Animal Toxins: How is Complexity Represented in Databases?

Peptide toxins synthesized by venomous animals have been extensively studied in the last decades. To be useful to the scientific community, this knowledge has been stored, annotated and made easy to retrieve by several databases. The aim of this article is to present what type of information users can access from each database. ArachnoServer and ConoServer focus on spider toxins and cone snail toxins, respectively. UniProtKB, a generalist protein knowledgebase, has an animal toxin-dedicated annotation program that includes toxins from all venomous animals. Finally, the ATDB metadatabase compiles data and annotations from other databases and provides toxin ontology.

Web-based reference databases and subject gateways to locate current research information in agricultural and food sciences : a Finnish perspective

Selostus: Maatalous- ja elintarviketieteiden www-pohjaiset viitetietokannat ja aihehakemistot - suomalaisen tiedonetsijän näkökulma

A process for mining science & technology documents databases, illustrated for the case of "knowledge discovery and data mining"

This paper presents a process of mining research & development abstract databases to profile current status and to project potential developments for target technologies, The process is called "technology opportunities analysis." This article steps through the process using a sample data set of abstracts from the INSPEC database on the topic o "knowledge discovery and data mining." The paper offers a set of specific indicators suitable for mining such databases to understand innovation prospects. In illustrating the uses of such indicators, it offers some insights into the status of knowledge discovery research*.

trome, trEST and trGEN: databases of predicted protein sequences.

We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these two databases plus a new database (trome), which uses alignments of EST data to HTG or full genomes to generate virtual transcripts and coding sequences. This new database is of higher quality and since it contains the information in a much denser format it is of much smaller size. These new databases are in a Swiss-Prot-like format and are updated on a weekly basis (trEST and trGEN) or every 3 months (trome). They can be downloaded by anonymous ftp from ftp://ftp.isrec.isb-sib.ch/pub/databases.

Performance of Randomly Oriented, Fiber-Reinforced Roadway Soils, HR-211, 1982

Several primary techniques have been developed through which soil aggregate road material properties may be improved. Such techniques basically involve a mechanism of creating a continuous matrix system of soil and/or aggregate particles, interlocked through the use of some additive such as portland cement, lime, or bituminous products. Details by which soils are stabilized vary greatly, but they are dependent on the type of stabilizing agent and nature of the soil, though the overall approach to stabilization has the common feature that improvement is achieved by some mechanism(s) forcing individual particles to adhere to one another. This process creates a more rigid material, most often capable of resisting the influx of water during freezing, loss of strength due to high moisture content and particle dispersion during thawing, and loss of strength due to migration of fines and/or water by capillarity and pumping. The study reported herein, took a new and relatively different approach to strengthening of soils, i.e., improvement of roadway soils and/or soil-aggregate materials by structural reinforcement with randomly oriented fibers. The purpose of the study was to conduct a laboratory and field investigation into the potential of improving (a) soil-aggregate surfaced and subgrade materials, including those that are frost-prone and/or highly moisture susceptible, and (b) localized base course materials, by uniting such materials through fibrous reinforcement. The envisioned objective of the project was the development of a simple construction technique(s) that could be (a) applied on a selective basis to specific areas having a history of poor performance, or (b) used for improvement of potential base materials prior to surfacing. Little background information on such purpose and objective was available. Though the envisioned process had similarities to fibrous reinforced concrete, and to fibrous reinforced resin composites, the process was devoid of a cementitious binder matrix and thus highly dependent on the cohesive and frictional interlocking processes of a soil and/or aggregate with the fibrous reinforcement; a condition not unlike the introduction of reinforcing bars into a concrete sand/aggregate mixture without benefit of portland cement. Thus the study was also directed to answering some fundamental questions: (1) would the technique work; (2) what type or types of fibers are effective; (3) are workable fibers commercially available; and (4) can such fibers be effectively incorporated with conventional construction equipment, and employed in practical field applications? The approach to obtaining answers to these questions, was guided by the philosophy that an understanding of basic fundamentals was essential to developing a body of engineering knowledge, that would serve as the basis for eventual development of design procedures with fibrous products for the applications previously noted.

Paraphrase concept and typology. A linguistically based and computationally oriented approach

In this paper, we present a critical analysis of the state of the art in the definition and typologies of paraphrasing. This analysis shows that there exists no characterization of paraphrasing that is comprehensive, linguistically based and computationally tractable at the same time. The following sets out to define and delimit the concept on the basis of the propositional content. We present a general, inclusive and computationally oriented typology of the linguistic mechanisms that give rise to form variations between paraphrase pairs.

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored in databases and from automatic retrieval and integration methods. Once a reconstruction of the network of interactions is achieved, analysis of its structural features and its dynamic behaviour can take place. Mathematical modelling techniques are used to simulate the complex behaviour of cell signalling networks, which ultimately sheds light on the mechanisms leading to complex diseases or helps in the identification of drug targets. A variety of databases containing information on cell signalling pathways have been developed in conjunction with methodologies to access and analyse the data. In principle, the scenario is prepared to make the most of this information for the analysis of the dynamics of signalling pathways. However, are the knowledge repositories of signalling pathways ready to realize the systems biology promise? In this article we aim to initiate this discussion and to provide some insights on this issue.

