Stability analysis of mixtures of mutagenetic trees

<p>Abstract</p> <p>Background</p> <p>Mixture models of mutagenetic trees are evolutionary models that capture several pathways of ordered accumulation of genetic events observed in different subsets of patients. They were used to model HIV progression by accumulation of resistance mutations in the viral genome under drug pressure and cancer progression by accumulation of chromosomal aberrations in tumor cells. From the mixture models a genetic progression score (GPS) can be derived that estimates the genetic status of single patients according to the corresponding progression along the tree models. GPS values were shown to have predictive power for estimating drug resistance in HIV or the survival time in cancer. Still, the reliability of the exact values of such complex markers derived from graphical models can be questioned.</p> <p>Results</p> <p>In a simulation study, we analyzed various aspects of the stability of estimated mutagenetic trees mixture models. It turned out that the induced probabilistic distributions and the tree topologies are recovered with high precision by an EM-like learning algorithm. However, only for models with just one major model component, also GPS values of single patients can be reliably estimated.</p> <p>Conclusion</p> <p>It is encouraging that the estimation process of mutagenetic trees mixture models can be performed with high confidence regarding induced probability distributions and the general shape of the tree topologies. For a model with only one major disease progression process, even genetic progression scores for single patients can be reliably estimated. However, for models with more than one relevant component, alternative measures should be introduced for estimating the stage of disease progression.</p

Ten high-impact actions for integrated care system success

As the English NHS and social care system responds to current need and challenges, national policy remains that integrated care systems provide the best way forward to improved population health, reduced inequalities and per capita costs. Back in 2017 when Nottingham and Nottinghamshire was announced as an integrated care system (ICS) accelerator, with an early focus on Greater Nottingham and Rushcliffe, local leaders joined with Nottingham Business School in initiating a case study of the development. The predominant aim of the case study was to provide reflective insight and action learning to the local system. This case study has drawn from workshops, roundtables, interviews, document reviews and analysis. Pre COVID-19, the over-arching finding centred on the NHS and social care system not being ready for comprehensive and systemic change, in the prevailing policy and operational environment. This finding was based on both local experience and national evidence since 2017

Ten high-impact actions for integrated care success

Based on a case study from within Nottingham and Nottinghamshire. As the English NHS and social care system responds to current need and challenges, national policy remains that integrated care systems provide the best way forward to improved population health, reduced inequalities and per capita costs. Back in 2017 when Nottingham and Nottinghamshire was announced as an integrated care system (ICS) accelerator, with an early focus on Greater Nottingham and Rushcliffe, local leaders joined with Nottingham Business School in initiating a case study of the development. The predominant aim of the case study was to provide reflective insight and action learning to the local system

Loss of Mrap2 is associated with Sim1 deficiency and increased circulating cholesterol

Melanocortin receptor accessory protein 2 (MRAP2) is a transmembrane accessory protein predominantly expressed in the brain. Both global and brain-specific deletion of Mrap2 in mice results in severe obesity. Loss-of-function MRAP2 mutations have also been associated with obesity in humans. Although MRAP2 has been shown to interact with MC4R, a G protein-coupled receptor with an established role in energy homeostasis, appetite regulation and lipid metabolism, the mechanisms through which loss of MRAP2 causes obesity remains uncertain. In this study, we used two independently derived lines of Mrap2 deficient mice (Mrap2tm1a/tm1a) to further study the role of Mrap2 in the regulation of energy balance and peripheral lipid metabolism. Mrap2tm1a/tm1a mice have a significant increase in body weight, with increased fat and lean mass, but without detectable changes in food intake or energy expenditure. Transcriptomic analysis showed significantly decreased expression of Sim1, Trh, Oxt and Crh within the hypothalamic paraventricular nucleus of Mrap2tm1a/tm1a mice. Circulating levels of both high-density lipoprotein and low-density lipoprotein were significantly increased in Mrap2 deficient mice. Taken together, these data corroborate the role of MRAP2 in metabolic regulation and indicate that, at least in part, this may be due to defective central melanocortin signallin

Mapping HIV-1 Vaccine Induced T-Cell Responses: Bias towards Less-Conserved Regions and Potential Impact on Vaccine Efficacy in the Step Study

