Primary care usage at the end of life: a retrospective cohort study of cancer patients using linked primary and hospital care data

PURPOSE

Health service use is most intensive in the final year of a person's life, with 80% of this expenditure occurring in hospital. Close involvement of primary care services has been promoted to enhance quality end-of-life care that is appropriate to the needs of patients. However, the relationship between primary care involvement and patients' use of hospital care is not well described. This study aims to examine primary care use in the last year of life for cancer patients and its relationship to hospital usage.

METHODS

Retrospective cohort study in Victoria, Australia, using linked routine care data from primary care, hospital and death certificates. Patients were included who died related to cancer between 2008 and 2017.

RESULTS

A total of 758 patients were included, of whom 88% (n = 667) visited primary care during the last 6 months (median 9.1 consultations). In the last month of life, 45% of patients were prescribed opioids, and 3% had imaging requested. Patients who received home visits (13%) or anticipatory medications (15%) had less than half the median bed days in the last 3 months (4 vs 9 days, p < 0.001, 5 vs 10 days, p = 0.001) and 1 month of life (0 vs 2 days, p = 0.002, 0 vs 3 days, p < 0.001), and reduced emergency department presentations (32% vs 46%, p = 0.006, 31% vs 47% p < 0.001) in the final month.

CONCLUSION

This study identifies two important primary care processes-home visits and anticipatory medication-associated with reduced hospital usage and intervention at the end of life.

The Comet Assay as a Tool in Human Biomonitoring Studies of Environmental and Occupational Exposure to Chemicals-A Systematic Scoping Review

Biomonitoring of human populations exposed to chemical substances that can act as potential mutagens or carcinogens, may enable the detection of damage and early disease prevention. In recent years, the comet assay has become an important tool for assessing DNA damage, both in environmental and occupational exposure contexts. To evidence the role of the comet assay in human biomonitoring, we have analysed original research studies of environmental or occupational exposure that used the comet assay in their assessments, following the PRISMA-ScR method (preferred reporting items for systematic reviews and meta-analyses extension for scoping reviews). Groups of chemicals were designated according to a broad classification, and the results obtained from over 300 original studies (n = 123 on air pollutants, n = 14 on anaesthetics, n = 18 on antineoplastic drugs, n = 57 on heavy metals, n = 59 on pesticides, and n = 49 on solvents) showed overall higher values of DNA strand breaks in the exposed subjects in comparison with the unexposed. In summary, our systematic scoping review strengthens the relevance of the use of the comet assay in assessing DNA damage in human biomonitoring studies.

Deep learning model shows promise for detecting and grading sesamoiditis in horse radiographs

OBJECTIVE

The objective of this study was to develop a robust machine-learning approach for efficient detection and grading of sesamoiditis in horses using radiographs, specifically in data-limited conditions.

SAMPLE

A dataset of 255 dorsolateral-palmaromedial oblique (DLPMO) and dorsomedial-palmarolateral oblique (DMPLO) equine radiographs were retrospectively acquired from Hagyard Equine Medical Institute. These images were anonymized and classified into 3 categories of sesamoiditis severity (normal, mild, and moderate).

METHODS

This study was conducted from February 1, 2023, to August 31, 2023. Two RetinaNet models were used in a cascaded manner, with a self-attention module incorporated into the second RetinaNet's classification subnetwork. The first RetinaNet localized the sesamoid bone in the radiographs, while the second RetinaNet graded the severity of sesamoiditis based on the localized region. Model performance was evaluated using the confusion matrix and average precision (AP).

RESULTS

The proposed model demonstrated a promising classification performance with 92.7% accuracy, surpassing the base RetinaNet model. It achieved a mean average precision (mAP) of 81.8%, indicating superior object detection ability. Notably, performance metrics for each severity category showed significant improvement.

CLINICAL RELEVANCE

The proposed deep learning-based method can accurately localize the position of sesamoid bones and grade the severity of sesamoiditis on equine radiographs, providing corresponding confidence scores. This approach has the potential to be deployed in a clinical environment, improving the diagnostic interpretation of metacarpophalangeal (fetlock) joint radiographs in horses. Furthermore, by expanding the training dataset, the model may learn to assist in the diagnosis of pathologies in other skeletal regions of the horse.

Assay conditions for estimating differences in base excision repair activity with Fpg-modified comet assay

DNA repair is an essential agent in cancer development, progression, prognosis, and response to therapy. We have adapted a cellular repair assay based on the formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay to assess DNA repair kinetics. The removal of oxidized nucleobases over time (0-480 min) was analyzed in peripheral blood mononuclear cells (PBMCs) and 8 cell lines. DNA damage was induced by exposure to either Ro19-8022 plus visible light or potassium bromate (KBrO3). The initial amount of damage induced by Ro 19-8022 plus light varied between cell lines, and this was apparently associated with the rate of repair. However, the amount of DNA damage induced by KBrO3 varied less between cell types, so we used this agent to study the kinetics of DNA repair. We found an early phase of ca. 60 min with fast removal of Fpg-sensitive sites, followed by slower removal over the following 7 h. In conclusion, adjusting the initial damage at T0 to an equal level can be achieved by the use of KBrO3, which allows for accurate analysis of subsequent cellular DNA repair kinetics in the first hour after exposure.

The virulence of Dichelobacter nodosus, measured by the elastase test, is an important predictor for virulent footrot diagnosis in New South Wales sheep flocks

Ovine footrot is a contagious bacterial disease that causes foot lesions, and depending on the virulence of the causative strains, may lead to severe underrunning of the hoof and lameness. Virulent footrot can be identified, treated and controlled more effectively than less virulent benign forms. The in vitro elastase test for virulence of the causative bacteria, Dichelobacter nodosus, has been used to support clinical diagnosis. However, not all laboratory-designated virulent D. nodosus strains cause clinical signs of virulent footrot. This study evaluated retrospectively how well the elastase test supported clinical footrot diagnosis in 150 sheep flocks examined for suspect footrot in New South Wales between August 2020 and December 2021. Flocks were included if measures of clinical disease, environmental conditions and the virulence of D. nodosus isolates were available. Variation in the elastase activity result between D. nodosus isolated from the same flock made bacterial virulence hard to interpret, but calculating the mean elastase rate for all isolates from the same flock made correlations between bacterial virulence and flock footrot diagnosis possible. Simplifying bacterial virulence into whether there were any elastase-positive D. nodosus isolates before 12 days increased the predictive value of elastase results for virulent diagnosis, compared with using the first day that any isolate was elastase positive or the percentage of elastase-positive isolates by 12 days, but not all clinically virulent flocks had isolates with elastase activity before 12 days. Logistic regression models were fitted to identify the minimum number of predictors for virulent footrot diagnosis, with models suggesting that virulent footrot diagnosis was best predicted by adding the elastase test result and environmental conditions to the prevalence of severe foot lesions (score 4 and 5). However, performing the same analysis with different breeds, ages of sheep and seasons might highlight other factors important in the diagnosis of virulent footrot.

Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley

This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area.

