A New Validated Approach for Identifying Childhood Immunizations in Electronic Health Records in the United Kingdom.

BACKGROUND: Routinely collected electronic health records (EHR) offer a valuable opportunity to carry out research on immunization uptake, effectiveness, and safety, using large and representative samples of the population. In contrast to other drugs, vaccines do not require electronic prescription in many settings, which may lead to ambiguous coding of vaccination status and timing. METHODOLOGY: We propose a comprehensive algorithm to identifying childhood immunizations in routinely collected EHR. In order to deal with ambiguous coding, over-recording, and backdating in EHR, we suggest an approach combining a wide range of medical codes in combination to identify vaccination events and using appropriate wash-out periods and quality checks. We illustrate this approach on a cohort of children born between 2006 and 2014 followed up to the age of five in the Clinical Practice Research Datalink (CPRD) Aurum, a UK primary care dataset of EHR, and validate the results against national estimates of vaccine coverage by NHS Digital and Public Health England. RESULTS: Our algorithm reproduced estimates of vaccination coverage, which are comparable to official national estimates and allows to approximate the age at vaccination. Electronic prescription data only do not cover vaccination events sufficiently. CONCLUSION: Our new proposed method could be used to provide a more accurate estimation of vaccination coverage and timing of vaccination for researchers and policymakers using EHR. As with all observational research using real-world data, it is important that researchers understand the context of the used dataset used and the clinical practice of recording.

Adult intravenous sedation in general dental practice: indication, effectiveness and patient experiences.

Background Conscious sedation is an option in primary dental care for anxious patients or those undergoing extensive procedures. The objective of this retrospective service evaluation was to study the range of treatments delivered during sedation with intravenous midazolam, together with patient-reported experience measures.Methods Data from 100 consecutive patients treated under sedation at a single private dental practice were evaluated retrospectively. All patients were asked questions about their experience of sedation during a post-operative follow-up phone call.Results Over half of patients were treated under sedation due to anxiety. The mean dose of midazolam was 7.8 mg and the average treatment time was 1 hour 25 minutes. Of note, the average dose for the most extensive procedure - implant immediate full arch loading - was 11.7 mg; however, this equated to an average dose of 4.5 mg per hour. One patient needed supplemental oxygen; flumazenil was never required. Additionally, 91% of patients felt they had enough sedation, and 50% could remember the events of treatment.Conclusion With the British National Formulary recommending a maximum dose of 7.5 mg midazolam, this study demonstrates that this dose can be safely exceeded in dental treatment; therefore, a dose that accounts for the length of the procedure is a more valid approach. Moreover, patients undergoing a variety of dental treatments were satisfied with the amount of intravenous sedation received and age is not an absolute limit for sedating older people.

Volumetric Analysis of Peri-implant Tissue Change Over Time: Validating an Innovative 3D Method.

PURPOSE: To validate an innovative 3D volumetric method of evaluating tissue changes proposed by Lee et al in 2020 by comparing the results of this method-in which the scanned peri-implant surfaces were transformed, visualized, and analyzed as 3D objects-to the results reported by an existing method based on calculation of the mean distance between measured surfaces. The null hypothesis was that there was no statistically significant difference between the two methods. Additionally, the present study evaluated peri-implant tissue changes 5 years after single implant placement in the esthetic zone. MATERIALS AND METHODS: Both methods were applied to 11 oral implant site casts (6 maxillary central incisor sites, 5 maxillary lateral incisor sites) taken from 11 patients at crown placement and at follow-up examinations 5 years later. The methods are based on digital workflows in which the reference and 5-year casts are scanned and the resulting STL files are superimposed and analyzed for three regions of interest (mesial papilla, central area, and distal papilla). The volumetric changes reported by the Lee et al method and the mean distance method were calculated and compared using the Spearman rank correlation coefficient (P < .01) and the Wilcoxon signed-rank test (P < .05). RESULTS: The correlation between the two sets of measurements was very high (Spearman rank correlation coefficient = 0.885). The new volumetric method indicated a mean volume loss of 2.82 mm3 (SD: 5.06), while the method based on the measurement of mean distance showed a mean volume loss of 2.92 mm3 (SD: 4.43; Wilcoxon signed-rank test result: P = .77). No statistically significant difference was found. The two methods gave equivalent results, and the null hypothesis was accepted. CONCLUSIONS: The new volumetric method was validated and can be considered a trustworthy tool.

