Three-Dimensional Aberration Analyses of Metasurface Flat Lenses

Plasmonics - Three-dimensional analyses of optical aberrations of metasurface flat lenses are presented via ray tracing. The ray tracing is performed on the basis of anomalous refraction/reflection...     

The application of fractal clustering to efficient molecular ray tracing on low-cost computers

Ray tracing is a powerful, and highly computer intensive means for generating high-quality molecular displays. A variety of simple, yet effective optimization strategies are described that allow large molecular models to be ray traced on microcomputers and low-cost desktop workstations. In particular, the method of fractal clustering provides a time and space-efficient means for spatially subdividing the molecular scene into a hierarchy of spherical bounding volumes, permitting ray-atom intersections to be determined by a form of binary search. An implementation of the algorithms, MolRay, is described which demonstrates that large structures may be ray traced in a reasonable time on a PC or small Unix workstation. Images generated by PC and Unix versions of MolRay are shown.     

Modelling the visual world of a velvet worm

In many animal phyla, eyes are small and provide only low-resolution vision for general orientation in the environment. Because these primitive eyes rarely have a defined image plane, traditional visual-optics principles cannot be applied. To assess the functional capacity of such eyes we have developed modelling principles based on ray tracing in 3D reconstructions of eye morphology, where refraction on the way to the photoreceptors and absorption in the photopigment are calculated incrementally for ray bundles from all angles within the visual field. From the ray tracing, we calculate the complete angular acceptance function of each photoreceptor in the eye, revealing the visual acuity for all parts of the visual field. We then use this information to generate visual filters that can be applied to high resolution images or videos to convert them to accurate representations of the spatial information seen by the animal. The method is here applied to the 0.1 mm eyes of the velvet worm Euperipatoides rowelli (Onychophora). These eyes of these terrestrial invertebrates consist of a curved cornea covering an irregular but optically homogeneous lens directly joining a retina packed with photoreceptive rhabdoms. 3D reconstruction from histological sections revealed an asymmetric eye, where the retina is deeper in the forward-pointing direction. The calculated visual acuity also reveals performance differences across the visual field, with a maximum acuity of about 0.11 cycles/deg in the forward direction despite laterally pointing eyes. The results agree with previous behavioural measurements of visual acuity, and suggest that velvet worm vision is adequate for orientation and positioning within the habitat.     

Angular sensitivity of the bee ommatidium

Summary Light propagation within the worker bee ommatidium is analyzed. The angular sensitivity of the ommatidium can be separated into a product of the bee's dioptric apparatus and rhabdom angular sensitivities. The discrepancy in angular sensitivity between recent electrophysiological measurements and ray tracing procedures for the worker bee arises because the field of view of the rhabdom is smaller than that of the optical system in front of it.I thank G. A. Horridge for suggesting this research, Simon Laughlin for providing the results of his recordings from the worker bee and J. W. Blamey for helpful discussion on optical systems.     

Neoblast-enriched fraction rescues eye formation in eye-defective planarian 'menashi' Dugesia ryukyuensis

Planarians are well known for their remarkable regenerative capacity. This capacity to regenerate is thought to be due to the presence of totipotent somatic stem cells known as ‘neoblasts’, which have particular morphological characteristics. The totipotency of neoblasts was supported by Baguñà's experiment, which involved the introduction of donor cells into irradiated hosts. However, since Baguñà's experiment did not include the use of a phenotypic marker, the donor cells could not be traced. In the current study, a genetic mutant planarian, menashi, an eye‐defective mutant that lacks the pigmented area in the eyes, was established. This planarian is excellent for tracing the fate of cells after their introduction into irradiated hosts. To investigate the differentiation potency more directly, a neoblast‐rich fraction obtained from normal worms was transplanted into an X‐ray‐irradiated menashi strain. Planarians that survive X‐ray irradiation were developed, and we observed the pigment of the area in the eyes of the regenerating planarians. This result suggests that the neoblast‐rich fraction contains cells that can proliferate and differentiate. These cells can replace the cells and structures lost by X‐ray irradiation and ablation, and they can also differentiate into eye pigment cells.     

