingwerf ME, Abdulrahman N, Pas KGH, Thomas G, Brandsma AM, Davids J, Rottier SJ, Roy van Zuidewijn D, Hawkins R, Ong HI, Li Y, Desmond B, Winstanley J, Martins M, Rosete M, Americano M, Santos M, Frade S, Senhorinho R, Peixoto R, Alagoa João A, Alves-Vale C, Lamas M, O'Connor DB, Hoo M, Gopaul A, Scanlon K, O'Dwyer N, Negoi I, Jovanović M, Panyko A, De Lima H, Van Vuuren S, Curchod P, Gaspar S, Imadalou L, Mutlu D, Akyol C, Uygur FA, Eray IC, Biyiklioglu O, Çetin MF, Isik AE, Karip B, Dogan H, Sarıgül L, Tunc E, Aydin T, Bodur S, Karabulut K, Francis AA, Al-hadithi A, To N, Lau ISF, Smith E, Mahapatra S, McAuliffe O, Francis AA, Imam L, Akram B, Hossaini S, Davies R, Ko M, Collins J, Pandya A, Reilly S, Archer J, Auty C, Roche CD, Livie J, Chaudhry FA, Ntakomyti E, Diallo R, Bylinski T, Wright J, Lawday S, Masiha E, Tung J, Shirazi B, Neilson A, Epton S, Patel N, Trussell S, Couldrey A, Donnelly C, Eftychiou S. Safety and efficacy of non-steroidal anti-inflammatory drugs to reduce ileus after colorectal surgery. Br J Surg 2020; 107:e161-e169. [PMID: 31595986 DOI: 10.1002/bjs.11326] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/06/2019] [Accepted: 07/04/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Ileus is common after elective colorectal surgery, and is associated with increased adverse events and prolonged hospital stay. The aim was to assess the role of non-steroidal anti-inflammatory drugs (NSAIDs) for reducing ileus after surgery. METHODS A prospective multicentre cohort study was delivered by an international, student- and trainee-led collaborative group. Adult patients undergoing elective colorectal resection between January and April 2018 were included. The primary outcome was time to gastrointestinal recovery, measured using a composite measure of bowel function and tolerance to oral intake. The impact of NSAIDs was explored using Cox regression analyses, including the results of a centre-specific survey of compliance to enhanced recovery principles. Secondary safety outcomes included anastomotic leak rate and acute kidney injury. RESULTS A total of 4164 patients were included, with a median age of 68 (i.q.r. 57-75) years (54·9 per cent men). Some 1153 (27·7 per cent) received NSAIDs on postoperative days 1-3, of whom 1061 (92·0 per cent) received non-selective cyclo-oxygenase inhibitors. After adjustment for baseline differences, the mean time to gastrointestinal recovery did not differ significantly between patients who received NSAIDs and those who did not (4·6 versus 4·8 days; hazard ratio 1·04, 95 per cent c.i. 0·96 to 1·12; P = 0·360). There were no significant differences in anastomotic leak rate (5·4 versus 4·6 per cent; P = 0·349) or acute kidney injury (14·3 versus 13·8 per cent; P = 0·666) between the groups. Significantly fewer patients receiving NSAIDs required strong opioid analgesia (35·3 versus 56·7 per cent; P < 0·001). CONCLUSION NSAIDs did not reduce the time for gastrointestinal recovery after colorectal surgery, but they were safe and associated with reduced postoperative opioid requirement.
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Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A. Accurate annotation of human protein-coding small open reading frames. Nat Chem Biol 2019; 16:458-468. [PMID: 31819274 PMCID: PMC7085969 DOI: 10.1038/s41589-019-0425-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022]
Abstract
Functional protein-coding small open reading frames (smORFs) are emerging as an important class of genes. However, the number of translated smORFs in the human genome is unclear because proteogenomic methods are not sensitive enough, and, as we show, Ribo-Seq strategies require additional measures to ensure comprehensive and accurate smORF annotation. Here, we integrate de novo transcriptome assembly and Ribo-Seq into an improved workflow that overcomes obstacles with previous methods to more confidently annotate thousands of smORFs. Evolutionary conservation analyses suggest that hundreds of smORF-encoded microproteins are likely functional. Additionally, many smORFs are regulated during fundamental biological processes, such as cell stress. Peptides derived from smORFs are also detectable on human leukocyte antigen complexes, revealing smORFs as a source of antigens. Thus, by including additional validation into our smORF annotation workflow, we accurately identify thousands of unannotated translated smORFs that will provide a rich pool of unexplored, functional human genes.