A new neonatal BCG vaccination pathway in England: a mixed methods evaluation of its implementation.

INTRODUCTION: The introduction of a national evaluation of newborn screening for Severe Combined Immunodeficiency (SCID) in England triggered a change to the selective Bacillus Calmette-Guerin (BCG) vaccination programme delivery pathway, as this live attenuated vaccine is contraindicated in infants with SCID. The neonatal BCG vaccination programme is a targeted programme for infants at increased risk of tuberculosis and used to be offered shortly after birth. Since September 2021 the BCG vaccine is given to eligible infants within 28 days of birth, when the SCID screening outcome is available. We explore the experiences of those implementing the new pathway, and how they made sense of, engaged with, and appraised the change. METHODS: A mixed-methods evaluation was conducted between October 2022 and February 2023. This involved national online surveys with BCG commissioners and providers and qualitative semi-structured interviews with commissioners, providers, and Child Health Information System stakeholders in two urban areas. Survey data was analysed using descriptive statistics and interview data was analysed thematically. The data was triangulated using Normalization Process Theory as a guiding framework. RESULTS: Survey respondents (n = 65) and qualitative interviewees (n = 16) revealed that making sense of the new pathway was an iterative process. Some expressed a desire for more direction on how to implement the new pathway. The perceived value of the change varied from positive, ambivalent, to concerned. Some felt well-prepared and that improvements to data capture, eligibility screening, and accountably brought by the change were valuable. Others were concerned about the feasibility of the 28-day target, reductions in vaccination coverage, increased resource burden, and the outcome of the SCID evaluation. New collaborations and communities of practice were required to facilitate the change. Three main challenges in implementing the pathway and meeting the 28-day vaccination target were identified: appointment non-attendance; appointment and data systems; and staffing and resourcing. Feedback mechanisms were informal and took place in tandem with implementation. CONCLUSION: The new NHS neonatal BCG service specification has created an effective structure for monitoring and managing the BCG vaccination programme, but further work is required to support delivery of the 28-day vaccination target and improve uptake rates.

Pregnant women and measles: we need to be vigilant during outbreaks.

A number of countries including the UK are currently experiencing large outbreaks of measles affecting mainly young children but also adolescents and young adults. Women of childbearing age are a particular group of concern because the 1988 Wakefield Lancet paper, which falsely asserted a connection between the MMR vaccine and autism, was associated with a large and sharp decline in childhood MMR uptake over several years. This has left large cohorts of non-immune adolescents and young adults (born between 1998 and 2004), including young women who are now of childbearing age and remain susceptible to measles as well as rubella. Pregnant mothers are at higher risk of serious complications, such as pneumonia, with adverse pregnancy complications including fetal loss, premature birth, and neonatal death. Measles infection may also result in subacute sclerosing panencephalitis (SSPE), a very rare but very severe and invariably fatal neurodegenerative complication that typically manifests many years after acute measles infection but can have a short-onset latency with a fulminant course in pregnant women. Here, we summarise the epidemiology of measles infection, factors associated with the current measles outbreaks, as well as the risks and outcomes of measles, including SSPE, in pregnancy. We propose an algorithm for clinical management of measles infection in pregnancy. We also highlight the importance of early liaison with local health protection teams for risk assessment, diagnosis and management of suspected measles in pregnancy and close contacts as well as susceptible pregnant women exposed to a person with measles in the community.

SERS Microsensors for the Study of pH Regulation in Cystic Fibrosis Patient-Derived Airway Cultures.

Acidification of the airway surface liquid in the respiratory system could play a role in the pathology of Cystic Fibrosis, but its low volume and proximity to the airway epithelium make it a challenging biological environment in which to noninvasively collect pH measurements. To address this challenge, we explored surface enhanced Raman scattering microsensors (SERS-MS), with a 4-mercaptobenzoic acid (MBA) pH reporter molecule, as pH sensors for the airway surface liquid of patient-derived in vitro models of the human airway. Using air-liquid interface (ALI) cultures to model the respiratory epithelium, we show that SERS-MS facilitates the optical measurement of trans-epithelial pH gradients between the airway surface liquid and the basolateral culture medium. SERS-MS also enabled the successful quantification of pH changes in the airway surface liquid following stimulation of the Cystic Fibrosis transmembrane conductance regulator (CFTR, the apical ion channel that is dysfunctional in Cystic Fibrosis airways). Finally, the influence of CFTR mutations on baseline airway surface liquid pH was explored by using SERS-MS to measure the pH in ALIs grown from Cystic Fibrosis and non-Cystic Fibrosis donors.

