The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy.

While the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood. Here we investigate the structure of actively transcribed chromatin and the architecture of its interaction with active RNA polymerase. For this analysis, we have used super-resolution microscopy to image the Drosophila melanogaster Y loops which represent huge, several megabases long, single transcription units. The Y loops provide a particularly amenable model system for transcriptionally active chromatin. We find that, although these transcribed loops are decondensed they are not organised as extended 10nm fibres, but rather they largely consist of chains of nucleosome clusters. The average width of each cluster is around 50nm. We find that foci of active RNA polymerase are generally located off the main fibre axis on the periphery of the nucleosome clusters. Foci of RNA polymerase and nascent transcripts are distributed around the Y loops rather than being clustered in individual transcription factories. However, as the RNA polymerase foci are considerably less prevalent than the nucleosome clusters, the organisation of this active chromatin into chains of nucleosome clusters is unlikely to be determined by the activity of the polymerases transcribing the Y loops. These results provide a foundation for understanding the topological relationship between chromatin and the process of gene transcription.

Transparent teamwork: The practice of supervision and delegation within the multi-tiered nursing team.

Supervision and delegation are important leadership skills that nurses require when practising within the multi-tiered nursing team. In response to increasing demands globally on healthcare systems, Nursing Assistants are becoming more prevalent members of the nursing workforce in the acute care setting. An exploratory descriptive research design was used to examine supervision and delegation of Nursing Assistants in an acute hospital setting in Victoria, Australia. It was found that supervision and delegation in the context of a multi-tier nursing team required a complex assessment and decision-making process which was influenced by multiple factors. This research promotes developing transparent nursing practices and mutual understanding in the multi-tier nursing team to facilitate effective supervision and delegation based on informed decision-making and culture of openness and trust. Pre-registration education and continuing education and support for nurses are important to build transparent supervision and delegation practices and teamwork, empowering the nursing team to practice to their full scope of practice to provide high-quality patient care.

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells.

Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ∼100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 megabases. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications.

A human origin strain Lactobacillus acidophilus DDS-1 exhibits superior in vitro probiotic efficacy in comparison to plant or dairy origin probiotics.

Background: The health benefits of probiotics are well established and known to be strain-specific. However, the role of probiotics obtained from different origins and their efficacy largely remains unexplored. The aim of this study is to investigate the in vitro efficacy of probiotics from different origins. Methods: Probiotic strains utilized in this study include Lactobacillus acidophilus DDS-1 (human origin), Bifidobacterium animalis ssp. lactis UABla-12 (human origin), L. plantarum UALp-05 (plant origin) and Streptococcus thermophilus UASt-09 (dairy origin). Screening assays such as in vitro digestion simulation, adhesion, cell viability and cytokine release were used to evaluate the probiotic potential. Results: All strains showed good resistance in the digestion simulation process, especially DDS-1 and UALp-05, which survived up to a range of 107 to 108 CFU/mL from an initial concentration of 109 CFU/mL. Two human colonic mucus-secreting cells, HT-29 and LS174T, were used to assess the adhesion capacity, cytotoxicity/viability, and cytokine quantification. All strains exhibited good adhesion capacity. No significant cellular cytotoxicity or loss in cell viability was observed. DDS-1 and UALp-05 significantly upregulated anti-inflammatory IL-10 and downregulated pro-inflammatory TNF-α cytokine production. All the strains were able to downregulate IL-8 cytokine levels. Conclusion: Of the 4 strains tested, DDS-1 demonstrated superior survival rates, good adhesion capacity and strong immunomodulatory effect under different experimental conditions.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome. Several approaches were used to assess submissions, including ROC AUC (area under receiver operating characteristic curve), probability rankings, the number of correct predictions, and statistical significance simulations. Overall, we found that prediction of individual traits is difficult, relying on a strong knowledge of trait frequency within the general population, whereas matching genomes to trait profiles relies heavily upon a small number of common traits including ancestry, blood type, and eye color. When a rare genetic disorder is present, profiles can be matched when one or more pathogenic variants are identified. Prediction accuracy has improved substantially over the last 6 years due to improved methodology and a better understanding of features.

