Security Analysis and Improvement of ‘a More Secure Anonymous User Authentication Scheme for the Integrated EPR Information System’

Over the past few years, secure and privacy-preserving user authentication scheme has become an integral part of the applications of the healthcare systems. Recently, Wen has designed an improved user authentication system over the Lee et al.’s scheme for integrated electronic patient record (EPR) information system, which has been analyzed in this study. We have found that Wen’s scheme still has the following inefficiencies: (1) the correctness of identity and password are not verified during the login and password change phases; (2) it is vulnerable to impersonation attack and privileged-insider attack; (3) it is designed without the revocation of lost/stolen smart card; (4) the explicit key confirmation and the no key control properties are absent, and (5) user cannot update his/her password without the help of server and secure channel. Then we aimed to propose an enhanced two-factor user authentication system based on the intractable assumption of the quadratic residue problem (QRP) in the multiplicative group. Our scheme bears more securities and functionalities than other schemes found in the literature.     

Data processing and exchange tools to facilitate chemical genetic screening processes

Due to the development of chemical genomics, the screening of chemical libraries is used more and more by research laboratories to identify small molecule inhibitors or activators of cell functions. To facilitate the treatment and archiving of screening data, we developed a multiuser web application called Elisa Data Exchanger (EDE). The program is able to automatically identify which chemical compounds were tested. Several data exchange formats can be generated for visualization, printing, charting, or exporting to chemical analysis software. These data exchange functions allow for a comparison of results obtained from screening several targets in order to select the most specific compounds. EDE is freely available online at https://ibph.pharma.univ-montpl.fr/ede/ (login: evalede, password: loginede).     

麻疹减毒活疫苗国家参考品的制备及标定

为了制备麻疹减毒活疫苗国家参考品,选用国内麻疹疫苗生产株沪191制备麻疹疫苗参考品。生产过程中严格控制精密性、水分含量,对候选参考品进行鉴别试验、水分含量、病毒滴度及无菌检查等检验。检验合格后组织进行候选参考品病毒滴度协作标定,共有5个实验室参加了协作标定。协作标定完成后,对实验室内变异、实验室间变异及国际参考品在不同实验室间的变异进行了分析。此外还对疫苗进行了热稳定性和实时稳定性分析。结果显示经5个实验室协作标定后,麻疹减毒活疫苗国家参考品的滴度为4.96±0.26 lgCC ID50/m l,实验室内部变异在1.09%～4.64%之间,实验室间变异为2.62%。国际参考品在不同实验室间的变异为4.19%。稳定性考核数据表明制备的参考品具有较好的稳定性,符合作为麻疹减毒活疫苗国家参考品的要求,滴度为4.96±0.26 lgCC ID50/m l。     

The MetaFMF website: a high quality tool for meta-analysis of FMF

We present here the MetaFMF database (freely accessible at http://fmf.igh.cnrs.fr/metaFMF/index_us.html) that attempts to gather and unify, in a common resource, data on phenotype-genotype correlation in familial Mediterranean fever (FMF). A single accession form, including a large number of quality controls, has been implemented such that data, collected worldwide, are included in an homogeneous manner. The inclusion criterion has the objective to avoid interpretational bias: patients will be included only if they bear at least two mutations. The clinical form has been set up by an International editorial board (12 FMF expert centres), which guarantees the validity of the data. Data are anonymous and submitted by a secure interface, in which the researcher is logged in with a specific ID and password. A pilot study on 211 patients has shown the feasibility and relevance of this project. We anticipate that the use of MetaFMF will enable reliable assessment of phenotype-genotype correlations in FMF, and define a set of severe versus mild mutations/genotypes. It should also highlight reasons for previous inconsistencies in such correlations.     

