Germination experiments are becoming increasingly complex and they are now routinely involving several experimental factors. Recently, a two-step approach utilizing meta-analysis methodology has been proposed for the estimation of hierarchical models suitable for describing data from such complex experiments. Step 1 involves fitting models to data from each sub-experiment, whereas Step 2 involves combination estimates from all model fits obtained in Step 1. However, one shortcoming of this approach was that visualization of resulting fitted germination curves was difficult. Here, we describe in detail an improved two-step analysis that allows visualization of cumulated data together with fitted curves and confidence bands. Also, we demonstrate in detail, through two examples, how to carry out the statistical analysis in practice.

Les déficits neuropsychologiques consécutifs à l’alcoolo-dépendance affectent principalement la mémoire épisodique, la mémoire de travail et les capacités visuospatiales, ainsi que les fonctions exécutives et motrices [1,2]. Ces déficits présents notamment en début de sevrage peuvent conduire à un bénéfice limité des ateliers psychothérapeutiques et entraver le maintien de l’abstinence des patients alcoolo-dépendants [3,4]. Ainsi, une évaluation neuropsychologique étendue conduite après sevrage semble essentielle afin d’orienter la prise en charge clinique de ces patients. Cependant, peu de services d’addictologie ont les ressources humaines et financières pour conduire une telle évaluation chez chaque patient. L’objectif de cette étude était donc d’examiner la validité et les qualités psychométriques d’un outil de dépistage : le BEARNI (pour Brief Examination of Alcohol-Related Neuropsychological Impairments). Cet outil a été spécialement développé pour être accessible au personnel soignant non psychologue dans l’objectif de conduire un dépistage rapide des déficits neuropsychologiques consécutifs à l’alcoolo-dépendance. Une batterie neuropsychologique étendue a servi de référence (gold standard) pour déterminer le profil cognitif des patients alcoolo-dépendants et examiner les qualités psychométriques du BEARNI. L’analyse factorielle exploratoire a permis de valider la structure interne de BEARNI en mettant en évidence 5 facteurs expliquant 60 % de la variabilité et reflétant les capacités visuospatiales, les fonctions exécutives, la mémoire verbale et la mémoire de travail verbale. La standardisation de chacun des sub-tests et des scores totaux à BEARNI, conduite par l’intermédiaire de courbes ROC, a mis en évidence que cet outil de dépistage présente une bonne efficacité diagnostique dans le dépistage des atteintes cognitives et motrices présentes chez les patients alcoolo-dépendants après sevrage. Cette étude montre la pertinence de l’utilisation de BEARNI en pratique clinique pour détecter la présence de troubles neuropsychologiques chez les patients alcoolo-dépendants et permettre d’orienter ceux ayant besoin d’une évaluation neuropsychologique étendue.

New dietary-based concepts are needed for treatment and effective prevention of overweight and obesity. The primary objective was to investigate if reduction in appetite is associated with improved weight loss maintenance. This cohort study was nested within the European Commission project Satiety Innovation (SATIN). Participants achieving ≥8% weight loss during an initial 8-week low-energy formula diet were included in a 12-week randomised double-blind parallel weight loss maintenance intervention. The intervention included food products designed to reduce appetite or matching controls along with instructions to follow national dietary guidelines. Appetite was assessed by ad libitum energy intake and self-reported appetite evaluations using visual analogue scales during standardised appetite probe days. These were evaluated at the first day of the maintenance period compared with baseline (acute effects after a single exposure of intervention products) and post-maintenance compared with baseline (sustained effects after repeated exposures of intervention products) regardless of randomisation. A total of 181 participants (forty-seven men and 134 women) completed the study. Sustained reduction in 24-h energy intake was associated with improved weight loss maintenance (R 0·37; P = 0·001), whereas the association was not found acutely (P = 0·91). Suppression in self-reported appetite was associated with improved weight loss maintenance both acutely (R −0·32; P = 0·033) and sustained (R −0·33; P = 0·042). Reduction in appetite seems to be associated with improved body weight management, making appetite-reducing food products an interesting strategy for dietary-based concepts.

