Novel methods for early phase clinical trials

Early phase clinical trials are conducted with limited time and patient resources. Despite design restrictions, patient safety must be prioritised and trial conclusions must be accurate; maximising a promising treatment’s chance of success in later largescale, long-term trials. Increasing the efficiency of early phase clinical trials, through utilising available data more effectively, can lead to improved decision making during, and as a result of, the trial. This thesis contains three distinct pieces of research; each of which proposes a novel, early phase clinical trial design with this overall objective. The initial focus of the thesis is on dose-escalation. In the single-agent setting, subgroups of the population, between which the reaction to treatment may differ, are accounted for in dose-escalation. This is achieved using a Bayesian model-based approach to dose-escalation with spike and slab priors in order to identify a recommended dose of the treatment (for use in later trials) in each subgroup. Accounting for a potential subgroup effect in a dose-escalation trial can yield safety benefits for patients within, and post- trial due to subgorup-specific dosing which should improve the benefit-risk ratio of the treatment.Dual-agent dose-escalation is considered next. In the dual-agent setting, singleagent data, including toxicity and pharmacokinetic exposure information, is available. This information is used to define escalation rules that combine the outputs of independent dose-toxicity and dose-exposure models which are fitted to emerging trial data. This solution is practical to implement and reduces the subjectivity that currently surrounds the use of exposure data in dose-escalation. In addition, escalation decisions and consistency of the final recommended dose-pair are improved. The focus of the third piece of research changes. In this work, Bayesian sample size calculations for single-arm and randomised phase II trials with time-to-event endpoints are considered. Calculation of the sample size required for a trial is based on a proportional hazards assumption and utilises historical data on the control (and experimental) treatments. The sample sizes obtained are consistent with those currently used in practice while better accounting for available information and uncertainty in parameter estimates of the time-to-event distribution. Investigating allocation ratio’s in the randomised setting provides a basis for deciding whether a control arm is indeed necessary. That is, in a randomised trial, whether it is necessary for any patients to be randomised to the control treatment arm

Dose-escalation strategies which utilise subgroup information

Dose‐escalation trials commonly assume a homogeneous trial population to identify a single recommended dose of the experimental treatment for use in future trials. Wrongly assuming a homogeneous population can lead to a diluted treatment effect. Equally, exclusion of a subgroup that could in fact benefit from the treatment can cause a beneficial treatment effect to be missed. Accounting for a potential subgroup effect (ie, difference in reaction to the treatment between subgroups) in dose‐escalation can increase the chance of finding the treatment to be efficacious in a larger patient population. A standard Bayesian model‐based method of dose‐escalation is extended to account for a subgroup effect by including covariates for subgroup membership in the dose‐toxicity model. A stratified design performs well but uses available data inefficiently and makes no inferences concerning presence of a subgroup effect. A hypothesis test could potentially rectify this problem but the small sample sizes result in a low‐powered test. As an alternative, the use of spike and slab priors for variable selection is proposed. This method continually assesses the presence of a subgroup effect, enabling efficient use of the available trial data throughout escalation and in identifying the recommended dose(s). A simulation study, based on real trial data, was conducted and this design was found to be both promising and feasible

Threat analysis for more effective lion conservation

We use comparable 2005 and 2018 population data to assess threats driving the decline of lion Panthera leo populations, and review information on threats structured by problem tree and root cause analysis. We define 11 threats and rank their severity and prevalence. Two threats emerged as affecting both the number of lion populations and numbers within them: livestock depredation leading to retaliatory killing of lions, and bushmeat poaching leading to prey depletion. Our data do not allow determination of whether any specific threat drives declines faster than others. Of 20 local extirpations, most were associated with armed conflicts as a driver of proximate threats. We discuss the prevalence and severity of proximate threats and their drivers, to identify priorities for more effective conservation of lions, other carnivores and their prey

Modeling to predict factor VIII levels associated with zero bleeds in patients with severe hemophilia A initiated on tertiary prophylaxis

