A bit of a song & dance - first class folk music, food, heritage, art & curiosities. 10 years plus three Festival gatherings 15 -17th August 2025 #FolkEast
Articles by Nicholas Sanderson
Clinical validation of an optimised metagenomic nanopore sequencing method for detecting viral respiratory pathogens
3 Results In total 382 respiratory samples were retrieved, divided temporally into separate sample sets: a) a derivation (n=38 clinical samples, tested in aliquots to produce n=104 sequences); and b) a validation set (n=344 clinical samples, each tested once to produce n=344 individual sequences). Derivation Set: Defining thresholds for quality control The derivation set included 104 sequencing results from 38 samples, all with pathogens detected on multiplex PCR testing (Table 1, Fig.2).
Bispecific chimeric autoantibody receptor T cells eliminate acetylcholine receptor-specific B cells in myasthenia gravis models
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Abstract Myasthenia gravis (MG) is an autoimmune neuromuscular disorder mediated by autoantibodies targeting the nicotinic acetylcholine receptor (nAChR), which can lead to severe disability and life-threatening crises. Current therapies rely on broad immunosuppression and fail to achieve sustained remission in the majority of patients.
By Niels von Wardenburg, Gregorio Spagni, S. Momsen Reincke, Hans-Christian Kornau, Marie A. Homeyer, Sonja Blumenau, Maria Stecklum, Dietmar Schmitz, Andreas Pelz, Valentina Damato, Nicholas Sanderson, Tobias Derfuss, Minh Pham, Kevin C. O’Connor, Andreas Meisel, Harald Prüss, Stephanie Wernick, Viktoria Zinnow, Amelya Keles Slevogt, Lucie Y. Li
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Nature
Verified
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods
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Abstract The majority of SARS-CoV-2 genomes obtained during the pandemic were derived by amplifying overlapping windows of the genome (‘tiled amplicons’), reconstructing their sequences and fitting them together. This leads to systematic errors in genomes unless the software is both aware of the amplicon scheme and of the error modes of amplicon sequencing.
By Martin Hunt, Angie S Hinrichs, Daniel Anderson, Lily Karim, Bethany L Dearlove, Bede Constantinides, Philip Fowler, Teresa Street, Benjamin Kotzen, Nicola De Maio, Reuben Ayivor-Djanie, Matthew Bashton, Andreas Bergthaler, Stefan A. Boers, Alexander T. Dilthey, Kwabena Obeng Duedu, Lukas Endler, Ilka Engelmann, Ngiambudulu M. Francisco, Jonas Fuchs, Etienne Z. Gnimpieba, Jones Gyamfi, Matthew Huska, Hanna Jarva, Ravi Kant, Marie Lataretu, Gathsaurie Neelika Malavige, Niranjan Nagarajan, Marcus Panning, Peter K. Quashie, Diyanath Ranasinghe, James Emmanuel San, Nicholas Sanderson, Bryan Tegomoh, Olli Vapalahti, Andreas Walker, Robert Wilkinson, Carolyn Williamson, Tulio de Oliveira, Derrick W Crook, Russell B. Corbett-Detig, Jeff Knaggs, Dennis Heemskerk, Satu Kurkela, Brigitte Montes
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Nature
Verified
Myelin antigen capture in the CNS by B cells expressing EBV latent membrane protein 1 leads to demyelinating lesion formation
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Keywords B cells multiple sclerosis Epstein-Barr virus latent membrane protein 1 myelin oligodendrocyte glycoprotein demyelination neurotropic infection activation-induced cell death CD40L tissue antigen capture Introduction Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS).
By Hyein Kim, Mika Schneider, Yakine Raach, Panajotis Karypidis, Julien Roux, Georgios Perdikaris, Sebastian Holdermann, Laila Kulsvehagen, Anne-Catherine Lecourt, Kerstin Narr, Roman Sankowski, Martin Diebold, Ewelina Bartoszek-Kandler, Josef P. Kapfhammer, Gert Zimmer, Anne-Katrin Pröbstel, Marco Prinz, Ludwig Kappos, Nicholas Sanderson, Tobias Derfuss
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Cell Press
Verified
Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey
Article metrics loading... /content/journal/mgen/10.1099/mgen.0.001340 Download as PowerPoint /deliver/fulltext/mgen/11/1/mgen001340.html?itemId=/content/journal/mgen/10.1099/mgen.0.001340&mimeType=html&fmt=ahah References Perin J, Mulick A, Yeung D, Villavicencio F, Lopez G et al. Global, regional, and national causes of under-5 mortality in 2000-19: an updated systematic analysis with implications for the Sustainable Development Goals.