The study aimed at assessing stunting, wasting and breast-feeding as correlates of body composition in Cambodian children. As part of a nutrition trial (ISRCTN19918531), fat mass (FM) and fat-free mass (FFM) were measured using 2H dilution at 6 and 15 months of age. Of 419 infants enrolled, 98 % were breastfed, 15 % stunted and 4 % wasted at 6 months. At 15 months, 78 % were breastfed, 24 % stunted and 11 % wasted. Those not breastfed had lower FMI at 6 months but not at 15 months. Stunted children had lower FM at 6 months and lower FFM at 6 and 15 months compared with children with length-for-age z ≥0. Stunting was not associated with height-adjusted indexes fat mass index (FMI) or fat-free mass index (FFMI). Wasted children had lower FM, FFM, FMI and FFMI at 6 and 15 months compared with children with weight-for-length z (WLZ) ≥0. Generally, FFM and FFMI deficits increased with age, whereas FM and FMI deficits decreased, reflecting interactions between age and WLZ. For example, the FFM deficits were –0·99 (95 % CI –1·26, –0·72) kg at 6 months and –1·44 (95 % CI –1·69; –1·19) kg at 15 months (interaction, P<0·05), while the FMI deficits were –2·12 (95 % CI –2·53, –1·72) kg/m2 at 6 months and –1·32 (95 % CI –1·77, –0·87) kg/m2 at 15 months (interaction, P<0·05). This indicates that undernourished children preserve body fat at the detriment of fat-free tissue, which may have long-term consequences for health and working capacity.

Early nutrition and growth have been found to be important early exposures for later development. Studies of crude growth in terms of weight and length/height, however, cannot elucidate how body composition (BC) might mediate associations between nutrition and later development. In this study, we aimed to examine the relation between fat mass (FM) or fat-free mass (FFM) tissues at birth and their accretion during early infancy, and later developmental progression. In a birth cohort from Ethiopia, 455 children who have BC measurement at birth and 416 who have standardised rate of BC growth during infancy were followed up for outcome variable, and were included in the statistical analysis. The study sample was restricted to mothers living in Jimma town who gave birth to a term baby with a birth weight ≥1500 g and no evident congenital anomalies. The relationship between the exposure and outcome variables was examined using linear-mixed regression model. The finding revealed that FFM at birth was positively associated with global developmental progression from 1 to 5 years (β=1·75; 95 % CI 0·11, 3·39) and from 4 to 5 years (β=1·34; 95 % CI 0·23, 2·44) in the adjusted model. Furthermore, the rate of postnatal FFM tissue accretion was positively associated with development at 1 year of age (β=0·50; 95 % CI 0·01, 0·99). Neither fetal nor postnatal FM showed a significant association. In conclusion, fetal, rather than postnatal, FFM tissue accretion was associated with developmental progression. Intervention studies are needed to assess whether nutrition interventions increasing FFM also increase cognitive development.

In recent years germination experiments have become more and more complex. Typically, they are replicated in time as independent runs and at each time point they involve hierarchical, often factorial experimental designs, which are now commonly analysed by means of linear mixed models. However, in order to characterize germination in response to time elapsed, specific event-time models are needed and mixed model extensions of these models are not readily available, neither in theory nor in practice. As a practical workaround we propose a two-step approach that combines and weighs together results from event-time models fitted separately to data from each germination test by means of meta-analytic random effects models. We show that this approach provides a more appropriate appreciation of the sources of variation in hierarchically structured germination experiments as both between- and within-experiment variation may be recovered from the data.

