Formalizing concepts of species, sex and developmental stage in anatomical ontologies

MOTIVATION: Anatomy ontologies have a growing role in bioinformatics-for example, in indexing gene expression data in model organisms. To relate or draw conclusions from data so indexed, anatomy ontologies must be equipped with the formal vocabulary that would allow statements about meronomy to be qualified by constraints such as part of the male or part at the embryonic stage. Lacking such a vocabulary, anatomists have built this information into the structure of the ontology or into anatomical terms. For example, in the FlyBase anatomy for drosophila, the term larval abdominal segment encodes the stage in the term, while the terms male genital disc and female genital disc encode the sex. It remains implicit that a fly has one and only one of these parts during its larval stage. Such indicators of context can and should be represented explicitly in the ontology. RESULTS: The framework we have defined for anatomical ontologies allows the canonical anatomy structures of a given species to be those common to all sexes, and to have either male, female or hermaphrodite parts--but not combinations of the latter. Temporal aspects of development are addressed by associating a stage with organism parts and requiring a connected anatomy to have parts that exist at a common stage. Both sex and anatomical stage are represented by attributes. This formalization clarifies ontological structure and meaning and increases the capacity for formal reasoning about anatomy. The framework also supports generalizations such as vertebrate and invertebrate, thereby allowing the representation of anatomical structures that are common across a sub-phylum.     

Photosynthesis in leaves of the juvenile and adult phase of ivy (Hedera helix)

Abstract Photosynthetic and anatomical parameters of leaves from the juvenile and adult part of an ivy plant (Hedera helix L.) have been determined and compared with each other. Light-saturated net photosynthesis (per unit leaf area) was about 1.5 times higher in adult leaves than in juvenile ones. The lower photosynthetic capacity of juvenile leaves was caused by a lower stomatal and especially a lower residual conductance to the CO₂-transfer. This corresponds with anatomical features of the leaves, i.e. lower stomatal frequency, fewer chloroplasts per cell, and – most important – thinner leaves, as well as with a less efficient photosynthetic apparatus measured as Hill reaction of isolated broken chloroplasts and activity of ribulose bisphosphate carboxylase. No differences in the respiration in light (relative to net photosynthesis) and in the CO₂-compensation concentration could be detected between the two leaf types. These observed anatomical and photosynthetic parameters of the juvenile and adult ivy leaves resemble those reported for shade and sun leaves, respectively, although the leaves investigated originated from the same light environment.     

鹅掌柴花蜜腺的发育解剖学研究

对鹅掌柴(Scheffler octophylla Harms．)花蜜腺的发育进行解剖结构观察。鹅掌柴花盘蜜腺位于下位子房上方环绕花柱基部。蜜腺由分泌表皮、产蜜组织组成,心皮维管束与其相邻并发出一些伸入蜜腺基部的短分枝。蜜腺起源于心皮原基基部外侧的几层细胞。鹅掌柴花蜜腺为淀粉型蜜腺,淀粉粒为许多微小颗粒聚集成的复粒。原蜜汁由蜜腺基部维管束的筛管提供,达产蜜组织细胞和表皮细胞后以淀粉粒的形式贮藏。泌出的蜜汁一部分来自淀粉粒的降解,一部分来自泌蜜期输入的原蜜汁。表皮和产蜜组织细胞均具泌蜜功能。泌出的蜜汁大部分通过气孔排出,还有部分由角质层渗出。     

Angiosperm wood evolution and the potential contribution of paleontological data

Wood anatomy is often viewed as a source of independent data that may be used to assess evolutionary relationships among angiosperms. Comparative anatomical studies document suites of correlated characters that have been interpreted as general evolutionary trends, of which several have been asserted to be irreversible. Paleobotanical data summarized by Wheeler and Baas provide broad chronological corroboration of some wood anatomical trends, such as evolution from scalariform to simple perforation plates and long to short vessel elements. However, the focus on general evolutionary trends rather than on analyzing character distribution patterns in a cladistic phylogenetic context obscures a more detailed understanding of the evolution of wood anatomical features. Patterns of character evolution, including the assertions of irreversibility, need to be tested through cladistic analyses. In this paper selected wood anatomical features from families of Magnoliidae and “lower” Hamamelididae are summarized and mapped onto previously published cladograms as a preliminary means of testing previous hypotheses of wood evolution. The results show that many of the characters are homoplasious and have evolved both in accord with, and counter to, the hypothesized general trends in different groups of flowering plants. In general, changes that confirm generalized trends are more common than changes that are counter to those trends. Future studies should combine wood anatomical characters with other features as part of a cladistic analysis. Fossil woods have not yet contributed significantly to phylogenetic studies, but in the very few cases where they have been linked to fossil reproductive structures, the woods have provided a better understanding of wood anatomy in early members of some families. Data from fossil wood expand the diversity of anatomical structure known in some angiosperm taxa and thus provide additional evidence that might be used in phylogenetic analyses. Fossil woods have the greatest potential to affect phylogenetic analyses where they can be linked to other fossil organs. The best chance for establishing such a linkage is through the study of fossil charcoalified woods that co-occur with other dispersed mesofossils.     