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Pennington M, Ring H, Howlett J, Smith C, Redley M, Murphy C, Hook R, Platt A, Gilbert N, Jones E, Kelly J, Pullen A, Mander A, Donaldson C, Rowe S, Wason J, Irvine F. The impact of an epilepsy nurse competency framework on the costs of supporting adults with epilepsy and intellectual disability: findings from the EpAID study. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2019; 63:1391-1400. [PMID: 31397022 PMCID: PMC7613974 DOI: 10.1111/jir.12679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND The development of a nurse-led approach to managing epilepsy in adults with an intellectual disability (ID) offers the potential of improved outcomes and lower costs of care. We undertook a cluster randomised trial to assess the impact on costs and outcomes of the provision of ID nurses working to a designated epilepsy nurse competency framework. Here, we report the impact of the intervention on costs. METHOD Across the United Kingdom, eight sites randomly allocated to the intervention recruited 184 participants and nine sites allocated to treatment as usual recruited 128 participants. Cost and outcome data were collected mainly by telephone interview at baseline and after 6 months. Total costs at 6 months were compared from the perspective of health and social services and society, with adjustments for pre-specified participant and cluster characteristics at baseline including costs. Missing data were imputed using multiple imputation. Uncertainty was quantified by bootstrapping. RESULTS The intervention was associated with lower per participant costs from a health and social services perspective of -£357 (2014/2015 GBP) (95% confidence interval -£986, £294) and from a societal perspective of -£631 (95% confidence interval -£1473, £181). Results were not sensitive to the exclusion of accommodation costs. CONCLUSIONS Our findings suggest that the competency framework is unlikely to increase the cost of caring for people with epilepsy and ID and may reduce costs.
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Holmes RD, Steele JG, Exley C, Vernazza CR, Donaldson C. Use of programme budgeting and marginal analysis to set priorities for local NHS dental services: learning from the north east of England. J Public Health (Oxf) 2019; 40:e578-e585. [PMID: 29726998 DOI: 10.1093/pubmed/fdy075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/13/2018] [Indexed: 11/12/2022] Open
Abstract
Background Priority setting is necessary where competing demands exceed the finite resources available. The aim of the study was to develop and test a prioritization framework based upon programme budgeting and marginal analysis (PBMA) as a tool to assist National Health Service (NHS) commissioners in their management of resources for local NHS dental services. Methods Twenty-seven stakeholders (5 dentists, 8 commissioners and 14 patients) participated in a case-study based in a former NHS commissioning organization in the north of England. Stakeholders modified local decision-making criteria and applied them to a number of different scenarios. Results The majority of financial resources for NHS dental services in the commissioning organization studied were allocated to primary care dental practitioners' contracts in perpetuity, potentially constraining commissioners' abilities to shift resources. Compiling the programme budget was successful, but organizational flux and difficulties engaging local NHS commissioners significantly impacted upon the marginal analysis phase. Conclusions NHS dental practitioners' contracts resemble budget-silos which do not facilitate local resource reallocation. 'Context-specific' factors significantly challenged the successful implementation and impact of PBMA. A local PBMA champion embedded within commissioning organizations should be considered. Participants found visual depiction of the cost-value ratio helpful during their initial priority setting deliberations.