Multilocus sequence typing for global surveillance of meningococcal disease

The global surveillance of bacterial pathogens is particularly important for bacteria with diverse and dynamic populations that cause periodic epidemics or pandemics. The isolate characterization methods employed for surveillance should: (1) generate unambiguous data; (2) be readily implemented in a variety of scenarios and be reproducible among laboratories; (3) be scalable and preferably available in a high throughput format; and (4) be cost effective. Multilocus sequence typing (MLST) was designed to meet these criteria and has been implemented effectively for a wide range of microorganisms. The 'Impact of meningococcal epidemiology and population biology on public health in Europe (EU-MenNet)' project had amongst its objectives: (1) to disseminate meningococcal MLST and sequence-based typing throughout Europe by establishing a centre for training and data generation, and (2) to produce a comprehensive Europe-wide picture of meningococcal disease epidemiology for the first time. Data produced from the project have shown the distribution of a relatively small number of STs, clonal complexes and PorA types that account for a large proportion of the disease-associated isolates in Europe. The project demonstrates how molecular typing can be combined with epidemiological data via the Internet for global disease surveillance.     

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases

MOTIVATION: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. RESULTS: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. AVAILABILITY: http://www.molgenis.nl     

Design and Implementation of an Interactive Web-Based Near Real-Time Forest Monitoring System

This paper describes an interactive web-based near real-time (NRT) forest monitoring system using four levels of geographic information services: 1) the acquisition of continuous data streams from satellite and community-based monitoring using mobile devices, 2) NRT forest disturbance detection based on satellite time-series, 3) presentation of forest disturbance data through a web-based application and social media and 4) interaction of the satellite based disturbance alerts with the end-user communities to enhance the collection of ground data. The system is developed using open source technologies and has been implemented together with local experts in the UNESCO Kafa Biosphere Reserve, Ethiopia. The results show that the system is able to provide easy access to information on forest change and considerably improves the collection and storage of ground observation by local experts. Social media leads to higher levels of user interaction and noticeably improves communication among stakeholders. Finally, an evaluation of the system confirms the usability of the system in Ethiopia. The implemented system can provide a foundation for an operational forest monitoring system at the national level for REDD+ MRV applications.     

候选结核疫苗的评价模型

卡介苗作为目前唯一批准使用的预防结核疫苗,由于无法提供充足的保护力,目前结核病依然是严重危害人类健康的传染病,因此筛选优质候选疫苗迫在眉睫。所有候选疫苗进入临床试验前必须评价其安全性、免疫原性以及有效性。评价结果在一定程度上也预示候选疫苗在人体的免疫作用,也是目前评价候选疫苗是否优于传统卡介苗的依据。论述候选结核疫苗临床试验前所使用的体内和体外评价模型。对评价模型的充分认识将提高候选疫苗评价数据对人体临床试验的预测意义,也可更具体地执行实验动物的替代、减少和优化原则。     

Vaccine stability study design and analysis to support product licensure

Stability evaluation supporting vaccine licensure includes studies of bulk intermediates as well as final container product. Long-term and accelerated studies are performed to support shelf life and to determine release limits for the vaccine. Vaccine shelf life is best determined utilizing a formal statistical evaluation outlined in the ICH guidelines, while minimum release is calculated to help assure adequate potency through handling and storage of the vaccine. In addition to supporting release potency determination, accelerated stability studies may be used to support a strategy to recalculate product expiry after an unintended temperature excursion such as a cold storage unit failure or mishandling during transport. Appropriate statistical evaluation of vaccine stability data promotes strategic stability study design, in order to reduce the uncertainty associated with the determination of the degradation rate, and the associated risk to the customer.     

HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees

MOTIVATION: Numerous database management systems have been developed for processing various taxonomic data bases on biological classification or phylogenetic information. In this paper, we present an integrated system to deal with interacting classifications and phylogenies concerning particular taxonomic groups. RESULTS: An information-theoretic view (taxon view) has been applied to capture taxonomic concepts as taxonomic data entities. A data model which is suitable for supporting semantically interacting dynamic views of hierarchic classifications and a query method for interacting classifications have been developed. The concept of taxonomic view and the data model can also be expanded to carry phylogenetic information in phylogenetic trees. We have designed a prototype taxonomic database system called HICLAS (HIerarchical CLAssification System) based on the concept of taxon view, and the data models and query methods have been designed and implemented. This system can be effectively used in the taxonomic revisionary process, especially when databases are being constructed by specialists in particular groups, and the system can be used to compare classifications and phylogenetic trees. AVAILABILITY: Freely available at the WWW URL: http://aims.cps.msu.edu/hiclas/ CONTACT: pramanik@cps.msu.edu; lotus@wipm.whcnc.ac.cn     

