Content-based image retrieval system using neural networks

An effective image retrieval system is developed based on the use of neural networks (NNs). It takes advantages of association ability of multilayer NNs as matching engines which calculate similarities between a user's drawn sketch and the stored images. The NNs memorize pixel information of every size-reduced image (thumbnail) in the learning phase. In the retrieval phase, pixel information of a user's drawn rough sketch is inputted to the learned NNs and they estimate the candidates. Thus the system can retrieve candidates quickly and correctly by utilizing the parallelism and association ability of NNs. In addition, the system has learning capability: it can automatically extract features of a user's drawn sketch during the retrieval phase and can store them as additional information to improve the performance. The software for querying, including efficient graphical user interfaces, has been implemented and tested. The effectiveness of the proposed system has been investigated through various experimental tests.     

A new interactive computerized data base and retrieval system.

A new computerized data base and retrieval system for a minicomputer has been devised for storing and retrieving clinical data. It features interactive terminal input and output using a pagination scheme as well as a subset mapping scheme for interactive retrieval. The pagination system, file structuring and retrieval system are discussed.     

Retrieving mutation-specific information for human proteins in UniProt/Swiss-Prot Knowledgebase

The UniProt/Swiss-Prot Knowledgebase records about 30,500 variants in 5,664 proteins (Release 52.2). Most of these variants are manually curated single amino acid polymorphisms (SAPs) with references to the literature. In order to keep the list of published documents related to SAPs up to date, an automatic information retrieval method is developed to recover texts mentioning SAPs. The method is based on the use of regular expressions (patterns) and rules for the detection and validation of mutations. When evaluated using a corpus of 9,820 PubMed references, the precision of the retrieval was determined to be 89.5% over all variants. It was also found that the use of nonstandard mutation nomenclature and sequence positional correction is necessary to retrieve a significant number of relevant articles. The method was applied to the 5,664 proteins with variants. This was performed by first submitting a PubMed query to retrieve articles using gene or protein names and a list of mutation-related keywords; the SAP detection procedure was then used to recover relevant documents. The method was found to be efficient in retrieving new references on known polymorphisms. New references on known SAPs will be rendered accessible to the public via the Swiss-Prot variant pages.     

LC-MS/MS测定单抗药动学参数的样品前处理方法研究进展

随着生物技术药物研发的大力开展,单抗类药物的药动学评价越来越受到重视。对近年来应用LC-MS/MS检测单抗类药物药动 学特征的文献进行归纳,总结其样品前处理的不同方法及各自优缺点和适用范围,为单抗类药物LC-MS/MS检测方法的进一步研究提供 参考。     

A microcomputer based program for the storage and retrieval of experimental animal information

A microcomputer based program for the storage and selective retrieval of experimental animal information has been developed for use on any system which runs under CP/M system software. The program has been designed to be completely conversational, to communicate with the user in French, English, or Spanish, and to allow the user to define the data format and the alphanumeric coding scheme.     

A real-time and dynamic biological information retrieval and analysis system (BIRAS)

The aim of this study is to design a biological information retrieval and analysis system (BIRAS) based on the Internet. Using the specific network protocol, BIRAS system could send and receive information from the Entrez search and retrieval system maintained by National Center for Biotechnology Information (NCBI) in USA. The literatures, nucleotide sequence, protein sequences, and other resources according to the user-defined term could then be retrieved and sent to the user by pop up message or by E-mail informing automatically using BIRAS system. All the information retrieving and analyzing processes are done in real-time. As a robust system for intelligently and dynamically retrieving and analyzing on the user-defined information, it is believed that BIRAS would be extensively used to retrieve specific information from large amount of biological databases in now days. The program is available on request from the corresponding author.     

A Multiple Relevance Feedback Strategy with Positive and Negative Models

A commonly used strategy to improve search accuracy is through feedback techniques. Most existing work on feedback relies on positive information, and has been extensively studied in information retrieval. However, when a query topic is difficult and the results from the first-pass retrieval are very poor, it is impossible to extract enough useful terms from a few positive documents. Therefore, the positive feedback strategy is incapable to improve retrieval in this situation. Contrarily, there is a relatively large number of negative documents in the top of the result list, and it has been confirmed that negative feedback strategy is an important and useful way for adapting this scenario by several recent studies.In this paper, we consider a scenario when the search results are so poor that there are at most three relevant documents in the top twenty documents. Then, we conduct a novel study of multiple strategies for relevance feedback using both positive and negative examples from the first-pass retrieval to improve retrieval accuracy for such difficult queries. Experimental results on these TREC collections show that the proposed language model based multiple model feedback method which is generally more effective than both the baseline method and the methods using only positive or negative model.     