Background Factor VIII (FVIII) trough levels > 1 IU/dL in patients with severe hemophilia A receiving regular prophylaxis may optimize bleed protection. Objectives In this post hoc analysis of patients receiving tertiary prophylaxis for approximately 1 year, the relationship between estimated FVIII levels and reported bleeds was investigated to predict the potential for zero bleeds. Methods Sixty-three patients (median [range] age, 28 [7–59] years) with severe hemophilia A (229 bleeds) were included. FVIII levels at time of each bleed were estimated from single-dose individual pharmacokinetics. The highest estimated FVIII level at which patients experienced a bleed was considered the “potentially effective trough level” for that bleed type. Kaplan–Meier estimates of proportions of patients with no bleeds above certain estimated FVIII levels were determined. Those not experiencing a bleed in the trial were assumed to have a bleed at 0 IU/dL (pragmatic approach) or at their median trough level (conservative approach). Results Kaplan–Meier estimates based on pragmatic approach predicted zero all bleeds, joint bleeds, and spontaneous joint bleeds in 1 year in 40, 43, and 63% of patients, respectively, when the potentially effective trough FVIII level was set at 1 IU/dL. Between 1 and 10 IU/dL, every 1 IU/dL rise in estimated FVIII level was associated with an additional 2% of patients having zero all bleeds. Conclusion This post hoc analysis confirms benefits with trough levels of approximately 1 to 3 IU/dL in most patients starting tertiary prophylaxis; prophylaxis with higher trough levels may help patients to achieve zero bleeds

Culturally-adapted Family Intervention (CaFI) for African-Caribbeans diagnosed with schizophrenia and their families : a feasibility study protocol of implementation and acceptability

Background African-Caribbeans in the UK have the highest schizophrenia incidence and greatest inequity in access to mental health services of all ethnic groups. The National Institute for Health and Care Excellence (NICE) highlights this crisis in care and urgent need to improve evidence-based mental healthcare, experiences of services and outcomes for this group. Family intervention (FI) is clinically and cost-effective for the management of schizophrenia but it is rarely offered. Evidence for FI with minority ethnic groups generally, and African-Caribbeans in particular, is lacking. This study aims to test the feasibility and acceptability of delivering Culturally-adapted Family Intervention (CaFI) to African-Caribbean service users diagnosed with schizophrenia. Methods/Design This is a feasibility cohort design study. Over a 12-month intervention period, 30 service users and their families, recruited from hospital and community settings, will receive ten one-hourly sessions of CaFI. Where biological families are absent, access to the intervention will be optimised through ‘family support members’; trusted individuals nominated by service users or study volunteers. We shall collect data on eligibility, uptake, retention and attrition and assess the utility and feasibility of collecting various outcome measures including readmission, service engagement, working alliance, clinical symptoms and functioning, perceived criticism, psychosis knowledge, familial stress and economic costs. Measures will be collected at baseline, post-intervention and at 3-month follow-up using validated questionnaires and standardised interviews. Admission rates and change in care management will be rated by independent case note examination. Variability in the measures will inform sample size estimates for a future trial. Independent raters will assess fidelity to the intervention in 10 % of sessions. Feedback at the end of each session along with thematically-analysed qualitative interviews will examine CaFI’s acceptability to service users, families and healthcare professionals. Discussion This innovative response to inequalities in mental healthcare experienced by African-Caribbeans diagnosed with schizophrenia might improve engagement in services, access to evidence-based interventions and clinical outcomes. Successful implementation of CaFI in this group could pave the way for better engagement and provision across marginalised groups and therefore has potentially important implications for commissioning and service delivery in ethnically diverse populations. This study will demonstrate whether the approach is feasible and acceptable and can be implemented with fidelity in different settings

Is there an elephant in the room? A Response to Batavia et al

Non peer reviewe

Consequences Matter : Compassion in Conservation Means Caring for Individuals, Populations and Species

Funding This research received no external funding. Acknowledgments The manuscript benefitted from significant input from Dan Brockington, J.B. Callicott, Peter Coals, Tim Hodgetts, David Macdonald and Jeremy Wilson. Conflicts of Interest The authors declare no conflict of interest.Peer reviewedPublisher PD