Long-term cryopreservation of potassium bromate positive assay controls for measurement of oxidatively damaged DNA by the Fpg-modified comet assay: results from the hCOMET ring trial

The formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay is widely used for the measurement of oxidatively generated damage to DNA. However, there has not been a recommended long-term positive control for this version of the comet assay. We have investigated potassium bromate as a positive control for the Fpg-modified comet assay because it generates many Fpg-sensitive sites with a little concurrent generation of DNA strand breaks. Eight laboratories used the same procedure for the treatment of monocytic THP-1 cells with potassium bromate (0, 0.5, 1.5, and 4.5 mM) and subsequent cryopreservation in a freezing medium consisting of 50% foetal bovine serum, 40% RPMI-1640 medium, and 10% dimethyl sulphoxide. The samples were analysed by the Fpg-modified comet assay three times over a 3-year period. All laboratories obtained a positive concentration-response relationship in cryopreserved samples (linear regression coefficients ranging from 0.79 to 0.99). However, there was a wide difference in the levels of Fpg-sensitive sites between the laboratory with the lowest (4.2% Tail DNA) and highest (74% Tail DNA) values in THP-1 cells after exposure to 4.5 mM KBrO3. In an attempt to assess sources of inter-laboratory variation in Fpg-sensitive sites, comet images from one experiment in each laboratory were forwarded to a central laboratory for visual scoring. There was high consistency between measurements of %Tail DNA values in each laboratory and the visual score of the same comets done in the central laboratory (r = 0.98, P < 0.001, linear regression). In conclusion, the results show that potassium bromate is a suitable positive comet assay control.

DNA strand break levels in cryopreserved mononuclear blood cell lines measured by the alkaline comet assay: results from the hCOMET ring trial

The comet assay is widely used in biomonitoring studies for the analysis of DNA damage in leukocytes and peripheral blood mononuclear cells. Rather than processing blood samples directly, it can be desirable to cryopreserve whole blood or isolated cells for later analysis by the comet assay. However, this creates concern about artificial accumulation of DNA damage during cryopreservation. In this study, 10 laboratories used standardized cryopreservation and thawing procedures of monocytic (THP-1) or lymphocytic (TK6) cells. Samples were cryopreserved in small aliquots in 50% foetal bovine serum, 40% cell culture medium, and 10% dimethyl sulphoxide. Subsequently, cryopreserved samples were analysed by the standard comet assay on three occasions over a 3-year period. Levels of DNA strand breaks in THP-1 cells were increased (four laboratories), unaltered (four laboratories), or decreased (two laboratories) by long-term storage. Pooled analysis indicates only a modest positive association between storage time and levels of DNA strand breaks in THP-1 cells (0.37% Tail DNA per year, 95% confidence interval: -0.05, 0.78). In contrast, DNA strand break levels were not increased by cryopreservation in TK6 cells. There was inter-laboratory variation in levels of DNA strand breaks in THP-1 cells (SD = 3.7% Tail DNA) and TK6 reference sample cells (SD = 9.4% Tail DNA), whereas the intra-laboratory residual variation was substantially smaller (i.e. SD = 0.4%-2.2% Tail DNA in laboratories with the smallest and largest variation). In conclusion, the study shows that accumulation of DNA strand breaks in cryopreserved mononuclear blood cell lines is not a matter of concern.

Inter-laboratory variation in measurement of DNA damage by the alkaline comet assay in the hCOMET ring trial

The comet assay is a simple and versatile method for measurement of DNA damage in eukaryotic cells. More specifically, the assay detects DNA migration from agarose gel-embedded nucleoids, which depends on assay conditions and the level of DNA damage. Certain steps in the comet assay procedure have substantial impact on the magnitude of DNA migration (e.g. electric potential and time of electrophoresis). Inter-laboratory variation in DNA migration levels occurs because there is no agreement on optimal assay conditions or suitable assay controls. The purpose of the hCOMET ring trial was to test potassium bromate (KBrO3) as a positive control for the formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay. To this end, participating laboratories used semi-standardized protocols for cell culture (i.e. cell culture, KBrO3 exposure, and cryopreservation of cells) and comet assay procedures, whereas the data acquisition was not standardized (i.e. staining of comets and image analysis). Segregation of the total variation into partial standard deviation (SD) in % Tail DNA units indicates the importance of cell culture procedures (SD = 10.9), comet assay procedures (SD = 12.3), staining (SD = 7.9) and image analysis (SD = 0.5) on the overall inter-laboratory variation of DNA migration (SD = 18.2). Future studies should assess sources of variation in each of these steps. On the positive side, the hCOMET ring trial demonstrates that KBrO3 is a robust positive control for the Fpg-modified comet assay. In conclusion, the hCOMET ring trial has demonstrated a high reproducibility of detecting genotoxic effects by the comet assay, but inter-laboratory variation of DNA migration levels is a concern.

Visual comet scoring revisited: a guide to scoring comet assay slides and obtaining reliable results

Measurement of DNA migration in the comet assay can be done by image analysis or visual scoring. The latter accounts for 20%-25% of the published comet assay results. Here we assess the intra- and inter-investigator variability in visual scoring of comets. We include three training sets of comet images, which can be used as reference for researchers who wish to use visual scoring of comets. Investigators in 11 different laboratories scored the comet images using a five-class scoring system. There is inter-investigator variation in the three training sets of comets (i.e. coefficient of variation (CV) = 9.7%, 19.8%, and 15.2% in training sets I-III, respectively). However, there is also a positive correlation of inter-investigator scoring in the three training sets (r = 0.60). Overall, 36% of the variation is attributed to inter-investigator variation and 64% stems from intra-investigator variation in scoring between comets (i.e. the comets in training sets I-III look slightly different and this gives rise to heterogeneity in scoring). Intra-investigator variation in scoring was also assessed by repeated analysis of the training sets by the same investigator. There was larger variation when the training sets were scored over a period of six months (CV = 5.9%-9.6%) as compared to 1 week (CV = 1.3%-6.1%). A subsequent study revealed a high inter-investigator variation when premade slides, prepared in a central laboratory, were stained and scored by investigators in different laboratories (CV = 105% and 18%-20% in premade slides with comets from unexposed and hydrogen peroxide-exposed cells, respectively). The results indicate that further standardization of visual scoring is desirable. Nevertheless, the analysis demonstrates that visual scoring is a reliable way of analysing DNA migration in comets.

High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia

The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.

Comparison of comet-based approaches to assess base excision repair

DNA repair plays an essential role in maintaining genomic stability, and can be assessed by various comet assay-based approaches, including the cellular repair assay and the in vitro repair assay. In the cellular repair assay, cells are challenged with a DNA-damaging compound and DNA damage removal over time is assessed. In the in vitro repair assay, an early step in the repair process is assessed as the ability of a cellular extract to recognize and incise damaged DNA in substrate nucleoids from cells treated with a DNA-damaging compound. Our direct comparison of both assays in eight cell lines and human peripheral blood lymphocytes indicated no significant relationship between these DNA repair assays (R2 = 0.084, P = 0.52). The DNA incision activity of test cells measured with the in vitro repair assay correlated with the background level of DNA damage in the untreated test cells (R2 = 0.621, P = 0.012). When extracts were prepared from cells exposed to DNA-damaging agents (10 mM KBrO3 or 1 µM Ro 19-8022 plus light), the incision activity was significantly increased, which is in line with the notion that base excision repair is inducible. The data presented suggest that the two assays do not measure the same endpoint of DNA repair and should be considered as complementary.

Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets

Phosphorylation is a post-translational modification of great interest to researchers due to its relevance in many biological processes. LC-MS/MS techniques have enabled high-throughput data acquisition, with studies claiming identification and localization of thousands of phosphosites. The identification and localization of phosphosites emerge from different analytical pipelines and scoring algorithms, with uncertainty embedded throughout the pipeline. For many pipelines and algorithms, arbitrary thresholding is used, but little is known about the actual global false localization rate in these studies. Recently, it has been suggested to use decoy amino acids to estimate global false localization rates of phosphosites, among the peptide-spectrum matches reported. Here, we describe a simple pipeline aiming to maximize the information extracted from these studies by objectively collapsing from peptide-spectrum match to the peptidoform-site level, as well as combining findings from multiple studies while maintaining track of false localization rates. We show that the approach is more effective than current processes that use a simpler mechanism for handling phosphosite identification redundancy within and across studies. In our case study using eight rice phosphoproteomics data sets, 6368 unique sites were confidently identified using our decoy approach compared to 4687 using traditional thresholding in which false localization rates are unknown.