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).     

Forgetting, reminding, and remembering: the retrieval of lost spatial memory

Retrograde amnesia can occur after brain damage because this disrupts sites of storage, interrupts memory consolidation, or interferes with memory retrieval. While the retrieval failure account has been considered in several animal studies, recent work has focused mainly on memory consolidation, and the neural mechanisms responsible for reactivating memory from stored traces remain poorly understood. We now describe a new retrieval phenomenon in which rats' memory for a spatial location in a watermaze was first weakened by partial lesions of the hippocampus to a level at which it could not be detected. The animals were then reminded by the provision of incomplete and potentially misleading information—an escape platform in a novel location. Paradoxically, both incorrect and correct place information reactivated dormant memory traces equally, such that the previously trained spatial memory was now expressed. It was also established that the reminding procedure could not itself generate new learning in either the original environment, or in a new training situation. The key finding is the development of a protocol that definitively distinguishes reminding from new place learning and thereby reveals that a failure of memory during watermaze testing can arise, at least in part, from a disruption of memory retrieval.     

Properties of fast endocytosis at hippocampal synapses

Regulation of synaptic transmission is a widespread means for dynamic alterations in nervous system function. In several cases, this regulation targets vesicular recycling in presynaptic terminals and may result in substantial changes in efficiency of synaptic transmission. Traditionally, experimental accessibility of the synaptic vesicle cycle in central neuronal synapses has been largely limited to the exocytotic side, which can be monitored with electrophysiological responses to neurotransmitter release. Recently, physiological measurements on the endocytotic portion of the cycle have been made possible by the introduction of styryl dyes such as FM1-43 as fluorescent markers for recycling synaptic vesicles. Here we demonstrate the existence of fast endocytosis in hippocampal nerve terminals and derive its kinetics from fluorescence measurements using dyes with varying rates of membrane departitioning. The rapid mode of vesicular retrieval was greatly speeded by exposure to staurosporine or elevated extracellular calcium. The effective time-constant for retrieval can be < 2 seconds under appropriate conditions. Thus, hippocampal synapses capitalize on efficient mechanisms for endocytosis and their vesicular retrieval is subject to modulatory control.     

Method for Coding Data on Protozoan Strains for Computers

SYNOPSIS. Traditionally, observations on the nature of protozoa have been published in periodicals or books, or remain buried in research notebooks. The retrieval and processing of information on a particular species or strain are dependent solely upon individual investigators. Although various modern methods have been applied to the study of protozoa, no attempt has been made to develop a system with which information on protozoan strains can be stored, retrieved easily, and processed for various analyses by computer technology. Based upon an existing system for encoding data on bacterial strains, a complementary system applicable to protozoan strains was developed and is described herein.     

Co-occurring words and retrieval efficiency: finding information about alternatives to animal testing in relation to skin irritation testing

Words appearing in abstracts of scientific articles are often useful as search terms, particularly those words and word patterns that are unique to the relevant field of endeavour. In view of the heightened interest in obtaining information about alternatives to animal testing, efforts directed toward enhancing retrieval of pertinent references from the biomedical literature are warranted. Words and phrases, and word-phrase co-occurrences describing methods of experimentation in abstracts about alternatives to skin-irritation testing in animals, were evaluated with regard to retrieval efficiency in the National Library of Medicine database, Toxline(. Precision of retrieval was defined as the number of pertinent references found in the total number of citations retrieved. Retrieval precision values ranged from 0.25% to 100%.     

The case against HIV antibody testing of refugees and immigrants.

Computers are now widely used in medical practice for accounting and secretarial tasks. However, it has been much more difficult to use computers in more physician-related activities of daily practice. I investigated the Desqview multitasking system on a 386 computer as a solution to this problem. Physician-directed tasks of management of patient charts, retrieval of reference information, word processing, appointment scheduling and office organization were each managed by separate programs. Desqview allowed instantaneous switching back and forth between the various programs. I compared the time and cost savings and the need for physician input between Desqview 386, a 386 computer alone and an older, XT computer. Desqview significantly simplified the use of computer programs for medical information management and minimized the necessity for physician intervention. The time saved was 15 minutes per day; the costs saved were estimated to be $5000 annually.     