Social Annotation Valence: The Impact on Online Informed Consent Beliefs and Behavior.

BACKGROUND: Social media, mobile and wearable technology, and connected devices have significantly expanded the opportunities for conducting biomedical research online. Electronic consent to collecting such data, however, poses new challenges when contrasted to traditional consent processes. It reduces the participant-researcher dialogue but provides an opportunity for the consent deliberation process to move from solitary to social settings. In this research, we propose that social annotations, embedded in the consent form, can help prospective participants deliberate on the research and the organization behind it in ways that traditional consent forms cannot. Furthermore, we examine the role of the comments' valence on prospective participants' beliefs and behavior. OBJECTIVE: This study focuses specifically on the influence of annotations' valence on participants' perceptions and behaviors surrounding online consent for biomedical research. We hope to shed light on how social annotation can be incorporated into digitally mediated consent forms responsibly and effectively. METHODS: In this controlled between-subjects experiment, participants were presented with an online consent form for a personal genomics study that contained social annotations embedded in its margins. Individuals were randomly assigned to view the consent form with positive-, negative-, or mixed-valence comments beside the text of the consent form. We compared participants' perceptions of being informed and having understood the material, their trust in the organization seeking the consent, and their actual consent across conditions. RESULTS: We find that comment valence has a marginally significant main effect on participants' perception of being informed (F2=2.40, P=.07); specifically, participants in the positive condition (mean 4.17, SD 0.94) felt less informed than those in the mixed condition (mean 4.50, SD 0.69, P=.09). Comment valence also had a marginal main effect on the extent to which participants reported trusting the organization (F2=2.566, P=.08). Participants in the negative condition (mean 3.59, SD 1.14) were marginally less trusting than participants exposed to the positive condition (mean 4.02, SD 0.90, P=.06). Finally, we found that consent rate did not differ across comment valence conditions; however, participants who spent less time studying the consent form were more likely to consent when they were exposed to positive-valence comments. CONCLUSIONS: This work explores the effects of adding a computer-mediated social dimension, which inherently contains human emotions and opinions, to the consent deliberation process. We proposed that augmenting the consent deliberation process to incorporate multiple voices can enable individuals to capitalize on the knowledge of others, which brings to light questions, problems, and concerns they may not have considered on their own. We found that consent forms containing positive valence annotations are likely to lead participants to feel less informed and simultaneously more trusting of the organization seeking consent. In certain cases where participants spent little time considering the content of the consent form, participants exposed to positive valence annotations were even more likely to consent to the study. We suggest that these findings represent important considerations for the design of future electronic informed consent mechanisms.

Persistence of Human Papillomavirus, Overexpression of p53, and Outcomes of Patients After Endoscopic Ablation of Barrett's Esophagus.

We investigated the role of high-risk human papillomavirus (hr-HPV) in patients with Barrett's dysplasia and adenocarcinoma (EAC). Clearance vs persistence of HPV (DNA, E6 or E7 mRNA, and p16INK4A protein) and overexpression or mutation of p53 were determined for 40 patients who underwent endotherapy for Barrett's dysplasia or EAC. After ablation, dysplasia or neoplasia was eradicated in 34 subjects (24 squamous, 10 intestinal metaplasia). Six patients had detectable lesions after treatment; 2 were positive for transcriptionally active hr-HPV, and 4 had overexpression of p53. Before endotherapy, 15 patients had biologically active hr-HPV, 13 cleared the infection with treatment, and dysplasia or EAC was eliminated from 12 patients. One patient who cleared HPV after ablation acquired a p53 mutation, and their cancer progressed. Of 13 patients with overexpression of p53 before treatment, 10 cleared the p53 abnormality after ablation with eradication of dysplasia or neoplasia, whereas 3 of 13 had persistent p53 mutation-associated dysplasia after endotherapy (P = .004). Immunohistochemical and sequence analyses of p53 produced concordant results for 36 of 40 samples (90%). Detection of dysplasia or neoplasia after treatment was associated with HPV persistence or continued p53 overexpression.