Scanning electron microscope study of the communications between the anterior chamber and the sinus venosus sclerae in primates

We have studied the morphology of the anatomical structures that permit communication between the anterior chamber and the sinus venosus sclerae. Examination of the posterior or inner wall of this canal, represented by the sclerocorneal trabecula, in 15 species of primates and 5 adult humans, has enabled us to observe the existence of some small orifices or stomata that are the outermost part of the so-called Sondermann's canals, which in our opinion are made by the successive confluence of the interstices worked in the interior of the sclerocorneal trabecula by means of contraction of the longitudinal portion of the ciliary muscle.     

高寒地区不同海拔藏茴香茎解剖结构比较研究

采用石蜡切片法,分别对5种不同海拔高度藏茴香茎初生解剖结构进行比较研究,并用一维和二维(面积)的度量指标进行观测,以期探索随海拔升高,藏茴香茎结构的变化规律,从而探讨藏茴香对高寒气候的适应性,为藏茴香这一食用、药用植物资源开发利用提供基础资料。结果表明:藏茴香茎的初生结构由表皮、皮层、维管柱构成,随着海拔升高,藏茴香茎的表皮厚度、髓厚度、髓射线宽度以及通气组织的面积逐渐增加,而维管组织与基本组织的比值不断缩小,皮层的细胞层数、厚度逐渐下降;维管束的数量、厚度不断降低,但维管束的发育程度和导管的直径有逐渐增加的趋势。藏茴香茎表皮的不断增厚,可以减少植物体内热量的散失,并有效地降低强紫外线对植物造成的伤害。基本组织比例的增加,有利于贮藏更多的生理调节性物质,增加植物的抗寒能力;通气组织逐渐发达,可极大地降低空气在植物体内的扩散阻力,形成氧气由地上部运输到地下部的通道,还可增加植物体的浮力,减轻了植物体比重,对植物体起到了良好的支撑作用。藏茴香茎解剖结构随海拔的变化,体现了植物对环境的适应性。研究中发现的随着海拔升高,茎皮层的细胞层数和厚度以及茎中维管束的数量和厚度均下降,但维管束的发育程度和导管直径增加的现象,还有待于进一步研究。     

Biochemical Studies on the Formation of the Silkprotein

A large part, about 70 per cent, of the silkproteins produced by one silkworm is directly derived from the proteins of the mulberry leaves (direct formation), but some part of the silk-proteins, about 30 per cent, is also derived from the tissue proteins and body fluid proteins, in relation to the metamorphosis of the silkworm larva (indirect formation); there are two pathways in the formation of the silkproteins during the growth of the silkworm larva, i.e., direct formation and indirect formation.     

Errors and difficulties in the x-ray diagnosis of osteogenic sarcoma of the long tubular bones

In some cases radiodiagnosis of osteogenic sarcoma is associated with some difficulties resulting from a variety of its x-ray picture. The main factor that influences the x-ray manifestations of osteogenic sarcoma, is a neoplastic bone formation which reflects the morphological essence of this tumor. Other signs depend on a tumor site in one or another anatomical part of the tubular bone, on rates and type ot tumor growth. In some cases the combination of these signs ensures reliable diagnosis. However, along side with typical forms of osteogenic sarcoma there are also other ones which do not fit into the classical concept of this tumor type resulting in diagnostic difficulties and errors.     

