Replacing animal experiments: choices, chances and challenges

Replacing animal procedures with methods such as cells and tissues in vitro, volunteer studies, physicochemical techniques and computer modelling, is driven by legislative, scientific and moral imperatives. Non-animal approaches are now considered as advanced methods that can overcome many of the limitations of animal experiments. In testing medicines and chemicals, in vitro assays have spared hundreds of thousands of animals. In contrast, academic animal use continues to rise and the concept of replacement seems less well accepted in university research. Even so, some animal procedures have been replaced in neurological, reproductive and dentistry research and progress is being made in fields such as respiratory illnesses, pain and sepsis. Systematic reviews of the transferability of animal data to the clinical setting may encourage a fresh look for novel non-animal methods and, as mainstream funding becomes available, more advances in replacement are expected.     

PowerPoint in the classroom

Points of View (POV) addresses issues faced within life science education. Cell Biology Education has launched the POV feature to present two or more opinions published in tandem on a common topic. We consider POVs to be "Op-Ed" pieces designed to stimulate thought and dialog on significant educational issues. Each author has the opportunity to revise a POV after reading drafts of the other POVs. In this issue, we ask the question, "Is PowerPoint the best instructional medium to use in your class?" Everyone seems to have an opinion on Microsoft, but the intellectual merits of using PowerPoint (or similar software) is a growing question as states and institutions put more and more money into information technology and distance learning. Four POVs are presented: 1) David Keefe and James Willett provide their case why PowerPoint is an ideal teaching software. Keefe is an educational researcher at the Center for Technology in Learning at SRI International. Willett is a professor at George Mason University in the Departments of Microbial and Molecular Bioscience; as well as Bioinformatics and Computational Biology. 2) Kim McDonald highlights the causes of PowerPointlessness, a term which indicates the frequent use of PowerPoint as a crutch rather than a tool. She is a Bioscience Educator at the Shodor Education Foundation, Inc. 3) Diana Voss asks readers if PowerPoint is really necessary to present the material effectively or not. Voss is a Instructional Computing Support Specialist at SUNY Stony Brook. 4) Cynthia Lanius takes a light-hearted approach to ask whether PowerPoint is a technological improvement or just a change of pace for teacher and student presentations. Lanius is a Technology Integration Specialist in the Sinton (Texas) Independent School District. The authors span the range of teaching experiences and settings from which they bring different points of view to the debate. Readers are encouraged to participate in the online discussion forum hosted by CBE at www.cellbioed.org/discussion/public/main.cfm and/or contact the authors directly.     

Hypercard-based data management tools for molecular biologists

I have designed a Macintosh data management system for molecularbiologists. This system, called DataMinder, can be used to storeinformation about oligonucleotides, nucleic acid or proteinsequences, recombinant DNA clones, cells, reagents and protocols.DataMinder is not limited to data storage. A number of utilitiesfor data analysis are provided, including those for the evaluationof oligonucleotides for use as hybridization probes or primersfor DNA synthesis, and a variety of sequence editing features.Context-sensitive help is available on-line. DataMinder is simpleto use and to customize and allows for sharing of database informationacross a computer network.     

微机医学图像库

建立一个微机医学图像库,使（微机医学图像库）能象普通数据库一样便于管理和使用,材料和方法,开发硬件为５８６－９０机和ＥｐｓｏｎｓＥＳ－８００ｃ扫描仪,开发应用软件为Ｗｉｎｄｏｗｓ３．１的ＧＵＩ为开发环境,以Ｆｏｘｐｒｏ２．６为开发语言,Ｐｏｗｅｒｐｏｉｎｔ４．０（以后简称ＰＰＴ）为图像工具。     

COMPUTER ANALYSIS OF BIRD SOUNDS: A GUIDE TO CURRENT METHODS

ABSTRACT

Bioacoustics researchers can use a computer as a powerful tool to measure, classify, compare and synthetise sounds. Vocalisations on tape are commonly converted to a digital format suitable for a computer by using an analogue to digital converter and then a Fourier transformation. Alternatively, sonagrams can be measured, for example by using a digitising pad or an image analysis system. Correlations and indices of similarity have been used to compare sounds, but variations in both the time and frequency dimensions of a noise are a problem. A solution may be the use of pattern recognition methods such as elastic matching and time warping. These methods are briefly described and assessed.     

Cytomat-R: a computer-controlled multiple laser source multiparameter flow cytophotometer system.