Effects of atorvastatin on oxidative stress in chronic kidney disease.

AIM: Statins have pleiotropic effects that include attenuation of oxidative stress that may be relevant for chronic kidney disease (CKD) patients. We investigated the effect of long-term atorvastatin therapy on oxidative stress biomarkers in CKD patients. METHODS: This was a pre-specified secondary analysis of data from a randomized, double-blind, placebo-controlled trial (Lipid lowering and Onset of Renal Disease, LORD) in CKD patients. Participants received 10 mg/day atorvastatin (n = 47) or placebo (n = 39) for 3 years. Plasma measures (total F2-isoprostanes, malondialdehyde. protein carbonyls, uric acid, glutathione peroxidase (GPx) activity and total antioxidant capacity (TAC) ) were performed at baseline and at 3 years. Age and sex matched participants (n = 34) with normal kidney function were controls. RESULTS: CKD patients had significantly (P < 0.05) increased F2-isoprostanes and uric acid and decreased GPx activity compared with controls. When comparing the treatment (atorvastatin (A) vs placebo (P) ) change from baseline to 3 years, there were no significant differences (P > 0.05) in the group difference of the change values: (mean (95% CI), F2-isoprostanes = 5.3 (-29.2 to 39.8) pg/mL, protein carbonyls = 0.03 (-0.13 to 0.19) nmol/mg, GPx activity = -0.10 (-4.73 to 4.52) (U/L), uric acid = 8.8 (-33.9 to 51.6) µmol/L or TAC = -0.03 (-0.10 to 0.04) mmol/L. A significant difference (P = 0.04) in the change in malondialdehyde between groups, 1.52(0.09 to 2.96) µmol/L, was due to a large decrease in the placebo group. CONCLUSION: CKD patients had elevated oxidative stress that was not attenuated by atorvastatin 10 mg/day for 3 years.

A public resource facilitating clinical use of genomes.

Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the Personal Genome Project choose to forgo privacy via our institutional review board- approved "open consent" process. The contribution of public data and samples facilitates both scientific discovery and standardization of methods. We present our findings after enrollment of more than 1,800 participants, including whole-genome sequencing of 10 pilot participant genomes (the PGP-10). We introduce the Genome-Environment-Trait Evidence (GET-Evidence) system. This tool automatically processes genomes and prioritizes both published and novel variants for interpretation. In the process of reviewing the presumed healthy PGP-10 genomes, we find numerous literature references implying serious disease. Although it is sometimes impossible to rule out a late-onset effect, stringent evidence requirements can address the high rate of incidental findings. To that end we develop a peer production system for recording and organizing variant evaluations according to standard evidence guidelines, creating a public forum for reaching consensus on interpretation of clinically relevant variants. Genome analysis becomes a two-step process: using a prioritized list to record variant evaluations, then automatically sorting reviewed variants using these annotations. Genome data, health and trait information, participant samples, and variant interpretations are all shared in the public domain-we invite others to review our results using our participant samples and contribute to our interpretations. We offer our public resource and methods to further personalized medical research.

Informing the Design of Direct-to-Consumer Interactive Personal Genomics Reports.

BACKGROUND: In recent years, people who sought direct-to-consumer genetic testing services have been increasingly confronted with an unprecedented amount of personal genomic information, which influences their decisions, emotional state, and well-being. However, these users of direct-to-consumer genetic services, who vary in their education and interests, frequently have little relevant experience or tools for understanding, reasoning about, and interacting with their personal genomic data. Online interactive techniques can play a central role in making personal genomic data useful for these users. OBJECTIVE: We sought to (1) identify the needs of diverse users as they make sense of their personal genomic data, (2) consequently develop effective interactive visualizations of genomic trait data to address these users' needs, and (3) evaluate the effectiveness of the developed visualizations in facilitating comprehension. METHODS: The first two user studies, conducted with 63 volunteers in the Personal Genome Project and with 36 personal genomic users who participated in a design workshop, respectively, employed surveys and interviews to identify the needs and expectations of diverse users. Building on the two initial studies, the third study was conducted with 730 Amazon Mechanical Turk users and employed a controlled experimental design to examine the effectiveness of different design interventions on user comprehension. RESULTS: The first two studies identified searching, comparing, sharing, and organizing data as fundamental to users' understanding of personal genomic data. The third study demonstrated that interactive and visual design interventions could improve the understandability of personal genomic reports for consumers. In particular, results showed that a new interactive bubble chart visualization designed for the study resulted in the highest comprehension scores, as well as the highest perceived comprehension scores. These scores were significantly higher than scores received using the industry standard tabular reports currently used for communicating personal genomic information. CONCLUSIONS: Drawing on multiple research methods and populations, the findings of the studies reported in this paper offer deep understanding of users' needs and practices, and demonstrate that interactive online design interventions can improve the understandability of personal genomic reports for consumers. We discuss implications for designers and researchers.

