Guidelines for depositors : The UKCCSRC data and information life cycle

The UKCCSRC funds projects to promote the implementation of Carbon Capture and Storage (CCS) and require data from these projects to be lodged in the UKCCSRC Data and Information Archive. Natural Environment Research Council (NERC), the Engineering and Physical Sciences Research Council (EPSRC) and other research funders also provide grants for CCS scientific research. All research council grant holders have to abide by the conditions of the grant and follow their research council expectations such as the NERC Data Policy and EPSRC Research Framework. These policies place a duty on grant holders to offer a copy of their datasets to the appropriate Data Centre. The UKCCSRC Data and Information Archive is a component of the National Geoscience Data Centre1 (NGDC), hosted within the British Geological Survey (BGS). CCS data collected by UKCCSRC and EPSRC-funded projects must be deposited in the UKCCSRC Data Archive in addition to any home institution requirements. CCS data from projects supported by NERC and other funding streams can also be deposited with the UKCCSRC Data Archive, on a voluntary basis, under the same terms and conditions as a UKCCSRC-funded research. This document explains the benefits that this deposit offers, describes the process of depositing information, and provides information about other sources of relevant information

Using OGC API standards for marine data delivery : MEDIN Pilot Project

This report is the published product of a pilot project by the British Geological Survey (BGS), commissioned by Marine Environmental Data and Information Network (MEDIN) to investigate the implementation of the OGC API – Environmental Data Retrieval (OGC API – EDR) standard to deliver data externally from the MEDIN Geology and Geophysics Data Archive Centre (DAC). The report details the method and technologies used in the attempt to deliver BGS DAC data using the OGC API – EDR standard. This report could be used as an OGC API implementation guide for other DACs and as guidance on contributing to existing Open-Source projects. The report also detail aspects of the OGC API – EDR that made it inappropriate to use for some marine environmental data, and any areas where the standard was ambiguous or challenging to implement. Also included are recommendations on how well the OGC API – EDR can support direct access to data for MEDIN, including which data types/formats can be supported. BGS did not have sufficient resource to deliver an OGC API – EDR endpoint at the completion of the project but did implement OGC API – Features with Common Query Language (CQL) endpoint which offers similar functionality but uses different syntax. OGC API – Features + CQL was meant to be an intermediary step to delivering OGC API – EDR. BGS were unable to deliver OGCI – EDR as after spending time exploring the standard in depth it was shown to be more complex than anticipated. However, through the process of this endeavour we have made incremental steps forward towards EDR, and we were able to make a major contribution to an Open-Source Project which will benefit many geospatial data publishers and users

A randomised, double-blind, parallel-group trial to assess mercaptopurine versus placebo to prevent or delay recurrence of Crohn's disease following surgical resection (TOPPIC)

Crohn’s disease (CD) is a chronic, relapsing, inflammatory bowel disease. Up to 65% of patients with CD require an operation to control the disease within 10 years. Both endoscopic and clinical recurrence is common within 2 years of operation, with re-operation rates cumulating at 5% of patients per year

The effectiveness and cost-effectiveness of minimal access surgery amongst people with gastro-oesophageal reflux disease – a UK collaborative study