DrivR-Base: a feature extraction toolkit for variant effect prediction model construction.

MOTIVATION: Recent advancements in sequencing technologies have led to the discovery of numerous variants in the human genome. However, understanding their precise roles in diseases remains challenging due to their complex functional mechanisms. Various methodologies have emerged to predict the pathogenic significance of these genetic variants. Typically, these methods employ an integrative approach, leveraging diverse data sources that provide important insights into genomic function. Despite the abundance of publicly available data sources and databases, the process of navigating, extracting, and pre-processing features for machine learning models can be highly challenging and time-consuming. Furthermore, researchers often invest substantial effort in feature extraction, only to later discover that these features lack informativeness. RESULTS: In this article, we introduce DrivR-Base, an innovative resource that efficiently extracts and integrates molecular information (features) related to single nucleotide variants. These features encompass information about the genomic positions and the associated protein positions of a variant. They are derived from a wide array of databases and tools, including structural properties obtained from AlphaFold, regulatory information sourced from ENCODE, and predicted variant consequences from Variant Effect Predictor. DrivR-Base is easily deployable via a Docker container to ensure reproducibility and ease of access across diverse computational environments. The resulting features can be used as input for machine learning models designed to predict the pathogenic impact of human genome variants in disease. Moreover, these feature sets have applications beyond this, including haploinsufficiency prediction and the development of drug repurposing tools. We describe the resource's development, practical applications, and potential for future expansion and enhancement. AVAILABILITY AND IMPLEMENTATION: DrivR-Base source code is available at https://github.com/amyfrancis97/DrivR-Base.

Mediators of change in psychological interventions for adult offenders with personality disorders: A scoping review of the literature.

Offenders with personality disorder cause disproportionate harm to society and pose significant challenges for those responsible for their care and rehabilitation. Personality disorders are heterogeneous in terms of symptoms, as well as their pathways to offending behaviour. Thus, there is limited evidence regarding effective interventions. One solution might be to focus on how interventions are delivered as well as what is delivered. Within the non-offender personality disorder literature, the identification of potential mediators of change has enabled interventions to focus on 'how' they are delivered (e.g., therapeutic alliance) rather than the intervention itself. We explore the evidence and present a scoping review of the available literature on the mechanisms of change in psychological treatments for offenders with personality disorder. Only one study was found in the scoping review, highlighting a significant gap in the evidence base. We discuss the implications of this finding and potential future directions.

Multivariate canonical correlation analysis identifies additional genetic variants for chronic kidney disease.

Chronic kidney diseases (CKD) have genetic associations with kidney function. Univariate genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with estimated glomerular filtration rate (eGFR) and blood urea nitrogen (BUN), two complementary kidney function markers. However, it is unknown whether additional SNPs for kidney function can be identified by multivariate statistical analysis. To address this, we applied canonical correlation analysis (CCA), a multivariate method, to two individual-level CKD genotype datasets, and metaCCA to two published GWAS summary statistics datasets. We identified SNPs previously associated with kidney function by published univariate GWASs with high replication rates, validating the metaCCA method. We then extended discovery and identified previously unreported lead SNPs for both kidney function markers, jointly. These showed expression quantitative trait loci (eQTL) colocalisation with genes having significant differential expression between CKD and healthy individuals. Several of these identified lead missense SNPs were predicted to have a functional impact, including in SLC14A2. We also identified previously unreported lead SNPs that showed significant correlation with both kidney function markers, jointly, in the European ancestry CKDGen, National Unified Renal Translational Research Enterprise (NURTuRE)-CKD and Salford Kidney Study (SKS) datasets. Of these, rs3094060 colocalised with FLOT1 gene expression and was significantly more common in CKD cases in both NURTURE-CKD and SKS, than in the general population. Overall, by using multivariate analysis by CCA, we identified additional SNPs and genes for both kidney function and CKD, that can be prioritised for further CKD analyses.

