Dealing with many correlated covariates in capture–recapture models

Capture–recapture models for estimating demographic parameters allow covariates to be incorporated to better understand population dynamics. However, high-dimensionality and multicollinearity can hamper estimation and inference. Principal component analysis is incorporated within capture–recapture models and used to reduce the number of predictors into uncorrelated synthetic new variables. Principal components are selected by sequentially assessing their statistical significance. We provide an example on seabird survival to illustrate our approach. Our method requires standard statistical tools, which permits an efficient and easy implementation using standard software.     

Kinetics and metabolic specificities of Vero cells in bioreactor cultures with serum-free medium

The aim of this study was to understand the metabolism kinetics of Vero cells grown on microcarriers in bioreactors in serum-free medium (SFM). We sought to determine what nutrients are essential for Vero cells and how they are consumed. Contrary to glucose and to most of the amino acids, glutamine and serine were very quickly depleted in this medium and can be supposed to be responsible for cell apoptosis. Lactate and ammonium ions did not reach toxic levels for Vero cells. We payed more attention to the lactate metabolism. Usually we observed that after about 2 days lactate was consumed in serum-containing media, but its concentration plateaud in SFM. Moreover, the addition of serum in SFM provoked lactate consumption and the rate of glucose and glutamine consumption was twice as high as in the SFM not supplemented with serum. The depletion of glutamine and serine and the metabolic deviations leading to a shortage of intermediate products required for other metabolic pathways probably contribute to the lower cell yield and higher cell death rate in SFM. This revised version was published online in July 2006 with corrections to the Cover Date.     

Promoting lab culture to enhance academic resilience during crises

The COVID‐19 pandemic has heavily impacted academics’ professional and personal lives, forcing many research groups (labs) to shift from an academic system primarily based on in‐person work to an almost full‐time remote workforce during lockdowns. Labs are generally characterized by a strong lab culture that underpins all research and social activities of its members. Lab culture traditionally builds on the pillars of in‐person communication, knowledge sharing, and all social and professional activities that promote collaboration, team building, scientific productivity, and well‐being. Here, we use the experience of our research group facing the COVID‐19 pandemic to illustrate how proactively reinforcing lab culture and its positive outcomes have been essential to our lab when transitioning from an in‐person to a remote lab environment, and through its ongoing evolution toward a hybrid remote/in‐person model. We argue that the proactive promotion of lab culture in research groups can foster academic resilience during crises, helping research groups to maintain their capacity to conduct scientific activities while preserving a sustainable life/work balance and a healthy mental condition.     

Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2011-31 January 2012

This article documents the addition of 473 microsatellite marker loci and 71 pairs of single‐nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross‐tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax.     

Statistical ecology comes of age

The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1–4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.     

A simple field method to identify foot strike pattern during running

Identifying foot strike patterns in running is an important issue for sport clinicians, coaches and footwear industrials. Current methods allow the monitoring of either many steps in laboratory conditions or only a few steps in the field. Because measuring running biomechanics during actual practice is critical, our purpose is to validate a method aiming at identifying foot strike patterns during continuous field measurements. Based on heel and metatarsal accelerations, this method requires two uniaxial accelerometers. The time between heel and metatarsal acceleration peaks (THM) was compared to the foot strike angle in the sagittal plane (α_foot) obtained by 2D video analysis for various conditions of speed, slope, footwear, foot strike and state of fatigue. Acceleration and kinematic measurements were performed at 1000 Hz and 120 Hz, respectively, during 2-min treadmill running bouts. Significant correlations were observed between THM and α_foot for 14 out of 15 conditions. The overall correlation coefficient was r=0.916 (P<0.0001, n=288). The THM method is thus highly reliable for a wide range of speeds and slopes, and for all types of foot strike except for extreme forefoot strike during which the heel rarely or never strikes the ground, and for different footwears and states of fatigue. We proposed a classification based on THM: FFS<−5.49 ms<MFS<15.2 ms<RFS. With only a few precautions being necessary to ensure appropriate use of this method, it is reliable for distinguishing rearfoot and non-rearfoot strikers in situ.     

Abundance of rare and elusive species: Empirical investigation of closed versus spatially explicit capture–recapture models with lynx as a case study

Effective conservation and management require reliable monitoring methods and estimates of abundance to prioritize human and financial investments. Camera trapping is a non-invasive sampling method allowing the use of capture–recapture (CR) models to estimate abundance while accounting for the difficulty of detecting individuals in the wild. We investigated the relative performance of standard closed CR models and spatially explicit CR models (SECR) that incorporate spatial information in the data. Using simulations, we considered 4 scenarios comparing low versus high detection probability and small versus large populations and contrasted abundance estimates obtained from both approaches. Standard CR and SECR models both provided minimally biased abundance estimates, but precision was improved when using SECR models. The associated confidence intervals also provided better coverage than their non-spatial counterpart. We concluded SECR models exhibit better statistical performance than standard closed CR models and allow for sound management strategies based on density maps of activity centers. To illustrate the comparison, we considered the Eurasian lynx (Lynx lynx) as a case study that provided the first abundance estimates of a local population in France. © 2012 The Wildlife Society.     

Detecting and estimating density dependence in wildlife populations

We review methods for detecting and assessing the strength of density dependence based on 2 types of approaches: surveys of population size and studies of life history traits, in particular demographic parameters. For the first type of studies, methods neglecting uncertainty in population size should definitely be abandoned. Bayesian approaches to simple state-space models accounting for uncertainty in population size are recommended, with some caution because of numerical difficulties and risks of model misspecification. Realistic state-space models incorporating features such as environmental covariates, age structure, etc., may lack power because of the shortness of the time series and the simultaneous presence of process and sampling variability. In all cases, complementing the population survey data with some external information, with priority on the intrinsic growth rate, is highly recommended. Methods for detecting density dependence in life history traits are generally conservative (i.e., tend to underestimate the strength of density dependence). Among approaches to correct for this effect, the state-space formulation of capture–recapture models is again the most promising. Foreseeable developments will exploit integrated monitoring combining population size surveys and individual longitudinal data in refined state-space models, for which a Bayesian approach is the most straightforward statistical treatment. One may thus expect an integration of various types of models that will make it possible to look at density dependence as a complex biological process interacting with other processes rather than in terms of a simple equation; modern statistical and modeling tools make such a synthesis within reach. © 2012 The Wildlife Society.     

Determination of the enantiomers of chlorpheniramine and its main monodesmethyl metabolite in urine using achiral–chiral liquid chromatography

The enantiomers of chlorpheniramine and its monodesmethyl metabolite were determined separately in urine by using a coupled achiral–chiral chromatographic system. The two enantiomers of the studied compound and the internal standard were separated from the biological matrix on a cyanopropyl column and reinjected into a chiral amylose AD column where the two enantiomers were separated and quantified by UV detection. The method was validated for chlorpheniramine and for the metabolite within the range 0–1000 ng/ml. It was also applied in a pilot pharmacokinetic study to samples from a volunteer given 8 mg of racemic chlorpheniramine by mouth.