DNA methylation-based age prediction using massively parallel sequencing data and multiple machine learning models

The field of DNA intelligence focuses on retrieving information from DNA evidence that can help narrow down large groups of suspects or define target groups of interest. With recent breakthroughs on the estimation of geographical ancestry and physical appearance, the estimation of chronological age comes to complete this circle of information. Recent studies have identified methylation sites in the human genome that correlate strongly with age and can be used for the development of age-estimation algorithms. In this study, 110 whole blood samples from individuals aged 11–93 years were analysed using a DNA methylation quantification assay based on bisulphite conversion and massively parallel sequencing (Illumina MiSeq) of 12 CpG sites. Using this data, 17 different statistical modelling approaches were compared based on root mean square error (RMSE) and a Support Vector Machine with polynomial function (SVMp) model was selected for further testing. For the selected model (RMSE = 4.9 years) the mean average error (MAE) of the blind test (n = 33) was calculated at 4.1 years, with 52% of the samples predicting with less than 4 years of error and 86% with less than 7 years. Furthermore, the sensitivity of the method was assessed both in terms of methylation quantification accuracy and prediction accuracy in the first validation of this kind. The described method retained its accuracy down to 10 ng of initial DNA input or ∼2 ng bisulphite PCR input. Finally, 34 saliva samples were analysed and following basic normalisation, the chronological age of the donors was predicted with less than 4 years of error for 50% of the samples and with less than 7 years of error for 70%

Curation of the Video Art Exhibition in the Museum

The goal of this thesis is to illustrate the importance of video art through a spatial and aesthetic phenomenological framework, revealing the critical nature of aesthetic experiences for forming meaning between art-objects and viewers facilitated through acts of curation. Video art, emerging in the 1960s and heavily intertwined with the museum, marks a unique, novel, and profound disruption of the representative regime of aesthetic experiences and objects through its nature to question cultural systems of the world as a radical medium. By evolving from anti-art movements in tandem with technological innovations, video was distant from art history, discourse, and tradition, allowing for women and people of color to work liberated from fine art limitations and set a new precedent for the art and museum community. Video art allows us to shape the future of the museum, curatorial practices, and aesthetic experiences as well as set a greater model for inclusion of voices often lost in the traditional art institution

Building the English health visitor workforce as a result of the Health Visitor Implementation Plan 2011-2015: a survey study of career progression and retention for newly qualified health visitors

Aim: This study aimed to explore the extent to which health visitors who trained and qualified in both Greater London and the South West of England between September 2011 and January 2016 were employed in health visiting posts and have remained in the profession. Background: In 2011, the UK Government launched the Health Visitor Implementation Plan ‘A Call to Action’ (Department of Health, 2011) to develop the health visitor workforce by training 4200 health visitors over a four-year period. By April 2015, 4000 additional health visitors were trained, but the total workforce has since fallen back to pre-Implementation Plan size. Methods: Data were collected using a survey, completed online by participants. All participants had undertaken a health visitor education programme at one of two participating universities. The survey was distributed in January 2017 and completed by 180 individuals. Quantitative data were analysed using SPSS; association was assessed using individual chi-square tests or Fisher’s exact test. Free-text responses were thematically analysed. Findings: Most (153; 87%) participants were still working as health visitors. Length of time spent working in the community prior to completing health visitor training was associated with staying in the role ( χ2 (with Fisher’s exact test = 7.998, P = .027). Current pay was associated with attrition from the health visitor workforce ( χ2 (with Fisher’s exact test) = 67.559, P < .001.). The majority who had left the health visitor role were on higher pay bands in their new post compared to those that had stayed (12; 60%). Bronfenbrenner’s (1979) theory of socio-ecological development was used as a framework to interpret the results. While participants made an active choice to join the profession, leaving was influenced more by factors outside their control. To influence health visitor retention, both local and strategic changes are required

Incorporating multiparametric MRI staging and the new histological Grade Group system improves risk-stratified detection of bone metastasis in prostate cancer

