bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dissimilarity matrix between protein atom classes based
on Gaussian mixtures
Authors: Rantanen Ville-Veikko , Gyllenberg Mats , Koski Timo , Johnson Mark S. 
Published: September 2002

Abstract
Motivation: Previously, Rantanen et al. (2001; J. Mol. Biol., 313, 197–214) constructed a protein atom–ligand fragment interaction library embodying experimentally solved, high-resolution three-dimensional (3D) structural data from the Protein Data Bank (PDB). The spatial locations of protein atoms that surround ligand fragments were modeled with Gaussian mixture models, the parameters of which were estimated with the expectation-maximization (EM) algorithm. In the validation analysis of this library, there was strong indication that the protein atom classification, 24 classes, was too large and that a reduction in the classes would lead to improved predictions.
Results: Here, a dissimilarity (distance) matrix that is suitable for comparison and fusion of 24 pre-defined protein atom classes has been derived. Jeffreys' distances between Gaussian mixture models are used as a basis to estimate dissimilarities between protein atom classes. The dissimilarity data are analyzed both with a hierarchical clustering method and independently by using multidimensional scaling analysis. The results provide additional insight into the relationships between different protein atom classes, giving us guidance on, for example, how to readjust protein atom classification and, thus, they will help us to improve protein--ligand interaction predictions.
Contact: vira@utu.fi
* To whom correspondence should be addressed.
VIZARD: analysis of Affymetrix Arabidopsis
GeneChip® data
Authors: Moseyko Nick , Feldman Lewis J. 
Published: September 2002

Abstract
Summary: The Affymetrix GeneChip® Arabidopsis genome array has proved to be a very powerful tool for the analysis of gene expression in Arabidopsis thaliana, the most commonly studied plant model organism. VIZARD is a Java program created at the University of California, Berkeley, to facilitate analysis of Arabidopsis GeneChip® data. It includes several integrated tools for filtering, sorting, clustering and visualization of gene expression data as well as tools for the discovery of regulatory motifs in upstream sequences. VIZARD also includes annotation and upstream sequence databases for the majority of genes represented on the Affymetrix Arabidopsis GeneChip® array.
Availability: VIZARD is available free of charge for educational, research, and not-for-profit purposes, and can be downloaded at http://www.anm.f2s.com/research/vizard/
Contact: moseyko@uclink4.berkeley.edu
* To whom correspondence should be addressed.
SEGE: A database on ‘intron less/single exonic’ genes from eukaryotes
Authors: Sakharkar Meena K. , Kangueane Pandjassarame , Petrov Dmitri A. , Kolaskar A. S. , Subbiah S. 
Published: September 2002

Abstract
Summary: Eukaryotes have both ‘intron containing’ and ‘intron less’ genes. Several databases are available for ‘intron containing’ genes in eukaryotes. In this note, we describe a database for‘ intron less’ genes from eukaryotes. ‘Intron less’ eukaryotic genes having prokaryotic architecture will help to understand gene evolution in a much simpler way unlike ‘intron containing’ genes.
Availability: SEGE is available at http://intron.bic.nus.edu.sg/seg/
Contact: mmeena@ntu.edu.sg
* To whom correspondence should be addressed.
UniBLAST: a system to filter, cluster, and display BLAST
results and assign unique gene annotation
Authors: Zhou Yan , Huang Guyang Matthew , Wei Liping 
Published: September 2002

Abstract
Motivation: More and more often, a gene is epitomized by a large number of sequences in GenBank. This high redundancy makes it very difficult to identify a unique best match for a query sequence from its BLAST results. We developed a novel program UniBLAST that filters out uninformative hits, clusters the redundant hits, groups the hits by LocusLink, and graphically displays the results. We also implemented a scoring function in UniBLAST to assign a unique gene name to a query sequence. UniBLAST significantly increases the efficiency of gene annotation.
Availability: The program is available at http://south.genomics.org.cn/software/uniblast/index.html
Contact: uniblast@genomics.org.cnwei@nexusgenomics.com
* To whom correspondence should be addressed.
Parallelized multiple alignment
Authors: Kleinjung Jens , Douglas Nigel , Heringa Jaap 
Published: September 2002

