bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advancing post‐genome data and system integration through machine learning
Authors: Azuaje Francisco 
Published: September 2002

AbstractResearch on biological data integration has traditionally focused on the
development of systems for the maintenance and interconnection of databases.
In the next few years, public and private biotechnology organisations will
expand their actions to promote the creation of a post‐genome semantic web.
It has commonly been accepted that artificial intelligence and data mining
techniques may support the interpretation of huge amounts of integrated data.
But at the same time, these research disciplines are contributing to the creation of
content markup languages and sophisticated programs able to exploit the constraints
and preferences of user domains. This paper discusses a number of issues on
intelligent systems for the integration of bioinformatic resources. Copyright
© 2001 John Wiley & Sons, Ltd.
SNP and mutation data on the Web – hidden treasures for uncovering.
Authors: Barnes Michael R 
Published: September 2002

AbstractSNP data has grown exponentially over the last two years, SNP database
evolution has matched this growth, as initial development of several independent
SNP databases has given way to one central SNP database, dbSNP. Other SNP
databases have instead evolved to complement this central database by providing
gene specific focus and an increased level of curation and analysis on subsets
of data, derived from the central data set. By contrast, human mutation data,
which has been collected over many years, is still stored in disparate sources,
although moves are afoot to move to a similar central database. These developments
are timely, human mutation and polymorphism data both hold complementary keys
to a better understanding of how genes function and malfunction in disease.
The impending availability of a complete human genome presents us with an
ideal framework to integrate both these forms of data, as our understanding
of the mechanisms of disease increase, the full genomic context of variation
may become increasingly significant. Copyright © 2001 John Wiley &
Sons, Ltd.
Discovery of single nucleotide polymorphisms and mutations by Pyrosequencing
Authors: Ronaghi Mostafa , Elahi Elahe 
Published: September 2002

AbstractComparative genomics, analyzing variation among individual genomes, is
an area of intense investigation. DNA sequencing is usually employed to look
for polymorphisms and mutations. Pyrosequencing, a real‐time DNA sequencing
method, is emerging as a popular platform for comparative genomics. Here we
review the use of this technology for mutation scanning, polymorphism discovery
and chemical haplotyping. We describe the methodology and accuracy of this
technique and discuss how to reduce the cost for large‐scale analysis. Copyright © 2002 John Wiley & Sons, Ltd.
From gene regulation to gene function: regulatory networks in Bacillus subtilis
Authors: Harwood Colin R , Moszer Ivan 
Published: September 2002

AbstractBacillus subtilis is a sporulating Gram‐positive bacterium that
lives primarily in the soil and associated water sources. The publication
of the B. subtilis genome sequence and subsequent systematic functional
analysis and gene regulation programmes, together with an extensive understanding
of its biochemistry and physiology, makes this micro‐organism a prime candidate
in which to model regulatory networks in silico. In this paper we discuss
combined molecular biological and bioinformatical approaches that are being
developed to model this organism's responses to changes in its environment. Copyright © 2001 John Wiley & Sons, Ltd.
RIBDB: An SRS based infrastructure for REALIS
Authors: Rice Peter , Jassal Bijay , de Daruvar Antoine 
Published: September 2002

AbstractThe REALIS project is an EU‐funded consortium for the post genomic analysis
of the food pathogen Listeria monocytogenes. The data generated by
the consortium members is stored under the RIBDB database, a system built
using SRS which integrates consortium data, public databases, and applications
for analysis. RIBDB is available to all consortium members through a web server,
with the option of installing a local mirror of the main server for local
analysis. Copyright © 2001 John Wiley & Sons, Ltd.
Ontology based document enrichment in bioinformatics
Authors: Stevens Robert 
Published: September 2002