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Donaldson C, Winder T, Caudron C, White RS. Crustal seismic velocity responds to a magmatic intrusion and seasonal loading in Iceland's Northern Volcanic Zone. SCIENCE ADVANCES 2019; 5:eaax6642. [PMID: 31807704 PMCID: PMC6881157 DOI: 10.1126/sciadv.aax6642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/23/2019] [Indexed: 05/31/2023]
Abstract
Seismic noise interferometry is an exciting technique for studying volcanoes, providing a continuous measurement of seismic velocity changes (dv/v), which are sensitive to magmatic processes that affect the surrounding crust. However, understanding the exact mechanisms causing changes in dv/v is often difficult. We present dv/v measurements over 10 years in central Iceland, measured using single-station cross-component correlation functions from 51 instruments across a range of frequency bands. We observe a linear correlation between changes in dv/v and volumetric strain at stations in regions of both compression and dilatation associated with the 2014 Bárðarbunga-Holuhraun dike intrusion. Furthermore, a clear seasonal cycle in dv/v is modeled as resulting from elastic and poroelastic responses to changing snow thickness, atmospheric pressure, and groundwater level. This study comprehensively explains variations in dv/v arising from diverse crustal stresses and highlights the importance of deformation modeling when interpreting dv/v, with implications for volcano and environmental monitoring worldwide.
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Choi SH, Martinez TF, Kim S, Donaldson C, Shokhirev MN, Saghatelian A, Jones KA. CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability. Genes Dev 2019; 33:418-435. [PMID: 30819820 PMCID: PMC6446539 DOI: 10.1101/gad.322339.118] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/22/2019] [Indexed: 01/23/2023]
Abstract
Here, Choi et al. show that CDK12, the RNA polymerase II C-terminal domain kinase, which regulates genome stability, expression of DNA repair genes, and cancer cell drug resistance, also phosphorylates the mRNA 5′ cap-binding repressor 4E-BP1 to promote translation of mTORC1-dependent mRNAs. Using RIP-seq and Ribo-seq, the authors found that CDK12 regulates binding of eIF4G to many mTORC1 target mRNAs, and identified specific CDK12 “translation-only” target mRNAs. The RNA polymerase II (RNAPII) C-terminal domain kinase, CDK12, regulates genome stability, expression of DNA repair genes, and cancer cell resistance to chemotherapy and immunotherapy. In addition to its role in mRNA biosynthesis of DNA repair genes, we show here that CDK12 phosphorylates the mRNA 5′ cap-binding repressor, 4E-BP1, to promote translation of mTORC1-dependent mRNAs. In particular, we found that phosphorylation of 4E-BP1 by mTORC1 (T37 and T46) facilitates subsequent CDK12 phosphorylation at two Ser–Pro sites (S65 and T70) that control the exchange of 4E-BP1 with eIF4G at the 5′ cap of CHK1 and other target mRNAs. RNA immunoprecipitation coupled with deep sequencing (RIP-seq) revealed that CDK12 regulates release of 4E-BP1, and binding of eIF4G, to many mTORC1 target mRNAs, including those needed for MYC transformation. Genome-wide ribosome profiling (Ribo-seq) further identified specific CDK12 “translation-only” target mRNAs, including many mTORC1 target mRNAs as well as many subunits of mitotic and centromere/centrosome complexes. Accordingly, confocal imaging analyses revealed severe chromosome misalignment, bridging, and segregation defects in cells deprived of CDK12 or CCNK. We conclude that the nuclear RNAPII-CTD kinase CDK12 cooperates with mTORC1, and controls a specialized translation network that is essential for mitotic chromosome stability.
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Abstract
Bone mineral density measurements have been criticized on the grounds that they are not a worth-while screening tool. In this paper we argue that bone mineral measurements can be an efficient diagnostic tool even if they are not of proven value for screening. There is complex relationship between the costs of a measurement, the intervention and the predictive value of the test all of which must be accounted for when assessing the value of a bone density measurement. For bone density measurements to be used for screening, a wider evaluation needs to be undertaken compared with that for their use as a diagnostic tool. We address some common objections, for example, that low compliance with screening would undermine efficiency, and show that these are not relevant. Evaluations of screening need to address issues that are likely to affect efficiency.