Effects of atorvastatin on biomarkers of inflammation in chronic kidney disease.

BACKGROUND: Chronic kidney disease (CKD) is associated with inflammation. The effects of atorvastatin on biomarkers of inflammation were assessed in CKD patients in the LORD trial. METHODS: 117 patients with serum creatinine >120 µmol/L were randomized to receive atorvastatin 10 mg/day (56) or placebo (61) and followed for a mean of 2.5 years. 33 individuals with normal kidney function were controls. Outcomes included comparison of changes in pentraxin-3 (PTX3), TNF-α, CRP, IL-6, IL-8, and IL-10 between atorvastatin and placebo-treated patients. RESULTS: At baseline, compared with controls, CKD patients had increased PTX3 (mean, 1.08 vs. 0.58 ng/mL; p < 0.001), CRP (4.9 vs. 1.5 mg/L; p < 0.001), IL-8 (6.00 vs. 4.58 pg/mL; p = 0.001), IL-10 (59.0 vs. 17.6 pg/mL; p = 0.007), and TNF-α (18.0 vs. 5.6 ng/mL; p < 0.001). In patients with raised baseline plasma IL-6/8/10 and/or PTX3 the eGFR decline during the trial was significantly less in those treated with atorvastatin compared to placebo (mean change, -3.36; vs. + 1.25 mL/min/1.73 m2/year; difference, 4.61 95% CI 0.98 - 8.25; p = 0.002), whilst those without raised inflammatory biomarkers showed no difference. Placebo treated patients with raised TNF-α levels had no eGFR decline (p > 0.90), whereas in atorvastatin-treated patients eGFR declined (p = 0.05). CONCLUSIONS: CKD patients with inflammation treated with atorvastatin had significantly less eGFR decline. Larger studies using statin therapy, specifically enrolling CKD patients with inflammation, may be worthwhile exploring.

Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.

Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date (< 1,000 base pairs). We use family inheritance state analysis to control sequencing error and inform family-wide haplotype phasing, allowing quantification of genome-wide compound heterozygosity. We develop a sequence-based methodology for Human Leukocyte Antigen typing that contributes to disease risk prediction. Finally, we advance methods for analysis of disease and pharmacogenomic risk across the coding and non-coding genome that incorporate phased variant data. We show these methods are capable of identifying multigenic risk for inherited thrombophilia and informing the appropriate pharmacological therapy. These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.

Establishing breath as a biomarker platform-take home messages from the Breath Biopsy Conference 2023.

The annual Breath Biopsy Conference hosted by Owlstone Medical gathers together the leading experts, early career researchers, and physicians working with breath as a biomarker platform for clinical purposes. The current topics in breath research are discussed and presented, and an overarching topical theme is identified and discussed as part of an expert panel to close the conference. The profiling of normal breath composition and the establishment of standards for analyzing breath compared to background signal were two important topics that were major focuses of this conference, as well as important innovative progress that has been made since last year, including the development of a non-invasive breath test for lung cancer and liver disease. This meeting report offers an overview of the key take-home messages from the various presentations, posters, and discussions from the conference.

Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters.

