Darren Smith
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View article: Oral microbiomes as forensic markers of origin and migration: Insights from an underrepresented population, Nigeria
Oral microbiomes as forensic markers of origin and migration: Insights from an underrepresented population, Nigeria Open
The oral microbiome is shaped by environmental and host-associated factors, suggesting its utility for human profiling in forensics, particularly as an indicator of geographic origin and human migration. Using high-throughput sequencing an…
View article: Spatiotemporal development of late and moderate preterm infant gut and oral microbiomes and impact of gestational age on early colonization
Spatiotemporal development of late and moderate preterm infant gut and oral microbiomes and impact of gestational age on early colonization Open
Microbiome research focusing on late and moderate preterm infants (LMPT; 32 to 36 weeks gestation) is limited, despite rising LMPT births, large healthcare burdens, and increased risks of multiple morbidities, potentially microbially relat…
View article: Interpretation guidance for MHRA regulatory considerations for phage therapeutic products
Interpretation guidance for MHRA regulatory considerations for phage therapeutic products Open
On 4 June 2025, the MHRA published ‘Regulatory considerations for therapeutic use of bacteriophages in the UK’. This was in response to recommendations made by the House of Commons Science, Innovation and Technology Committee Inquiry into …
View article: Understanding the Clinical Characteristics and Timeliness of Diagnosis for Patients Diagnosed With Long Covid: A Retrospective Observational Cohort Study From North West London
Understanding the Clinical Characteristics and Timeliness of Diagnosis for Patients Diagnosed With Long Covid: A Retrospective Observational Cohort Study From North West London Open
Background Long Covid is a multisystem condition first identified in the Covid‐19 pandemic, characterised by a wide range of symptoms including fatigue, breathlessness and cognitive impairment. Considerable disagreement exists in who is mo…
View article: Genomic analysis of Aeromonas species isolated from retail foods suggests an under-investigated population
Genomic analysis of Aeromonas species isolated from retail foods suggests an under-investigated population Open
The genus Aeromonas includes species capable of causing disease in a range of hosts, including humans. With some species implicated in outbreaks of illness, these bacteria are considered emerging foodborne pathogens. This study examined Ae…
View article: Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk
Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk Open
Bacteriophages and lipids in human milk may benefit preterm infant health by modulating gut microbiomes. Here, we present a protocol for analyzing the phageome and lipidome in preterm milk using shotgun metagenomics and untargeted lipidomi…
View article: PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB
PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB Open
BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The varied BREX T…
View article: PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB
PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB Open
BREX ( B acte r iophage Ex clusion) systems, identified through shared identity with Pgl ( P hage G rowth L imitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The vari…
View article: Profiling the Enterobacterales Community Isolated from Retail Foods in England
Profiling the Enterobacterales Community Isolated from Retail Foods in England Open
Enterobacterales include foodborne pathogens of importance to public health and are often targeted in food surveillance programs as both safety and hygiene indicators. Furthermore, Enterobacterales are important in the context of antimicro…
View article: Spatial and temporal epidemiology of SARS-CoV-2 virus lineages in Teesside, UK, in 2020: effects of socio-economic deprivation, weather, and lockdown on lineage dynamics
Spatial and temporal epidemiology of SARS-CoV-2 virus lineages in Teesside, UK, in 2020: effects of socio-economic deprivation, weather, and lockdown on lineage dynamics Open
Background : SARS-CoV-2 emerged in the UK in January 2020. The UK government introduced control measures including national ‘lockdowns’ and local ‘tiers’ in England to control virus transmission. As the outbreak continued, new variants wer…
View article: Understanding the clinical characteristics and timeliness of diagnosis for patients diagnosed with Long COVID: A retrospective observational cohort study from North West London
Understanding the clinical characteristics and timeliness of diagnosis for patients diagnosed with Long COVID: A retrospective observational cohort study from North West London Open
Background Long COVID is a multisystem condition first identified in the COVID-19 pandemic characterised by a wide range of symptoms including fatigue, breathlessness and cognitive impairment. Considerable disagreement exists in who is mos…
View article: Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence
Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence Open
Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognise and methylate 6 bp non-palindromic motifs within the host genome, and preve…
View article: Unelicitable Backdoors in Language Models via Cryptographic Transformer Circuits
Unelicitable Backdoors in Language Models via Cryptographic Transformer Circuits Open
The rapid proliferation of open-source language models significantly increases the risks of downstream backdoor attacks. These backdoors can introduce dangerous behaviours during model deployment and can evade detection by conventional cyb…
View article: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny Open
The SARS-CoV-2 genome occupies a unique place in infection biology – it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has bee…
View article: Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence
Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence Open
Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognize and methylate 6 bp non-palindromic motifs within the host genome, and preve…
View article: Influence of maternal folate depletion on Art3 DNA methylation in the murine adult brain; potential consequences for brain and neurocognitive health
Influence of maternal folate depletion on Art3 DNA methylation in the murine adult brain; potential consequences for brain and neurocognitive health Open
The developmental origins of health and disease hypothesis suggest early-life environment impacts health outcomes throughout the life course. In particular, epigenetic marks, including DNA methylation, are thought to be key mechanisms thro…
View article: The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies Open
Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented i…
View article: Controlling bacterial growth and inactivation using thin film-based surface acoustic waves
Controlling bacterial growth and inactivation using thin film-based surface acoustic waves Open
We introduced the use of piezoelectric thin film based ZnO/Si SAW devices. We explored the mechanisms of bacterial growth and inactivation caused by varied RF powers, ZnO concentrations, and thermal effects via thin film SAW technology.