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Toellner H, Hughes G, Beswick W, Crooks MG, Donaldson C, Forrest I, Hart SP, Leonard C, Major M, Simpson AJ, Chaudhuri N. Early clinical experiences with nintedanib in three UK tertiary interstitial lung disease centres. Clin Transl Med 2017; 6:41. [PMID: 29101500 PMCID: PMC5670096 DOI: 10.1186/s40169-017-0172-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/22/2017] [Indexed: 01/09/2023] Open
Abstract
Background Nintedanib has been shown to slow disease progression in patients with idiopathic pulmonary fibrosis (IPF). It was approved by the National Institute for Health and Care Excellence (NICE) in January 2016 for IPF patients with a forced vital capacity (FVC) of 50–80% in the United Kingdom (UK). Aim To report real world data about our early clinical experience using nintedanib in 187 patients with a multi-disciplinary (MDT) diagnosis of IPF in a manufacturer funded patient in need scheme (three UK centres) prior to NICE approval. Methods All patients with a MDT diagnosis of IPF from December 2014 to January 2016 commenced on nintedanib were included. Demographic details, adverse events (AEs) and where available lung function results were retrospectively collected from clinical letters. Results 187 patients (76% males) with a median age of 72 years (49–89) were treated with nintedanib. The average pre-treatment FVC was 81.1 ± 19.8% and diffusion capacity of the lungs for carbon monoxide was 43.9 ± 15% (n = 82). Fifty percent of patients started nintedanib because they were ineligible for pirfenidone due to an FVC > 80%. The median treatment course was 8 ± 4 months. The majority of patients experienced 1–3 AEs with nintedanib (52%, n = 97). The most frequent AEs were diarrhoea (50%), nausea (36%), reduced appetite (24%), tiredness (20%) and gastro-oesophageal reflux (18%). The majority of AEs resulted in no change in treatment (64%, n = 461). 21% (n = 150) of AEs resulted in a dose reduction and 13% (n = 94) necessitated discontinuation of treatment. 1 in 5 patients discontinued treatment either temporarily or on a permanent basis during the monitoring period. In a select cohort of patients, a statistically significant greater proportion of patients remained stable or improved and a lower proportion declined, as depicted by FVC changes of > 5% after nintedanib commencement (P < 0.05 using Chi squared test). Conclusions Nintedanib is well tolerated and has an acceptable safety profile. Only 8% of those reporting diarrhoea discontinued treatment either on a temporary or permanent basis. There were no signals with respect to increased cardiovascular morbidity or major bleeding risk. This is in keeping with the INPULSIS clinical trial findings but in a real world cohort.
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Boers PM, Donaldson C, Zagami AS, Lambert GA. Naratriptan Has a Selective Inhibitory Effect on Trigeminovascular Neurones at Central 5-HT1A and 5-HT1B/1D Receptors in the Cat: Implications for Migraine Therapy. Cephalalgia 2016; 24:99-109. [PMID: 14728705 DOI: 10.1111/j.1468-2982.2004.00636.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The triptans are agonists at serotonin(5-HT) 1B/1D receptors; however, they are also active at 5-HT1A and 5-HT1F receptors. We conducted this series of experiments to further elucidate the site of action of naratriptan using a well-established animal model of trigeminovascular stimulation. Following electrical stimulation of the superior sagittal sinus of the cat, single cell responses ( n = 83) were recorded in the trigeminal nucleus caudalis. Most cells (91%) also responded to electrical and mechanical stimulation of cutaneous or mucosal facial receptive fields. The micro-iontophoretic application of naratriptan resulted in a significant suppression of the response to sagittal sinus stimulation (response suppressed by 47 ± 4%, P < 0.001). The effect of naratriptan was significantly attenuated by application of either the 5-HT1B/1D receptor antagonist GR-127935 ( P < 0.001) or the 5-HT1A antagonist WAY-100635 ( P < 0.05). The response of single cells to receptive field stimulation was also suppressed by microiontophoretic application of naratriptan, but by only 20 ± 3%. Intravenous administration of naratriptan resulted in a similar selective suppression of sagittal sinus vs. receptive field responses in trigeminal neurones. These results indicate that naratriptan has a central effect in the trigeminovascular system, selectively inhibiting afferent activity in craniovascular neurones, via both 5-HT1B/1D and 5-HT1A receptors.