The 'experimental stable' of the BCG vaccine: safety, efficacy, proof, and standards, 1921-1933

The anti-tuberculosis BCG (Bacille Calmette-Guérin) vaccine was conceived and developed between 1905 and 1921 at Pasteur Institutes in France. Between 1921 and A. Calmette's death in 1933, the vaccine went through a first period of national and international production and distribution for its use in humans. In France these activities were exclusively carried out by Calmette and his collaborators at the Pasteur Institute in Paris. Initially improvised production in a small room in the cellar gave way in 1931 to the construction of the spacious and magnificent 'New laboratories for research on tuberculosis and the preparation of the BCG' within the premises of the Pasteur Institute. Presentation and image-building of the vaccine in France insisted on the fact that the BCG was not a commercial specialty but distributed free of charge. The technical monopoly of its production nevertheless lay with the Paris Pasteur Institute and standardization of scientific proof of safety, efficacy and stability was dominated by that Institute in France. In contrast, the international production and distribution of the vaccine was entrusted and transferred, free of charge, to trustworthy laboratories outside France. Multiplication of producers and users led to an increased need for standardization. For this process the analysis distinguishes between the standardization of scientific proof concerning safety, efficacy and stability of the vaccine and standardization of its medical uses. Whereas standardization was rather successful in the inter-war period in France, the international efforts remained rather unsuccessful. Only after world war II under Scandinavian leadership and in the context of mass vaccination programs supported by the WHO and UNICEF was the international standardization effectively implemented and succeeded at least to some extend.     

Experience with BXGrid: a data repository and computing grid for biometrics research

Research in the field of biometrics depends on the effective management and analysis of many terabytes of digital data. The quality of an experimental result is often highly dependent upon the sheer amount of data marshalled to support it. However, the current state of the art requires researchers to have a heroic level of expertise in systems software to perform large scale experiments. To address this, we have designed and implemented BXGrid, a data repository and workflow abstraction for biometrics research. The system is composed of a relational database, an active storage cluster, and a campus computing grid. End users interact with the system through a high level abstraction of four stages: Select, Transform, AllPairs, and Analyze. A high degree of availability and reliability is achieved through transparent fail over, three phase operations, and independent auditing. BXGrid is currently in daily production use by an active biometrics research group at the University of Notre Dame. We discuss our experience in constructing and using the system and offer lessons learned in conducting collaborative research in e-Science.     

Recombinant DNA laboratory data manager using DBASE III+

The use of recombinant DNA technology in clinical and research laboratories involves diverse information management functions such as keeping track of patient samples, blot membranes, polymerase chain reaction products and test results. We report here the use of a PC-based database manager (DBASE III+, Ashton-Tate) for the coordinated maintenance of these functions. We have implemented a menu driven interface, developed using DBASE's programming language, which provides a data entry and maintenance system. The system is easily learned by technologists and saves time and reduces data handling errors compared to a manual method. The system can rapidly look up data and produce customized worksheets or reports correlating all available clinical and laboratory information. We will provide a copy of the program disc to interested parties.     

Integration of nonchemical treatments for control of postharvest pyralid moths (Lepidoptera: Pyralidae) in almonds and raisins

We propose a treatment strategy combining an initial disinfestation treatment with one of three protective treatments as an alternative for chemical fumigation of almonds and raisins for control of postharvest insect populations. Initial disinfestation treatments using low oxygen controlled atmosphere (0.4% O2) were designed to disinfest product of field populations of pyralid moths; navel orangeworm, Amyelois transitella (Walker), in almonds and raisin moth, Cadra figulilella (Gregson), in raisins. The protective treatments were cold storage (10 degrees C), controlled atmosphere (5% O2) storage, and application of the Indianmeal moth granulosis virus, and were designed to prevent establishment of Indianmeal moth, Plodia interpunctella (Hübner). The initial disinfestation treatment was effective against laboratory populations of navel orangeworm and raisin moth. Efficacy of protective treatments was determined by exposure of commodities to laboratory Indianmeal moth populations at levels far higher than those found in commercial storage facilities. All three protective treatments prevented development of damaging Indianmeal moth populations as measured by pheromone trap catches and evaluation of product samples. Quality analysis by commercial laboratories showed that overall product quality for all protective treatments was maintained at levels acceptable by industry standards.     