Theoretical accuracy of model-based shape matching for measuring natural knee kinematics with single-plane fluoroscopy

Quantification of knee motion under dynamic, in vivo loaded conditions is necessary to understand how knee kinematics influence joint injury, disease, and rehabilitation. Though recent studies have measured three-dimensional knee kinematics by matching geometric bone models to single-plane fluoroscopic images, factors limiting the accuracy of this approach have not been thoroughly investigated. This study used a three-step computational approach to evaluate theoretical accuracy limitations due to the shape matching process alone. First, cortical bone models of the femur tibia/fibula, and patella were created from CT data. Next, synthetic (i.e., computer generated) fluoroscopic images were created by ray tracing the bone models in known poses. Finally, an automated matching algorithm utilizing edge detection methods was developed to align flat-shaded bone models to the synthetic images. Accuracy of the recovered pose parameters was assessed in terms of measurement bias and precision. Under these ideal conditions where other sources of error were eliminated, tibiofemoral poses were within 2 mm for sagittal plane translations and 1.5 deg for all rotations while patellofemoral poses were within 2 mm and 3 deg. However, statistically significant bias was found in most relative pose parameters. Bias disappeared and precision improved by a factor of two when the synthetic images were regenerated using flat shading (i.e., sharp bone edges) instead of ray tracing (i.e., attenuated bone edges). Analysis of absolute pose parameter errors revealed that the automated matching algorithm systematically pushed the flat-shaded bone models too far into the image plane to match the attenuated edges of the synthetic ray-traced images. These results suggest that biased edge detection is the primary factor limiting the theoretical accuracy of this single-plane shape matching procedure.     

Personal computer-based visualization of molecular models by available ray-tracing software

Developed primarily for the graphic arts, ray-tracing algorithms offer a high level of flexibility with reference to photorealistic and surrealistic image rendering. The utility of these programs is further enhanced by portability (i.e., compatibility with a number of operating systems), accessibility through various sources, and low cost. This report documents, through the use of existing software, the application of these ray-tracing attributes to molecular graphics on a desktop computer. This application is especially pertinent in view of rapid speed enhancements in personal computers (PCs), which have enabled molecular modeling and dynamics on these systems. In this regard, ray tracing on a PC provides enhanced capabilities for molecular graphics rendering that are potentially equivalent to those achieved by workstations.     

萤火虫复眼光学模型重叠成象的研究与模拟

以北京萤火虫复眼结构与生理参数为依据,基于已知的梯度折射率透镜特征,对复眼的整个光学系统进行模型化.模型的尺寸与折射率分布依据实际晶锥的测量值.通过对模型复眼的光线追迹,证明北京萤火虫复眼是一个折射重叠型复眼.重叠孔径以内入射的平行光线在视网膜水平形成一半宽度为一定值的模糊圈.利用计算机光线追迹模拟了复眼的重叠成象过程,随着象平面与晶锥近端距离的增加,信号光线的数目也逐渐增加,信噪比逐渐提高,在视网膜水平达到最大值.     

三维辐射传输模型在森林生态系统研究中的应用与展望

太阳辐射是森林生态系统功能与服务得以维持并发展的基础, 对森林中的辐射传输过程进行建模对于理解森林生态系统过程具有重要意义。近年来, 三维辐射传输模型的迅速发展使得冠层辐射能量分布格局与动态的准确模拟成为可能。为更好地理解三维辐射传输模型以使其更有效地服务于森林生态系统研究, 该文从模型的原理、应用及发展趋势3个角度展开论述。首先简要介绍了辐射度方法、光线追踪法等森林三维辐射传输模型常用的原理及目前代表性的模型, 然后总结了三维辐射传输模型在森林生态系统研究中的应用, 最后对模型未来如何通过提高易用性、增加多模型耦合等方式更好地应用于森林生态系统研究进行了展望。随着森林生态系统大数据的积累与过程模型的不断完善, 三维辐射传输模型将在未来森林生态理论研究与实践中发挥更加重要的作用。     

Lineage tracing

Lineage tracing is the identification of all progeny of a single cell. Although its origins date back to developmental biology of invertebrates in the 19(th) century, lineage tracing is now an essential tool for studying stem cell properties in adult mammalian tissues. Lineage tracing provides a powerful means of understanding tissue development, homeostasis, and disease, especially when it is combined with experimental manipulation of signals regulating cell-fate decisions. Recently, the combination of inducible recombinases, multicolor reporter constructs, and live-cell imaging has provided unprecedented insights into stem cell biology. Here we discuss the different experimental strategies currently available for lineage tracing, their associated caveats, and new opportunities to integrate lineage tracing with the monitoring of intracellular signaling pathways.     

