A Bayesian approach for event predictions in clinical trials with time-to-event outcomes.

In clinical trials with time-to-event outcome as the primary endpoint, the end of study date is often based on the number of observed events, which drives the statistical power and the sample size calculation. It is of great value for study sponsors to have a good understanding of the recruitment process and the event milestones to manage the logistical tasks, which require a considerable amount of resources. The objective of the proposed statistical approach is to predict, as accurately as possible, the timing of an analysis planned once a target number of events is collected. The method takes into account the enrollment, the time to event, and the time to censor processes, using Weibull models in a Bayesian framework. We also consider a possible delay in the event reporting by the investigators, and covariates may also be included. Several metrics can be obtained, such as the probability of study completion at specific timepoints or the credible interval of the date of study completion. The approach was applied to oncology trials, with progression-free survival as primary outcome. A retrospective analysis shows the accuracy of the approach on these examples, as well as the benefit of updating the predictive probability of study completion as data are accumulating or new information becomes available. We also evaluated the performances of the proposed method in a comprehensive simulation study.

Dielectric Spectroscopy Analysis of Liquid Crystals Recovered from End-of-Life Liquid Crystal Displays.

In the present work, the dielectric properties of recycled liquid crystals (LCs) (non-purified, purified, and doped with diamond nanoparticles at 0.05, 0.1, and 0.2 wt%) were investigated. The studied LC mixtures were obtained from industrial recycling of end-of-life LC displays presenting mainly nematic phases. Dielectric measurements were carried out at room temperature on a frequency range from 0.1 to 106 Hz using an impedance analyzer. The amplitude of the oscillating voltage was fixed at 1 V using cells with homogeneous and homeotropic alignments. Results show that the dielectric anisotropy of all purified samples presents positive values and decreases after the addition of diamond nanoparticles to the LC mixtures. DC conductivity values were obtained by applying the universal law of dielectric response proposed by Jonscher. In addition, conductivity of the doped LC mixtures is lower than that of the undoped and non-purified LC.

Intraspecific and interspecific adaptive latitudinal cline in Brassicaceae seed oil traits.

PREMISE OF THE STUDY: Nearly all seed plants rely on stored seed reserves before photosynthesis can commence. Natural selection for seed oil traits must have occurred over 319 million years of evolution since the first seed plant ancestor. Accounting for the biogeographic distribution of seed oil traits is fundamental to understanding the mechanisms of adaptive evolution in seed plants. However, the evolution of seed oils is poorly understood. We provide evidence of the adaptive nature of seed oil traits at the intraspecific and interspecific levels in Brassicaceae-an oilseed-rich and economically important plant family. METHODS: Univariate statistics, Pearson's correlation, multiple regression, generalized linear mixed model analysis, and phylogenetic autocorrelation tests on seed oil traits of 360 accessions of Arabidopsis thaliana and 216 Brassicaceae species helped provide evidence of the adaptive nature of seed oil traits. KEY RESULTS: At higher latitudes, both seed oil content and unsaturated fatty acids have selective advantages in Arabidopsis thaliana (intraspecific-level), while only unsaturated fatty acids have selective advantages across 216 Brassicaceae species (interspecific-level). The seed oil patterns fit within the theoretical framework of the gradient model. Seed oil content increases significantly from temperate to subtropical to tropical regions in Brassicaceae herbs. Absence of phylogenetic signals for seed oil traits and high seed oil content in four tribes of Brassicaceae were observed. CONCLUSIONS: Multiple seed oil traits are adaptive in nature and follow a gradient model. Consistent evolutionary patterns of seed oil traits were observed at the intraspecific and interspecific levels in Brassicaceae. Seed oil traits change with latitude and across biomes, suggesting selection. The absence of a phylogenetic signal for seed oil traits and the occurrence of high seed oil content in four Brassicaceae tribes provides evidence of the adaptive nature of seed oil traits in Brassicaceae.

Implementation of adaptive methods in early-phase clinical trials.

