419 results on '"James Shepherd"'
Search Results
2. A shortcut to the thermodynamic limit for quantum many-body calculations of metals
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Laura Weiler, Andreas Grüneis, Tobias Schäfer, James Shepherd, Sai Kumar Ramadugu, and Tina Mihm
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Computer Networks and Communications ,0103 physical sciences ,Computer Science (miscellaneous) ,02 engineering and technology ,021001 nanoscience & nanotechnology ,010306 general physics ,0210 nano-technology ,01 natural sciences ,Computer Science Applications - Abstract
Computationally efficient and accurate quantum mechanical approximations to solve the many-electron Schrödinger equation are crucial for computational materials science. Methods such as coupled cluster theory show potential for widespread adoption if computational cost bottlenecks can be removed. For example, extremely dense k-point grids are required to model long-range electronic correlation effects, particularly for metals. Although these grids can be made more effective by averaging calculations over an offset (or twist angle), the resultant cost in time for coupled cluster theory is prohibitive. We show here that a single special twist angle can be found using the transition structure factor, which provides the same benefit as twist averaging with one or two orders of magnitude reduction in computational time. We demonstrate that this not only works for metal systems but also is applicable to a broader range of materials, including insulators and semiconductors.
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- 2021
3. Seoul Virus Associated with Pet Rats, Scotland, UK, 2019
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Katherine Smollett, Stephen Carmichael, Rory Gunson, Jane Osborne, Hector Maxwell-Scott, James Shepherd, E. Thomson, Ana da Silva Filipe, Rajiv Shah, Eoghan C.W. Farmer, Alasdair MacLean, Andrew E. Blunsum, Shirin Ashraf, and Emma Aarons
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Microbiology (medical) ,Lineage (genetic) ,Epidemiology ,Seoul hantavirus ,Infectious and parasitic diseases ,RC109-216 ,Biology ,Kidney ,Virus ,hantavirus ,hemorrhagic fever with renal syndrome ,Animals ,Humans ,viruses ,Hantavirus ,Seoul virus ,Whole genome sequencing ,viral zoonoses ,Seoul Virus Associated with Pet Rats, Scotland, UK, 2019 ,Dispatch ,Virology ,United Kingdom ,Rats ,Infectious Diseases ,Scotland ,whole-genome sequencing ,Medicine ,hantavirus infections ,SEOV ,pets ,Hantavirus Infection - Abstract
We describe a case of hemorrhagic fever with renal syndrome caused by Seoul virus in a woman in Scotland, UK. Whole-genome sequencing showed the virus belonged to a lineage characterized by recent international expansion, probably driven by trade in pet rats.
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- 2021
4. 1897. The Decline of Respiratory Viruses During the SARS-CoV-2 Pandemic: Public Health Interventions vs. Viral Competition?
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Waleed Malik, Ritche Hao, and James Shepherd
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Infectious Diseases ,Oncology - Abstract
Background With the spread of the SARS-CoV-2 pandemic in 2020 and the attendant global precautions such as masking, travel restrictions and social distancing, the WHO FluNet data indicated a decline in flu rates. The CDC data for the 2020-2021 season showed the same decline in US flu as well as other respiratory viruses. Two hypotheses to explain the observed phenomenon are the impact of non-pharmaceutical interventions (NPI) to prevent SARS-CoV-2 infection and suppression of other respiratory viruses by SARS-CoV-2 through a form of resource competition. Methods We conducted a study using the EPIC Slicer Dicer analytics tool and the Yale Internal Medicine COVID-19 Database to retrieve data from the Yale New Haven Health System (YNHHS). We tabulated the total number of positive and negative tests for SARS-CoV-2 and a panel of respiratory viruses from September 2, 2018 to April 30, 2022 to cover pre- and peri-pandemic periods. These results were divided into three age groups: ≤12, 13-59, and ≥60. Epidemic curves of each virus with respect to each other, the season, and the introduction of NPIs were constructed to help differentiate between the two hypotheses. Results Pre-pandemic data from 09/2018 to 02/2020 revealed seasonal spikes in influenza A and B with 254 positive weekly influenza A/B tests from 11/2018 to 02/2019 for a positivity rate of 7.97% and 481 positive weekly tests (10.53% positivity rate [PR]) from November 2019 to February 2020. There were only 0.35 positive weekly influenza A/B tests (0.05% PR) from 11/2020 to 02/2021 with 2018 positive weekly tests (6.45% PR) for SARS-CoV-2 over the same period. From 11/2020 to 02/2021, there were 56 positive weekly influenza A/B tests (1.44% PR) and 4347 positive weekly SARS-CoV-2 tests (10.35% PR). From 07/2021 to 11/2021, there was an increased rate of positive RSV tests (82 per week, 15.76% PR) and rhinovirus tests (58 per week, 18.73% PR). There were 803 positive weekly tests (2.53% positivity rate) for SARS-CoV-2 over this same period. Conclusion Since the start of the SARS-CoV-2 pandemic, the number of positive tests for influenza A/B and seasonal respiratory viruses have not reached pre-pandemic levels across the YNHHS. However, rates of influenza and other respiratory viruses have increased since the relaxation of NPIs. Disclosures All Authors: No reported disclosures.
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- 2022
5. Risk factors for Crimean-Congo Haemorrhagic Fever (CCHF) virus exposure in farming communities in Uganda
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Stella A. Atim, Shirin Ashraf, Sandra Belij-Rammerstorfer, Anna R Ademun, Patrick Vudriko, Teddy Nakayiki, Marc Niebel, James Shepherd, Stephen Balinandi, Gladys Nakanjako, Andrew Abaasa, Paul C.D. Johnson, Steven Odongo, Martin Esau, Milton Bahati, Pontiano Kaleebu, Julius J Lutwama, Charles Masembe, Teresa Lambe, Emma C. Thomson, and Robert Tweyongyere
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Microbiology (medical) ,Goats ,Agriculture ,Infectious Diseases ,Dogs ,Cross-Sectional Studies ,Ticks ,Risk Factors ,Hemorrhagic Fever Virus, Crimean-Congo ,Animals ,Humans ,Female ,Cattle ,Hemorrhagic Fever, Crimean ,Uganda - Abstract
Background: \ud Crimean-Congo Haemorrhagic Fever (CCHF) is an emerging human-health threat causing sporadic outbreaks in livestock farming communities. However, the full extent and the risks associated with exposure of such communities has not previously been well-described.\ud \ud Methods: \ud We collected blood samples from 800 humans, 666 cattle, 549 goats and 32 dogs in districts within and outside Ugandan cattle corridor in a cross-sectional survey, and tested for CCHFV-specific IgG antibodies using Enzyme-Linked Immunosorbent Assays. Sociodemographic and epidemiological data were recorded using structured questionnaire. Ticks were collected to identify circulating nairoviruses by metagenomic sequencing.\ud \ud Results: \ud CCHFV seropositivity was in 221/800 (27·6%) in humans, 612/666 (91·8%) in cattle, 413/549 (75·2%) in goats and 18/32 (56·2%) in dogs. Human seropositivity was associated with livestock farming (AOR=5·68, p50 ticks: AOR=3·52, p=0·004). CCHFV was identified in multiple tick pools of Rhipicephalus appendiculatus.\ud \ud Interpretation: \ud The very high CCHF seropositivity especially among livestock farmers and multiple regional risk factors associated exposures, including collecting/eating engorged ticks previously unrecognised, highlights need for further surveillance and sensitisation and control policies against the disease.
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- 2022
6. Effect of statin therapy on muscle symptoms: an individual participant data meta-analysis of large-scale, randomised, double-blind trials
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Christina Reith, Colin Baigent, Lisa Blackwell, Jonathan Emberson, Enti Spata, Kelly Davies, Heather Halls, Lisa Holland, Kate Wilson, Jane Armitage, Charlie Harper, David Preiss, Alistair Roddick, Anthony Keech, John Simes, Rory Collins, Elizabeth Barnes, Jordan Fulcher, William G Herrington, Adrienne Kirby, Borislava Mihaylova, Rachel O'Connell, Pierre Amarenco, Philip Barter, D John Betteridge (deceased), Michael Blazing, Jackie Bosch, Louise Bowman, Eugene Braunwald, Christopher P Cannon, Michael Clearfield, Stuart Cobbe, Helen M Colhoun, Björn Dahlöf, Barry Davis, James de Lemos, John R Downs, Paul N Durrington, Bengt Fellström, Ian Ford, Maria Grazia Franzosi, John Fuller (deceased), Curt Furberg, Robert Glynn, David Gordon, Antonio Gotto Jr, Richard Grimm, Ajay Gupta, C Morton Hawkins, Graham A Hitman, Hallvard Holdaas (deceased), Alan Jardine, J Wouter Jukema, John JP Kastelein, Sharon Kean, John Kjekshus, Genell Knatterud (deceased), Robert H Knopp (deceased), Wolfgang Koenig, Michael Koren, Vera Krane, Martin Landray, John LaRosa, Roberto Latini, Eva Lonn, Donata Lucci, Jean MacFadyen, Peter Macfarlane, Stephen MacMahon, Aldo Maggioni, Roberto Marchioli, Ian Marschner, Lemuel Moyé, Sabina Murphy, Andrew Neil, Enrico B Nicolis, Chris Packard, Sarah Parish, Terje R Pedersen, Richard Peto, Marc Pfeffer, Neil Poulter, Sara Pressel, Jeffrey Probstfield, Mahboob Rahman, Paul M Ridker, Michele Robertson, Frank Sacks, Naveed Sattar, Roland Schmieder, Patrick W Serruys, Peter Sever, John Shaw (deceased), James Shepherd (deceased), Lara Simpson, Peter Sleight (deceased), Luigi Tavazzi, Gianni Tognoni, Andrew Tonkin, Stella Trompet, Christoph Wanner, Hans Wedel, Stephen Weis, K Michael Welch, Harvey White, John Wikstrand, Lars Wilhelmsen, Stephen Wiviott, Robin Young, Salim Yusuf, Faiez Zannad, Hiroyuki Arashi, Robert Byington, Robert Clarke, Marcus Flather, Uri Goldbourt, Shinya Goto, Jemma Hopewell, Kees Hovingh, Patricia Kearney, George Kitas, Connie Newman, Marc S Sabatine, Greg Schwartz, Liam Smeeth, Jonathan Tobert, John Varigos, Junichi Yamaguchi, Vascular Medicine, ACS - Atherosclerosis & ischemic syndromes, ACS - Pulmonary hypertension & thrombosis, Experimental Vascular Medicine, ACS - Amsterdam Cardiovascular Sciences, and Collaboration, Cholesterol Treatment Trialists'
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Male ,Muscles ,Australia ,Humans ,Female ,General Medicine ,Myalgia ,Hydroxymethylglutaryl-CoA Reductase Inhibitors ,Middle Aged ,Atherosclerosis ,Randomized Controlled Trials as Topic - Abstract
Background: Statin therapy is effective for the prevention of atherosclerotic cardiovascular disease and is widely prescribed, but there are persisting concerns that statin therapy might frequently cause muscle pain or weakness. We aimed to address these through an individual participant data meta-analysis of all recorded adverse muscle events in large, long-term, randomised, double-blind trials of statin therapy. Methods: Randomised trials of statin therapy were eligible if they aimed to recruit at least 1000 participants with a scheduled treatment duration of at least 2 years, and involved a double-blind comparison of statin versus placebo or of a more intensive versus a less intensive statin regimen. We analysed individual participant data from 19 double-blind trials of statin versus placebo (n=123 940) and four double-blind trials of a more intensive versus a less intensive statin regimen (n=30 724). Standard inverse-variance-weighted meta-analyses of the effects on muscle outcomes were conducted according to a prespecified protocol. Findings: Among 19 placebo-controlled trials (mean age 63 years [SD 8], with 34 533 [27·9%] women, 59 610 [48·1%] participants with previous vascular disease, and 22 925 [18·5%] participants with diabetes), during a weighted average median follow-up of 4·3 years, 16 835 (27·1%) allocated statin versus 16 446 (26·6%) allocated placebo reported muscle pain or weakness (rate ratio [RR] 1·03; 95% CI 1·01–1·06). During year 1, statin therapy produced a 7% relative increase in muscle pain or weakness (1·07; 1·04–1·10), corresponding to an absolute excess rate of 11 (6–16) events per 1000 person-years, which indicates that only one in 15 ([1·07–1·00]/1·07) of these muscle-related reports by participants allocated to statin therapy were actually due to the statin. After year 1, there was no significant excess in first reports of muscle pain or weakness (0·99; 0·96–1·02). For all years combined, more intensive statin regimens (ie, 40–80 mg atorvastatin or 20–40 mg rosuvastatin once per day) yielded a higher RR than less intensive or moderate-intensity regimens (1·08 [1·04–1·13] vs 1·03 [1·00–1·05]) compared with placebo, and a small excess was present (1·05 [0·99–1·12]) for more intensive regimens after year 1. There was no clear evidence that the RR differed for different statins, or in different clinical circumstances. Statin therapy yielded a small, clinically insignificant increase in median creatine kinase values of approximately 0·02 times the upper limit of normal. Interpretation: Statin therapy caused a small excess of mostly mild muscle pain. Most (>90%) of all reports of muscle symptoms by participants allocated statin therapy were not due to the statin. The small risks of muscle symptoms are much lower than the known cardiovascular benefits. There is a need to review the clinical management of muscle symptoms in patients taking a statin. Funding: British Heart Foundation, Medical Research Council, Australian National Health and Medical Research Council.
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- 2022
7. A Near-Deterministic Mutational Hotspot in Pseudomonas fluorescens Is Constructed by Multiple Interacting Genomic Features
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Matthew James Shepherd, Tiffany B. Taylor, and James Horton
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Mutation bias ,Genetics ,predicting evolution ,mutation hotspot ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics - Abstract
Mutation—whilst stochastic—is frequently biased toward certain loci. When combined with selection, this results in highly repeatable and predictable evolutionary outcomes. Immotile variants of the bacterium Pseudomonas fluorescens (SBW25) possess a “mutational hotspot” that facilitates repeated occurrences of an identical de novo single nucleotide polymorphism when re-evolving motility, where ≥95% independent lines fix the mutation ntrB A289C. Identifying hotspots of similar potency in other genes and genomic backgrounds would prove valuable for predictive evolutionary models but to do so we must understand the genomic features that enable such a hotspot to form. Here, we reveal that genomic location, local nucleotide sequence, gene strandedness, and presence of mismatch repair proteins operate in combination to facilitate the formation of this mutational hotspot. Our study therefore provides a framework for utilizing genomic features to predict and identify hotspot positions capable of enforcing near-deterministic evolution.
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- 2022
8. Non-epidemic HCV genotypes in low- and middle-income countries and the risk of resistance to current direct-acting antiviral regimens
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Lucrece Ahovegbe, Marc Niebel, James Shepherd, E. Thomson, and Rajiv Shah
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0301 basic medicine ,Hepatitis C Virus ,SVR ,Genotype ,Elimination ,Hepatitis C virus ,Genotypes ,Resistance ,HCV genotypes ,Drug Resistance ,Hepacivirus ,Biology ,medicine.disease_cause ,Antiviral Agents ,Virus ,03 medical and health sciences ,0302 clinical medicine ,Directly Acting Antivirals ,medicine ,Sequencing ,Humans ,Developing Countries ,Subtypes ,Genetic diversity ,Hepatology ,Resistance (ecology) ,Thematic Miniseries on HCV cure ,Virology ,Clinical trial ,030104 developmental biology ,Low and middle income countries ,030211 gastroenterology & hepatology - Abstract
Summary The hepatitis C virus (HCV) is an extremely diverse virus, subtypes of which are distributed variably around the world. Viral genotypes may be divided into epidemic subtypes; those that have become prevalent globally, and endemic subtypes that have a more limited distribution, mainly in Africa and Asia. The high variability of endemic strains reflects evolutionary origins in the locations where they are found. This increased genetic diversity raises the possibility of resistance to pan-genotypic direct-acting antiviral regimens. While many endemic subtypes respond well to direct-acting antiviral therapies, others, for example genotypes 1l, 3b and 4r, do not respond as well as predicted. Many genotypes that are rare in high-income countries but common in other parts of the world have not yet been fully assessed in clinical trials. Further sequencing and clinical studies in sub-Saharan Africa and Asia are indicated to monitor response to treatment and to facilitate the World Health Organization’s 2030 elimination strategy.