GOBASE--a database of mitochondrial and chloroplast information

GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over 130 000 mitochondrial sequences, an increase of 37% over the previous release, and more than 30 000 chloroplast sequences in a new auxiliary database. To handle this flood of new data, we have designed and implemented GOpop, a Java system for population and verification of the database. We have also implemented a more powerful and flexible user interface using the PHP programming language. http://megasun.bch.umontreal.ca/gobase/gobase.html.     

An introduction and study design

Under the sponsorship of the International Programme on Chemical Safety (IPCS), 17 laboratories from diverse regions of the world participated in evaluating the utility of four plant bioassays for detecting genetic hazards of environmental chemicals. The bioassays included in this collaborative study were: Arabidopsis thaliana embryo and chlorophyll assay and Tradescantia stamen hair assay, Tradescantia paludosa micronucleus assay and Vicia Faba root tip assay. Four to six laboratories participated in the performance of each of the bioassays. All laboratories participating in a particular bioassay were supplied with uniform plant material as well as standardized protocol. Five direct acting water soluble test chemicals, i.e. maleic hydrazide, methyl nitrosourea, ethyl methanesulfonate, sodium azide and azidoglycerol, were selected for this study. The study was designed to be completed in three phases. Ethyl methanesulfonate was used as a positive control and has already been reported earlier (Sandhu et al., 1991). The data from the remaining four chemicals used for the evaluation of four plant test systems in the first phase of the collaborative study are reported in this issue.     

An ontology for bioinformatics applications.

MOTIVATION: An ontology of biological terminology provides a model of biological concepts that can be used to form a semantic framework for many data storage, retrieval and analysis tasks. Such a semantic framework could be used to underpin a range of important bioinformatics tasks, such as the querying of heterogeneous bioinformatics sources or the systematic annotation of experimental results. RESULTS: This paper provides an overview of an ontology [the Transparent Access to Multiple Biological Information Sources (TAMBIS) ontology or TaO] that describes a wide range of bioinformatics concepts. The present paper describes the mechanisms used for delivering the ontology and discusses the ontology's design and organization, which are crucial for maintaining the coherence of a large collection of concepts and their relationships. AVAILABILITY: The TAMBIS system, which uses a subset of the TaO described here, is accessible over the Web via http://img.cs.man.ac.uk/tambis (although in the first instance, we will use a password mechanism to limit the load on our server). The complete model is also available on the Web at the above URL.     

The technology of the Global HIV Vaccine Research Cryorepository

This paper gives an overview of our developments in the fields of cryotechnology and cryoelectronics for managing biological samples stored over liquid nitrogen, fields that are essential to a central cryostorage facility for AIDS related material used in worldwide collaborative research. As a fundamental part of this project we have developed new electronic cryovials and carrier plates attached to Flash memory chips, so that a redundant and portable set of data is present with each sample. The recovery of peripheral blood mononuclear cells (PBMCs) after cryopreservation in the new cryosubstrates showed, especially for small sample volumes (0.1 ml), an increased viability in comparison to the preservation in standard cryovials. The electronic cryosubstrates interface with a dedicated laboratory workflow management system for reproducible and standardized sample processing. This system can read standard operating procedures (SOPs) stored on each sample's memory chip. Finally, we have developed a polymorphic cryoelectronic infrastructure for sample storage tanks. This cryoelectronic system has been integrated in a hermetic storage and semiautomatic handling environment. The new technologies provide state‐of‐the‐art sample identification, documentation and tracking that brings added value to each sample. The first application of these technologies is in a worldwide collaborative research towards the production of an AIDS vaccine. The functionality and versatility of the technologies will lead to an essential optimization of sample and data exchange for global clinical studies by ensuring a high degree of standardization between laboratories.     

Deep within the filarial genome: progress of the filarial genome project.

Four years ago, a WHO/United Nations Development Programme/World Bank-sponsored genome project to study the filarial lymphatic nematode parasite Brugia malayi was initiated. The project took as its aims gene discovery for drug target and vaccine candidate identification, genome mapping, dissemination of genomic data to the world community and training of endemic country partners in genomic research. In this article, the principal investigators in the laboratories behind the project describe the background to the project, the data now emerging and goals for the future. Open access to filarial genome data is emphasized.