Species‐level, metagenomic and proteomic analysis of microbe‐immune interactions in severe asthma
1 INTRODUCTION Asthma is a complex, heterogenous disease.
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing
Article metrics loading... /content/journal/mgen/10.1099/mgen.0.001246 Download as PowerPoint /deliver/fulltext/mgen/10/5/mgen001246.html?itemId=/content/journal/mgen/10.1099/mgen.0.001246&mimeType=html&fmt=ahah References Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L et al. Genomics for public health and international surveillance of antimicrobial resistance.
Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23
Highlights • Nanopore sequencing is a reproducible tool for influenza surveillance. • Inter-regional transmission of influenza was common across the UK. • Influenza anti-viral resistance was rare. • In 1 year most infections were genetically similar, hindering transmission studies. • Hospital-acquired infections are likely a key source of nosocomial transmission. Abstract We evaluated Nanopore sequencing for influenza surveillance.
Bird Tunes - FolkEast
Bird Tunes - A new suite of folk tunes from Miranda Rutter with Rob Harbron
Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing
Article metrics loading... /content/journal/mgen/10.1099/mgen.0.001208 Download as PowerPoint /deliver/fulltext/mgen/10/3/mgen001208.html?itemId=/content/journal/mgen/10.1099/mgen.0.001208&mimeType=html&fmt=ahah References Unemo M, Shafer WM. Antimicrobial resistance in Neisseria gonorrhoeae in the 21st century: past, evolution, and future. Clin Microbiol Rev 2014; 27:587–613 [View Article] [PubMed] [Google Scholar] Omeershffudin UNM, Kumar S.
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing
Abstract Whole genome reconstruction of bacterial pathogens has become an import tool for tracking antimicrobial resistance spread, however accurate and complete assemblies have only been achievable using hybrid long and short-read sequencing. We have previously found the Oxford Nanopore Technologies (ONT) R10.4/kit12 flowcells produced improved assemblies over the R9.4.1/kit10, however they contained too many errors compared to hybrid Illumina-ONT assemblies.
Playing for their Pint
Sold Out /Been and gone
Year Round FolkEast - FolkEast
FolkEast is for life, not just for summer. Find out about events we run in Suffolk outside of the usual August shenanigans.
Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals
Highlights • Current surveillance definitions underestimate SARS-CoV-2 nosocomial acquisition. • Many cases of SARS-CoV-2 diagnosed within the first week of hospital admission were acquired in hospital. • Whole genome sequencing revealed most nosocomial transmission occurs from a relatively limited number of highly infectious individuals. • The majority of epidemiologically defined outbreaks consisted of multiple genomic introductions.
Stantec set to bring micro-mobility hubs to cities for e-bikes and e-scooters
Parking and e-charging hubs, designed to improve micro-mobility and autonomous vehicle infrastructure, will be offered through Stantec’s new automated mobility practice, GenerationAV By now, every municipal planner knows there’s a lot of kit involved in making transport “smart” — from sensors, to screens, to payment points, to the vehicles themselves.
COVID-19 stimulus spending needs to be wise to the perils of road building
In times of economic crisis, stimulus spending is important. But spending it wisely is even more important. In the midst of the climate and public health crisis you’d think we’d be on a recovery better path than we are today. Efforts to get the economy running again have long-lasting legacies It is well established logic that in times of economic downturns, Governments step in to stimulate the economy.
Optimized use of Oxford Nanopore flowcells for hybrid assemblies
Article metrics loading... /content/journal/mgen/10.1099/mgen.0.000453 References Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B et al. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother 2018; 73:1121–1137 [View Article][PubMed] [Google Scholar] George S, Pankhurst L, Hubbard A, Votintseva A, Stoesser N et al.
Toronto Region Board of Trade debuts regional analysis — Nick Sanderson Consulting
The Economic Blueprint Institute, the Toronto Region Board of Trade’s data and research arm, has published its playbook for planning a regional recovery, called Shaping Our Future. Concept map showing the different economic districts of the Toronto Region The Economic Blueprint Institute report identifies three "transformations" and a set of "critical activations" that will bear down against the Toronto region’s challenges and help it bounce back from the pandemic.