Simulation of photon transport in a three-dimensional leaf: implications for photosynthesis

A model to evaluate photon transport within leaves and the implications for photosynthesis are investigated. A ray tracing model, Raytran, was used to produce absorption profiles within a virtual dorsiventral plant leaf oriented in two positions (horizontal/vertical) and illuminated on one of its two faces (adaxial/abaxial). Together with chlorophyll profiles, these absorption profiles feed a simple photosynthesis model that calculates the gross photosynthetic rate as a function of the incident irradiance. The differences observed between the four conditions are consistent with the literature: horizontal‐adaxial leaves, which are commonly found in natural conditions, have the greatest light use efficiency. The absorption profile obtained with horizontal‐abaxial leaves lies below this, but above those obtained for vertical leaves. The latter present similar gross photosynthetic rates when irradiated on either the adaxial or abaxial surfaces. Vertical profiles of photosynthetic rates across the leaf confirm that carbon fixation occurs mainly in the palisade parenchyma, that the leaf anatomy is integral to its function and that leaves cannot be considered as a single homogeneous unit. Finally, the relationships between leaf structure, orientation and photosynthesis are discussed.     

Epidemic Contact Tracing via Communication Traces

Traditional contact tracing relies on knowledge of the interpersonal network of physical interactions, where contagious outbreaks propagate. However, due to privacy constraints and noisy data assimilation, this network is generally difficult to reconstruct accurately. Communication traces obtained by mobile phones are known to be good proxies for the physical interaction network, and they may provide a valuable tool for contact tracing. Motivated by this assumption, we propose a model for contact tracing, where an infection is spreading in the physical interpersonal network, which can never be fully recovered; and contact tracing is occurring in a communication network which acts as a proxy for the first. We apply this dual model to a dataset covering 72 students over a 9 month period, for which both the physical interactions as well as the mobile communication traces are known. Our results suggest that a wide range of contact tracing strategies may significantly reduce the final size of the epidemic, by mainly affecting its peak of incidence. However, we find that for low overlap between the face-to-face and communication interaction network, contact tracing is only efficient at the beginning of the outbreak, due to rapidly increasing costs as the epidemic evolves. Overall, contact tracing via mobile phone communication traces may be a viable option to arrest contagious outbreaks.     

405 nm versus 633 nm for protoporphyrin IX excitation in fluorescence‐guided stereotactic biopsy of brain tumors

Fluorescence diagnosis may be used to improve the safety and reliability of stereotactic brain tumor biopsies using biopsy needles with integrated fiber optics. Based on 5‐aminolevulinic‐acid‐induced protoporphyrin IX (PpIX) fluorescence, vital tumor tissue can be localized in vivo during the excision procedure to reduce the number of necessary samples for a reliable diagnosis. In this study, the practical suitability of two different PpIX excitation wavelengths (405 nm, 633 nm) was investigated on optical phantoms. Violet excitation at 405 nm provides a 50‐fold higher sensitivity for the bulk tumor; this factor increases up to 100 with decreasing fluorescent volume as shown by ray tracing simulations. Red excitation at 633 nm, however, is noticeably superior with regard to blood layers obscuring the fluorescence. Experimental results on the signal attenuation through blood layers of well‐defined thicknesses could be confirmed by ray tracing simulations. Typical interstitial fiber probe measurements were mimicked on agarose‐gel phantoms. Even in direct contact, blood layers of 20–40 µm between probe and tissue must be expected, obscuring 405‐nm‐excited PpIX fluorescence almost completely, but reducing the 633‐nm‐excited signal only by 25.5%. Thus, 633 nm seems to be the wavelength of choice for PpIX‐assisted detection of high‐grade gliomas in stereotactic biopsy.

PpIX signal attenuation through clinically relevant blood layers for 405 nm (violet) and 633 nm (red) excitation.     

Role of gravitation-dependent systems in visual tracing

In 31 astronauts under conditions of free falling, when the visual functions proper were preserved, the precision and speedy parameters of all the forms of visual tracing (saccades, smooth tracing) became worse, and in a number of cases a complete disintegration of the smooth tracing reflex occurred as well as a 2-fold and greater enhancement of the time for fixing the stare at a target. In the beginning of adaptation to altered gravitation conditions, a transition of the smooth visual tracing into the strategy of saccadic approximation, occurs. These disorders were shown to be due to a vestibular deprivation.     

Reliability of cardiotocography in predicting baby's condition at birth.