*Corresponding author randomised arm of the trial (178 allocated to surgical management,179 allocated to continued, but optimised,medical management) and 453 recruited to the parallel non-randomised preference arm (261 chose surgical management, 192 chose to continue with best medical management). The type of fundoplication was left to the discretion of the surgeon. Main outcome measures: Participants completed a baseline reflux questionnaire, developed specifically for this study, containing a disease-specific outcome measure, the Short Form with 36 Items (SF-36), the EuroQol-5 Dimensions (EQ-5D) and the Beliefs about Medicines and Surgery questionnaires (BMQ/BSQ).Postal questionnaires were completed at participant specific time intervals after joining the trial (equivalent to approximately 3 and 12 months after surgery).Intraoperative data were recorded by the surgeons and all other in-hospital data were collected by the research nurse. At the end of the study period, participants completed a discrete choice experiment questionnaire. Results: The randomised groups were well balanced at entry. Participants had been taking GORD medication for a median of 32 months; the mean age of participants was 46 years and 66% were men. Of 178 randomised to surgery, 111 (62%) actually had fundoplication.There was a mixture of clinical and personal reasons why some patients did not have surgery, sometimes Objectives: To evaluate the clinical effectiveness, costeffectiveness and safety of a policy of relatively early laparoscopic surgery compared with continued medical management amongst people with gastro-oesophageal reflux disease (GORD) judged suitable for both policies. Design: Relative clinical effectiveness was assessed by a randomised trial (with parallel non-randomised preference groups) comparing a laparoscopic surgerybased policy with a continued medical management policy. The economic evaluation compared the costeffectiveness of the two management policies in order to identify the most efficient provision of future care and describe the resource impact that various policies for fundoplication would have on the NHS.Setting: A total of 21 hospitals throughout the UK with a local partnership between surgeon(s) and gastroenterologist(s) who shared the secondary care of patients with GORD.Participants: The 810 participants, who were identified retrospectively or prospectively via their participating clinicians, had both documented evidence of GORD (endoscopy and/or manometry/24-hour pH monitoring) and symptoms for longer than 12 months. In addition,the recruiting clinician(s) was clinically uncertain about which management policy was best.Intervention: Of the 810 eligible patients who consented to participate, 357 were recruited to the related to long waiting times. A total or partial wrap procedure was performed depending on surgeon preference. Complications were uncommon and there were no deaths associated with surgery. By the equivalent of 12 months after surgery, 38% in the randomised surgical group (14% amongst those who had surgery) were taking reflux medication compared with 90% in the randomised medical group. There were substantial differences (one-third to one-half standard deviation) favouring the randomised surgical group across the health status measures, the size depending on assumptions about the proportion that actually had fundoplication. These differences were the same or somewhat smaller than differences observed at 3 months. The lower the reflux score, the worse the symptoms at trial entry and the larger the benefit observed after surgery. The preference surgical group had the lowest reflux scores at baseline. These scores improved substantially after surgery, and by 12 months they were better than those in the preference medical group. The BMQ/BSQ and discrete choice experiment did distinguish the preference groups from each other and from the randomised groups. The latter indicated that the risk of serious complications was the most important single attribute of a treatment option. A within trial cost-effectiveness analysis suggested that the surgery policy was more costly (mean £2049) but also more effective [+0.088 quality-adjusted life-years (QALYs)]. The estimated incremental cost per QALY was £19,000–£23,000, with a probability between 46% (when 62% received surgery) and 19% (when all received surgery) of cost-effectiveness at a threshold of £20,000 per QALY. Modelling plausible longer-term scenarios (such as lifetime benefit after surgery) indicated a greater likelihood (74%) of costeffectiveness at a threshold of £20,000, but applying a range of alternative scenarios indicated wide uncertainty.The expected value of perfect information was greatest for longer-term quality of life and proportions of surgical patients requiring medication.Conclusions: Amongst patients requiring long-term medication to control symptoms of GORD, surgical management significantly increases general and refluxspecific health-related quality of life measures, at least up to 12 months after surgery. Complications of surgery were rare. A surgical policy is, however, more costly than continued medical management. At a threshold of £20,000 per QALY it may well be cost-effective, especially when putative longer-term benefits are taken into account, but this is uncertain.The more troublesome the symptoms, the greater the potential benefit from surgery. Uncertainty about cost-effectiveness would be greatly reduced by more reliable information about relative longer-term costs and benefits of surgical and medical policies. This could be through extended follow-up of the reflux trial cohorts or of other cohorts of fundoplication patients.Peer reviewedPublisher PD

HLA-DP on Epithelial Cells Enables Tissue Damage by NKp44⁺ Natural Killer Cells in Ulcerative Colitis

Background &amp; Aims: Ulcerative colitis (UC) is characterized by severe inflammation and destruction of the intestinal epithelium, and is associated with specific risk single nucleotide polymorphisms in HLA class II. Given the recently discovered interactions between subsets of HLA-DP molecules and the activating natural killer (NK) cell receptor NKp44, genetic associations of UC and HLA-DP haplotypes and their functional implications were investigated. Methods: HLA-DP haplotype and UC risk association analyses were performed (UC: n = 13,927; control: n = 26,764). Expression levels of HLA-DP on intestinal epithelial cells (IECs) in individuals with and without UC were quantified. Human intestinal 3-dimensional (3D) organoid cocultures with human NK cells were used to determine functional consequences of interactions between HLA-DP and NKp44. Results: These studies identified HLA-DPA1∗01:03-DPB1∗04:01 (HLA-DP401) as a risk haplotype and HLA-DPA1∗01:03-DPB1∗03:01 (HLA-DP301) as a protective haplotype for UC in European populations. HLA-DP expression was significantly higher on IECs of individuals with UC compared with controls. IECs in human intestinal 3D organoids derived from HLA-DP401pos individuals showed significantly stronger binding of NKp44 compared with HLA-DP301pos IECs. HLA-DP401pos IECs in organoids triggered increased degranulation and tumor necrosis factor production by NKp44+ NK cells in cocultures, resulting in enhanced epithelial cell death compared with HLA-DP301pos organoids. Blocking of HLA-DP401–NKp44 interactions (anti-NKp44) abrogated NK cell activity in cocultures. Conclusions: We identified an UC risk HLA-DP haplotype that engages NKp44 and activates NKp44+ NK cells, mediating damage to intestinal epithelial cells in an HLA-DP haplotype–dependent manner. The molecular interaction between NKp44 and HLA-DP401 in UC can be targeted by therapeutic interventions to reduce NKp44+ NK cell–mediated destruction of the intestinal epithelium in UC.</p

