Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors.

BACKGROUND: Transcription factor (TF) binding to regulatory DNA sites is a key determinant of cell identity within multi-cellular organisms and has been studied extensively in relation to site affinity and chromatin modifications. There has been a strong focus on the inference of TF-gene regulatory networks and TF-TF physical interaction networks. Here, we present a third type of TF network, the spatial network of co-localized TF binding sites within the three-dimensional genome. RESULTS: Using published canonical Hi-C data and single-cell genome structures, we assess the spatial proximity of a genome-wide array of potential TF-TF co-localizations in human and mouse cell lines. For individual TFs, the abundance of occupied binding sites shows a positive correspondence with their clustering in three dimensions, and this is especially apparent for weak TF binding sites and at enhancer regions. An analysis between different TF proteins identifies significantly proximal pairs, which are enriched in reported physical interactions. Furthermore, clustering of different TFs based on proximity enrichment identifies two partially segregated co-localization sub-networks, involving different TFs in different cell types. Using data from both human lymphoblastoid cells and mouse embryonic stem cells, we find that these sub-networks are enriched within, but not exclusive to, different chromosome sub-compartments that have been identified previously in Hi-C data. CONCLUSIONS: This suggests that the association of TFs within spatial networks is closely coupled to gene regulatory networks. This applies to both differentiated and undifferentiated cells and is a potential causal link between lineage-specific TF binding and chromosome sub-compartment segregation

PUTTING THE PASS IN CLASS: IN-CLASS PEER MENTORING ON CAMPUS AND ONLINE

We analyse the introduction of peer mentors into classrooms to understand how in-class mentoring supports students’ learning in first-year courses. Peer mentors are high-achieving students who have completed the same course previously, and are hired and trained by the university to facilitate Peer Assisted Study Sessions (PASS). PASS sessions give students the opportunity to deepen their understanding through revision and active learning and are typically held outside of class time. In contrast, our trial embedded peer mentors into the classes for Professional Scientific Thinking, a large (~250 students) workshop-based course at the University of Newcastle. Analysis of Blackboard analytics, student responses to Brookfield’s Critical Incident Questionnaire and peer mentors’ journals found that during face-to-face workshops, peer mentors role-modelled ideal student behaviour (e.g. asking questions), rather than act as additional teachers. This helped students new to university to better understand how to interact and learn effectively in class. Moving classes online mid-semester reshaped mentors’ roles, including through the technical aspects of their work and their engagement with students – adaptations that were essential for supporting students to also adapt effectively to changed learning circumstances. This study highlights the benefits of embedding student mentors in classrooms, both on campus and online

A video-feedback parenting intervention to prevent enduring behaviour problems in at-risk children aged 12-36 months: the Healthy Start, Happy Start RCT.