This paper discusses results from the second phase of the European Ice Sheet Modelling Initiative (EISMINT). It reports the intercomparison of ten operational ice-sheet models and uses a series of experiments to examine the implications of thermomechanical coupling for model behaviour. A schematic, circular ice sheet is used in the work which investigates both steady states and the response to stepped changes in climate. The major finding is that the radial symmetry implied in the experimental design can, under certain circumstances, break down with the formation of distinct, regularly spaced spokes of cold ice which extended from the interior of the ice sheet outward to the surrounding zone of basal melt. These features also manifest themselves in the thickness and velocity distributions predicted by the models. They appear to be a common feature to all of the models which took part in the intercomparison, and may stem from interactions between ice temperature, flow and surface form. The exact nature of these features varies between models, and their existence appears to be controlled by the overall thermal regime of the ice sheet. A second result is that there is considerable agreement between the models in their predictions of global-scale response to imposed climate change.

As cases of resistance to herbicides escalate worldwide, there is increasingdemand from growers to test for weed resistance and learn how to manage it.Scientists have developed resistance-testing protocols for numerousherbicides and weed species. Growers need immediate answers and scientistsare faced with the daunting task of testing an increasingly large number ofsamples across a variety of species and herbicides. Quick tests have been,and continue to be, developed to address this need, although classical testsare still the norm. Newer methods involve molecular techniques. Whereas theclassical whole-plant assay tests for resistance regardless of themechanism, many quick tests are limited by specificity to an herbicide, modeof action, or mechanism of resistance. Advancing knowledge in weed biologyand genomics allows for refinements in sampling and testing protocols. Thus,approaches in resistance testing continue to diversify, which can confoundthe less experienced. We aim to help weed science practitioners resolvequestions pertaining to the testing of herbicide resistance, starting withfield surveys and sampling methods, herbicide screening methods, dataanalysis, and, finally, interpretation. More specifically, this articlediscusses approaches for sampling plants for resistance confirmation assays,provides brief overviews on the biological and statistical basis fordesigning and analyzing dose–response tests, and discusses alternativeprocedures for rapid resistance confirmation, including molecular-basedassays. Resistance confirmation procedures often need to be slightlymodified to suit a specific situation; thus, the general requirements aswell as pros and cons of quick assays and DNA-based assays are contrasted.Ultimately, weed resistance testing research, as well as resistancemanagement decisions arising from research, needs to be practical, feasible,and grounded in science-based methods.

Advances in statistical software allow statistical methods for nonlinear regression analysis of dose-response curves to be carried out conveniently by non-statisticians. One such statistical software is the program R with the drc extension package. The drc package can: (1) simultaneously fit multiple dose-response curves; (2) compare curve parameters for significant differences; (3) calculate any point along the curve at the response level of interest, commonly known as an effective dose (e.g., ED30, ED50, ED90), and determine its significance; and (4) generate graphs for publications or presentations. We believe that the drc package has advantages that include: the ability to relatively simply and quickly compare multiple curves and select ED-levels easily along the curve with relevant statistics; the package is free of charge and does not require licensing fees, and the size of the package is only 70 MB. Therefore, our objectives are to: (1) provide a review of a few common issues in dose-response-curve fitting, and (2) facilitate the use of up-to-date statistical techniques for analysis of dose-response curves with this software. The methods described can be utilized to evaluate chemical and non-chemical weed control options. Benefits to the practitioners and academics are also presented.

There are various reasons for using statistics, but perhaps the most important is that the biological sciences are empirical sciences. There is always an element of variability that can only be dealt with by applying statistics. Essentially, statistics is a way to summarize the variability of data so that we can confidently say whether there is a difference among treatments or among regression parameters and tell others about the variability of the results. To that end, we must use the most appropriate statistics to get a “correct” picture of the experimental variability, and the best way of doing that is to report the size of the parameters or the means and their associated standard errors or confidence intervals. Simply declaring that the yields were 1 or 2 ton ha−1 does not mean anything without associated standard errors for those yields. Another driving force is that no journal will accept publications without the data having been subjected to some kind of statistical analysis.