HLA-DP on Epithelial Cells Enables Tissue Damage by NKp44⁺ Natural Killer Cells in Ulcerative Colitis

Background &amp; Aims: Ulcerative colitis (UC) is characterized by severe inflammation and destruction of the intestinal epithelium, and is associated with specific risk single nucleotide polymorphisms in HLA class II. Given the recently discovered interactions between subsets of HLA-DP molecules and the activating natural killer (NK) cell receptor NKp44, genetic associations of UC and HLA-DP haplotypes and their functional implications were investigated. Methods: HLA-DP haplotype and UC risk association analyses were performed (UC: n = 13,927; control: n = 26,764). Expression levels of HLA-DP on intestinal epithelial cells (IECs) in individuals with and without UC were quantified. Human intestinal 3-dimensional (3D) organoid cocultures with human NK cells were used to determine functional consequences of interactions between HLA-DP and NKp44. Results: These studies identified HLA-DPA1∗01:03-DPB1∗04:01 (HLA-DP401) as a risk haplotype and HLA-DPA1∗01:03-DPB1∗03:01 (HLA-DP301) as a protective haplotype for UC in European populations. HLA-DP expression was significantly higher on IECs of individuals with UC compared with controls. IECs in human intestinal 3D organoids derived from HLA-DP401pos individuals showed significantly stronger binding of NKp44 compared with HLA-DP301pos IECs. HLA-DP401pos IECs in organoids triggered increased degranulation and tumor necrosis factor production by NKp44+ NK cells in cocultures, resulting in enhanced epithelial cell death compared with HLA-DP301pos organoids. Blocking of HLA-DP401–NKp44 interactions (anti-NKp44) abrogated NK cell activity in cocultures. Conclusions: We identified an UC risk HLA-DP haplotype that engages NKp44 and activates NKp44+ NK cells, mediating damage to intestinal epithelial cells in an HLA-DP haplotype–dependent manner. The molecular interaction between NKp44 and HLA-DP401 in UC can be targeted by therapeutic interventions to reduce NKp44+ NK cell–mediated destruction of the intestinal epithelium in UC.</p

Phenotype and genotype of 87 patients with Mowat-Wilson syndrome and recommendations for care

Mowat-Wilson syndrome (MWS) is a rare intellectual disability/multiple congenital anomalies syndrome caused by heterozygous mutation of the ZEB2 gene. It is generally underestimated because its rarity and phenotypic variability sometimes make it difficult to recognize. Here, we aimed to better delineate the phenotype, natural history, and genotype-phenotype correlations of MWS.MethodsIn a collaborative study, we analyzed clinical data for 87 patients with molecularly confirmed diagnosis. We described the prevalence of all clinical aspects, including attainment of neurodevelopmental milestones, and compared the data with the various types of underlying ZEB2 pathogenic variations.ResultsAll anthropometric, somatic, and behavioral features reported here outline a variable but highly consistent phenotype. By presenting the most comprehensive evaluation of MWS to date, we define its clinical evolution occurring with age and derive suggestions for patient management. Furthermore, we observe that its severity correlates with the kind of ZEB2 variation involved, ranging from ZEB2 locus deletions, associated with severe phenotypes, to rare nonmissense intragenic mutations predicted to preserve some ZEB2 protein functionality, accompanying milder clinical presentations.ConclusionKnowledge of the phenotypic spectrum of MWS and its correlation with the genotype will improve its detection rate and the prediction of its features, thus improving patient care.GENETICS in MEDICINE advance online publication, 4 January 2018; doi:10.1038/gim.2017.221

Argo data 1999-2019: two million temperature-salinity profiles and subsurface velocity observations from a global array of profiling floats.