BACKGROUND: Behaviour problems emerge early in childhood and place children at risk for later psychopathology. OBJECTIVES: To evaluate the clinical effectiveness and cost-effectiveness of a parenting intervention to prevent enduring behaviour problems in young children. DESIGN: A pragmatic, assessor-blinded, multisite, two-arm, parallel-group randomised controlled trial. SETTING: Health visiting services in six NHS trusts in England. PARTICIPANTS: A total of 300 at-risk children aged 12-36 months and their parents/caregivers. INTERVENTIONS: Families were allocated in a 1 : 1 ratio to six sessions of Video-feedback Intervention to promote Positive Parenting and Sensitive Discipline (VIPP-SD) plus usual care or usual care alone. MAIN OUTCOME MEASURES: The primary outcome was the Preschool Parental Account of Children's Symptoms, which is a structured interview of behaviour symptoms. Secondary outcomes included caregiver-reported total problems on the Child Behaviour Checklist and the Strengths and Difficulties Questionnaire. The intervention effect was estimated using linear regression. Health and social care service use was recorded using the Child and Adolescent Service Use Schedule and cost-effectiveness was explored using the Preschool Parental Account of Children's Symptoms. RESULTS: In total, 300 families were randomised: 151 to VIPP-SD plus usual care and 149 to usual care alone. Follow-up data were available for 286 (VIPP-SD, n = 140; usual care, n = 146) participants and 282 (VIPP-SD, n = 140; usual care, n = 142) participants at 5 and 24 months, respectively. At the post-treatment (primary outcome) follow-up, a group difference of 2.03 on Preschool Parental Account of Children's Symptoms (95% confidence interval 0.06 to 4.01; p = 0.04) indicated a positive treatment effect on behaviour problems (Cohen's d = 0.20, 95% confidence interval 0.01 to 0.40). The effect was strongest for children's conduct [1.61, 95% confidence interval 0.44 to 2.78; p = 0.007 (d = 0.30, 95% confidence interval 0.08 to 0.51)] versus attention deficit hyperactivity disorder symptoms [0.29, 95% confidence interval -1.06 to 1.65; p = 0.67 (d = 0.05, 95% confidence interval -0.17 to 0.27)]. The Child Behaviour Checklist [3.24, 95% confidence interval -0.06 to 6.54; p = 0.05 (d = 0.15, 95% confidence interval 0.00 to 0.31)] and the Strengths and Difficulties Questionnaire [0.93, 95% confidence interval -0.03 to 1.9; p = 0.06 (d = 0.18, 95% confidence interval -0.01 to 0.36)] demonstrated similar positive treatment effects to those found for the Preschool Parental Account of Children's Symptoms. At 24 months, the group difference on the Preschool Parental Account of Children's Symptoms was 1.73 [95% confidence interval -0.24 to 3.71; p = 0.08 (d = 0.17, 95% confidence interval -0.02 to 0.37)]; the effect remained strongest for conduct [1.07, 95% confidence interval -0.06 to 2.20; p = 0.06 (d = 0.20, 95% confidence interval -0.01 to 0.42)] versus attention deficit hyperactivity disorder symptoms [0.62, 95% confidence interval -0.60 to 1.84; p = 0.32 (d = 0.10, 95% confidence interval -0.10 to 0.30)], with little evidence of an effect on the Child Behaviour Checklist and the Strengths and Difficulties Questionnaire. The primary economic analysis showed better outcomes in the VIPP-SD group at 24 months, but also higher costs than the usual-care group (adjusted mean difference £1450, 95% confidence interval £619 to £2281). No treatment- or trial-related adverse events were reported. The probability of VIPP-SD being cost-effective compared with usual care at the 24-month follow-up increased as willingness to pay for improvements on the Preschool Parental Account of Children's Symptoms increased, with VIPP-SD having the higher probability of being cost-effective at willingness-to-pay values above £800 per 1-point improvement on the Preschool Parental Account of Children's Symptoms. LIMITATIONS: The proportion of participants with graduate-level qualifications was higher than among the general public. CONCLUSIONS: VIPP-SD is effective in reducing behaviour problems in young children when delivered by health visiting teams. Most of the effect of VIPP-SD appears to be retained over 24 months. However, we can be less certain about its value for money. TRIAL REGISTRATION: Current Controlled Trials ISRCTN58327365. FUNDING: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 25, No. 29. See the NIHR Journals Library website for further project information.NIHR HTA programm

Interventions to improve social circumstances of people with mental health conditions: a rapid evidence synthesis

BACKGROUND: Poor social circumstances can induce, exacerbate and prolong symptoms of mental health conditions, while having a mental health condition can also lead to worse social outcomes. Many people with mental health conditions prioritise improvement in social and functional outcomes over reduction in clinical symptoms. Interventions that improve social circumstances in this population should thus be considered a priority for research and policy. METHODS: This rapid evidence synthesis reports on randomised controlled trials of interventions to improve social circumstances across eight social domains (Housing and homelessness; money and basic needs; work and education; social isolation and connectedness; family, intimate and caring relationships; victimisation and exploitation; offending; and rights, inclusion and citizenship) in people with mental health conditions. Economic evaluations were also identified. A comprehensive, stepped search approach of the Cochrane library, MEDLINE, Embase, PsycINFO, Web of Science and Scopus was conducted. RESULTS: One systematic review and 102 randomised controlled trials were included. We did not find RCT evidence for interventions to improve family, intimate and caring relationships and only one or two trials for each of improving money and basic needs, victimisation and exploitation, and rights, inclusion and citizenship. Evidence from successful interventions in improving homelessness (Housing First) and employment (Individual Placement and Support) suggests that high-intensity interventions which focus on the desired social outcome and provide comprehensive multidisciplinary support could influence positive change in social circumstances of people with mental health conditions. Objective social isolation could be improved using a range of approaches such as supported socialisation and social skills training but interventions to reduce offending showed few benefits. Studies with cost and cost-effectiveness components were generally supportive of interventions to improve housing and vocational outcomes. More research is needed to ensure that social circumstances accompanied by high risks of further exacerbation of mental health conditions are adequately addressed. CONCLUSIONS: Although there is a large body of literature examining how to support some aspects of life for people with mental health conditions, more high-quality evidence is required in other social domains. Integration into mental health services of interventions targeting social circumstances could significantly improve a number of social outcomes

Rapid exome sequencing as a first-tier test in neonates with suspected genetic disorder:results of a prospective multicenter clinical utility study in the Netherlands