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- 2021
9. Risk scores for predicting early antiretroviral therapy mortality in sub-Saharan Africa to inform who needs intensification of care: a derivation and external validation cohort study
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Rosanna Boyd, Yuliang Liu, George Bicego, Peter Ehrenkranz, Alison D. Grant, Sherri L. Pals, Anand Date, Alice Maida, Goabaone Rankgoane-Pono, Ray W. Shiraishi, Tefera Agizew, Heather Alexander, Unami Mathebula, Salome Charalambous, Tedd V. Ellerbrock, Katherine Fielding, Courtney Emerson, James Shepherd, Alyssa Finlay, Christopher Serumola, Anikie Mathoma, Charles Holmes, Pontsho Pono, and Andrew F. Auld
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0301 basic medicine ,Adult ,Male ,medicine.medical_specialty ,Sub saharan ,Human immunodeficiency virus (HIV) ,Clinical scores ,lcsh:Medicine ,HIV Infections ,medicine.disease_cause ,Risk Assessment ,Cohort Studies ,Predictive models ,03 medical and health sciences ,0302 clinical medicine ,Acquired immunodeficiency syndrome (AIDS) ,Risk Factors ,Internal medicine ,Secondary Prevention ,Medicine ,Humans ,030212 general & internal medicine ,Derivation ,Stage (cooking) ,Mortality ,Africa South of the Sahara ,Acquired immuno-deficiency syndrome ,business.industry ,lcsh:R ,External validation ,Reproducibility of Results ,HIV ,General Medicine ,medicine.disease ,Prognosis ,030112 virology ,Antiretroviral therapy ,Anti-Retroviral Agents ,Female ,business ,Cohort study ,Research Article - Abstract
BackgroundClinical scores to determine early (6-month) antiretroviral therapy (ART) mortality risk have not been developed for sub-Saharan Africa (SSA), home to 70% of people living with HIV. In the absence of validated scores, WHO eligibility criteria (EC) for ART care intensification are CD4 MethodsWe used Botswana XPRES trial data for adult ART enrollees to develop CD4-independent and CD4-dependent multivariable prognostic models for 6-month mortality. Scores were derived by rescaling coefficients. Scores were developed using the first 50% of XPRES ART enrollees, and their accuracy validated internally and externally using South African TB Fast Track (TBFT) trial data. Predictive accuracy was compared between scores and WHO EC.ResultsAmong 5553 XPRES enrollees, 2838 were included in the derivation dataset; 68% were female and 83 (3%) died by 6 months. Among 1077 TBFT ART enrollees, 55% were female and 6% died by 6 months. Factors predictive of 6-month mortality in the derivation dataset atp 37.5 °C (2 points). The same variables plus CD4 ConclusionsSensitivity of the CD4-independent score was nearly twice that of WHO stage in predicting 6-month mortality and could be used in settings lacking CD4 testing to inform ART care intensification. The CD4-dependent score improved specificity versus WHO EC. Both scores should be considered for scale-up in SSA.
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- 2020
10. Machine learning for a finite size correction in periodic coupled cluster theory calculations
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James Shepherd, Tina Mihm, and Laura Weiler
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Physics::Atomic and Molecular Clusters ,General Physics and Astronomy ,FOS: Physical sciences ,Physical and Theoretical Chemistry ,Computational Physics (physics.comp-ph) ,Physics - Computational Physics - Abstract
We introduce a straightforward Gaussian process regression (GPR) model for the transition structure factor of metal periodic coupled cluster singles and doubles (CCSD) calculations. This is inspired by the method introduced by Liao and Gr\"uneis for interpolating over the transition structure factor to obtain a finite size correction for CCSD [J. Chem. Phys. 145, 141102 (2016)], and by our own prior work using the transition structure factor to efficiently converge CCSD for metals to the thermodynamic limit [Nat. Comput. Sci. 1, 801 (2021)]. In our CCSD-FS-GPR method to correct for finite size errors, we fit the structure factor to a 1D function in the momentum transfer, $G$. We then integrate over this function by projecting it onto a k-point mesh to obtain comparisons with extrapolated results. Results are shown for lithium, sodium, and the uniform electron gas., Comment: 7 pages, 2 figures
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- 2022
11. Descriptive comparison of admission characteristics between pandemic waves and multivariable analysis of the association of the Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 with disease severity in inner London
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Keith Morris, Judith Breuer, NgeeKeong Tan, Eric Witele, Sophie Hunter, Monica Panca, Aleks Marek, Paul Flowers, Gaia Nebbia, Sam Haldenby, Jacqui Prieto, Gee Yen Shin, Fiona Mapp, Andrew Copas, Mark Hopkins, Oliver Stirrup, Adam Witney, Kenneth Laing, May Rabuya, Vasa Curcin, Alison Holmes, Mohammad Raza, Wenjuan Wang, Rachel Williams, David Robertson, Julie Samuel, Rory Gunson, Helen Wheeler, Alexander J Keeley, Paul Randell, Cariad Evans, Tabassum Khan, Michelle Ramsay, Darren Smith, James Price, Sarah Francis, Shazaad Ahmad, Finola Higgins, Eleni Nastouli, Abhinav Kumar, Katie Johnson, Sharon Glaysher, Scott Elliott, Rebecca Gregory, Matthew D Parker, Helen Umpleby, Emanuela Pelosi, Emma Thomson, Anna Riddell, Yanzhong Wang, David Harrington, Alexandra Bailey, Nikunj Mahida, Charlotte Williams, Tanzina Haque, David G Partridge, Yusri Taha, Adrienn Angyal, Catherine Houlihan, James Shepherd, Hayley Colton, Chris Davis, Adela Alcolea-Medina, Themoula Charalampous, Beatrix Kele, Irene Monahan, Guy Mollett, Sunando Roy, Joshua Taylor, Sophie Weller, Eleri Wilson-Davies, Joseph Hughes, Tabitha Mahungu, Cassie Pope, Samuel Robson, Kordo Saeed, Luke Snell, James Blackstone, Leanne Hockey, Georgia Marley, Christine Peters, Flavia Flaviani, Bindi Patel, Rahul Batra, Jennifer Hart, Nadua Bayzid, Marius Cotic, Luke Green, Amy State, Alison Cope, Peijun Zhang, Max Whiteley, Marta Gallis Ramalho, Stella Christou, Paige Wolverson, Joe Heffer, Nikki Smith, Salman Goudarzi, Kate Cook, Katie Loveson, Buddhini Samaraweera, Stephen Aplin, Sarah Jeremiah, Matthew Harvey, Thea Sass, Dan Frampton, Matt Byott, Judith Heaney, Ana da Silva Filipe, Thushan de Silva, Jonathan Edgeworth, Luke B Snell, Leonardo de Jongh, Teresa Cutino-Moguel, Raghavendran Kulasegaran-Shylini, Claire E. Broad, Dola Owoyemi, Clare Coffey, Martina Cummins, Tyrra D’Souza, Emily Goldstein, Emilie Shepherd, Katherine Smollett, Alice Broos, Stephen Carmichael, Nicholas Suarez, Sreenu Vattipally, Ioulia Tsatsani, Jacqueline McTaggart, Stephanie McEnhill, Adela Medina, Jörg Saßmannshausen, Sulekha Gurung, Anu Augustine, Sid Mookerjee, Krystal Johnson, Thilipan Thaventhiran, Damien Mine, Isa Ahmad, Anitha Ramanathan, Anu Chawla, Alistair Derby, Becky Taylor, Charles Numbere, Jenifer Mason, Nicholas Machin, Julie Cawthorne, Ryan George, James Montgomery, Deborah McKew, Angela Cobb, Maria Leader, Shirelle Burton-Fanning, Lydia Taylor, Matthew Bashton, Matthew Crown, Matthew Loose, Patrick McClure, Mitch Clarke, Elaine Baxter, Carl Yates, Irfan Aslam, Vicki Fleming, Michelle Lister, Johnny Debebe, Nadine Holmes, Christopher Moore, Matt Carlile, Dianne Irish-Tavares, Mia De Mesa, Vicky Pang, Jelena Heaphy, Wendy Chatterton, Monika Pusok, Tranprit Saluja, Zahira Maqsood, Angie Williams, Debbie Devonport, Lucy Palinkas, Diane Thomlinson, Julie Booth, Ashok Dadrah, Amanda Symonds, Cassandra Craig, Benjamin B Lindsey, Benjamin H Foulkes, Stavroula F Louka, Phillip Ravencroft, Sharon Hsu, Nasar Ali, Rasha Raghei, Samantha E Hansford, Hailey R Hornsby, Phil Wade, Kay Cawthron, Maqsood Khan, Amber Ford, Imogen Wilson, Kate Harrington, Nic Tinker, Sally Nyinza, Adhyana Mahanama, Siona Silviera, Christopher Fearn, Claudia Cardosa Pereira, Vaz Malik, Gema Martinez-Garcia, Leila Hail, Ndifreke Atang, Helen Francis, Milica Rajkov, Rachel McComish, Alyson MacNeil, Alif Tamuri, Stefan Piatek, Snell, Luke B [0000-0002-6263-9497], Wang, Wenjuan [0000-0002-1879-7332], Charalampous, Themoula [0000-0002-8914-5868], Nebbia, Gaia [0000-0002-7524-1947], Wang, Yanzhong [0000-0002-0768-1676], and Apollo - University of Cambridge Repository
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SARS-CoV-2 ,public health ,B100 ,COVID-19 ,General Medicine ,A300 ,Severity of Illness Index ,virology ,B900 ,London ,Medicine ,Humans ,RNA, Viral ,epidemiology ,Pandemics - Abstract
BackgroundThe Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 emerged and became the dominant circulating variant in the UK in late 2020. Current literature is unclear on whether the Alpha variant is associated with increased severity. We linked clinical data with viral genome sequence data to compare admitted cases between SARS-CoV-2 waves in London and to investigate the association between the Alpha variant and the severity of disease.MethodsClinical, demographic, laboratory and viral sequence data from electronic health record systems were collected for all cases with a positive SARS-CoV-2 RNA test between 13 March 2020 and 17 February 2021 in a multisite London healthcare institution. Multivariate analysis using logistic regression assessed risk factors for severity as defined by hypoxia at admission.ResultsThere were 5810 SARS-CoV-2 RNA-positive cases of which 2341 were admitted (838 in wave 1 and 1503 in wave 2). Both waves had a temporally aligned rise in nosocomial cases (96 in wave 1 and 137 in wave 2). The Alpha variant was first identified on 15 November 2020 and increased rapidly to comprise 400/472 (85%) of sequenced isolates from admitted cases in wave 2. A multivariate analysis identified risk factors for severity on admission, such as age (OR 1.02, 95% CI 1.01 to 1.03, for every year older; pConclusionsOur analysis is the first in hospitalised cohorts to show increased severity of disease associated with the Alpha variant. The number of nosocomial cases was similar in both waves despite the introduction of many infection control interventions before wave 2.
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- 2022
12. Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study
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Harry D Wilson, Elaine O'Toole, Andrew Bassett, Moritz U. G. Kraemer, Beth Blane, Scott Goodwin, Giri Shankar, Joseph Hughes, Lucy R. Frost, Alicia Thornton, Scott Elliott, Tammy V Merrill, Sheila Waugh, Alexander Adams, Peter Muir, Graciela Sluga, Rebecca Williams, Hannah Dent, Christophe Fraser, Shavanthi Rajatileka, John C. Hartley, Luke B Snell, Benjamin J Cogger, Lance Turtle, Alex Makunin, John A. Todd, Victoria Wright, Daniela De Angelis, James McKenna, Dinesh Aggarwal, Jonathan K. Ball, Jillian Durham, Garren Scott, Thushan I de Silva, Veena Raviprakash, Hannah M Pymont, Jason Coombes, Anita Lucaci, Luke R. Green, Leigh M Jackson, Hermione J. Webster, Louis du Plessis, David A. Jackson, Minal Patel, Áine O'Toole, Ravi Gupta, Marc Niebel, Garry Scarlett, Rajiv Shah, Guy Mollett, Kathy Li, Rory Gunson, Matthew Bashton, Carl Jones, Sara Kumziene-Summerhayes, Zoltan Molnar, Siona Silveira, Malte L Pinckert, Catherine Ludden, Angeliki Karamani, Leanne Kane, Brendan A I Payne, Alan McNally, Clare M. McCann, Holli Carden, Mohammad Raza, Alison E. Mather, Kate B. Cook, Amy Gaskin, David J. Williams, Shaun R. Seaman, Christopher I. Jones, Gilberto Betancor, Matthew T. G. Holden, Jennifier Liddle, Meera Unnikrishnan, Angie Green, Ben Taylor, Kelly Bicknell, Alexander J. Trotter, Emma Meader, Leanne M Kermack, Nathaniel Storey, Michelle Cronin, Sally Forrest, Sarah Jeremiah, Asad Zaidi, M Morgan, Alasdair MacLean, Thomas R. Connor, Johnathan M Evans, Rachael Stanley, Ryan P George, Nadine Holmes, Richard H. Myers, Christine Sambles, Bernardo Gutierrez, Jeffrey K. J. Cheng, Tim Wyatt, Natasha Jesudason, Lindsay Coupland, Monika Pusok, Manon Ragonnet-Cronin, Jenifer Mason, Joshua Maksimovic, Russell Hope, Alison Holmes, David Simpson, Radoslaw Poplawski, Amelia Joseph, Erwan Acheson, James Bonfield, Mara K. N. Lawniczak, Sascha Ott, Lesley-Anne Williams, Jessica Lynch, Graham P. Taylor, Anita Kenyon, Elizabeth Wastenge, Megan Mayhew, Adhyana I K Mahanama, Stavroula F Louka, Chloe Bishop, Esther Robinson, Darren Smith, Anne M. Presanis, Matthew Carlile, Thomas D Stanton, Dennis Wang, Katerina Galai, Adam P Westhorpe, Flavia Flaviani, Michelle Wantoch, Max Whiteley, Yann Bourgeois, Matthew Gemmell, Mary Ramsay, A Lloyd, Simon Thelwall, Hannah C. Howson-Wells, Joseph G. Chappell, Steve Paterson, Gary Eltringham, Robert Impey, Siddharth Mookerjee, Steven Platt, Emma Swindells, Laura Letchford, Alex Alderton, Lee Graham, Safiah Afifi, David C. Lee, Cassie Breen, Melisa Louise Fenton, Benita Percival, Adrian W Signell, Tanya Golubchik, Ian B Vipond, Eleri Wilson-Davies, Angie Lackenby, Laura Atkinson, Sarojini Pandey, Nazreen F. Hadjirin, Michael A Chapman, Huw Gulliver, Joana Dias, Grant Hall, Antony D Hale, Hassan Hartman, Alp Aydin, Louise Smith, Ashok Dadrah, Johnny Debebe, Sarah Walsh, Stephanie W. Lo, Andrew Bosworth, Bridget Knight, Hannah E Bridgewater, Nadua Bayzid, Gemma L. Kay, Richard Gregory, Sally Kay, Ellena Brooks, Andre Charlett, Georgina M McManus, Riaz Jannoo, Victoria Blakey, Carol Scott, Rachel Nelson, Liz Ratcliffe, Gerry Tonkin-Hill, Verity Hill, Joanne D. Stockton, Danielle Leek, Steven Leonard, Stephanie Hutchings, Jonathan D. Moore, Kathryn Ann Harris, Sophie Jones, Venkat Sivaprakasam, Amy Plimmer, Tanzina Haque, Katherine L. Bellis, Khalil Abudahab, Dianne Irish-Tavares, Gaia Nebbia, Kathryn A Jackson, Stephen W Attwood, Daniel Mair, Sreenu Vattipally, Susanne Stonehouse, Ian Merrick, Lucille Rainbow, Mathew A. Beale, Angela Helen Beckett, Ember Hilvers, Thomas Helmer, Jenna Nichols, Giselda Bucca, Salman Goudarzi, Christopher Ruis, Surendra Parmar, Angela Cowell, Alberto C Cerda, Divya K. Shah, Judith Heaney, E. Thomson, Kyriaki Nomikou, Nicole Pacchiarini, Katherine L Harper, Fatima Downing, M. Estée Török, Michelle L Michelsen, Aaron R. Jeffries, Jennifer Collins, Christopher Williams, Katie F. Loveson, Steven Rudder, Theocharis Tsoleridis, Robert Davies, David Robertson, Katherine Smollett, Kathryn McCluggage, Liam