人类股骨断面面积与形状的不对称性——基于三维激光扫描的形态测量分析

人类股骨横断面面积、形状及其左右侧差异记载的人类演化、人群差异及生存活动的重要信息一直为古人类学研究所关注。多年来, 对股骨断面的研究通常采用破坏性地切割或者制作模型的方法。本文利用三维激光表面扫描技术, 无损、快捷、方便地获取了20对现代中国人左右侧股骨外轮廓的三维数据, 采用CAD软件及几何形态测量方法对两侧股骨断面轮廓的大小及形状进行了对比和分析。初步研究结果发现: 两侧股骨的横断面相对面积差异极其显著, 绝对面积差异不显著, 不对称方式表现为波动不对称性, 而不是偏向不对称性; 个体之间两侧股骨横断面外轮廓形状的波动不对称性极其显著, 偏向不对称性虽有差异但不显著; 平均形状和面积分析结果似乎表明股骨稍有偏左侧优势。虽然本文所采用的标本量有限, 所得出的结论需要更多标本的进一步验证, 但是, 本文的研究结果提示利用三维激光扫描技术获取股骨横断面外轮廓数据, 并采用形态测量方法分析确实能够揭示出一些以往研究方法不能发现的重要信息, 这种研究骨骼不对称性的新方法值得进一步的应用。     

3D虚拟复原精度的差异对头骨测量数值的影响——以Mimics软牛为例

近年来,根据三维软件虚拟复原的头骨来获取测量数据的方法被越来越多地应用在古生物,特别是古人类学的研究中,然而对于三维软件不同精度虚拟复原的头骨,其测量数值是否有差异,研究者并不是很清楚。本文以Mimics软件为例,根据其复原模型简化规则,选择未精简的最佳精度模型作为标准进行配对t检验或非参数检验,通过对43例云南人头骨的顶骨矢状弦长、颅周长、头盖部面积、乳突小房表面积、颅容量、乳突小房体积等六个测量项目的对比和分析,对Mimics软件低、中、高、最佳四种精度3D虚拟复原头骨间的测量差异进行了研究。结果显示：颅周长、头盖部面积、颅容量、乳突小房体积四项的所有简化精度模型的测量数据均与最佳精度模型测量数据的差异具有显著性;而除高精度组外,顶骨矢状弦长及乳突小房表面积的其余精度组测量数据均与最佳精度组差异具有显著性;此外,顶骨矢状弦长、颅周长、头盖部面积、颅容量的简化精度与最佳精度的测量差异占比均小于3%.而乳突小房表面积的低精度与最佳精度测量差异占比可超过50%,乳突小房体积的低精度与最佳精度测量差异占比可超过120%。这一结果提示我们,在测量Mimics复原的三维模型时,体量大差异小的测量项可以在较低精度的复原模型上进行测量;而对头骨内部腔窦这样体量小表面粗糙的结构,复原模型的精度选择及测量数据比较需要格外谨慎。     

Improving the spatial orientation of human teeth using a virtual 3D approach

Since teeth are resistant to decomposition processes, they provide important and at times unique sources of information about fossil humans. Fortunately, dental remains reflect significant evolutionary changes. These changes make a very important and often exclusive contribution to the definition of new taxa or the attribution of fossil specimens to existing taxa.The traditional approach to dental morphometric analyses usually focuses on the recording of several measures of the tooth with calipers, especially the two basic crown diameters (buccolingual and mesiodistal). However, since these measures do not adequately represent the complex morphology of the tooth, 2D images and 3D digital models of dental morphology have been used. For both types of analysis, the possibility of correctly comparing homologous teeth depends on the adoption of a common orientation system. The lack of such a system makes it difficult to compare the results of different studies.Here we describe a new method for orienting teeth specifically devised for the upper and lower first molar (M1). Samples of unworn maxillary (n = 15) and mandibular (n = 15) first molars of modern humans were scanned with a Roland Picza 3D digitizer. The 3D virtual models were used to compare our new orientation method with those proposed in the literature. The new orientation system, which meets a geometric criterion, is based on three points identified on the cervical line and ensures acceptable repeatability of the spatial positioning and orientation independent of the shape and wear of the first molar under investigation. This orientation system is a first step toward the creation of a virtual set of hominid and fossil human first molars, which will allow us to make comparisons via a sophisticated and noninvasive approach. This pilot study also provides guidelines to extend the new methodology to the other types of teeth.     

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access.     

