3D genital shape complexity in female marine mammals

Comparisons of 3D shapes have recently been applied to diverse anatomical structures using landmarking techniques. However, discerning evolutionary patterns can be challenging for structures lacking homologous landmarks. We used alpha shape analyses to quantify vaginal shape complexity in 40 marine mammal specimens including cetaceans, pinnipeds, and sirenians. We explored phylogenetic signal and the potential roles of natural and sexual selection on vaginal shape evolution. Complexity scores were consistent with qualitative observations. Cetaceans had a broad range of alpha complexities, while pinnipeds were comparatively simple and sirenians were complex. Intraspecific variation was found. Three‐dimensional surface heat maps revealed that shape complexity was driven by invaginations and protrusions of the vaginal wall. Phylogenetic signal was weak and metrics of natural selection (relative neonate size) and sexual selection (relative testes size, sexual size dimorphism, and penis morphology) did not explain vaginal complexity patterns. Additional metrics, such as penile shape complexity, may yield interesting insights into marine mammal genital coevolution. We advocate for the use of alpha shapes to discern patterns of evolution that would otherwise not be possible in 3D anatomical structures lacking homologous landmarks.     

Creation of accurate 3D models of harbor porpoises (Phocoena phocoena) using 3D photogrammetry

Creating accurate 3D models of marine mammals is valuable for assessment of body condition, computational fluids dynamics models of locomotion, and for education. However, the methods for creating 3D models are not well-developed. We used photography and video to create 3D photogrammetry models of harbor porpoises (Phocoena phocoena). We accessed one live adult female (155.5 cm total length), and two dead animals, one juvenile (110 cm total length) and one calf (88 cm total length). We accessed the two dead individuals through a stranding network in Germany, and the live individual through the Fjord and Baelt research center in Denmark. For all porpoises, we used still photographs from hand-held cameras, drone video, and synchronized GoPro videos to create 3D photogrammetric models. We used Blender software, and other 3D reconstruction software, to recreate the 3D body meshes, and confirmed the accuracy of each of the 3D body meshes by comparing digital measures on the 3D models to original measures taken on the specimens. We also provide a colored, animated version of the live harbor porpoise for educational purposes. These open-access 3D models can be used to develop methods to study body morphometrics and condition, and to study bioenergetics and locomotion costs.     

Vitamin D content in Alaskan Arctic zooplankton,fishes, and marine mammals

We postulated that dietary ingestion of vitamin D may be used by some Alaskan Arctic marine mammal species in addition to, or instead of, cutaneous production to meet nutritional requirements. Zooplankton (n=5) sampled near Kaktovik, Alaska, contained no measurable vitamin D₂ or D₃, but did contain provitamin D (7‐dehydrocholesterol), the cutaneous precursor for previtamin D₃ in mammals. Fillets and livers from five fish species were sampled near Barrow, Alaska, and evaluated for vitamin D₃ content (no vitamin D₂ was detected). Differences in vitamin D₃ content appeared significant (P≤0.10) among fish livers (Kruskal‐Wallis [H test]=8.25, df=4, P=0.08) and among fish fillets (H=7.80, df=4, P=0.01). We also found significant differences in several pairwise comparisons (Mann‐Whitney U‐test) of vitamin D₃ levels in fillets and livers. Blubber from six species of marine mammals had no detectable vitamin D₂. The H test results for blubber vitamin D₃ concentration were highly significant: 28.12, df=5, P<0.001. There were also significant differences in vitamin D₃ content from blubber in pairwise comparisons of primarily invertebrate feeders (bowhead whale (Balaena mysticetus) [mean=4.20 SD±1.10 ng/g], and Pacific walrus (Odobenus rosmarus divergens) [5.43±2.82 ng/g]) vs. primarily piscivorous feeders (ringed seal (Phoca hispida) [746.57±493.00 ng/g] and beluga whale (Delphinapterus leucas) [426.00±174.92 ng/g]) and a semiaquatic terrestrial carnivore (polar bear (Ursus maritimus) [406.17±311.70 ng/g]). The bearded seal (Erignathus barbatus) had intermediate blubber vitamin D₃ concentration (156.83±139.25 ng/g), which may reflect an intermediate‐type feeding strategy or an artifact of the small sample size. Zoo Biol 23:33–43, 2004. © 2004 Wiley‐Liss, Inc.     

Development and validation of a generic 3D model of the distal femur

The development and validation of a virtual generic 3D model of the distal femur using computer graphical methods is presented. The synthesis of the generic model requires the following steps: acquisition of bony 3D morphology using standard computed tomography (CT) imaging; alignment of 3D models reconstructed from CT images with a common coordinate system; computer graphical sectioning of the models; extraction of bone contours from the image sections; combining and averaging of extracted contours; and 3D reconstruction of the averaged contours.