Crawford, Inigo Martincorena, Charlotte Beaver, Oliver Megram, Karla Spellman, Sam Haldenby, Emma Betteridge, William D. Fuller, Will P. M. Rowe, Cherian Koshy, Tim E. A. Peto, Alison Cox, Natasha Johnson, Tanya Curran, Sharif Shaaban, Tamyo Mbisa, Cordelia Langford, Eric Witele, Andrew J. Page, Christoph Puethe, Nicola Reynolds, Paul W Bird, Louise Aigrain, Ronan Lyons, Amy Trebes, Sally Corden, Steven Rushton, Jack Cd Lee, Jane Greenaway, Hibo Asad, Amanda Bradley, Mohammed O Hassan-Ibrahim, Shane McCarthy, Fei Sang, Matthew Loose, Hannah Jones, Keith D. James, Chloe L Fisher, Chrystala Constantinidou, Alex G. Richter, Jane A. H. Masoli, Michael Gallagher, Vicki M. Fleming, Anna Price, Amy Ash, Michaela John, Alex Zarebski, Fenella D. Halstead, John Danesh, Christine Kitchen, Aminu S Jahun, Mark Whitehead, Julianne R Brown, Catherine Bresner, Marius Cotic, Stefanie V Lensing, Nick Levene, Louissa R Macfarlane-Smith, Wendy Hogsden, Cressida Auckland, Eleanor Drury, Richard Eccles, Jennifer Hart, Seema Nickbakhsh, Alisha Davies, David M. Aanensen, Shirelle Burton-Fanning, Ben Farr, Buddhini Samaraweera, Sarah Wyllie, Hannah Lowe, Richard J. Orton, Martin D. Curran, Carol Churcher, Karen Oliver, Elihu Aranday-Cortes, Wen Yew, Thanh Le-Viet, Matthew Parker, Katherine A Twohig, Shahjahan Miah, Samuel M. Nicholls, G MacIntyre-Cockett, Tranprit Saluja, Charlotte Nelson, Vicki Chalker, Roberto Amato, Ellen Higginson, Timothy M. Freeman, Christopher W Holmes, Yasmin Chaudhry, Elias Allara, Alec Birchley, Iraad Bronner, Emma Moles-Garcia, Angus I. Best, Anna L. Casey, Audrey Farbos, Nicholas W Machin, David W Eyre, Tim Boswell, Charlotte A Williams, Elen De Lacy, Matthew J. Bull, Matilde Mori, Carmen F. Manso, Peijun Zhang, Sahar Eldirdiri, Dimitris Grammatopoulos, Corin Yeats, Claudia Wierzbicki, David G Partridge, Kordo Saeed, Nichola Duckworth, David J. Studholme, Harmeet K Gill, Juan Ledesma, Thomas R. A. Davis, Sushmita Sridhar, Clive Graham, Husam Osman, Julian A. Hiscox, Helen Adams, Christopher Fearn, Fabrícia F. Nascimento, Ulf Schaefer, James W. Harrison, Andrew J. Nelson, Joshua Quick, Mohammad Tauqeer Alam, Liam Prestwood, Nikos Manesis, Julian Tang, Justin O'Grady, Sophia T Girgis, Louise Berry, Gemma Clark, Marina Escalera Zamudio, Karlie Fallon, Tim J Sloan, Joanne Watkins, Clare Pearson, Andrew D Beggs, Rachel Williams, Luke Bedford, Trevor Robinson, Nicholas M Redshaw, Richard Hopes, Mirko Menegazzo, Katherine Twohig, Gabrielle Vernet, Steven Liggett, Mariateresa de Cesare, Derrick W. Crook, Dominic P. Kwiatkowski, Mark Kristiansen, Miren Iturriza-Gomara, Christopher I. Moore, Claire Cormie, Olivia Boyd, Nikki Smith, Noel Craine, Kathleen A. Williamson, John Boyes, Sian Ellard, Cristina V. Ariani, Wendy Chatterton, David Bonsall, Kevin Lewis, David Jorgensen, Ian Harrison, Christopher Jackson, Martin P McHugh, Danni Weldon, Michael A. Quail, Amita Patel, Lily Geidelberg, Myra Hosmillo, Judith Breuer, Cariad Evans, Edward Barton, Trudy Workman, Derek Fairley, Vineet Patel, Daniel Bradshaw, Robin Manley, Scott Aj Thurston, John Sillitoe, Monique Andersson, Sharon J. Peacock, Jamie Lopez-Bernal, Thomas Thompson, Nabil-Fareed Alikhan, Ben Temperton, Paul Baker, Robin J Moll, Laura Gifford, Nicholas J. Loman, Jayna Raghwani, Jacqui Prieto, Andrew Hesketh, Oliver G. Pybus, Adela Alcolea-Medina, David Buck, Gregory R Young, Alistair C. Darby, Sónia Gonçalves, Aileen G. Rowan, Tabitha Mahungu, Nicholas Ellaby, Jon-Paul Keatley, Lily Tong, Robert Beer, Martyn Guest, Lisa J Levett, Ali R Awan, Iliana Georgana, Paul E Brown, Li Xu-McCrae, Stephen P. Kidd, Sara Rey, Shazaad Ahmad, Danielle C. Groves, Tetyana I. Vasylyeva, David F. Bibby, Nathan Moore, Fiona Ashcroft, Igor Starinskij, Hannah Paul, Claire McMurray, Michael Spencer Chapman, Carlos Balcazar, Joanna Warwick-Dugdale, Pinglawathee Madona, Edith Vamos, Lesley Shirley, Kate Templeton, Luke Foulser, Igor Siveroni, Ewan M. Harrison, Sian Morgan, Diana Rajan, S Taylor, Laia Fina, Naomi Park, Sarah J. O'Brien, Alessandro M Carabelli, Angela Marchbank, Sunando Roy, Leonardo de Oliveira Martins, Steve Palmer, Jonathan Hubb, Alexander J Keeley, Francesc Coll, Malorie Perry, Paul J. Parsons, Anthony Underwood, Patawee Asamaphan, William L Hamilton, Tommy Nyberg, Sophie Palmer, Amanda Symmonds, Anoop Chauhan, Robert Johnson, Christopher J. R. Illingworth, James Shepherd, Wendy Smith, Rich Livett, Rachel Blacow, Margaret Hughes, Jeremy Mirza, Joanne Watts, Jonathan D. Edgeworth, Sarah François, Sue Edwards, Adrienn Angyal, Thomas N. Williams, Marta Gallis, Lauren Gilbert, Paul Randell, Kate Johnson, Eileen Gallagher, Nick Cortes, Yusri Taha, Leah Ensell, Emanuela Pelosi, Stefan Rooke, Michelle Lister, Ana da Silva Filipe, Cassandra S Malone, Themoula Charalampous, Benjamin B Lindsey, Natalie Groves, Colin Smith, Ross J Harris, Rebekah E Wilson, Stephen Bonner, Richard Stark, Sharon Campbell, Nicola Sheriff, Helen L Lowe, Rachel Jones, Ben Warne, Rose K Davidson, Declan Bradley, Ian Johnston, Jeffrey C. Barrett, Joshua B Singer, Shirin Aliabadi, Andrew Whitwham, Patrick McClure, Samuel Robson, Sharon Glaysher, Robert J. Munn, Emma L. Wise, Laura Baxter, Kim S Smith, Catherine Moore, Bree Gatica-Wilcox, Alice Broos, Sarah Essex, David Baker, Manjinder Khakh, Dorota Jamrozy, Rachel Tucker, Ian Goodfellow, S.E. Moses, Nicola Cumley, Robin Howe, Meera Chand, James I. Price, Marina Gourtovaia, Debra Padgett, Jaime Tovar-Corona, Stephen L. Michell, Matthew J. Dorman, Lizzie Meadows, David Heyburn, Iona Willingham, Rocio Martinez Nunez, Grace Taylor-Joyce, Claire M Bewshea, Anita Justice, Simon Cottrell, Rebecca C H Brown, Jamie Young, Gavin Dabrera, Matthew Wyles, Stephen Carmichael, Lisa Berry, Frances Bolt, Andrew Rambaut, Samir Dervisevic, Erik M. Volz, Rahul Batra, Caoimhe McKerr, Samantha McGuigan, Katie Jones, Mailis Maes, Rebecca Dewar, Mary Sinnathamby, Joel Southgate, and Lynn Monaghan
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medicine.medical_specialty ,business.industry ,Proportional hazards model ,Public health ,Hazard ratio ,Attendance ,C500 ,Vaccination ,Infectious Diseases ,Relative risk ,Internal medicine ,Cohort ,medicine ,business ,Cohort study - Abstract
Background: \ud The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes.\ud \ud Methods: \ud This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status.\ud \ud Findings: \ud Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low.\ud \ud Interpretation: \ud This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant.\ud \ud Funding: \ud Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research.
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- 2022
13. DIY Fraud Investigation and Access to Justice: A Case Study
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David William James Shepherd
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Political science ,050901 criminology ,0502 economics and business ,05 social sciences ,Justice (ethics) ,0509 other social sciences ,Criminology ,Law ,050203 business & management - Abstract
Access to justice for fraud victims remains an enduring problem in the UK. Law enforcement agencies have limited capacity and capabilities for delivering criminal justice. Civil justice is so expensive that it is only an option for those with deep pockets or lucky enough to find competent professionals who are willing to work under a conditional fee arrangement (no-win-no-fee). This article describes the progress of a fraud case from a victim’s perspective through both the criminal and civil justice systems in the UK. The experiences describe incompetence in law enforcement, dishonesty and incompetence amongst lawyers and other professionals, and fractured, self-centred justice systems that poorly serve the public in England and Wales.
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- 2020
14. Effect of tuberculosis screening and retention interventions on early antiretroviral therapy mortality in Botswana: a stepped-wedge cluster randomized trial
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Alison D. Grant, Anikie Mathoma, Tefera Agizew, Rosanna Boyd, Tedd V. Ellerbrock, Anand Date, Alyssa Finlay, Heather Alexander, Andrew F. Auld, Sherri L. Pals, Goabaone Rankgoane-Pono, Pontsho Pono, James Shepherd, Katherine Fielding, Christopher Serumola, and Unami Mathebula
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Adult ,Male ,0301 basic medicine ,medicine.medical_specialty ,Tuberculosis ,Xpert MTB/RIF ,Psychological intervention ,lcsh:Medicine ,Tuberculosis screening ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,medicine ,Humans ,Mass Screening ,Stepped wedge ,Prospective Studies ,030212 general & internal medicine ,Cluster randomised controlled trial ,Mortality ,Botswana ,business.industry ,Hazard ratio ,lcsh:R ,Mycobacterium tuberculosis ,General Medicine ,medicine.disease ,Survival Analysis ,030112 virology ,Antiretroviral therapy ,Confidence interval ,Anti-Retroviral Agents ,Intensified tuberculosis case finding ,Female ,business ,Research Article - Abstract
Background Undiagnosed tuberculosis (TB) remains the most common cause of HIV-related mortality. Xpert MTB/RIF (Xpert) is being rolled out globally to improve TB diagnostic capacity. However, previous Xpert impact trials have reported that health system weaknesses blunted impact of this improved diagnostic tool. During phased Xpert rollout in Botswana, we evaluated the impact of a package of interventions comprising (1) additional support for intensified TB case finding (ICF), (2) active tracing for patients missing clinic appointments to support retention, and (3) Xpert replacing sputum-smear microscopy, on early (6-month) antiretroviral therapy (ART) mortality. Methods At 22 clinics, ART enrollees > 12 years old were eligible for inclusion in three phases: a retrospective standard of care (SOC), prospective enhanced care (EC), and prospective EC plus Xpert (EC+X) phase. EC and EC+X phases were implemented as a stepped-wedge trial. Participants in the EC phase received SOC plus components 1 (strengthened ICF) and 2 (active tracing) of the intervention package, and participants in the EC+X phase received SOC plus all three intervention package components. Primary and secondary objectives were to compare all-cause 6-month ART mortality between SOC and EC+X and between EC and EC+X phases, respectively. We used adjusted analyses, appropriate for study design, to control for baseline differences in individual-level factors and intra-facility correlation. Results We enrolled 14,963 eligible patients: 8980 in SOC, 1768 in EC, and 4215 in EC+X phases. Median age of ART enrollees was 35 and 64% were female. Median CD4 cell count was lower in SOC than subsequent phases (184/μL in SOC, 246/μL in EC, and 241/μL in EC+X). By 6 months of ART, 461 (5.3%) of SOC, 54 (3.2%) of EC, and 121 (3.0%) of EC+X enrollees had died. Compared with SOC, 6-month mortality was lower in the EC+X phase (adjusted hazard ratio, 0.77; 95% confidence interval, 0.61–0.97, p = 0.029). Compared with EC enrollees, 6-month mortality was similar among EC+X enrollees. Conclusions Interventions to strengthen ICF and retention were associated with lower early ART mortality. This new evidence highlights the need to strengthen ICF and retention in many similar settings. Similar to other trials, no additional mortality benefit of replacing sputum-smear microscopy with Xpert was observed. Trial registration Retrospectively registered: ClinicalTrials.gov (NCT02538952)
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- 2020
15. The media, personal digital criminal legacies and the experience of offenders convicted of occupational fraud and corruption
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Mark Button, Dean Blackbourn, Emma Beatty, and David William James Shepherd
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Coping (psychology) ,Health (social science) ,Public Administration ,Sociology and Political Science ,Social Psychology ,Digital era ,media_common.quotation_subject ,medicine.medical_treatment ,corruption ,050801 communication & media studies ,Prison ,Criminology ,Health(social science) ,Newspaper ,0508 media and communications ,Political science ,medicine ,offenders ,media_common ,Rehabilitation ,business.industry ,050901 criminology ,05 social sciences ,Public sector ,media impact ,resettlement ,White-collar crime ,white-collar crime ,Content analysis ,fraud ,0509 other social sciences ,business ,Law - Abstract
Purpose The purpose of this paper is to explore the impact of media coverage on offenders convicted of occupational fraud and corruption in the UK. It examines the extent of media coverage and provides insights into the experiences of offenders. Design/methodology/approach The study is based upon interviews with 17 convicted offenders, and on a content analysis of one national and two regional newspapers in the UK. Findings The findings suggest that offenders convicted of occupational crime and corruption are more likely to experience media coverage than previously assumed and that personal digital criminal legacies create long-term labels which lead to economic strains and social fractures that hinder productive reintegration into society. Research limitations/implications The research is limited by a small sample frame in the UK. Nevertheless, the findings suggest further research is required as they have important implications for privacy and rehabilitation. Practical implications In particular, offenders and their families need support in dealing with their personal digital criminal legacies, accessing their privacy rights and coping with the strains created by online stigmatisation. From a policy perspective, the existing regulatory framework that supports rehabilitation in the UK, especially the increasingly archaic Rehabilitation of Offenders Act 1974, requires close examination and debate to ensure it is fit for the digital era. The findings also suggest that policies, practices and responsibilities of the public sector in employing offenders need to be examined. Originality/value It is a rare study of white-collar offenders after their release from prison. The findings are of relevance to criminal justice policy makers, rehabilitation services and academics.