AbstractControlled vocabularies are common within bioinformatics resources. They
can be used to give a summary of the knowledge held about a particular entity.
They are also used to constrain values given for particular attributes of
an entity. This helps create a shared understanding of a domain and aids increased
precision and recall during querying of resources. Ontologies can also provide
such facilities, but can also enhance their utility. Controlled vocabularies
are often simply lists of words, but may be viewed as a kind of ontology.
Ideally ontologies are structurally enriched with relationships between terms
within the vocabulary. Use of such rich forms of vocabularies in database
annotation could enhance those resources usability by both humans and computers.
The representation of the knowledge content of biological resources in a computationally
accessible form opens the prospect of greater support for a biologist investigating
new data. Copyright © 2002 John Wiley & Sons, Ltd.
Many Genbank entries for complete microbial genomes violate the Genbank standard
Authors: Karp Peter D. 
Published: September 2002

AbstractA survey of Genbank entries for complete microbial genomes reveals that the majority do not conform to the Genbank standard. Typical deviations from the Genbank standard include records with information in incorrect fields, addition of extraneous and confusing information within a field, and omission of useful fields. This situation results from two principal causes: genome centres do not submit Genbank records in the proper form and the Genbank, EMBL and DDBJ staffs do not enforce the database standards that they have defined. Copyright © 2001 John Wiley & Sons, Ltd.
Cryptosporidium parvum genome project
Authors: Abrahamsen Mitchell S. 
Published: September 2002

AbstractA lack of basic understanding of parasite biology has been a limiting factor in designing effective means of treating and preventing disease caused by Cryptosporidium parvum. Since the genomic DNA sequence encodes all of the heritable information responsible for development, disease pathogenesis, virulence, species permissiveness and immune resistance, a comprehensive knowledge of the C. parvum genome will provide the necessary information required for cost‐effective and targeted research into disease prevention and treatment. With the recent advances in high‐throughput automated DNA sequencing capabilities, large‐scale genomic sequencing has become a cost‐effective and time‐efficient approach to understanding the biology of an organism. In addition, the continued development and implementation of new software tools that can scan raw sequences for signs of genes and then identify clues as to potential functions, has provided the final realization of the potential rewards of genome sequencing. To further our understanding of C. parvum biology, we have initiated a random shotgun sequencing approach to obtain the complete sequence of the IOWA isolate of C. parvum. Our progress to date has demonstrated that sequencing of the C. parvum genome will be an efficient and cost‐effective method for gene discovery of this important eukaryotic pathogen. This will allow for the identification of key metabolic and immunological features of the organism that will provide the basis for future development of safe and effective strategies for prevention and treatment of disease in AIDS patients, as well as immunocompetent hosts. Moreover, by obtaining the complete sequence of the C. parvum genome, effective methods for subspecific differentiation (strain typing) and epidemiologic surveillance (strain tracking) of this pathogen can be developed. Copyright © 2001 John Wiley & Sons, Ltd.
Abundant expression of the microtubule‐associated protein, ensconsin (E‐MAP‐115), alters the cellular response to Taxol
Authors: Gruber Dorota , Faire Kathleen , Bulinski J. Chloë 
Published: September 2002

AbstractCorrelation between expression level of a microtubule‐associated protein called ensconsin (E‐MAP‐115) and degree of Taxol sensitivity in several cultured cell lines prompted us to investigate potential cause‐and‐effect relationships between ensconsin level and Taxol action. We used human MCF‐7 or HeLa cells, which are sensitive to low Taxol concentrations (LD50 of 30–35 and 3.5 nM, respectively) to prepare stably transfected populations of cells expressing heterogeneous levels of ensconsin chimeras, either green fluorescent protein (GFP) conjugated to full‐length ensconsin (GFP‐Ensc) or to ensconsin's microtubule‐binding domain (GFP‐EMTB). Both a subjective microscopic assay, i.e., scoring fluorescence of GFP‐ensconsin chimeras following Taxol treatment, and a quantitative immunobiochemical assay, i.e., measuring level of GFP‐ensconsin chimera in cells surviving treatment with Taxol, showed that cells expressing higher levels of GFP‐ensconsin chimera were killed more readily by Taxol concentrations approaching the LD50. In contrast, in TC‐7 cells, which are relatively insensitive to Taxol (LD50 > 600 nM), high‐level expression of GFP‐EMTB conferred no significant susceptibility to killing by Taxol. However, heightening the Taxol sensitivity of GFP‐EMTB‐TC‐7 cells by pre‐incubating cells with the p‐glycoprotein inhibitor, verapamil, did result in selective killing of cells highly expressing GFP‐EMTB. Taken together, results obtained in MCF‐7, HeLa, and TC‐7 cells suggest that elevated ensconsin level bestowed a selective disadvantage upon Taxol‐sensitive cells. To probe potential mechanisms by which ensconsin could alter the Taxol response, we isolated microtubules from HeLa cells that were or were not pretreated with Taxol. In vivo Taxol treatment significantly tightened microtubule‐binding of ensconsin, suggesting that Taxol alters ensconsin's microtubule‐binding properties and may, in turn, alter the Taxol response of the microtubules. Our data support the hypothesis that Taxol works synergistically or in concert with microtubule‐binding proteins in bringing about deleterious effects on the microtubule cytoskeleton. Cell Motil. Cytoskeleton 49:115–129, 2001. © 2001 Wiley‐Liss, Inc.
Remodeling of the proximal segment of crayfish motor nerves following transection
Authors: Pearce Joanne , Govind C.K. 
Published: September 2002

