利用C++ Builder实现肿瘤遗传信息数据库的查询和利用

利用C＋＋ Builder,Microsoft SQL Server 2000数据库和ADO控件构建了肿瘤遗传信息的查询系统。先在数据库中建立肿瘤的生物信息表,通过C＋＋ Builder编写代码,添加ADO控件及其属性设置实现数据库的访问和信息查询。     

A genetic code Boolean structure. II. The genetic information system as a Boolean information system

A Boolean structure of the genetic code where Boolean deductions have biological and physicochemical meanings was discussed in a previous paper. Now, from these Boolean deductions we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory. In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96×10²⁵ bits per kg. In addition to this, for the experimental estimations of the minimum energy dissipation in genetic logic operations, we present two postulates: (1) the energy E _i (i = 1, 2, ..., 20) of amino acids in the messages conveyed by proteins is proportional to the value of information, and (2) amino acids are distributed according to their energy E _i so the amino acid population in proteins follows a Boltzmann distribution. Specifically, in the genetic message carried by the DNA from the genomes of living organisms, we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.     

Analysis of the morphological substrate of information processing in the striatum based on organizational characteristics of its afferent projections

By the method of axonal transport of the retrograde markers, the afferent projections, coming from functionally different cortical and subcortical structures to various segments of the caudate nucleus, were investigated in the putamen and the nucleus accumbens of the dog brain. On the basis of the determined peculiarities of the spatail organization of these projections, the morphological aspects of the segregated and convergent conducting and processing of the information in the striatum, which underlie their functioning, were analyzed.     

GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections

The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.     

Approach to modeling of a regional ecological system and spatial relations of its components based on integrated interdisciplinary information

An approach to spatial analysis and modeling of relations between components of a regional ecosystem is exemplified by the Altai ecoregion. Problems of pretreatment of heterogeneous geographical data are considered in order to make them fit for the conjugate spatial analysis. Emphasis is placed on problems of unification of thematically diversified information. Possibilities of carrying out multiple parameter complex analysis of information files within the framework of regional interdisciplinary research are demonstrated.     

Prediction model for knee osteoarthritis based on genetic and clinical information

Introduction  

Osteoarthritis (OA) is the most common bone and joint disease influenced by genetic and environmental factors. Recent association studies have uncovered the genetic factors behind OA, its susceptibility genes, which would enable us to predict disease occurrence based on genotype information. However, most previous studies have evaluated the effects of only a single susceptibility gene, and hence prediction based on such information is not as reliable. Here, we constructed OA-prediction models based on genotype information from a case-control association study and tested their predictability.     

Evolution of hominoids and the search for a genetic basis for creating humanness

The phylogenetic relationship of human and apes are reviewed. The history of molecular phylogenetic studies in this field is then discussed, as is the role of natural selection at the molecular level. It is argued that approximately 10,000 genetic changes are responsible for creating human specific phenotypes. A genome-wide comparison is necessary to decipher those changes.     

Ethical issues raised by personalized nutrition based on genetic information

Four principles are taken as basis for the ethical analysis: autonomy, nonmaleficence, beneficence, and justice. Health is understood as a limited aspect of wellbeing. Food is understood as an important aspect of wellbeing, not only an instrument for health. Modern society is characterized by a tendency to identify wellbeing with external rather than subjective circumstances, to identify wellbeing with health, and to create exaggerated health expectations. Based upon this understanding, aspects of personalized nutrition are discussed: genetic testing, counselling, and development of special dietary products. Today the predictive value of genetic tests for personal nutrition is limited, and experimental at best. Recommendations for the future: Personalized nutrition must be based on solid knowledge. Phenotypic analyses should be used when adequate. When a genetic test can have a clear advantage, this should be preferred. Opportunistic screening should only be used when clearly beneficial. Specially trained persons should collect information from genetic tests and carry through councelling on a personal basis. Marketing of genetic tests directly sold to the public should be discouraged. Development of special products for personalized nutrition may be necessary in some cases. However, this may also lead to a medicalization of diet.     

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool

BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules. A new version of BRAGI has been developed that is supported on Windows, Linux and SGI. The user interface has been rewritten to give the standard 'look and feel' of the chosen operating system and to provide a more intuitive, easier usage. A large number of new features have been added. Information from public databases such as SWISS-PROT, InterPro, DALI and OMIM can be displayed in the 3D viewer. Structures can be searched for homologous sequences using the NCBI BLAST server.     