The flow of bile in the human cystic duct

Clinical studies suggest that the flow of bile in the biliary system may be a contributing factor in the pathogenesis of cholelithiasis, but little is known about its transport mechanism. This paper reports a numerical study of steady flow in human cystic duct models. In order to obtain parametric data on the effects of various anatomical features in the cystic duct, idealised models were constructed, first with staggered baffles in a channel to represent the valves of Heister and lumen. The qualitative consistency of these findings are validated by modelling two of the real cystic ducts obtained from operative cholangiograms. Three-dimensional (3D) models were also constructed to further verify the two-dimensional (2D) results. It was found that the most significant geometric parameter affecting resistance is the baffle clearance (lumen size), followed by the number of baffles (number of folds in the valves of Heister), whilst the least significant ones are the curvature of the cystic duct and the angle between the neck and the gallbladder. The study presented here forms part of a larger project to understand the functions of the human cystic duct, especially the influence of its various anatomical structures on the resistance to bile flow, so that it may aid the assessment of the risk of stone formation in the gallbladder.     

Properties of the celiac trunk--anatomical study

Although anatomical properties and vessel variations of the celiac trunk are well explored in the literature, there is not so much information on the arterial diameters, and this data is important for surgical procedures and angiographic examinations. The aim of this study was to investigate properties of the celiac trunk in humans by using anatomical dissection. Ninety cadavers were dissected for the celiac trunk identification and arterial diameter measurements. The results of anatomical examination showed that in 72% of all cases the celiac trunk divides into the splenic artery and the common hepatic artery, while the left gastric artery arises as a first branch and had origin between aorta, all over the celiac trunk up to a bifurcation. From the 90 cadavers, 4 presented anatomical variations. Where normal anatomy was present, the mean length of the celiac trunk was 1.9 +/- 0.08 cm and its mean arterial diameter was 0.78 +/- 0.08 cm. The splenic artery had the largest diameter (0.61 +/- 0.05 cm) and the left gastric artery had the smallest diameter (0.38 +/- 0.03 cm). Our data represent original results about anatomical variations and arterial diameter of the celiac trunk and its main branches provided by anatomical dissection.     

Thresholds for 60 Hz magnetic field stimulation of peripheral nerves in human subjects

The goal of the research reported here is to narrow the range of uncertainty about peripheral nerve stimulation (PNS) thresholds associated with whole body magnetic field exposures at 50/60 Hz. This involved combining PNS thresholds measured in human subjects exposed to pulsed magnetic gradient fields with calculations of electric fields induced in detailed anatomical models of the body by that same exposure system. PNS thresholds at power frequencies (50/60 Hz) can be predicted from these data due to the wide range of pulse durations (70 mus to 1 ms), the length of the pulse trains (several tens of ms), and the exposure of a large part of the body to the magnetic field. These data together with the calculations of the rheobase electric field exceeded in 1% (E(1%)) of two anatomical body models, lead to a median PNS detection threshold of 47.9 +/- 4.4 mT for a uniform 60 Hz magnetic field exposure coronal to the body. The threshold for the most sensitive 1% of the population is about 27.8 mT. These values are lower than PNS thresholds produced by magnetic fields with sagittal and vertical orientations or nonuniform exposures.     

中国蒺藜科植物黄酮类化学成分分析 及其化学分类学意义

采用薄层层析和高效毛细管电泳(HPCE)等方法,对中国蒺藜科5属的代表性植物中的黄酮类成分进行了分析研究,并结合其它分类学性状进行了初步讨论,我们同意(1)支持Engler(1931)骆驼蓬亚科(Peganoideae)地位;(2)支持Takhtajan(1987)白刺科(Nitrariaceae)的恢复;(3)支持EI-Hadidi(1977)刺蒺藜科(Tribulaceae)的建立。     

Anatomical Cross-Sectional Areas and Volumes of the Muscles of the Lower Extremities

The maximum anatomical muscle cross-sectional areas and volumes of the muscles in the lower part of the body, thigh, and shank were measured by magnetic resonance imaging. The largest cross-sectional areas were 145.65 and 63 cm² in m. gluteus maximus and m. vastus, respectively, referred to as mm. adductors. In the thigh, m. vastus had the largest volume, 1505 ± 271 cm³, and in the shank, m. soleus had the largest volume, 552 ± 64 cm³. Close correlations (0.50 < R < 0.75) between the maximum areas of the lower extremity muscles were evidence for a certain relationship between the muscle cross-sections. A multiple regression equation was formulated to calculate the maximum anatomical cross-sectional areas and volumes in the muscles of the lower extremities with respect to some anthropometric parameters.     