A standard numerical experiment featuring the Ross Ice Shelf, Antarctica, is presented as a test package for the development and intercomparison of ice-shelf models. The emphasis of this package is solution of stress-equilibrium equations for an ice-shelf velocity consistent with present observations. As a demonstration, we compare five independently developed ice-shelf models based on finite-difference and finite-element methods. Our results suggest that there is little difference between finite-element and finite-difference methods in capturing the basic, large-scale flow features of the ice shelf. We additionally show that the fit between model and observed velocity depends strongly on the ice-shelf temperature field, for which there is presently little observational control. The main differences between model results are due to the equations being solved, the boundary conditions at the ice from and the discretization method (finite element vs finite difference).

Plant responses to various doses of herbicides usually follow a sigmoid model where the potency is given by the 50% inhibition (I 50) value. To assess the potency of a herbicide under a range of environmental conditions, a series of independent bioassays are necessary to account for assay-to-assay variation. Analysis has conventionally been done by separate analysis of the individual bioassays or by simply pooling data. Analyzing the individual bioassays separately throws up relevant information on interassay variation. Such a model becomes too complex because a full set of model parameters is needed for each data set. Pooling data instead, and analyzing the bioassay jointly, inflates parameter uncertainty because of oversimplification. Such a simple model would have too few variables, and the fixed-effect estimates would be more uncertain because they would be explaining the interassay random effects. This means that the underlying statistical model is not realistic. Therefore, we propose a new technique of intermediate complexity that outperforms either technique and provides biologically realistic estimates that allow us to compare herbicide potencies. With this technique, we simultaneously analyze independent experiments by using a combination of nonlinear regression and mixed models. The case study uses a group of independently run bioassays with two photosystem II–inhibiting herbicides, diuron and bentazon, by measuring the oxygen evolution of thylakoid membranes. The introduction of random elements in the nonlinear regression parameters reduces the uncertainty in the parameters of interest. We demonstrate that it is possible to pool data from independent experiments to assess which parameters can be assigned a random element, to conduct hypothesis testing, and to calculate stable confidence limits and thus obtain a more precise interpretation of the biologically relevant parameters, such as I 50, compared with the conventional nonlinear regression models of the individual bioassays.

For the first time high-quality coverage of the ERS-1 radar altimeter provides a very accurate surface topographic map covering 80% of the Antarctic ice sheet that can contribute significantly to glaciological studies such as ice-sheet flow modelling. The topography allows estimation of the ice-flow direction, the balance velocity and the basal shear stress. A relationship between shear stress, basal temperature and a parameter related to strain rate helps in mapping the behaviour anomalies of these parameters. Longitudinal stress, sliding, bedrock topography and variation in the pre-exponential factor of the flow law are found to play a major role in the ice-flow pattern. This relation can also be used to estimate rheological parameters: the Glen exponent n is found to be 1 for T < −10°C and 3–4 for higher temperatures, where Q is found to be 70 kJ mol−1.

The Southern Alps – Ligurian basin junction is one of the most active seismic areas in Western Europe countries. The topographic and the structural setting of this region is complex because of (i) its position between the high topography of the Southern Alps and the deep, narrow Ligurian oceanic basin, and (ii) the large number of structures inherited from the Alpine orogeny. Historical seismicity reveals about twenty moderate-size earthquakes (up to M=6.0), mostly distributed along the Ligurian coast and the Vésubie valley. A recent geodetic experiment shows a significant strain rate during the last 50 years in the area between the Argentera massif and the Mediterranean coastline. Results of this experiment suggest a N-S shortening of about 2-4 mm/yr over the network, this shortening direction is consistent with the seismological (P-axes of earthquakes) and the microtectonic data. The Pennic front (E-NE of the Argentera massif) and the northern Ligurian margin are the most seismically active areas. In the Nice arc and in the Argentera massif, some seismic lineaments correspond to faults identified in the field (such as theTaggia-Saorge fault or the Monaco-Sospel fault). In the western part of the Alpes Maritimes, no seismic activity is recorded in the Castellane arc. In the field, geological evidence, such as offsets of recent alluvial sediments, recent fault breccia, speleothem deformations, radon anomalies and others indicates recent deformation along these faults. Nevertheless, to this date active fault scarps have not been identified: this probably results from a relatively high erosion rate versus deformation rate and from the lack of Quaternary markers. We also suspect the presence of two hidden active faults, one in the lower Var valley (Nice city area) and the other one at the base of the Argentera crustal thrust-sheet. Offshore, along the northern Ligurian margin, the seismic reflection data shows traces of Quaternary extensional deformation, but the accuracy of the data does not yet allow the construction of a structural map nor does it allow the determination of the continuity between the offshore and onshore structures. From these data set we propose a preliminary map of 11 active faults and we discuss the questions which remain unsolved in the perspective of seismic hazard evaluations.