Integrated View of Baseline Protein Expression in Human Tissues

The availability of proteomics datasets in the public domain, and in the PRIDE database, in particular, has increased dramatically in recent years. This unprecedented large-scale availability of data provides an opportunity for combined analyses of datasets to get organism-wide protein abundance data in a consistent manner. We have reanalyzed 24 public proteomics datasets from healthy human individuals to assess baseline protein abundance in 31 organs. We defined tissue as a distinct functional or structural region within an organ. Overall, the aggregated dataset contains 67 healthy tissues, corresponding to 3,119 mass spectrometry runs covering 498 samples from 489 individuals. We compared protein abundances between different organs and studied the distribution of proteins across these organs. We also compared the results with data generated in analogous studies. Additionally, we performed gene ontology and pathway-enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point, we have integrated the protein abundance results into the resource Expression Atlas, where they can be accessed and visualized either individually or together with gene expression data coming from transcriptomics datasets. We believe this is a good mechanism to make proteomics data more accessible for life scientists.

Factors Associated with Success of Ream-and-Run Arthroplasty at a Minimum of Five Years

BACKGROUND

Ream-and-run arthroplasty offers improvement in shoulder pain and function for patients with primary glenohumeral arthritis who wish to avoid limitations associated with a polyethylene glenoid component. Longer-term clinical outcome assessments of the ream-and-run procedure are sparse in the literature. This study aims to present minimum 5-year functional outcomes in a large cohort following ream-and-run arthroplasty to determine factors associated with clinical success and reoperation.

METHODS

Patients undergoing ream-and-run surgery with a minimum of 5-years and mean of 7.6 ± 2.1 years of follow-up were collected through a retrospective review of a prospectively maintained database from a single academic institution. To assess clinical outcomes, the Simple Shoulder Test (SST) was administered and assessed for minimum clinically important difference achievement as well as the necessity for open revision surgery. Factors associated with a p<0.1 on univariate analysis were included in a multivariate analysis.

RESULTS

A total of 201 patients of 228 patients (88%) consented for long-term follow-up were included in our analysis. Average age was 59.4 ± 8.8 years, and 93% of patients were male with the majority having the diagnosis of osteoarthritis (79%) or capsulorrhaphy arthropathy (10%). SST scores improved from a mean of 4.9 ± 2.5 preoperatively to a mean of 10.2 ± 2.6 at latest follow-up. 165 patients (82%) reached the minimal clinically important difference of the SST of 2.6. Male sex (p=0.020), non-diabetes (p=0.080), and lower preoperative SST (p<0.001) were included in the multivariate analysis. Male sex (p=0.010) and lower preoperative SST scores (p≤0.001) were associated with clinically important improvements in SST scores on the multivariate analysis. Twenty-two patients (11%) required open revision surgery. Younger age (p<0.001), female sex (p=0.055), and higher preoperative pain scores (p=0.023) were included in the multivariate analysis. Only younger age was predictive of open revision surgery (p=0.003).

CONCLUSIONS

Ream and run arthroplasty can provide significant and clinically important improvements in clinical outcomes at minimum 5-year follow-up. Successful clinical outcomes were significantly associated with male sex and lower preoperative SST scores. Reoperation was more common in younger patients.

Genotoxic effects of occupational exposure to glass fibres - A human biomonitoring study

As part of a large human biomonitoring study, we conducted occupational monitoring in a glass fibre factory in Slovakia. Shopfloor workers (n = 80), with a matched group of administrators in the same factory (n = 36), were monitored for exposure to glass fibres and to polycyclic aromatic hydrocarbons (PAHs). The impact of occupational exposure on chromosomal aberrations, DNA damage and DNA repair, immunomodulatory markers, and the role of nutritional and lifestyle factors, as well as the effect of polymorphisms in metabolic and DNA repair genes on genetic stability, were investigated. The (enzyme-modified) comet assay was employed to measure DNA strand breaks (SBs) and apurinic sites, oxidised and alkylated bases. Antioxidant status was estimated by resistance to H₂O₂-induced DNA damage. Base excision repair capacity was measured with an in vitro assay (based on the comet assay). Exposure of workers to fibres was low, but still was associated with higher levels of SBs, and SBs plus oxidised bases, and higher sensitivity to H₂O₂. Multivariate analysis showed that exposure increased the risk of high levels of SBs by 20%. DNA damage was influenced by antioxidant enzymes catalase and glutathione S-transferase (measured in blood). DNA repair capacity was inversely correlated with DNA damage and positively with antioxidant status. An inverse correlation was found between DNA base oxidation and the percentage of eosinophils (involved in the inflammatory response) in peripheral blood of both exposed and reference groups. Genotypes of XRCC1 variants rs3213245 and rs25487 significantly decreased the risk of high levels of base oxidation, to 0.50 (p = 0.001) and 0.59 (p = 0.001), respectively. Increases in DNA damage owing to glass fibre exposure were significant but modest, and no increases were seen in chromosome aberrations or micronuclei. However, it is of concern that even low levels of exposure to these fibres can cause significant genetic damage.

Calibration of the comet assay using ionising radiation

Several trials have attempted to identify sources of inter-laboratory variability in comet assay results, aiming at achieving more equal responses. Ionising radiation induces a defined level of DNA single-strand breaks (per dose/base pairs) and is used as a reference when comparing comet results but relies on accurately determined radiation doses. In this ring test we studied the significance of dose calibrations and comet assay protocol differences, with the object of identifying causes of variability and how to deal with them. Eight participating laboratories, using either x-ray or gamma radiation units, measured dose rates using alanine pellet dosimeters that were subsequently sent to a specialised laboratory for analysis. We found substantial deviations between calibrated and nominal (uncalibrated) dose rates, with up to 46% difference comparing highest and lowest values. Three additional dosimetry systems were employed in some laboratories: thermoluminescence detectors and two aqueous chemical dosimeters. Fricke's and Benzoic Acid dosimetry solutions gave reliable quantitative dose estimations using local equipment. Mononuclear cells from fresh human blood or mammalian cell lines were irradiated locally with calibrated (alanine) radiation doses and analysed for DNA damage using a standardised comet assay protocol and a lab-specific protocol. The dose response of eight laboratories, calculated against calibrated radiation doses, was linear with slope variance CV= 29% with the lab-specific protocol, reduced to CV= 16% with the standard protocol. Variation between laboratories indicate post-irradiation repair differences. Intra-laboratory variation was very low judging from the dose response of 8 donors (CV=4%). Electrophoresis conditions were different in the lab-specific protocols explaining some dose response variations which were reduced by systematic corrections for electrophoresis conditions. The study shows that comet assay data obtained in different laboratories can be compared quantitatively using calibrated radiation doses and that systematic corrections for electrophoresis conditions are useful.

