La Rochelle Université

Considerable time and effort can be saved by simultaneously amplifying multiple sequences in a single reaction, a process referred to as multiplex polymerase chain reaction (PCR). Multiplex PCR requires that primers lead to amplification of unique regions of DNA, both in individual pairs and in combinations of many primers, under a single set of reaction conditions. In addition, methods must be available for the analysis of each individual amplification product from the mixture of all the products. Multiplex PCR is becoming a rapid and convenient screening assay in both the clinical and the research laboratory. The development of an efficient multiplex PCR usually requires strategic planning and multiple attempts to optimize reaction conditions. For a successful multiplex PCR assay, the relative concentration of the primers, concentration of the PCR buffer, balance between the magnesium chloride and deoxynucleotide concentrations, cycling temperatures, and amount of template DNA and Taq DNA polymerase are important. An optimal combination of annealing temperature and buffer concentration is essential in multiplex PCR to obtain highly specific amplification products. Magnesium chloride concentration needs only to be proportional to the amount of dNTP, while adjusting primer concentration for each target sequence is also essential. The list of various factors that can influence the reaction is by no means complete. Optimization of the parameters discussed in the present review should provide a practical approach toward resolving the common problems encountered in multiplex PCR (such as spurious amplification products, uneven or no amplification of some target sequences, and difficulties in reproducing some results). Thorough evaluation and validation of new multiplex PCR procedures is essential. The sensitivity and specificity must be thoroughly evaluated using standardized purified nucleic acids. Where available, full use should be made of external and internal quality controls, which must be rigorously applied. As the number of microbial agents detectable by PCR increases, it will become highly desirable for practical purposes to achieve simultaneous detection of multiple agents that cause similar or identical clinical syndromes and/or share similar epidemiological features.

In this communication we introduce marmap, a package designed for downloading, plotting and manipulating bathymetric and topographic data in R. marmap can query the ETOPO1 bathymetry and topography database hosted by the NOAA, use simple latitude-longitude-depth data in ascii format, and take advantage of the advanced plotting tools available in R to build publication-quality bathymetric maps. Functions to query data (bathymetry, sampling information…) are available interactively by clicking on marmap maps. Bathymetric and topographic data can also be used to calculate projected surface areas within specified depth/altitude intervals, and constrain the calculation of realistic shortest path distances. Such information can be used in molecular ecology, for example, to evaluate genetic isolation by distance in a spatially-explicit framework.

Agricultural landscape homogenization has detrimental effects on biodiversity and key ecosystem services. Increasing agricultural landscape heterogeneity by increasing seminatural cover can help to mitigate biodiversity loss. However, the amount of seminatural cover is generally low and difficult to increase in many intensively managed agricultural landscapes. We hypothesized that increasing the heterogeneity of the crop mosaic itself (hereafter "crop heterogeneity") can also have positive effects on biodiversity. In 8 contrasting regions of Europe and North America, we selected 435 landscapes along independent gradients of crop diversity and mean field size. Within each landscape, we selected 3 sampling sites in 1, 2, or 3 crop types. We sampled 7 taxa (plants, bees, butterflies, hoverflies, carabids, spiders, and birds) and calculated a synthetic index of multitrophic diversity at the landscape level. Increasing crop heterogeneity was more beneficial for multitrophic diversity than increasing seminatural cover. For instance, the effect of decreasing mean field size from 5 to 2.8 ha was as strong as the effect of increasing seminatural cover from 0.5 to 11%. Decreasing mean field size benefited multitrophic diversity even in the absence of seminatural vegetation between fields. Increasing the number of crop types sampled had a positive effect on landscape-level multitrophic diversity. However, the effect of increasing crop diversity in the landscape surrounding fields sampled depended on the amount of seminatural cover. Our study provides large-scale, multitrophic, cross-regional evidence that increasing crop heterogeneity can be an effective way to increase biodiversity in agricultural landscapes without taking land out of agricultural production.