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- 2019
16. Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant
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Mohammad Raza, Alison E. Mather, Gilberto Betancor, Ian Merrick, Ben Taylor, Mathew A. Beale, Helen Ward, Samir Dervisevic, Michelle Cronin, Aaron R. Jeffries, Louise Smith, Steven Rudder, Mara K. N. Lawniczak, Sascha Ott, Ashok Dadrah, Luke Bedford, Gabrielle Vernet, Erik M. Volz, Rahul Batra, Johnny Debebe, Caoimhe McKerr, Samantha McGuigan, Oliver Megram, Katie Jones, Mailis Maes, Rebecca Dewar, Emma Swindells, Robert E. Johnson, Myra Hosmillo, Wen C Yew, Vineet Patel, Scott Aj Thurston, Matthew Bashton, Luke B Snell, Lynn Monaghan, David Buck, Gregory R Young, Garren Scott, Louis du Plessis, Sara Kumziene-Summerhayes, David M. Aanensen, Carl Jones, Nadine Holmes, Bernardo Gutierrez, Elizabeth Wastenge, Stavroula F Louka, Dennis Wang, Richard I. Gregory, M. Estée Török, Alistair C. Darby, Ulf Schaefer, Marc Niebel, David Robertson, E. Thomson, Carol Churcher, Patrick C McClure, Scott Elliott, Sarah Jeremiah, Katerina Galai, Matthew W. Loose, Megan Mayhew, Adhyana I K Mahanama, Angeliki Karamani, Naomi R Park, David J. Williams, Lance Turtle, Lucy R. Frost, Alicia Thornton, Jennifier Liddle, M Morgan, Tim Wyatt, Paul W Bird, Chloe Bishop, Esther Robinson, Alasdair MacLean, Inigo Martincorena, Bridget A. Knight, Emma Meader, Thomas R. Connor, Hermione J. Webster, Peter Muir, Sarah Walsh, Stephanie W. Lo, Andrew Bosworth, Hannah E Bridgewater, David Simpson, Radoslaw Poplawski, Angus I. Best, David Baker, Laura Letchford, Cassie Breen, Yann Bourgeois, Matthew Gemmell, Nikki Smith, Alison Holmes, Iliana Georgana, Christophe Fraser, Natasha Jesudason, Johnathan M Evans, Rachael Stanley, Lesley-Anne Williams, Jessica Lynch, Hannah Lowe, Eleri Wilson-Davies, Paul A. Baker, Alex Makunin, James Bonfield, Helen Adams, Christopher Fearn, Peter J. Diggle, Harry D Wilson, Carmen F. Manso, Nichola Duckworth, D Haw, Anna L. Casey, Audrey Farbos, Sam Haldenby, Vicki Chalker, Roberto Amato, Elen De Lacy, Ben Farr, Eric Witele, Buddhini Samaraweera, G MacIntyre-Cockett, Husam Osman, Jane Greenaway, Justin O'Grady, Sally Forrest, Andrew Nelson, Monika Pusok, A Lloyd, Edward Barton, James W. Harrison, Sophie Palmer, Amanda Symmonds, James Shepherd, Nazreen F. Hadjirin, Stephen L. Michell, Mohammed O Hassan-Ibrahim, Fiona Ashcroft, Daniel Mair, Richard H. Myers, Dianne Irish-Tavares, Hannah C. Howson-Wells, Jacqui Prieto, Christine Sambles, Andrew Hesketh, Alp Aydin, Sónia Gonçalves, Tabitha Mahungu, Tanzina Haque, Nicholas Ellaby, Karen Oliver, Hannah Paul, Joanne Watts, Claire McMurray, Lisa J Levett, Darren Smith, Simon Cottrell, Joanna Warwick-Dugdale, Pinglawathee Madona, Matthew J. Dorman, Lizzie Meadows, Ali R Awan, Leanne M Kermack, Jennifer Hart, Angie Lackenby, Carol Scott, Michael Spencer Chapman, Lucille Rainbow, Kyriaki Nomikou, Julianne R Brown, Juan Ledesma, Adam P Westhorpe, Giri Shankar, Karlie Fallon, Tim J Sloan, Joanne Watkins, Robert Impey, Sue Edwards, Rebecca C H Brown, Robin J Moll, Karla Spellman, Laura Gifford, Jamie Young, Adrienn Angyal, Graham Phillip Taylor, Robin Manley, Gavin Dabrera, Michelle Wantoch, Rachel Williams, David Heyburn, Mirko Menegazzo, Derrick W. Crook, Gaia Nebbia, Rachel Nelson, Elaine O'Toole, Luke Foulser, Katherine L Harper, Fatima Downing, Hassan Hartman, Nathan Moore, Gemma L. Kay, Matthew Wyles, Thanh Le-Viet, Edith Vamos, John Sillitoe, Lesley Shirley, Nicholas J. Loman, Iona Willingham, Elihu Aranday-Cortes, Ian B Vipond, Jeremy Mirza, Alberto C Cerda, Michelle L Michelsen, Steven Riley, Alison Cox, Igor Siveroni, Nadua Bayzid, Shavanthi Rajatileka, Giselda Bucca, Benjamin J Cogger, Tim Boswell, Matthew J. Bull, Stephen Carmichael, Lisa Berry, Frances Bolt, Kylie E. C. Ainslie, Martyn Guest, Sarojini Pandey, Katherine L. Bellis, Shane A. McCarthy, Christopher Ruis, Fei Sang, David Bonsall, Danni Weldon, Alex Alderton, Lee Graham, Amy Trebes, Sally Corden, Adrian W Signell, Tanya Golubchik, Huw Gulliver, Rocio Martinez Nunez, Dinesh Aggarwal, Tanya Curran, Jonathan K. Ball, Sharif Shaaban, Paul Randell, Jillian Durham, Alec Birchley, Matilde Mori, Joana Dias, Katherine A Twohig, Grant Hall, Antony D Hale, Alan McNally, Jonathan D. Edgeworth, Safiah Afifi, Andrew Rambaut, Katherine Smollett, David N. Lee, Tamyo Mbisa, Shahjahan Miah, Steven Rushton, Grace Taylor-Joyce, Hannah M Pymont, Chloe L Fisher, Cordelia Langford, Alex G. Richter, Jane A. H. Masoli, Michael Gallagher, Vicki M. Fleming, Kathleen A. Williamson, Anna Price, Holli Carden, Khalil Abudahab, Joanne D. Stockton, Meera Unnikrishnan, Jennifer Collins, Emma Moles-Garcia, Michaela John, Christine Kitchen, Tranprit Saluja, Ian Harrison, Lily Tong, Thomas G. Thompson, Thomas Helmer, Amita Patel, Siona Silveira, Deborah Ashby, Claire M Bewshea, Anita Justice, Brendan A I Payne, Alexander J. Trotter, Nikos Manesis, Katie F. Loveson, Cristina V. Ariani, Wendy Chatterton, Robert J. Munn, Julian A. Hiscox, Robert Beer, Judith Breuer, Caroline E. Walters, Liam Crawford, Ara Darzi, Will P. M. Rowe, Cariad Evans, Matthew Parker, Tammy V Merrill, Louise Aigrain, Joshua Quick, Leigh M Jackson, Samuel M. Nicholls, Jonathan W. Moore, John A Hartley, Graham P. Taylor, Cherian Koshy, Shirelle Burton-Fanning, Sheila Waugh, Catherine Moore, Danielle C. Groves, Peijun Zhang, Sahar Eldirdiri, Derek Fairley, Tim E. A. Peto, Jack Cd Lee, Sharon Glaysher, Liam Prestwood, Hannah Dent, Anita Kenyon, Stephen P. Kidd, Nick Levene, Igor Starinskij, Joseph G. Chappell, Steve Paterson, Gary Eltringham, Laia Fina, Angela Marchbank, Daniel Bradshaw, Marina Escalera Zamudio, Scott Goodwin, Andrew D Beggs, Seema Nickbakhsh, Trevor Robinson, Christina Atchison, David K. Jackson, Kathy Li, Rory Gunson, Sunando Roy, Graham S Cooke, Steven Liggett, Yasmin Chaudhry, Anoop Chauhan, Ben Temperton, Mariateresa de Cesare, Paul E Brown, Li Xu-McCrae, Martin P McHugh, Catherine Ludden, Wendy Smith, Danielle Leek, Divya K. Shah, Judith Heaney, Dominic P. Kwiatkowski, Kate M. Johnson, Robin Howe, Malorie Perry, Tetyana I. Vasylyeva, David F. Bibby, Haowei Wang, Steve Palmer, Nicholas W Machin, Charlotte A Williams, Bree Gatica-Wilcox, Angie Green, John A. Todd, Paul Elliott, Noel Craine, Jeffrey K. J. Cheng, Kate Templeton, Jonathan Hubb, Joshua Maksimovic, Christl A. Donnelly, Monique Andersson, Christopher Holmes, Dimitris Grammatopoulos, Christopher B. Williams, David G Partridge, Aminu S Jahun, Alexander Adams, Marius Cotic, Sarah Essex, Christopher J. Moore, Trudy Workman, Nicola Sheriff, Helen L Lowe, Ewan M. Harrison, Dorota Jamrozy, Rachel Jones, Ellen Higginson, Erwan Acheson, Christopher R. Jones, Oliver G. Pybus, Francesc Coll, Sian Morgan, Paul J. Parsons, Patawee Asamaphan, Veena Raviprakash, Andrew R. Bassett, Declan Bradley, Laura Atkinson, Anthony Underwood, Graciela Sluga, Sally Kay, Ellena Brooks, Oliver Eales, Andrew Whitwham, Surendra Parmar, Angela Cowell, Nicole Pacchiarini, Theocharis Tsoleridis, Jason Coombes, Robert Davies, Flavia Flaviani, Benita Percival, Jenna Nichols, Natasha M. Johnson, Salman Goudarzi, Hibo Asad, Amanda Bradley, Hannah Jones, Chrystala Constantinidou, Georgina M McManus, Minal Patel, Steven Leonard, Rebecca Williams Bmbs, Andrew J. Page, Christoph Puethe, Nicola Reynolds, Amy Ash, John Danesh, Corin Yeats, Claudia Wierzbicki, Kordo Saeed, John Boyes, Michael A. Quail, Sharon J. Peacock, Nabil-Fareed Alikhan, Jon-Paul Keatley, Claudio Fronterre, Garry Scarlett, James McKenna, Thushan I de Silva, Malte L Pinckert, Kate B. Cook, Amy Gaskin, Rajiv Shah, Matthew T. G. Holden, Sophie J Prosolek, Nathaniel Storey, Ryan P George, Lindsay Coupland, Jenifer Mason, Matthew Carlile, Thomas D Stanton, Guy Mollett, Siddharth Mookerjee, Mary Ramsay, Steven Platt, Stephen W Attwood, Susanne Stonehouse, Sophie Jones, Venkat Sivaprakasam, Amy Plimmer, Mark Whitehead, Catherine Bresner, Stefanie V Lensing, Louissa R Macfarlane-Smith, Colin P. Smith, Wendy Hogsden, Charlotte Nelson, Ian Johnston, Jeffrey C. Barrett, Joshua B Singer, Samuel Robson, Zoltán Molnár, Emma L. Wise, Sian Ellard, Kim S Smith, Alice Broos, Manjinder Khakh, Kathryn A Jackson, Claire Cormie, Rachel Tucker, Ian Goodfellow, S.E. Moses, Nicola Cumley, Meera Chand, Debra Padgett, Cassandra S Malone, James V. Price, Themoula Charalampous, Ronan A Lyons, Natalie Groves, Stefan Rooke, Rebekah E Wilson, Stephen Bonner, Richard Stark, Sharon Campbell, Michelle Lister, Carlos Balcazar, Ana da Silva Filipe, Ben Warne, Thomas N. Williams, Marta Gallis, Lauren Gilbert, Rose K Davidson, Angela Helen Beckett, Ember Hilvers, Kathryn McCluggage, Eileen Gallagher, Charlotte Beaver, Nick Cortes, Alisha Davies, Yusri Taha, Leah Ensell, Emanuela Pelosi, Elias Allara, Cressida Auckland, Eleanor Drury, Richard Eccles, Adela Alcolea-Medina, William L Hamilton, Rich Livett, Rachel Blacow, Margaret Hughes, Sarah François, Melisa Louise Fenton, Liz Ratcliffe, Verity Hill, Stephanie Hutchings, Kathryn Ann Harris, Emma Betteridge, William D. Fuller, Sophia T Girgis, Louise Berry, Gemma Clark, Nicholas M Redshaw, Richard Hopes, Leonardo de Oliveira Martins, Alexander J Keeley, Beth Blane, Wendy S. Barclay, Victoria Wright, Anita Lucaci, Luke R. Green, Fenella D. Halstead, Sarah Wyllie, Iraad F. Bronner, Áine O'Toole, Ravi Gupta, Leanne Kane, Clare M. McCann, Michael R Chapman, David W Eyre, Kelly Bicknell, Aileen G. Rowan, Sara Rey, Shazaad Ahmad, Diana Rajan, S Taylor, Sarah J. O'Brien, Alessandro M Carabelli, Amelia Joseph, Max Whiteley, Riaz Jannoo, Victoria Blakey, Martin D. Curran, David J. Studholme, Harmeet K Gill, Thomas R. A. Davis, Sushmita Sridhar, Clive Graham, Julian Tang, Clare Pearson, Mark Kristiansen, Miren Iturriza-Gomara, National Institute for Health Research, and UK Research and Innovation
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Delta ,Adult ,Male ,2019-20 coronavirus outbreak ,COVID-19 Vaccines ,Vaccination Coverage ,Coronavirus disease 2019 (COVID-19) ,Adolescent ,General Science & Technology ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Vaccine Efficacy ,Biology ,Young Adult ,Exponential growth ,Ethnicity ,Prevalence ,Humans ,Child ,Aged ,Family Characteristics ,Multidisciplinary ,High prevalence ,COVID-19 Genomics UK (COG-UK) Consortium11‡ ,SARS-CoV-2 ,Age Factors ,COVID-19 ,Middle Aged ,Virology ,Hospitalization ,England ,Socioeconomic Factors ,COVID-19 Nucleic Acid Testing ,Child, Preschool ,Female ,Self Report - Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.
- Published
- 2021
17. The SARS-CoV-2 Alpha variant is associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis
- Author
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Alasdair Campbell, David Robertson, Samantha Lycett, John Haughney, Ruth Forrester, James Shepherd, Martin P McHugh, David J Pascall, Sharif Shabaan, Ben Parcell, Katherine Smollett, Rachel M Blacow, Rory Gunson, Guy Mollett, Ludmila Fjodorova, Emily Goldstein, Ana Da Silva Filipe, Noha El Sakka, Naomi Bulteel, Matthew T. G. Holden, Eddie A. James, Chris Davis, Patrick Honour, Joseph Hughes, Sarah Clifford, Tim Lewis, Yusuke Onishi, and Robyn Campbell
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medicine.medical_specialty ,Lineage (genetic) ,business.industry ,Transmission (medicine) ,Internal medicine ,Severity of illness ,Medicine ,Alpha (ethology) ,Clinical severity ,Odds ratio ,Disease ,business ,Viral load - Abstract
Background The B.1.1.7 (Alpha) SARS-CoV-2 variant of concern was associated with increased transmission relative to other variants present at the time of its emergence and several studies have shown an association between the B.1.1.7 lineage infection and increased 28-day mortality. However, to date none have addressed the impact of infection on severity of illness or the need for oxygen or ventilation. Methods In this prospective clinical cohort sub-study of the COG-UK consortium, 1475 samples from hospitalised and community cases collected between the 1st November 2020 and 30th January 2021 were collected. These samples were sequenced in local laboratories and analysed for the presence of B.1.1.7-defining mutations. We prospectively matched sequence data to clinical outcomes as the lineage became dominant in Scotland and modelled the association between B.1.1.7 infection and severe disease using a 4-point scale of maximum severity by 28 days: 1. no support, 2. oxygen, 3. ventilation and 4. death. Additionally, we calculated an estimate of the growth rate of B.1.1.7-associated infections following introduction into Scotland using phylogenetic data. Results B.1.1.7 was responsible for a third wave of SARS-CoV-2 in Scotland, and rapidly replaced the previously dominant second wave lineage B.1.177) due to a significantly higher transmission rate (∼5 fold). Of 1475 patients, 364 were infected with B.1.1.7, 1030 with B.1.177 and 81 with other lineages. Our cumulative generalised linear mixed model analyses found evidence (cumulative odds ratio: 1.40, 95% CI: 1.02, 1.93) of a positive association between increased clinical severity and lineage (B.1.1.7 versus non-B.1.1.7). Viral load was higher in B.1.1.7 samples than in non-B.1.1.7 samples as measured by cycle threshold (Ct) value (mean Ct change: -2.46, 95% CI: -4.22, -0.70). Conclusions The B.1.1.7 lineage was associated with more severe clinical disease in Scottish patients than co-circulating lineages. Funding COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. Funding was also provided by UKRI through the JUNIPER consortium (grant number MR/V038613/1). Sequencing and bioinformatics support was funded by the Medical Research Council (MRC) core award (MC UU 1201412).
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- 2021
18. Author response: Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data
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Aleksandra Marek, Alexander J Keeley, Oliver Stirrup, Thushan I de Silva, Judith Breuer, Joshua B Singer, Matthew Parker, Asif U. Tamuri, Benjamin B Lindsey, Christine Peters, David G Partridge, James Blackstone, E. Thomson, Joseph Hughes, Francesc Coll, and James Shepherd
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medicine.medical_specialty ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Epidemiology ,Sequencing data ,medicine ,business ,Virology - Published
- 2021
19. White Collar Criminals’ Experience of Imprisonment in England and Wales: Revisiting the ‘special Sensitivity’ Debate
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David William James Shepherd, Dean Blackbourn, Mark Button, and Dennis Gough
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White (horse) ,History ,Sociology and Political Science ,Social Psychology ,050901 criminology ,05 social sciences ,Criminology ,Collar ,Clinical Psychology ,0501 psychology and cognitive sciences ,0509 other social sciences ,Imprisonment ,Law ,050104 developmental & child psychology - Abstract
This article explores white collar criminals’ experience of imprisonment in England and Wales. Based upon interviews with 13 convicted offenders after they had completed their imprisonment, it is the first study to date of this kind in England and Wales (all others have been based in prison). It offers a unique impartial insight of prisoners’ experience, beyond the influence of the prison walls. The paper explores the experience around the largely American ‘special sensitivity’ debate, over whether such offenders are more sensitive to prison. The research uncovers both positive experiences, labelled ‘good’, but also negative, labelled ‘bad’ (non-violent experiences) and ‘ugly’ (violent experiences). Overall the findings reveal it is difficult to apply the special sensitivity hypothesis universally to this group of offenders.
