Analysis of in vivo responses by mixed-effect models reference

Présentation PosterInternational audienceObjectives. In in vivo experimentation, the large intra-group variability between animals is a major obstacle that prevents to detect significant therapeutic effects of treatment factors. Our objective is to assess a new statistical method able to better estimate and characterize the additive effects of the combination of an oncolytic virus (TG6002) and the prodrug flucytosine (5-FC) associated in an anti-cancer treatment. The experimental data are kinetics of tumor growth collected during in vivo assays carried out on mice. Methods. The experimental set up is decomposed into four main steps. Firstly, a full factorial design of experiments is proposed. TG6002 was tested at four concentrations in combination or not with 5-FC. Eight groups of 13 mice are randomly affected to each experimental condition. Secondly, we propose a mixed-effect model to describe the kinetic growth of the mean tumor diameter. In a third step, the model parameters are determined with a maximum likelihood estimator based on an expectation-maximization algorithm. Finally, effects of the two examined components are assessed with a Wald test.Results. With our model-based approach, we show a 3% reduction of the therapeutic response time due to 5-FC and a division by five of the growth delay with TG6002.Conclusion. Results confirm the practical relevance of mixed-effect kinetic models to increase the statistical power of statistical tests applied to in vivo studies and efficacy of the combination TG6002 with 5-FC

First-in-human phase I study of pictilisib (GDC-0941), a potent pan-class I phosphatidylinositol-3-kinase (PI3K) inhibitor, in patients with advanced solid tumors.

PURPOSE: This first-in-human dose-escalation trial evaluated the safety, tolerability, maximal-tolerated dose (MTD), dose-limiting toxicities (DLT), pharmacokinetics, pharmacodynamics, and preliminary clinical activity of pictilisib (GDC-0941), an oral, potent, and selective inhibitor of the class I phosphatidylinositol-3-kinases (PI3K). PATIENTS AND METHODS: Sixty patients with solid tumors received pictilisib at 14 dose levels from 15 to 450 mg once-daily, initially on days 1 to 21 every 28 days and later, using continuous dosing for selected dose levels. Pharmacodynamic studies incorporated (18)F-FDG-PET, and assessment of phosphorylated AKT and S6 ribosomal protein in platelet-rich plasma (PRP) and tumor tissue. RESULTS: Pictilisib was well tolerated. The most common toxicities were grade 1-2 nausea, rash, and fatigue, whereas the DLT was grade 3 maculopapular rash (450 mg, 2 of 3 patients; 330 mg, 1 of 7 patients). The pharmacokinetic profile was dose-proportional and supported once-daily dosing. Levels of phosphorylated serine-473 AKT were suppressed >90% in PRP at 3 hours after dose at the MTD and in tumor at pictilisib doses associated with AUC >20 h·μmol/L. Significant increase in plasma insulin and glucose levels, and >25% decrease in (18)F-FDG uptake by PET in 7 of 32 evaluable patients confirmed target modulation. A patient with V600E BRAF-mutant melanoma and another with platinum-refractory epithelial ovarian cancer exhibiting PTEN loss and PIK3CA amplification demonstrated partial response by RECIST and GCIG-CA125 criteria, respectively. CONCLUSION: Pictilisib was safely administered with a dose-proportional pharmacokinetic profile, on-target pharmacodynamic activity at dose levels ≥100 mg and signs of antitumor activity. The recommended phase II dose was continuous dosing at 330 mg once-daily.This study was supported by Genentech Inc. The Drug Development Unit, The Royal Marsden NHS Foundation Trust, and The Institute of Cancer Research (London) is supported in part by programme grants from Cancer Research UK. Support was also provided by Experimental Cancer Medicine Center grants (to The Institute of Cancer Research and the Cancer Research UK Center), the National Institute for Health Research Biomedical Research Center (jointly to The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research) and the Wellcome Trust (grant 090952/Z/09/Z to Dr. Ang). Paul Workman is a Cancer Research UK Life Fellow.Originally published by the American Association for Cancer Research in Clinical Cancer Research January 1, 2015 21; 77 http://dx.doi.org/10.1158/1078-0432.CCR-14-094

A decision aid to rule out pneumonia and reduce unnecessary prescriptions of antibiotics in primary care patients with cough and fever