Ancient migrations in Southeast Asia The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McColl et al. sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations. Science , this issue p. 92 , p. 88 ; see also p. 31

Contrasting regional changes in Southern Ocean sea ice have occurred over the last 30 years with distinct regional effects on ecosystem structure and function. Quantifying how Antarctic predators respond to such changes provides the context for predicting how climate variability/change will affect these assemblages into the future. Over an 11-year time-series, we examine how inter-annual variability in sea ice concentration and advance affect the foraging behaviour of a top Antarctic predator, the southern elephant seal. Females foraged longer in pack ice in years with greatest sea ice concentration and earliest sea ice advance, while males foraged longer in polynyas in years of lowest sea ice concentration. There was a positive relationship between near-surface meridional wind anomalies and female foraging effort, but not for males. This study reveals the complexities of foraging responses to climate forcing by a poleward migratory predator through varying sea ice property and dynamic anomalies.

Text detection and recognition in a natural environment are key components of many applications, ranging from business card digitization to shop indexation in a street. This competition aims at assessing the ability of state-of-the-art methods to detect Multi-Lingual Text (MLT) in scene images, such as in contents gathered from the Internet media and in modern cities where multiple cultures live and communicate together. This competition is an extension of the Robust Reading Competition (RRC) which has been held since 2003 both in ICDAR and in an online context. The proposed competition is presented as a new challenge of the RRC. The dataset built for this challenge largely extends the previous RRC editions in many aspects: the multi-lingual text, the size of the dataset, the multi-oriented text, the wide variety of scenes. The dataset is comprised of 18,000 images which contain text belonging to 9 languages. The challenge is comprised of three tasks related to text detection and script classification. We have received a total of 16 participations from the research and industrial communities. This paper presents the dataset, the tasks and the findings of this RRC-MLT challenge.

The Paris agreement target of limiting global surface warming to 1.5-2°C compared to pre-industrial levels by 2100 will heavily impact the ocean. While ambitious mitigation and adaptation are both needed, the ocean provides major opportunities for action to reduce climate change globally and its impacts on vital ecosystems and ecosystem services. A comprehensive and systematic assessment of 13 global- and local-scale, ocean-based measures was performed to help steer the development and implementation of technologies and actions towards a sustainable outcome. We show that (1) all measures have tradeoffs and multiple criteria must be used for a comprehensive assessment of their potential, (2) greatest benefit is derived by combining global and local solutions, some of which could be implemented or scaled-up immediately, (3) some measures are too uncertain to be recommended yet, (4) political consistency must be achieved through effective cross-scale governance mechanisms, (5) scientific effort must focus on effectiveness, co-benefits, disbenefits, and costs of poorly tested as well as new and emerging measures.

Vehicular Adhoc Networks (VANETs) have been attracted a lot of research recent years. Although VANETs are deployed in reality offering several services, the current architecture has been facing many difficulties in deployment and management because of poor connectivity, less scalability, less flexibility and less intelligence. We propose a new VANET architecture called FSDN which combines two emergent computing and network paradigm Software Defined Networking (SDN) and Fog Computing as a prospective solution. SDN-based architecture provides flexibility, scalability, programmability and global knowledge while Fog Computing offers delay-sensitive and location-awareness services which could be satisfy the demands of future VANETs scenarios. We figure out all the SDN-based VANET components as well as their functionality in the system. We also consider the system basic operations in which Fog Computing are leveraged to support surveillance services by taking into account resource manager and Fog orchestration models. The proposed architecture could resolve the main challenges in VANETs by augmenting Vehicle-to-Vehicle (V2V), Vehicle-to-Infrastructure (V2I), Vehicle-to-Base Station communications and SDN centralized control while optimizing resources utility and reducing latency by integrating Fog Computing. Two use-cases for non-safety service (data streaming) and safety service (Lane-change assistance) are also presented to illustrate the benefits of our proposed architecture.

Mixture of Gaussians is a widely used approach for background modeling to detect moving objects from static cameras. Numerous improvements of the original method developed by Stauffer and Grimson [1] have been proposed over the recent years and the purpose of this paper is to provide a survey and an original classification of these improvements. We also discuss relevant issues to reduce the computation time. Firstly, the original MOG are reminded and discussed following the challenges met in video sequences. Then, we categorize the different improvements found in the literature. We have classified them in term of strategies used to improve the original MOG and we have discussed them in term of the critical situations they claim to handle. After analyzing the strategies and identifying their limitations, we conclude with several promising directions for future research. Keywords: Background modeling, foreground detection, mixture of gaussians

Summary The status of small cetaceans in the North Sea and adjacent waters has been of concern for many years. Shipboard and aerial line transect surveys were conducted to provide accurate and precise estimates of abundance as a basis for conservation strategy in European waters. The survey, known as SCANS (Small Cetacean Abundance in the North Sea), was conducted in summer 1994 and designed to generate precise and unbiased abundance estimates. Thus the intensity of survey was high, and data collection and analysis methods allowed for the probability of detection of animals on the transect line being less than unity and, for shipboard surveys, also allowed for animal movement in response to the survey platform. Shipboard transects covered 20 000 km in an area of 890 000 km 2 . Aerial transects covered 7000 km in an area of 150 000 km 2 . Three species dominated the data. Harbour porpoise Phocoena phocoena were encountered throughout the survey area except in the Channel and the southern North Sea. Whitebeaked dolphin Lagenorhynchus albirostris and minke whale Balaenoptera acutorostrata were found mainly in the north‐western North Sea. Phocoena phocoena abundance for the entire survey area was estimated as 341 366 [coefficient of variation (CV) = 0·14; 95% confidence interval (CI) = 260 000–449 000]. The estimated number of B. acutorostrata was 8445 (CV = 0·24; 95% CI 5000–13 500). The estimate for L. albirostris based on confirmed sightings of this species was 7856 (CV = 0·30; 95% CI = 4000–13 000). When Atlantic whitesided dolphin Lagenorhynchus acutus and Lagenorhynchus spp. sightings were included, this estimate increased to 11 760 (CV = 0·26; 95% CI 5900–18 500). Shortbeaked common dolphin Delphinus delphis were found almost exclusively in the Celtic Sea. Abundance was estimated as 75 450 (CV = 0·67; 95% CI = 23 000–149 000). Current assessments and recommendations by international fora concerning the impact on P. phocoena of bycatch in gillnet fisheries in the North Sea and adjacent waters are based on these estimates.

The European Union (EU) Habitats Directive requires Member States to monitor and maintain at favourable conservation status those species identified to be in need of protection, including all cetaceans. In July 2005 we surveyed the entire EU Atlantic continental shelf to generate robust estimates of abundance for harbour porpoise and other cetacean species. The survey used line transect sampling methods and purpose built data collection equipment designed to minimise bias in estimates of abundance. Shipboard transects covered 19,725 km in sea conditions ⩽Beaufort 4 in an area of 1,005,743 km2. Aerial transects covered 15,802 km in good/moderate conditions (⩽Beaufort 3) in an area of 364,371 km2. Thirteen cetacean species were recorded; abundance was estimated for harbour porpoise (375,358; CV = 0.197), bottlenose dolphin (16,485; CV = 0.422), white-beaked dolphin (16,536; CV = 0.303), short-beaked common dolphin (56,221; CV = 0.234) and minke whale (18,958; CV = 0.347). Abundance in 2005 was similar to that estimated in July 1994 for harbour porpoise, white-beaked dolphin and minke whale in a comparable area. However, model-based density surfaces showed a marked difference in harbour porpoise distribution between 1994 and 2005. Our results allow EU Member States to discharge their responsibilities under the Habitats Directive and inform other international organisations concerning the assessment of conservation status of cetaceans and the impact of bycatch at a large spatial scale. The lack of evidence for a change in harbour porpoise abundance in EU waters as a whole does not exclude the possibility of an impact of bycatch in some areas. Monitoring bycatch and estimation of abundance continue to be essential.

from 1993 to 2012 is consistent with independent estimates from satellite altimetry, leading to overall acceleration larger than previously suggested. This feature is geographically dominated by the Indian Ocean-Southern Pacific region, marking a transition from lower-than-average rates before 1990 toward unprecedented high rates in recent decades. We demonstrate that VLM corrections, area weighting, and our use of a common reference datum for tide gauges may explain the lower rates compared with earlier GMSL estimates in approximately equal proportion. The trends and multidecadal variability of our GMSL curve also compare well to the sum of individual contributions obtained from historical outputs of the Coupled Model Intercomparison Project Phase 5. This, in turn, increases our confidence in process-based projections presented in the Fifth Assessment Report of the Intergovernmental Panel on Climate Change.

