Multi-Atlas Based Adaptive Active Contour Model with Application to Organs at Risk Segmentation in Brain MR Images

BackgroundAccurate delineation of organs at risk (OARs) is critical in radiotherapy. Manual delineation is tedious and suffers from both interobserver and intraobserver variability. Automatic segmentation of brain MR images has a wide range of applications in brain tumor radiotherapy. In this paper, we propose a multi-atlas based adaptive active contour model for OAR automatic segmentation in brain MR images.MethodsThe proposed method consists of two parts: multi-atlas based OAR contour initiation and an adaptive edge and local region based active contour evolution. In the adaptive active contour model, we define an energy functional with an adaptive edge intensity fitting force which is responsible for evaluating contour inwards or outwards, and a local region intensity fitting force which guides the evolution of the contour.ResultsExperimental results show that the proposed method achieved more accurate segmentation results in brainstem, eyes and lens automatic segmentation with the Dice Similar Coefficient (DSC) value of 87.19%, 91.96%, 77.11% respectively. Besides, the dosimetric parameters also demonstrate the high consistency of the manual OAR delineations and the auto segmentation results of the proposed method in brain tumor radiotherapy.ConclusionsThe geometric and dosimetric evaluations show the desirable performance of the proposed method on the application of OARs segmentations in brain tumor radiotherapy.     

Parallels and contrasts between intermittently freezing and drying streams: From individual adaptations to biodiversity variation

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Cranial and mandibular morphology of Middle Pleistocene cave bears (Ursus deningeri): implications for diet and evolution

ABSTRACT

Deninger’s bears (Ursus deningeri) have been studied less frequently than Ursus spelaeus s.l. Our objective is to present, for the first time, an analysis of the skull shape of U. deningeri.

Bear crania and mandibles were digitised with a Microscribe or CT-scanned and the surface models subsequently landmarked. The landmarks were chosen based on a compromise between functional morphology and sample size.

Results show that U. deningeri and U. spelaeus mandibles display very similar morphologies and allometric trajectories, both to each other and to Ailuropoda melanoleuca. It is inferred that masticatory adaptations to a herbivorous diet were already present in the Middle Pleistocene. U. deningeri displays a cranial morphology that is similar to that of U. spelaeus when comparing all species, but U. deningeri has a relatively narrower and dorsoventrally lower zygomatic arch than U. spelaeus, although the masticatory signal is less strong in the skull.

We observe intraspecific differences between different populations of U. deningeri, which could parallel the genetic diversity found in U. spelaeus. The intraspecific differences found within U. deningeri may be temporal and/or geographical in nature and could be related to the evolution of the Late Pleistocene cave bear, but this hypothesis remains to be tested.     

Homosemiosis, mimicry and superficial similarity: notes on the conceptualization of independent emergence of similarity in biology

Independent phenotypic emergence of superficially similar traits is a phenomenon frequently reported from investigations in the whole biota. Superficial similarity (including mimicry) is frequently explained as results of selective forces (predation or external environment). However, the mechanisms underlying independent (polyphyletic) emergence of similar phenotypic features remain largely unknown. A part of superficial similarity may emerge due to the occasional re-activation of latent genetic and/or developmental precursors. A specific kind of superficial similarity is represented by the phenomenon of mimicry that presupposes the attendance of a particular animal-interpreter. Despite diversity of ways how mimetic patterns are generated, they are structurally similar and often bear a common semantic message for an interpreter (predator); therefore, the term “homosemiosis” is proposed for such cases of sign-mediated correspondences where congruence of meaning appears.

Low congruence between the diversity of Waxcap (Hygrocybe spp.) fungi and vascular plants in semi-natural grasslands

The diversity of fungi in semi-natural grasslands is poorly known, partly due to difficulties in species identification in the field but also because there are few specialists available. Diversity assessments of grassland fungi would be facilitated if a potential surrogate group for fungal diversity could be identified. The aim of this study was to assess whether plant diversity patterns in semi-natural grasslands are congruent with diversity patterns of Waxcap (Hygrocybe spp.) fungi. Waxcaps, together with several other groups of fungi (e.g. the genera Entoloma, Dermoloma, Camarophyllopsis, and the families Clavariaceae and Geoglossaceae) have habitat requirements similar to many plants typical for semi-natural grasslands and they are all threatened by ceased management and nutrient enrichment. Diversity data from 31 semi-natural grasslands in southern Sweden were used to examine if there is congruence in species richness, nestedness, β-diversity and species composition between plants and Hygrocybe fungi. Species richness of Hygrocybe was significantly positively correlated with plant richness, although the relationship was not strong (r²=0.14). Both plant and Hygrocybe species composition was significantly nested, i.e. species-poor sites contain a subset of species from species-rich sites, which suggests that rare species mostly occur in the species-rich sites. A species similarity analysis between the grassland sites showed that there is low overlap between species composition of plants and Hygrocybe, indicating that conservation decisions based solely on plants may not fulfil the requirements of the Hygrocybe species. The conclusion is that there is low congruence between plant and Hygrocybe species diversity, making plants a poor surrogate group for Hygrocybe fungi, and probably also for other grassland fungi.     