AbstractTransected crustacean motor axons consist of a soma‐endowed proximal segment that regenerates and a soma‐less distal segment that survives for up to a year. We report on the anatomical remodeling of the proximal segment of phasic motor nerves innervating the deep flexor muscles in the abdomen of adult crayfish following transection. The intact nerve with 10 phasic axons and its two branches with subsets of 6 and 7 of these 10 axons undergo several remodeling changes. First, the transected nerve displays many more and smaller axon profiles than the 6 and 7 axons of the intact nerve, approximately 100 and 300 profiles in the two branches of a preparation transected 8 weeks previously. Serial images of the transected nerve denote that the proliferation of profiles is due to several orders of axon sprouting primary, secondary, and tertiary branches. The greater proliferation of axon sprouts, their smaller size, and the absence of intervening glia in the one nerve branch compared with the other branch denote that sprouting is more advanced in this branch. Second, the axon sprouts are regionally differentiated; thus, although in most regions the sprouts are basically axon‐like, with a cytoskeleton of microtubules and peripheral mitochondria, in some regions they appear nerve terminal‐like and are characterized by numerous clear synaptic vesicles, a few dense‐core vesicles, and dispersed mitochondria. Both regions possess active zone dense bars with clustered synaptic vesicles found opposite other sprouts, glia, hemocytes, and connective tissue, but because the opposing membranes are not differentiated into a synaptic contact, the active zones are extrasynaptic. Third, some of the transected axons display a glial cell nucleus denoting assimilation of an adaxonal glial cell by the transected axons. Fourth, within the nerve trunk are a few myocytes and muscle fibers. These most likely originate from adjoining and intimately connected hemocytes, because such transformation occurs during muscle repair. In a crustacean nerve, however, where muscle is clearly misplaced, its presence implies an instructive role for motor nerves in muscle formation. J. Comp. Neurol. 450:61–72, 2002. © 2002 Wiley‐Liss, Inc.
Ultrastructural organization of lamprey reticulospinal synapses in three dimensions
Authors: Gustafsson Jenny S. , Birinyi András , Crum John , Ellisman Mark , Brodin Lennart , Shupliakov Oleg 
Published: September 2002

AbstractThe giant reticulospinal synapse in lamprey provides a unique model to study synaptic vesicle traffic. The axon permits microinjections, and the active zones are often separated from each other, which makes it possible to track vesicle cycling at individual release sites. However, the proportion of reticulospinal synapses with individual active zones (“simple synapses”) is unknown and a quantitative description of their organization is lacking. Here, we report such data obtained by serial section analysis, intermediate‐voltage electron microscopy, and electron tomography. The simple synapse was the most common type (78%). It consisted of one active zone contacting one dendritic process. The remaining synapses were “complex,” mostly containing one vesicle cluster and two to three active zones synapsing with distinct dendritic shafts. Occasional axosomatic synapses with multiple active zones forming synapses with the same cell were also observed. The vast majority of active zones in all synapse types contained both chemical and electrotonic synaptic specializations. Quantitative analysis of simple synapses showed that the majority had active zones with a diameter of 0.8–1.8 μm. The number of synaptic vesicles and the height of the vesicle cluster in middle sections of serially cut synapses correlated with the active zone length within, but not above, this size range. Electron tomography of simple synapses revealed small filaments between the clustered synaptic vesicles. A single vesicle could be in contact with up to 12 filaments. Another type of filament, also associated with synaptic vesicles, emerged from dense projections. Up to six filaments could be traced from one dense projection. J. Comp. Neurol. 450:167–182, 2002. © 2002 Wiley‐Liss, Inc.
Three‐dimensional cartography of functional territories in the human striatopallidal complex by using calbindin immunoreactivity
Authors: Karachi Carine , François Chantal , Parain Karine , Bardinet Eric , Tandé Dominique , Hirsch Etienne , Yelnik Jérôme 
Published: September 2002