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Ma J, Diedrich JK, Jungreis I, Donaldson C, Vaughan J, Kellis M, Yates JR, Saghatelian A. Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. Anal Chem 2016; 88:3967-75. [PMID: 27010111 DOI: 10.1021/acs.analchem.6b00191] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Computational, genomic, and proteomic approaches have been used to discover nonannotated protein-coding small open reading frames (smORFs). Some novel smORFs have crucial biological roles in cells and organisms, which motivates the search for additional smORFs. Proteomic smORF discovery methods are advantageous because they detect smORF-encoded polypeptides (SEPs) to validate smORF translation and SEP stability. Because SEPs are shorter and less abundant than average proteins, SEP detection using proteomics faces unique challenges. Here, we optimize several steps in the SEP discovery workflow to improve SEP isolation and identification. These changes have led to the detection of several new human SEPs (novel human genes), improved confidence in the SEP assignments, and enabled quantification of SEPs under different cellular conditions. These improvements will allow faster detection and characterization of new SEPs and smORFs.
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Erchegyi J, Wang L, Gulyas J, Samant M, Perrin MH, Lewis K, Miller C, Vaughan J, Donaldson C, Fischer W, Low W, Yakabi S, Karasawa H, Taché Y, Rivier C, Rivier J. Characterization of Multisubstituted Corticotropin Releasing Factor (CRF) Peptide Antagonists (Astressins). J Med Chem 2016; 59:854-66. [PMID: 26789203 DOI: 10.1021/acs.jmedchem.5b00926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
CRF mediates numerous stress-related endocrine, autonomic, metabolic, and behavioral responses. We present the synthesis and chemical and biological properties of astressin B analogues {cyclo(30-33)[D-Phe(12),Nle(21,38),C(α)MeLeu(27,40),Glu(30),Lys(33)]-acetyl-h/r-CRF(9-41)}. Out of 37 novel peptides, 17 (2, 4, 6-8, 10, 11, 16, 17, 27, 29, 30, 32-36) and 16 (3, 5, 9, 12-15, 18, 19, 22-26, 28, 31) had k(i) to CRF receptors in the high picomolar and low nanomole ranges, respectively. Peptides 1, 2, and 11 inhibited h/rCRF and urocortin 1-induced cAMP release from AtT20 and A7r5 cells. When Astressin C 2 was administered to adrenalectomized rats at 1.0 mg subcutaneously, it inhibited ACTH release for >7 d. Additional rat data based on the inhibitory effect of (2) on h/rCRF-induced stimulation of colonic secretory motor activity and urocortin 2-induced delayed gastric emptying also indicate a safe and long-lasting antagonistic effect. The overall properties of selected analogues may fulfill the criteria expected from clinical candidates.
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Vernazza CR, Steele JG, Whitworth JM, Wildman JR, Donaldson C. Factors affecting direction and strength of patient preferences for treatment of molar teeth with nonvital pulps. Int Endod J 2014; 48:1137-46. [PMID: 25400281 DOI: 10.1111/iej.12413] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 11/12/2014] [Indexed: 11/29/2022]
Abstract
AIM To elicit the factors affecting willingness to pay (WTP) values for the preferred options of participants for dealing with a molar tooth with a nonvital pulp, a common but difficult problem. METHODOLOGY A total of 503 patients were recruited from dental practices in the North East of England and interviewed. Their preferred treatment option for a molar tooth with a nonvital pulp (endodontics, extraction and various prosthetic restorative options) and WTP for this preferred option were elicited. Factors affecting preferred option and WTP were analysed using econometric modelling. RESULTS Overall, 53% of the sample wished to save the tooth with a mean WTP of £373. The variance in WTP was high. Of those opting for extraction, the majority chose to leave a gap or have an implant. The preferred option was influenced by previous treatment experience. WTP was only influenced by having a low income. CONCLUSIONS The high level of variance in WTP and its relatively unpredictable nature pose difficult questions for policy makers trying to ensure the delivery of an equitable service. For dentists, it is important not to make assumptions about patient preference and strength of preference when making decisions. Ideally, WTP values should be considered alongside effectiveness data, and those on costs, in policy making.