Analysis of Qa-1bPeptide Binding Specificity and the Capacity of Cd94/Nkg2a to Discriminate between Qa-1–Peptide Complexes

The major histocompatibility complex class Ib protein, Qa-1b, serves as a ligand for murine CD94/NKG2A natural killer (NK) cell inhibitory receptors. The Qa-1b peptide-binding site is predominantly occupied by a single nonameric peptide, Qa-1 determinant modifier (Qdm), derived from the leader sequence of H-2D and L molecules. Five anchor residues were identified in this study by measuring the peptide-binding affinities of substituted Qdm peptides in experiments with purified recombinant Qa-1b. A candidate peptide-binding motif was determined by sequence analysis of peptides eluted from Qa-1 that had been folded in the presence of random peptide libraries or pools of Qdm derivatives randomized at specific anchor positions. The results indicate that Qa-1b can bind a diverse repertoire of peptides but that Qdm has an optimal primary structure for binding Qa-1b. Flow cytometry experiments with Qa-1b tetramers and NK target cell lysis assays demonstrated that CD94/NKG2A discriminates between Qa-1b complexes containing peptides with substitutions at nonanchor positions P4, P5, or P8. Our findings suggest that it may be difficult for viruses to generate decoy peptides that mimic Qdm and raise the possibility that competitive replacement of Qdm with other peptides may provide a novel mechanism for activation of NK cells

A comprehensive candidate gene approach identifies genetic variation associated with osteosarcoma

<p>Abstract</p> <p>Background</p> <p>Osteosarcoma (OS) is a bone malignancy which occurs primarily in adolescents. Since it occurs during a period of rapid growth, genes important in bone formation and growth are plausible modifiers of risk. Genes involved in DNA repair and ribosomal function may contribute to OS pathogenesis, because they maintain the integrity of critical cellular processes. We evaluated these hypotheses in an OS association study of genes from growth/hormone, bone formation, DNA repair, and ribosomal pathways.</p> <p>Methods</p> <p>We evaluated 4836 tag-SNPs across 255 candidate genes in 96 OS cases and 1426 controls. Logistic regression models were used to estimate the odds ratios (OR) and 95% confidence intervals (CI).</p> <p>Results</p> <p>Twelve SNPs in growth or DNA repair genes were significantly associated with OS after Bonferroni correction. Four SNPs in the DNA repair gene <it>FANCM </it>(ORs 1.9-2.0, <it>P </it>= 0.003-0.004) and 2 SNPs downstream of the growth hormone gene <it>GH1 </it>(OR 1.6, <it>P </it>= 0.002; OR 0.5, <it>P </it>= 0.0009) were significantly associated with OS. One SNP in the region of each of the following genes was significant: <it>MDM2</it>, <it>MPG</it>, <it>FGF2</it>, <it>FGFR3</it>, <it>GNRH2</it>, and <it>IGF1</it>.</p> <p>Conclusions</p> <p>Our results suggest that several SNPs in biologically plausible pathways are associated with OS. Larger studies are required to confirm our findings.</p

Quantitative High-Throughput Screening Identifies 8-Hydroxyquinolines as Cell-Active Histone Demethylase Inhibitors

Small molecule modulators of epigenetic processes are currently sought as basic probes for biochemical mechanisms, and as starting points for development of therapeutic agents. N(epsilon)-Methylation of lysine residues on histone tails is one of a number of post-translational modifications that together enable transcriptional regulation. Histone lysine demethylases antagonize the action of histone methyltransferases in a site- and methylation state-specific manner. N(epsilon)-Methyllysine demethylases that use 2-oxoglutarate as co-factor are associated with diverse human diseases, including cancer, inflammation and X-linked mental retardation; they are proposed as targets for the therapeutic modulation of transcription. There are few reports on the identification of templates that are amenable to development as potent inhibitors in vivo and large diverse collections have yet to be exploited for the discovery of demethylase inhibitors