Enzymatic Processing of DNA-Protein Crosslinks.

DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of mechanisms and can significantly impede essential cellular processes such as transcription and replication. For this reason, anti-cancer drugs that form DPCs have proven effective in cancer therapy. While cells rely on numerous different processes to remove DPCs, the molecular mechanisms responsible for orchestrating these processes remain obscure. Having this insight could potentially be harnessed therapeutically to improve clinical outcomes in the battle against cancer. In this review, we describe the ways cells enzymatically process DPCs. These processing events include direct reversal of the DPC via hydrolysis, nuclease digestion of the DNA backbone to delete the DPC and surrounding DNA, proteolytic processing of the crosslinked protein, as well as covalent modification of the DNA-crosslinked proteins with ubiquitin, SUMO, and Poly(ADP) Ribose (PAR).

COVID-19 vaccination coverage for half a million non-EU migrants and refugees in England.

Despite evidence suggesting that some migrants are at risk of under-immunization and have experienced severe health inequities during the pandemic, data are limited on migrants' COVID-19 vaccine coverage globally. Here we linked data from non-European Union migrants and resettled refugees to the national COVID-19 vaccination dataset in England. We estimated patterns in second and third dose delays and overdue doses between 12 December 2020 and 20 April 2022 by age, visa type and ethnicity. Of the 465,470 linked records, 91.8% (427,073/465,470) of migrants received a second dose and 51.3% (238,721/465,470) received a third. Refugees had the highest risk of delayed second (adjusted odds ratio 1.66; 95% confidence interval 1.55-1.79) and third dose (1.55; 1.43-1.69). Black migrants were twice as likely to have a second dose delayed (2.37; 2.23-2.54) than white migrants, but this trend reversed for the third dose. Older migrants (>65 years) were four times less likely to have received their second or third dose compared with the general population in England aged >65 or older. Policymakers, researchers and practitioners should work to understand and address personal and structural barriers to vaccination for diverse migrant populations.

Ubiquitin signaling and the proteasome drive human DNA-protein crosslink repair.

DNA-protein crosslinks (DPCs) are large cytotoxic DNA lesions that form following exposure to chemotherapeutic drugs and environmental chemicals. Nucleotide excision repair (NER) and homologous recombination (HR) promote survival following exposure to DPC-inducing agents. However, it is not known how cells recognize DPC lesions, or what mechanisms selectively target DPC lesions to these respective repair pathways. To address these questions, we examined DPC recognition and repair by transfecting a synthetic DPC lesion comprised of the human oxoguanine glycosylase (OGG1) protein crosslinked to double-stranded M13MP18 into human cells. In wild-type cells, this lesion is efficiently repaired, whereas cells deficient in NER can only repair this lesion if an un-damaged homologous donor is co-transfected. Transfected DPC is subject to rapid K63 polyubiquitination. In NER proficient cells, the DPC is subject to K48 polyubiquitination, and is removed via a proteasome-dependent mechanism. In NER-deficient cells, the DNA-conjugated protein is not subject to K48 polyubiquitination. Instead, the K63 tag remains attached, and is only lost when a homologous donor molecule is present. Taken together, these results support a model in which selective addition of polyubiquitin chains to DNA-crosslinked protein leads to selective recruitment of the proteasome and the cellular NER and recombinational DNA repair machinery.

Carbon availability affects already large species-specific differences in chemical composition of ectomycorrhizal fungal mycelia in pure culture.

Although ectomycorrhizal (ECM) contribution to soil organic matter processes receives increased attention, little is known about fundamental differences in chemical composition among species, and how that may be affected by carbon (C) availability. Here, we study how 16 species (incl. 19 isolates) grown in pure culture at three different C:N ratios (10:1, 20:1, and 40:1) vary in chemical structure, using Fourier transform infrared (FTIR) spectroscopy. We hypothesized that C availability impacts directly on chemical composition, expecting increased C availability to lead to more carbohydrates and less proteins in the mycelia. There were strong and significant effects of ECM species (R2 = 0.873 and P = 0.001) and large species-specific differences in chemical composition. Chemical composition also changed significantly with C availability, and increased C led to more polysaccharides and less proteins for many species, but not all. Understanding how chemical composition change with altered C availability is a first step towards understanding their role in organic matter accumulation and decomposition.