The generic models reconstructed from the averaged contours of six cadaver femora were validated by comparing their surface geometry on a point to point basis with that of the CT reconstructed reference models. The mean errors ranged from 0.99 to 2.5 mm and were in agreement with the qualitative assessment of the models.     

Characterization of measurement errors using structure‐from‐motion and photogrammetry to measure marine habitat structural complexity

Habitat structural complexity is one of the most important factors in determining the makeup of biological communities. Recent advances in structure‐from‐motion and photogrammetry have resulted in a proliferation of 3D digital representations of habitats from which structural complexity can be measured. Little attention has been paid to quantifying the measurement errors associated with these techniques, including the variability of results under different surveying and environmental conditions. Such errors have the potential to confound studies that compare habitat complexity over space and time. This study evaluated the accuracy, precision, and bias in measurements of marine habitat structural complexity derived from structure‐from‐motion and photogrammetric measurements using repeated surveys of artificial reefs (with known structure) as well as natural coral reefs. We quantified measurement errors as a function of survey image coverage, actual surface rugosity, and the morphological community composition of the habitat‐forming organisms (reef corals). Our results indicated that measurements could be biased by up to 7.5% of the total observed ranges of structural complexity based on the environmental conditions present during any particular survey. Positive relationships were found between measurement errors and actual complexity, and the strength of these relationships was increased when coral morphology and abundance were also used as predictors. The numerous advantages of structure‐from‐motion and photogrammetry techniques for quantifying and investigating marine habitats will mean that they are likely to replace traditional measurement techniques (e.g., chain‐and‐tape). To this end, our results have important implications for data collection and the interpretation of measurements when examining changes in habitat complexity using structure‐from‐motion and photogrammetry.     

基于Agisoft PhotoScan的石器三维建模与应用

打制石器是了解古人类认知、技术、行为等信息的重要物质载体之一,如何能够更加方便地观察绘制、测量以及展示石器是旧石器时代考古学中基础的研究内容。目前多视角影像三维重建技术在中国考古界应用越来越广泛,尤其是Agisoft PhotoScan软件的应用。相比其他类型遗物,石器的形制及片疤样式具有独特性,在建模过程难度较大。我们经过反复尝试,总结出了一套基于Agisoft PhotoScan软件,专门针对打制石器且易于掌握的建模方式,并从观察绘图、数字化、展示三个方面探讨了石器三维模型的应用。     

Underwater photogrammetry for close‐range 3D imaging of dry‐sensitive objects: The case study of cephalopod beaks

• Technical advances in 3D imaging have contributed to quantifying and understanding biological variability and complexity. However, small, dry‐sensitive objects are not easy to reconstruct using common and easily available techniques such as photogrammetry, surface scanning, or micro‐CT scanning. Here, we use cephalopod beaks as an example as their size, thickness, transparency, and dry‐sensitive nature make them particularly challenging. We developed a new, underwater, photogrammetry protocol in order to add these types of biological structures to the panel of photogrammetric possibilities.
• We used a camera with a macrophotography mode in a waterproof housing fixed in a tank with clear water. The beak was painted and fixed on a colored rotating support. Three angles of view, two acquisitions, and around 300 pictures per specimen were taken in order to reconstruct a full 3D model. These models were compared with others obtained with micro‐CT scanning to verify their accuracy.
• The models can be obtained quickly and cheaply compared with micro‐CT scanning and have sufficient precision for quantitative interspecific morphological analyses. Our work shows that underwater photogrammetry is a fast, noninvasive, efficient, and accurate way to reconstruct 3D models of dry‐sensitive objects while conserving their shape. While the reconstruction of the shape is accurate, some internal parts cannot be reconstructed with photogrammetry as they are not visible. In contrast, these structures are visible using reconstructions based on micro‐CT scanning. The mean difference between both methods is very small (10⁻⁵ to 10⁻⁴ mm) and is significantly lower than differences between meshes of different individuals.
• This photogrammetry protocol is portable, easy‐to‐use, fast, and reproducible. Micro‐CT scanning, in contrast, is time‐consuming, expensive, and nonportable. This protocol can be applied to reconstruct the 3D shape of many other dry‐sensitive objects such as shells of shellfish, cartilage, plants, and other chitinous materials.