T cell directed HIV vaccines are based upon the induction of CD8+ T cell memory responses that would be effective in inhibiting infection and subsequent replication of an infecting HIV-1 strain, a process that requires a match or near-match between the epitope induced by vaccination and the infecting viral strain. We compared the frequency and specificity of the CTL epitope responses elicited by the replication-defective Ad5 gag/pol/nef vaccine used in the Step trial with the likelihood of encountering those epitopes among recently sequenced Clade B isolates of HIV-1. Among vaccinees with detectable 15-mer peptide pool ELISpot responses, there was a median of four (one Gag, one Nef and two Pol) CD8 epitopes per vaccinee detected by 9-mer peptide ELISpot assay. Importantly, frequency analysis of the mapped epitopes indicated that there was a significant skewing of the T cell response; variable epitopes were detected more frequently than would be expected from an unbiased sampling of the vaccine sequences. Correspondingly, the most highly conserved epitopes in Gag, Pol, and Nef (defined by presence in >80% of sequences currently in the Los Alamos database www.hiv.lanl.gov) were detected at a lower frequency than unbiased sampling, similar to the frequency reported for responses to natural infection, suggesting potential epitope masking of these responses. This may be a generic mechanism used by the virus in both contexts to escape effective T cell immune surveillance. The disappointing results of the Step trial raise the bar for future HIV vaccine candidates. This report highlights the bias towards less-conserved epitopes present in the same vaccine used in the Step trial. Development of vaccine strategies that can elicit a greater breadth of responses, and towards conserved regions of the genome in particular, are critical requirements for effective T-cell based vaccines against HIV-1

Antimicrobial ‘inks’ for 3D printing: block copolymer-silver nanoparticle composites synthesised using supercritical CO2

Silver nanoparticles (AgNP) are widely exploited for their effective antimicrobial activity against a range of pathogens. Their high efficacy in this regard has seen the global demand for AgNP in consumer products steadily increase in recent years, necessitating research into novel low environmental impact synthesis approaches. Here we present a new synthetic methodology to produce polymer-AgNP composite microparticles using supercritical carbon dioxide (scCO2) and avoiding use of any petrochemically derived solvents. Poly(methyl methacrylate)-poly(4-vinylpyridine) (PMMA-b-P4VP) block copolymers were synthesised via RAFT-mediated dispersion polymerisation in scCO2, with in situ thermal degradation of various amounts of a CO2-soluble silver complex. Selective interaction of the silver with the pyridinyl moieties of the block copolymer allowed the formation of AgNP, dispersed within the block copolymer microparticles, leading to homogeneous composites. The by-products of the reaction were also removed by extracting with a flow of CO2 to yield a clean dry product in a single process. The composites were found to be non-cytotoxic and proved to have good antimicrobial activity against two bacterial strains. Though no significant activity was seen for at least the first 24 hours, inhibition of bacterial growth afterwards proved to be extremely persistent, with inhibition observed even after 15 days. Finally, the microparticulate nature of the synthesised composites was exploited and tested for compatibility in the Laser Sintering (LS) 3D printing process. Composite microparticles were fused to produce solid objects, without aggregation of the AgNP. With further optimisation, these composites could prove to be an incredibly versatile ‘ink’ that may be used within additive manufacturing and 3D printing to rapidly produce bespoke medical devices with inherent antimicrobial activity

Role of Self‐Assembly Conditions and Amphiphilic Balance on Nanoparticle Formation of PEG‐PDLLA Copolymers in Aqueous Environments

The production of well-defined and reproducible poly-meric nanoparticles (NPs), in terms of size and stability in biological environments, is undoubtedly a fundamental challenge in the formulation of novel and more effective nanomedicines. The adoption of PEGylated lactide (LA) block copolymers as biodegradable and biocompatible nanocarriers at different clinical stages has rendered these materials an attractive polymeric platform to be exploited and their formulation is further understood. In the present work, we synthesized a library of linear polyethyl-ene glycol-poly(D,L-lactide) block copolymers with different lengths of LA (15, 25, 50, and 100 LA units) via simple and metal-free ring-opening polymerization, in order to alter the amphi-philic balance of the different macromolecules. The produced polymers were formulated into NPs while varying a series of key parameters in the solvent displacement process, including solvent:nonsolvent ratios and the nature of the two media, and the effect on size and stability was assessed. In addition, stability to protein-NPs interaction and aggregation was studied, highlighting the different NP final properties according to the nature of the amphiphilic balance and nanoformulation conditions. Therefore, we have illustrated a systematic and methodo-logical process to optimize a series of NPs parameters balancing particle size, size distribution, surface charge, and stability to guide future works in the nanoformulation field

