Silhouette-based object phenotype recognition using 3D shape priors

This paper tackles the novel challenging problem of 3D object phenotype recognition from a single 2D silhouette. To bridge the large pose (articulation or deformation) and camera viewpoint changes between the gallery images and query image, we propose a novel probabilistic inference algorithm based on 3D shape priors. Our approach combines both generative and discriminative learning. We use latent probabilistic generative models to capture 3D shape and pose variations from a set of 3D mesh models. Based on these 3D shape priors, we generate a large number of projections for different phenotype classes, poses, and camera viewpoints, and implement Random Forests to efficiently solve the shape and pose inference problems. By model selection in terms of the silhouette coherency between the query and the projections of 3D shapes synthesized using the galleries, we achieve the phenotype recognition result as well as a fast approximate 3D reconstruction of the query. To verify the efficacy of the proposed approach, we present new datasets which contain over 500 images of various human and shark phenotypes and motions. The experimental results clearly show the benefits of using the 3D priors in the proposed method over previous 2D-based methods. © 2011 IEEE.

基于SPEM2XPDL模型转换的软件过程执行

SPEM(software process engineering metamodel)是国际标准化组织制定的标准元模型,正日益成为软件过程建模领域的行业标准,但在过程执行方面,SPEM还存在不足.将软件过程看作是一种特殊的工作流,提出了一种应用工作流运行机制支持软件过程执行的方法.通过将SPEM模型转换为XPDL(XML process definition language)模型,利用XPDL引擎支持SPEM模型的执行.制定了SPEM和XPDL之间的映射规则,设计了转换算法并开发了转换引擎.该方法被应用在SoftPM项目中,成功地基于XPDL引擎Shark实现了对软件过程模型的执行支持.

SPEM2XPDL模型转换研究

将软件过程技术与工作流技术相结合,严格定义了SPEM2XPDL模型转换规则,设计并实现了一个SPEM2XPDL模型转换引擎.此引擎将SPEM描述的软件过程转换为符合工作流定义(XPDL)的工作流过程,从而可基于工作流管理系统对软件过程提供执行支持.SPEM模型经引擎转换后在工作流管理系统Shark上的成功执行表明了引擎的可用性.

The complete amino acid sequence of growth hormone and partial amino acid sequence of prolactin and somatolactin from sea perch (Lateolabrax japonicus)

Growth hormone (GH), prolactin (PRL) and somatolactin (SL) were purified simultaneously under alkaline condition (pH 9.0) from pituitary glands of sea perch (Lateolabrax japonicas) by a two-step procedure involving gel filtration on Sephadex G-100 and reverse-phase high-performance liquid chromatography (rpHPLC). At each step of purification, fractions were monitored by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and by immunoblotting with chum salmon GH. PRL and SL antisera. The yields of sea perch GH, PRL and SL were 4.2, 1.0 and 0.28 mg/g wet tissue, respectively. The molecular weights of 19,200 and 20,370 Da were estimated by SDS-PAGE for sea perch GH and PRL, respectively. Two forms of sea perch SL were found: one (28,400 Da) is probably glycosylated, while the other one (23,200 Da) is believed to be deglycosylated. GH bioactivity was examined by an in vivo assay. Intraperitoneal injection of sea perch GH at a dose of 0.01 and 0.1 mug/g body weight at 7-day intervals resulted in a significant increase in body weight and length of juvenile rainbow trout. The complete sea-perch GH amino acid sequence of 187 residues was determined by sequencing fragments cleaved by chemicals and enzymes. Alignment of sea-perch GH with those of other fish GHs revealed that sea-perch GH is most similar to advanced marine fish, such as tuna, gilthead sea bream, yellowfin porgy, red sea bream, bonito and yellow tail with 98.4, 96.2%, 95.7%, 95.2%, 94.1% and 91% sequence identity, respectively. Sea-perch GH has low identity to Atlantic cod (76.5%), hardtail (73.3%), flounder (68.4%), chum salmon (66.3%), carp (54%) and blue shark (38%). Partial amino-acid sequences of 127 of sea-perch PRL and the N-terminal of 16 amino-acid sequence of sea-perch SL have been determined. The data show that sea-perch PRL has a slightly higher sequence identity with tilapia PRL( 73.2%) than with chum salmon PRL(70%) in this 127 amino-acid sequence. (C) 2001 Elsevier Science B.V. All rights reserved.