Factors associated with COVID-19 vaccine uptake in adolescents: a national cross-sectional study, August 2021-January 2022, England.

OBJECTIVES: To assess socioeconomic and geographical factors associated with COVID-19 vaccine uptake in pupils attending state-funded secondary schools in England. DESIGN: Cross-sectional observational study. SETTING: State-funded schools in England. PARTICIPANTS: Pupils aged 12-17 years attending state-funded schools in England for the academic year 2021/2022. OUTCOME MEASURES: Demographic, socioeconomic and geographical factors associated with vaccination uptake. We linked individual-level data from the English Schools Census to the National Immunisation Management System to obtain COVID-19 vaccination status of 3.2 million adolescents. We used multivariable logistic regression to assess demographic, socioeconomic and geographical factors associated with vaccination. RESULTS: By 9 January 2022, 56.8% of adolescents aged 12-17 years old had received at least one dose, with uptake increasing from 48.7% in those aged 12 years old to 77.2% in those aged 17 years old. Among adolescents aged 12-15 years old, there were large variations in vaccine uptake by region and ethnic group. Pupils who spoke English as an additional language (38.2% vs 55.5%), with special educational needs (48.1% vs 53.5%), eligible for free school meals (35.9% vs 58.9%) and lived in more deprived areas (36.1% in most deprived vs 70.3% in least deprived) had lower vaccine uptake. Socioeconomic variables had greater impact on the odds of being vaccinated than geographical variables. School-level analysis found wide variation in vaccine uptake between schools even within the same region. Schools with higher proportions of pupils eligible for free school meals had lower vaccine uptake. CONCLUSIONS: We found large differences in vaccine uptake by geographical region and ethnicity. Socioeconomic variables had a greater impact on the odds of being vaccinated than geographical variables. Further research is required to identify evidence-based interventions to improve vaccine uptake in adolescents.

Mobilisation of jerboa kidney gene networks during dehydration and opportunistic rehydration.

Desert animals have evolved systems that enable them to thrive under dry conditions. Focusing on the kidney, we have investigated the transcriptomic adaptations that enable a desert rodent, the Lesser Egyptian Jerboa (Jaculus jaculus), to withstand water deprivation and opportunistic rehydration. Analysis of the whole kidney transcriptome showed many differentially expressed genes in the Jerboa kidney, 6.4% of genes following dehydration and an even greater number (36.2%) following rehydration compared to control. Genes correlated with the rehydration condition included many ribosomal protein coding genes suggesting a concerted effort to accelerate protein synthesis when water is made available. We identify an increase in TGF-beta signaling antagonists in dehydration (e.g., GREM2). We also describe expression of multiple aquaporin and solute carrier transporters mapped to specific nephron segments. The desert adapted renal transcriptome presented here is a valuable resource to expand our understanding of osmoregulation beyond that derived from model organisms.

Immediately loaded full arch implant rehabilitation and oral health-related quality of life: A retrospective cohort study from primary dental care.

AIMS: This study evaluates patient-centered outcomes in patients undergoing full-arch rehabilitation, with immediate loading of implants. Using the Oral Health Impact Profile questionnaire pre-and post-treatment, it assesses the hypothesis that immediate full arch loading significantly improves quality of life. METHODOLOGY: A dataset was defined as: 20 consecutive patients from a research database who had undergone IFAL surgery (maxilla, mandible, or both) and definitive restoration by a single clinician, and completed the OHIP-14 questionnaire prior to treatment and after restoration. RESULTS: Pre (T0 ) and post (T1 ) treatment questionnaires were analyzed from 20 consecutive patients in whom a total of 160 implants were placed. The mean T0 score was 26.7, and mean T1 score 4.6. Differences were statistically significant (p = 0.00008). Greatest improvements were seen in psychological discomfort and disability, and pain. Worsening quality of life was shown by questions relating to speech in six patients and taste in three patients. CONCLUSION: This study demonstrates that overall IFAL significantly improves tooth-related quality of life. It suggests reasons for patients to seek treatment while providing evidence to manage expectations, such as possible implications on speech, thus supporting informed consent of future patients in a primary care setting.