The introduction of rapid exome sequencing (rES) for critically ill neonates admitted to the neonatal intensive care unit has made it possible to impact clinical decision-making. Unbiased prospective studies to quantify the impact of rES over routine genetic testing are, however, scarce. We performed a clinical utility study to compare rES to conventional genetic diagnostic workup for critically ill neonates with suspected genetic disorders. In a multicenter prospective parallel cohort study involving five Dutch NICUs, we performed rES in parallel to routine genetic testing for 60 neonates with a suspected genetic disorder and monitored diagnostic yield and the time to diagnosis. To assess the economic impact of rES, healthcare resource use was collected for all neonates. rES detected more conclusive genetic diagnoses than routine genetic testing (20% vs. 10%, respectively), in a significantly shorter time to diagnosis (15 days (95% CI 10–20) vs. 59 days (95% CI 23–98, p &lt; 0.001)). Moreover, rES reduced genetic diagnostic costs by 1.5% (€85 per neonate). Conclusion: Our findings demonstrate the clinical utility of rES for critically ill neonates based on increased diagnostic yield, shorter time to diagnosis, and net healthcare savings. Our observations warrant the widespread implementation of rES as first-tier genetic test in critically ill neonates with disorders of suspected genetic origin.What is Known:• Rapid exome sequencing (rES) enables diagnosing rare genetic disorders in a fast and reliable manner, but retrospective studies with neonates admitted to the neonatal intensive care unit (NICU) indicated that genetic disorders are likely underdiagnosed as rES is not routinely used.• Scenario modeling for implementation of rES for neonates with presumed genetic disorders indicated an expected increase in costs associated with genetic testing.What is New:• This unique prospective national clinical utility study of rES in a NICU setting shows that rES obtained more and faster diagnoses than conventional genetic tests.• Implementation of rES as replacement for all other genetic tests does not increase healthcare costs but in fact leads to a reduction in healthcare costs.</p

Prognostic Significance of MYC Rearrangement and Translocation Partner in Diffuse Large B-Cell Lymphoma : A Study by the Lunenburg Lymphoma Biomarker Consortium

PURPOSE: MYC rearrangement (MYC-R) occurs in approximately 10% of diffuse large B-cell lymphomas (DLBCLs) and has been associated with poor prognosis in many studies. The impact of MYC-R on prognosis may be influenced by the MYC partner gene (immunoglobulin [IG] or a non-IG gene). We evaluated a large cohort of patients through the Lunenburg Lymphoma Biomarker Consortium to validate the prognostic significance of MYC-R (single-, double-, and triple-hit status) in DLBCL within the context of the MYC partner gene. METHODS: The study cohort included patients with histologically confirmed DLBCL morphology derived from large prospective trials and patient registries in Europe and North America who were uniformly treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone therapy or the like. Fluorescence in situ hybridization for the MYC, BCL2, BCL6, and IG heavy and light chain loci was used, and results were correlated with clinical outcomes. RESULTS: A total of 5,117 patients were identified of whom 2,383 (47%) had biopsy material available to assess for MYC-R. MYC-R was present in 264 (11%) of 2,383 patients and was associated with a significantly shorter progression-free and overall survival, with a strong time-dependent effect within the first 24 months after diagnosis. The adverse prognostic impact of MYC-R was only evident in patients with a concurrent rearrangement of BCL2 and/or BCL6 and an IG partner (hazard ratio, 2.4; 95% CI, 1.6 to 3.6; P < .001). CONCLUSION: The negative prognostic impact of MYC-R in DLBCL is largely observed in patients with MYC double hit/triple-hit disease in which MYC is translocated to an IG partner, and this effect is restricted to the first 2 years after diagnosis. Our results suggest that diagnostic strategies should be adopted to identify this high-risk cohort, and risk-adjusted therapeutic approaches should be refined further

Mixed-methods study protocol for an evaluation of the mental health transition navigator model in child and adolescent mental health services : the Navigator Evaluation Advancing Transitions (NEAT) study