Intestinal serotonin (5-hydroxytrypamine, 5-HT) metabolism is thought to play a role in gut functions by regulating motility, permeability and other functions of the intestine. In the present study, we investigated the effect of tryptophan (TRP), the precursor of 5-HT, supplementation on intestinal barrier functions and non-alcoholic fatty liver disease (NAFLD). An established mouse model of NAFLD induced by feeding a fructose-rich diet (N group) was used in the present study. TRP was administered orally for 8 weeks to C57BL/6J control or NAFLD mice. NAFLD-related liver parameters (hepatic TAG and Oil Red O staining), intestinal barrier parameters (tight-junction protein occludin and portal plasma lipopolysaccharides (LPS)) and 5-HT-related parameters (5-HT, 5-HT transporter (SERT) and motility) were measured. We observed reduced duodenal occludin protein concentrations (P= 0·0007), high portal plasma LPS concentrations (P= 0·005) and an elevated liver weight:body weight ratio (P= 0·01) in the N group compared with the parameters in the control group. TRP supplementation led to an increase in occludin concentrations (P= 0·0009) and consecutively reduced liver weight:body weight ratio (P= 0·009) as well as overall hepatic fat accumulation in the N group (P= 0·05). In addition, the N group exhibited reduced SERT protein expression (P= 0·002), which was normalised by TRP supplementation (P= 0·02). For the first time, our data indicate that oral TRP supplementation attenuates experimental NAFLD in mice. The underlying mechanisms are not clear, but probably involve stabilisation of the intestinal barrier in the upper small intestine and amelioration of the dysregulated intestinal serotonergic system.

Chilli peppers have been shown to enhance diet-induced thermogenesis (DIT) and reduce energy intake (EI) in some studies, but there are few data on other pungent spices. The primary aim of the present study was to test the acute effects of black pepper (pepper), ginger, horseradish and mustard in a meal on 4 h postprandial DIT. The secondary aim was to examine the effects on subjective appetite measures, ad libitum EI and energy balance. In a five-way placebo-controlled, single-blind, cross-over trial, twenty-two young (age 24·9 (sd 4·6) years), normal-weight (BMI 21·8 (sd 2·1) kg/m2) males were randomly assigned to receive a brunch meal with either pepper (1·3 g), ginger (20 g), horseradish (8·3 g), mustard (21 g) or no spices (placebo). The amounts of spices were chosen from pre-testing to make the meal spicy but palatable. No significant treatment effects were observed on DIT, but mustard produced DIT, which tended to be larger than that of placebo (14 %, 59 (se 3) v. 52 (se 2) kJ/h, respectively, P= 0·08). No other spice induced thermogenic effects approaching statistical significance. Subjective measures of appetite (P>0·85), ad libitum EI (P= 0·63) and energy balance (P= 0·67) also did not differ between the treatments. Finally, horseradish decreased heart rate (P= 0·048) and increased diastolic blood pressure (P= 0·049) compared with placebo. In conclusion, no reliable treatment effects on appetite, EI or energy balance were observed, although mustard tended to be thermogenic at this dose. Further studies should explore the possible strength and mechanisms of the potential thermogenic effect of mustard actives, and potential enhancement by, for example, combinations with other food components.