Chromatin state is thought to impart regulatory function to the underlying DNA sequence. This can be established through histone modifications and chromatin organisation, but exactly how these factors relate to one another to regulate gene expression is unclear. In this study, we have used super-resolution microscopy to image the Y loops of Drosophila melanogaster primary spermatocytes, which are enormous transcriptionally active chromatin fibres, each representing single transcription units that are individually resolvable in the nuclear interior. We previously found that the Y loops consist of regular clusters of nucleosomes, with an estimated median of 54 nucleosomes per cluster with wide variation.In this study, we report that the histone modifications H3K4me3, H3K27me3, and H3K36me3 are also clustered along the Y loops, with H3K4me3 more associated with diffuse chromatin compared to H3K27me3. These histone modifications form domains that can be stretches of Y loop chromatin micrometres long, or can be in short alternating domains. The different histone modifications are associated with different sizes of chromatin clusters and unique morphologies. Strikingly, a single chromatin cluster almost always only contains only one type of the histone modifications that were labelled, suggesting exclusivity, and therefore regulation at the level of individual chromatin clusters. The active mark H3K36me3 is more associated with actively elongating RNA polymerase II than H3K27me3, with polymerase often appearing on what are assumed to be looping regions on the periphery of chromatin clusters.These results provide a foundation for understanding the relationship between chromatin state, chromatin organisation, and transcription regulation - with potential implications for pause-release dynamics, splicing complex organisation and chromatin dynamics during polymerase progression along a gene.

Characteristics and Health Care Utilization of Patients With Housing Insecurity in the ED.

Importance: Unstable housing and homelessness can exacerbate adverse health outcomes leading to increased risk of chronic disease, injury, and disability. However, emergency departments (EDs) have no universal method to identify those at risk of or currently experiencing homelessness. Objective: To describe the extent of housing insecurity among patients who seek care in an urban ED, including chief concerns, demographics, and patterns of health care utilization. Design, Setting, and Participants: This cross-sectional study included all adult patients presenting to the ED at Vanderbilt University Medical Center (VUMC), an urban tertiary care, level I trauma center in the Southeast US, from January 5 to May 16, 2023. Main Outcomes and Measures: The primary outcome was the proportion of ED visits at which patients screened positive for housing insecurity. Secondary outcomes included prevalence of insecurity by chief concerns, demographics, and patterns of health care utilization. Results: Of all 23 795 VUMC ED visits with screenings for housing insecurity (12 465 visits among women [52%]; median age, 47 years [IQR, 32-48 years]), in 1185 (5%), patients screened positive for current homelessness or housing insecurity (660 unique patients); at 22 610 visits (95%), the screening result was negative. Of visits with positive results, the median age of patients was 46 years (IQR, 36-55 years) and 829 (70%) were among male patients. Suicide and intoxication were more common chief concerns among visits at which patients screened positive (132 [11%] and 118 [10%], respectively) than among those at which patients screened negative (220 [1%] and 335 [2%], respectively). Visits with positive results were more likely to be among patients who were uninsured (395 [33%] vs 2272 [10%]) and had multiple visits during the study period. A higher proportion of positive screening results occurred between 8 pm and 6 am. The social work team assessed patients at 919 visits (78%) with positive screening results. Conclusions and Relevance: In this cross-sectional study of 23 795 ED visits, at 5% of visits, patients screened positive for housing insecurity and were more likely to present with a chief concern of suicide, to be uninsured, and to have multiple visits during the study period. This analysis provides a call for other institutions to introduce screening and create tailored care plans for patients experiencing housing insecurity to achieve equitable health care.

Prediction of Effectiveness and Toxicities of Immune Checkpoint Inhibitors Using Real-World Patient Data.