- Published
- 2019
20. Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface
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Joseph Hughes, Oliver Stirrup, Alison Taylor, Natasha Johnson, Kathy Li, Rory Gunson, James Shepherd, Josh Singer, Jennifer S Lees, Yasmin A Parr, Judith G Breuer, Aislynn Taggart, Timothy Willem Jones, Y. Mun Woo, David Robertson, Patrick B. Mark, Igor Starinskij, Vattipally B. Sreenu, Marc Niebel, E. Thomson, Elihu Aranday-Cortes, Scott T W Morris, Ana da Silva Filipe, Natasha Jesudason, Daniel Mair, Jamie P. Traynor, Rajiv Shah, Kyriaki Nomikou, Antonia Ho, Zoe Cousland, Kirstyn Brunker, Alasdair MacLean, Colin C. Geddes, Peter C. Thomson, Sarah E. McDonald, Stephen Carmichael, Jonathan Price, Jenna Nichols, Carlos Varon Lopez, Patawee Asamaphan, Lily Tong, Katherine Smollett, Mair, Daniel [0000-0001-7169-9080], Nomikou, Kyriaki [0000-0002-7013-1853], Niebel, Marc [0000-0003-2515-6151], Shah, Rajiv [0000-0002-2827-5108], Jones, Timothy PW [0000-0001-6147-6748], Starinskij, Igor [0000-0001-8585-5929], Mark, Patrick B [0000-0003-3387-2123], and Apollo - University of Cambridge Repository
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medicine.medical_specialty ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Infection control ,Renal Dialysis ,Epidemiology ,medicine ,Humans ,Molecular Epidemiology ,SARS-CoV-2 ,business.industry ,Transmission (medicine) ,fungi ,COVID-19 ,Outbreak ,Bayes Theorem ,Renal dialysis unit ,Hospitals ,Community hospital ,Rapid sequencing ,Haemodialysis ,Increased risk ,Genetic epidemiology ,Emergency medicine ,Dialysis unit ,Nosocomial ,business - Abstract
ObjectivesPatients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium.MethodsWe combined geographical, temporal and genomic sequence data from the community and hospital to estimate the probability of infection originating from within the dialysis unit, the hospital or the community using Bayesian statistical modelling and compared these results to the details of epidemiological investigations.ResultsOf 671 patients, 60 (8.9%) became infected with SARS-CoV-2, of whom 16 (27%) died. Within-unit and community transmission were both evident and an instance of transmission from the wider hospital setting was also demonstrated.ConclusionsNear-real-time SARS-CoV-2 sequencing data can facilitate tailored infection prevention and control measures, which can be targeted at reducing risk in these settings.
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- 2021
21. Iron-Catalyzed Halogen Exchange of Trifluoromethyl Arenes
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Florence Williams, James Shepherd, Hayley Petras, Emily Landgreen, and Andreas Dorian
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We report the facile production of ArCF2X and ArCX3 from ArCF3 using catalytic iron(III)halides, which constitutes the first iron-catalyzed halogen exchange for non-aromatic CF bonds. Theoretical calculations suggest direct activation of C–F bonds by iron coordination. ArCX3 and ArCF2X products of the reaction are synthetically valuable due to their diversification potential. In particular, bromo-, chloro-, and iododifluoromethyl arenes (ArCF2Br, ArCF2Cl, ArCF2I, respectively) provide access to a myriad of difluoromethyl arene derivatives (ArCF2R). To optimize for mono-halogen exchange, a statistical method called Design of Experiments was used. Optimized parameters were successfully applied to electron rich and electron deficient aromatic substrates, and to the late stage diversification of flufenoxuron, a commercial insecticide.
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- 2021
22. Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2
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Rachel M. Colquhoun, David Robertson, Stephen Carmichael, Gianluigi Rossi, Tom Stanton, Andrew Rambaut, James Shepherd, Stefan Rooke, Ana da Silva Filipe, Amy Shepherd, Alasdair MacLean, Elihu Aranday-Cortes, Carlos E Balcazar-Lopez, Verity Hill, Igor Starinskij, Lu Lu, Katherine Smollett, Kathy Li, Michael Gallagher, Kathleen A. Williamson, John T. McCrone, Rory Gunson, Ben Jackson, Thomas C Williams, Rebecca Dewar, Kirstyn Brunker, Rhys Inward, Sharif Shaaban, Martin P McHugh, Kate Templeton, Seb Cotton, Mark E. J. Woolhouse, Daniel Balaz, Alice Broos, Sarah E. McDonald, Rajiv Shah, Jenna Nichols, Lily Tong, Thomas Doherty, Rowland R. Kao, Áine O'Toole, Natasha Johnson, Patawee Asamaphan, Yasmin A Parr, Vattipally B. Sreenu, E. Thomson, Marc Niebel, Natasha Jesudason, Daniel Mair, Kyriaki Nomikou, Emily Scher, Matthew T. G. Holden, Samantha Lycett, and Joseph Hughes
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medicine.medical_specialty ,education.field_of_study ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Public health ,Population ,National health service ,Quarter (United States coin) ,Geography ,Epidemiology ,medicine ,Health board ,education ,Demography - Abstract
The second SARS virus, SARS-CoV-2, emerged in December 2019, and within a month was globally distributed. It was first introduced into Scotland in February 2020 associated with returning travellers and visitors. By March it was circulating in communities across the UK, and to control COVID-19 cases, and prevent overwhelming of the National Health Service (NHS), a ‘lockdown’ was introduced on 23rd March 2020 with a restriction of people’s movements. To augment the public health efforts a large-scale genome epidemiology effort (as part of the COVID-19 Genomics UK (COG-UK) consortium) resulted in the sequencing of over 5000 SARS-CoV-2 genomes by 18th August 2020 from Scottish cases, about a quarter of the estimated number of cases at that time. Here we quantify the geographical origins of the first wave introductions into Scotland from abroad and other UK regions, the spread of these SARS-CoV-2 lineages to different regions within Scotland (defined at the level of NHS Health Board) and the effect of lockdown on virus ‘success’. We estimate that approximately 300 introductions seeded lineages in Scotland, with around 25% of these lineages composed of more than five viruses, but by June circulating lineages were reduced to low levels, in line with low numbers of recorded positive cases. Lockdown was, thus, associated with a dramatic reduction in infection numbers and the extinguishing of most virus lineages. Unfortunately since the summer cases have been rising in Scotland in a second wave, with >1000 people testing positive on a daily basis, and hospitalisation of COVID-19 cases on the rise again. Examining the available Scottish genome data from the second wave, and comparing it to the first wave, we find that while some UK lineages have persisted through the summer, the majority of lineages responsible for the second wave are new introductions from outside of Scotland and many from outside of the UK. This indicates that, while lockdown in Scotland is directly linked with the first wave case numbers being brought under control, travel-associated imports (mostly from Europe or other parts of the UK) following the easing of lockdown are responsible for seeding the current epidemic population. This demonstrates that the impact of stringent public health measures can be compromised if following this, movements from regions of high to low prevalence are not minimised.
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- 2021
23. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity
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Erik Volz, Verity Hill, John T. McCrone, Anna Price, David Jorgensen, Áine O’Toole, Joel Southgate, Robert Johnson, Ben Jackson, Fabricia F. Nascimento, Sara M. Rey, Samuel M. Nicholls, Rachel M. Colquhoun, Ana da Silva Filipe, James Shepherd, David J. Pascall, Rajiv Shah, Natasha Jesudason, Kathy Li, Ruth Jarrett, Nicole Pacchiarini, Matthew Bull, Lily Geidelberg, Igor Siveroni, Ian Goodfellow, Nicholas J. Loman, Oliver G. Pybus, David L. Robertson, Emma C. Thomson, Andrew Rambaut, Thomas R. Connor, Cherian Koshy, Emma Wise, Nick Cortes, Jessica Lynch, Stephen Kidd, Matilde Mori, Derek J. Fairley, Tanya Curran, James P. McKenna, Helen Adams, Christophe Fraser, Tanya Golubchik, David Bonsall, Catrin Moore, Sarah L. Caddy, Fahad A. Khokhar, Michelle Wantoch, Nicola Reynolds, Ben Warne, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Michaela John, Robert Beer, Safiah Afifi, Sian Morgan, Angela Marchbank, Christine Kitchen, Huw Gulliver, Ian Merrick, Martyn Guest, Robert Munn, Trudy Workman, William Fuller, Catherine Bresner, Luke B. Snell, Themoula Charalampous, Gaia Nebbia, Rahul Batra, Jonathan Edgeworth, Samuel C. Robson, Angela Beckett, Katie F. Loveson, David M. Aanensen, Anthony P. Underwood, Corin A. Yeats, Khalil Abudahab, Ben E.W. Taylor, Mirko Menegazzo, Gemma Clark, Wendy Smith, Manjinder Khakh, Vicki M. Fleming, Michelle M. Lister, Hannah C. Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Paul Bird, Thomas Helmer, Karlie Fallon, Christopher Holmes, Julian Tang, Veena Raviprakash, Sharon Campbell, Nicola Sheriff, Matthew W. Loose, Nadine Holmes, Christopher Moore, Matthew Carlile, Victoria Wright, Fei Sang, Johnny Debebe, Francesc Coll, Adrian W. Signell, Gilberto Betancor, Harry D. Wilson, Theresa Feltwell, Charlotte J. Houldcroft, Sahar Eldirdiri, Anita Kenyon, Thomas Davis, Oliver Pybus, Louis du Plessis, Alex Zarebski, Jayna Raghwani, Moritz Kraemer, Sarah Francois, Stephen Attwood, Tetyana Vasylyeva, M. Estee Torok, William L. Hamilton, Ian G. Goodfellow, Grant Hall, Aminu S. Jahun, Yasmin Chaudhry, Myra Hosmillo, Malte L. Pinckert, Iliana Georgana, Anna Yakovleva, Luke W. Meredith, Samuel Moses, Hannah Lowe, Felicity Ryan, Chloe L. Fisher, Ali R. Awan, John Boyes, Judith Breuer, Kathryn Ann Harris, Julianne Rose Brown, Divya Shah, Laura Atkinson, Jack C.D. Lee, Adela Alcolea-Medina, Nathan Moore, Nicholas Cortes, Rebecca Williams, Michael R. Chapman, Lisa J. Levett, Judith Heaney, Darren L. Smith, Matthew Bashton, Gregory R. Young, John Allan, Joshua Loh, Paul A. Randell, Alison Cox, Pinglawathee Madona, Alison Holmes, Frances Bolt, James Price, Siddharth Mookerjee, Aileen Rowan, Graham P. Taylor, Manon Ragonnet-Cronin, Rob Johnson, Olivia Boyd, Erik M. Volz, Kirstyn Brunker, Katherine L. Smollett, Joshua Quick, Claire McMurray, Joanne Stockton, Sam Nicholls, Will Rowe, Radoslaw Poplawski, Rocio T. Martinez-Nunez, Jenifer Mason, Trevor I. Robinson, Elaine O'Toole, Joanne Watts, Cassie Breen, Angela Cowell, Catherine Ludden, Graciela Sluga, Nicholas W. Machin, Shazaad S.Y. Ahmad, Ryan P. George, Fenella Halstead, Venkat Sivaprakasam, James G. Shepherd, Patawee Asamaphan, Marc O. Niebel, Kathy K. Li, Rajiv N. Shah, Natasha G. Jesudason, Yasmin A. Parr, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N. Carmichael, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Igor Starinskij, Richard J. Orton, Joseph Hughes, Sreenu Vattipally, Joshua B. Singer, Antony D. Hale, Louissa R. Macfarlane-Smith, Katherine L. Harper, Yusri Taha, Brendan A.I. Payne, Shirelle Burton-Fanning, Sheila Waugh, Jennifer Collins, Gary Eltringham, Kate E. Templeton, Martin P. McHugh, Rebecca Dewar, Elizabeth Wastenge, Samir Dervisevic, Rachael Stanley, Reenesh Prakash, Claire Stuart, Ngozi Elumogo, Dheeraj K. Sethi, Emma J. Meader, Lindsay J. Coupland, Will Potter, Clive Graham, Edward Barton, Debra Padgett, Garren Scott, Emma Swindells, Jane Greenaway, Andrew Nelson, Wen C. Yew, Paola C. Resende Silva, Monique Andersson, Robert Shaw, Timothy Peto, Anita Justice, David Eyre, Derrick Crooke, Sarah Hoosdally, Tim J. Sloan, Nichola Duckworth, Sarah Walsh, Anoop J. Chauhan, Sharon Glaysher, Kelly Bicknell, Sarah Wyllie, Ethan Butcher, Scott Elliott, Allyson Lloyd, Robert Impey, Nick Levene, Lynn Monaghan, Declan T. Bradley, Elias Allara, Clare Pearson, Peter Muir, Ian B. Vipond, Richard Hopes, Hannah M. Pymont, Stephanie Hutchings, Martin D. Curran, Surendra Parmar, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Meera Chand, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Alicia Thornton, Richard Myers, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Ian Harrison, Hassan Hartman, Nikos Manesis, Vineet Patel, Chloe Bishop, Vicki Chalker, Husam Osman, Andrew Bosworth, Esther Robinson, Matthew T.G. Holden, Sharif Shaaban, Alec Birchley, Alexander Adams, Alisha Davies, Amy Gaskin, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Catherine Moore, Chris Williams, David Heyburn, Elen De Lacy, Ember Hilvers, Fatima Downing, Giri Shankar, Hannah Jones, Hibo Asad, Jason Coombes, Joanne Watkins, Johnathan M. Evans, Laia Fina, Laura Gifford, Lauren Gilbert, Lee Graham, Malorie Perry, Mari Morgan, Michelle Cronin, Noel Craine, Rachel Jones, Robin Howe, Sally Corden, Sara Rey, Sara Kumziene-Summerhayes, Sarah Taylor, Simon Cottrell, Sophie Jones, Sue Edwards, Justin O’Grady, Andrew J. Page, John Wain, Mark A. Webber, Alison E. Mather, David J. Baker, Steven Rudder, Muhammad Yasir, Nicholas M. Thomson, Alp Aydin, Ana P. Tedim, Gemma L. Kay, Alexander J. Trotter, Rachel A.J. Gilroy, Nabil-Fareed Alikhan, Leonardo de Oliveira Martins, Thanh Le-Viet, Lizzie Meadows, Anastasia Kolyva, Maria Diaz, Andrew Bell, Ana Victoria Gutierrez, Ian G. Charles, Evelien M. Adriaenssens, Robert A. Kingsley, Anna Casey, David A. Simpson, Zoltan Molnar, Thomas Thompson, Erwan Acheson, Jane A.H. Masoli, Bridget A. Knight, Andrew Hattersley, Sian Ellard, Cressida Auckland, Tabitha W. Mahungu, Dianne Irish-Tavares, Tanzina Haque, Yann Bourgeois, Garry P. Scarlett, David G. Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Steven Liggett, Paul Baker, Sarah Essex, Ronan A. Lyons, Laura G. Caller, Sergi Castellano, Rachel J. Williams, Mark Kristiansen, Sunando Roy, Charlotte A. Williams, Patricia L. Dyal, Helena J. Tutill, Yasmin N. Panchbhaya, Leysa M. Forrest, Paola Niola, Jacqueline Findlay, Tony T. Brooks, Artemis Gavriil, Lamia Mestek-Boukhibar, Sam Weeks, Sarojini Pandey, Lisa Berry, Katie Jones, Alex Richter, Andrew Beggs, Colin P. Smith, Giselda Bucca, Andrew R. Hesketh, Ewan M. Harrison, Sharon J. Peacock, Sophie Palmer, Carol M. Churcher, Katherine L. Bellis, Sophia T. Girgis, Plamena Naydenova, Beth Blane, Sushmita Sridhar, Chris Ruis, Sally Forrest, Claire Cormie, Harmeet K. Gill, Joana Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Leanne M. Kermack, Nazreen F. Hadjirin, Dinesh Aggarwal, Luke Griffith, Tracey Swingler, Rose K. Davidson, Thomas Williams, Carlos E. Balcazar, Michael D. Gallagher, Áine O'Toole, Stefan Rooke, Rachel Colquhoun, Jordan Ashworth, J.T. McCrone, Emily Scher, Xiaoyu Yu, Kathleen A. Williamson, Thomas D. Stanton, Stephen L. Michell, Claire M. Bewshea, Ben Temperton, Michelle L. Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W. Harrison, Christine M. Sambles, David J. Studholme, Aaron R. Jeffries, Alistair C. Darby, Julian A. Hiscox, Steve Paterson, Miren Iturriza-Gomara, Kathryn A. Jackson, Anita O. Lucaci, Edith E. Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Lance Turtle, Sam T. Haldenby, Richard Gregory, Matthew Gemmell, Dominic Kwiatkowski, Thushan I. de Silva, Nikki Smith, Adrienn Angyal, Benjamin B. Lindsey, Danielle C. Groves, Luke R. Green, Dennis Wang, Timothy M. Freeman, Matthew D. Parker, Alexander J. Keeley, Paul J. Parsons, Rachel M. Tucker, Rebecca Brown, Matthew Wyles, Chrystala Constantinidou, Meera Unnikrishnan, Sascha Ott, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Richard Stark, Laura Baxter, Mohammad T. Alam, Paul E. Brown, Patrick C. McClure, Joseph G. Chappell, Theocharis Tsoleridis, Jonathan Ball, Dimitris Grammatopoulos, David Buck, John A. Todd, Angie Green, Amy Trebes, George MacIntyre-Cockett, Mariateresa de Cesare, Cordelia Langford, Alex Alderton, Roberto Amato, Sonia Goncalves, David K. Jackson, Ian Johnston, John Sillitoe, Steve Palmer, Mara Lawniczak, Matt Berriman, John Danesh, Rich Livett, Lesley Shirley, Ben Farr, Mike Quail, Scott Thurston, Naomi Park, Emma Betteridge, Danni Weldon, Scott Goodwin, Rachel Nelson, Charlotte Beaver, Laura Letchford, David A. Jackson, Luke Foulser, Liz McMinn, Liam Prestwood, Sally Kay, Leanne Kane, Matthew J. Dorman, Inigo Martincorena, Christoph Puethe, Jon-Paul Keatley, Gerry Tonkin-Hill, Christen Smith, Dorota Jamrozy, Mathew A. Beale, Minal Patel, Cristina Ariani, Michael Spencer-Chapman, Eleanor Drury, Stephanie Lo, Shavanthi Rajatileka, Carol Scott, Keith James, Sarah K. Buddenborg, Duncan J. Berger, Gaurang Patel, Maria V. Garcia-Casado, Thomas Dibling, Samantha McGuigan, Hazel A. Rogers, Adam D. Hunter, Emily Souster, Alexandra S. Neaverson, Medical Research Council (MRC), Pascall, David [0000-0002-7543-0860], and Apollo - University of Cambridge Repository
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Genome ,Genetic analysis ,0302 clinical medicine ,Clade ,11 Medical and Health Sciences ,Genetics ,0303 health sciences ,education.field_of_study ,Phylogenetic tree ,Virulence ,C500 ,COG-UK Consortium ,C700 ,Transmissibility (vibration) ,3. Good health ,founder effect ,Spike Glycoprotein, Coronavirus ,epidemiology ,Viral load ,Population ,Glycine ,B100 ,Genomics ,Genome, Viral ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,evolution ,Humans ,education ,030304 developmental biology ,Aspartic Acid ,Whole Genome Sequencing ,Biochemistry, Genetics and Molecular Biology(all) ,SARS-CoV-2 ,COVID-19 ,spike ,The COVID-19 Genomics UK Consortium ,A300 ,06 Biological Sciences ,United Kingdom ,Amino Acid Substitution ,Evolutionary biology ,Mutation ,Biological dispersal ,030217 neurology & neurosurgery ,Founder effect ,Developmental Biology - Abstract
Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant., Graphical Abstract, Highlights • Increasing frequency of SARS-CoV-2 D614G is consistent with a selective advantage • Phylodynamic analyses do not show significantly different growth of D614G clusters • There is no association of D614G replacement with greater severity of infection • The D614G replacement is associated with higher viral loads and younger patient age, Analysis of the spread and frequency of SARS-CoV-2 D614G in the United Kingdom suggests a selective advantage for this strain that is associated with higher viral loads in younger patients but not higher COVID-19 clinical severity or mortality.