Do protein–protein interaction databases identify moonlighting proteins?

One of the most striking results of the human (and mammalian) genomes is the low number of protein-coding genes. To-date, the main molecular mechanism to increase the number of different protein isoforms and functions is alternative splicing. However, a less-known way to increase the number of protein functions is the existence of multifunctional, multitask, or ‘‘moonlighting’’, proteins. By and large, moonlighting proteins are experimentally disclosed by serendipity. Proteomics is becoming one of the very active areas of biomedical research, which permits researchers to identify previously unseen connections among proteins and pathways. In principle, protein–protein interaction (PPI) databases should contain information on moonlighting proteins and could provide suggestions to further analysis in order to prove the multifunctionality. As far as we know, nobody has verified whether PPI databases actually disclose moonlighting proteins. In the present work we check whether well-established moonlighting proteins present in PPI databases connect with their known partners and, therefore, a careful inspection of these databases could help to suggest their different functions. The results of our research suggest that PPI databases could be a valuable tool to suggest multifunctionality.

On the Selection of Non-Invasive Methods Based on Speech Analysis Oriented to Automatic Alzheimer Disease Diagnosis

The work presented here is part of a larger study to identify novel technologies and biomarkers for early Alzheimer disease (AD) detection and it focuses on evaluating the suitability of a new approach for early AD diagnosis by non-invasive methods. The purpose is to examine in a pilot study the potential of applying intelligent algorithms to speech features obtained from suspected patients in order to contribute to the improvement of diagnosis of AD and its degree of severity. In this sense, Artificial Neural Networks (ANN) have been used for the automatic classification of the two classes (AD and control subjects). Two human issues have been analyzed for feature selection: Spontaneous Speech and Emotional Response. Not only linear features but also non-linear ones, such as Fractal Dimension, have been explored. The approach is non invasive, low cost and without any side effects. Obtained experimental results were very satisfactory and promising for early diagnosis and classification of AD patients.

Mission-Oriented Dust Control and Surface Improvement Processes for Unpaved Roads, HR-194, 1981

Six subject areas prompted the broad field of inquiry of this mission-oriented dust control and surface improvement project for unpaved roads: • DUST--Hundreds of thousands of tons of dust are created annually by vehicles on Iowa's 70,000 miles of unpaved roads and streets. Such dust is often regarded as a nuisance by Iowa's highway engineers. • REGULATIONS--Establishment of "fugitive dust" regulations by the Iowa DEQ in 1971 has created debates, conferences, legal opinions, financial responsibilities, and limited compromises regarding "reasonable precaution" and "ordinary travel," both terms being undefined judgment factors. • THE PUBLIC--Increased awareness by the public that regulations regarding dust do in fact exist creates a discord of telephone calls, petitions, and increasing numbers of legal citations. Both engineers and politicians are frustrated into allowing either the courts or regulatory agencies to resolve what is basically a professional engineering responsibility. • COST--Economics seldom appear as a tenet of regulatory strategies, and in the case of "fugitive dust," four-way struggles often occur between the highway professions, political bodies, regulatory agencies, and the general public as to who is responsible, what can be done, how much it will cost, or why it wasn't done yesterday. • CONFUSION--The engineer lacks authority, and guidelines and specifications to design and construct a low-cost surf acing system are nebulous, i.e., construct something between the present crushed stone/gravel surface and a high-type pavement. • SOLUTION--The engineer must demonstrate that dust control and surface improvement may be engineered at a reasonable cost to the public, so that a higher degree of regulatory responsibility can be vested in engineering solutions.

Culture in infancy : an account of a way the object "sculpts" early development.

The
 aim
 of
 this
 paper
 is
 to
 bring
 into
 consideration
 a
 way
 of
 studying
 culture
 in
 infancy.
 An
 emphasis 
is 
put 
on
 the
 role 
that 
the 
material 
object 
plays 
in 
early 
interactive
 processes. 
Accounted
 as
 a
 cultural
 artefact,
 the
 object
 is
 seen
 as
 a
 fundamental
 element
 within
 triadic
 mother‐object‐ infant
 interactions
 and
 is
 believed
 to
 be
 a
 driving
 force
 both
 for
 communicative
 and
 cognitive
 development.
 In
 order
 to
 reconsider
 the
 importance
 of
 the
 object
 in
 child
 development
 and
 to
 present
 an 
approach
 of 
studying
object
 construction,
accounts 
in 
literature 
on 
early 
communication
 development
 and
 the
 importance
 of
 the
 object
 are
 reviewed
 and
 discussed
 under
 the
 light
 of
 the
 cultural 
specificity 
of 
the 
material 
object.