A Software Architecture for Multi-Cellular System Simulations on Graphics Processing Units

The first aim of simulation in virtual environment is to help biologists to have a better understanding of the simulated system. The cost of such simulation is significantly reduced compared to that of in vivo simulation. However, the inherent complexity of biological system makes it hard to simulate these systems on non-parallel architectures: models might be made of sub-models and take several scales into account; the number of simulated entities may be quite large. Today, graphics cards are used for general purpose computing which has been made easier thanks to frameworks like CUDA or OpenCL. Parallelization of models may however not be easy: parallel computer programing skills are often required; several hardware architectures may be used to execute models. In this paper, we present the software architecture we built in order to implement various models able to simulate multi-cellular system. This architecture is modular and it implements data structures adapted for graphics processing units architectures. It allows efficient simulation of biological mechanisms.     

Human Performance in a Realistic Instrument-Control Task during Short-Term Microgravity

Previous studies have documented the detrimental effects of microgravity on human sensorimotor skills. While that work dealt with simple, laboratory-type skills, we now evaluate the effects of microgravity on a complex, realistic instrument-control skill. Twelve participants controlled a simulated power plant during the short-term microgravity intervals of parabolic flight as well as during level flight. To this end they watched multiple displays, made strategic decisions and used multiple actuators to maximize their virtual earnings from the power plant. We quantified control efficiency as the participants’ net earnings (revenue minus expenses), motor performance as hand kinematics and dynamics, and stress as cortisol level, self-assessed mood and self-assessed workload. We found that compared to normal gravity, control efficiency substantially decreased in microgravity, hand velocity slowed down, and cortisol level and perceived physical strain increased, but other stress and motor scores didn’t change. Furthermore, control efficiency was not correlated with motor and stress scores. From this we conclude that realistic instrument control was degraded in short-term microgravity. This degradation can’t be explained by the motor and/or stress indicators under study, and microgravity affected motor performance differently in our complex, realistic skill than in the simple, laboratory-type skills of earlier studies.     

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。     

Accessible haptic technology for drug design applications

Structure-based drug design is a creative process that displays several features that make it closer to human reasoning than to machine automation. However, very often the user intervention is limited to the preparation of the input and analysis of the output of a computer simulation. In some cases, allowing human intervention directly in the process could improve the quality of the results by applying the researcher intuition directly into the simulation. Haptic technology has been previously explored as a useful method to interact with a chemical system. However, the need of expensive hardware and the lack of accessible software have limited the use of this technology to date. Here we are reporting the implementation of a haptic-based molecular mechanics environment aimed for interactive drug design and ligand optimization, using an easily accessible software/hardware combination.     

Virtual Reality as an upper Limb Rehabilitation Approach

Cerebrovascular diseases seriously reduce the quality of life of patients. One of the priority tasks of restoring individual independency, daily living and social activity of patients is to restore basic motor skills such as the reaching, manipulating, and bimanual tasks an coordination. For successful recovery of movement necessary to conduct training in real environment, active participation of the patient, and interactive biofeedback that allows the patient to control the correct performance of motor tasks and adjust their own efforts. Evolution of computer technology gives an opportunity to improve the classical approaches in stroke rehabilitation. To make rehabilitation process met necessary terms, in everyday practice often used high technological devices, such as virtual reality (VR) systems. The technical basis of VR is an artificial three-dimensional environment that is created with computer and displayed on the screen. These technologies allow recreating the necessary training environment for motor skills relearning, as well as to provide interactive biofeedback and make rehabilitation process more intensive. This review present an information about history of VR technology developments, experience of upper limb rehabilitation using VR systems and comparative analysis of different VR based rehabilitation approaches.     

Advanced technologies in plastic surgery: how new innovations can improve our training and practice

Over the last two decades, virtual reality, haptics, simulators, robotics, and other "advanced technologies" have emerged as important innovations in medical learning and practice. Reports on simulator applications in medicine now appear regularly in the medical, computer science, engineering, and popular literature. The goal of this article is to review the emerging intersection between advanced technologies and surgery and how new technology is being utilized in several surgical fields, particularly plastic surgery. The authors also discuss how plastic and reconstructive surgeons can benefit by working to further the development of multimedia and simulated environment technologies in surgical practice and training.     