     

Fabrication of 3D calcium-alginate scaffolds for human glioblastoma modeling and anticancer drug response evaluation

The three-dimensional (3D) cell culture model has been increasingly used to study cancer biology and screen for anticancer agents due to its close mimicry to in vivo tumor biopsies. In this study, 3D calcium(Ca)-alginate scaffolds were developed for human glioblastoma cell culture and an investigation of the responses to two anticancer agents, doxorubicin and cordycepin. Compared to the 2D monolayer culture, glioblastoma cells cultured on these 3D Ca-alginate scaffolds showed reduced cell proliferation, increased tumor spheroid formation, enhanced expression of cancer stem cell genes (CD133, SOX2, Nestin, and Musashi-1), and improved expression of differentiation potential-associated genes (GFAP and β-tubulin III). Additionally, the vascularization potential of the 3D glioblastoma cells was increased, as indicated by a higher expression of tumor angiogenesis biomarker (VEGF) than in the cells in 2D culture. To highlight the application of Ca-alginate scaffolds, the 3D glioblastomas were treated with anticancer agents, including doxorubicin and cordycepin. The results demonstrated that the 3D glioblastomas presented a greater resistance to the tested anticancer agents than that of the cells in 2D culture. In summary, the 3D Ca-alginate scaffolds for glioblastoma cells that were developed in this study offer a promising platform for anticancer agent screening and the discovery of drug-resistant mechanisms of cancer.     

虚拟森林景观中林火蔓延模型及三维可视化表达

传统上的林火模拟通常只选用一种林火模型,用一个简单的椭圆预测林火蔓延时火场各个位置的情况,与现实中火灾蔓延状况相差甚远,而且以往的林火蔓延是基于二维可视化表达,表达信息有限.本系统采用现今运用最广泛的Rothermel模型,利用Huygen原理,并以改进的粒子系统方法三维模拟在不同的风速、坡度下林火在火场不同位置的扩散行为.采用该方法模拟林火扩散行为,不仅能实时显示受灾面积、火势蔓延的方向、火势大小,且能给人以真实感.并将该方法成功地应用于福建漳浦林区.     

Morphological analyses and 3D modeling of the tongue musculature of the chimpanzee (Pan troglodytes)

Knowledge of the comparative anatomy of tongue musculature is crucial to the discussion of the origin and the evolution of speech because of the indispensable role played by this organ in speech. However, the tongue musculature of primates has rarely been studied. In a previous study, the author analyzed human tongue musculature and developed a 3D model of this organ [Takemoto, Journal of Speech, Language, and Hearing Research 44:95-107, 2001]. In this study, the tongue musculature of chimpanzees was examined using methods similar to those used for humans. Results showed that tongue musculature was topologically the same for both humans and chimpanzees. As in humans, the tongue musculature of chimpanzees consisted of inner and outer regions. The inner musculature was composed of serial "structural units," made up of two types of laminae whose fibers were perpendicular to the tongue surface. The outer musculature was a thin layer of fibers oriented parallel to the surface and superficial to the inner musculature. Although the tongue musculature of humans and chimpanzees is similar, the external shapes differ: the chimpanzee tongue is flat, whereas the human tongue is round. Applying the muscular hydrostat theory to the external shape of the tongue suggests that the primary actions of the chimpanzee tongue are protrusion and retrusion, whereas the human tongue can be deformed in the oral cavity with a high degree of freedom. It is hypothesized that the evolution of the external shape of the tongue is one of the factors that led to the development of human speech. The results of this study suggest that modeling based on muscular hydrostatic theory of the effects of changes in external tongue shape on articulatory movements should be included in discussions on the origin of speech.     

组合式3D模型在骨科临床课教学中的应用及优势

骨科是一门抽象性及实践性较强的学科,如何提高直观性和可操作性是骨科临床课教学面临的主要问题之一。3D模型技术 具有高度仿真,立体,便捷的优势能很好的再现骨骼的立体结构及三维实体信息,为解决这一问题带来了希望。笔者结合多年的 临床及教学经验,自行设计了集解剖。骨折分型及手术治疗为一体的组合式股骨颈骨折模型,在同一模型上完整的实现了知识的 整合,不仅提高了直观性和生动性更具有很好的操作性,能显著提高授课效果,其优势是目前常用的骨骼标本模型和普通单一式 模型无法比拟的。该模型于第四届全国医学院校青年教师授课基本功比赛中进行了展示并获得一等奖及最受学员欢迎奖,具有 较好的应用及推广价值。本文就组合式3D模型的制作,授课效果及优势进行了全面的阐述,希望对提高骨科临床课教学效果及 提高青年教师教学水平有一定的帮助和启发作用。     