Emergence of Drug Resistance Is Associated with an Increased Risk of Death among Patients First Starting HAART

BACKGROUND: The impact of the emergence of drug-resistance mutations on mortality is not well characterized in antiretroviral-naïve patients first starting highly active antiretroviral therapy (HAART). Patients may be able to sustain immunologic function with resistant virus, and there is limited evidence that reduced sensitivity to antiretrovirals leads to rapid disease progression or death. We undertook the present analysis to characterize the determinants of mortality in a prospective cohort study with a median of nearly 5 y of follow-up. The objective of this study was to determine the impact of the emergence of drug-resistance mutations on survival among persons initiating HAART. METHODS AND FINDINGS: Participants were antiretroviral therapy naïve at entry and initiated triple combination antiretroviral therapy between August 1, 1996, and September 30, 1999. Marginal structural modeling was used to address potential confounding between time-dependent variables in the Cox proportional hazard regression models. In this analysis resistance to any class of drug was considered as a binary time-dependent exposure to the risk of death, controlling for the effect of other time-dependent confounders. We also considered each separate class of mutation as a binary time-dependent exposure, while controlling for the presence/absence of other mutations. A total of 207 deaths were identified among 1,138 participants over the follow-up period, with an all cause mortality rate of 18.2%. Among the 679 patients with HIV-drug-resistance genotyping done before initiating HAART, HIV-drug resistance to any class was observed in 53 (7.8%) of the patients. During follow-up, HIV-drug resistance to any class was observed in 302 (26.5%) participants. Emergence of any resistance was associated with mortality (hazard ratio: 1.75 [95% confidence interval: 1.27, 2.43]). When we considered each class of resistance separately, persons who exhibited resistance to non-nucleoside reverse transcriptase inhibitors had the highest risk: mortality rates were 3.02 times higher (95% confidence interval: 1.99, 4.57) for these patients than for those who did not exhibit this type of resistance. CONCLUSIONS: We demonstrated that emergence of resistance to non-nucleoside reverse transcriptase inhibitors was associated with a greater risk of subsequent death than was emergence of protease inhibitor resistance. Future research is needed to identify the particular subpopulations of men and women at greatest risk and to elucidate the impact of resistance over a longer follow-up period

The obesity-associated gene TMEM18 has a role in the central control of appetite and body weight regulation

An intergenic region of human chromosome 2 (2p25.3) harbors genetic variants which are among those most strongly and reproducibly associated with obesity. The gene closest to these variants is TMEM18, although the molecular mechanisms mediating these effects remain entirely unknown. Tmem18 expression in the murine hypothalamic paraventricular nucleus (PVN) was altered by changes in nutritional state. Germline loss of Tmem18 in mice resulted in increased body weight, which was exacerbated by high fat diet and driven by increased food intake. Selective overexpression of Tmem18 in the PVN of wild-type mice reduced food intake and also increased energy expenditure. We provide evidence that TMEM18 has four, not three, transmembrane domains and that it physically interacts with key components of the nuclear pore complex. Our data support the hypothesis that TMEM18 itself, acting within the central nervous system, is a plausible mediator of the impact of adjacent genetic variation on human adiposity.RL, YCLT, DR, GSHY, SOR and APC are funded by the Medical Research Council (MRC) Metabolic Disease Unit (MRC_MC_UU_12012/1) and animal work was carried out with the assistance of MRC Disease Model Core of the Wellcome Trust MRC Institute of Metabolic Sciences (MRC_MC_UU_12012/5 and Wellcome Trust Strategic Award (100574/Z/12/Z). F. Bosch is the recipient of an award from the ICREA Academia, Generalitat de Catalunya, Spain. Vector generation and production were funded by Ministerio de Economía y Competitividad (SAF 2014-54866-R), Spain. CD and DWL were supported by the Wellcome Trust (WT098051) and CD was supported by the Wellcome Trust PhD Programme for Clinicians (100679/Z/12/Z)