Seasonal Water Mass Evolution and Non-Redfield Dynamics Enhance CO2 Uptake in the Chukchi Sea

The Chukchi Sea is an increasing CO₂ sink driven by rapid climate changes. Understanding the seasonal variation of air-sea CO₂ exchange and the underlying mechanisms of biogeochemical dynamics is important for predicting impacts of climate change on and feedbacks by the ocean. Here, we present a unique data set of underway sea surface partial pressure of CO₂ (pCO₂) and discrete samples of biogeochemical properties collected in five consecutive cruises in 2014 and examine the seasonal variations in air-sea CO₂ flux and net community production (NCP). We found that thermal and non-thermal effects have different impacts on sea surface pCO₂ and thus the air-sea CO₂ flux in different water masses. The Bering summer water combined with meltwater has a significantly greater atmospheric CO₂ uptake potential than that of the Alaskan Coastal Water in the southern Chukchi Sea in summer, due to stronger biological CO₂ removal and a weaker thermal effect. By analyzing the seasonal drawdown of dissolved inorganic carbon (DIC) and nutrients, we found that DIC-based NCP was higher than nitrate-based NCP by 66%-84% and attributable to partially decoupled C and N uptake because of a variable phytoplankton stoichiometry. A box model with a non-Redfield C:N uptake ratio can adequately reproduce observed pCO₂ and DIC, which reveals that, during the intensive growing season (late spring to early summer), 30%-46% CO₂ uptake in the Chukchi Sea was supported by a flexible stoichiometry of phytoplankton. These findings have important ramification for forecasting the responses of CO₂ uptake of the Chukchi ecosystem to climate change.

In vivo Mammalian Alkaline Comet Assay: Method Adapted for Genotoxicity Assessment of Nanomaterials

The in vivo Comet assay measures the generation of DNA strand breaks under conditions in which the DNA will unwind and migrate to the anode in an electrophoresis assay, producing comet-like figures. Measurements are on single cells, which allows the sampling of a diversity of cells and tissues for DNA damaging effects. The Comet assay is the most common in vivo method for genotoxicity assessment of nanomaterials (NM). The Method outlined here includes a recommended step-by-step approach, consistent with OECD 489, taking into consideration the issues impacting assessment of NM, including choice of cells or systems, handling of NM test articles, dose determination, assay methods and data assessment. This method is designed to be used along with the accompanying “Common Considerations” paper, which discusses issues common to any genotoxicity assay using NM as a test article.

Predicting Pancreatic Cancer in the UK Biobank Cohort Using Polygenic Risk Scores and Diabetes Mellitus

BACKGROUND & AIMS

Diabetes mellitus (DM) is known to be associated with pancreatic ductal adenocarcinoma (PDAC), particularly new-onset DM (NODM). Others have developed polygenic risk scores (PRS) associated with PDAC risk. We aimed to compare the performance of these PRS in an independent cohort to determine if they can discriminate between NODM and long-standing DM patients with PDAC.

METHODS

Cases (1042) and matched cancer-free controls (10,420) were drawn from the UK Biobank. Five PRS models were calculated using single nucleotide polymorphisms (SNPs) from previous studies (Nakatochi, Galeotti, Molina, Jia, and Rashkin) and a combination of these. Regression models were used to assess the association between PDAC and PRS adjusted for ancestry, smoking, DM, waist circumference, and family history of digestive cancer. Receiver operator characteristic curves and area under the curve metrics (AUC) were used to assess the performance of each PRS for classifying PDAC risk.

RESULTS

The combined PRS model achieved the highest AUC (0.605), and significantly improved a clinical risk model in this cohort (AUC = 0.83; P = .0002). Individuals within the fifth quintile have a 2.74-fold increased risk of developing PDAC vs those in the first quintile (P < .001), and have a 3.05-fold increased risk of developing PDAC if they have DM vs those without DM (P < .001). The positive predictive value was 11.9% in participants without DM, 23.9% with long-standing DM, and 86.7% with NODM.

CONCLUSIONS

The PDAC-related common genetic variants are more strongly associated with DM. This PRS has the potential for targeting individuals with NODM for PDAC secondary screening measures.

Measuring aniseikonia and investigating neuroplasticity and image factors in amblyopia (MAGNIFY): study protocol for a randomised clinical trial

Background

Aniseikonia represents a potential barrier to neuroplasticity which may limit visual outcomes in children with anisometropic amblyopia. Full correction of refractive error is the first step in standard amblyopia treatment, which corrects for image focus but neglects image size differences.

Methods

The MAGNIFY study is a double-masked, randomised clinical trial investigating the effectiveness of aniseikonia correcting lenses in children at first diagnosis of significant anisometropia. We hypothesis that aniseikonia correction lenses will improve image clarity and reduce the retinal size differences producing better visual acuity and stereoacuity improvements after 15 weeks of optical treatment for children with anisometropia. Eligible children will be randomly allocated to the treatment group (aniseikonia-correcting spectacle lenses) or control group (standard spectacle lenses). Visual acuity and binocular functions will be assessed every 5 weeks during the 15-week optical treatment phase according to standard amblyopia treatment protocol.

Discussion

It is possible that correcting aniseikonia along with anisometropia at first diagnosis will promote binocularity as well as increase spectacle adherence by reducing visual discomfort, improving optical treatment outcomes. This could then reduce the need for additional amblyopia treatment such as patching or atropine, reducing the burden on hospital eye departments and potentially improving visual outcomes for children with amblyopia.

Trial registration

Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12620000061932. Registered on 24 January 2020. Protocol 15th November 2019, version one.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13063-022-06159-2.

Estimating the Health Effects of Adding Bicycle & Pedestrian Paths: Modeling At The Census Tract-Level (Preprint)

Background

Adding additional bicycle and pedestrian paths to an area can lead to improved health outcomes for residents over time. However, quantitatively determining which areas benefit more from bicycle and pedestrian paths, how many miles of bicycle and pedestrian paths are needed, and the health outcomes that may be most improved remain open questions.

Objective

Our work provides and evaluates a methodology that offers actionable insight for city-level planners, public health officials, and decision makers tasked with the question “To what extent will adding specified bicycle and pedestrian path mileage to a census tract improve residents’ health outcomes over time?”

Methods

We conducted a factor analysis of data from the American Community Survey, Center for Disease Control 500 Cities project, Strava, and bicycle and pedestrian path location and use data from two different cities (Norfolk, Virginia, and San Francisco, California). We constructed 2 city-specific factor models and used an algorithm to predict the expected mean improvement that a specified number of bicycle and pedestrian path miles contributes to the identified health outcomes.

Results

We show that given a factor model constructed from data from 2011 to 2015, the number of additional bicycle and pedestrian path miles in 2016, and a specific census tract, our models forecast health outcome improvements in 2020 more accurately than 2 alternative approaches for both Norfolk, Virginia, and San Francisco, California. Furthermore, for each city, we show that the additional accuracy is a statistically significant improvement (P<.001 in every case) when compared with the alternate approaches. For Norfolk, Virginia (n=31 census tracts), our approach estimated, on average, the percentage of individuals with high blood pressure in the census tract within 1.49% (SD 0.85%), the percentage of individuals with diabetes in the census tract within 1.63% (SD 0.59%), and the percentage of individuals who had >2 weeks of poor physical health days in the census tract within 1.83% (SD 0.57%). For San Francisco (n=49 census tracts), our approach estimates, on average, that the percentage of individuals who had a stroke in the census tract is within 1.81% (SD 0.52%), and the percentage of individuals with diabetes in the census tract is within 1.26% (SD 0.91%).

Conclusions

We propose and evaluate a methodology to enable decision makers to weigh the extent to which 2 bicycle and pedestrian paths of equal cost, which were proposed in different census tracts, improve residents’ health outcomes; identify areas where bicycle and pedestrian paths are unlikely to be effective interventions and other strategies should be used; and quantify the minimum amount of additional bicycle path miles needed to maximize health outcome improvements. Our methodology shows statistically significant improvements, compared with alternative approaches, in historical accuracy for 2 large cities (for 2016) within different geographic areas and with different demographics.

An examination of temporal trends in health behaviors among United States children, adolescents, and adults from 2005 to 2016

Introduction

Lifestyle-related health behaviors are major contributors to preventable chronic diseases. We aimed to characterize temporal trends in health behaviors of US children, adolescents, and adults and examine the association of sociodemographic characteristics with clustering of unhealthy behaviors.