BACKGROUND: Physicians fear missing cases of pneumonia and treat many patients with signs of respiratory infection unnecessarily with antibiotics. This is an avoidable cause for the increasing worldwide problem of antibiotic resistance. We developed a user-friendly decision aid to rule out pneumonia and thus reduce the rate of needless prescriptions of antibiotics. METHODS: This was a prospective cohort study in which we enrolled patients older than 18 years with a new or worsened cough and fever without serious co-morbidities. Physicians recorded results of a standardized medical history and physical examination. C-reactive protein was measured and chest radiographs were obtained. We used Classification and Regression Trees to derive the decision tool. RESULTS: A total of 621 consenting eligible patients were studied, 598 were attending a primary care facility, were 48 years on average and 50% were male. Radiographic signs for pneumonia were present in 127 (20.5%) of patients. Antibiotics were prescribed to 234 (48.3%) of patients without pneumonia. In patients with C-reactive protein values below 10 μg/ml or patients presenting with C-reactive protein between 11 and 50 μg/ml, but without dyspnoea and daily fever, pneumonia can be ruled out. By applying this rule in clinical practice antibiotic prescription could be reduced by 9.1% (95% confidence interval (CI): 6.4 to 11.8). CONCLUSIONS: Following validation and confirmation in new patient samples, this tool could help rule out pneumonia and be used to reduce unnecessary antibiotic prescriptions in patients presenting with cough and fever in primary care. The algorithm might be especially useful in those instances where taking a medical history and physical examination alone are inconclusive for ruling out pneumonia

Sensitivity of the West Antarctic Ice Sheet to +2 °C (SWAIS 2C)

The West Antarctic Ice Sheet (WAIS) presently holds enough ice to raise global sea level by 4.3 m if completely melted. The unknown response of the WAIS to future warming remains a significant challenge for numerical models in quantifying predictions of future sea level rise. Sea level rise is one of the clearest planet-wide signals of human-induced climate change. The Sensitivity of the West Antarctic Ice Sheet to a Warming of 2 ∘C (SWAIS 2C) Project aims to understand past and current drivers and thresholds of WAIS dynamics to improve projections of the rate and size of ice sheet changes under a range of elevated greenhouse gas levels in the atmosphere as well as the associated average global temperature scenarios to and beyond the +2 ∘C target of the Paris Climate Agreement. Despite efforts through previous land and ship-based drilling on and along the Antarctic margin, unequivocal evidence of major WAIS retreat or collapse and its causes has remained elusive. To evaluate and plan for the interdisciplinary scientific opportunities and engineering challenges that an International Continental Drilling Program (ICDP) project along the Siple coast near the grounding zone of the WAIS could offer (Fig. 1), researchers, engineers, and logistics providers representing 10 countries held a virtual workshop in October 2020. This international partnership comprised of geologists, glaciologists, oceanographers, geophysicists, microbiologists, climate and ice sheet modelers, and engineers outlined specific research objectives and logistical challenges associated with the recovery of Neogene and Quaternary geological records from the West Antarctic interior adjacent to the Kamb Ice Stream and at Crary Ice Rise. New geophysical surveys at these locations have identified drilling targets in which new drilling technologies will allow for the recovery of up to 200 m of sediments beneath the ice sheet. Sub-ice-shelf records have so far proven difficult to obtain but are critical to better constrain marine ice sheet sensitivity to past and future increases in global mean surface temperature up to 2 ∘C above pre-industrial levels. Thus, the scientific and technological advances developed through this program will enable us to test whether WAIS collapsed during past intervals of warmth and determine its sensitivity to a +2 ∘C global warming threshold (UNFCCC, 2015)

Endothelial Progenitor Cells, Cardiovascular Risk Factors, Cytokine Levels and Atherosclerosis – Results from a Large Population-Based Study