3D heart morphological changes in response to developmental temperature in zebrafish: More than ventricle roundness

A new, three‐dimensional geometric morphometric approach was assessed to study the effect of developmental temperature on fish heart shape utilizing geometric morphometrics of three‐dimensional landmarks captured on digitally reconstructed zebrafish hearts. This study reports the first three‐dimensional analysis of the fish heart and demonstrates significant shape modifications occurring after three developmental temperature treatments (T_D = 24, 28 or 32°C) at two distinct developmental stages (juvenile and adult fish). Elevation of T_D induced ventricle roundness in juveniles, males and females. Furthermore, significant differences that have not been described so far in heart morphometric indices (i.e., ventricle sphericity, bulbus arteriosus elongation and relative location, heart asymmetry) were identified. Sex proved to be a significant regulating factor of heart shape plasticity in response to T_D. This methodology offers unique benefits by providing a more precise representation of heart shape changes in response to developmental temperature that are otherwise not discernable with the previously described two‐dimensional methods. Our work provides the first evidence of three‐dimensional shape alterations of the zebrafish heart adding to the emerging rationale of temperature‐driven plastic responses of global warming and seasonal temperature disturbances in wild fish populations and in other ectothermic vertebrates as well (amphibians and reptiles).     

An accurate and effective FMM-based approach for freehand 3D ultrasound reconstruction

Freehand three-dimensional ultrasound imaging is a highly attractive research area because it is capable of volumetric visualization and analysis of tissues and organs. The reconstruction algorithm plays a key role to the construction of three-dimensional ultrasound volume data with higher image quality and faster reconstruction speed. However, a systematic approach to such problem is still missing. A new fast marching method (FMM) for three-dimensional ultrasound volume reconstruction using the tracked and hand-held probe is proposed in this paper. Our reconstruction approach consists of two stages: bin-filling stage and hole-filling stage. Each pixel in the B-scan images is traversed and its intensity value is assigned to its nearest voxel in the bin-filling stage. For the efficient and accurate reconstruction, we present a new hole-filling algorithm based on the fast marching method. Our algorithm advances the interpolation boundary along its normal direction and fills the area closest to known voxel points in first, which ensure that the structural details of image can be preserved. Experimental results on both ultrasonic abdominal phantom and in vivo urinary bladder of human subject and comparisons with some popular algorithms are used to demonstrate its improvement in both reconstruction accuracy and efficiency.     

Technical note: The use of 3D printing in dental anthropology collections

Objectives

Rapid prototyping (RP) technology is becoming more affordable, faster, and is now capable of building models with a high resolution and accuracy. Due to technological limitations, 3D printing in biological anthropology has been mostly limited to museum displays and forensic reconstructions. In this study, we compared the accuracy of different 3D printers to establish whether RP can be used effectively to reproduce anthropological dental collections, potentially replacing access to oftentimes fragile and irreplaceable original material.

Methods

We digitized specimens from the Yuendumu collection of Australian Aboriginal dental casts using a high‐resolution white‐light scanning system and reproduced them using four different 3D printing technologies: stereolithography (SLA); fused deposition modeling (FDM); binder‐jetting; and material‐jetting. We compared the deviations between the original 3D surface models with 3D print scans using color maps generated from a 3D metric deviation analysis.

Results

The 3D printed models reproduced both the detail and discrete morphology of the scanned dental casts. The results of the metric deviation analysis demonstrate that all 3D print models were accurate, with only a few small areas of high deviations. The material‐jetting and SLA printers were found to perform better than the other two printing machines.

Conclusions

The quality of current commercial 3D printers has reached a good level of accuracy and detail reproduction. However, the costs and printing times limit its application to produce large sample numbers for use in most anthropological studies. Nonetheless, RP offers a viable option to preserve numerically constraint fragile skeletal and dental material in paleoanthropological collections.

     