鲨鱼软骨抗血管生成多肽的分离纯化及其生物活性

以血管生成为靶点的抗肿瘤策略是抗肿瘤领域的研究热点，目前已经发现许多天然和化学合成的抗血管生成药物。鲨鱼软骨作为抗新生血管生成因子的重要来源的研究已有20多年的历史，很多研究显示鲨鱼软骨提取物有抗血管生成活性。但鲨鱼软骨活性多肽的完整分子结构一直未见报道；鲨鱼软骨活性多肽干扰血管生成通路的信号途径尚不明确。 本文应用盐酸胍抽提、丙酮分级沉淀、超滤、凝胶层析等分离技术，从青鲨（Prionace glauca）软骨中分离纯化并鉴定了一种新的具有抗新生血管生成活性的多肽。经SDS-PAGE和N-末端氨基酸序列分析显示，该多肽分子量为15500 Da，采用蛋白数据库分析表明该多肽是一种新发现的鲨鱼软骨多肽（Polypeptide from Prionace glauca，PG155）。 体外实验显示，PG155抑制内皮细胞生长因子（vascular endothelial growth factor，VEGF）介导的人脐静脉内皮细胞（human umbilical vein endothelial cell ，HUVEC）迁移和管腔形成，并呈剂量依赖关系。200 μg/ml PG155对牛主动脉内皮细胞（Bovine Aortic Endothelial Cells，BAECs）和HUVECs及以下癌细胞，包括人肝癌细胞（human hepatoma Bel-7402 cells，Bel-7402）、 口腔上皮癌细胞（human oral epidermoid carcinoma KB cells ，KB）、人结肠癌细胞（human colon cancer HCT-18 cells，HCT-18）和人乳腺癌细胞（human breast MCF7 cancer cells ，MCF7）的增殖均无抑制作用，说明PG155无细胞毒作用。20 μg/ml PG155显著抑制HUVEC的迁移和管腔形成；40-80 μg/ml PG155 对VEGF 介导的HUVEC的迁移和管腔形成几乎完全抑制。 体内实验显示，PG155显著抑制斑马鱼胚胎模型新生血管生成，并呈剂量依赖关系。形态学观察表明PG155显著抑制斑马鱼胚胎肠下静脉（subintestinal vessels， SIVs）的生长，随着浓度的升高SIVs的生长可受到完全抑制。碱性磷酸酶染色分析显示，在一定浓度范围内，PG155随着浓度的升高对斑马鱼胚胎整体血管生成抑制作用依次增强。160 μg/ml PG155会引起斑马鱼胚胎心脏功能障碍。 由海洋生物中发现新的肿瘤新生血管生成抑制剂国内外的报道较少，我们的工作表明鲨鱼软骨可作为血管生成抑制剂的重要来源，鲨鱼软骨活性多肽PG155由于具有极低的细胞毒作用，并能抑制VEGF介导的血管生成过程，有希望成为一类新型抗肿瘤药物。

Freezing behaviour facilitates bioelectric crypsis in cuttlefish faced with predation risk.

Cephalopods, and in particular the cuttlefish Sepia officinalis, are common models for studies of camouflage and predator avoidance behaviour. Preventing detection by predators is especially important to this group of animals, most of which are soft-bodied, lack physical defences, and are subject to both visually and non-visually mediated detection. Here, we report a novel cryptic mechanism in S. officinalis in which bioelectric cues are reduced via a behavioural freeze response to a predator stimulus. The reduction of bioelectric fields created by the freeze-simulating stimulus resulted in a possible decrease in shark predation risk by reducing detectability. The freeze response may also facilitate other non-visual cryptic mechanisms to lower predation risk from a wide range of predator types.

Encounter success of free-ranging marine predator movements across a dynamic prey landscape

Movements of wide-ranging top predators can now be studied effectively using satellite and archival telemetry. However, the motivations underlying movements remain difficult to determine because trajectories are seldom related to key biological gradients, such as changing prey distributions. Here, we use a dynamic prey landscape of zooplankton biomass in the north-east Atlantic Ocean to examine active habitat selection in the plankton-feeding basking shark Cetorhinus maximus. The relative success of shark searches across this landscape was examined by comparing prey biomass encountered by sharks with encounters by random-walk simulations of ‘model’ sharks. Movements of transmitter-tagged sharks monitored for 964 days (16754km estimated minimum distance) were concentrated on the European continental shelf in areas characterized by high seasonal productivity and complex prey distributions. We show movements by adult and sub-adult sharks yielded consistently higher prey encounter rates than 90% of random-walk simulations. Behavioural patterns were consistent with basking sharks using search tactics structured across multiple scales to exploit the richest prey areas available in preferred habitats. Simple behavioural rules based on learned responses to previously encountered prey distributions may explain the high performances. This study highlights how dynamic prey landscapes enable active habitat selection in large predators to be investigated from a trophic perspective, an approach that may inform conservation by identifying critical habitat of vulnerable species.