A multiple illumination wavelength multiparameter flow cytophotometer system, using laser sources and controlled by a small, general-purpose digital computer, has been produced for use in the development of new flow cytometric techniques. Three different laser wave-lengths can be used simultaneously to illuminate different regions of the flow chamber; as many as five measurements of light scattering at various angles, extinction, and fluorescence at one or more wavelengths can be made at each illuminated station. Cells in suspension may be examined at rates of 1000 cells/sec, with seven correlated optical measurements being recorded for each cell. A library of programs for data manipulation and statistical analysis make it possible to use the system to develop and implement cell characterization, counting and classification procedures for basic and clinical research applications.     

Technology in the teaching of neuroscience: enhanced student learning

The primary motivation for integrating any form of education technology into a particular course or curriculum should always be to enhance student learning. However, it can be difficult to determine which technologies will be the most appropriate and effective teaching tools. Through the alignment of technology-enhanced learning experiences with a clear set of learning objectives, teaching becomes more efficient and effective and learning is truly enhanced. In this article, I describe how I have made extensive use of technology in two neuroscience courses that differ in structure and content. Course websites function as resource centers and provide a forum for student interaction. PowerPoint presentations enhance formal lectures and provide an organized outline of presented material. Some lectures are also supplemented with interactive CD-ROMs, used in the presentation of difficult physiological concepts. In addition, a computer-based physiological recording system is used in laboratory sessions, improving the hands-on experience of group learning while reinforcing the concepts of the research method. Although technology can provide powerful teaching tools, the enhancement of the learning environment is still dependent on the instructor. It is the skill and enthusiasm of the instructor that determines whether technology will be used effectively.     

多视角三维重建技术在石制品研究中的应用

三维重建技术已广泛应用于考古发掘、研究、展示等各个领域。通过对石制品的三维重建,可以帮助我们获取更加精准的数据信息,一些过去只能估算的测量指标得以精准化,由此催生出许多新的研究方法。本文回顾了十几年来三维重建方法在石器分析研究中的实例,如石制品的表面积、体积测量,台面、砾石面/人工面、片疤的精确数值获取,以及三维空间中打击方向、角度的判定等等,有效推动了石制品的深入研究。不同的三维重建技术各有优劣,多视角三维重建技术不受设备、场地、人员技术要求的限制,能够快速、准确地建立石制品的三维模型,并且获取如面积、体积、角度等通常难以准确测量的数据信息,其生成的点云、数字高程模型、正射影像图等还可以导入其他软件拓展使用。该技术的诸多优点,使其可以成为旧石器考古发掘、研究的日常工具。     

ORBIT: an integrated environment for user-customized bioinformatics tools

MOTIVATION: There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. RESULTS: We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.     

A computational modeling for the detection of diabetic retinopathy severity

Prolonged diabetes ultimately leads to Diabetic Retinopathy (DR) which is one of the leading causes of preventable blindness in the world. Through advanced image analysis techniques are used for abnormalities detection in retina that define and correlate the severity of DR. A thorough study is done in this area in recent past years and on the basis of these studies we have developed a computer based prediction model that is used to determine the severity of DR. To identify severity DR, we have analyzed the human eye image. We have extracted some important features from human eye image i.e. Blood Artery, Optical disc, Exudates. Based on these image and data we have designed an automated system for the determination of DR severity. This automated DR severity assessment methods can be used to predict the clinical case and conditions when young clinicians would agree or disagree with their more experienced fellow members. The algorithms described in this study may be used in clinical practice to validate or invalidate the diagnoses. Algorithms or method developed here may also be used for pooling diagnostic knowledge for serving mankind. Here we have described a computational based low cost retinal diagnostic approach which can aid an ophthalmologist to quickly diagnose the various stages of DR. This system can accept retinal images and can successfully detect any pathological condition associated with DR.     

Unbiased and automated identification of a circulating tumour cell definition that associates with overall survival

Circulating tumour cells (CTC) in patients with metastatic carcinomas are associated with poor survival and can be used to guide therapy. Classification of CTC however remains subjective, as they are morphologically heterogeneous. We acquired digital images, using the CellSearch™ system, from blood of 185 castration resistant prostate cancer (CRPC) patients and 68 healthy subjects to define CTC by computer algorithms. Patient survival data was used as the training parameter for the computer to define CTC. The computer-generated CTC definition was validated on a separate CRPC dataset comprising 100 patients. The optimal definition of the computer defined CTC (aCTC) was stricter as compared to the manual CellSearch CTC (mCTC) definition and as a consequence aCTC were less frequent. The computer-generated CTC definition resulted in hazard ratios (HRs) of 2.8 for baseline and 3.9 for follow-up samples, which is comparable to the mCTC definition (baseline HR 2.9, follow-up HR 4.5). Validation resulted in HRs at baseline/follow-up of 3.9/5.4 for computer and 4.8/5.8 for manual definitions. In conclusion, we have defined and validated CTC by clinical outcome using a perfectly reproducing automated algorithm.     