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Andrews SW, Kabrah S, May JE, Donaldson C, Morse HR. Multiple myeloma: the bone marrow microenvironment and its relation to treatment. Br J Biomed Sci 2013; 70:110-20. [PMID: 24273897 DOI: 10.1080/09674845.2013.11669945] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Multiple myeloma is the most common haematological malignancy yet currently it remains incurable. For decades the mainstay in therapy has been non-targeted approaches including genotoxic agents and immunosuppressants. With myeloma predominantly affecting an elderly population, who are vulnerable to aggressive therapy, these non-specific approaches have resulted in poor survival. However, in recent years an explosion of collaborative research into myeloma has identified molecular interactions between myeloma cells and the bone marrow microenvironment as promoting myeloma development and associated complications such as bone lesions due to osteolysis. At the same time, a better understanding of the adhesion molecules, cytokines and signalling pathways involved in myeloma has led to the development of new targeted therapies, which are improving the quality of life for patients and significantly extending median patient survival. This review explores the current understanding of molecular pathways that promote myeloma progression and lead to bone destruction, with particular reference to the influence of interactions with the bone marrow microenvironment. It describes molecular targets for therapy with reference to the new therapeutics and their improved efficacy. While the outlook for myeloma patients has improved in recent years as a result of these new approaches, drug resistance remains a problem and future therapies will also need to address the molecular mechanisms of resistance in order to improve further the outcome for patients with this disease.
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Carr SM, Lhussier M, Forster N, Geddes L, Deane K, Pennington M, Visram S, White M, Michie S, Donaldson C, Hildreth A. An evidence synthesis of qualitative and quantitative research on component intervention techniques, effectiveness, cost-effectiveness, equity and acceptability of different versions of health-related lifestyle advisor role in improving health. Health Technol Assess 2011; 15:iii-iv, 1-284. [PMID: 21329611 DOI: 10.3310/hta15090] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND There is a need to identify and analyse the range of models developed to date for delivering health-related lifestyle advice (HRLA), or training, for effectiveness and cost-effectiveness in improving the health and well-being of individuals and communities in the UK, with particular reference to the reduction of inequalities. OBJECTIVES To identify the component intervention techniques of lifestyle advisors (LAs) in the UK and similar contexts, and the outcomes of HRLA interventions. DATA SOURCES Stakeholder views, secondary analysis of the National Survey of Health Trainer Activity, telephone survey of health trainer leads/coordinators. A search of a range of electronic databases was undertaken [including the Applied Social Sciences Index and Abstracts (ASSIA), EMBASE, NHS Economic Evaluation Database (NHS EED), MEDLINE, Psyc INFO, etc.], as well searching relevant journals and reference lists, conducted from inception to September 2008. REVIEW METHODS Identified studies were scanned by two reviewers and those meeting the following criteria were included: studies carrying out an evaluation of HRLA; those taking place in developed countries similar to the UK context; those looking at adult groups; interventions with the explicit aim of health improvement; interventions that involved paid or voluntary work with an individual or group of peers acting in an advisory role; advice delivered by post, online or electronically; training, support or counselling delivered to patients, communities or members of the public. After quality assessment, studies were selected for inclusion in the review. Data were abstracted from each study according to an agreed procedure and narrative, and realist and economic approaches were used to synthesise the data. Cost-effectiveness analysis of interventions was undertaken. RESULTS In total, 269 studies were identified but 243 were excluded. The 26 included studies addressing chronic care, mental health, breastfeeding, smoking, diet and physical activity, screening and human immunodeficiency virus (HIV) infection prevention. Overall, there was insufficient evidence to either support or refute the use of LAs to promote health and improve quality of life (QoL), and thus uncertainty about the interventions' cost-effectiveness. However, the economic analysis showed that LA interventions were cost-effective in chronic care and smoking cessation, inconclusive for breastfeeding and mental health and not cost-effective for screening uptake and diet/physical activity. LA interventions for HIV prevention were cost-effective, but not in a UK context. LIMITATIONS The wide variety of LA models, delivery settings and target populations prevented the reviewers from establishing firm causal relationships between intervention mode and study outcomes. CONCLUSIONS Evidence was variable, giving only limited support to LAs having a positive impact on health knowledge, behaviours and outcomes. Levels of acceptability appeared to be high. LAs acted as translational agents, sometimes removing barriers to prescribed behaviour or helping to create facilitative social environments. Reporting of processes of accessing or capitalising on indigenous knowledge was limited. Ambiguity was apparent with respect to the role and impact of lay and peer characteristics of the interventions. A future programme of research on HRLA could benefit from further emphasis on identification of needs, the broadening of population focus and intervention aims, the measurement of outcomes and the reviewing of evidence. FUNDING This study was funded by the Health Technology Assessment programme of the National Institute for Health Research.