Whose lane is it, anyway? Five ways COVID-19 might change city mobility
The pandemic lockdown has changed the way people get around town — changes that may be permanently rewriting the mobility agenda for Canadian cities in a post-COVID era Efforts to halt the spread of COVID-19 have changed the rhythms of our cities dramatically. Since Prime Minister Trudeau’s instruction to Canadians on March 23 to “Go home and stay home,” downtown office blocks and schools have emptied out, while access to essential services is rationed. Mobility paused but for essentials.
Pandemic Archives - Spacing Toronto
By Spacing Radio There have been two full, virtual City Council meetings since the COVID-19 outbreak in Toronto. Those meeting saw near-unanimous votes... Read More By Ian Chodikoff The ability to feed our communities as a result of COVID-19 has the potential to increase awareness of the economic, social and... Read More By Nicholas Sanderson In cities the world over, streets are being repurposed for people walking, cycling, and simply spending time outside. First Milan...
A how-to guide to redesign city streets during and after COVID
In cities the world over, streets are being repurposed for people walking, cycling, and simply spending time outside. First Milan, Bogota, then Oakland, Lima, Paris, New York, London. The list goes on. From east to west, Canadian cities are setting out similar plans. So how should cities start to re-plan their streets? Here is a four-step guide for our cities.
Two Lineages of KLRA with Contrasting Transcription Patterns Have Been Conserved at a Single Locus during Ruminant Speciation
Open Access Mark S. Gibson, Alasdair J. Allan, Nicholas D. Sanderson, James Birch, Simon Gubbins, Shirley A. Ellis and John A. Hammond J Immunol May 1, 2020, 204 (9) 2455-2463; DOI: https://doi.org/10.4049/jimmunol.1801363 Key Points Two divergent allele lineages of KLRA have become fixed in the cattle population. The two cattle KLRA allele lineages likely have contrasting functions. Abstract Cattle possess the most diverse repertoire of NK cell receptor genes among all mammals studied to date.
Two Lineages of KLRA with Contrasting Transcription Patterns Have Been Conserved at a Single Locus during Ruminant Speciation
Open Access Mark S. Gibson, Alasdair J. Allan, Nicholas D. Sanderson, James Birch, Simon Gubbins, Shirley A. Ellis and John A. Hammond J Immunol March 25, 2020, ji1801363; DOI: https://doi.org/10.4049/jimmunol.1801363 Key Points Two divergent allele lineages of KLRA have become fixed in the cattle population. The two cattle KLRA allele lineages likely have contrasting functions. Abstract Cattle possess the most diverse repertoire of NK cell receptor genes among all mammals studied to date.
Line-up - FolkEast
Angeline Morrison Band, Baskery, Bloomfield Family Band, Blowzabella, Bof!, Dhol Foundation, The Drystones, Fay Hield Trio, Folk Detectives, George Boomsma Band, Gigspanner Big Band, Granny's Attic, Hedera, Honey & the Bear, Jennifer Reid, Jim Moray Band, John & Lynne Ward, Katherine Priddy, The King Driscolls, Kyson Point, Kris Drever Band, Martin Carthy & Jon Wilks, Melrose Quartet, Mishra, Nick Hart & Tom Moore, Paper Sparrows, Peterloo Project, Rag Mama Rag, Rhythms of Migration - Freedom...
How long will can ride-hailing apps last?
Part two of Nick’s look at the state of ride hailing. Read part one here. It has been almost ten years since Uber was founded in San Francisco. In 2011, saw their first services and app launched, which was followed a year later by ride-hailing competitor Lyft. The bright future that every tech-happy urbanite had been longing for had arrived: you could book a taxi through your smartphone. Hallelujah. World saved.
What other cities can learn from Toronto’s ride-hailing experience
With British Columbia rolling out its ride-hailing regulations in August, Toronto City Council re-examining its bylaws, and Halifax looking to do the same, it seems like a good time to dive in on what we do and don’t know about ride-hailing in our cities. Part one of two pieces by Nick Sanderson exploring these issues. Part 2 can be found here. What’s happening in Toronto?
Analysis: the permanent King Street transit way is a model for all Toronto
King Street pilot by Wylie Poon The Toronto Streetcar, older or newer type, is an ever-present symbol of the city. The red, black and white TTC colours trundle along century old tracks, east and west, north and south and are a crucial part of the city’s fabric: 56 million trips were made by Streetcar in 2017. On one street, famous to Torontonians, streetcar ridership has jumped 17 per cent.
Is it time for Canadian cities to think about road pricing? Put it to the people and find out.