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- 2021
24. Victims of Cybercrime: Understanding the Impact Through Accounts
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Lisa Sugiura, Dean Blackbourn, Mark Button, David William James Shepherd, Victoria Wang, and Richard Kapend
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Cybercrime ,Continuum (measurement) ,Technological change ,media_common.quotation_subject ,Subject (philosophy) ,Sociology ,Paper based ,Criminology ,Seriousness ,Hacker ,media_common - Abstract
The technological changes of the last 30 years have facilitated a substantial increase in cybercrimes. The impact of these crimes on victims has not been the subject of extensive research. This paper based upon a British Home Office funded study draws upon the experience of 52 victims of computer misuse crime, which can be broadly grouped under hacking and computer virus related crimes. Drawing upon the interviews with these victims the researchers identified a continuum of three components founded upon the seriousness of the incident and the impact on the victim. These three categories included: incidents of inconvenience, crimes of inconvenience and serious crimes of personal violation or significant financial loss or fear of. The paper provides depth accounts of 15 of the 52 victims interviewed to illustrate this continuum.
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- 2021
25. Remdesivir induced viral RNA and subgenomic RNA suppression, and evolution of viral variants in SARS-CoV-2 infected patients
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Juanita Pang, Myerson P, de Silva Ti, Köeglmeier J, Judith Breuer, Caroline Dalton, Matthew Parker, E. Thomson, Rachel Williams, Grandjean L, Timothy Best, Florencia A T Boshier, Bynoe Pd, Richard A. Goldstein, Nele Alders, Stephanie Grunewald, Justin Penner, Alasdair Bamford, James Shepherd, Sunando Roy, Claire Frauenfelder, Joseph Hughes, and James Hatcher
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Viral replication ,Viral evolution ,Superinfection ,medicine ,RNA ,Drug resistance ,Biology ,medicine.disease_cause ,Virology ,Viral load ,Deep sequencing ,Subgenomic mRNA - Abstract
While changes in SARS-CoV-2 viral load over time have been documented, detailed information on the impact of remdesivir and how it might alter intra-host viral evolution is limited. Sequential viral loads and deep sequencing of SARS-CoV-2 recovered from the upper respiratory tract of hospitalised children revealed that remdesivir treatment suppressed viral RNA levels in one patient but not in a second infected with an identical strain. Evidence of drug resistance to explain this difference was not found. Reduced levels of subgenomic (sg) RNA during treatment of the second patient, suggest an additional effect of remdesivir on viral replication that is independent of viral RNA levels. Haplotype reconstruction uncovered persistent SARS-CoV-2 variant genotypes in four patients. We conclude that these are likely to have arisen from within-host evolution, and not co-transmission, although superinfection cannot be excluded in one case. Sample-to-sample heterogeneity in the abundances of variant genotypes is best explained by the presence of discrete viral populations in the lung with incomplete population sampling in diagnostic swabs. Such compartmentalisation is well described in serious lung infections caused by influenza and Mycobacterium tuberculosis and has been associated with poor drug penetration, suboptimal treatment and drug resistance. Our data provide evidence that remdesivir is able to suppress SARS-CoV-2 replication in vivo but that its efficacy may be compromised by factors reducing penetration into the lung. Based on data from influenza and Mycobacterium tuberculosis lung infections we conclude that early use of remdesivir combined with other agents should now be evaluated.Summary SentenceDeep sequencing of longitudinal samples from SARS-CoV-2 infected paediatric patients identifies evidence of remdesivir-associated inhibition of viral replication in vivo and uncovers evidence of within host evolution of distinct viral genotypes.
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- 2020
26. Detection of Southern Beech Heavy Flowering Using Sentinel-2 Imagery
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Ben Jolly, James Shepherd, Jan Schindler, John Dymond, and Terry Greene
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General Earth and Planetary Sciences - Abstract
The southern beech (genus Fuscospora and Lophozonia) forest in New Zealand periodically has “mast” years, during which very large volumes of seeds are produced. This excessive seed production results in a population explosion of rodents and mustelids, which then puts pressure on native birds. To protect the birds, extra pest controls, costing in the order of NZD 20 million, are required in masting areas. To plan pest control and keep it cost-effective, it would be helpful to have a map of the masting areas. In this study, we developed a remote sensing method for the creation of a national beech flowering map. It used a temporal sequence of Sentinel-2 satellite imagery to determine areas in which a yellow index, which was based on red and green reflectance (red-green)/(red + green), was higher than normal in spring. The method was used to produce national maps of heavy beech flowering for the years 2017 to 2021. In 2018, which was a major beech masting year, of the 4.1 million ha of beech forest in New Zealand, 27.6% was observed to flower heavily. The overall classification accuracy of the map was 90.8%. The method is fully automated and could be used to help to identify areas of potentially excessive seed fall across the whole of New Zealand, several months in advance of when pest control would be required.
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- 2022
27. COVID-19 and telemedicine
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James Shepherd
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2019-20 coronavirus outbreak ,Telemedicine ,Coronavirus disease 2019 (COVID-19) ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,medicine ,Medical emergency ,medicine.disease ,business - Published
- 2021
28. periscope: sub-genomic RNA identification in SARS-CoV-2 Genomic Sequencing Data
- Author
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Lily Tong, Elihu Aranday-Cortes, Chris Davis, Danielle C. Groves, Abha Chopra, Laura Carrilero, David G Partridge, Simon B. Mallal, Dennis Wang, James Shepherd, E. Thomson, Joe Heffer, Jenna Nichols, Matthew Wyles, T.I. de Silva, Shay Leary, Alexander J Keeley, Luke R. Green, Mohammad Raza, Cariad Evans, Sahan Bennett, Alain Kohl, Nikki Smith, Benjamin B Lindsey, Rachel Tucker, Parker, Karen C. Johnson, Ana da Silva Filipe, Paul J. Parsons, Adrienn Angyal, Silvana Gaudieri, and Rebecca Brown
- Subjects
Untranslated region ,Open reading frame ,Start codon ,Regulatory sequence ,Transcription (biology) ,RNA ,Computational biology ,Biology ,Genome ,Subgenomic mRNA - Abstract
We have developed periscope, a tool for the detection and quantification of sub-genomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed “sub-genomic RNAs”. sgRNAs are produced through discontinuous transcription which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L which is located in the 5’ UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5’ end of all sgRNA. We applied periscope to 1,155 SARS-CoV-2 genomes from Sheffield, UK and validated our findings using orthogonal datasets and in vitro cell systems. Using a simple local alignment to detect reads which contain the leader sequence we were able to identify and quantify reads arising from canonical and non-canonical sgRNA. We were able to detect all canonical sgRNAs at expected abundances, with the exception of ORF10. A number of recurrent non-canonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/− cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing datasets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA.
- Published
- 2020
29. Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence
- Author
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Kathy Li, Rory Gunson, Antonia Ho, David Robertson, Elihu Aranday-Cortes, Daniel Mair, Katherine Smollett, Igor Starinskij, Kyriaki Nomikou, Natasha Johnson, Sarah E. McDonald, Vattipally B. Sreenu, Sharif Shaaban, Patawee Asamaphan, E. Thomson, Jenna Nichols, Carlos Balcazar, Joseph Hughes, Marc Niebel, Michael Gallagher, Kirstyn Brunker, Elizabeth Wastnedge, E. Carol McWilliam Leitch, Martin P McHugh, Massimo Palmarini, Natasha Jesudason, Kate Templeton, Áine O'Toole, Lily Tong, Matthew T. G. Holden, Joshua B Singer, Rajiv Shah, James Shepherd, Yasmin A Parr, Thomas C Williams, Richard J. Orton, Stephen Carmichael, Andrew Rambaut, Alasdair MacLean, Rebecca Dewar, Stefan Rooke, and Ana da Silva Filipe
- Subjects
medicine.medical_specialty ,Coronavirus disease 2019 (COVID-19) ,European travel ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Outbreak ,law.invention ,Geography ,Infectious disease (medical specialty) ,law ,Quarantine ,Epidemiology ,medicine ,Contact tracing ,Demography - Abstract
SARS-CoV-2, the causative agent of COVID-19, emerged in Wuhan, China in December 2019 and spread rapidly throughout the world. Understanding the introductions of this new coronavirus in different settings may assist control efforts and the establishment of frameworks to support rapid response in future infectious disease outbreaks.We investigated the first four weeks of emergence of the SARS-CoV-2 virus in Scotland after the first case reported on the 1st March 2020. We obtained full genome sequences from 452 individuals with a laboratory-confirmed diagnosis of COVID-19, representing 20% of all cases until 1st April 2020 (n=2310). This permitted a genomic epidemiology approach to study the introductions and spread of the SARS-2 virus in Scotland.From combined phylogenetic and epidemiological analysis, we estimated at least 113 introductions of SARS-CoV-2 into Scotland during this period. Clusters containing multiple sequences suggestive of onward transmission occurred in 48/86 (56%). 42/86 (51%) clusters had no known international travel history indicating undetected introductions.The majority of viral sequences were most closely related to those circulating in other European countries, including Italy, Austria and Spain. Travel-associated introductions of SARS-CoV-2 into Scotland predated travel restrictions in the UK and other European countries. The first local transmission occurred three days after the first case. A shift from travel-associated to sustained community transmission was apparent after only 11 days. Undetected introductions occurred prior to the first known case of COVID-19. Earlier travel restrictions and quarantine measures might have resulted in fewer introductions into Scotland, thereby reducing the number of cases and the subsequent burden on health services. The high number of introductions and transmission rates were likely to have impacted on national contact tracing efforts. Our results also demonstrate that local real-time genomic epidemiology can be used to monitor transmission clusters and facilitate control efforts to restrict the spread of COVID-19.FundingMRC (MC UU 1201412), UKRI/Wellcome (COG-UK), Wellcome Trust Collaborator Award (206298/Z/17/Z – ARTIC Network; TCW Wellcome Trust Award 204802/Z/16/ZResearch in contextEvidence before this studyCoronavirus disease-2019 (COVID-19) was first diagnosed in Scotland on the 1st of March 2020 following the emergence of the causative severe acute respiratory system coronavirus 2 (SARS-CoV-2) virus in China in December 2019. During the first month of the outbreak in Scotland, 2310 positive cases of COVID-19 were detected, associated with 1832 hospital admissions, 207 intensive care admissions and 126 deaths. The number of introductions into Scotland and the source of those introductions was not known prior to this study.Added value of this studyUsing a combined phylogenetic and epidemiological approach following real-time next generation sequencing of 452 SARS-CoV-2 samples, it was estimated that the virus was introduced to Scotland on at least 113 occasions, mostly from other European countries, including Italy, Austria and Spain. Localised outbreaks occurred in the community across multiple Scottish health boards, within healthcare facilities and an international conference and community transmission was established rapidly, before local and international lockdown measures were introduced.
- Published
- 2020
30. Exploring the extent of openness of open government data – a critique of open government datasets in the UK
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Victoria Wang and David William James Shepherd
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Open government ,Government ,Sociology and Political Science ,Download ,open government ,Social change ,Global Leadership ,open data ,RCUK ,Social Sciences(all) ,Library and Information Sciences ,Public administration ,granularity ,embargoover12 ,EPSRC ,Politics ,Open data ,Open government data ,Political science ,Openness to experience ,ordinary citizen ,data.gov.uk ,Law ,EP/N27825/1 - Abstract
The claim of the open government data (OGD) movement is that it would add considerable value to the political, economic and social development of nations. Thus, during the past few years, governments around the world have been under increasing pressure to release data to encourage citizen participation in government. In the UK, the government publishes its data on the data.gov.uk website for the public to find, view, download and interrogate. 1 In this paper, we evaluate the extent of openness of OGD in the UK – a recognised global leader in the OGD movement – by examining a sample of 400 datasets listed on this website. The examination uses an ‘ordinary citizen’ test, which is developed based on the original eight Sebastopol principles of open data. Our examination discovers that existing prevalent measures of openness of data are inadequate. Our findings demonstrate that the majority of the published government resources on the website are informational rather than granular data. In fact, only a small minority of these advertised as open data are actually open, which severely limits their open government utilities.
- Published
- 2020
31. Detection of New Zealand Kauri Trees with AISA Aerial Hyperspectral Data for Use in Multispectral Monitoring
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Norton, Jane J. Meiforth, Henning Buddenbaum, Joachim Hill, James Shepherd, and David A.
- Subjects
hyperspectral ,airborne ,optical remote sensing ,pixel-based ,Random Forest ,AISA Fenix ,Waitakere Ranges ,kauri dieback disease - Abstract
The endemic New Zealand kauri trees (Agathis australis) are of major importance for the forests in the northern part of New Zealand. The mapping of kauri locations is required for the monitoring of the deadly kauri dieback disease (Phytophthora agathidicida (PTA)). In this study, we developed a method to identify kauri trees by optical remote sensing that can be applied in an area-wide campaign. Dead and dying trees were separated in one class and the remaining trees with no to medium stress symptoms were defined in the two classes “kauri” and “other”. The reference dataset covers a representative selection of 3165 precisely located crowns of kauri and 21 other canopy species in the Waitakere Ranges west of Auckland. The analysis is based on an airborne hyperspectral AISA Fenix image (437–2337 nm, 1 m2 pixel resolution). The kauri spectra show characteristically steep reflectance and absorption features in the near-infrared (NIR) region with a distinct long descent at 1215 nm, which can be parameterised with a modified Normalised Water Index (mNDWI-Hyp). With a Jeffries–Matusita separability over 1.9, the kauri spectra can be well separated from 21 other canopy vegetation spectra. The Random Forest classifier performed slightly better than Support Vector Machine. A combination of the mNDWI-Hyp index with four additional spectral indices with three red to NIR bands resulted in an overall pixel-based accuracy (OA) of 91.7% for crowns larger 3 m diameter. While the user’s and producer’s accuracies for the class “kauri” with 94.6% and 94.8% are suitable for management purposes, the separation of “dead/dying trees” from “other” canopy vegetation poses the main challenge. The OA can be improved to 93.8% by combining “kauri” and “dead/dying” trees in one class, separate classifications for low and high forest stands and a binning to 10 nm bandwidths. Additional wavelengths and their respective indices only improved the OA up to 0.6%. The method developed in this study allows an accurate location of kauri trees for an area-wide mapping with a five-band multispectral sensor in a representative selection of forest ecosystems.