$\textbf{BACKGROUND}$: There remains uncertainty on the need for bone staging in men with intermediate-risk prostate cancer. Current guidelines do not use mpMRI-staging information and rely on historic pathology grading. $\textbf{METHODS}$: We investigated the ability of mpMRI and the new Grade Group system to better predict bone metastasis status in a retrospective cohort study of 438 men with prostate cancer undergoing baseline mpMRI and isotope bone scintigraphy (BS). $\textbf{RESULTS}$: Including mpMRI-staging information significantly increased the specificity of bone metastasis detection from 3.0% to 24.2% (P<0.01) and sensitivity from 89.2% to 97.3%. The new Grade Group score demonstrated progressive increase in bone metastasis rates (P<0.001). A novel risk-stratification model combining Grade Groups, PSA and mpMRI staging shows promise in predicting bone metastasis and could potentially reduce BS usage by 22.4%-34.7%. $\textbf{CONCLUSIONS}$: Incorporating the new Grade Group system and mpMRI staging more accurately identified bone metastatic risk and suggests men with Grade Group ⩽2 and/or without radiological T3 disease could safely avoid routine bone staging.We thank research support from the National Institute of Health Research, Cambridge Biomedical Research Centre, Cancer Research UK, Cancer Research UK and the Engineering and Physical Sciences Research Council Imaging Centre in Cambridge and Manchester and the Cambridge Experimental Cancer Medicine Centre

Evolution and oncological outcomes of a contemporary radical prostatectomy practice in a UK regional tertiary referral centre

Objective To investigate the clinical and pathological trends over a ten-year period for robotic-assisted laparoscopic prostatectomy (RALP) in a UK regional tertiary referral centre. Patients and Methods 1500 consecutive patients underwent RALP between October 2005 and January 2015. Prospective data was collected on clinic-pathological details at presentation as well as surgical outcomes and compared over time. Results The median(range) age of patients throughout the period was 62(35-78) years. The proportion of pre-operative high-grade cases (Gleason sum 8-10) rose from 4.6% in 2005-2008 to 18.2% in 2013-2015 (p<0.0001). In the same periods the proportion of clinical stage T3 cases operated on rose from 2.4% to 11.4% (p<0.0001). Median PSA at diagnosis did not alter significantly. Overall 11.6% of men in 2005-2008 were classified pre-operatively as high-risk by NICE criteria, compared to 33.6% in 2013-2015 (p<0.0001). The corresponding proportions for low-risk cases were 48.6% and 17.3% respectively. Final surgical pathology demonstrated an increase in tumour stage, Gleason grade and nodal status across time. The proportion of pT3 cases rose from 43.2% in 2005-2008 to 55.5% in 2013-15 (p=0.0007), Gleason grade 9-10 tumours increased from 1.8% to 9.1% (p=0.0002) and positive nodal status increased from 1.6% to 12.9% (p<0.0001) between the same periods. Despite this, positive surgical margin rates showed a downward trend in all pT groups across the different eras (p=0.72). Conclusion This study suggests that the patient profile for RALP in our unit is changing, with increasing proportions of higher-stage and more advanced disease being referred and operated on. Surgical margin outcomes however have remained good.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1111/bju.1351

Description of 3,180 courses of chelation with dimercaptosuccinic acid in children ≤ 5 y with severe lead poisoning in Zamfara, Northern Nigeria: a retrospective analysis of programme data.

BACKGROUND: In 2010, Médecins Sans Frontières (MSF) discovered extensive lead poisoning impacting several thousand children in rural northern Nigeria. An estimated 400 fatalities had occurred over 3 mo. The US Centers for Disease Control and Prevention (CDC) confirmed widespread contamination from lead-rich ore being processed for gold, and environmental management was begun. MSF commenced a medical management programme that included treatment with the oral chelating agent 2,3-dimercaptosuccinic acid (DMSA, succimer). Here we describe and evaluate the changes in venous blood lead level (VBLL) associated with DMSA treatment in the largest cohort of children ≤ 5 y of age with severe paediatric lead intoxication reported to date to our knowledge. METHODS AND FINDINGS: In a retrospective analysis of programme data, we describe change in VBLL after DMSA treatment courses in a cohort of 1,156 children ≤ 5 y of age who underwent between one and 15 courses of chelation treatment. Courses of DMSA of 19 or 28 d duration administered to children with VBLL ≥ 45 µg/dl were included. Impact of DMSA was calculated as end-course VBLL as a percentage of pre-course VBLL (ECP). Mixed model regression with nested random effects was used to evaluate the relative associations of covariates with ECP. Of 3,180 treatment courses administered, 36% and 6% of courses commenced with VBLL ≥ 80 µg/dl and ≥ 120 µg/dl, respectively. Overall mean ECP was 74.5% (95% CI 69.7%-79.7%); among 159 inpatient courses, ECP was 47.7% (95% CI 39.7%-57.3%). ECP after 19-d courses (n = 2,262) was lower in older children, first-ever courses, courses with a longer interval since a previous course, courses with more directly observed doses, and courses with higher pre-course VBLLs. Low haemoglobin was associated with higher ECP. Twenty children aged ≤ 5 y who commenced chelation died during the period studied, with lead poisoning a primary factor in six deaths. Monitoring of alanine transaminase (ALT), creatinine, and full blood count revealed moderate ALT elevation in <2.5% of courses. No clinically severe adverse drug effects were observed, and no laboratory findings required discontinuation of treatment. Limitations include that this was a retrospective analysis of clinical data, and unmeasured variables related to environmental exposures could not be accounted for. CONCLUSIONS: Oral DMSA was a pharmacodynamically effective chelating agent for the treatment of severe childhood lead poisoning in a resource-limited setting. Re-exposure to lead, despite efforts to remediate the environment, and non-adherence may have influenced the impact of outpatient treatment. Please see later in the article for the Editors' Summary