Toronto Streetcar in traffic by Wylie Poon Editor: With congestion grinding cities down and road pricing hitting political buffers, is there a better route to a solution? Spacing is pleased to introduce our newest urban issues correspondent, Nicholas Sanderson. Nick is an independent policy and communications consultant from the UK, currently working out of Toronto, specializing in transport and environment issues.
Traffic Archives - Spacing Toronto
By Nicholas Sanderson Editor: With congestion grinding cities down and road pricing hitting political buffers, is there a better route to a solution... Read More By Tricia Wood This is probably a pointless plea, but can we stop talking about congestion? Our conversations about transportation in Canadian urban... Read More By Tricia Wood When we plan for our transportation future, whether we’re talking at the municipal, regional or provincial level, there’s an elephant...
Control of Artifactual Variation in Reported Intersample Relatedness during Clinical Use of a Mycobacterium tuberculosis Sequencing Pipeline
ABSTRACTContact tracing requires reliable identification of closely related bacterial isolates. When we noticed the reporting of artifactual variation between Mycobacterium tuberculosis isolates during routine next-generation sequencing of Mycobacterium spp., we investigated its basis in 2,018 consecutive M. tuberculosis isolates.
Eurosurveillance | Gonorrhoea treatment failure caused by a Neisseria gonorrhoeae strain with combined ceftriaxone and high-level azithromycin resistance, England, February 2018
We describe a gonorrhoea case with combined high-level azithromycin resistance and ceftriaxone resistance. In February 2018, a heterosexual male was diagnosed with gonorrhoea in the United Kingdom following sexual intercourse with a locally resident female in Thailand and failed treatment with ceftriaxone plus doxycycline and subsequently spectinomycin. Resistance arose from two mechanisms combining for the first time in a genetic background similar to a commonly circulating strain.
Five key decisions facing the next generation of road pricing
The first Street Talk of 2018 put the issue of pay-per-mile road pricing to a panel of experts. Nicholas Sanderson sums up the choices city leaders will need to make in order to roll out road pricing. London’s Congestion Charge turns 15 this year. Its immediate impact was of fewer vehicles, less congestion, better air quality and reduced carbon emissions.
Can the Mayor treble London’s protected Cycle Superhighways by 2020?
Before the 2016 Mayoral election, all the main candidates committed to triple the extent of protected space for cycling, through the cycle superhighways programme. With 27 more months guaranteed in office, what does Sadiq Khan need to do to meet this commitment? The London Assembly Transport Committee are currently investigating the issue and here’s what we know and what’s needed.
M&S Energy names community fund winners - Environment Journal
A total of 25 projects will each receive up to £12,000 of funding from the fund for their local clean energy project. More than 150 projects entered this year’s competition, with 21 of the winners were determined by a public vote. The Sunshine for St Micheal’s hospice in Hereford (pictured) received 721 votes in the public vote and has been awarded £12,000.
Ministers urged to put catchment partnerships at heart of new environment plan - Environment Journal
The Chartered Institution of Water and Environmental Management (CIWEM) has today called on ministers to give more powers and resources to the 100-plus catchment partnerships, which currently exist across England. The catchment partnerships were introduced as a voluntary programme in 2011 and include local bodies, farmers and landowners, who work together to deliver the most effective ways to deliver flood and climate resilience.
Getting your message across - Environment Journal
At Bath and North East Somerset Council (B&NES) we think we have found one answer in a series of animated infographics. We’d been talking about customer needs and preferences for communication for a while. With our resident population as well as visitor numbers increasing yet with a finite amount of resource available to communicate key messages and handle queries, just how to do it was a question that was being asked more frequently and across a diverse range of services.
How walking and cycling can be used to pave the way for new homes - Environment Journal
Nowhere is this more acutely felt than in London. And the capital’s mayor, Sadiq Khan, is focused on tackling this housing crisis. But what has this got to do with walking and cycling, you ask? Potentially a lot. Here’s why. In London, the planning system rightly restricts new development to where there is public transport capacity or committed improvements.
How to ride the ‘rollercoaster’ of community energy - Environment Journal
Community Energy: A guide to community-based renewable-energy projects has been written by Gordon Cowtan and looks at the history of community energy in the UK and examines which projects have been successful and unsuccessful. Mr Cowtan was one of the founders of the Fintry Development Trust, set up in 2007 to help make local residents in the Scottish village reduce their energy use and tackle other issues like fuel poverty.