There has been constant development of novel statistical methods in the design of early-phase clinical trials since the introduction of model-based designs, yet the traditional or modified 3+3 algorithmic design remains the most widely used approach in dose-finding studies. Research has shown the limitations of this traditional design compared with more innovative approaches yet the use of these model-based designs remains infrequent. This can be attributed to several causes including a poor understanding from clinicians and reviewers into how the designs work, and how best to evaluate the appropriateness of a proposed design. These barriers are likely to be enhanced in the coming years as the recent paradigm of drug development involves a shift to more complex dose-finding problems. This article reviews relevant information that should be included in clinical trial protocols to aid in the acceptance and approval of novel methods. We provide practical guidance for implementing these efficient designs with the aim of augmenting a broader transition from algorithmic to adaptive model-guided designs. In addition we highlight issues to consider in the actual implementation of a trial once approval is obtained. Copyright © 2016 John Wiley & Sons, Ltd.

Characterization of a NADH-dependent glutamate dehydrogenase mutant of Arabidopsis demonstrates the key role of this enzyme in root carbon and nitrogen metabolism.

The role of NADH-dependent glutamate dehydrogenase (GDH) was investigated by studying the physiological impact of a complete lack of enzyme activity in an Arabidopsis thaliana plant deficient in three genes encoding the enzyme. This study was conducted following the discovery that a third GDH gene is expressed in the mitochondria of the root companion cells, where all three active GDH enzyme proteins were shown to be present. A gdh1-2-3 triple mutant was constructed and exhibited major differences from the wild type in gene transcription and metabolite concentrations, and these differences appeared to originate in the roots. By placing the gdh triple mutant under continuous darkness for several days and comparing it to the wild type, the evidence strongly suggested that the main physiological function of NADH-GDH is to provide 2-oxoglutarate for the tricarboxylic acid cycle. The differences in key metabolites of the tricarboxylic acid cycle in the triple mutant versus the wild type indicated that, through metabolic processes operating mainly in roots, there was a strong impact on amino acid accumulation, in particular alanine, γ-aminobutyrate, and aspartate in both roots and leaves. These results are discussed in relation to the possible signaling and physiological functions of the enzyme at the interface of carbon and nitrogen metabolism.

[Community-based screening: a motivating experience for drug users]. / Dépister hors les murs d’un centre de dépistage?: une expérience mobilisatrice pour des usagers de drogues.

OBJECTIVES: Hepatitis C virus infection (HCV) is a major public health problem among drug users. Screening for hepatitis C virus in this population is complicated. The aim of the study was to describe a community-based screening experience conducted by the Tours university hospital addiction medicine team. METHODS: Between 2008 and 2010, a free 14-day HCV, hepatitis B virus (HBV) and HIV community-based screening programme was conducted by the addiction medicine and prevention team. A questionnaire collected the main risk factors for transmission of these viruses and the subject's viral serology status. RESULTS: 76% of the 219 screened subjects reported being drug users. HCV prevalence was 20%. Risk factors for HCV infection were exclusive intravenous use and the use of several routes of administration. Among the 30 HCV patients with positive RNA, 83% were followed up. CONCLUSIONS: The prevalence of HCV infection was similar to that reported in the literature for drug users, whereas the number of patients treated and followed up was higher than in the literature. A community-based screening experience facilitated initiation and follow-up of medical care.

Sequence and functional analysis of the envelope glycoproteins of hepatitis C virus variants selectively transmitted to a new host.

Hepatitis C virus (HCV) remains a challenging public health problem worldwide. The identification of viral variants establishing de novo infections and definition of the phenotypic requirements for transmission would facilitate the design of preventive strategies. We explored the transmission of HCV variants in three cases of acute hepatitis following needlestick accidents. We used single-genome amplification of glycoprotein E1E2 gene sequences to map the genetic bottleneck upon transmission accurately. We found that infection was likely established by a single variant in two cases and six variants in the third case. Studies of donor samples showed that the transmitted variant E1E2 amino acid sequences were identical or closely related to those of variants from the donor virus populations. The transmitted variants harbored a common signature site at position 394, within hypervariable region 1 of E2, together with additional signature amino acids specific to each transmission pair. Surprisingly, these E1E2 variants conferred no greater capacity for entry than the E1E2 derived from nontransmitted variants in lentiviral pseudoparticle assays. Mutants escaping the antibodies of donor sera did not predominate among the transmitted variants either. The fitness parameters affecting the selective outgrowth of HCV variants after transmission in an immunocompetent host may thus be more complex than those suggested by mouse models. Human antibodies directed against HCV envelope effectively cross-neutralized the lentiviral particles bearing E1E2 derived from transmitted variants. These findings provide insight into the molecular mechanisms underlying HCV transmission and suggest that viral entry is a potential target for the prevention of HCV infection.