EPC number and functionality are assumed to reflect the endogenous vascular repair capacity with the EPC pool declining in higher ages and being exhausted by unfavorable life-style and risk factors. This intriguing and clinically highly relevant concept, however, has so far been derived from small case-control studies and patient series.In the population-based Bruneck Study EPC number and EPC-colony forming units (EPC-CFU) were assessed as part of the fourth follow-up evaluation (2005) in 571 and 542 subjects, respectively. EPC number declined with age (p = 0.013), was significantly lower in women (p = 0.006) and higher in subjects on statin, hormone replacement or ACE inhibitor/angiotensin-receptor blockers, and correlated positively with moderate alcohol consumption. Unexpectedly, a positive relation between EPC number and several vascular risk factors emerged. In a step forward multivariate linear regression analysis EPC number was independently related with SDF1alpha, MMP-9, triglycerides, alcohol consumption, and Hba1c. EPC-CFU in turn was related to SDF1alpha and diastolic blood pressure. Moreover, EPC number showed a significant positive association with the Framingham risk score (P = 0.001). Finally, there was an inverse association between EPC number and common carotid artery intima-media thickness (p = 0.02) and the carotid artery atherosclerosis score (p = 0.059).Our population-based data confirm the decline of EPC number with advancing age and lend first epidemiological support to a role of SDF-1alpha and MMP9 in EPC differentiation, mobilization and homing, but are conflict with the view that EPC number is unfavorably affected by cardiovascular risk factors. EPC number increases with the cardiovascular risk estimated by the Framingham risk score (FRS), which in the absence of similar changes for EPC-CFU. Finally, we demonstrate a significant inverse association between EPC number and extent of carotid atherosclerosis even though this association was only of moderate strength and not entirely consistent in other vascular territories

Mutation analysis of the MDM4 gene in German breast cancer patients

<p>Abstract</p> <p>Background</p> <p>MDM4 is a negative regulator of p53 and cooperates with MDM2 in the cellular response to DNA damage. It is unknown, however, whether <it>MDM4 </it>gene alterations play some role in the inherited component of breast cancer susceptibility.</p> <p>Methods</p> <p>We sequenced the whole <it>MDM4 </it>coding region and flanking untranslated regions in genomic DNA samples obtained from 40 German patients with familial breast cancer. Selected variants were subsequently screened by RFLP-based assays in an extended set of breast cancer cases and controls.</p> <p>Results</p> <p>Our resequencing study uncovered two <it>MDM4 </it>coding variants in 4/40 patients. Three patients carried a silent substitution at codon 74 that was linked with another rare variant in the 5'UTR. No association of this allele with breast cancer was found in a subsequent screening of 133 patients with bilateral breast cancer and 136 controls. The fourth patient was heterozygous for the missense substitution D153G which is located in a less conserved region of the MDM4 protein but may affect a predicted phosphorylation site. The D153G substitution only partially segregated with breast cancer in the family and was not identified on additional 680 chromosomes screened.</p> <p>Conclusion</p> <p>This study did not reveal clearly pathogenic mutations although it uncovered two new unclassified variants at a low frequency. We conclude that there is no evidence for a major role of <it>MDM4 </it>coding variants in the inherited susceptibility towards breast cancer in German patients.</p

Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis

<p>Abstract</p> <p>Background</p> <p>Protein-protein interaction (PPI) data sets generated by high-throughput experiments are contaminated by large numbers of erroneous PPIs. Therefore, computational methods for PPI validation are necessary to improve the quality of such data sets. Against the background of the theory that most extant PPIs arose as a consequence of gene duplication, the sensitive search for homologous PPIs, i.e. for PPIs descending from a common ancestral PPI, should be a successful strategy for PPI validation.</p> <p>Results</p> <p>To validate an experimentally observed PPI, we combine FASTA and PSI-BLAST to perform a sensitive sequence-based search for pairs of interacting homologous proteins within a large, integrated PPI database. A novel scoring scheme that incorporates both quality and quantity of all observed matches allows us (1) to consider also tentative paralogs and orthologs in this analysis and (2) to combine search results from more than one homology detection method. ROC curves illustrate the high efficacy of this approach and its improvement over other homology-based validation methods.</p> <p>Conclusion</p> <p>New PPIs are primarily derived from preexisting PPIs and not invented <it>de novo</it>. Thus, the hallmark of true PPIs is the existence of homologous PPIs. The sensitive search for homologous PPIs within a large body of known PPIs is an efficient strategy to separate biologically relevant PPIs from the many spurious PPIs reported by high-throughput experiments.</p

Natriuretic peptides and integrated risk assessment for cardiovascular disease: an individual-participant-data meta-analysis