View article: Building a future for phage-based technologies—a thought leadership approach to accelerating progress in the UK
Building a future for phage-based technologies—a thought leadership approach to accelerating progress in the UK Open
Antimicrobial resistance is a global issue that threatens our ability to effectively manage and treat bacteria in the context of human health, animal health, and the environment. Bacteriophages provide a viable and necessary alternative to…
View article: The core phageome and its interrelationship with preterm human milk lipids
The core phageome and its interrelationship with preterm human milk lipids Open
Phages and lipids in human milk (HM) may benefit preterm infant health by preventing gastrointestinal pathobiont overgrowth and microbiome modulation. Lipid association may promote vertical transmission of phages to the infant. Despite thi…
View article: LoRA Fine-tuning Efficiently Undoes Safety Training in Llama 2-Chat 70B
LoRA Fine-tuning Efficiently Undoes Safety Training in Llama 2-Chat 70B Open
AI developers often apply safety alignment procedures to prevent the misuse of their AI systems. For example, before Meta released Llama 2-Chat - a collection of instruction fine-tuned large language models - they invested heavily in safet…
View article: BadLlama: cheaply removing safety fine-tuning from Llama 2-Chat 13B
BadLlama: cheaply removing safety fine-tuning from Llama 2-Chat 13B Open
Llama 2-Chat is a collection of large language models that Meta developed and released to the public. While Meta fine-tuned Llama 2-Chat to refuse to output harmful content, we hypothesize that public access to model weights enables bad ac…
View article: Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey
Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey Open
The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until …
View article: Chronic supplementation of a multi-ingredient herbal supplement increases speed of cognitive task performance alongside changes in the urinary metabolism of dopamine and the gut microbiome in cognitively intact older adults experiencing subjective memory decline: a randomized, placebo controlled, parallel groups investigation
Chronic supplementation of a multi-ingredient herbal supplement increases speed of cognitive task performance alongside changes in the urinary metabolism of dopamine and the gut microbiome in cognitively intact older adults experiencing subjective memory decline: a randomized, placebo controlled, parallel groups investigation Open
Background The effects of herbs on brain function are often investigated in isolation, yet herbal preparations are often complex combinations of phytochemicals, designed to target widespread mechanisms. Objective To assess the effects of c…
View article: Vanillin Cross-Linked Chitosan Film with Controlled Release of Green Tea Polyphenols for Active Food Packaging
Vanillin Cross-Linked Chitosan Film with Controlled Release of Green Tea Polyphenols for Active Food Packaging Open
We report a novel cross-linked chitosan composite film containing vanillin, glycerol, and green tea extract. The effects of vanillin-mediated cross-linking and the incorporation of antimicrobial green tea polyphenols were investigated. The…
View article: Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias
Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias Open
[This corrects the article DOI: 10.1371/journal.ppat.1011461.].
View article: Built environment microbiomes transition from outdoor to human-associated communities after construction and commissioning
Built environment microbiomes transition from outdoor to human-associated communities after construction and commissioning Open
The microbiota of the built environment is linked to usage, materials and, perhaps most importantly, human health. Many studies have attempted to identify ways of modulating microbial communities within built environments to promote health…