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- 2019
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32. Co-offending and bribery: the recruitment of participants to corrupt schemes and the implications for prevention
- Author
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David William James Shepherd, Mark Button, and Dean Blackbourn
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Corruption ,Prevention ,Strategy and Management ,media_common.quotation_subject ,05 social sciences ,Co offending ,Criminology ,Public domain ,Bribery ,050501 criminology ,0501 psychology and cognitive sciences ,Business ,Resident pathogen theory ,Law ,Safety Research ,050104 developmental & child psychology ,0505 law ,media_common - Abstract
This paper explores the rarely researched areas of co-offending and bribery. Based upon interviews with six persons convicted of bribery-related offences and other cases in the public domain, the paper explores how previously ‘clean’ persons are recruited to corrupt schemes. In doing so, the paper draws on Reason’s resident pathogen theory on safety and uniquely applies it to bribery. The paper also identifies common recruitment techniques used by corruptors and proposes pathogen network analysis as a novel method for enhancing bribery prevention.
- Published
- 2018
33. 'The Higher You Fly, the Further You Fall': White-Collar Criminals, 'Special Sensitivity' and the Impact of Conviction in the United Kingdom
- Author
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Mark Button, Dean Blackbourn, and David William James Shepherd
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050402 sociology ,Health (social science) ,media_common.quotation_subject ,white collar offenders ,Prison ,Criminology ,Pathology and Forensic Medicine ,Collar ,0504 sociology ,special sensitvity ,Applied Psychology ,0505 law ,media_common ,White (horse) ,05 social sciences ,embargoover12 ,Mental health ,conviction ,impact ,050501 criminology ,Conviction ,Psychological resilience ,Psychology ,Law ,Sentence ,Criminal justice - Abstract
The resilience of some high-profile white-collar criminals in the media gaze after prison may lead some to conclude, particularly as some research also supports this notion, that this group of offenders generally manages well after conviction. Research in this area is, however, small and largely American. The authors seek to add to this small body of research by offering findings on the impact of conviction on 17 UK convicted white-collar criminals after completion of their sentence. It provides a unique insight into the consequences of conviction, showing that although there were some offenders who did experience limited impact and coped well, there was also a significant group who suffered a decline in status, financial losses, negative media coverage, and relationship and mental health problems, to name some. The authors argue more research is needed on this group and their needs as they are often neglected by the criminal justice system.
- Published
- 2017
34. Derivation and external validation of a risk score for predicting HIV-associated tuberculosis to support case finding and preventive therapy scale-up: A cohort study
- Author
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Tefera Agizew, Yasmeen Hanifa, Heather Alexander, Unami Mathebula-Modongo, Yuliang Liu, Anand Date, Rosanna Boyd, Andrew D. Kerkhoff, Andrew F. Auld, Robin Wood, George Bicego, Anikie Mathoma, Goabaone Rankgoane-Pono, Alison D. Grant, Salome Charalambous, Alyssa Finlay, Pontsho Pono, Katherine Fielding, Tedd V. Ellerbrock, James Shepherd, Ray W. Shiraishi, and Christopher Serumola
- Subjects
Bacterial Diseases ,Male ,Epidemiology ,Economics ,Antitubercular Agents ,Social Sciences ,HIV Infections ,Economic Geography ,Logistic regression ,Biochemistry ,Machine Learning ,Medical Conditions ,Mathematical and Statistical Techniques ,Risk Factors ,Preventive Health Services ,Medicine and Health Sciences ,Prevalence ,Mass Screening ,Public and Occupational Health ,Subclinical infection ,Clinical Trials as Topic ,Botswana ,Framingham Risk Score ,Geography ,Coinfection ,Statistics ,General Medicine ,Middle Aged ,Prognosis ,Vaccination and Immunization ,Infectious Diseases ,Anti-Retroviral Agents ,Physical Sciences ,Medicine ,Tuberculosis Diagnosis and Management ,Low and Middle Income Countries ,Female ,Fast track ,Research Article ,Cohort study ,Adult ,Computer and Information Sciences ,medicine.medical_specialty ,Tuberculosis ,Immunology ,Antiretroviral Therapy ,Research and Analysis Methods ,Risk Assessment ,HIV Long-Term Survivors ,Antiviral Therapy ,Artificial Intelligence ,Diagnostic Medicine ,Predictive Value of Tests ,Internal medicine ,medicine ,Humans ,Hemoglobin ,Statistical Methods ,Medical prescription ,business.industry ,Biology and Life Sciences ,Proteins ,Reproducibility of Results ,Tropical Diseases ,medicine.disease ,Early Diagnosis ,Medical Risk Factors ,Earth Sciences ,Preventive Medicine ,business ,Body mass index ,Mathematics ,Forecasting - Abstract
Background Among people living with HIV (PLHIV), more flexible and sensitive tuberculosis (TB) screening tools capable of detecting both symptomatic and subclinical active TB are needed to (1) reduce morbidity and mortality from undiagnosed TB; (2) facilitate scale-up of tuberculosis preventive therapy (TPT) while reducing inappropriate prescription of TPT to PLHIV with subclinical active TB; and (3) allow for differentiated HIV–TB care. Methods and findings We used Botswana XPRES trial data for adult HIV clinic enrollees collected during 2012 to 2015 to develop a parsimonious multivariable prognostic model for active prevalent TB using both logistic regression and random forest machine learning approaches. A clinical score was derived by rescaling final model coefficients. The clinical score was developed using southern Botswana XPRES data and its accuracy validated internally, using northern Botswana data, and externally using 3 diverse cohorts of antiretroviral therapy (ART)-naive and ART-experienced PLHIV enrolled in XPHACTOR, TB Fast Track (TBFT), and Gugulethu studies from South Africa (SA). Predictive accuracy of the clinical score was compared with the World Health Organization (WHO) 4-symptom TB screen. Among 5,418 XPRES enrollees, 2,771 were included in the derivation dataset; 67% were female, median age was 34 years, median CD4 was 240 cells/μL, 189 (7%) had undiagnosed prevalent TB, and characteristics were similar between internal derivation and validation datasets. Among XPHACTOR, TBFT, and Gugulethu cohorts, median CD4 was 400, 73, and 167 cells/μL, and prevalence of TB was 5%, 10%, and 18%, respectively. Factors predictive of TB in the derivation dataset and selected for the clinical score included male sex (1 point), ≥1 WHO TB symptom (7 points), smoking history (1 point), temperature >37.5°C (6 points), body mass index (BMI) 10) yielded TB prevalence of 1%, 1%, 2%, and 6% in the lowest risk group and 33%, 22%, 26%, and 32% in the highest risk group for XPRES, XPHACTOR, TBFT, and Gugulethu cohorts, respectively. At clinical score ≥2, the number needed to screen (NNS) ranged from 5.0 in Gugulethu to 11.0 in XPHACTOR. Limitations include that the risk score has not been validated in resource-rich settings and needs further evaluation and validation in contemporary cohorts in Africa and other resource-constrained settings. Conclusions The simple and feasible clinical score allowed for prioritization of sensitivity and NPV, which could facilitate reductions in mortality from undiagnosed TB and safer administration of TPT during proposed global scale-up efforts. Differentiation of risk by clinical score cutoff allows flexibility in designing differentiated HIV–TB care to maximize impact of available resources., Andrew Auld and colleagues evaluate a clinical score for active tuberculosis in persons with HIV infection., Author summary Why was this study done? Tuberculosis (TB) remains the most common cause of death among people living with HIV (PLHIV) and is often undiagnosed at time of death. Rapid scale-up of tuberculosis preventive therapy (TPT) to 13 million PLHIV in low- and middle-income countries (LMICs) has been proposed for 2021; however, active TB is commonly asymptomatic and therefore missed by current WHO-recommended 4-symptom TB screening rules. Therefore, more sensitive TB screening tools are needed to better facilitate early TB diagnosis and safer scale-up of TPT to PLHIV by avoiding TPT prescription to clients with asymptomatic active TB, who need TB treatment. What did the researchers do and find? We derived a TB risk score for PLHIV from XPRES trial data and validated the score on 3 external datasets. We prioritized high sensitivity and ability to correctly rule out TB (i.e., high negative predictive value (NPV)) at key time points in care such as HIV clinic enrollment and before TPT prescription. Both logistic regression and random forest machine learning approaches were used to identify the 6 most important predictors, commonly available in LMIC clinic settings. In the external datasets, TB risk score ≥2 had higher sensitivity (87% to 97%) than WHO 4-symptom screening rule and increased NPV by 0.3% to 1.7%. Three risk groups were identified by the score, with active TB prevalence in external datasets ranging from 1% to 6% in the lowest to 22% to 32% in the highest risk groups. What do these findings mean? Following further validation, this clinical score could improve early detection of active TB to reduce morbidity and mortality from undiagnosed TB. Use of the clinical score cutoff of ≥2 during the proposed TPT scale-up for 13 million PLHIV could potentially avoid many thousands of PLHIV with active TB being inappropriately prescribed TPT. By differentiating 3 risk groups, the score also allows for the development of differentiated service delivery models suitable for LMIC.
- Published
- 2021
35. Phylogenetic diversity of Mycobacterium tuberculosis in two geographically distinct locations in Botswana - The Kopanyo Study
- Author
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Chawangwa Modongo, Nicola M. Zetola, Alyssa Finlay, Xiao Jun Wen, James Shepherd, Joyce Basotli, Patrick K. Moonan, John E. Oeltmann, Rosanna Boyd, and Eleanor S. Click
- Subjects
0301 basic medicine ,Microbiology (medical) ,Veterinary medicine ,Genotype ,Lineage (evolution) ,030106 microbiology ,Population ,Microbiology ,Mycobacterium tuberculosis ,03 medical and health sciences ,South Africa ,Genetics ,Cluster Analysis ,Humans ,Tuberculosis ,education ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,education.field_of_study ,Molecular Epidemiology ,Botswana ,biology ,Phylogenetic tree ,Molecular epidemiology ,Genetic Variation ,biology.organism_classification ,Bacterial Typing Techniques ,Interspersed Repetitive Sequences ,Variable number tandem repeat ,Phylogenetic diversity ,030104 developmental biology ,Infectious Diseases ,Mycobacterium tuberculosis complex ,Tandem Repeat Sequences - Abstract
Mycobacterium tuberculosis complex (MTBC) is divided into several major phylogenetic lineages, with differential distribution globally. Using population-based data collected over a three year period, we performed 24-locus Mycobacterial Interspersed Repeat Unit – Variable Number Tandem Repeat (MIRU-VNTR) genotyping on all culture isolates from two districts of the country that differ in tuberculosis (TB) incidence (Gaborone, the capital, and Ghanzi in the Western Kalahari). The study objective was to characterize the molecular epidemiology of TB in these districts. Overall phylogenetic diversity mirrored that reported from neighboring Republic of South Africa, but differences in the two districts were marked. All four major lineages of M. tuberculosis were found in Gaborone, but only three of the four major lineages were found in Ghanzi. Strain diversity was lower in Ghanzi, with a large proportion (38%) of all isolates having an identical MIRU-VNTR result, compared to 6% of all isolates in Gaborone with the same MIRU-VNTR result. This study demonstrates localized differences in strain diversity by two districts in Botswana, and contributes to a growing characterization of MTBC diversity globally.
- Published
- 2019
36. Organisational inhibitions to addressing occupational fraud:a theory of differential rationalisation
- Author
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David William James Shepherd and Mark Button
- Subjects
ComputingMilieux_THECOMPUTINGPROFESSION ,Sociology and Political Science ,Social Psychology ,050901 criminology ,05 social sciences ,Rationalisation ,ComputingMilieux_LEGALASPECTSOFCOMPUTING ,Criminology ,embargoover12 ,culture ,Clinical Psychology ,neutralisation ,prevention ,occupational fraud ,ComputerApplications_GENERAL ,ComputingMilieux_COMPUTERSANDSOCIETY ,0501 psychology and cognitive sciences ,Sociology ,0509 other social sciences ,Positive economics ,rationalisation ,Law ,050104 developmental & child psychology - Abstract
This article examines organizational inhibitions in relation to addressing occupational fraud. The a priori assumption would be if an organization discovers occupational fraud it would deal with it. However, this research illustrates, drawing upon 24 semi-structured interviews, two case studies and participant observation, a range of avoidant rationalizations constructed by representatives of organizational victims to justify not tackling occupational fraud. These rationalizations bear great similarity to the rationalizations constructed by offenders, and the article argues they constitute a theory of differential rationalization. The research may have wider relevance to explaining why organizations fail to deal with other negative behaviors.
- Published
- 2019
37. Septuagint, Targum and Beyond Comparing Aramaic and Greek Versions from Jewish Antiquity
- Author
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David James Shepherd, Jan Joosten, Michaël van der Meer, Théologie protestante (TP), and Université de Strasbourg (UNISTRA)
- Subjects
[SHS.RELIG]Humanities and Social Sciences/Religions - Published
- 2019
38. The psychology of the corrupt: some preliminary findings
- Author
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Mark Button, Claire Nee, David William James Shepherd, Dean Blackbourn, and Sharon Leal
- Subjects
occupational corruption ,media_common.quotation_subject ,050109 social psychology ,Economics, Econometrics and Finance(all) ,Impulsivity ,white collar crime ,Psychological Techniques ,Risk appetite ,medicine ,Sensation seeking ,Personality ,0501 psychology and cognitive sciences ,media_common ,05 social sciences ,White-collar crime ,Eysenck Personality Questionnaire ,Scale (social sciences) ,psychological profile ,medicine.symptom ,Psychology ,General Economics, Econometrics and Finance ,Law ,050104 developmental & child psychology ,Clinical psychology - Abstract
Purpose This paper aims to present findings based on the psychological profile of 17 offenders who have been convicted of occupational fraud, bribery or related offences. It provides findings on their specific psychological profiles using well-established psychological techniques to gauge personality. The study is also aimed to provide the foundations for further research on such profiles, which could eventually provide a screening tool to identify individuals who might be a higher risk of engaging in corrupt behaviours for organisations. Design/methodology/approach The research is based upon 17 interviews with white-collar offenders who were also asked to complete an Eysenck Personality Questionnaire to identify their profile. Findings This study postulates that sensation seeking, risk appetite, impulsivity and lower non-aggressive self-regulation dominate the E scale traits of white-collar offenders. Originality/value This paper is very much original in its design with few studies having been performed in this area.
- Published
- 2019
39. Mathematical modelling of the pre-oxidation of a uranium carbide fuel pellet
- Author
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Bruce C. Hanson, Michael Fairweather, James Shepherd, and Peter J. Heggs
- Subjects
Materials science ,Differential equation ,General Chemical Engineering ,Nuclear engineering ,Radiochemistry ,Radius ,010402 general chemistry ,010403 inorganic & nuclear chemistry ,7. Clean energy ,01 natural sciences ,0104 chemical sciences ,Computer Science Applications ,chemistry.chemical_compound ,chemistry ,Mass transfer ,Pellet ,Uranium oxide ,Uranium carbide ,Limiting oxygen concentration ,Current (fluid) - Abstract
Uranium carbide is a candidate fuel for future nuclear reactors. However, for it to be implemented in a closed fuel cycle, an outline for its reprocessing is necessary. One proposed method is to oxidise the uranium carbide into uranium oxide which can then be reprocessed using current infrastructure. A mathematical model describing the heat and mass transfer processes involved in such an oxidation has been constructed. The available literature was consulted for reaction coefficients and information on reaction products. A stable and convergent numerical solution has been developed using a combination of finite-difference approximations of the differential equations. Completion times of approximately 3-30h are predicted given a spherical pellet with a radius of 9.35mm under varying initial conditions. The transient temperature distribution throughout the system is predicted, with a maximum temperature of 1458°C observed from an initial temperature of 500°C at an oxygen concentration of 3.15mol m‾³.