AbstractThis anatomic study presents an analysis of the distribution of calbindin immunohistochemistry in the human striatopallidal complex. Entire brains were sectioned perpendicularly to the mid‐commissural line into 70‐μm‐thick sections. Every tenth section was immunostained for calbindin. Calbindin labeling exhibited a gradient on the basis of which three different regions were defined: poorly labeled, strongly labeled, and intermediate. Corresponding contours were traced in individual sections and reformatted as three‐dimensional structures. The poorly labeled region corresponded to the dorsal part of the striatum and to the central part of the pallidum. The strongly labeled region included the ventral part of the striatum, the subcommissural part of the external pallidum but also the adjacent portion of its suscommissural part, and the anterior pole of the internal pallidum. The intermediate region was located between the poorly and strongly labeled regions. As axonal tracing and immunohistochemical studies in monkeys show a similar pattern, poorly, intermediate, and strongly labeled regions were considered as the sensorimotor, associative, and limbic territories of the human striatopallidal complex, respectively. However, the boundaries between these territories were not sharp but formed gradients of labeling, which suggests overlapping between adjacent territories. Similarly, the ventral boundary of the striatopallidal complex was blurred, suggesting a structural intermingling with the substantia innominata. This three‐dimensional partitioning of the human striatopallidal complex could help to define functional targets for high‐frequency stimulation with greater accuracy and help to identify new stimulation sites. J. Comp. Neurol. 450:122–134, 2002. © 2002 Wiley‐Liss, Inc.
Distribution of cholecystokinin, calcitonin gene‐related peptide, neuropeptide Y, and galanin in the primary gustatory nuclei of the goldfish
Authors: Farrell William J. , Böttger Bärbel , Ahmadi Ferogh , Finger Thomas E. 
Published: September 2002

AbstractCholecystokinin (CCK), neuropeptide Y (NPY), calcitonin gene‐related peptide (CGRP), and galanin all are known to have central effects on food intake. Immunocytochemistry was used to examine the presence of these substances within the primary gustatory nuclei of the goldfish, including the vagal lobe, which is a large, laminated structure composed of discrete sensory, fiber, and motor layers. The vagal lobes receive primary afferent input from the gustatory portion of the vagus nerve and contain reflex circuitry involved in the ingestion or rejection of potential food items. Immunohistochemistry indicates a heavy concentration of CCK‐, CGRP‐, NPY‐, and galanin‐immunoreactive fibers in the capsular fiber layer as well as in deeper sensory layers of the vagal lobe. CGRP immunoreactivity throughout the sensory layers and capsular immunoreactivity for CCK are greatly reduced 1–2 weeks following vagus nerve transection, indicating that the majority of these fibers are primary sensory afferents. In contrast, NPY and galanin immunoreactivity in the capsular fiber layer and reactivity for CCK, NPY, and galanin in the deeper sensory and fiber layers are relatively unaffected by vagus transection. CCK‐, NPY‐, and galanin‐immunoreactive fibers and puncta also were present in the motor layers, as were CGRP‐immunoreactive motor somata. CCK‐immunoreactive cell bodies are present in layer III and layer VII/VIII of the vagal lobe and in the superficial granular layer of the lateral subnucleus of the commissural nucleus of Cajal, which is caudally contiguous with the vagal lobe. J. Comp. Neurol. 450:103–114, 2002. © 2002 Wiley‐Liss, Inc.
Imposition of essential boundary conditions by displacement constraint equations in meshless methods
Authors: Zhang Xiong , Liu Xin , Lu Ming‐Wan , Chen Yong 
Published: September 2002