Teaching the Blind to Find Their Way by Playing Video Games

Computer based video games are receiving great interest as a means to learn and acquire new skills. As a novel approach to teaching navigation skills in the blind, we have developed Audio-based Environment Simulator (AbES); a virtual reality environment set within the context of a video game metaphor. Despite the fact that participants were naïve to the overall purpose of the software, we found that early blind users were able to acquire relevant information regarding the spatial layout of a previously unfamiliar building using audio based cues alone. This was confirmed by a series of behavioral performance tests designed to assess the transfer of acquired spatial information to a large-scale, real-world indoor navigation task. Furthermore, learning the spatial layout through a goal directed gaming strategy allowed for the mental manipulation of spatial information as evidenced by enhanced navigation performance when compared to an explicit route learning strategy. We conclude that the immersive and highly interactive nature of the software greatly engages the blind user to actively explore the virtual environment. This in turn generates an accurate sense of a large-scale three-dimensional space and facilitates the learning and transfer of navigation skills to the physical world.     

ElePhant: an anatomic-electronic simulation system for the evaluation of computer assisted interventions and surgical education]

BACKGROUND: Suitable simulation systems providing realistic conditions are required for preclinical evaluation of computer assisted interventions and surgical training. Techniques are necessary for an objective detection of injuries to the structures at risk. The aim of this study was the technical realization of a simulation system for the ENT intervention, mastoidectomy.MATERIALS AND METHODS: The basis of the simulation system was a CT scan of a cadaver skull. Using 3D printing, an anatomical phantom with realistic bone-like properties was created. Electronic detection systems were integrated into the structures at risk. A study with 16 ENT surgeons was conducted to prove the system's suitability for surgical training.RESULTS: The creation of simulation systems for the objective evaluation of surgical intervention qualities is feasible. A modular structure enables economic and simple replacement of the simulation area. The modules are cost effective and reproducible with high accuracy. The present study shows that the simulation system can be applied in surgical education and evaluation as an alternative to cadavers.CONCLUSION: Objective evaluation of injured structures at risk can be realized in real time. The simulation system permits preclinical evaluation studies of computer assisted instruments and surgical education. Reproducibility of the results makes multi-center studies possible.     

Modeling and simulating biogeochemical cycles: the BCS freeware

The use of simulation is a scientifically-recognized way of studying biogeochemical cycles, mainly when consecutive disturbances are made. As a pedagogical tool, simulation helps students gain insight into the response dynamics of the respective biogeochemical cycle. The development of simulation tools for educational purposes has not progressed much for the last couple of decades, despite advances in computer science. Trying to fill in that gap, this paper presents the biogeochemical cycles simulator (BCS) freeware, a more user-friendly replacement for older simulators. The BCS is a light-weight, user-friendly, Windows®-based simulator. Using the sulfur biogeochemical cycle as an example, the simulation results from two sequential disturbances were compared with those of the former tools: the sum of relative errors between the three tools was never greater than 2.7%. Moreover, a real-world event (Mount Pinatubo’s Eruption 1991) was also simulated, giving similar results to those actually measured. The major improvements made include: a friendly graphical user interface, unlimited number of reservoirs, direct input of mass fluxes, multi-disturbance assessment, and fully customizable plots. The BCS freeware has been used in case studies, in a biogeochemical cycles course of a B.S. in Chemistry at the University of São Paulo, Brazil. Simulations helped students to develop decision-making and group-working skills, as well as enhanced data interpretation. Moreover, the students were able to recognize how even small disturbances can cause short- and long-term impacts on biogeochemical cycles. A set of possible strategies for using BCS as an educational tool is also provided in this work.

     

Objective fidelity evaluation in multisensory virtual environments: auditory cue fidelity in flight simulation

We argue that objective fidelity evaluation of virtual environments, such as flight simulation, should be human-performance-centred and task-specific rather than measure the match between simulation and physical reality. We show how principled experimental paradigms and behavioural models to quantify human performance in simulated environments that have emerged from research in multisensory perception provide a framework for the objective evaluation of the contribution of individual cues to human performance measures of fidelity. We present three examples in a flight simulation environment as a case study: Experiment 1: Detection and categorisation of auditory and kinematic motion cues; Experiment 2: Performance evaluation in a target-tracking task; Experiment 3: Transferrable learning of auditory motion cues. We show how the contribution of individual cues to human performance can be robustly evaluated for each task and that the contribution is highly task dependent. The same auditory cues that can be discriminated and are optimally integrated in experiment 1, do not contribute to target-tracking performance in an in-flight refuelling simulation without training, experiment 2. In experiment 3, however, we demonstrate that the auditory cue leads to significant, transferrable, performance improvements with training. We conclude that objective fidelity evaluation requires a task-specific analysis of the contribution of individual cues.     