Direct, rapid effects of 25-hydroxyvitamin D3 on isolated intestinal cells

Scattered reports in the literature have suggested that the metabolite 25-hydroxyvitamin D(3) [25(OH)D(3)] has biological activity. In the present work, perfusion of isolated duodenal loops of normal chickens with 100 nM 25(OH)D(3) resulted in enhanced transport of (45)Ca within 2 min relative to the vehicle controls. We then tested the effect of a range of 25(OH)D(3) concentrations on (45)Ca handling by isolated intestinal cells in time course studies. Following a basal uptake period, cell suspensions from 7-week old chicks were treated either with 25, 100, or 300 nM 25(OH)D(3), or the vehicle ethanol (0.01%, final concentration). Both 25 and 100 nM 25(OH)D(3) resulted in a significant (P < 0.05) reduction in (45)Ca levels, relative to controls, between 1-10 min after treatment, while 300 nM 25(OH)D(3) resulted in a significant increase in (45)Ca levels, relative to controls, after 10 min of incubation. The effect of 100 nM 25(OH)D(3) (a physiological level) on cell calcium was abolished by the presence of 6.5 nM 24,25-dihydroxyvitamin D(3). In cell preparations from 14- or 28-week old birds 100nM 25(OH)D(3) had no effect, relative to vehicle controls. Incubation of cells with 2 microM BAY K8644, a calcium channel activator, stimulated (45)Ca uptake within 3 min relative to vehicle controls (P < 0.05), while addition of either 20 microM forskolin or 100 nM phorbol ester (stimulators of the PKA and PKC pathways, respectively) resulted in enhanced radionuclide levels after 10 min of incubation (P < 0.05, relative to corresponding controls). Finally, cells were treated with 100 nM 25(OH)D(3) or vehicle and samples taken at various times for analyses of protein kinase C and A activities. No effect of 25(OH)D(3) on protein kinase C activity was observed, while protein kinase A activity was stimulated to nearly 200% of controls at 1 min after 25(OH)D(3) addition (P < 0.05, relative to corresponding controls) and began declining at 3 min, returning to control levels 5 min after additions. We conclude that 25(OH)D(3) has a direct effect on calcium handling in enterocytes of young animals that may in part be mediated by the protein kinase A signal transduction pathway.     

三维几何形态学概述及其在昆虫学中的应用

长期以来二维（two-dimensional, 2D）数据是几何形态学（geometric morphometrics）分析的最主要的数据类型,在推动几何形态学的发展过程中起到了奠基性的作用,并也解决了很多重大的科学问题,展示了几何形态学强大的科学计算能力与问题解决能力。但有些特殊的科学问题或者特殊的形态结构,无法通过二维数据完美解决,亟需大规模、大尺度三维（three-dimensional, 3D）数据的支持,这对几何形态学的三维化发展提出需求。更重要的是,随着三维数据获取成本的日渐降低,大量三维数据涌现出来。因此,三维几何形态学应运而生。本文对三维几何形态学的原理及其应用进行了概述,重点探讨了三维几何形态学与二维几何形态学的异同点,并对前者的两个发展阶段（少量样本的形态模拟与准定量比较及大量样本的定量比较）进行了概述,评价了四维数据和有限元等方法的应用,指出了该方法在昆虫学领域的发展潜力,最后对该方法在样本量增加、硬件提升、数据分辨率提高、新算法的开发、分析结果的呈现及3D打印等方面的发展趋势进行了展望。     

D3S1358、D21S11和FGA复合扩增系统的研究

目的：研究D3S1358、D21S11和FGA3个STR基因座复合扩增的最佳体系。方法：设计正交实验优化复合扩增最佳反应条件,然后采用聚丙烯酰胺凝胶电泳分离显带技术检测扩增片段。结果：获得复合扩增条件各反应因素较为满意的参数。     

Spatial integration using a 3D virtual environment with humans

Spatial integration refers to the superimposition of two separate spatial relationships between cues (C1–C2 and C2–C3) by a common linking element (C2). This linkage creates a new spatial relationship between cues that were never paired together (C1–C3). Several authors obtained conflicting results on spatial integration in both humans and animals. Using a dynamic 3D virtual environment, we provide the first clear evidence that humans can integrate two spatial relationships into a new spatial relationship that guides spatial navigation. This research is discussed in light of a spatial version of the temporal coding hypothesis (Savastano and Miller, 1998).     

Design,synthesis and biological evaluation of bitopic arylpiperazine-hexahydro-pyrazinoquinolines as preferential dopamine D3 receptor ligands

Three series of bitobic arylpiperazine-phenyl-hexahydropyrazinoquino- lines analogues were designed, synthesizedand evaluated as a novel class of selective ligands for the dopamine D3 receptor. Compounds 15a (K_i of 11.7 ± 1.8 and 373 nM at D3 and D2, respectively), 15c (K_i of 5.49 and 264 nM at D3 and D2, respectively), 15e (K_i of 14.9 and 325 nM at D3 and D2, respectively), 15i (K_i of 13.8 and 401 nM at D3 and D2, respectively) and 15l (K_i of 13.6 and 870 nM at D3 and D2, respectively) were found to demonstrate good binding affinity and selectivity, and especially compound 15c showeda similar binding affinity and selectivity compared with the contrast drug BP897.     