- Published
- 2015
40. ‘The iceberg beneath the sea':fraudsters and their punishment through non-criminal justice in the ‘fraud justice network’ in England and Wales
- Author
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Dean Blackbourn, Mark Button, and David William James Shepherd
- Subjects
Government ,punishment ,Sociology and Political Science ,Punishment ,media_common.quotation_subject ,Contempt ,05 social sciences ,Criminology ,embargoover12 ,0506 political science ,fraud justice network ,Political science ,Political Science and International Relations ,050602 political science & public administration ,050501 criminology ,fraudsters ,offenders ,Christian ministry ,Justice (ethics) ,Law ,0505 law ,Criminal justice ,media_common - Abstract
This paper illustrates the substantial role of non-criminal justice bodies in punishing persons for fraud related behaviours in England and Wales. It illustrates the substantial role of government regulators, delegated regulators, self-regulators, fraudster databases and the use of contempt of court in civil courts in dealing with fraudsters. Using data from the Ministry of Justice, the number of persons sanctioned for fraud offences are juxtaposed against data drawn from the regulatory bodies within the broader ‘fraud justice network’. The paper shows that over one million individuals are sanctioned for fraud offences each year and the great majority do not trouble the criminal justice system.
- Published
- 2018
41. Preventing occupational corruption:utilising situational crime prevention techniques and theory to enhance organisational resilience
- Author
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Mark Button, David William James Shepherd, Martin Tunley, and Dean Blackbourn
- Subjects
occupational corruption ,Corruption ,business.industry ,Mechanism (biology) ,Strategy and Management ,media_common.quotation_subject ,Best practice ,05 social sciences ,situational crime prevention ,bribery ,Public relations ,corruption-proofing ,Variety (cybernetics) ,Power (social and political) ,Crime prevention ,occupational fraud ,050501 criminology ,Situational ethics ,Resilience (network) ,Psychology ,business ,Law ,Safety Research ,0505 law ,media_common - Abstract
Corruption of all types including occupational corruption causes immense damage to society. Though a number of guides have been published which offer prevention advice, there is very little original criminological research which connects theory to best practice. This paper demonstrates that Clarke’s situational crime prevention framework provides a mechanism for operatively analysing specific situations to design and implement prevention methods. The study analyses a variety of techniques, based upon a survey and interviews with counter-corruption professionals, to offers insights into their utilisation and effectiveness. To achieve meaningful implementation of the techniques, counter-corruption managers need the delegated power and support of the executive leadership.
- Published
- 2018
42. The Barriers to the Opening of Government Data in the UK – A View From the Bottom
- Author
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Mark Button, Victoria Wang, and David William James Shepherd
- Subjects
impression management ,Open Government Data (OGD) ,EP/N027825/1 ,Public Administration ,Sociology and Political Science ,Public administration ,privacy ,Civil servants ,UK government ,Sociology ,benefit paradox ,Open government ,Government ,business.industry ,Communication ,RCUK ,EPSRC ,Publishing ,Impression management ,Position (finance) ,business ,EP/N028139/1 ,Library and Information Science ,Information Systems - Abstract
This paper explores some of the key barriers to Open Government Data (OGD) that responsible civil servants in the UK face as they try to comply with the UK-led OGD initiative. Empirically, we provide a quantitative analysis of the resources published on the government’s central OGD portal, data.gov.uk, and a unique insight into the publishing of OGD in the UK based on 22 interviews with responsible individuals at the operational level of publishing OGD. Our findings reveal that while the barriers to open government information have been substantially reduced, the barriers to open government data persist. Even the most enthusiastic responsible individuals face considerable obstacles in publishing OGD. Further, a key barrier to OGD in the UK is its impression management strategy based on its informational rather than data orientation. Due to the UK’s pioneering position in the OGD initiative, these findings are relevant to understanding and improving OGD programmes at local, national and international levels. The findings may subsequently lead to evidence-based strategies and policies.
- Published
- 2018
43. Tuberculosis incidence after 36 months’ isoniazid prophylaxis in HIV-infected adults in Botswana
- Author
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Zegabriel Tedla, James Shepherd, Samba Nyirenda, Thabisa Sibanda, Nong Shang, Tefera Agizew, Taraz Samandari, Barudi Mosimaneotsile, Oaitse I. Motsamai, and Charles E. Rose
- Subjects
Adult ,Male ,medicine.medical_specialty ,Tuberculosis ,Immunology ,Antitubercular Agents ,Placebo-controlled study ,Tuberculin ,HIV Infections ,Article ,law.invention ,Placebos ,Double-Blind Method ,Randomized controlled trial ,law ,Internal medicine ,Isoniazid ,Humans ,Immunology and Allergy ,Medicine ,Botswana ,business.industry ,Incidence ,Incidence (epidemiology) ,Hazard ratio ,medicine.disease ,Confidence interval ,Surgery ,Infectious Diseases ,Cohort ,Female ,Pre-Exposure Prophylaxis ,business - Abstract
Objective Thirty-six months of isoniazid preventive therapy (36IPT) was superior to 6 months of IPT (6IPT) in preventing tuberculosis (TB) among HIV-infected adults in Botswana. We assessed the posttrial durability of this benefit. Design A 36-month double-blind placebo controlled trial (1 : 1 randomization) with recruitment between November 2004 and July 2006 and observation until June 2011. Methods One thousand, nine hundred and ninety-five participants were followed in eight public health clinics. Twenty-four percent had a tuberculin skin test ≥5 mm (TST-positive). A minimum CD4 lymphocyte count was not required for enrolment. Antiretroviral therapy (ART) was provided in accordance with Botswana guidelines; 72% of participants retained by June 2011 had initiated ART. Multivariable analysis using Cox regression analysis included treatment arm, TST status, ART as a time-dependent variable and CD4 cell count at baseline and updated at 36 months. Results In the posttrial period, 2.13 and 2.14 per 100 person-years accumulated, whereas 0.93 and 1.13% TB incidence rates were observed in the 36IPT and 6IPT arms, respectively (P = 0.52). The crude hazard ratio of TB during the trial and posttrial was 0.57 [95% confidence intervals (CI) 0.33, 0.99] and 0.82 (95% CI 0.46, 1.49), and when restricted to TST-positive participants was 0.26 (95% CI 0.08, 0.80) and 0.40 (95% CI 0.15, 1.08), respectively. Multivariable analysis showed that ART use was associated with reduced death (adjusted hazard ratio 0.36, 95% CI 0.17-0.75) but not TB (0.92, 95% CI 0.55-1.53) in the posttrial period. Conclusion The benefit of 36IPT for TB prevention declined posttrial in this cohort. Adjunctive measures are warranted to prevent TB among HIV-infected persons receiving long-term ART in TB-endemic settings.
- Published
- 2015
44. Mathematical Model of the Oxidation of a Uranium Carbide Fuel Pellet Including an Adherent Product Layer
- Author
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James Shepherd, Michael Fairweather, Peter J. Heggs, and Bruce C. Hanson
- Subjects
Materials science ,Applied Mathematics ,Oxide ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Rate-determining step ,7. Clean energy ,Carbide ,Reaction rate ,chemistry.chemical_compound ,020401 chemical engineering ,chemistry ,Chemical engineering ,Modeling and Simulation ,Mass transfer ,Forensic engineering ,Uranium carbide ,0204 chemical engineering ,Diffusion (business) ,0210 nano-technology ,Carbon monoxide - Abstract
Uranium carbide is a candidate fuel for Generation IV nuclear reactors. However, like any candidate fuel, a reprocessing route should be established before implementation. One proposed method involves a pre-oxidation step, where the carbide fuel is oxidized to an oxide and then reprocessed as normal. A mathematical model has been developed to simulate such an oxidation using finite difference approximations of the heat and mass transfer processes occurring. Available literature was consulted to provide coefficients for the reaction rates and importantly the diffusion of oxygen through the adherent oxide layer that forms on the carbide: the rate limiting step. The transient temperature, oxygen and carbon monoxide distributions through the system are modeled in order to predict oxidation completion times and the temperatures reached. It was found that for a spherical pellet of radius 0.935 cm, the oxidation can take from 1 to 19 h depending on the oxidation conditions and reach temperatures of up to 1556 °C. A robust model results that offers increased understanding of a process crucial to the sustainable use of carbide fuels in energy generation.
- Published
- 2017
45. Increase in anti-tuberculosis drug resistance in Botswana: results from the fourth National Drug Resistance Survey
- Author
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Joconiah Chirenda, Heather J. Menzies, R. Makombe, James Shepherd, O. Kachuwaire, Kevin P. Cain, T. Maribe, B. Kim, K. Radisowa, C. Sentle, V. Anisimova, S. El-Halabi, Marcus A. Bachhuber, E. Bile, Taraz Samandari, G. Moalosi, Victoria M. Gammino, and J. Basotli
- Subjects
Adult ,Male ,Pulmonary and Respiratory Medicine ,medicine.medical_specialty ,Time Factors ,Tuberculosis ,Adolescent ,Antitubercular Agents ,Microbial Sensitivity Tests ,Drug resistance ,Article ,Mycobacterium tuberculosis ,Young Adult ,Anti tuberculosis ,Drug Resistance, Multiple, Bacterial ,Internal medicine ,Tuberculosis, Multidrug-Resistant ,Humans ,Medicine ,Young adult ,Child ,Tuberculosis, Pulmonary ,Aged ,Aged, 80 and over ,Botswana ,biology ,business.industry ,Transmission (medicine) ,Mycobacterial culture ,Sputum ,Middle Aged ,biology.organism_classification ,medicine.disease ,Surgery ,Treatment Outcome ,Infectious Diseases ,Child, Preschool ,Health Care Surveys ,Female ,medicine.symptom ,business - Abstract
Setting Although approximately 0.5 million cases of multidrug-resistant tuberculosis (MDR-TB) occur globally each year, surveillance data are limited. Botswana is one of the few high TB burden countries to have carried out multiple anti-tuberculosis drug resistance surveys (in 1995-1996, 1999 and 2002). Objective In 2007-2008, we conducted the fourth national survey of anti-tuberculosis drug resistance in Botswana to assess anti-tuberculosis drug resistance, including trends over time. In the previous survey, 0.8% (95%CI 0.4-1.5) of new patients and 10.4% (95%CI 5.6-17.3) of previously treated patients had MDR-TB. Design During the survey period, eligible specimens from all new sputum-smear positive TB patients and from all TB patients with history of previous anti-tuberculosis treatment underwent mycobacterial culture and anti-tuberculosis drug susceptibility testing (DST). Results Of 924 new TB patients and 137 with previous anti-tuberculosis treatment with DST results, respectively 23 (2.5%, 95%CI 1.6-3.7) and 9 (6.6%, 95%CI 3.3-11.7) had MDR-TB. The proportion of new TB patients with MDR-TB has tripled in Botswana since the previous survey. Conclusion Combatting drug-resistant TB will require the scale-up of MDR-TB diagnosis and treatment to prevent the transmission of MDR-TB and strengthening of general TB control to prevent the emergence of resistance.
- Published
- 2014
46. Evaluating the case for greater use of private prosecutions in England and Wales for fraud offences
- Author
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Alison Wakefield, David William James Shepherd, Graham Brooks, Chris Lewis, and Mark Button
- Subjects
Sociology and Political Science ,Law ,Political science ,Political Science and International Relations ,Sanctions ,Criminology ,Sentencing ,Policing-and-criminal-investigations ,Private prosecution - Abstract
This paper considers the challenges and opportunities that exist in England and Wales for the use of private prosecutions for Fraud. It considers the need for sanctions against fraudsters: looks at the prosecution landscape as it has evolved, especially during the 21st century: considers the legal basis for private prosecution and gives a brief history of its extent. The advantages and disadvantages associated with private prosecution are considered and recommendations made on the changes needed before there could be significant developments in the use of private prosecutions.
- Published
- 2014
47. Housing benefit for service charges in sheltered housing schemes: an exercise in semantics or an application of reality?
- Author
-
James Shepherd and Paul Sandford
- Subjects
Advanced and Specialized Nursing ,Community and Home Care ,Service (business) ,Health (social science) ,Housing Benefit ,Public economics ,business.industry ,Level of service ,Rehabilitation ,Legislation ,Public relations ,Semantics ,Tribunal ,Sheltered housing ,Value (economics) ,business - Abstract
PurposeThis paper aims to give guidance on the level of service charges that can be claimed by residents in sheltered housing as part of their housing benefit claims.Design/methodology/approachThe paper reviews the relevant legislation and recent opinions and rulings of both the Upper Tribunal and the Supreme Court.FindingsA broad based non arithmetical approach must be taken, particularly as many key words are not statutorily defined.Originality/valueClaimants, advocates and decision makers should use the guidance outlined when considering housing benefit claims by sheltered housing residents.
- Published
- 2012
48. Accumulation of large very low density lipoprotein in plasma during intravenous infusion of a chylomicron-like triglyceride emulsion reflects competition for a common lipolytic pathway
- Author
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Christopher J. Packard, Philip J. Stewart, Johan Björkegren, Muriel J. Caslake, James Shepherd, Fredrik Karpe, Dorothy Bedford, L Foster, and Anders Hamsten
- Subjects
medicine.medical_specialty ,Very low-density lipoprotein ,Triglyceride ,Apolipoprotein B ,biology ,nutritional and metabolic diseases ,QD415-436 ,Cell Biology ,Biochemistry ,digestive system ,chemistry.chemical_compound ,Endocrinology ,chemistry ,Internal medicine ,Emulsion ,medicine ,biology.protein ,polycyclic compounds ,Ingestion ,Lipolysis ,Density gradient ultracentrifugation ,lipids (amino acids, peptides, and proteins) ,Chylomicron - Abstract
Very low density lipoproteins (VLDL) are produced in the liver and contain apolipoprotein (apo) B-100 and endogenous lipids. By contrast, ingestion of fat leads to formation of chylomicrons containing apoB-48 secreted from the intestine. In this study, a 60-min intravenous infusion of a chylomicron-like triglyceride emulsion was given to healthy young men to examine whether competition between chylomicrons and VLDL for the same lipolytic pathway explains the increase in VLDL seen after meals. The responses of two major VLDL subfractions were determined by measuring the concentrations of apoB-100 in fractions of triglyceride-rich lipoproteins with Svedberg flotation rates of 60-400 (large VLDL) and 20-60 (small VLDL) that were separated from plasma by density gradient ultracentrifugation. A threefold elevation in plasma triglycerides was observed during the infusion together with a consistent linear increase of large VLDL. The rate at which large VLDL accumulated in plasma differed markedly among individuals and was not enhanced by doubling of the infusion rate. The response of small VLDL was more heterogeneous; however, a decrease was seen in most subjects. The combined pattern for the two VLDL species is what would be expected if large VLDL particles are the precursors of smaller VLDL species and if lipolysis of large VLDL is inhibited through competition from the triglyceride emulsion. The extent to which the triglyceride emulsion inhibited the lipolysis of VLDL and/or influenced the synthesis rate of large VLDL was estimated from simultaneous stable isotope studies. The emulsion caused a 75-90% block of the conversion of large VLDL apoB to small VLDL apoB and there was no sign of enhanced synthesis of large VLDL after infusion of the triglyceride emulsion. The corollary of these findings is that chylomicrons and their remnants impede the normal lipolytic degradation of VLDL and could thereby be indirectly implicated in the generation of atherogenic remnant lipoproteins.
- Published
- 2016
49. A Novel Electrical Based Breach Detection System for Flexible Pipe
- Author
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William James Shepherd, Phil Nott, John Mcnab, Syed Zakir Ahmed, and Phil Harley
- Subjects
Steady state (electronics) ,Computer science ,business.industry ,Mechanical engineering ,Structural engineering ,business ,Corrosion - Abstract
An outer shield breach is the most common form of damage that can occur to a subsea flexible pipe during both installation and operation. Definitive and accurate detection and location of such damage is imperative in triggering the appropriate repair response. The overall aim is to minimise corrosion damage to the carbon steel strength elements in the pipe annulus, which occurs from the resulting ingress of seawater. GE Oil & Gas, in collaboration with Photon Fire Ltd have developed a new method of detecting seawater in a subsea flexible pipe annulus. This paper describes a novel breach detection system developed to monitor pipes using very low energy electrical signals appropriate for use in hazardous areas. The technique provides an enduring record of the occurrence of a breach and the extent of the subsequent flooding. A brief outline of the development programme is presented. The work involved determining the sensing technique used, development of appropriate electronic instrumentation, the optimised method for installing the sensor into the riser, and bespoke connection to the instrumentation. A prototype system, approved for use in Hazardous Area ATEX zone zero has been implemented on midscale pipe samples and the transient and steady state ‘scans’ of the pipe have been investigated. A summary of the test results and a proposed testing regime is presented. Results show that using this technique can accurately determine that a breach has occurred in the wall of the riser and the extent of the flooding.
- Published
- 2016
50. Drilling Safe Wells Through Efficient, Rapid and Site Specific Planningto Manage Risks & Improve Performance
- Author
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Muhammad R. Tayab, Suhail Valappil, Sultan Al Yammani, and James Shepherd
- Published
- 2016
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