BACKGROUND: Guidelines for primary prevention of cardiovascular diseases focus on prediction of coronary heart disease and stroke. We assessed whether or not measurement of N-terminal-pro-B-type natriuretic peptide (NT-proBNP) concentration could enable a more integrated approach than at present by predicting heart failure and enhancing coronary heart disease and stroke risk assessment. METHODS: In this individual-participant-data meta-analysis, we generated and harmonised individual-participant data from relevant prospective studies via both de-novo NT-proBNP concentration measurement of stored samples and collection of data from studies identified through a systematic search of the literature (PubMed, Scientific Citation Index Expanded, and Embase) for articles published up to Sept 4, 2014, using search terms related to natriuretic peptide family members and the primary outcomes, with no language restrictions. We calculated risk ratios and measures of risk discrimination and reclassification across predicted 10 year risk categories (ie, <5%, 5% to <7·5%, and ≥7·5%), adding assessment of NT-proBNP concentration to that of conventional risk factors (ie, age, sex, smoking status, systolic blood pressure, history of diabetes, and total and HDL cholesterol concentrations). Primary outcomes were the combination of coronary heart disease and stroke, and the combination of coronary heart disease, stroke, and heart failure. FINDINGS: We recorded 5500 coronary heart disease, 4002 stroke, and 2212 heart failure outcomes among 95 617 participants without a history of cardiovascular disease in 40 prospective studies. Risk ratios (for a comparison of the top third vs bottom third of NT-proBNP concentrations, adjusted for conventional risk factors) were 1·76 (95% CI 1·56-1·98) for the combination of coronary heart disease and stroke and 2·00 (1·77-2·26) for the combination of coronary heart disease, stroke, and heart failure. Addition of information about NT-proBNP concentration to a model containing conventional risk factors was associated with a C-index increase of 0·012 (0·010-0·014) and a net reclassification improvement of 0·027 (0·019-0·036) for the combination of coronary heart disease and stroke and a C-index increase of 0·019 (0·016-0·022) and a net reclassification improvement of 0·028 (0·019-0·038) for the combination of coronary heart disease, stroke, and heart failure. INTERPRETATION: In people without baseline cardiovascular disease, NT-proBNP concentration assessment strongly predicted first-onset heart failure and augmented coronary heart disease and stroke prediction, suggesting that NT-proBNP concentration assessment could be used to integrate heart failure into cardiovascular disease primary prevention. FUNDING: British Heart Foundation, Austrian Science Fund, UK Medical Research Council, National Institute for Health Research, European Research Council, and European Commission Framework Programme 7

Developing Freedom: Thomas Jefferson, the State, and Human Capability

Thomas Jefferson is often invoked as an advocate of limited government and a defender of individual rights. This article argues that rights were Jefferson’s starting place. Jefferson also believed that American citizens should have opportunities to develop the capabilities necessary to enjoy the full use of their rights. Rather than thinking about Jefferson as progovernment or antigovernment, this article concludes that we must understand the particular kind of government Jefferson desired, the ends he had in mind, and why and how those ends differed from his Federalist predecessors. A better understanding of Jefferson’s statecraft not only offers a new perspective on the relationship between government and rights in Jefferson’s thought but also how and why Jeffersonians in power used the state to promote individual freedom

Addressing climate change with behavioral science: a global intervention tournament in 63 countries

Effectively reducing climate change requires marked, global behavior change. However, it is unclear which strategies are most likely to motivate people to change their climate beliefs and behaviors. Here, we tested 11 expert-crowdsourced interventions on four climate mitigation outcomes: beliefs, policy support, information sharing intention, and an effortful tree-planting behavioral task. Across 59,440 participants from 63 countries, the interventions’ effectiveness was small, largely limited to nonclimate skeptics, and differed across outcomes: Beliefs were strengthened mostly by decreasing psychological distance (by 2.3%), policy support by writing a letter to a future-generation member (2.6%), information sharing by negative emotion induction (12.1%), and no intervention increased the more effortful behavior—several interventions even reduced tree planting. Last, the effects of each intervention differed depending on people’s initial climate beliefs. These findings suggest that the impact of behavioral climate interventions varies across audiences and target behaviors