虚拟生物实验室实例

虚拟生物实验室在生物课程资源中有巨大并且尚未开发的潜力。它对于不同级别学生的学习都是有利的。介绍了虚拟生物实验室的一些实例。并展望了其应用前景。     

Cognitive Ergonomics in Virtual Environments: Development of an Intuitive and Appropriate Input Device for Navigating in a Virtual Maze

For patients suffering from mild cognitive impairments, the navigation through a virtual maze should be as intuitive and efficient as possible in order to minimize cognitive and physical strain. This paper discusses the appropriateness of interaction devices for being used for easy navigation tasks. Information gained from human centered evaluation was used to develop an intuitive and ergonomic interaction device. Two experiments examined the usability of tracked interaction devices. Usability problems with the devices are discussed. The findings from the experiments were translated into general design guidance, in addition to specific recommendations. A new device was designed on the basis of these recommendations and its usability was evaluated in a second experiment. The results were used to develop a lightweight interaction device for navigation in the virtual maze.     

中国主要农产品虚拟要素贸易网络结构特征分析

据虚拟水概念定义虚拟要素,并将其划分为虚拟资源要素和虚拟生态要素两类,选取虚拟资源要素中的耕地要素和虚拟生态要素中的化肥/农药要素为研究对象,定量分析2002—2016年以粮食贸易为载体的虚拟耕地、虚拟化肥/农药要素的贸易量,构建虚拟要素贸易网络,通过复杂网络的研究方法,结果表明:2002—2016年我国主要农产品虚拟耕地、化肥/农药要素的贸易总量呈下降趋势,降幅分别约25.51%、8.01%;虚拟耕地要素网络节点入度较大的为长江中下游、华南、西南地区,出度较大的为黄淮海和东北地区,虚拟化肥/农药要素网络与之相反;地区间节点强度的差异性大,虚拟耕地要素差值最大可达1459.56万hm~2,虚拟化肥/农药要素达61.38万t;二者网络节点度和强度的累积分布均符合幂律分布规律,其尾部的"重尾"现象揭示了节点度和强度的高可变性以及网络结构的脆弱性;虚拟耕地要素的输入区网络同配,输出区网络异配,揭示了地区间耕地要素的流动既呈集聚又有分散的态势,虚拟化肥/农药要素网络节点相关性皆为减函数,网络异配,揭示了虚拟化肥/农药要素在八大区域间联通的状况。网络结构特征分析为研究网络抗毁性特征和网络的优化调控机制奠定基础,为中国粮食贸易格局和粮价制定以及各个地区的农业种植结构调整提供理论依据。     

Virtual human hand: model and kinematics

The human hand plays an important role in daily life. It is the interface between the human and the exterior world by positioning, orienting, touching and grasping objects. The human hand has multiple degrees of freedom (DOFs) to enable mobility and dexterity. A virtual human hand model can be inserted into CAD (Computer Aided Design) models to assess the manipulation capabilities in the early design stage to reduce design time and cost. Joystick assessment is one of the important design cases. This study is a first step towards a comprehensive hand simulation tool to simulate the manipulation and grasping of objects. This paper presents a novel 25 DOFs' hand skeletal model based on hand anatomy and hand kinematics: (1) joint range of motion, (2) Denavit–Hartenberg method to define the joint relationship and (3) finger workspace determination. Novelty for this hand model includes arching the palm with the four DOFs added in the carpometacarpal and wrist joints for the ring and small fingers.     