Methods

The study population included 46,793 participants from the 2005 to 2016 National Health and Nutrition Examination Survey from three age groups: children (aged 2–11), adolescents (aged 12–19), and adults (aged ≥20). We calculated weighted prevalences of unhealthy behaviors—poor diet quality, low physical activity, screentime, fast food consumption, smoking (adolescents and adults), alcohol use, and short sleep duration (adults)—for each survey wave to examine temporal trends across age groups. Multivariable logistic regression estimated associations of sociodemographic characteristics with unhealthy behavior clustering (≥2 behaviors), stratified by age.

Results

Results of the study demonstrated that between 2005 and 2016, the proportion of children and adolescents not meeting the physical activity guidelines increased and screentime increased among all ages. Dietary quality improved and smoking prevalence declined among adolescents and adults, while fast food consumption declined among adolescents. Unhealthy behavior clustering among children increased by 13%. The odds of unhealthy behavior clustering were higher among children and adolescents that were older, non-Hispanic Black, or lived in unmarried households, and among adults who were younger, non-Hispanic black, had lower educational attainment, were uninsured or had public insurance, and had lower poverty-to-income ratios.

Conclusion

The findings suggest that screentime and physical inactivity are growing areas of concern in the U.S. population, and that disparities in adherence to multiple healthy behaviors may contribute to disparities in chronic diseases.

A pooled analysis of molecular epidemiological studies on modulation of DNA repair by host factors

Levels of DNA damage represent the dynamics between damage formation and removal. Therefore, to better interpret human biomonitoring studies with DNA damage endpoints, an individual's ability to recognize and properly remove DNA damage should be characterized. Relatively few studies have included DNA repair as a biomarker and therefore, assembling and analyzing a pooled database of studies with data on base excision repair (BER) was one of the goals of hCOMET (EU-COST CA15132). A group of approximately 1911 individuals, was gathered from 8 laboratories which run population studies with the comet-based in vitro DNA repair assay. BER incision activity data were normalized and subsequently correlated with various host factors. BER was found to be significantly higher in women. Although it is generally accepted that age is inversely related to DNA repair, no overall effect of age was found, but sex differences were most pronounced in the oldest quartile (>61 years). No effect of smoking or occupational exposures was found. A body mass index (BMI) above 25 kg/m² was related to higher levels of BER. However, when BMI exceeded 35 kg/m², repair incision activity was significantly lower. Finally, higher BER incision activity was related to lower levels of DNA damage detected by the comet assay in combination with formamidopyrimidine DNA glycosylase (Fpg), which is in line with the fact that oxidatively damaged DNA is repaired by BER. These data indicate that BER plays a role in modulating the steady-state level of DNA damage that is detected in molecular epidemiological studies and should therefore be considered as a parallel endpoint in future studies.

Short- and long-term reproducibility of the COMET assay for measuring DNA damage biomarkers in frozen blood samples of the EPIC-Heidelberg cohort

The comet assay is widely used for quantification of genomic damage in humans. Peripheral blood derived mononuclear cells (PBMCs) are the most often used cell type for this purpose. Since the comet assay can be performed in an enhanced throughput format, it can be applied to large sample collections such as biobanks. The European Prospective Investigation into Cancer and Nutrition (EPIC) study is one of the largest existing prospective cohort studies, and the German Cancer Research Institute (DKFZ) in Heidelberg is a participating center with 25.000 frozen blood samples stored from around 25 years ago, enabling retrospective assessment of disease risk factors. However, experience with decades long frozen samples in the comet assay is so far missing. In Heidelberg, 800 study participants were re-invited twice between 2010 and 2012 to donate further blood samples. Here, we analyzed 299 Heidelberg-EPIC samples, compiled from frozen PBMC and buffy coat preparations selected from the different sampling time points. In addition, 47 frozen PBMC samples from morbidly obese individuals were included. For buffy coat samples, we observed a poor correlation between DNA damage in the same donors assessed at two sampling time points. Additionally, no correlation between DNA damage in buffy coat samples and PBMCs was found. For PBMCs, a good correlation was observed between samples of the same donors at the two time points. DNA damage was not affected by age and smoking status, but high BMI (>30; obesity) was associated with increased DNA damage in PBMCs. There was no indication for a threshold of a certain BMI for increased DNA damage. In conclusion, while 25 year-long stored buffy coat preparations may require adaptation of certain experimental parameters such as cell density and electrophoresis conditions, frozen PBMC biobank samples can be analyzed in the comet assay even after a decade of storage.

Clinical and Descriptive Study of Orofacial Clefts in Colombia: 2069 Patients From Operation Smile Foundation

OBJECTIVE

To describe the population of patients with cleft lip and/or palate (CL/P) in terms of cleft phenotypes, gender, age, ethnic group, family history, clinical presentation (syndromic vs nonsyndromic), some environmental and behavioral factors, and some clinical features.

DESIGN

Descriptive retrospective study.

SETTING

Patients attending the genetics counseling practice in Operation Smile Foundation, Bogotá, Colombia, for over 8 years.

PARTICIPANTS

No screening was conducted. All patients requiring clinical genetics assessment in Operation Smile Foundation were included in the study.

RESULTS

Left cleft lip and palate (CLP) and nonsyndromic forms were the most frequent types of malformations in this population. Psychomotor retardation and heart disease were the most frequent comorbidities in these patients. A low proportion of mothers exposed to passive smoking during pregnancy was observed and low birth weight accounted for an important number of cases. Aarskog, velocardiofacial, and orofaciodigital syndromes were the most frequent syndromic forms of CLP in this population.

CONCLUSIONS

In this study, the most frequent type of CL/P was the nonsyndromic complete left CLP. Aarskog, velocardiofacial, and orofaciodigital syndromes were the most frequent syndromic forms of CL/P in this population.

Development of a Spectacle Wear Monitor System: SpecsOn Monitor

Purpose

This study aimed to custom design, build, and test a removable device that accurately and objectively monitors adherence to spectacle wear in preschool children participating in clinical trials. This work will provide researchers with the tools to investigate the effect of adherence to optical treatment in conditions relating to refractive error, such as anisometropia, amblyopia, myopia, and accommodative esotropia, where spectacle wearing behaviors are of interest.

Methods

Several sensors were considered in the design of the SpecsOn monitor. The final version included two temperature sensors, one that measures skin temperature through an infrared sensor directed at the wearer's temple on the spectacle arm and the other measuring device temperature. The difference between the two temperature readings is used to determine if the spectacles were worn. The SpecsOn monitor was tested in two phases in adult participants (laboratory n = 10 and real world n = 5).

Results

Results from both phases showed good agreement between the objective measurement of wear based on skin and device temperature differences and participants’ manually logged wear times. The custom built SpecsOn monitor was 99% successful in accurately detecting spectacle wear in our adult cohort.

Conclusions

The SpecsOn monitor offers a convenient, accurate, and reliable system to monitor spectacle adherence. The devices were comfortable, secure, and unobtrusive to wear, and fitted easily to a variety of frame styles.

Translational Relevance

Easy access to spectacle compliance information from the SpecsOn monitor during the optical treatment phase will optimize visual outcomes and provide detailed clinical data to support decision making on the need and timing of additional therapies, improving treatment efficiency.

DNA damage in circulating leukocytes measured with the comet assay may predict the risk of death

The comet assay or single cell gel electrophoresis, is the most common method used to measure strand breaks and a variety of other DNA lesions in human populations. To estimate the risk of overall mortality, mortality by cause, and cancer incidence associated to DNA damage, a cohort of 2,403 healthy individuals (25,978 person-years) screened in 16 laboratories using the comet assay between 1996 and 2016 was followed-up. Kaplan–Meier analysis indicated a worse overall survival in the medium and high tertile of DNA damage (p < 0.001). The effect of DNA damage on survival was modelled according to Cox proportional hazard regression model. The adjusted hazard ratio (HR) was 1.42 (1.06–1.90) for overall mortality, and 1.94 (1.04–3.59) for diseases of the circulatory system in subjects with the highest tertile of DNA damage. The findings of this study provide epidemiological evidence encouraging the implementation of the comet assay in preventive strategies for non-communicable diseases.