Seasonal movements and behaviour of basking sharks from archival tagging: No evidence of winter hibernation

Habitat selection processes in highly migratory animals such as sharks and whales are important to understand because they influence patterns of distribution, availability and therefore catch rates. However, spatial strategies remain poorly understood over seasonal scales in most species, including, most notably, the plankton-feeding basking shark Cetorhinus maximus. It was proposed nearly 50 yr ago that this globally distributed species migrates from coastal summer-feeding areas of the northeast Atlantic to hibernate during winter in deep water on the bottom of continental-shelf slopes. This view has perpetuated in the literature even though the 'hibernation theory' has not been tested directly. We have now tracked basking sharks for the first time over seasonal scales (1.7 to 6.5 mo) using 'pop-up' satellite archival transmitters. We show that they do not hibernate during winter but instead undertake extensive horizontal (up to 3400 km) and vertical (> 750 m depth) movements to utilise productive continental-shelf and shelf-edge habitats during summer, autumn and winter. They travel long distances (390 to 460 km) to locate temporally discrete productivity 'hotspots' at shelf-break fronts, but at no time were prolonged movements into open-ocean regions away from shelf waters observed. Basking sharks have a very broad vertical diving range and can dive beyond the known range of planktivorous whales. Our study suggests this species can exploit shelf and slope-associated zooplankton communities in mesopelagic (200 to 1000 m) as well as epipelagic habitat (0 to 200 m).

Basking sharks and oceanographic fronts: quantifying associations in the north‐east Atlantic

Understanding the mechanisms linking oceanographic processes and marine vertebrate habitat use is critical to effective management of populations of conservation concern. The basking shark Cetorhinus maximus has been shown to associate with oceanographic fronts – physical interfaces at the transitions between water masses – to exploit foraging opportunities resulting from aggregation of zooplankton. However, the scale, significance and variability of these observed associations have not yet been established. Here, we quantify the influence of mesoscale (10s – 100s km) frontal activity on habitat use over timescales of weeks to months. We use animal-mounted archival tracking with composite front mapping via Earth Observation (EO) remote sensing to provide an oceanographic context to individual shark movements. We investigate levels of association with fronts occurring over two spatio-temporal scales, (i) broad-scale seasonally persistent frontal zones and (ii) contemporaneous mesoscale thermal and chl-a fronts. Using random walk simulations and logistic regression within an iterative generalised linear mixed modelling (GLMM) framework, we find that seasonal front frequency is a significant predictor of shark presence. Temporally-matched oceanographic metrics also indicate that sharks demonstrate a preference for productive regions, and associate with contemporaneous thermal and chl-a fronts more frequently than could be expected at random. Moreover, we highlight the importance of cross-frontal temperature change and persistence, which appear to interact to affect the degree of prey aggregation along thermal fronts. These insights have clear implications for understanding the preferred habitats of basking sharks in the context of anthropogenic threat management and marine spatial planning in the northeast Atlantic.

Basking sharks and oceanographic fronts: quantifying associations in the north-east Atlantic

Understanding the mechanisms linking oceanographic processes and marine vertebrate habitat use is critical to effective management of populations of conservation concern. The basking shark Cetorhinus maximus has been shown to associate with oceanographic fronts – physical interfaces at the transitions between water masses – to exploit foraging opportunities resulting from aggregation of zooplankton. However, the scale, significance and variability of these observed associations have not yet been established. Here, we quantify the influence of mesoscale (10s – 100s km) frontal activity on habitat use over timescales of weeks to months. We use animal-mounted archival tracking with composite front mapping via Earth Observation (EO) remote sensing to provide an oceanographic context to individual shark movements. We investigate levels of association with fronts occurring over two spatio-temporal scales, (i) broad-scale seasonally persistent frontal zones and (ii) contemporaneous mesoscale thermal and chl-a fronts. Using random walk simulations and logistic regression within an iterative generalised linear mixed modelling (GLMM) framework, we find that seasonal front frequency is a significant predictor of shark presence. Temporally-matched oceanographic metrics also indicate that sharks demonstrate a preference for productive regions, and associate with contemporaneous thermal and chl-a fronts more frequently than could be expected at random. Moreover, we highlight the importance of cross-frontal temperature change and persistence, which appear to interact to affect the degree of prey aggregation along thermal fronts. These insights have clear implications for understanding the preferred habitats of basking sharks in the context of anthropogenic threat management and marine spatial planning in the northeast Atlantic.