中国棱子芹属16种1变种的果实特征及其分类学意义

采用石蜡切片法对中国棱子芹属植物16种1变种进行了果实外部形态和解剖特征观察,研究了分生果大小、果棱形状、油管数目、胚乳形状等特征,文中探讨了部分棱子芹属植物的分类地位,为该属的系统分类研究及分类问题的解决提供了佐证。主要结论如下:(1)棱子芹属植物果实解剖特征在种间存在明显差异,在种内性状比较稳定。(2)所研究的棱子芹属植物果实在外部形态和解剖结构表现出较高的多态性和一定的规律性,可以为棱子芹属近缘种的鉴定提供重要的参考性状。(3)结合果棱性状、油管数目等解剖结构和前人分子系统学研究证据,研究认为真正的棱子芹属植物其成熟果实外果皮膨胀,果棱远端具空囊,中果皮和维管束形成的内棱较不显著。     

南京2号人类头骨化石的复位和形态

南京2号人类头骨化石仅保留部分的额骨、顶骨、枕骨和颞骨,为一不完整的颅盖骨。其顶骨和枕骨有数条断裂缝,各断块之间有程度不一的错动,致使该颅盖骨显得外形异常。本项研究是对该颅盖骨的错动部分进行复位,结果表明,南京2号头骨有较大的顶骨、较小的上枕鳞相对宽度、可能较大的颅容量。这些形态提示该头骨与直立人有所不同而与早期智人相近。该头骨所具有的角圆枕、颞鳞顶缘形状、枕骨圆枕发育程度、枕骨的枕平面与项平面过渡情况、枕内隆突点与枕外隆突点的距离、头骨骨壁厚度、脑膜中动脉分支情况、头骨枕面观之轮廓线样式等形态细节,还很难作为可靠的依据把南京2号头骨鉴定为直立人。南京2号头骨很大可能是属于智人亚种(Homo sapiens sapiens)中的一员。     

The emergence of somatotopic maps of the body in S1 in rats: the correspondence between functional and anatomical organization

Most of what we know about cortical map development and plasticity comes from studies in mice and rats, and for the somatosensory cortex, almost exclusively from the whisker-dominated posteromedial barrel fields. Whiskers are the main effector organs of mice and rats, and their representation in cortex and subcortical pathways is a highly derived feature of murine rodents. This specialized anatomical organization may therefore not be representative of somatosensory cortex in general, especially for species that utilize other body parts as their main effector organs, like the hands of primates. For these reasons, we examined the emergence of whole body maps in developing rats using electrophysiological recording techniques. In P5, P10, P15, P20 and adult rats, multiple recordings were made in the medial portion of S1 in each animal. Subsequently, these functional maps were related to anatomical parcellations of S1 based on a variety of histological stains. We found that at early postnatal ages (P5) medial S1 was composed almost exclusively of the representation of the vibrissae. At P10, other body part representations including the hindlimb and forelimb were present, although these were not topographically organized. By P15, a clear topographic organization began to emerge coincident with a reduction in receptive field size. By P20, body maps were adult-like. This study is the first to describe how topography of the body develops in S1 in any mammal. It indicates that anatomical parcellations and functional maps are initially incongruent but become tightly coupled by P15. Finally, because anatomical and functional specificity of developing barrel cortex appears much earlier in postnatal life than the rest of the body, the entire primary somatosensory cortex should be considered when studying general topographic map formation in development.     

L’appareil urogénital mâle dans les planches anatomiques d’André Vésale (1514–1564)

Vesalius was perceptive, methodical and brilliant, and the greatest anatomist of all times. He created the anatomical nomenclature of organs that is still used today. He elaborated more than 300 remarkable anatomical illustrations, some of which are devoted to the male urogenital tract, providing valuable information about the state of knowledge on urology and andrology at the time.     

A carnivorous niche for Java Man? A preliminary consideration of the abundance of fossils in Middle Pleistocene Java

Considering anatomical and archaeological aspects of Homo erectus, it is likely that meat of vertebrates was an important part in its diet. Unfortunately, no or hardly any information is available for Java Man (Homo erectus). Therefore, in this paper, the Number of Identified Specimens (NISP) of five Middle Pleistocene Javanese sites are examined, and the Minimum Number of Individuals (MNI) from two of them are calculated, to acquire information about the possible ecological role of Javanese Homo erectus. Although one has to be extremely careful with the interpretation of fossil bone assemblages in order to try to gain some insight about the abundance of species in palaeocommunities, it is argued that both the NISP and the MNI indicate that the bone accumulations reflect at least two trophic levels in the ecological pyramid, that of primary and secondary consumers. The occurrences of the remains of Homo erectus are comparable with the quantity of secondary consumers, i.e., large carnivores. This could suggest that this species had, as an omnivore, a carnivorous niche, in Java.