Distance decay of similarity among European urban floras: the impact of anthropogenic activities on β diversity

Aim We examine how two categories of non‐native species (archaeophyte and neophyte, introduced before and after ad 1500, respectively) have had different impacts on β diversity across European urban floras. Our goal is to use the unique biological perspective provided by urban areas, and the contrasting historical and geographical perspectives provided by archaeophytes and neophytes, to infer how non‐native species will impact upon β diversity in the future. Location Twenty‐two urban areas located in seven European countries. Methods We used the β‐sim dissimilarity index to estimate the level of β diversity for 231 unique pair‐wise combinations of 22 urban floras. We examined bivariate plots of dissimilarity by geographical separation of city centres to evaluate distance decay of similarity for native species, archaeophytes and neophytes. Results Based on average percentages, 52.8% (SD = 8.2%) of species in the urban floras were identified as non‐native with 28.3% (SD = 6.9%) classified as neophytes and 24.5% (SD = 4.9%) as archaeophytes. Relative to native species, across urban floras, archaeophytes were associated with higher compositional similarity and weaker distance decay patterns, whereas neophytes were associated with lower compositional similarity and stronger distance decay patterns. Main conclusions Across European urban floras, archaeophytes and neophytes occurred in similar numbers but archaeophytes were consistently associated with lower β diversity and neophytes with higher β diversity. Thus, the impact of non‐native species on β diversity can be determined, at least in part, through their historical and geographical associations with anthropogenic activities. If archaeophytes represent the long‐term biogeographical outcome for human commensal species, neophytes could develop similar patterns. The consequences, however, are likely to be more substantial ecologically and geographically due to the increasing numbers of neophytes and their global anthropogenic associations. Nevertheless, at present, our findings suggest that, based on occurrence information, neophytes have not achieved this state with European urban floras retaining regionally distinct assemblages of neophytes.     

Characterization of zygotic and nucellar seedlings from sour orange-like citrus rootstock candidates using RAPD and EST-SSR markers

A series of crosses designed for introgression of mandarin (Citrus reticulata Blanco) and pummelo (C. maxima Merr.) germplasm, to develop an alternative rootstock to sour orange (C. aurantium L.), were carried out. It is necessary to identify those hybrids that yield nucellar seedlings for rootstock propagation. Rootstocks can be developed through traditional plant breeding methods; however, the ability to screen and select for economically important traits (such as production of true nucellar seedlings) in an efficient fashion is limited by the difficulties of screening techniques based on whole plant performance. To address these problems, we have used randomly amplified polymorphic DNA (RAPD) and fluorescently labeled expressed sequence tag simple sequence repeat (EST-SSR) molecular markers. A total of 204 individual seedlings obtained from 34 hybrid parental plants were successfully characterized using five RAPD primers. Ten hybrid parents and their progenies, found to be genetically similar among themselves, were selected for more scrutiny using eight EST-SSR primer pairs. The degrees of genetic similarity (nucellars) among progeny seedlings were determined and compared with that of their parents. The mean genetic similarity varied from 67–99% among the selected rootstock candidates screened. The genetic similarity relationship identified using RAPD and EST-SSR molecular markers was highly concordant (p = 0.001). Two elite rootstock candidates (B6R5T56; B6R11T129) that seem to be ideal for future mandarin and pummelo derived rootstock breeding programs have been identified. Our results indicate that either RAPD or EST-SSR analyses could be equally successful in identifying true nucellars among the progenies obtained from introgression crosses of mandarin and pummelo, thus improving the accuracy of early selection in a citrus rootstock breeding program.     

The decay of similarity with geographical distance in parasite communities of vertebrate hosts

Aim The rate at which similarity in species composition decays with increasing distance was investigated among communities of parasitic helminths in different populations of the same host species. Rates of distance decay in similarity of parasite communities were compared between populations of fish and mammal hosts, which differ with respect to their vagility and potential to disperse parasite species over large distances. Location Data on helminth communities were compiled for several populations of three mammalian host species (Ondatra zibethicus, Procyon lotor and Canis latrans) and three fish host species (Perca flavescens, Catostomus commersoni and Esox lucius) from continental North America. Methods Distances between localities and similarity in the composition of helminth communities, the latter computed using the Jaccard index, were calculated for all possible pairs of host populations within each host species. Similarity values were then regressed against distance to see if they decayed at exponential rates, as reported for plant communities; the significance of the regressions was assessed using randomization tests. Results The number of hosts examined per population did not correlate with the number of helminth species found per population, and thus sampling effort is unlikely to have confounded the results. In four (two mammals and two fish) of the six host species, similarity in helminth communities decayed exponentially with distance. When the log of similarity is plotted against untransformed distance, the slopes obtained for the two fish species are lower than those obtained for the two mammalian host species. Main conclusions Similarity in the composition of parasite communities appears to decay exponentially with increasing distance in some host species, but not in all host species. The rate of decay is not necessarily associated with the vagility of the host. Although distance decay of similarity is generally occurring, it seems that other ecological processes, related either to the host or its habitat, can obscure it.     

-3/2方自疏法则的机理与普适性

根据植物构件性理论,对经验规律-3/2方自疏法则进行了理论推导,对-3/2方自疏法则以前不能解释的实验结果进行了理论分析,并以春小麦（Triticum aestiunm L.）为材料,设置了4个密度梯度的实验,定期测定个体形态及种群数量指标,证明了-3/2方自疏法法则对春小麦作物种群的适用性,同时,基于所测定的植株形态数据,结合数值的量纲变化特点对-3/2方自疏法则的普适性进行了理论解释。     

新疆山地苔藓植物区系相似性的数量分析

应用相似性系数分析方法,对新疆阿尔泰山、天山和昆仑山苔藓植物区系间的相似性进行了定量研究。结果表明：阿尔泰山与天山苔藓植物区系之间的相似性最大,其科、属、种的相似性系数分别为86．11％,64．45％和50．45％,表明阿尔泰山与天山苔藓植物区系有较近的亲缘关系;昆仑山与天山苔藓植物区系间的相似性大于它与阿尔泰山间的相似性。上述结果与对三大山地气候条件的分析结果相一致。