3D immuno-confocal image reconstruction of fibroblast cytoskeleton and nucleus architecture

Computational models of cellular structures generally rely on simplifying approximations and assumptions that limit biological accuracy. This study presents a comprehensive image processing pipeline for creating unified three-dimensional (3D) reconstructions of the cell cytoskeletal networks and nuclei. Confocal image stacks of these cellular structures were reconstructed to 3D isosurfaces (Imaris), then tessellations were simplified to reduce the number of elements in initial meshes by applying quadric edge collapse decimation with preserved topology boundaries (MeshLab). Geometries were remeshed to ensure uniformity (Instant Meshes) and the resulting 3D meshes exported (ABAQUS) for downstream application. The protocol has been applied successfully to fibroblast cytoskeletal reorganisation in the scleral connective tissue of the eye, under mechanical load that mimics internal eye pressure. While the method herein is specifically employed to reconstruct immunofluorescent confocal imaging data, it is also more widely applicable to other biological imaging modalities where accurate 3D cell structures are required.     

Segmentation of 3D tubular objects with adaptive front propagation and minimal tree extraction for 3D medical imaging

We present a new fast approach for segmentation of thin branching structures, like vascular trees, based on Fast-Marching (FM) and Level Set (LS) methods. FM allows segmentation of tubular structures by inflating a “long balloon” from a user given single point. However, when the tubular shape is rather long, the front propagation may blow up through the boundary of the desired shape close to the starting point. Our contribution is focused on a method to propagate only the useful part of the front while freezing the rest of it. We demonstrate its ability to segment quickly and accurately tubular and tree-like structures. We also develop a useful stopping criterion for the causal front propagation. We finally derive an efficient algorithm for extracting an underlying 1D skeleton of the branching objects, with minimal path techniques. Each branch being represented by its centerline, we automatically detect the bifurcations, leading to the “Minimal Tree” representation. This so-called “Minimal Tree” is very useful for visualization and quantification of the pathologies in our anatomical data sets. We illustrate our algorithms by applying it to several arteries datasets.     

Characterization of 3D pluripotent stem cell aggregates and the impact of their properties on bioprocessing

Pluripotent stem cells (PSCs) have been traditionally expanded on a two-dimensional (2D) surface and require substrates coated with extracellular matrix (ECM) proteins. Recently, PSCs have been successfully expanded in suspension as undifferentiated PSC aggregates, which offer a means for large-scale production. Toward lineage-specific differentiation, PSCs can form aggregate-like structures known as embryoid bodies (EBs). The morphology and size of EBs have been shown to significantly affect the differentiation into specific lineages and three-dimensional (3D) tissue development, thus efforts have been devoted to form size-controlled EBs. The integration of both PSC expansion and differentiation in suspension promotes PSC-derived cell production in bioreactors. However, the cellular organization and differentiation potential of PSC aggregates, as well as the role of the cues provided by the reactors to regulate EB fate, have yet to be fully understood. Despite these challenges, integrated PSC aggregate-based culture provides a platform for a simple, scalable bioprocess for the potential application of PSCs in regenerative medicine, disease modeling, and drug discovery.     

3D representation and analysis of enthesis morphology

This comparison of methods for assessing the development of muscle insertion sites, or entheses, suggests that three‐dimensional (3D) quantification of enthesis morphology can produce a picture of habitual muscle use patterns in a past population that is similar to one produced by ordinal scores for describing enthesis morphology. Upper limb skeletal elements (humeri, radii, and ulnae) from a sample of 24 middle‐aged adult males from the Pottery Mound site in New Mexico were analyzed for both fibrous and fibrocartilaginous enthesis development with three different methods: ordinal scores, two‐dimensional (2D) area measurements, and 3D surface areas. The methods were compared using tests for asymmetry and correlations among variables in each quantitative data set. 2D representations of enthesis area did not agree as closely as ordinal scores and 3D surface areas did regarding which entheses were significantly asymmetrical. There was significant correlation between 3D and 2D data, but correlation coefficients were not consistently high. Intraobserver error was also assessed for the 3D method. Cronbach's alpha values fell between 0.68 and 0.73, and error rates for all entheses fell between 10% and 15%. Marginally acceptable intraobserver error and the analytic versatility of 3D images encourage further investigation of using 3D scanning technology for quantifying enthesis development. Am J Phys Anthropol 152:417–424, 2013. © 2013 Wiley Periodicals, Inc.