A Bayesian dose-finding design for drug combination clinical trials based on the logistic model.

In early phase dose-finding cancer studies, the objective is to determine the maximum tolerated dose, defined as the highest dose with an acceptable dose-limiting toxicity rate. Finding this dose for drug-combination trials is complicated because of drug-drug interactions, and many trial designs have been proposed to address this issue. These designs rely on complicated statistical models that typically are not familiar to clinicians, and are rarely used in practice. The aim of this paper is to propose a Bayesian dose-finding design for drug combination trials based on standard logistic regression. Under the proposed design, we continuously update the posterior estimates of the model parameters to make the decisions of dose assignment and early stopping. Simulation studies show that the proposed design is competitive and outperforms some existing designs. We also extend our design to handle delayed toxicities.

Resolving the role of plant glutamate dehydrogenase: II. Physiological characterization of plants overexpressing the two enzyme subunits individually or simultaneously.

Glutamate dehydrogenase (GDH; EC 1.4.1.2) is able to carry out the deamination of glutamate in higher plants. In order to obtain a better understanding of the physiological function of GDH in leaves, transgenic tobacco (Nicotiana tabacum L.) plants were constructed that overexpress two genes from Nicotiana plumbaginifolia (GDHA and GDHB under the control of the Cauliflower mosiac virus 35S promoter), which encode the α- and ß-subunits of GDH individually or simultaneously. In the transgenic plants, the GDH protein accumulated in the mitochondria of mesophyll cells and in the mitochondria of the phloem companion cells (CCs), where the native enzyme is normally expressed. Such a shift in the cellular location of the GDH enzyme induced major changes in carbon and nitrogen metabolite accumulation and a reduction in growth. These changes were mainly characterized by a decrease in the amount of sucrose, starch and glutamine in the leaves, which was accompanied by an increase in the amount of nitrate and Chl. In addition, there was an increase in the content of asparagine and a decrease in proline. Such changes may explain the lower plant biomass determined in the GDH-overexpressing lines. Overexpressing the two genes GDHA and GDHB individually or simultaneously induced a differential accumulation of glutamate and glutamine and a modification of the glutamate to glutamine ratio. The impact of the metabolic changes occurring in the different types of GDH-overexpressing plants is discussed in relation to the possible physiological function of each subunit when present in the form of homohexamers or heterohexamers.

Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea (Pisum sativum L.) and to Enhance Plant Biomass Production.

The application of bacterial bio-inputs is a very attractive alternative to the use of mineral fertilisers. In ploughed soils including a crop rotation pea, we observed an enrichment of bacterial communities with Sphingomonas (S.) sediminicola. Inoculation experiments, cytological studies, and de novo sequencing were used to investigate the beneficial role of S. sediminicola in pea. S. sediminicola is able to colonise pea plants and establish a symbiotic association that promotes plant biomass production. Sequencing of the S. sediminicola genome revealed the existence of genes involved in secretion systems, Nod factor synthesis, and nitrogenase activity. Light and electron microscopic observations allowed us to refine the different steps involved in the establishment of the symbiotic association, including the formation of infection threads, the entry of the bacteria into the root cells, and the development of differentiated bacteroids in root nodules. These results, together with phylogenetic analysis, demonstrated that S. sediminicola is a non-rhizobia that has the potential to develop a beneficial symbiotic association with a legume. Such a symbiotic association could be a promising alternative for the development of more sustainable agricultural practices, especially under reduced N fertilisation conditions.

Sphingomonas sediminicola Dae20 Is a Highly Promising Beneficial Bacteria for Crop Biostimulation Due to Its Positive Effects on Plant Growth and Development.