Place illusion and plausibility can lead to realistic behaviour in immersive virtual environments

In this paper, I address the question as to why participants tend to respond realistically to situations and events portrayed within an immersive virtual reality system. The idea is put forward, based on the experience of a large number of experimental studies, that there are two orthogonal components that contribute to this realistic response. The first is ‘being there’, often called ‘presence’, the qualia of having a sensation of being in a real place. We call this place illusion (PI). Second, plausibility illusion (Psi) refers to the illusion that the scenario being depicted is actually occurring. In the case of both PI and Psi the participant knows for sure that they are not ‘there’ and that the events are not occurring. PI is constrained by the sensorimotor contingencies afforded by the virtual reality system. Psi is determined by the extent to which the system can produce events that directly relate to the participant, the overall credibility of the scenario being depicted in comparison with expectations. We argue that when both PI and Psi occur, participants will respond realistically to the virtual reality.     

Stimulation of Cortisol During Mental Task Performance in a Provocative Virtual Environment

Fully immersive and stereoscopic Virtual Environments (VE) represent a powerful multimedia tool for laboratory-based simulations of distinct scenarios including scenarios for evaluating stressful situations resembling reality. Thus far, cortisol secretion as a neuroendocrine parameter of stress has not been evaluated within a Virtual Reality (VR)-based paradigm. In this study 94 healthy volunteers were subjected to a provocative VR-paradigm and a cognitive stress task. Provocative in this context means the VE was designed to provoke physiological reactions (cortisol secretion) within the respective users by purpose. It was tested (a) if a fully dynamic VE as opposed to a static VE can be regarded as a stressor and (b) if such a fully dynamic VE can modify an additional response to a cognitive stressor presented within the VE additionally. Furthermore, possible gender-related impacts on cortisol responses were assessed. A significant cortisol increase was observed only after the combined application of the fully dynamic VE and the cognitive stressor, but not after application of the dynamic VE or the cognitive stressor alone. Cortisol reactivity was greater for men than for women. We conclude that a fully dynamic VE does not affect cortisol secretion per se, but increases cortisol responses to a dual task paradigm that includes performance of a stressful mental task. This provides the basis for the application of VR-based technologies in neuroscientific research, including the assessment of the human Hypothalamus-Pituitary-Adrenal (HPA) axis regulation.     

E-Learning as a new tool in bioinformatics teaching

In recent years, virtual learning is growing rapidly. Universities, colleges, and secondary schools are now delivering training and education over the internet. Beside this, resources available over the WWW are huge and understanding the various techniques employed in the field of Bioinformatics is increasingly complex for students during implementation. Here, we discuss its importance in developing and delivering an educational system in Bioinformatics based on e-learning environment.     

Real cells - virtual computers

Now it is quite usual to use real computers to simulte virtual cells. I suggest that real cells (e.g. cells cultured in vitro ) might be considered and used as molecular automata. As an imaginary experience, a molecular automata can be built, using real cells and a chemical inert molecule. I suggest that one could be able to test statistical properties of a 2D gas trapped in a box using this sort of automata. Moreover, I would conjecture that any possible algorithm can be implemented in such molecular automata.     

A Functional Magnetic Resonance Imaging (fMRI) Study of Cue-Induced Smoking Craving in Virtual Environments

Smokers who are exposed to smoking-related cues show cardiovascular reactivity and smoking craving compared with their responses to neutral cues, and increased cue reactivity predicts decreased likelihood of successful cessation. Several brain imaging studies suggested four candidate brain regions that might differ in gray matter volumes and densities between smokers and nonsmokers. However, in these studies, smokers were only exposed to smoking-related objects. In our pilot study utilizing a virtual reality (VR) technique, virtual environments (VEs) were more immersive and evoked smoking craving more effectively than traditionally used methods. In this study, we sought to test whether smokers could experience cue-induced smoking craving inside the MRI scanner by using the VR system. The smoking cue reactivity scenario was based in part on our preliminary task and consisted of 2D and 3D (or VE) conditions. The group mean of participants had increased activity in the prefrontal cortex (PFC), left anterior cingulate gyrus (ACC), left supplementary motor area, left uncus, right inferior temporal gyrus, right lingual gyrus, and right precuneus in the 2D condition. Areas of differential activation in the 3D condition were as follows: left superior temporal gyrus, right superior frontal gyrus, and left inferior occipital gyrus in the 3D condition. This finding is consistent with those of previous studies of nicotine craving showing PFC and ACC activation. However, in the 3D condition, the PFC including the superior frontal gyrus as well as the superior temporal gyrus, inferior occipital gyrus, and cerebellum were activated. Therefore, in the 3D condition, participants seemed to have more attention, visual balance, and coordinating movement than in the 2D condition.     