AbstractOne of major difficulties in the implementation of meshless methods is the imposition of essential boundary conditions as the approximations do not pass through the nodal parameter values. As a consequence, the imposition of essential boundary conditions in meshless methods is quite awkward. In this paper, a displacement constraint equations method (DCEM) is proposed for the imposition of the essential boundary conditions, in which the essential boundary conditions is treated as a constraint to the discrete equations obtained from the Galerkin methods. Instead of using the methods of Lagrange multipliers and the penalty method, a procedure is proposed in which unknowns are partitioned into two subvectors, one consisting of unknowns on boundary Γu, and one consisting of the remaining unknowns. A simplified displacement constraint equations method (SDCEM) is also proposed, which results in a efficient scheme with sufficient accuracy for the imposition of the essential boundary conditions in meshless methods. The present method results in a symmetric, positive and banded stiffness matrix. Numerical results show that the accuracy of the present method is higher than that of the modified variational principles. The present method is a exact method for imposing essential boundary conditions in meshless methods, and can be used in Galerkin‐based meshless method, such as element‐free Galerkin methods, reproducing kernel particle method, meshless local Petrov–Galerkin method. Copyright © 2001 John Wiley & Sons, Ltd.
A variational theory of the Hessian equation
Authors: Chou Kai‐Seng , Wang Xu‐Jia 
Published: September 2002

AbstractBy studying a negative gradient flow of certain Hessian functionals we establish the existence of critical points of the functionals and consequently the existence of ground states to a class of nonhomogenous Hessian equations. To achieve this we derive uniform, first‐ and second‐order a priori estimates for the elliptic and parabolic Hessian equations. Our results generalize well‐known results for semilinear elliptic equations and the Monge‐Ampère equation. © 2001 John Wiley & Sons, Inc.
Which paradigm should I use? An analytical comparison of the client–server, remote evaluation and mobile agent paradigms
Authors: Puliafito Antonio , Riccobene Salvatore , Scarpa Marco 
Published: September 2002

AbstractIn this paper we deal with the study of the actual convenience of using the agent programming paradigm for accesssing distributed service. We try to point out the benefits of such a communication paradigm, by providing an analytical study of its basic features in comparison with the client–server approach and remote evaluation. The aim of the paper is to show how the Petri net analysis technique can be used for deciding whether to use traditional client/server, remote evaluation or mobile agents paradigm in designing a particular evaluation. So, we present several models of non‐Markovian Petri nets, which have been solved through the WebSPN tool, and we provide a close comparison between the agents technique, the client‐server and the remote evaluation communication paradigm. The results that we have obtained show how agents must not always be considered the only solution to any communication issue, since in several cases their use might even reveal a drawback. We also focus out attention on providing some practical remarks, which can help the developer during the design in order to select the communication paradigm which best suits the features of the application that has to be developed. Copyright © 2001 John Wiley & Sons, Ltd.
Emmerald: a fast matrix–matrix multiply using Intel's SSE instructions
Authors: Aberdeen Douglas , Baxter Jonathan 
Published: September 2002

AbstractGeneralized matrix–matrix multiplication forms the kernel of many mathematical algorithms, hence a faster matrix–matrix multiply immediately benefits these algorithms. In this paper we implement efficient matrix multiplication for large matrices using the Intel Pentium single instruction multiple data (SIMD) floating point architecture. The main difficulty with the Pentium and other commodity processors is the need to efficiently utilize the cache hierarchy, particularly given the growing gap between main‐memory and CPU clock speeds. We give a detailed description of the register allocation, Level 1 and Level 2 cache blocking strategies that yield the best performance for the Pentium III family. Our results demonstrate an average performance of 2.09 times faster than the leading public domain matrix–matrix multiply routines and comparable performance with Intel's SIMD small matrix–matrix multiply routines. Copyright © 2001 John Wiley & Sons, Ltd.