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wong, A. P. S., Wijffels, S. E., Riser, S. C., Pouliquen, S., Hosoda, S., Roemmich, D., Gilson, J., Johnson, G. C., Martini, K., Murphy, D. J., Scanderbeg, M., Bhaskar, T. V. S. U., Buck, J. J. H., Merceur, F., Carval, T., Maze, G., Cabanes, C., Andre, X., Poffa, N., Yashayaev, I., Barker, P. M., Guinehut, S., Belbeoch, M., Ignaszewski, M., Baringer, M. O., Schmid, C., Lyman, J. M., McTaggart, K. E., Purkey, S. G., Zilberman, N., Alkire, M. B., Swift, D., Owens, W. B., Jayne, S. R., Hersh, C., Robbins, P., West-Mack, D., Bahr, F., Yoshida, S., Sutton, P. J. H., Cancouet, R., Coatanoan, C., Dobbler, D., Juan, A. G., Gourrion, J., Kolodziejczyk, N., Bernard, V., Bourles, B., Claustre, H., D'Ortenzio, F., Le Reste, S., Le Traon, P., Rannou, J., Saout-Grit, C., Speich, S., Thierry, V., Verbrugge, N., Angel-Benavides, I. M., Klein, B., Notarstefano, G., Poulain, P., Velez-Belchi, P., Suga, T., Ando, K., Iwasaska, N., Kobayashi, T., Masuda, S., Oka, E., Sato, K., Nakamura, T., Sato, K., Takatsuki, Y., Yoshida, T., Cowley, R., Lovell, J. L., Oke, P. R., van Wijk, E. M., Carse, F., Donnelly, M., Gould, W. J., Gowers, K., King, B. A., Loch, S. G., Mowat, M., Turton, J., Rama Rao, E. P., Ravichandran, M., Freeland, H. J., Gaboury, I., Gilbert, D., Greenan, B. J. W., Ouellet, M., Ross, T., Tran, A., Dong, M., Liu, Z., Xu, J., Kang, K., Jo, H., Kim, S., & Park, H. Argo data 1999-2019: two million temperature-salinity profiles and subsurface velocity observations from a global array of profiling floats. Frontiers in Marine Science, 7, (2020): 700, doi:10.3389/fmars.2020.00700.In the past two decades, the Argo Program has collected, processed, and distributed over two million vertical profiles of temperature and salinity from the upper two kilometers of the global ocean. A similar number of subsurface velocity observations near 1,000 dbar have also been collected. This paper recounts the history of the global Argo Program, from its aspiration arising out of the World Ocean Circulation Experiment, to the development and implementation of its instrumentation and telecommunication systems, and the various technical problems encountered. We describe the Argo data system and its quality control procedures, and the gradual changes in the vertical resolution and spatial coverage of Argo data from 1999 to 2019. The accuracies of the float data have been assessed by comparison with high-quality shipboard measurements, and are concluded to be 0.002°C for temperature, 2.4 dbar for pressure, and 0.01 PSS-78 for salinity, after delayed-mode adjustments. Finally, the challenges faced by the vision of an expanding Argo Program beyond 2020 are discussed.AW, SR, and other scientists at the University of Washington (UW) were supported by the US Argo Program through the NOAA Grant NA15OAR4320063 to the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) at the UW. SW and other scientists at the Woods Hole Oceanographic Institution (WHOI) were supported by the US Argo Program through the NOAA Grant NA19OAR4320074 (CINAR/WHOI Argo). The Scripps Institution of Oceanography's role in Argo was supported by the US Argo Program through the NOAA Grant NA15OAR4320071 (CIMEC). Euro-Argo scientists were supported by the Monitoring the Oceans and Climate Change with Argo (MOCCA) project, under the Grant Agreement EASME/EMFF/2015/1.2.1.1/SI2.709624 for the European Commission

HLA-DQA1*05 carriage associated with development of anti-drug antibodies to infliximab and adalimumab in patients with Crohn's Disease

Anti-tumor necrosis factor (anti-TNF) therapies are the most widely used biologic drugs for treating immune-mediated diseases, but repeated administration can induce the formation of anti-drug antibodies. The ability to identify patients at increased risk for development of anti-drug antibodies would facilitate selection of therapy and use of preventative strategies.This article is freely available via Open Access. Click on Publisher URL to access the full-text

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery