Learning Probabilistic Features for Robotic Navigation Using Laser Sensors

SLAM is a popular task used by robots and autonomous vehicles to build a map of an unknown environment and, at the same time, to determine their location within the map. This paper describes a SLAM-based, probabilistic robotic system able to learn the essential features of different parts of its environment. Some previous SLAM implementations had computational complexities ranging from O(Nlog(N)) to O(N²), where N is the number of map features. Unlike these methods, our approach reduces the computational complexity to O(N) by using a model to fuse the information from the sensors after applying the Bayesian paradigm. Once the training process is completed, the robot identifies and locates those areas that potentially match the sections that have been previously learned. After the training, the robot navigates and extracts a three-dimensional map of the environment using a single laser sensor. Thus, it perceives different sections of its world. In addition, in order to make our system able to be used in a low-cost robot, low-complexity algorithms that can be easily implemented on embedded processors or microcontrollers are used.     

Fuzzy ART-based place recognition for visual loop closure detection

The automatic place recognition problem is one of the key challenges in SLAM approaches for loop closure detection. Most of the appearance-based solutions to this problem share the idea of image feature extraction, memorization, and matching search. The weakness of these solutions is the storage and computational costs which increase drastically with the environment size. In this regard, the major constraints to overcome are the required visual information storage and the complexity of similarity computation. In this paper, a novel formulation is proposed that allows the computation time reduction while no visual information are stored and matched explicitly. The proposed solution relies on the incremental building of a bio-inspired visual memory using a Fuzzy ART network. This network considers the properties discovered in primate brain. The performance evaluation of the proposed method has been conducted using two datasets representing different large scale outdoor environments. The method has been compared with RatSLAM and FAB-MAP approaches and has demonstrated a decreased time and storage costs with broadly comparable precision recall performance.     

Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max

Background

Quantitative trait locus (QTL) mapping is an efficient approach to discover the genetic architecture underlying complex quantitative traits. However, the low density of molecular markers in genetic maps has limited the efficiency and accuracy of QTL mapping. In this study, specific length amplified fragment sequencing (SLAF-seq), a new high-throughput strategy for large-scale SNP discovery and genotyping based on next generation sequencing (NGS), was employed to construct a high-density soybean genetic map using recombinant inbred lines (RILs, Luheidou2 × Nanhuizao, F_5:8). With this map, the consistent QTLs for isoflavone content across various environments were identified.

Results

In total, 23 Gb of data containing 87,604,858 pair-end reads were obtained. The average coverage for each SLAF marker was 11.20-fold for the female parent, 12.51-fold for the male parent, and an average of 3.98-fold for individual RILs. Among the 116,216 high-quality SLAFs obtained, 9,948 were polymorphic. The final map consisted of 5,785 SLAFs on 20 linkage groups (LGs) and spanned 2,255.18 cM in genome size with an average distance of 0.43 cM between adjacent markers. Comparative genomic analysis revealed a relatively high collinearity of 20 LGs with the soybean reference genome. Based on this map, 41 QTLs were identified that contributed to the isoflavone content. The high efficiency and accuracy of this map were evidenced by the discovery of genes encoding isoflavone biosynthetic enzymes within these loci. Moreover, 11 of these 41 QTLs (including six novel loci) were associated with isoflavone content across multiple environments. One of them, qIF20-2, contributed to a majority of isoflavone components across various environments and explained a high amount of phenotypic variance (8.7% - 35.3%). This represents a novel major QTL underlying isoflavone content across various environments in soybean.

Conclusions

Herein, we reported a high-density genetic map for soybean. This map exhibited high resolution and accuracy. It will facilitate the identification of genes and QTLs underlying essential agronomic traits in soybean. The novel major QTL for isoflavone content is useful not only for further study on the genetic basis of isoflavone accumulation, but also for marker-assisted selection (MAS) in soybean breeding in the future.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1086) contains supplementary material, which is available to authorized users.     

Spatial mapping memory: methods used to determine the existence and type of cognitive maps in arboreal mammals

1. Researchers have used multiple methods to understand spatial mapping memory used by arboreal mammals for orientation: the change-point test, measures of path tortuosity, field experiments with feeding platforms, nearest-neighbour feeding tree methods, complex calculations of travel route parameters, and theoretical models.
2. This literature review provides details of all of these methods, highlights previous results from spatial mapping memory studies, and discusses perspectives for future studies.
3. Previous studies have shown that various arboreal mammals, mostly in the order Primates, can memorise spatial environments using a cognitive map. Two types of maps are characterised: the topological map, based on landmarks and reused routes, and the Euclidean map, including the ability to create shortcuts by measuring distances and distinguishing between directions. Most of the studies showed that mammals do not travel randomly but, due to the difficulty of determining which spatial map is used, the use of cognitive maps remains hypothetical.
4. When studying spatial mapping memory, data collection and analysis should account for the species’ characteristics, such as the home-range size, food preferences, and types of movements. The role of sensory cues (visual, auditory, olfactory) is crucial to understanding spatial orientation. The most relevant way to determine how arboreal mammals orientate themselves in space is by using a mix of methods: random theoretical models, collecting data in a controlled environment, measuring different parameters of travel patterns, and considering the use of sensory cues and environmental factors of the study sites.
5. Research pertaining to spatial mapping memory in arboreal mammals and forest-dwelling mammals is important for understanding cognitive abilities in mammal species, and more studies are needed in mammals of various orders.

     

QTL mapping with near-isogenic lines in maize

A set of 89 near-isogenic lines (NILs) of maize was created using marker-assisted selection. Nineteen genomic regions, identified by restriction fragment length polymorphism loci and chosen to represent portions of all ten maize chromosomes, were introgressed by backcrossing three generations from donor line Tx303 into the B73 genetic background. NILs were genotyped at an additional 128 simple sequence repeat loci to estimate the size of introgressions and the amount of background introgression. Tx303 introgressions ranged in size from 10 to 150 cM, with an average of 60 cM. Across all NILs, 89% of the Tx303 genome is represented in targeted and background introgressions. The average proportion of background introgression was 2.5% (range 0–15%), significantly lower than the expected value of 9.4% for third backcross generation lines developed without marker-assisted selection. The NILs were grown in replicated field evaluations in two years to map QTLs for flowering time traits. A parallel experiment of testcrosses of each NIL to the unrelated inbred, Mo17, was conducted in the same environments to map QTLs in NIL testcross hybrids. QTLs affecting days to anthesis, days to silking, and anthesis-silk interval were detected in both inbreds and hybrids in both environments. The testing environments differed dramatically for drought stress, and different sets of QTLs were detected across environments. Furthermore, QTLs detected in inbreds were typically different from QTLs detected in hybrids, demonstrating the genetic complexity of flowering time. NILs can serve as a valuable genetic mapping resource for maize breeders and geneticists. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

邻体干扰模型的改进及其在营林中的应用

 本文研究了植物群落中优势种个体间的相互干扰问题。在前人工作基础上提出了邻体干扰指数的改进模型及野外资料搜集方法。保证了数学模型的逻辑一致性,增加了生态学的解释意义。本文还讨论了邻体干扰效应模型的选择问题,进而提出了约束条件下的材积增长的数学优化模型。以四川省重庆市缙云山马尾松林为例,进行了实例研究。     

Simultaneous Optimization of Robot Structure and Control System Using Evolutionary Algorithm

The simultaneous optimization of a robot structure and control system to realize effective mobility in an outdoor environment is investigated. Recently, various wheeled mechanisms with passive and/or active linkages for outdoor environments have been developed and evaluated. We developed a mobile robot having six active wheels and passive linkage mechanisms, and experimentally verified its maneuverability in an indoor environment. However, there are various obstacles in outdoor environment and the travel ability of a robot thus depends on its mechanical structure and control system.We proposed a method of simultaneously optimizing mobile robot structure and control system using an evolutionary algorithm. Here, a gene expresses the parameters of the structure and control system. A simulated mobile robot and controller are based on these parameters and the behavior of the mobile robot is evaluated for three typical obstacles. From the evaluation results, new genes are created and evaluated repeatedly. The evaluation items are travel distance, travel time, energy consumption, control accuracy, and attitude of the robot.Effective outdoor travel is achieved around the 80th generation, after which, other parameters are optimized until the 300th generation. The optimized gene is able to pass through the three obstacles with low energy consumption, accurate control, and stable attitude.     

不同生长环境下水稻最上节间长度QTL定位研究

利用由98 个家系组成的 Nipponbare/Kasalath//Nipponbare 回交重组自交系(backcross inbred lines, BIL)作图群体(BC1F12和BC1F13)和复合区间作图方法(CIM), 在3种不同的生长环境下对水稻最上节间长度进行了 QTL 分析。结果表明, 3种不同的生长环境共检测到 13 个 QTL , 分布于第 1, 2, 3, 5, 6, 8, 10, 11 染色体上, 解释性状变异的 3.97%～15.21%。其中qUIL-6在3种不同生长环境中均检测到, qUIL-1a, qUIL-3a, qUIL-3b和 qUIL-10a 等4个位点在两种不同生长环境中均被检测到, 说明这些 QTL 位点受环境影响较小, 表达较为稳定。     

High-Resolution Physical Map of the Immunoglobulin λ Variant Gene Cluster Assembled by Quantitative DNA Fiber Mapping

Quantitative DNA fiber mapping (QDFM) allows rapid construction of near-kilobase-resolution physical maps by hybridizing specific probes to individual stretched DNA molecules. We evaluated the utility of QDFM for the large-scale physical mapping of a rather unstable, repeat-rich 850-kb region encompassing the immunoglobulin λ variant (IGLV) gene segments. We mapped a minimal tiling path composed of 32 cosmid clones to three partially overlapping yeast artificial chromosome (YAC) clones and determined the physical size of each clone, the extent of overlap between clones, and contig orientation, as well as the sizes of gaps between adjacent contigs. Regions of germline DNA for which we had no YAC coverage were characterized by cosmid to cosmid hybridizations. Compared to other methods commonly used for physical map assembly, QDFM is a rapid, versatile technique delivering unambiguous data necessary for map closure and preparation of sequence-ready minimal tiling paths.     

Environment Recognition System Based on Multiple Classification Analyses for Mobile Robots

Various mechanisms have recently been developed that combine linkage mechanisms and wheels. In particular, the combination of passive linkage mechanisms and small wheels is a main research trend because standard wheeled mobile mechanisms find it difficult to move on rough terrain. In our previous research, a six-wheel mobile robot employing a passive linkage mechanism has been developed to enhance maneuverability and was able to climb over a 0.20 m bump and stairs. We designed a hybrid velocity and torque controller using a neural network since simple velocity controllers fail to climb up. In this paper, we propose an environment recognition system for a wheeled mobile robot that consists of multiple classification analyses to make the robot more adaptive to various environments by selecting a suitable system such as decision making, navigation and controller using the result of the environment recognition system. We evaluate the recognition performance in operation environments; slopes, bumps and stairs by comparing principle component, k-means and self-organizing map analyses.     

Neighborhood health‐promoting resources and obesity risk (the multi‐ethnic study of atherosclerosis)

Objective:

While behavioral change is necessary to reverse the obesity epidemic, it can be difficult to achieve and sustain in unsupportive residential environments. This study hypothesized that environmental resources supporting walking and a healthy diet are associated with reduced obesity incidence.

Design and Methods:

Data came from 4,008 adults aged 45‐84 at baseline who participated in a neighborhood ancillary study of the Multi‐Ethnic Study of Atherosclerosis. Participants were enrolled at six study sites at baseline (2000‐2002) and neighborhood scales were derived from a supplementary survey that asked community residents to rate availability of healthy foods and walking environments for a 1‐mile buffer area. Obesity was defined as BMI ≥ 30 kg/m². Associations between incident obesity and neighborhood exposure were examined using proportional hazards and generalized linear regression.

Results:

Among 4,008 nonobese participants, 406 new obesity cases occurred during 5 years of follow‐up. Neighborhood healthy food environment was associated with 10% lower obesity incidence per s.d. increase in neighborhood score. The association persisted after adjustment for baseline BMI and individual‐level covariates (hazard ratio (HR) 0.88, 95% confidence interval (CI): 0.79, 0.97), and for correlated features of the walking environment but CIs widened to include the null (HR 0.89, 95% CI: 0.77, 1.03). Associations between neighborhood walking environment and lower obesity were weaker and did not persist after adjustment for correlated neighborhood healthy eating amenities (HR 0.98, 95% CI: 0.84, 1.15).

Conclusions:

Altering the residential environment so that healthier behaviors and lifestyles can be easily chosen may be a precondition for sustaining existing healthy behaviors and for adopting new healthy behaviors.     

Efficient mapping of ligand migration channel networks in dynamic proteins

For many proteins such as myoglobin, the binding site lies in the interior, and there is no obvious route from the exterior to the binding site in the average structure. Although computer simulations for a limited number of proteins have found some transiently open channels, it is not clear if there exist more channels elsewhere or how the channels are regulated. A systematic approach that can map out the whole ligand migration channel network is lacking. Ligand migration in a dynamic protein resembles closely a well-studied problem in robotics, namely, the navigation of a mobile robot in a dynamic environment. In this work, we present a novel robotic motion planning inspired approach that can map the ligand migration channel network in a dynamic protein. The method combines an efficient spatial mapping of protein inner space with a temporal exploration of protein structural heterogeneity, which is represented by a structure ensemble. The spatial mapping of each conformation in the ensemble produces a partial map of protein inner cavities and their inter-connectivity. These maps are then merged to form a super map that contains all the channels that open dynamically. Results on the pathways in myoglobin for gaseous ligands demonstrate the efficiency of our approach in mapping the ligand migration channel networks. The results, obtained in a significantly less amount of time than trajectory-based approaches, are in agreement with previous simulation results. Additionally, the method clearly illustrates how and what conformational changes open or close a channel.     

Effects of individual size,local competition and canopy closure on the stem volume growth in a monoclonal Japanese cedar (<Emphasis Type="Italic">Cryptomeria japonica</Emphasis> D. Don) plantation

We studied how the dominant factor affecting stem volume growth changes during stand development in a monoclonal stand of Cryptomeria japonica D. Don. Stem analysis was used to compare growth history of trees in an unthinned plot (closed canopy) and a thinned plot (open canopy). In the unthinned plot, the dominant factor affecting stem volume growth was basal area (BA) before canopy closure, whereas neighborhood competition index (CI) was the dominant factor after canopy closure. In contrast, the dominant factor affecting stem volume in the thinned plot was BA throughout stand development. Spearman’s rank correlation coefficient between BA and CI continued to increase after canopy closure and size rank among individuals became increasingly fixed. Our results indicated that stem volume growth shifts from size-dependent to competition-dependent growth at canopy closure. The apparent correlation between tree size and growth rate observed in many previous studies may be the result of competition-mediated positive feedback between size and growth.     

Comparative mapping of QTLs for agronomic traits of rice across environments by using a doubled-haploid population

We report here the RFLP mapping of quantitative trait loci (QTLs) which affect some important agronomic traits in cultivated rice. An anther culture-derived doubled-haploid (DH) population was established from a cross between indica and japonica rice varieties. A molecular linkage map comprising 137 markers was constructed based on this population which covered the rice genome at intervals of 14.8 cM on average. The linkage map was used to locate QTLs for such important agronomic traits as heading date, plant height, number of spikelets per panicle, number of grains per panicle, 1 000-grain weight and the percentage of seed set, by interval mapping. Evidence of genotype-by-environment interaction was found by comparing QTL maps of the same population grown in three diverse environments. A total of 22 QTLs for six agronomic traits was detected which were significant in at least one environment, but only seven were significant in all three environments; seven were significant in two environments and eight could only be detected in a single environment. However, QTLs-by-environment interaction was trait dependent. QTLs for spikelets and grains per panicle were common across environments while traits like heading date and plant height were more sensitive to environment. Received: 22 February 1996 / Accepted: 10 May 1996     