Basking sharks and oceanographic fronts: quantifying associations in the north-east Atlantic

Understanding the mechanisms linking oceanographic processes and marine vertebrate habitat use is critical to effective management of populations of conservation concern. The basking shark Cetorhinus maximus has been shown to associate with oceanographic fronts – physical interfaces at the transitions between water masses – to exploit foraging opportunities resulting from aggregation of zooplankton. However, the scale, significance and variability of these observed associations have not yet been established. Here, we quantify the influence of mesoscale (10s – 100s km) frontal activity on habitat use over timescales of weeks to months. We use animal-mounted archival tracking with composite front mapping via Earth Observation (EO) remote sensing to provide an oceanographic context to individual shark movements. We investigate levels of association with fronts occurring over two spatio-temporal scales, (i) broad-scale seasonally persistent frontal zones and (ii) contemporaneous mesoscale thermal and chl-a fronts. Using random walk simulations and logistic regression within an iterative generalised linear mixed modelling (GLMM) framework, we find that seasonal front frequency is a significant predictor of shark presence. Temporally-matched oceanographic metrics also indicate that sharks demonstrate a preference for productive regions, and associate with contemporaneous thermal and chl-a fronts more frequently than could be expected at random. Moreover, we highlight the importance of cross-frontal temperature change and persistence, which appear to interact to affect the degree of prey aggregation along thermal fronts. These insights have clear implications for understanding the preferred habitats of basking sharks in the context of anthropogenic threat management and marine spatial planning in the northeast Atlantic.

Ocean-wide tracking of pelagic sharks reveals extent of overlap with longline fishing hotspots

Overfishing is arguably the greatest ecological threat facing the oceans, yet catches of many highly migratory fishes including oceanic sharks remain largely unregulated with poor monitoring and data reporting. Oceanic shark conservation is hampered by basic knowledge gaps about where sharks aggregate across population ranges and precisely where they overlap with fishers. Using satellite tracking data from six shark species across the North Atlantic, we show that pelagic sharks occupy predictable habitat ‘hotspots’ of high space use. Movement modelling showed sharks preferred habitats characterised by strong sea-surface-temperature gradients (fronts) over other available habitats. However, simultaneous Global Positioning System (GPS) tracking of the entire Spanish and Portuguese longline-vessel fishing fleets show an 80% overlap of fished areas with hotspots, potentially increasing shark susceptibility to fishing exploitation. Regions of high overlap between oceanic tagged sharks and longliners included the North Atlantic Current/Labrador Current convergence zone and the Mid-Atlantic Ridge south-west of the Azores. In these main regions, and sub-areas within them, shark/vessel co-occurrence was spatially and temporally persistent between years, highlighting how broadly the fishing exploitation efficiently ‘tracks’ oceanic sharks within their space-use hotspots year-round. Given this intense focus of longliners on shark hotspots our study argues the need for international catch limits for pelagic sharks and identifies a future role of combining fine-scale fish and vessel telemetry to inform the ocean-scale management of fisheries.

Coprolites from the Cretaceous Bearpaw Formation of Saskatchewan

Coprolites from the Beechy Member of the Cretaceous Bearpaw Formation, southern Saskatchewan, presumably deposited by one or more species of mosasaur or large fish/shark, were recovered and analyzed using SEM/EDS. The data reveal the presence of pseudomorphous coccoid bacteria, potential filamentous bacteria, bacterial endospores and filamentous fungi. No recorded fossil plant or bone material could be identified, either within the highly compressed coprolitic mat-flattened full coprolite bolus - of recovered marine sediment encased in a mixed mat of hematite-apatite primary minerals heavily coated with Ca-smectite and nontronite, or the full coprolite bolus. The presence of fossil bacteria with morphological characteristics similar to those of endospores in other environments suggests that only robust microbial forms such as these survive diagenesis, partly with some carbon still intact, the remainder replaced with silica and iron. The data support the view that coprolites can serve as a useful source of information on the ancient microbial world. © 2012 Elsevier Ltd.