Prolonged Grief and Bereavement Supports Within a Caregiver Population Who Transition Through a Palliative Care Program in British Columbia, Canada

OBJECTIVE

To determine the prevalence of prolonged grief disorder (PGD), and self-reported resilience among bereaved caregivers within a palliative care program that serves a large region of the Lower Mainland in British Columbia, Canada. Additionally, to discern effective bereavement supports utilized by caregivers following the loss of a loved one.

METHODS

A descriptive study using both quantitative and qualitative methods. Sociodemographic information (n = 427) was collected from bereaved caregivers 3 months after their loss. PGD and resilience were prospectively assessed 12 months post-loss using the prolonged grief scale (PG-13, n = 212) and brief resilience scale (BRS, n = 215), respectively. A qualitative thematic analysis was conducted on responses to the open-ended question on what bereavement services or activities caregivers found helpful in coping with the loss of a loved one.

RESULTS

Of the 212 individuals that completed the PG-13, 4.7% met diagnostic criteria for PGD, 27.4% were moderate risk, and 67.9% were low risk for PGD. Of the 215 caregivers that completed the BRS, 48.4% had low resilience, 51.6% had normal resilience, and 0% had high resilience. The major themes of formal supports, informal supports, and self-care activities emerged from caregiver comments regarding effective bereavement supports.

CONCLUSION

The incidence of PGD in caregivers is low within the Fraser Health Palliative Care program. Bereaved caregivers mainly utilize existing social networks and activities to cope with their loss. Focusing on a community-based approach to supports may improve bereavement experiences and lower rates of prolonged grief.

Potassium bromate as positive assay control for the Fpg-modified comet assay

The comet assay is a popular assay in biomonitoring studies. DNA strand breaks (or unspecific DNA lesions) are measured using the standard comet assay. Oxidative stress-generated DNA lesions can be measured by employing DNA repair enzymes to recognise oxidatively damaged DNA. Unfortunately, there has been a tendency to fail to report results from assay controls (or maybe even not to employ assay controls). We believe this might have been due to uncertainty as to what really constitutes a positive control. It should go without saying that a biomonitoring study cannot have a positive control group as it is unethical to expose healthy humans to DNA damaging (and thus potentially carcinogenic) agents. However, it is possible to include assay controls in the analysis (here meant as a cryopreserved sample of cells i.e. included in each experiment as a reference sample). In the present report we tested potassium bromate (KBrO3) as a positive comet assay control for the formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay. Ten laboratories used the same procedure for treatment of monocytic THP-1 cells with KBrO3 (0.5, 1.5 and 4.5 mM for 1 h at 37°C) and subsequent cryopreservation. Results from one laboratory were excluded in the statistical analysis because of technical issues in the Fpg-modified comet assay. All other laboratories found a concentration-response relationship in cryopreserved samples (regression coefficients from 0.80 to 0.98), although with different slopes ranging from 1.25 to 11.9 Fpg-sensitive sites (%DNA in tail) per 1 mM KBrO3. Our results demonstrate that KBrO3 is a suitable positive comet assay control.

Application of the comet assay for the evaluation of DNA damage in mature sperm

DNA integrity is considered an important parameter of semen quality and is of significant value as a predictor of male fertility. Currently, there are several methods that can assess sperm DNA integrity. One such assay is the comet assay, or single-cell gel electrophoresis, which is a simple, sensitive, reliable, quick and low-cost technique that is used for measuring DNA strand breaks and repair at the level of individual cells. Although the comet assay is usually performed with somatic cells from different organs, the assay has the ability to detect genotoxicity in germ cells at different stages of spermatogenesis. Since the ability of sperm to remove DNA damage differs between the stages, interpretation of the results is dependent on the cells used. In this paper we give an overview on the use and applications of the comet assay on mature sperm and its ability to detect sperm DNA damage in both animals and humans. Overall, it can be concluded that the presence in sperm of significantly damaged DNA, assessed by the comet assay, is related to male infertility and seems to reduce live births. Although there is some evidence that sperm DNA damage also has a long-term impact on offspring's health, this aspect of DNA damage in sperm is understudied and deserves further attention. In summary, the comet assay can be applied as a useful tool to study effects of genotoxic exposures on sperm DNA integrity in animals and humans.

Application of Next Generation Quality/Statistical Process Control and Expert-Led Case Review to Increase the Consistency of Diagnostic Rates in Precancerous Colorectal Polyps

BACKGROUND

Prior work suggests high interrater variability in the pathologist diagnostic rate (PDR) of the precancerous polyp sessile serrated adenoma (SSA).

OBJECTIVES

To improve the diagnostic consistency in the pathological evaluation of colorectal polyp specimens with diagnostic rate awareness, using funnel plots (FPs)/control charts (CCs), and a focused group case review.

METHODS

All colorectal polyp specimen (CRPS) reports September 2015 to August 2017 were analyzed at one institution. PDRs were extracted using a hierarchical free-text string matching algorithm and visualized using FPs, showing pathologist specimen volume versus PDR, and CCs, showing pathologist versus normed PDR. The FPs/CCs were centered on the group median diagnostic rate (GMDR). Pathologists were shown their baseline SSA diagnostic rate in relation to the practice, and in January 2017, there was a focused group case review/open discussion of approximately 40 sequential cases signed as SSA with a gastrointestinal pathology expert.

RESULTS

Nine pathologists interpreted more than 250 CRPSs per year. FPs/CCs for the first and second years showed 6/4 and 3/1 P < .05/P < .001 pathologist outliers, respectively, in relation to the GMDR for SSA and 0/0 and 0/0 P < .05/P < .001 pathologist outliers, respectively, in relation to the GMDR for tubular adenoma (TA). An in silico kappa (ISK) for SSA improved from 0.52 to 0.62.

CONCLUSION

Diagnostic rate awareness facilitated by FPs/CCs coupled with focused expert-led reviews may help calibrate PDR. Variation in SSA PDRs still remains high in relation to TA. ISK represents an intuitive, useful metric and Next Generation Quality/Statistical Process Control a promising approach for objectively increasing diagnostic consistency.

Systemic acidemia impairs cardiac function in critically Ill patients

BACKGROUND

Acidemia, is associated with reduced cardiac function in animals, but no studies showing an effect of acidemia on cardiac function in humans are reported. In the present study, we examined the effect of acidemia on cardiac function assessed with transpulmonary thermodilution technique with integrated pulse contour analysis (Pulse Contour Cardiac Output, PiCCO™) in a large cohort of critically ill patients.

METHODS

This was a prospective multicenter observational cross-sectional study of 297 patients from 6 intensive care units in London, England selected from all patients admitted consecutively between May 2018 and March 2019. Measurements of lowest plasma pH and concurrent assessment of cardiac function were obtained.