INTRODUCTION: Transition from child and adolescent mental health services (CAMHS) to community or adult mental health services (AMHS) is a highly problematic health systems hurdle, especially for transition-aged youth. A planned and purposeful transition process is often non-existent or experienced negatively by youth and their caregivers. Stakeholders, including youth and their caregivers, have demanded interventions to support more effective transitions, such a transition navigator. The transition navigator model uses a navigator to facilitate complex transitions from acute care CAMHS to community or AMHS. However, despite the widespread implementation of this model, there has been no evaluation of the programme, hindering its scalability. This paper describes the study protocol of the Navigator Evaluation Advancing Transitions study that aims to collaborate with patients, caregivers and clinicians in the evaluation of the navigator model. METHODS AND ANALYSIS: A pre and post mixed-method study will be conducted, using the Triple Aim Framework, to evaluate the navigator model. We will recruit participants from one large tertiary and two community hospitals in Toronto, Canada. For the quantitative portion of the study, we will recruit a sample of 45 youth (15 at each site), aged 16-18, and their caregivers at baseline (referral to navigator) (T1) and 6 months (T2). Youth and caregiver participants will complete a set of standardised measures to assess mental health, service utilisation, and satisfaction outcomes. For the qualitative portion of the study, semistructured interviews will be conducted at 6 months (T2) with youth, their caregivers and clinicians to better understand their experience and satisfaction with the model. ETHICS AND DISSEMINATION: Research Ethics Board (REB) approval has been obtained from the lead research sites, the University of Toronto and the Hospital for Sick Children. The results of the study will be reported in peer-reviewed publications, webinars and conferences and to all relevant stakeholders

Peri-operative red blood cell transfusion in neonates and infants: NEonate and Children audiT of Anaesthesia pRactice IN Europe: A prospective European multicentre observational study

BACKGROUND: Little is known about current clinical practice concerning peri-operative red blood cell transfusion in neonates and small infants. Guidelines suggest transfusions based on haemoglobin thresholds ranging from 8.5 to 12 g dl-1, distinguishing between children from birth to day 7 (week 1), from day 8 to day 14 (week 2) or from day 15 (≥week 3) onwards. OBJECTIVE: To observe peri-operative red blood cell transfusion practice according to guidelines in relation to patient outcome. DESIGN: A multicentre observational study. SETTING: The NEonate-Children sTudy of Anaesthesia pRactice IN Europe (NECTARINE) trial recruited patients up to 60 weeks' postmenstrual age undergoing anaesthesia for surgical or diagnostic procedures from 165 centres in 31 European countries between March 2016 and January 2017. PATIENTS: The data included 5609 patients undergoing 6542 procedures. Inclusion criteria was a peri-operative red blood cell transfusion. MAIN OUTCOME MEASURES: The primary endpoint was the haemoglobin level triggering a transfusion for neonates in week 1, week 2 and week 3. Secondary endpoints were transfusion volumes, 'delta haemoglobin' (preprocedure - transfusion-triggering) and 30-day and 90-day morbidity and mortality. RESULTS: Peri-operative red blood cell transfusions were recorded during 447 procedures (6.9%). The median haemoglobin levels triggering a transfusion were 9.6 [IQR 8.7 to 10.9] g dl-1 for neonates in week 1, 9.6 [7.7 to 10.4] g dl-1 in week 2 and 8.0 [7.3 to 9.0] g dl-1 in week 3. The median transfusion volume was 17.1 [11.1 to 26.4] ml kg-1 with a median delta haemoglobin of 1.8 [0.0 to 3.6] g dl-1. Thirty-day morbidity was 47.8% with an overall mortality of 11.3%. CONCLUSIONS: Results indicate lower transfusion-triggering haemoglobin thresholds in clinical practice than suggested by current guidelines. The high morbidity and mortality of this NECTARINE sub-cohort calls for investigative action and evidence-based guidelines addressing peri-operative red blood cell transfusions strategies. TRIAL REGISTRATION: ClinicalTrials.gov, identifier: NCT02350348

Machine learning algorithms performed no better than regression models for prognostication in traumatic brain injury

Objective: We aimed to explore the added value of common machine learning (ML) algorithms for prediction of outcome for moderate and severe traumatic brain injury. Study Design and Setting: We performed logistic regression (LR), lasso regression, and ridge regression with key baseline predictors in the IMPACT-II database (15 studies, n = 11,022). ML algorithms included support vector machines, random forests, gradient boosting machines, and artificial neural networks and were trained using the same predictors. To assess generalizability of predictions, we performed internal, internal-external, and external validation on the recent CENTER-TBI study (patients with Glasgow Coma Scale <13, n = 1,554). Both calibration (calibration slope/intercept) and discrimination (area under the curve) was quantified. Results: In the IMPACT-II database, 3,332/11,022 (30%) died and 5,233(48%) had unfavorable outcome (Glasgow Outcome Scale less than 4). In the CENTER-TBI study, 348/1,554(29%) died and 651(54%) had unfavorable outcome. Discrimination and calibration varied widely between the studies and less so between the studied algorithms. The mean area under the curve was 0.82 for mortality and 0.77 for unfavorable outcomes in the CENTER-TBI study. Conclusion: ML algorithms may not outperform traditional regression approaches in a low-dimensional setting for outcome prediction after moderate or severe traumatic brain injury. Similar to regression-based prediction models, ML algorithms should be rigorously validated to ensure applicability to new populations