A new bioinformatic approach to detect common 3D sites in protein structures

An innovative bioinformatic method has been designed and implemented to detect similar three-dimensional (3D) sites in proteins. This approach allows the comparison of protein structures or substructures and detects local spatial similarities: this method is completely independent from the amino acid sequence and from the backbone structure. In contrast to already existing tools, the basis for this method is a representation of the protein structure by a set of stereochemical groups that are defined independently from the notion of amino acid. An efficient heuristic for finding similarities that uses graphs of triangles of chemical groups to represent the protein structures has been developed. The implementation of this heuristic constitutes a software named SuMo (Surfing the Molecules), which allows the dynamic definition of chemical groups, the selection of sites in the proteins, and the management and screening of databases. To show the relevance of this approach, we focused on two extreme examples illustrating convergent and divergent evolution. In two unrelated serine proteases, SuMo detects one common site, which corresponds to the catalytic triad. In the legume lectins family composed of >100 structures that share similar sequences and folds but may have lost their ability to bind a carbohydrate molecule, SuMo discriminates between functional and non-functional lectins with a selectivity of 96%. The time needed for searching a given site in a protein structure is typically 0.1 s on a PIII 800MHz/Linux computer; thus, in further studies, SuMo will be used to screen the PDB.     

基于三维卷积神经网络的肺结节探测与定位方法

提出一种基于三维卷积神经网络对肺部计算机断层扫描图像(CT)进行肺结节自动探测及定位的方法.基于开源数据集LUNA16开展研究,对数据进行像素归一化、坐标转换等预处理,对正样本使用随机平移、旋转和翻转的方式进行扩充,对负样本进行随机采样.搭建了三维卷积神经网络并在训练过程中调整网络参数,直到得到性能最佳的网络.此外还设...     

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。     

Mathematical modeling of cell growth in a 3D scaffold and validation of static and dynamic cultures

Tissue engineering, an immensely important field in contemporary clinical practices, aims at the repair or replacement of damaged tissues. The mathematical model proposed herein shows the distribution and growth of cells in their characteristic time in a 3D scaffold model. This study contributes to the progress of simulation techniques in static and dynamic cultures of bone tissue. Brinkman, nutrient transport, and cell growth equations are brought together to quantify the growth behavior of cells. However, when a static culture is being studied, the Brinkman equation is eliminated. The model was validated by experimental cell culture using 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide assay and scanning electron microscopy. Then, static and dynamic cultures were compared to assess the cell density and cell distribution in the scaffold. Cell counting after 21 days of cell culture showed that the number of cells increased 42‐fold in static and 53.5‐fold in dynamic cultures, which was in good agreement with our model estimations (37‐fold increase in the number of cells in static and 49‐fold increase in dynamic cultures). In conclusion, our mathematical model could predict cell distribution and growth in the scaffold.     

一种新型高通量三维脑细胞芯片的研制及农药神经毒性评价应用

为了模拟体内脑组织细胞的三维生长环境,高效开展脑疾病和有关药物的研究工作,文中设计和制造了一种新型高通量三维脑细胞芯片.芯片由多孔滤网和三维脑细胞颗粒构成,装载于常规的96孔细胞培养板上使用.多孔滤网和细胞颗粒模具采用计算机建模、3D打印阳模、琼脂糖-PDMS两次翻模等技术制造,三维脑细胞颗粒是将小鼠胚胎脑细胞与海藻酸...     

大鼠肠道系统的高分辨解剖数据集及三维模型的构建

利用冰冻铣切技术获取的大鼠腹部的断面图像,构建了大鼠肠道系统的高分辨解剖数据集及三维模型,该数据集及模型具有信息丰富等特点.本工作为开展高等动物肠道系统功能与结构关系的"定量研究及系统整合"提供了基础.     

Outflow boundary conditions for 3D simulations of non-periodic blood flow and pressure fields in deformable arteries

The simulation of blood flow and pressure in arteries requires outflow boundary conditions that incorporate models of downstream domains. We previously described a coupled multidomain method to couple analytical models of the downstream domains with 3D numerical models of the upstream vasculature. This prior work either included pure resistance boundary conditions or impedance boundary conditions based on assumed periodicity of the solution. However, flow and pressure in arteries are not necessarily periodic in time due to heart rate variability, respiration, complex transitional flow or acute physiological changes. We present herein an approach for prescribing lumped parameter outflow boundary conditions that accommodate transient phenomena. We have applied this method to compute haemodynamic quantities in different physiologically relevant cardiovascular models, including patient-specific examples, to study non-periodic flow phenomena often observed in normal subjects and in patients with acquired or congenital cardiovascular disease. The relevance of using boundary conditions that accommodate transient phenomena compared with boundary conditions that assume periodicity of the solution is discussed.