超快速CT模拟胃镜的临床应用初探

目的：探讨模拟CT胃镜对常见胃部病变的应用价值。材料和方法：对50例已行内镜检查的患者行CT模拟胃镜检查,男33例,女17例,年龄24－70岁之间。全部病例均经手术或胃镜病理证实。将获得的二维图像输送至工作站,使用Insight软件包进行三维重建。结果：早期胃癌和进展期胃癌检出率分别为60％、100％,检出息肉3例,恶性淋巴瘤、平滑肌瘤和平滑肌肉瘤各1例,排除了3例胃镜诊断的粘膜下隆起病变,仅检出了7例溃疡中的2例。结论;模拟CT胃镜是探查胃部新生物的一种有效的诊断方法。     

On the way to building an integrated computational environment for the study of developmental patterns and genetic diseases

Genetic diseases and developmental patterns should be studied on several levels: from macroscale (organs and tissues) to nanoscale (cells, genes, proteins). Due to the overwhelming complexity of the life science data, it is common that disparate data pieces are meticulously stored but never fully analyzed or correlated. We have begun to develop a novel methodology based on virtual reality techniques for the study of these phenomena. Our key approach to knowledge integration is a top-down mapping of data onto visual contexts. For each organism that we want to study, a structural model is created and used as a visual "wireframe" onto which other data types are superimposed in a top-down assembly. Data analysis tools, visual controls, and queries are enabled so that users can interactively explore data. Our visualization technology gives users an opportunity to map disparate data onto a common model, and search visually for hitherto unknown patterns and correlations contained within the data. It is our goal to eventually transform genomics research from measuring various data pieces analytically into a fully interactive exploration of combined data in a 4D immersive visual environment that best matches a researcher's intuition.     

Receptor-based virtual screening evaluation for the identification of estrogen receptor β ligands

Abstract

In this paper, a receptor-based virtual screening study for the identification of estrogen receptor β (ERβ) ligands was developed. Starting from a commercial database of 400?000 molecules, only six compounds resulted to be potential active ligands of ERβ. Interestingly, all the six molecules possess scaffolds that had already been reported in known ERβ ligands. Therefore, the results obtained herein confirm the reliability of our virtual screening procedure, thus encouraging the application of this protocol to larger commercial databases in order to identify new ERβ ligands.     

虚拟现实技术在健康医疗领域的应用

介绍虚拟现实技术的发展历程及基本概况,综述VR/AR技术在临床技能培训与教育、康复治疗、心理治疗及远程医疗等方面的应用研究,提出健康医疗领域虚拟技术的应用还处于起步阶段,未来将在疾病诊疗、手术模拟、远程医疗、健康管理监测等方面不断发展,对提高医护工作人员的服务水平、改善患者就医体验有重大的意义。     

The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign

Structure-based virtual screening (SBVS) protocols were developed to find cyclooxygenase-2 (COX-2) inhibitors using the Protein-Ligand ANT System (PLANTS) docking software. The directory of useful decoys (DUD) dataset for COX-2 was used to retrospectively validate the protocols; the DUD consists of 426 known inhibitors in 13289 decoys. Based on criteria used in the article describing DUD datasets, the default protocol showed poor results. However, having ARG513 as a hydrogen bond anchor increased the quality of the SBVS protocol. The modified protocol showed results that could be well considered, with a maximum enrichment factor (EF(max)) value of 32.2.     