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Haque K, Truman C, Dittmer I, Donaldson C, Laundy G, Dudley J, Hows J, Bradley B. Quantitation of cyclosporine-sensitive and -resistant allospecific cytotoxic cells at birth. Transpl Int 2011. [DOI: 10.1111/j.1432-2277.2000.tb02086.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Baker R, Bateman I, Donaldson C, Jones-Lee M, Lancsar E, Loomes G, Mason H, Odejar M, Pinto Prades JL, Robinson A, Ryan M, Shackley P, Smith R, Sugden R, Wildman J. Weighting and valuing quality-adjusted life-years using stated preference methods: preliminary results from the Social Value of a QALY Project. Health Technol Assess 2010; 14:1-162. [PMID: 20525460 DOI: 10.3310/hta14270] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES To identify characteristics of beneficiaries of health care over which relative weights should be derived and to estimate relative weights to be attached to health gains according to characteristics of recipients of these gains (relativities study); and to assess the feasibility of estimating a willingness-to-pay (WTP)-based value of a quality-adjusted life-year (QALY) (valuation study). DESIGN Two interview-based surveys were administered - one (for the relativities study) to a nationally representative sample of the population in England and the other (for the valuation study) to a smaller convenience sample. SETTING The two surveys were administered by the National Centre for Social Research (NatCen) in respondents' homes. PARTICIPANTS 587 members of the public were interviewed for the relativities study and 409 for the valuation study. METHODS In the relativities study, in-depth qualitative work and considerations of policy relevance resulted in the identification of age and severity of illness as relevant characteristics. Scenarios reflecting these, along with additional components reflecting gains in QALYs, were presented to respondents in a series of pairwise choices using two types of question: discrete choice and matching. These questions were part of a longer questionnaire (including attitudinal and sociodemographic questions), which was administered face to face using a computer-assisted personal interview. In the valuation study, respondents were asked about their WTP to avoid/prevent different durations of headache or stomach illness and to value these states on a scale (death = 0; full health = 1) using standard gamble (SG) questions. RESULTS Discrete choice results showed that age and severity variables did not have a strong impact on respondents' choices over and above the health (QALY) gains presented. In contrast, matching showed age and severity impacts to be strong: depending on method of aggregation, gains to some groups were weighted three to four times more highly than gains to others. Results from the WTP and SG questions were combined in different ways to arrive at values of a QALY. These vary from values which are in the vicinity of the current National Institute for Health and Clinical Excellence (NICE) threshold to extremely high values. CONCLUSIONS With respect to relative weights, more research is required to explore methodological differences with respect to age and severity weighting. On valuation, there are particular issues concerning the extent to which 'noise' and 'error' in people's responses might generate extreme and unreliable figures. Methods of aggregation and measures of central tendency were issues in both weighting and valuation procedures and require further exploration.
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