Memory retrieval as a p-adic dynamical system

We propose a mathematical model of the memory retrieval process based on dynamical systems over a metric space of p-adic numbers representing a configuration 'space of ideas' in which two ideas are close if they have a sufficiently long common root. Our aim is to suggest a new way of conceptualizing human memory retrieval that might be useful for simulation purposes or for the construction of artificial intelligence devices, as well as for a deeper understanding of the process itself. The dynamical system is assumed to be located in a blackbox processing unit (the 'subconscious') and controlled by an interface control unit (the 'conscious') that fixes parameters in the dynamical system and starts its iteration by sending an initial generating idea to it. We show that even simple p-adic dynamical systems admit behavioral scenarios that could explain some of the essential features of the human memory retrieval process.     

Memory involves far more than 'consolidation'

The observation that retrieval returns a stable memory into a labile state cannot be readily explained by any simple version of consolidation theory. This finding has been interpreted as evidence for the need to reconsolidate a memory after reactivating it. However, as we discuss in this commentary, other behavioural observations indicate that even this modification to consolidation theory may be insufficient to describe the dynamic properties of memory.     

An Object-Oriented Programming System for the Integration of Internet-Based Bioinformatics Resources

The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.     

A distinct role for norepinephrine in memory retrieval

A role for norepinephrine in learning and memory has been elusive and controversial. A longstanding hypothesis states that the adrenergic nervous system mediates enhanced memory consolidation of emotional events. We tested this hypothesis in several learning tasks using mutant mice conditionally lacking norepinephrine and epinephrine, as well as control mice and rats treated with adrenergic receptor agonists and antagonists. We find that adrenergic signaling is critical for the retrieval of intermediate-term contextual and spatial memories, but is not necessary for the retrieval or consolidation of emotional memories in general. The role of norepinephrine in retrieval requires signaling through the beta(1)-adrenergic receptor in the hippocampus. The results demonstrate that mechanisms of memory retrieval can vary over time and can be different from those required for acquisition or consolidation. These findings may be relevant to symptoms in several neuropsychiatric disorders as well as the treatment of cardiac failure with beta blockers.     

Multidimensional spectroscopic data correlation in the conformation transition of biological macromolecules

A computerized spectrophotometer system which is capable of simultaneously obtaining three spectral dimensions, that is, the absorbance, the circular dichroism and the fluorescence intensity, from one sample solution has been developed for the purpose of attaining a higher resolving power in the study of conformational transitions of biological macromolecules. Measurement conditions, such as the wavelength, the temperature, pH or the concentration of reagents in the sample solution, can be scanned according to a sequence that is set just prior to the measurement. A computer-driven micro-injector and a pH electrode directly immersed in the sample solution make it possible to obtain a titration curve in parallel to the optical measurement. All the data taken are stored on a magnetic disk for later retrieval. They can be processed and displayed in any required form. The helix-coil transitions of a polynucleotide caused by temperature and those of a polypeptide caused by pH, and the denaturation of proteins caused by guanidine hydrochloride, were studied by this measuring system. The continuous plotting of transition profiles and the correlation diagrams among different spectral dimensions has proved to be a good way of demonstrating the existence of different modes of transition.     

Fragmentation or Transportation: Mode of Large-Prey Retrieval in Arboreal and Ground Nesting Ants

Foraging strategy of ant workers has been studied from several aspects, however, the mode of prey retrieval and factors affecting it have been rarely studied to date, even thought it is an important aspect for understanding ant foraging strategy. We investigated the behavioral response against large prey for 44 ant species of 34 genera belonging to eight subfamilies in Japan, Malaysia and Indonesia. Workers of most arboreal ants cut-up large prey at the site of prey capture, and individual workers retrieve the smaller pieces to the nests. In contrast, in most ground-living species, a group of workers retrieve large prey cooperatively without fragmentation. On the ground, parts of the prey item were often robbed by other ant species during this process, while such interference was rare on trees. The significance of the relation between nest site and mode of prey retrieval is discussed.