Antagonistic Pleiotropy and Fitness Trade-Offs Reveal Specialist and Generalist Traits in Strains of Canine Distemper Virus

Theoretically, homogeneous environments favor the evolution of specialists whereas heterogeneous environments favor generalists. Canine distemper is a multi-host carnivore disease caused by canine distemper virus (CDV). The described cell receptor of CDV is SLAM (CD150). Attachment of CDV hemagglutinin protein (CDV-H) to this receptor facilitates fusion and virus entry in cooperation with the fusion protein (CDV-F). We investigated whether CDV strains co-evolved in the large, homogeneous domestic dog population exhibited specialist traits, and strains adapted to the heterogeneous environment of smaller populations of different carnivores exhibited generalist traits. Comparison of amino acid sequences of the SLAM binding region revealed higher similarity between sequences from Canidae species than to sequences from other carnivore families. Using an in vitro assay, we quantified syncytia formation mediated by CDV-H proteins from dog and non-dog CDV strains in cells expressing dog, lion or cat SLAM. CDV-H proteins from dog strains produced significantly higher values with cells expressing dog SLAM than with cells expressing lion or cat SLAM. CDV-H proteins from strains of non-dog species produced similar values in all three cell types, but lower values in cells expressing dog SLAM than the values obtained for CDV-H proteins from dog strains. By experimentally changing one amino acid (Y549H) in the CDV-H protein of one dog strain we decreased expression of specialist traits and increased expression of generalist traits, thereby confirming its functional importance. A virus titer assay demonstrated that dog strains produced higher titers in cells expressing dog SLAM than cells expressing SLAM of non-dog hosts, which suggested possible fitness benefits of specialization post-cell entry. We provide in vitro evidence for the expression of specialist and generalist traits by CDV strains, and fitness trade-offs across carnivore host environments caused by antagonistic pleiotropy. These findings extend knowledge on CDV molecular epidemiology of particular relevance to wild carnivores.     

Genotype-environment interaction for quantitative trait loci affecting life span in Drosophila melanogaster

The nature of genetic variation for Drosophila longevity in a population of recombinant inbred lines was investigated by estimating quantitative genetic parameters and mapping quantitative trait loci (QTL) for adult life span in five environments: standard culture conditions, high and low temperature, and heat-shock and starvation stress. There was highly significant genetic variation for life span within each sex and environment. In the analysis of variance of life span pooled over sexes and environments, however, the significant genetic variation appeared in the genotype x sex and genotype x environment interaction terms. The genetic correlation of longevity across the sexes and environments was not significantly different from zero in these lines. We estimated map positions and effects of QTL affecting life span by linkage to highly polymorphic roo transposable element markers, using a multiple-trait composite interval mapping procedure. A minimum of 17 QTL were detected; all were sex and/or environment-specific. Ten of the QTL had sexually antagonistic or antagonistic pleiotropic effects in different environments. These data provide support for the pleiotropy theory of senescence and the hypothesis that variation for longevity might be maintained by opposing selection pressures in males and females and variable environments. Further work is necessary to assess the generality of these results, using different strains, to determine heterozygous effects and to map the life span QTL to the level of genetic loci.     

Comparative mapping of QTLs for agronomic traits of rice across environments using a doubled haploid population

We report here the RFLP mapping of quantitative triat loci (QTLs) that affect some important agronomic traits in cultivated rice. An anther culturederived doubled haploid (DH) population was established from a cross between an indica and a japonica rice variety. On the basis of this population a molecular linkage map comprising 137 markers was constructed that covered the rice genome at intervals of 14.8cM on average. Interval mapping of the linkage map was used to locate QTLs for such important agronomic traits as heading date, plant height, number of spikelets per panicle, number of grains Per panicle, 1000-grain weight and percentage of seed set. Evidence of genotype-byenvironment interaction was found by comparing QTL maps of the same population grown in three diverse environments. A total of 22 QTLs for six agronomic traits were detected that were significant in at least one environment, but only 7 were significant in all three environments, 7 were significant in two environments and 8 could only be detected in a single environment. However, QTL-by-environment interaction was traitdependent. QTLs for spikelets and grains per panicle were common across environments, while traits like heading date and plant height were more sensitive to environment.     