虚拟细胞

虚拟细胞是20世纪末在国外刚刚兴起的一种细胞生物学研究方法,主要是通过计算机建立人工细胞模型,模拟细胞内外环境,从而进行生物学的研究和探索。虚拟细胞包含了多门学科前沿的研究成果,具有十分重要的意义。现从其发展历程、应用及其对生物学工作者的关系等方面进行综述。     

Homology modelling,virtual screening and molecular dynamics of the MARK3 KA1 domain for cancer drug design

Structural homology modelling was done with the software AMPS, MODELLER, PROCHECK, WHATIF AND VERIFY-3D to generate a quality model of human MARK3. Macromolecular docking simulations seem to confirm recent data in the literature and in MARK3 there does not occur intramolecular interactions between the associated kinase domain KA1 and the catalytic domain. Using virtual screening, we were able to identify and suggest the principal residues of MARK3 which interact with the ligands in addition to those reported in the literature. The pharmacophoric model obtained from Discovery Studio coincides with those obtained by molecular interaction fields, indicating the principal ligand residues of the MARK3 KA1 domain. Using virtual screening with pharmacophoric constraints as well as molecular dynamics, the most stable compounds in the ligand site as well as their potential toxicities were used to select potential inhibitors for further in vitro and in vivo investigations of human MARK3 KA1 domain, which could eventually pass to the market to be used for the treatment of head and neck cancer.     

虚拟草地生态系统的建立方法

通过分析草地生态系统的要素及其关系,将其抽象为多维的虚拟空间,综合应用草地生态学原理、地理信息系统技术、数据库技术、网络技术、软件技术以及JAVA语言,集成基础科学数据和动态信息,在国际互联网上构建了完全开放和共享的、具有10维空间的虚拟草地生态系统.系统实现了空间-属性的双向复合查询和分析、牧草信息检索等主要功能.结果表明,该虚拟系统包含信息量大、运行稳定,为业界提供了一个方便、快捷的信息查询和空间分析的共享平台.该系统是我国在互联网上第一个基于WebGIS技术的虚拟草地生态系统,为建设我国数字草原提供技术支持.     

Virtual resource development in the glycosciences

The development of Internet-based virtual resources is a relatively new area of scientific and technical activity that is currently undergoing rapid expansion. Major factors fuelling recent growth include the emergence of multimedia capabilities through the rapid evolution of the World Wide Web, the reduction in cost of high quality personal computers and graphics workstations and the provision of mass-marketed provider services. Prior to 1995 the presence of Internet resources in the glycosciences was virtually non-existent. Existing scientific knowledge was primarily made available on the Net through the provision of databases from gopher and ftp sites. A particular example in the glycosciences is the Carbbank database of biological carbohydrate sequences. We will describe here our efforts in 1994–95 in establishing The Glycoscience Network (TGN, http://bellatrix.pcl.ox.ac.uk/TGN/). These activities included the establishment of a newsgroup, mailing lists, Web resources and the running of the First Electronic Glycoscience Conference (EGC-1, http://bellatrix.pcl.ox.ac.uk/egc/). EGC-1 included many novel initiatives in the glycosciences including electronic posters and papers, a Virtual Conference Centre, a Web-based hyperglossary, Virtual Trade and Employment Centres, refereed electronic publishing, and the creation of a Virtual Reality Gallery. We would like to look towards the near future and discuss several initiatives in virtual resource creation that we believe will have significant scientific impact on the glycosciences including the development of bioinformatics-based servers, sophisticated interactive databases, and videoconferencing. Furthermore, we cherish the belief that these resources will foster international scientific collaboration and progress of an extent never previously possible. Finally, we indulge in speculation and make some suggestions on the form and long-term impact of Glycoscience Virtual Resources. We predict that their development may completely reconstruct the scientific environment that we work in as scientists and we reflect on the probable benefits and pitfalls to be encountered.This paper was presented at the First Electronic Glycoscience Conference (EGCI) on the World Wide Web, September 1995.