Can digital image classification be used as a standardised method for surveying peatland vegetation cover?

The ability to carry out systematic, accurate and repeatable vegetation surveys is an essential part of long-term scientific studies into ecosystem biodiversity and functioning. However, current widely used traditional survey techniques such as destructive harvests, pin frame quadrats and visual cover estimates can be very time consuming and are prone to subjective variations. We investigated the use of digital image techniques as an alternative way of recording vegetation cover to plant functional type level on a peatland ecosystem. Using an established plant manipulation experimental site at Moor House NNR (an Environmental Change Network site), we compared visual cover estimates of peatland vegetation with cover estimates using digital image classification methods, from 0.5 m × 0.5 m field plots. Our results show that digital image classification of photographs taken with a standard digital camera can be used successfully to estimate dwarf-shrub and graminoid vegetation cover at a comparable level to field visual cover estimates, although the methods were less effective for lower plants such as mosses and lichens. Our study illustrates the novel application of digital image techniques to provide a new way of measuring and monitoring peatland vegetation to the plant functional group level, which is less vulnerable to surveyor bias than are visual field surveys. Furthermore, as such digital techniques are highly repeatable, we suggest that they have potential for use in long-term monitoring studies, at both plot and landscape scales.     

Enzymes as reagents in clinical chemistry

Clinical chemistry is concerned with the measurement of substances in biological matter, predominantly blood, serum or plasma. Significant, though small, changes may take place as a prelude to a life-threatening situation. Therefore analytical techniques in clinical chemistry must be sensitive, specific and rapid. Many features of an enzyme-catalysed reaction are incorporated in the design of diagnostic reagents. The specificity of an enzyme may be employed to measure a substrate, or to remove interferents in another reaction. The measurement of substances that act as cofactors, inhibitors or activators can be achieved by the use of the appropriate enzyme. Finally, the enzyme, as a catalyst, can be used as a label in various immunoassay techniques. Clinical chemistry tests are carried out in a wide variety of environments, from the large laboratory undertaking many hundreds of analyses down to a clinic performing only a few tests. Enzymes are therefore employed in analytical systems based on widely differing presentations. Thus enzymes may be employed in a solution medium, immobilized on a surface of the reaction vessel or in a reagent strip. The requirements imposed on the reagent enzyme may be different in all of these situations.     

The promise of machine learning in predicting treatment outcomes in psychiatry

For many years, psychiatrists have tried to understand factors involved in response to medications or psychotherapies, in order to personalize their treatment choices. There is now a broad and growing interest in the idea that we can develop models to personalize treatment decisions using new statistical approaches from the field of machine learning and applying them to larger volumes of data. In this pursuit, there has been a paradigm shift away from experimental studies to confirm or refute specific hypotheses towards a focus on the overall explanatory power of a predictive model when tested on new, unseen datasets. In this paper, we review key studies using machine learning to predict treatment outcomes in psychiatry, ranging from medications and psychotherapies to digital interventions and neurobiological treatments. Next, we focus on some new sources of data that are being used for the development of predictive models based on machine learning, such as electronic health records, smartphone and social media data, and on the potential utility of data from genetics, electrophysiology, neuroimaging and cognitive testing. Finally, we discuss how far the field has come towards implementing prediction tools in real‐world clinical practice. Relatively few retrospective studies to‐date include appropriate external validation procedures, and there are even fewer prospective studies testing the clinical feasibility and effectiveness of predictive models. Applications of machine learning in psychiatry face some of the same ethical challenges posed by these techniques in other areas of medicine or computer science, which we discuss here. In short, machine learning is a nascent but important approach to improve the effectiveness of mental health care, and several prospective clinical studies suggest that it may be working already.     