PURPOSE: Although immune checkpoint inhibitors (ICIs) have improved outcomes in certain patients with cancer, they can also cause life-threatening immunotoxicities. Predicting immunotoxicity risks alongside response could provide a personalized risk-benefit profile, inform therapeutic decision making, and improve clinical trial cohort selection. We aimed to build a machine learning (ML) framework using routine electronic health record (EHR) data to predict hepatitis, colitis, pneumonitis, and 1-year overall survival. METHODS: Real-world EHR data of more than 2,200 patients treated with ICI through December 31, 2018, were used to develop predictive models. Using a prediction time point of ICI initiation, a 1-year prediction time window was applied to create binary labels for the four outcomes for each patient. Feature engineering involved aggregating laboratory measurements over appropriate time windows (60-365 days). Patients were randomly partitioned into training (80%) and test (20%) sets. Random forest classifiers were developed using a rigorous model development framework. RESULTS: The patient cohort had a median age of 63 years and was 61.8% male. Patients predominantly had melanoma (37.8%), lung cancer (27.3%), or genitourinary cancer (16.4%). They were treated with PD-1 (60.4%), PD-L1 (9.0%), and CTLA-4 (19.7%) ICIs. Our models demonstrate reasonably strong performance, with AUCs of 0.739, 0.729, 0.755, and 0.752 for the pneumonitis, hepatitis, colitis, and 1-year overall survival models, respectively. Each model relies on an outcome-specific feature set, though some features are shared among models. CONCLUSION: To our knowledge, this is the first ML solution that assesses individual ICI risk-benefit profiles based predominantly on routine structured EHR data. As such, use of our ML solution will not require additional data collection or documentation in the clinic.

Transcriptionally active human papillomavirus is strongly associated with Barrett's dysplasia and esophageal adenocarcinoma.

OBJECTIVES: The role of human papillomavirus (HPV) in Barrett's esophagus (BE) remains unclear. The few studies that have previously investigated HPV and esophageal adenocarcinoma (EAC) or BE have produced either negative data or positive results of doubtful clinical/etiological significance or have detected only low-risk HPV types. We therefore prospectively determined the prevalence of biologically active HPV in esophageal epithelium of patients representing the Barrett's metaplasia-dysplasia-adenocarcinoma sequence. METHODS: HPV DNA was estimated by nested PCR and viral transcriptional activity detected by E6/7 oncogene mRNA expression and p16INK4A immunohistochemistry in fresh frozen and paraffin-embedded esophageal biopsies of patients with BE, Barrett's dysplasia (BD), and EAC, as well as controls. Biopsies were obtained from the transformation zone (squamocolumnar junction (SCJ)) and the lesion, or corresponding site in controls, i.e., 2 cm above the gastroesophageal junction (GEJ). RESULTS: Of the 261 patients, 81 were positive for HPV DNA. In controls and BE, the virus was mostly detected at the transformation zone. Compared with controls (18.0%), HPV positivity was significantly more common in BD (68.6%, incidence rate ratio (IRR) 2.94, 95% confidence interval (CI) 1.78-4.85, P<0.001) and EAC (66.7%, IRR 2.87, 95% CI 1.69-4.86, P<0.001), but not in BE (22.1%, IRR 1.06, 95% CI 0.60-1.85, P=0.85). Of the patients, 92.6% were high-risk (HR) HPV, i.e., types 16 and 18. Again, p16INK4A positivity was greatest in BD and EAC and much less in BE patients (44.1%, IRR 17.0 (95% CI 4.86-59.6, P<0.001), 44.4%, 17.0 (95% CI 4.87-59.4, P<0.001), and 10.6%, 3.93 (95% CI 1.01-15.3, P=0.048) respectively). In 66 HPV DNA-positive patients tested for E6/E7 mRNA, none of the control (n=16) or BE (n=13) individuals were positive, whereas 9/22 BD and 9/15 EAC patients demonstrated oncogene expression (P<0.001). When HPV DNA, p16INK4A, and E6/E7 mRNA were all positive, there was a very strong association with disease severity (SCJ: odds ratio (OR) 104, 95% CI 20.3-529, P<0.001; lesion: OR 62.2, 95% CI 12.4-311, P<0.001) than when all were negative. CONCLUSIONS: Transcriptionally active HR-HPV was strongly associated with BD and EAC, but was largely biologically irrelevant in BE and controls, suggesting a potential role in esophageal carcinogenesis. These data provide robust justification for further detailed longitudinal, interventional, and molecular studies.