A prospective study of 6825 labours was undertaken to determine the relation between the Apgar scores of the babies at one minute and the cardiotocograph tracing in labour. The sensitivity of an abnormal tracing was 35.2% for babies who needed intermittent positive pressure ventilation and 20.0% for babies who did not but who had Apgar scores of less than 7. The sensitivity of an abnormal tracing for all babies with an Apgar score of less than 7 was 23.2%. The positive predictive value of an abnormal tracing was 8.7% for babies who needed intermittent positive pressure ventilation and 18.7% for babies who did not but who had an Apgar score of less than 7. The positive predictive value of an abnormal tracing was 27.4% for all babies with an Apgar score of less than 7. The specificity of the tracing was 93.4% for babies with an Apgar score of 7 or over. The relatively high incidence of false positive predictions might be explained on the grounds that abnormalities in the cardiotocograph tracing are a more sensitive indicator of hypoxia than the Apgar score. False negative predictions might have been due to adverse factors other than hypoxia--for example, fetal trauma, compression of the head, infection, and analgesia in labour. These findings suggest that the current overdependence on fetal monitoring by cardiotocography alone should be examined and that other reliable indicators for non-hypoxic fetal distress should be sought.     

Optimal mix of screening and contact tracing for endemic diseases

Two common means of controlling infectious diseases are screening and contact tracing. Which should be used, and when? We consider the problem of determining the cheapest mix of screening and contact tracing necessary to achieve a desired endemic prevalence of a disease or to identify a specified number of cases. We perform a partial equilibrium analysis of small-scale interventions, assuming that prevalence is unaffected by the intervention; we develop a full equilibrium analysis where we compare the long-term cost of various combinations of screening and contact tracing needed to achieve a given equilibrium prevalence; and we solve the problem of minimizing the total costs of identifying and treating disease cases plus the cost of untreated disease cases. Our analysis provides several insights. First, contact tracing is only cost effective when prevalence is below a threshold value. This threshold depends on the relative cost per case found by screening versus contact tracing. Second, for a given contact tracing policy, the screening rate needed to achieve a given prevalence or identify a specified number of cases is a decreasing function of disease prevalence. As prevalence increases above the threshold (and contact tracing is discontinued), the screening rate jumps discontinuously to a higher level. Third, these qualitative results hold when we consider unchanged or changed prevalence, and short-term or long-term costs.     

A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures

The present paper describes a comprehensive protocol for manual tracing of the set of brain regions comprising the medial temporal lobe (MTL): amygdala, hippocampus, and the associated parahippocampal regions (perirhinal, entorhinal, and parahippocampal proper). Unlike most other tracing protocols available, typically focusing on certain MTL areas (e.g., amygdala and/or hippocampus), the integrative perspective adopted by the present tracing guidelines allows for clear localization of all MTL subregions. By integrating information from a variety of sources, including extant tracing protocols separately targeting various MTL structures, histological reports, and brain atlases, and with the complement of illustrative visual materials, the present protocol provides an accurate, intuitive, and convenient guide for understanding the MTL anatomy. The need for such tracing guidelines is also emphasized by illustrating possible differences between automatic and manual segmentation protocols. This knowledge can be applied toward research involving not only structural MRI investigations but also structural-functional colocalization and fMRI signal extraction from anatomically defined ROIs, in healthy and clinical groups alike.     

北京萤火虫复眼的模型小眼设计与光线追迹

以实际的北京萤火虫复眼结构与生理参数与依据,基于已知的ＧＲＩＮ透镜特征,把小眼的整个光学系统分成几个部分被模型化。模型中,在晶体柱部分使用了一个径向梯度折射率透镜柱具有的抛物线轮廓折射率公式;在晶锥末端所接的半椭球ＧＲＩＮ透镜部分,使用了一个径向梯度和纵向梯度分布都存在的折射率公式．模型的尺寸与折射率的大小根据实际晶锥的测量值．通过对模型小眼的光线追迹,证明模型小眼基本上是一个平行光入射,年行光出射的望远镜系统．小眼光学系统的前半部分把入射的平行光束聚焦到中间焦点,而这个点的位置恰好位于实际晶锥的腰的部位,而光线再次经过晶锥近端以后又以大致平行光束从晶锥末端出射。此模型小眼的最大入射角为３０度,在这个入射角内其角放大率基本上是相同的。随着对平行入射光束与小眼光轴的角度的增加,所产生的中间像越来越远离晶锥光轴。