Applications of computer vision and machine learning techniques for digitized herbarium specimens: A systematic literature review

Herbaria contain the treasure of millions of specimens that have been preserved for several years for scientific studies. To increase the rate of scientific discoveries, digitization of these specimens is currently ongoing to facilitate the easy access and sharing of data to a wider scientific community. Online digital repositories such as Integrated Digitized Biocollection and the Global Biodiversity Information Facility have already accumulated millions of specimen images yet to be explored. This presents the perfect time to take advantage of the opportunity to automate the identification process and increase the rate of novel discoveries using computer vision (CV) and machine learning (ML) techniques. In this study, a systematic literature review of more than 70 peer-reviewed publications was conducted focusing on the application of computer vision and machine learning techniques to digitized herbarium specimens. The study categorizes the different techniques and applications that are commonly used for digitized herbarium specimens and highlights existing challenges together with their potential solutions. We hope this study will serve as a firm foundation for new researchers in the relevant disciplines and will also be enlightening to both computer science and ecology experts.     

Lessons Learned from Implementing a Wet Laboratory Molecular Training Workshop for Beach Water Quality Monitoring

Rapid molecular testing methods are poised to replace many of the conventional, culture-based tests currently used in fields such as water quality and food science. Rapid qPCR methods have the benefit of being faster than conventional methods and provide a means to more accurately protect public health. However, many scientists and technicians in water and food quality microbiology laboratories have limited experience using these molecular tests. To ensure that practitioners can use and implement qPCR techniques successfully, we developed a week long workshop to provide hands-on training and exposure to rapid molecular methods for water quality management. This workshop trained academic professors, government employees, private industry representatives, and graduate students in rapid qPCR methods for monitoring recreational water quality. Attendees were immersed in these new methods with hands-on laboratory sessions, lectures, and one-on-one training. Upon completion, the attendees gained sufficient knowledge and practice to teach and share these new molecular techniques with colleagues at their respective laboratories. Key findings from this workshop demonstrated: 1) participants with no prior experience could be effectively trained to conduct highly repeatable qPCR analysis in one week; 2) participants with different desirable outcomes required exposure to a range of different platforms and sample processing approaches; and 3) the collaborative interaction amongst newly trained practitioners, workshop leaders, and members of the water quality community helped foster a cohesive cohort of individuals which can advocate powerful cohort for proper implementation of molecular methods.     

Stereotactic systems and procedures for depth electrode placement: technical aspects

The authors describe the conversion of the Leksell spherical system to that of the orthogonal approach for depth electrode placement, by the addition of relatively simple devices to the main frame. These modifications have created the need for new instrumentation such as teleradiology with laser beam centering and the use of an all-purpose stereotactic chair. The main device used for the orthogonal approach is an instrument and electrode carrier moving on sliding side bars. This system can also take advantage of the newer imaging techniques, such as CT scanning, digital angiography and NMR, by the addition of computer markers which are interchangeable with the frame side bars.     

Virtual telepathology in Egypt,applications of WSI in Cairo University

Telepathology, the practice of pathology at a long distance, has advanced continuously since 1986. Today, fourth-generation telepathology systems, so-called virtual slide telepathology systems, are being used for education applications. Both conventional and innovative surgical pathology diagnostic services are being designed and implemented as well. We have a successful experience in Egypt in applying the static & dynamic techniques in a pilot project between the Italian Hospital in Cairo (NPO) and the Civico Hospital in Palermo This project began in 2003 and continued till now. In 2004, centers in Venice, London and Pittsburgh participated actively in our project. During the past seven years we consulted on many problematic pathological cases with these different specialized pathological centers in Italy, UK & USA. In addition to the highly specialized scientific value of consulting on the cases and exchanging knowledge, we saved a lot of time and money and succeeded in providing our patients with a better medical service. In view of this success we have already established a new Digital Telepathology unit (DTU) in the pathology department, Cairo University, using the latest technique of telepathology which is Whole Slide Imaging (WSI) since one year. This unit is considered the first Digital pathology unit in all the universities of the whole Middle East. During the passed year we created a digital pathology library for the under graduate students using the WSI technique and changed the teaching method of the histopathology slides to be completely digital. We are building another digital pathology library (for post graduate candidates) which will be available to all pathology candidates in Egyptian universities & universities in the surrounding Arabic countries. We are also creating a digital pathology network between pathology centers in the Middle East for exchanging knowledge & telepathology.     

A high accuracy linear rate meter.

By implementing analog computer techniques using digital circuits, an instantaneous rate meter was built with approximately 100 times the accuracy of commercially available rate meters. The circuit is accurate to within +/- 0.2 events/min over a range of rates of 0.2-900 epm. Modifications can be made to provide a digital display of rate. The circuit design techniques used in developing the rate meter may be used to generate a wide variety of functions of time with very high accuracy.