基于知识库的植物害虫鉴别计算机辅助系统

在收集大量国内和外来害虫资料及图谱的基础上,采用Visual Basic6.0作为系统开发语言,模拟专家鉴别害虫的思路,建立了3个适合于害虫鉴别的计算机辅助鉴别模式,分别为计算机二叉分类检索表模式、外部特征组合鉴别模式和图谱显示辅助鉴别模式。     

Quantum-like model of processing of information in the brain based on classical electromagnetic field

We propose a model of quantum-like (QL) processing of mental information. This model is based on quantum information theory. However, in contrast to models of "quantum physical brain" reducing mental activity (at least at the highest level) to quantum physical phenomena in the brain, our model matches well with the basic neuronal paradigm of the cognitive science. QL information processing is based (surprisingly) on classical electromagnetic signals induced by joint activity of neurons. This novel approach to quantum information is based on representation of quantum mechanics as a version of classical signal theory which was recently elaborated by the author. The brain uses the QL representation (QLR) for working with abstract concepts; concrete images are described by classical information theory. Two processes, classical and QL, are performed parallely. Moreover, information is actively transmitted from one representation to another. A QL concept given in our model by a density operator can generate a variety of concrete images given by temporal realizations of the corresponding (Gaussian) random signal. This signal has the covariance operator coinciding with the density operator encoding the abstract concept under consideration. The presence of various temporal scales in the brain plays the crucial role in creation of QLR in the brain. Moreover, in our model electromagnetic noise produced by neurons is a source of superstrong QL correlations between processes in different spatial domains in the brain; the binding problem is solved on the QL level, but with the aid of the classical background fluctuations.     

Real-time unconstrained object recognition: a processing pipeline based on the mammalian visual system

The mammalian visual system is still the gold standard for recognition accuracy, flexibility, efficiency, and speed. Ongoing advances in our understanding of function and mechanisms in the visual system can now be leveraged to pursue the design of computer vision architectures that will revolutionize the state of the art in computer vision.     

Analysis of the morphological substrate of information processing in the dog brain pallidal complex based on organizational characteristics of its afferent projections

Projections from functionally diverse cortical and subcortical structures (cortex, amygdaloid body, substantia nigra, ventral tegmental area, and thalamus) to the pallidum (globus pallidus, entopeduncular nucleus and ventral pallidum) were studied in dogs using the method of axonal transport of the retrograde markers. Anatomical aspects of both the functional heterogeneity of the pallidal structures and integrative processing of information which underlie the mechanisms of adaptive behavior, were analyzed on the basis of the results obtained.     

Geographical information system parallelization for spatial big data processing: a review

With the increasing interest in large-scale, high-resolution and real-time geographic information system (GIS) applications and spatial big data processing, traditional GIS is not efficient enough to handle the required loads due to limited computational capabilities.Various attempts have been made to adopt high performance computation techniques from different applications, such as designs of advanced architectures, strategies of data partition and direct parallelization method of spatial analysis algorithm, to address such challenges. This paper surveys the current state of parallel GIS with respect to parallel GIS architectures, parallel processing strategies, and relevant topics. We present the general evolution of the GIS architecture which includes main two parallel GIS architectures based on high performance computing cluster and Hadoop cluster. Then we summarize the current spatial data partition strategies, key methods to realize parallel GIS in the view of data decomposition and progress of the special parallel GIS algorithms. We use the parallel processing of GRASS as a case study. We also identify key problems and future potential research directions of parallel GIS.     

Posttranslational processing of the LDL receptor and its genetic disruption in familial hypercholesterolemia

Synthesis of the low density lipoprotein (LDL) receptor was studied by incubation of cultured human fibroblasts with 35S-methionine followed by immunoprecipitation with a monoclonal antireceptor antibody. The receptor was synthesized as a precursor with an apparent molecular weight of 120 kilodaltons (kd) that was converted to a mature form of 160 kd. This novel form of processing occurred 15-30 min after synthesis and did not appear to be due to the simple addition of N-linked oligosaccharide chains. Fibroblasts from a child with the phenotype of homozygous familial hypercholesterolemia showed a disruption in receptor processing. This child has two different mutant alleles at the LDL receptor locus. One allele, inherited from his heterozygous mother, produces an abnormal 120 kd protein that cannot be processed to the mature 160 kd form. The other allele, inherited from his heterozygous father, produces a receptor that is synthesized as an elongated 170 kd precursor which undergoes a 40 kd increase in molecular weight to form an abnormally large receptor of 210 kd.