Campaign aims to make EVs the ‘new normal’ by 2030 - Environment Journal
The EV100 campaign will be launched today at an event in New York and aims to use the collective buying of multinationals to accelerate the take up of EVs around the globe. Among the first companies to sign up to the campaign are Heathrow Airport, IKEA and Unilever. The companies have all promised to fast-track their rollout and integrate EVs directly into their owned or leased fleets by 2030.
Balancing precaution and innovation in post-Brexit environmental law - Environment Journal
The precautionary principle was defined in the 1992 Rio Conference on the Environment. It stated: ‘In order to protect the environment, the precautionary approach shall be widely applied by States according to their capability.
Mayor Khan’s strategy puts health at the heart of transport. Can we get Londoners walking and cycling? - Environment Journal
Earlier in the year, Transport for London set about finding a way of quantifying how much travel in London could be made by foot or bike. They took data on all of the journeys Londoners made each day, stripped out those already walked or cycled and those that were too long, or involved carrying heavy tools and equipment, and a few other criteria. The idea was they would find out how many journeys could be reasonably cycled.
Coffee cup and plastic bottle inquiry relaunched - Environment Journal
The committee launched an inquiry into plastic bottles and coffee cups earlier this year during the last parliament, but the general election was called before it could complete its research. Now the new committee has decided it should be relaunched and has asked for evidence to be submitted by September 29. The inquiry will look at the environmental impact of coffee cups and plastic bottles, along with the challenges in recycling such products.
When will London adopt pay-as-you-go road pricing?
On 21 June, Sadiq Khan, published a draft of the Mayor's Transport Strategy, and some newspaper editors got very excited. The Sun’s headline claimed “London motorists will pay-as-you-go and won’t have anywhere to park”; the Times was more measured with “Drivers in London face first pay-as-you-go road charge”. Unfortunately, neither of these headlines are entirely accurate. So what’s really being mooted in the draft strategy and what might it mean?
Home is where the smart is - Environment Journal
It might sound like something ripped from the pages of a Jules Verne novel, but the prospect of a home that thinks for itself, generates power itself and is also able to sell electricity back to the grid when demand allows is now a reality, although a lot of the technology involved is still in its infancy.
Veolia offers hope in the war against coffee cups - Environment Journal
The service will be available to both existing Veolia customers and new customers and aims to collect the cups as soon as customers have finished their drink in a bid to increase recycling rates. The company says multiple options are available, including an in-house recycling bin, which has been purposely designed to enable the consumer to drain any remaining liquid from their cup and separate the lid, sleeve and cup to minimise contamination.
Oxford City Council demands action on clean air - Environment Journal
In its official response to the Government’s Draft Air Quality Action Plan, the city council has demanded more funding for local authorities to implement innovative new products, such as NO2-reducing road surfaces. The local authority has also called on the Government to set up a network for councils to share information and best practice, as well as introduce a scrappage scheme to encourage drivers to take high-emitting vehicles off the road.
Sadiq’s most important strategy as Mayor - Environment Journal
First off, the transport strategy is no simple declaration. At 361 pages, Boris’s strategy came two years after his election in 2008. After one year Sadiq’s first draft is good progress in developing policies to cover off a vast range of services: the Underground, Overground, TfL run railways, DLR, trams, buses, cycle hire, taxis, London’s main roads and funding to London’s boroughs to spend on their streets, for instance.
Art for the environment - Environment Journal
Some 20 years ago, when I was writing my first environmental management plan for The Australian National University – a strategy to make our campus infrastructure more sustainable – I was approached by John Reid an artist and academic from the school of art, with (what seemed to me) an odd suggestion. He proposed that we have artists and musicians collaborate with scientists and facilities managers to highlight environmental issues facing society and promote the objectives of the university plan.
Rethinking waste crime - Environment Journal
Despite significant additional funding and renewed vigour by governments and the regulators to tackle the issue, waste crime is more entrenched than ever. It continues to undermine investment, growth and jobs within the waste and resources industry, blights communities and threatens our natural environment.
Thugs, knotweed and nuisance - Environment Journal
Japanese knotweed has been described as ‘a real thug’ by the Royal Horticultural Society and there is no denying that it is the bully of the plant world. It destroys other native species, grows voraciously and can force itself through concrete causing damage to buildings and infrastructure. It is expensive and time-consuming to eradicate completely. As a result, its presence on or in the vicinity of a property can stop lenders from providing finance to potential purchasers.
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