A program for simulated rodent surgical training

For the inexperienced individual, learning surgical techniques can be taxing. The authors developed a rodent surgery dry lab training program to assist educational and research institutions in providing low-stress training for basic surgical techniques using handmade, cost-effective simulation models. The program not only helps students develop essential skills in basic surgery, but also fulfills the mandate of the 3Rs by allowing students to repeatedly practice and refine their skills on models rather than live animals. This type of training is a valuable tool in bridging the gap between computer training and training with live animals.     

基于群体协同交互式学习模式的“微生物生理学”虚拟仿真实验教学方法

随着我国虚拟仿真实验教学工作的开展,群组式学习模式被越来越多地探讨并应用到实际教学中,但将此学习模式与虚拟仿真类实验课程相结合进行教学研究的实例相对较少。针对微生物类实验实践教学中存在的典型问题,以哈尔滨工业大学“微生物生理学”研究生精品课程建设研究为例,提出基于群体协同交互式学习模式的“微生物生理学”虚拟仿真实验教学研究,以期打造微生物学科一流实验/实践类教学课程。本文阐述了群体协同交互式学习模式的内涵、构成要素及优势,论述了群体协同交互式学习模式在“微生物生理学”虚拟仿真实验教学中的实现过程,并总结了该模式的不足与未来发展方向。     

An investigative laboratory course in human physiology using computer technology and collaborative writing

Active investigative student-directed experiences in laboratory science are being encouraged by national science organizations. A growing body of evidence from classroom assessment supports their effectiveness. This study describes four years of implementation and assessment of an investigative laboratory course in human physiology for 65 second-year students in sports medicine and biology at a small private comprehensive college. The course builds on skills and abilities first introduced in an introductory investigations course and introduces additional higher-level skills and more complex human experimental models. In four multiweek experimental modules, involving neuromuscular, reflex, and cardiovascular physiology, by use of computerized hardware/software with a variety of transducers, students carry out self-designed experiments with human subjects and perform data collection and analysis, collaborative writing, and peer editing. In assessments, including standard course evaluations and the Salgains Web-based evaluation, student responses to this approach are enthusiastic, and gains in their skills and abilities are evident in their comments and in improved performance.     

Using System Emulation to Model Next-Generation Shared Virtual Memory Clusters

Recently much effort has been spent on providing a shared address space abstraction on clusters of small-scale symmetric multiprocessors. However, advances in technology will soon make it possible to construct these clusters with larger-scale cc-NUMA nodes, connected with non-coherent networks that offer latencies and bandwidth comparable to interconnection networks used in hardware cache-coherent systems. The shared memory abstraction can be provided on these systems in software across nodes and hardware within nodes.Recent simulation results have demonstrated that certain features of modern system area networks can be used to greatly reduce shared virtual memory (SVM) overheads [5,19]. In this work we leverage these results and we use detailed system emulation to investigate building future software shared memory clusters. We use an existing, large-scale hardware cache-coherent system with 64 processors to emulate a complete future cluster. We port our existing infrastructure (communication layer and shared memory protocol) on this system and study the behavior of a set of real applications. We present results for both 32- and 64-processor system configurations.We find that: (i) System emulation is invaluable in quantifying potential benefits from changes in the technology of commodity components. More importantly, it reveals potential problems in future systems that are easily overlooked in simulation studies. Thus, system emulation should be used along with other modeling techniques (e.g., simulation, implementation) to investigate future trends. (ii) Our work shows that current SVM protocols can only partially take advantage of faster interconnects and wider nodes due to operating system and architectural implications. We quantify the related issues and identify the areas where more research is required for future SVM clusters.     