Association of blood lead level with neurological features in 972 children affected by an acute severe lead poisoning outbreak in Zamfara State, northern Nigeria.

BACKGROUND: In 2010, Médecins Sans Frontières (MSF) investigated reports of high mortality in young children in Zamfara State, Nigeria, leading to confirmation of villages with widespread acute severe lead poisoning. In a retrospective analysis, we aimed to determine venous blood lead level (VBLL) thresholds and risk factors for encephalopathy using MSF programmatic data from the first year of the outbreak response. METHODS AND FINDINGS: We included children aged ≤5 years with VBLL ≥45 µg/dL before any chelation and recorded neurological status. Odds ratios (OR) for neurological features were estimated; the final model was adjusted for age and baseline VBLL, using random effects for village of residence. 972 children met inclusion criteria: 885 (91%) had no neurological features; 34 (4%) had severe features; 47 (5%) had reported recent seizures; and six (1%) had other neurological abnormalities. The geometric mean VBLLs for all groups with neurological features were >100 µg/dL vs 65.9 µg/dL for those without neurological features. The adjusted OR for neurological features increased with increasing VBLL: from 2.75, 95%CI 1.27-5.98 (80-99.9 µg/dL) to 22.95, 95%CI 10.54-49.96 (≥120 µg/dL). Neurological features were associated with younger age (OR 4.77 [95% CI 2.50-9.11] for 1-<2 years and 2.69 [95%CI 1.15-6.26] for 2-<3 years, both vs 3-5 years). Severe neurological features were seen at VBLL <105 µg/dL only in those with malaria. INTERPRETATION: Increasing VBLL (from ≥80 µg/dL) and age 1-<3 years were strongly associated with neurological features; in those tested for malaria, a positive test was also strongly associated. These factors will help clinicians managing children with lead poisoning in prioritising therapy and developing chelation protocols

Models predicting survival to guide treatment decision-making in newly diagnosed primary non-metastatic prostate cancer: a systematic review.

OBJECTIVES: Men diagnosed with non-metastatic prostate cancer require standardised and robust long-term prognostic information to help them decide on management. Most currently-used tools use short-term and surrogate outcomes. We explored the evidence base in the literature on available pre-treatment, prognostic models built around long-term survival and assess the accuracy, generalisability and clinical availability of these models. DESIGN: Systematic literature review, pre-specified and registered on PROSPERO (CRD42018086394). DATA SOURCES: MEDLINE, Embase and The Cochrane Library were searched from January 2000 through February 2018, using previously-tested search terms. ELIGIBILITY CRITERIA: Inclusion required a multivariable model prognostic model for non-metastatic prostate cancer, using long-term survival data (defined as ≥5 years), which was not treatment-specific and usable at the point of diagnosis. DATA EXTRACTION AND SYNTHESIS: Title, abstract and full-text screening were sequentially performed by three reviewers. Data extraction was performed for items in the CHecklist for critical Appraisal and data extraction for systematic Reviews of prediction Modelling Studies checklist. Individual studies were assessed using the new Prediction model Risk Of Bias ASsessment Tool. RESULTS: Database searches yielded 6581 studies after deduplication. Twelve studies were included in the final review. Nine were model development studies using data from over 231 888 men. However, only six of the nine studies included any conservatively managed cases and only three of the nine included treatment as a predictor variable. Every included study had at least one parameter for which there was high risk of bias, with failure to report accuracy, and inadequate reporting of missing data common failings. Three external validation studies were included, reporting two available models: The University of California San Francisco (UCSF) Cancer of the Prostate Risk Assessment score and the Cambridge Prognostic Groups. Neither included treatment effect, and both had potential flaws in design, but represent the most robust and usable prognostic models currently available. CONCLUSION: Few long-term prognostic models exist to inform decision-making at diagnosis of non-metastatic prostate cancer. Improved models are required to inform management and avoid undertreatment and overtreatment of non-metastatic prostate cancer.The Urology Foundation - Research Scholarship