FINDINGS

There was a significant difference between two pH categories (pH ≤ 7.28 vs. pH > 7.28) for the following variables of cardiac function: SVI (difference in means 32.7; 95% CI: 21 to 45 mL/m2; p < 0.001); GEF (18; 95% CI: 11 to 26%; p < 0.001), dPmax (-331; 95% CI: -510 to -153 mmHg/s; p = 0.001), CFI (0.7; 95% CI: 0.2 to 1.3 1/min; p = 0.01) and CPI (0.09; 95% CI: 0.03 to 0.15 W/m2; p < 0.001). However, there was no significant difference in CI (0.13; 95% CI: -0.20 to 0.47 L/min/m2; p = 0.12) between the pH categories. Also, a significant relationship was found between the quantitative pH and the following variables: SVI (132; 95% CI: 77 to 188 mL/m2; p < 0.001), GEF (74.7; 95% CI: 37.1 to 112.4%; p < 0.001), dPmax (-1587; 95% CI: -2361 to -815 mmHg/s; p < 0.001), CFI (3.5; 95% CI: 0.9 to 6.1 /min; p = 0.009), CPI (0.62; 95% CI: 0.36 to 0.88 W/m2; p < 0.001) and CI (regression coefficient 1.96; 95% CI:0.45 to 3.47 L/min/m2; p = 0.01).

INTERPRETATION

Acidemia is associated with impaired cardiac function in seriously ill patients hospitalized in the intensive care unit supporting the potential value of early diagnosis and improvement of arterial pH in these patients.

FUNDING

The study was partially supported by unrestricted funds from the UCLA School of Medicine.

Innovative Follow-up Strategies for Endometrial Cancer

Increasing recognition of the heterogeneous nature of endometrial cancer, the excellent prognosis of low-risk cases and improvements in risk stratification offer opportunities for innovative, personalised follow-up strategies. This review article outlines the evidence base for alternative follow-up strategies in the different risk categories of endometrial cancer, cancer survivorship programmes and considers future directions in endometrial cancer follow-up, including emerging new techniques, such as the liquid biopsy, and opportunities for combining molecular and clinicopathological features to personalise endometrial cancer follow-up.

Children are safe in schools: a review of the Irish experience of reopening schools during the COVID-19 pandemic

Objectives

Schools in the Republic of Ireland reopened to students and staff in late August 2020. We sought to determine the test positivity rate of close contacts of cases of coronavirus disease 2019 (COVID-19) in schools during the first half-term of the 2020/2021 academic year.

Methods

National-level data from the schools' testing pathway were interrogated to determine the positivity rate of close contacts of cases of COVID-19 in Irish primary, postprimary and special schools during the first half-term of 2020/2021 academic year. The positivity rates among adult and child close contacts were compared and the proportion of national cases of COVID-19 who were aged 4–18 years during the observation period was calculated to assess whether this proportion increased after schools reopened.

Results

Of all, 15,533 adult and child close contacts were tested for COVID-19 through the schools' testing pathway during the first half-term of the 2020/2021 academic year. Three hundred and ninety-nine close contacts tested positive, indicating a positivity rate of 2.6% (95% confidence interval: 2.3–2.8%). The positivity rates of child and adult close contacts were similarly low (2.6% vs 2.7%, P = 0.7). The proportion of all national cases of COVID-19 who were aged 4–18 years did not increase during the first half-term of the 2020/2021 school year.

Conclusions

The low positivity rate of close contacts of cases of COVID-19 in schools indicate that transmission of COVID-19 in Irish schools during the first half-term of the 2020/2021 academic year was low. These findings support policies to keep schools open during the pandemic.

High-Yield Mucosal Olfactory Ensheathing Cells Restore Loss of Function in Rat Dorsal Root Injury

In a previous study, we reported that no axons were crossing from the severed dorsal roots to the spinal cord using the rat dorsal rhizotomy paradigm. The injury caused ipsilateral deficits of forepaw function. An attempt to restore the function by transplanting cells containing 5% olfactory ensheathing cells (OECs) cultured from the olfactory mucosa did not succeed. However, obtaining OECs from the olfactory mucosa has an advantage for clinical application. In the present study, we used the same rhizotomy paradigm, but rats with an injury received cells from a modified mucosal culture containing around 20% OECs mixed in collagen. The forelimb proprioception assessment showed that 80% of the rats receiving the transplants had functional improvement over six weeks of the study. The adhesive removal test showed that the time taken for the rats to notice the adhesive label and remove it almost returned to the normal level after receiving the transplants. Transplanted cells were identified with the expression of green fluorescent protein (ZsGreen). Some regeneration fibres immunostained for neurofilament (NF) or traced by biotinylated dextran amine (BDA) in the injury area were associated with the transplanted cells. The evidence in this study improves the prospect of clinical application using OECs from the olfactory mucosa to treat CNS injuries.

Aarskog-Scott syndrome: phenotypic and genetic heterogeneity

Aarskog-Scott syndrome (AAS) is a rare developmental disorder which primarily affects males and has a relative prevalence of 1 in 25,000 in the general population. AAS patients usually present with developmental complications including short stature and facial, skeletal and urogenital anomalies. The spectrum of genotype-phenotype correlations in AAS is unclear and mutations of the FGD1 gene on the proximal short arm of chromosome X account for only 20% of the incidence of the disorder. Failure to identify pathogenic variants in patients referred for FGD1 screening suggests heterogeneity underlying pathophysiology of the condition. Furthermore, overlapping features of AAS with several other developmental disorders increase the complexity of diagnosis. Cytoskeletal signaling may be involved in the pathophysiology of AAS. The FGD1 protein family has a role in activation of CDC42 (Cell Division Control protein 42 homolog) which has a core function in remodeling of extracellular matrix and the transcriptional activation of many modulators of development. Therefore, mutations in components in the EGFR1 (Epidermal Growth Factor Receptor 1) signaling pathway, to which CDC42 belongs, may contribute to pathophysiology. Parallel sequencing strategies (so-called next generation sequencing or high throughput sequencing) enables simultaneous production of millions of sequencing reads that enormously facilitate cost-effective identification of cryptic mutations in heterogeneous monogenic disorders. Here we review the source of phenotypic and genetic heterogeneity in the context of AAS and discuss the applicability of next generation sequencing for identification of novel mutations underlying AAS.

Collection and storage of human white blood cells for analysis of DNA damage and repair activity using the comet assay in molecular epidemiology studies

DNA damage and repair activity are often assessed in blood samples from humans in different types of molecular epidemiology studies. However, it is not always feasible to analyse the samples on the day of collection without any type of storage. For instance, certain studies use repeated sampling of cells from the same subject or samples from different subjects collected at different time-points, and it is desirable to analyse all these samples in the same comet assay experiment. In addition, flawless comet assay analyses on frozen samples open up the possibility of using this technique on biobank material. In this article we discuss the use of cryopreserved peripheral blood mononuclear cells (PBMCs), buffy coat (BC) and whole blood (WB) for analysis of DNA damage and repair using the comet assay. The published literature and the authors' experiences indicate that various types of blood samples can be cryopreserved with only a minor effect on the basal level of DNA damage. There is evidence to suggest that WB and PBMCs can be cryopreserved for several years without much effect on the level of DNA damage. However, care should be taken when cryopreserving WB and BCs. It is possible to use either fresh or frozen samples of blood cells, but results from fresh and frozen cells should not be used in the same dataset. The article outlines detailed protocols for the cryopreservation of PBMCs, BCs and WB samples.

The micronucleus cytome assay - A fast tool for DNA damage screening in human conjunctival epithelial cells

PURPOSE

To assess whether the micronucleus cytome assay (MCyt) reliably detects DNA damage occurring in control and pathological superficial epithelial cells from human conjunctiva.

METHODS

Impression cytology samples from the bulbar conjunctiva of 33 healthy controls, eight patients with conjunctival intraepithelial neoplasia (CIN) and eight with mucous membrane pemphigoid (MMP) were examined using the MCyt modified for the ocular surface.