Predicting the size of the progeny mapping population required to positionally clone a gene

A key frustration during positional gene cloning (map-based cloning) is that the size of the progeny mapping population is difficult to predict, because the meiotic recombination frequency varies along chromosomes. We describe a detailed methodology to improve this prediction using rice (Oryza sativa L.) as a model system. We derived and/or validated, then fine-tuned, equations that estimate the mapping population size by comparing these theoretical estimates to 41 successful positional cloning attempts. We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size. We developed a meiotic recombination frequency map (MRFM) for approximately 1400 marker intervals in rice and anchored each published allele onto an interval on this map. We show that neighborhood recombination frequencies (R-map, >280-kb segments) extracted from the MRFM, in conjunction with the validated formulas, better predicted the mapping population size than the genome-wide average recombination frequency (R-avg), with improved results whether the recombination frequency was calculated as genes/cM or kb/cM. Our results offer a detailed road map for better predicting mapping population size in diverse eukaryotes, but useful predictions will require robust recombination frequency maps based on sampling more progeny.     

Flowering time quantitative trait Loci analysis of oilseed brassica in multiple environments and genomewide alignment with Arabidopsis

Most agronomical traits exhibit quantitative variation, which is controlled by multiple genes and are environmentally dependent. To study the genetic variation of flowering time in Brassica napus, a DH population and its derived reconstructed F(2) population were planted in 11 field environments. The flowering time varied greatly with environments; 60% of the phenotypic variation was attributed to genetic effects. Five to 18 QTL at a statistically significant level (SL-QTL) were detected in each environment and, on average, two new SL-QTL were discovered with each added environment. Another type of QTL, micro-real QTL (MR-QTL), was detected repeatedly from at least 2 of the 11 environments; resulting in a total of 36 SL-QTL and 6 MR-QTL. Sixty-three interacting pairs of loci were found; 50% of them were involved in QTL. Hundreds of floral transition genes in Arabidopsis were aligned with the linkage map of B. napus by in silico mapping; 28% of them aligned with QTL regions and 9% were consistent with interacting loci. One locus, BnFLC10, in N10 and a QTL cluster in N16 were specific to spring- and winter-cropped environments respectively. The number of QTL, interacting loci, and aligned functional genes revealed a complex genetic network controlling flowering time in B. napus.     

Detection of QTL for six yield-related traits in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis>) using DH and immortalized F<Subscript>2</Subscript> populations

The inheritance of yield-related traits in rapeseed (Brassica napus) is poorly understood, and the investigations on mapping of quantitative trait loci (QTL) for such traits are only few. QTL related to six traits were mapped which include plant height (PH), height of lowest primary effective branch (HPB), length of main inflorescence (LMI), silique length (SL), number of primary branches (FB) and silique density (SD). A set of 258 doubled haploid (DH) lines derivatives of a cross between a canola variety Quantum and a resynthesized B. napus line No.2127-17, and a fixed immortalized F₂ (designated as IF₂) population generated by randomly permutated intermating of these DHs were investigated. A genetic linkage map was constructed using 208 SSR and 189 SRAP markers for the DH population. Phenotypic data were collected from three environments for the two populations. Using composite interval mapping analyses, 30 and 22 significant QTL were repeatedly detected across environments for the six traits in the DH and IF₂ populations, respectively. Twenty-nine QTL were common between the two populations. The directions of parental contribution for all common QTL were the same, showing a great potential for marker-assisted selection in improving these traits. Some chromosomal regions harbor QTL for multiple traits, which were consistent with significant phenotypic correlations observed among traits. The results provided a better understanding of the genetic factors controlling yield-related traits in rapeseed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.