Trends in Neighborhood Social Cohesion among Families with Children during the COVID-19 Pandemic.

The onset of the coronavirus disease 2019 (COVID-19) pandemic had far-reaching economic and social consequences, affecting economic well-being, health, mobility, relationships, and daily routines. What effect did the COVID-19 pandemic have on neighborhood social cohesion? Drawing on data from the National Survey of Children's Health, the authors examine trends in neighborhood social cohesion as reported by caregivers of U.S. children from 2016 to 2021. Despite the substantial changes spurred by the COVID-19 pandemic, the authors find that the pandemic did not lead to a significant change in perceived neighborhood social cohesion. These findings reveal the durability of perceived neighborhood social cohesion, showing that it appears to be unaffected even by sizable changes in social and economic contexts. Moreover, the findings provide additional evidence of disparities in perceived neighborhood social cohesion across social groups and contribute to ongoing debates related to potential declines in neighborhood relationships.

Effectiveness of one dose of MVA-BN smallpox vaccine against mpox in England using the case-coverage method: an observational study.

BACKGROUND: The UK experienced a national outbreak of mpox (formerly known as monkeypox) disease that started in May, 2022, as did many other countries worldwide, with case numbers rising rapidly, mainly among gay, bisexual, and other men who have sex with men (GBMSM). To control the outbreak, Modified Vaccinia Ankara-Bavaria Nordic (MVA-BN), an attenuated smallpox vaccine, was offered to at-risk GBMSM. We aimed to assess the effectiveness of a single MVA-BN dose against symptomatic mpox disease in at-risk GBMSM. METHODS: In this case-coverage study, mpox cases in England were sent questionnaires collecting information on demographics, vaccination history, symptoms, and sexual orientation. Returned questionnaires were linked to laboratory data and a public health case management system (HP Zone) to obtain additional information on symptom onset and specimen date. Cases with a rash onset date (or alternative proxy) between July 4 and Oct 9, 2022, were included. Females, heterosexual men, and those with missing vaccination information were excluded. Vaccine effectiveness was calculated using the case-coverage method in which vaccine coverage among cases is compared with coverage in the eligible population, estimated from doses given to GBMSM and the estimated size of at-risk GBMSM. Sensitivity analyses included an increase and decrease of 20% differences in the estimated high-risk GBMSM population size. FINDINGS: By Nov 3, 2022, 1102 people had responded to questionnaires, of which 739 were excluded (52 females or self-declared male heterosexuals, 590 with an index date outside of the study period, and 97 missing a vaccination date). 363 cases were included in the analyses. Vaccine uptake among eligible GBMSM increased steadily from July, 2022, reaching 47% by Oct 9, 2022. Of the 363 confirmed cases, eight cases either did occur or were likely to have occurred at least 14 days after vaccination, 32 within 0-13 days after vaccination, and the rest were unvaccinated. The estimated vaccine effectiveness against symptomatic mpox at least 14 days after a single dose was 78% (95% CI 54 to 89) ranging from 71 to 85 in sensitivity analyses. Vaccine effectiveness within 0-13 days after vaccination was -4% (95% CI -50 to 29). INTERPRETATION: A single MVA-BN dose was highly protective against symptomatic mpox disease among at-risk GBMSM, making it a useful tool for mpox outbreak control when rapid protection is needed. For cases in which numbers at highest risk of infection exceed vaccine supply, there might be benefit in prioritising delivery of first doses. FUNDING: UK Health Security Agency.

SERS microsensors for pH measurements in the lumen and ECM of stem cell derived human airway organoids.

Patient derived organoids have the potential to improve the physiological relevance of in vitro disease models. However, the 3D architecture of these self-assembled cellular structures makes probing their biochemistry more complex than in traditional 2D culture. We explore the application of surface enhanced Raman scattering microsensors (SERS-MS) to probe local pH gradients within patient derived airway organoid cultures. SERS-MS consist of solid polymer cores decorated with surface immobilised gold nanoparticles which are functionalised with pH sensitive reporter molecule 4-mercaptobenzoic acid (MBA). We demonstrate that by mixing SERS-MS into the extracellular matrix (ECM) of airway organoid cultures the probes can be engulfed by expanding organoids and report on local pH in the organoid lumen and ECM.