Current agricultural practices rely heavily on synthetic fertilizers, which not only consume a lot of energy but also disrupt the ecological balance. The overuse of synthetic fertilizers has led to soil degradation. In a more sustainable approach, alternative methods based on biological interactions, such as plant growth-promoting bacteria (PGPRs), are being explored. PGPRs, which include both symbiotic and free-living bacteria, form mutualistic relationships with plants by enhancing nutrient availability, producing growth regulators, and regulating stress responses. This study investigated the potential of Sphingomonas sediminicola Dae20, an α-Proteobacteria species commonly found in the rhizosphere, as a beneficial PGPR. We observed that S. sediminicola Dae20 stimulated the root system and growth of three different plant species in the Brassicaceae family, including Arabidopsis thaliana, mustard, and rapeseed. The bacterium produced auxin, nitric oxide, siderophores and showed ACC deaminase activity. In addition to activating an auxin response in the plant, S. sediminicola Dae20 exhibited the ability to modulate other plant hormones, such as abscisic acid, jasmonic acid and salicylic acid, which are critical for plant development and defense responses. This study highlights the multifunctional properties of S. sediminicola Dae20 as a promising PGPR and underscores the importance of identifying effective and versatile beneficial bacteria to improve plant nutrition and promote sustainable agricultural practices.

Optimizing Crop Production with Bacterial Inputs: Insights into Chemical Dialogue between Sphingomonas sediminicola and Pisum sativum.

The use of biological inputs is an interesting approach to optimize crop production and reduce the use of chemical inputs. Understanding the chemical communication between bacteria and plants is critical to optimizing this approach. Recently, we have shown that Sphingomonas (S.) sediminicola can improve both nitrogen supply and yield in pea. Here, we used biochemical methods and untargeted metabolomics to investigate the chemical dialog between S. sediminicola and pea. We also evaluated the metabolic capacities of S. sediminicola by metabolic profiling. Our results showed that peas release a wide range of hexoses, organic acids, and amino acids during their development, which can generally recruit and select fast-growing organisms. In the presence of S. sediminicola, a more specific pattern of these molecules took place, gradually adapting to the metabolic capabilities of the bacterium, especially for pentoses and flavonoids. In turn, S. sediminicola is able to produce several compounds involved in cell differentiation, biofilm formation, and quorum sensing to shape its environment, as well as several molecules that stimulate pea growth and plant defense mechanisms.

PGPR-Soil Microbial Communities' Interactions and Their Influence on Wheat Growth Promotion and Resistance Induction against Mycosphaerella graminicola.

The efficiency of plant-growth-promoting rhizobacteria (PGPR) may not be consistently maintained under field conditions due to the influence of soil microbial communities. The present study aims to investigate their impact on three PGPR-based biofertilizers in wheat. We used the PGPR Paenibacillus sp. strain B2 (PB2), PB2 in co-inoculation with Arthrobacter agilis 4042 (Mix 2), or with Arthrobacter sp. SSM-004 and Microbacterium sp. SSM-001 (Mix 3). Inoculation of PB2, Mix 2, and Mix 3 into non-sterile field soil had a positive effect on root and aboveground dry biomass, depending on the wheat cultivar. The efficiency of the PGPR was further confirmed by the protection they provided against Mycosphaerella graminicola, the causal agent of Septoria leaf blotch disease. PB2 exhibited protection of ≥37.8%, while Mix 2 showed ≥47.9% protection in the four cultivars tested. These results suggest that the interactions between PGPR and native soil microbial communities are crucial for promoting wheat growth and protection. Additionally, high-throughput sequencing of microbial communities conducted 7 days after PGPR inoculations revealed no negative effects of PB2, Mix 2, and Mix 3 on the soil microbial community structure. Interestingly, the presence of Arthrobacter spp. appeared to mitigate the potential negative effect of PB2 on bacterial community and foster root colonization by other beneficial bacterial strains.

Impacts of environmental conditions, and allelic variation of cytosolic glutamine synthetase on maize hybrid kernel production.