Using Amphibians and Reptiles to learn the Process of Science

The National Research Council's document, Inquiry and the National Science Education Standards (2000) describes an elementary science classroom as one that is composed of learners who are engaged in scientific processes. In such a setting, children ask real-world questions and seek real-world solutions. As students pursue their inquiries, they often move away from science textbooks, and they implement mathematical skills, read literature, conduct research in electronic databases, write stories, and so forth in a larger context. What was originally a regular science lesson becomes an opportunity for integration across the curriculum. This article describes an integrated unit on bats and specifically addresses the National Science Education Standards.     

技能大赛背景下高职生物制药技术综合实训课程教学改革

综合实训是高职学生将理论知识与生产实践有机融合的重要教学环节。本文介绍了技能大赛背景下,学院生物制药技术专业立足“以赛促教、以赛促建、以赛促学、育训结合”特色,以青霉素发酵工艺实验为例,从教学目标、教学内容、教学方法、考核等内容进行的改革与实践,将发酵设备的实践操作与虚拟仿真软件相融合,双向交互式开展课程。突破发酵过程控制的主观依赖性,建立发酵过程参数控制的量化管理和评价,更有利于实现技能大赛与实践教学的高效融合。通过近几年的改革与实践,取得良好的教学效果,为同类课程基于技能大赛的教学实践改革提供了新的思路和借鉴。     

Training considerations for the intracoelomic implantation of electronic tags in fish with a summary of common surgical errors

Training is a fundamental part of all scientific and technical disciplines. This is particularly true for all types of surgeons. For surgical procedures, a number of skills are necessary to reduce mistakes. Trainees must learn an extensive yet standardized set of problem-solving and technical skills to handle challenges as they arise. There are currently no guidelines or consistent training methods for those intending to implant electronic tags in fish; this is surprising, considering documented cases of negative consequences of fish surgeries and information from studies having empirically tested fish surgical techniques. Learning how to do fish surgery once is insufficient for ensuring the maintenance or improvement of surgical skill. Assessment of surgical skills is rarely incorporated into training, and is needed. Evaluation provides useful feedback that guides future learning, fosters habits of self-reflection and self-remediation, and promotes access to advanced training. Veterinary professionals should be involved in aspects of training to monitor basic surgical principles. We identified attributes related to knowledge, understanding, and skill that surgeons must demonstrate prior to performing fish surgery including a “hands-on” assessment using live fish. Included is a summary of common problems encountered by fish surgeons. We conclude by presenting core competencies that should be required as well as outlining a 3-day curriculum for training surgeons to conduct intracoelomic implantation of electronic tags. This curriculum could be offered through professional fisheries societies as professional development courses.     

生态系统服务与景观格局集成研究综述

生态系统服务是综合科学和政策应用的有效工具,可用于应对人类干扰下的景观和生态系统服务的快速退化等复杂生态环境问题。综述生态系统服务与景观格局集成的学科发展、基础理论和模型开发的进展与存在的问题,建立可用的集成建模框架,并提出知识集成的概念框架:1)在要素层,"政策-决策—景观—生态系统服务—社会经济系统"的跨学科知识反馈环是集成理论基础; 2)在模型层,结构化、多层次的集成模拟模型是核心方法; 3)在数据层,多源数据集成是模拟模型的数据基础。集成生态系统服务与景观格局为区域生态环境治理实践提供了科学参考,能更好地应对生态系统服务科学与应用的挑战。     

INDISIM-YEAST: an individual-based simulator on a website for experimenting and investigating diverse dynamics of yeast populations in liquid media

Simulation modelling can be used to capture and mimic real-world microbial systems that, unlike the real-world, can then be experimented upon as a new kind of experimental milieu. Individual-based models, in which individuals interact dynamically with each other as structural elements in the model world, exemplify this view of simulation modelling. These models are more difficult to analyze, understand and communicate than traditional analytical models. It is good practice to provide executable versions that perform simulation results. INDISIM-YEAST, developed to deal with yeast populations in liquid media, models the evolution of a set of yeasts by setting up rules of behavior for each individual cell according to its own biological regulations and characteristics. The aim of this work is to develop and present a website from which INDISIM-YEAST is accessible, and how to carry out yeast simulations to further the skills associated with the use of this individual-based simulator. A good and useful way to analyze this yeast simulator is to experiment and explore the manner in which it reacts to changes in parameter values, initial conditions or assumptions. The application results in a very versatile program that could be used in controlled simulation experiments via the Internet.