RESULTS

The mean number of micronuclei (MNi) in control samples was 0.94 MNi/1000 epithelial cells, with no significant difference between conjunctival quadrants and independent of sex and age. The MCyt assay applied to CIN-affected eyes showed a significantly higher frequency of MNi (18.63/1000 cells), apoptotic cells, nuclear enlargement, multinucleated cells, and keratolysis compared with the corresponding unaffected paired eyes and with the control value. Although the mean MNi frequency in MMP eyes was also higher (1.73 MNi/1000 cells), it did not prove to be statistically different from the control samples. On the other hand, the MMP-affected eyes revealed significantly elevated percentages of cells with snake-like chromatin, multinucleated cells, apoptotic cells, and nuclear buds compared with controls.

CONCLUSIONS

Micronucleus cytome assay was adapted as a rapid screening test for genomic instability on the ocular surface. We have determined reference levels for MNi and other nuclear alterations on healthy conjunctiva and demonstrated that particularly frequencies of MNi are significantly elevated in conjunctiva affected by CIN. We demonstrate that MNi are more specific than other nuclear abnormalities and thus can be used for screening of ocular surface neoplasia.

Subdural extravasation of crystalloids and blood products through a scalp peripheral intravenous catheter into the subdural space of a neonate on veno-arterial extracorporeal membrane oxygenation

We describe a rare and devastating complication of a malpositioned scalp peripheral intravenous catheter (PIV) that resulted in subdural extravasation of infused fluids and midline shift in a critically ill neonate who required extracorporeal membrane oxygenation (ECMO). Recognition of increased intracranial pressure was hindered by the hemodynamic changes of being on ECMO and only identified by routine surveillance ultrasonography. Awareness of this complication may lead providers to seek alternate sites for vascular access in such patients, and encourage closer monitoring for this complication when an alternate site is unavailable.

Background prevalence of subclinical Shiga toxin-producing Escherichia coli in children attending childcare facilities in the Irish Midlands

BACKGROUND

Exclusion of asymptomatic shedders of Shiga toxin-producing Escherichia coli (STEC) from childcare facilities (CCFs) is a recognized measure to minimize risk of secondary transmission. This is predicated on factors including an assumption of low background prevalence of STEC amongst CCF attendees. There is a paucity of scientific evidence regarding the true prevalence of STEC in paediatric populations. The study aimed to develop and test a methodology to estimate background prevalence of STEC amongst CCF attendees at regional level in Ireland.

METHODS

Computerized Infectious Disease Reporting data were used to compile a list of outbreaks of STEC occurring in CCFs in the Irish Midlands since the introduction of polymerase chain reaction (PCR)-based testing. Laboratory data were used to determine background prevalence of STEC in screened children in each outbreak individually and across all outbreaks.

RESULTS

A pooled summary prevalence estimate of 2.9% (95% confidence interval 1.4-5.5%) was determined for the entire screened cohort across all outbreaks. Sensitivity analysis supported the validity of the estimate.

CONCLUSIONS

The relatively high prevalence estimate of 2.9% suggests that a public health risk assessment approach to return of prolonged asymptomatic shedders to the CCF may be appropriate in peak STEC season in the Midlands.

Clinical Aniseikonia in Anisometropia and Amblyopia

Purpose:

Clinically, aniseikonia (a perceived difference in shape and image size between the eyes) is often neglected in anisometropic amblyopia due to assumed measurement difficulties. Therefore, we currently lack evidence on whether correction of aniseikonia is beneficial. This study aimed to determine whether subjective aniseikonia is measurable in anisometropia with or without amblyopia.

Methods:

Participants (15–52 years) with Anisometropic Amblyopia (n = 7), Anisometropia without amblyopia (n = 6) and Isometropic Controls (n = 6) were recruited. Subjective aniseikonia was measured using three clinical techniques: Robertson Technique (RT) (penlight and Maddox rod), Aniseikonia Inspector Version 3 (AI3), and the New Aniseikonia Test booklet (NAT), and a psychophysical adaptive method, the Contrast-balanced Aniseikonia Test (CAT), where dichoptic contrast adjustments compensate for any suppression.

Results:

Eighteen participants completed all tests, one Anisometropic Amblyopia participant could only complete the CAT and NAT due to fusion loss. The Anisometropic Amblyopia group exhibited the most aniseikonia (range –1.50–+10.50%) followed by Anisometropic Controls (range –3.30–+4.50%) and Isometropic Controls (range –1.50–+3.28%). There was a significant trend of more subjective aniseikonia with increasing amounts of anisometropia across all four tests (AI3 r = 0.630, p = 0.005; NAT r = 0.542, p = 0.017; RT r = 0.499, p = 0.035; CAT r = 0.440, p = 0.059. Bland Altman analysis demonstrated clinically significant levels of variability between the tests.

Conclusions:

Subjective aniseikonia can be reliably measured in patients with anisometropia and suppression. Subjective aniseikonia measurement is recommended as four of the most commonly used clinical tests did not support the 1% per dioptre rule of thumb.

The enzyme-modified comet assay: Past, present and future

The enzyme-modified comet assay was developed in order to detect DNA lesions other than those detected by the standard version (single and double strand breaks and alkali-labile sites). Various lesion-specific enzymes, from the DNA repair machinery of bacteria and humans, have been combined with the comet assay, allowing detection of different oxidized and alkylated bases as well as cyclobutane pyrimidine dimers, mis-incorporated uracil and apurinic/apyrimidinic sites. The enzyme-modified comet assay has been applied in different fields - human biomonitoring, environmental toxicology, and genotoxicity testing (both in vitro and in vivo) - as well as in basic research. Up to now, twelve enzymes have been employed; here we describe the enzymes and give examples of studies in which they have been applied. The bacterial formamidopyrimidine DNA glycosylase (Fpg) and endonuclease III (EndoIII) have been extensively used while others have been used only rarely. Adding further enzymes to the comet assay toolbox could potentially increase the variety of DNA lesions that can be detected. The enzyme-modified comet assay can play a crucial role in the elucidation of the mechanism of action of both direct and indirect genotoxins, thus increasing the value of the assay in the regulatory context.

Sequencing era methods for identifying signatures of selection in the genome

Insights into genetic loci which are under selection and their functional roles contribute to increased understanding of the patterns of phenotypic variation we observe today. The availability of whole-genome sequence data, for humans and other species, provides opportunities to investigate adaptation and evolution at unprecedented resolution. Many analytical methods have been developed to interrogate these large data sets and characterize signatures of selection in the genome. We review here recently developed methods and consider the impact of increased computing power and data availability on the detection of selection signatures. Consideration of demography, recombination and other confounding factors is important, and use of a range of methods in combination is a powerful route to resolving different forms of selection in genome sequence data. Overall, a substantial improvement in methods for application to whole-genome sequencing is evident, although further work is required to develop robust and computationally efficient approaches which may increase reproducibility across studies.

Detection of Oxidised Purines and UV-induced Photoproducts in DNA of Single Cells, by Inclusion of Lesion-specific Enzymes in the Comet Assay

The comet assay (single cell gel electrophoresis) is a rapid, very sensitive method for the detection of DNA strand breaks at the level of single cells, which is now being applied in genotojricity testing. We modified this method for the detection of a variety of kinds of DNA lesion, by treating nucleoid DNA in the gel with either formamidopyrimidine-DNA glycosylase (which recognises ring opened purines, 8-hydroxyguanine and apurinic/apyrimidinic sites), or uvrABC excinuclease (uvrABC; which has a rather broad specificity, including bulky lesions and UV photoproducts). By using this modified assay, we demonstrate the removal of DNA strand breaks and oxidised purines upon incubating cells after treatment with hydrogen peroxide. This modification clearly increases the usefulness of the assay for the analysis of DNA damage and repair, for screening human populations for DNA damage, and for testing novel chemicals for genotoxicity.