Effect of hereditary haemochromatosis genotypes and iron overload on other trace elements.

PURPOSE: Hereditary haemochromatosis is a common genetic disorder involving dysregulation of iron absorption. There is some evidence to suggest that abnormal iron absorption and metabolism may influence the status of other important trace elements. In this study, the effect of abnormal HFE genotypes and associated iron overload on the status of other trace elements was examined. METHODS: Dietary data and blood samples were collected from 199 subjects (mean age = 55.4 years; range = 21-81 years). Dietary intakes, serum selenium, copper and zinc concentrations and related antioxidant enzymes (glutathione peroxidase and superoxide dismutase) in subjects with normal HFE genotype (n = 118) were compared to those with abnormal HFE genotype, with both normal iron status (n = 42) and iron overload (n = 39). RESULTS: For most dietary and biochemical variables measured, there were no significant differences between study groups. Red cell GPx was significantly higher in male subjects with normal genotypes and normal iron status compared to those with abnormal genotypes and normal iron status (P = 0.03) or iron overload (P = 0.001). Red cell GPx was also highest in normal women and significantly lower in the abnormal genotype and normal iron group (P = 0.016), but not in the iron overload group (P = 0.078). CONCLUSION: Although it may not be possible to exclude a small effect between the genotype groups on RBC GPx, overall, haemochromatosis genotypes or iron overload did not appear to have a significant effect on selenium, copper or zinc status.

Serum [25(OH)D] status, ankle strength and activity show seasonal variation in older adults: relevance for winter falls in higher latitudes.

BACKGROUND: seasonal variation exists in serum [25(OH)D] and physical activity, especially at higher latitudes, and these factors impact lower limb strength. This study investigates seasonal variation in leg strength in a longitudinal repeated measures design concurrently with serum vitamin D and physical activity. METHODS: eighty-eight community-dwelling independently mobile older adults (69.2 ± 6.5 years) were evaluated five times over a year, at the end of five consecutive seasons at latitude 41.1°S, recruited in two cohorts. Leg strength, serum [25(OH)D] and physical activity levels were measured. Time spent outside was recorded. Monthly falls diaries recorded falls. Data were analysed to determine annual means and percentage changes. RESULTS: significant variation in [25(OH)D] (±15%), physical activity (±13%), ankle dorsiflexion strength (±8%) and hours spent outside (±20%) (all P < 0.001) was demonstrated over the year, with maximums in January and February (mid-summer). Low mean ankle strength was associated with increased incidence of falling (P = 0.047). Quadriceps strength did not change (±2%; P = 0.53). CONCLUSION: ankle dorsiflexor strength varied seasonally. Increased ankle strength in summer may be influenced by increased levels of outdoors activity over the summer months. Reduced winter-time dorsiflexor strength may predispose older people to increased risk of tripping-related falls, and warrants investigation in a multi-faceted falls prevention programme.

Development and experimental application of an HPLC procedure for the determination of capsaicin and dihydrocapsaicin in serum samples from human subjects.

Total capsaicins are extracted from 2 mL aliquots of serum or plasma using methyl-isobutyl ketone, evaporation of the extract to dryness and reconstitution with 200 µL of acetonitrile. The HPLC mobile phase is 40:60 water:acetonitrile. The absorbance of the eluent is monitored at 205 nm. Standardisation uses a known mixture of pure capsaicin and dihydrocapsaicin. Accuracies are 98.9 and 100.6 % for capsaicin and dihydrocapsaicin respectively. Inter batch reproducibility for both is 15 %. The limits of detection are 2.6 and 3.8 ng/mL for capsaicin and dihydrocapsaicin respectively. Analyses of sera obtained previously from human subjects who had eaten chilli containing meals showed that in those that absorbed capsaicins (N = 30) then the median, mean and SD of their serum capsaicin were: 13.4, 18.9 and 16.3 ng/mL. The corresponding data for those sera (N = 13) that had measurable levels of dihydrocapsaicin were: 6.9, 7.5 and 3.6 ng/mL. This procedure is suitable for use in prospective studies of the metabolism of orally ingested chilli.