Cytosolic glutamine synthetase (GS1) is the enzyme mainly responsible of ammonium assimilation and reassimilation in maize leaves. The agronomic potential of GS1 in maize kernel production was investigated by examining the impact of an overexpression of the enzyme in the leaf cells. Transgenic hybrids exhibiting a three-fold increase in leaf GS activity were produced and characterized using plants grown in the field. Several independent hybrids overexpressing Gln1-3, a gene encoding cytosolic (GS1), in the leaf and bundle sheath mesophyll cells were grown over five years in different locations. On average, a 3.8% increase in kernel yield was obtained in the transgenic hybrids compared to controls. However, we observed that such an increase was simultaneously dependent upon both the environmental conditions and the transgenic event for a given field trial. Although variable from one environment to another, significant associations were also found between two GS1 genes (Gln1-3 and Gln1-4) polymorphic regions and kernel yield in different locations. We propose that the GS1 enzyme is a potential lead for producing high yielding maize hybrids using either genetic engineering or marker-assisted selection. However, for these hybrids, yield increases will be largely dependent upon the environmental conditions used to grow the plants.

Use of an anti-hepatitis C virus (HCV) IgG avidity assay to identify recent HCV infection.

There is no reliable and simple diagnostic marker available to diagnose recent hepatitis C virus (HCV) infection. It has been shown that the avidity of specific IgG antibody is low in primary viral infection and increases with time. We report the development of an anti-HCV avidity assay derived from a commercially available test. A panel of 117 sera was first examined for IgG avidity. It was composed of samples from patients with recent (group 1, n = 14), chronic (group 2, n = 70), and resolved (group 3, n = 33) HCV infections. Avidity index (AI) values observed in recently infected patients were significantly lower (12.0% +/- 9.2% [mean +/- standard deviation]) than those found in chronic carriers (83.1% +/- 15.2%). Using a threshold of 43.0%, this assay distinguished between groups 1 and 2 with very high sensitivity (98%) and specificity (100%). For group 3, a broader distribution of the AI values was observed (54.8% +/- 27.3%), suggesting that this index would not be useful in HCV RNA-negative patients. Blind validation of the test was carried out with a panel of 36 serum samples from 17 HCV seroconverters. The assay described here is a useful tool to distinguish recent from chronic infection in HCV-viremic patients.

Prevalence of hepatitis B and hepatitis C virus infections in France in 2004: social factors are important predictors after adjusting for known risk factors.

To monitor the prevalence of hepatitis B and hepatitis C a cross-sectional survey was conducted in 2004 among French metropolitan residents. A complex sampling design was used to enroll 14,416 adult participants aged 18-80 years. Data collected included demographic and social characteristics and risk factors. Sera were tested for anti-HCV, HCV-RNA, anti-HBc and HBsAg. Data were analyzed with SUDAAN software to provide weighted estimates for the French metropolitan resident population. The overall anti-HCV prevalence was 0.84% (95% CI: 0.65-1.10). Among anti-HCV positive individuals, 57.4% (95% CI: 43.2-70.5) knew their status. Factors associated independently with positive anti-HCV were drug use (intravenous and nasal), blood transfusion before 1992, a history of tattoos, low socioeconomic status, being born in a country where anti-HCV prevalence >2.5%, and age >29 years. The overall anti-HBc prevalence was 7.3% (95%: 6.5-8.2). Independent risk factors for anti-HBc were intravenous drug use, being a man who has sex with men, low socioeconomic status, a stay in a psychiatric facility or facility for the mentally disabled, <12 years of education, being born in a country where HBsAg prevalence >2%, age >29 and male sex. The HCV RNA and HBsAg prevalence were 0.53% (95% CI: 0.40-0.70) and 0.65% (95% CI: 0.45-0.93), respectively. Among HBsAg positive individuals, 44.8% (95% CI: 22.8-69.1) knew their status. Anti-HCV prevalence was close to the 1990s estimates whereas HBsAg prevalence estimate was greater than expected. Screening of hepatitis B and C should be strengthened and should account for social vulnerability.

Metabolic profiling of maize mutants deficient for two glutamine synthetase isoenzymes using 1H-NMR-based metabolomics.