Abstract Vertical land motions are a key element in understanding how sea levels have changed over the past century and how future sea levels may impact coastal areas. Ideally, to be useful in long‐term sea level studies, vertical land motion should be determined with standard errors that are 1 order of magnitude lower than the contemporary climate signals of 1 to 3 mm/yr observed on average in sea level records, either using tide gauges or satellites. This metrological requirement constitutes a challenge in geodesy. Here we review the most successful instrumental methods that have been used to determine vertical displacements at the Earth's surface, so that the objectives of understanding and anticipating sea levels can be addressed adequately in terms of accuracy. In this respect, the required level of uncertainty is examined in two case studies (global and local). A special focus is given to the use of the Global Positioning System (GPS) and to the combination of satellite radar altimetry with tide gauge data. We update previous data analyses and assess the quality of global satellite altimetry products available to the users for coastal applications. Despite recent advances, a near‐plateau level of accuracy has been reached. The major limitation is the realization of the terrestrial reference frame, whose physical parameters, the origin and the scale factor, are beyond the scope of a unique technique such as the GPS. Additional practical but nonetheless important issues are associated with the installation of GPS antennas, such as ensuring that there is no unknown differential vertical motion with the tide gauge.

Principal component analysis (PCA) is one of the most widely used dimension reduction techniques. A related easier problem is termed subspace learning or subspace estimation. Given relatively clean data, both are easily solved via singular value decomposition (SVD). The problem of subspace learning or PCA in the presence of outliers is called robust subspace learning (RSL) or robust PCA (RPCA). For long data sequences, if one tries to use a single lower-dimensional subspace to represent the data, the required subspace dimension may end up being quite large. For such data, a better model is to assume that it lies in a low-dimensional subspace that can change over time, albeit gradually. The problem of tracking such data (and the subspaces) while being robust to outliers is called robust subspace tracking (RST). This article provides a magazine-style overview of the entire field of RSL and tracking. In particular, solutions for three problems are discussed in detail: RPCA via sparse+low-rank (S+LR) matrix decomposition; RST via S+LR; robust subspace recovery (RSR). RSR assumes that an entire data vector is either an outlier or an inlier. The S+LR formulation instead assumes that outliers occur on only a few data vector indices and, hence, are well modeled as sparse corruptions.

We review the characteristics of sea level variability at the coast focussing on how it differs from the variability in the nearby deep ocean. Sea level variability occurs on all timescales, with processes at higher frequencies tending to have a larger magnitude at the coast due to resonance and other dynamics. In the case of some processes, such as the tides, the presence of the coast and the shallow waters of the shelves results in the processes being considerably more complex than offshore. However, 'coastal variability' should not always be considered as 'short spatial scale variability' but can be the result of signals transmitted along the coast from 1000s km away. Fortunately, thanks to tide gauges being necessarily located at the coast, many aspects of coastal sea level variability can be claimed to be better understood than those in the deep ocean. Nevertheless, certain aspects of coastal variability remain under-researched, including how changes in some processes (e.g., wave setup, river runoff) may have contributed to the historical mean sea level records obtained from tide gauges which are now used routinely in large-scale climate research.

International audience

In intensive farmland habitats, pollination of wild flowers and crops may be threatened by the widespread decline of pollinators. The honey bee decline, in particular, appears to result from the combination of multiple stresses, including diseases, pathogens, and pesticides. The reduction of semi-natural habitats is also suspected to entail floral resource scarcity for bees. Yet, the seasonal dynamics and composition of the honey bee diet remains poorly documented to date. In this study, we studied the seasonal contribution of mass-flowering crops (rapeseed and sunflower) vs. other floral resources, as well as the influence of nutritional quality and landscape composition on pollen diet composition over five consecutive years. From April to October, the mass of pollen and nectar collected by honey bees followed a bimodal seasonal trend, marked by a two-month period of low food supply between the two oilseed crop mass-flowerings (ending in May for rapeseed and July for sunflower). Bees collected nectar mainly from crops while pollen came from a wide diversity of herbaceous and woody plant species in semi-natural habitats or from weeds in crops. Weed species constituted the bulk of the honey bee diet between the mass flowering crop periods (up to 40%) and are therefore suspected to play a critical role at this time period. The pollen diet composition was related to the nutritional value of the collected pollen and by the local landscape composition. Our study highlights (1) a food supply depletion period of both pollen and nectar resources during late spring, contemporaneously with the demographic peak of honey bee populations, (2) a high botanical richness of pollen diet, mostly proceeding from trees and weeds, and (3) a pollen diet composition influenced by the local landscape composition. Our results therefore support the Agri-Environmental Schemes intended to promote honey bees and beekeeping sustainability through the enhancement of flower availability in agricultural landscapes.