INTRODUCTION: Maize mutants deficient for the expression of two genes encoding cytosolic glutamine synthetase (GS) isoenzymes GS1.3 and GS1.4 displayed reduced kernel number and kernel size, respectively, the effect of the mutation being cumulative in the double mutant. However, at maturity, shoot biomass production was not modified in all the mutants, indicating that the reaction catalysed by the enzyme is specifically involved in the control of grain yield. OBJECTIVE: To examine the physiological impact of the GS mutations on the leaf metabolic profile during the kernel filling period, during which nitrogen is remobilized from the shoots to be further exported to the kernels. METHODOLOGY: An (1)H-NMR spectroscopy metabolomic was applied to the investigation of metabolic change of the gln1.3, gln1.4 and gln1.3/1.4 double mutant. RESULTS: In the three GS mutants, an increase in the amount of several N-containing metabolites such as asparagine, alanine, threonine and phophatidylcholine was observed whatever the level of nitrogen fertilisation. In addition, we found an accumulation of phenylalanine and tyrosine, two metabolites involved the primary steps of the phenylpropanoid pathway. CONCLUSION: Changes in the metabolic profile of the GS mutants suggest that, when cytosolic GS activity is strongly reduced, either alternative metabolic pathways participate in the reassimilation of ammonium released during leaf protein remobilization or that premature leaf senescence is induced when kernel set and kernel filling are affected. The accumulation of phenylalanine and tyrosine in the mutant plants indicates that lignin biosynthesis is altered, thus possibly affecting ear development.

A quantitative genetic study for elucidating the contribution of glutamine synthetase, glutamate dehydrogenase and other nitrogen-related physiological traits to the agronomic performance of common wheat.

To better understand the genetic variability for nitrogen use efficiency in winter wheat is a necessity in the frame of the present economic and ecological context. The objective of this work was to investigate the role of the enzymes glutamine synthetase (GS) and glutamate dehydrogenase (GDH), and other nitrogen (N)-related physiological traits in the control of agronomic performance in wheat. A quantitative genetics approach was developed using the Arche x Récital population of doubled haploid lines grown for 3 years in the field. GS and GDH activities, ammonium, amino acid and protein contents were measured at different stages of plant development in different organs after flowering. Significant genotypic effects were observed for all measured physiological and agronomical traits. Heading date was negatively correlated with ammonium, amino acid, protein contents and GS activity in the flag leaf lamina. Grain protein content was positively correlated with both ammonium and amino acid content, and to a lesser extent with soluble protein content and GS activity. A total of 148 quantitative trait loci (QTLs) were detected, 104 QTLs for physiological traits and 44 QTLs for agronomic traits. Twenty-six QTLs were detected for GDH activity spread over 13 chromosomes and 25 QTLs for GS activity spread over 12 chromosomes. We found only a co-localization between a QTL for GS activity and GSe, a structural gene encoding cytosolic GS on chromosome 4B. A coincidence between a QTL for GDH activity and a gene encoding GDH was also found on chromosome 2B. QTL regions combining both physiological and agronomical QTLs were mainly identified on linkage groups 2A, 2B, 2D, 5A, 5B and 5D. This approach allowed us to propose possible functions of physiological traits to explain the variation observed for agronomic traits including yield and its components.

Phase I/II dose-finding design for molecularly targeted agent: Plateau determination using adaptive randomization.

Conventionally, phase I dose-finding trials aim to determine the maximum tolerated dose of a new drug under the assumption that both toxicity and efficacy monotonically increase with the dose. This paradigm, however, is not suitable for some molecularly targeted agents, such as monoclonal antibodies, for which efficacy often increases initially with the dose and then plateaus. For molecularly targeted agents, the goal is to find the optimal dose, defined as the lowest safe dose that achieves the highest efficacy. We develop a Bayesian phase I/II dose-finding design to find the optimal dose. We employ a logistic model with a plateau parameter to capture the increasing-then-plateau feature of the dose-efficacy relationship. We take the weighted likelihood approach to accommodate for the case where efficacy is possibly late-onset. Based on observed data, we continuously update the posterior estimates of toxicity and efficacy probabilities and adaptively assign patients to the optimal dose. The simulation studies show that the proposed design has good operating characteristics. This method is going to be applied in more than two phase I clinical trials as no other method is available for this specific setting. We also provide an R package dfmta that can be downloaded from CRAN website.