We present the DynTex database of high-quality dynamic texture videos. It consists of over 650 sequences of dynamic textures, mostly in everyday surroundings. Additionally, we propose a scheme for the manual annotation of the sequences based on a detailed analysis of the physical processes underlying the dynamic textures. Using this scheme we describe the texture sequences in terms of both visual structure and semantic content. The videos and annotations are made publicly available for scientific research.

UNLABELLED: In the frame of the French national research program PRIMEQUAL (inter-ministry program for better air quality in urban environments), measurements of outdoor and indoor pollution have been carried out in eight schools in La Rochelle (France) and its suburbs. The buildings were naturally ventilated by opening the windows, or mechanically ventilated, and showed various air permeabilities. Ozone, nitrogen oxides (NO and NO(2)), and airborne particle (particle counts within 15 size intervals ranging from 0.3 to 15 mum) concentrations were continuously monitored indoors and outdoors for two 2-week periods. The indoor humidity, temperature, CO(2) concentration (an indicator of occupancy), window openings and building permeability were also measured. The temporal profiles of indoor and outdoor concentrations show ozone and nitrogen oxides behave differently: NO and NO(2) indoor/outdoor concentration ratios (I/O) were found to vary in a range from 0.5 to 1, and from 0.88 to 1, respectively, but no correlation with building permeability was observed. On the contrary, I/O ratios of ozone vary in a range from 0 to 0.45 and seem to be strongly influenced by the building air-tightness: the more airtight the building envelope, the lower the ratio. Occupancy, through re-suspension of previously deposited particles and possible particle generation, strongly influences the indoor concentration level of airborne particles. However, this influence decreases with particle size, reflecting the way deposition velocities vary as a function of size. The influence of particle size on deposition and penetration across the building envelope is also discussed by analyzing the I/O ratios measured when the buildings were unoccupied, by comparing the indoor concentrations measured when the buildings were occupied and when they were not (O/U ratios), and by referring to previously published studies focussing on this topic. Except one case, I/O were found to vary in the range from 0.03 to 1.79. All O/U are greater than one and increase up to 100 with particle size. PRACTICAL IMPLICATIONS: Assessing children's total exposure requires the knowledge of outdoor and indoor air contaminant concentrations. The study presented here provides data on compared outdoor and indoor concentration levels in school buildings, as well as information on the parameters influencing the relationship between outdoor and indoor air quality. It may be used as a basis for estimating indoor concentrations from outdoor concentrations data, or as a first step in designing buildings sheltering children against atmospheric pollution.

A bstract The Argos satellite system is commonly used to track and relay behavioral data from marine mammals, but their underwater habit results in a high proportion of locations of non‐guaranteed accuracy (location classes (LC) O, A, and B). The accuracy of these locations is poorly documented in marine mammals. We assessed the accuracy of all LCs on four juvenile gray seals fitted with Argos satellite relay data loggers and held in captivity in an outdoor tank for a total of 61 seal‐days. Four hundred and twenty‐six locations were obtained from seals in captivity, and their latitude and longitude error was assessed before and after filtering, following MConnell et al. (1992). There was significantly more error in longitude than latitude in all LCs except I. C A. The ratio of the standard deviations of longitude : latitude ranged from 1.77 (LC 3) to 2.58 (LC 1). Filtering had very little effect on errors in LCs 3‐1, but in the remaining LCs filtering resulted in error reductions ranging from 8% to 63%. In LCs O, A, and B, error reduction was greater in the 95th percentile errors, especially in longitude. The averages of the latitude and longitude 68th percentile errors and those predicted by Argos (in brackets) were 226 (150), 372 (350), and 757 (1000) m for LCs 3, 2, and 1 respectively. Both latitude and longitude errors of LCs > O were normally distributed. Both filtered and unfiltered LC A locations were of a similar accuracy to LC 1 locations, and considerably better than LC O locations.