Abstract
Summary: Multiple sequence alignment is a frequently used technique for analyzing sequence relationships. Compilation of large alignments is computationally expensive, but processing time can be considerably reduced when the computational load is distributed over many processors. Parallel processing functionality in the form of single-instruction multiple-data (SIMD) technology was implemented into the multiple alignment program Praline by using ‘message passing interface’ (MPI) routines. Over the alignments tested here, the parallelized program performed up to ten times faster on 25 processors compared to the single processor version.
Availability: Example program code for parallelizing pairwise alignment loops is available from http://mathbio.nimr.mrc.ac.uk/~jkleinj/tools/mpicode. The‘ message passing interface’ package (MPICH) is available from http:/www.unix.mcs.anl.gov/mpi/mpich.
Contact: jhering@nimr.mrc.ac.uk
Supplementary information: Praline is accessible at http://mathbio.nimr.mrc.ac.uk/praline.
* To whom correspondence should be addressed.
OrthoGUI: graphical presentation of Orthostrapper results
Authors: Hollich Volker , Storm Christian E. V. , Sonnhammer Erik L. L 
Published: September 2002

Abstract
Summary: Orthostrapper is a program that calculates orthology support values for pairs of sequences in a multiple alignment (Storm and Sonnhammer, Bioinformatics, 18, 92–99, 2002). Here we present OrthoGUI, a web interface and display tool for Orthostrapper analysis. OrthoGUI visualizes the Orthostrapper output in both tabular and tree representations, and can also apply a clustering algorithm to identify groups of multiple orthologs, which are indicated by colour coding.
Availability: http://www.cgb.ki.se/OrthoGUI
Contact: erik.sonnhammer@cgb.ki.se
* To whom correspondence should be addressed.
A kinase sequence database: sequence alignments and family assignment
Authors: Buzko Oleksandr , Shokat Kevan M. 
Published: September 2002

Abstract
Summary: The Kinase Sequence Database (KSD) located at http://kinase.ucsf.edu/ksd contains information on 290 protein kinase families derived by profile-based clustering of the non-redundant list of sequences obtained from a GenBank-wide search. Included in the database are a total of 5041 protein kinases from over 100 organisms. Clustering into families is based on the extent of homology within the kinase catalytic domain (250–300 residues in length). Alignments of the families are viewed by interactive Excel-based sequence spreadsheets. In addition, KSD features evolutionary trees derived for each family and detailed information on each sequence as well as links to the corresponding GenBank entries. Sequence manipulation tools, such as evolutionary tree generation, novel sequence assignment, and statistical analysis, are also provided.
Availability: The kinase sequence database is a web-based service accessible at http://kinase.ucsf.edu/ksd
Contact: buzko@cmp.ucsf.edushokat@cmp.ucsf.edu/ksd
* To whom correspondence should be addressed.
PeCoP: automatic determination of persistently conserved positions in protein families
Authors: Friedberg Iddo , Margalit Hanah 
Published: September 2002

Abstract
Summary: PeCoP is a WWW-based service which accepts a protein sequence, and reports positions that are conserved in close and distant sequence family members. The collation of family members is performed using iterative PSI-BLAST runs. Examining positional conservation in close and distant family members enables a better selection of positions that may play a role in determining the protein's structure and function.
Availability: http://bioinformatics.org/pecop
Contact: idoerg@burnham.org
Supplementary information: http://bioinformatics.org/pecop/about_pecop
* To whom correspondence should be addressed at present address: The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
Applications of Tree-Maps to hierarchical biological data
Authors: McConnell Patrick , Johnson Kimberly , Lin Simon 
Published: September 2002

Abstract
Summary: A brief overview of Tree-Maps provides the basis for understanding two new implementations of Tree-Map methods. TreeMapClusterView provides a new way to view microarray gene expression data, and GenePlacer provides a view of gene ontology annotation data. We also discuss the benefits of Tree-Maps to visualize complex hierarchies in functional genomics.
Availability: Java class files are freely available at http://mendel.mc.duke.edu/bioinformatics/
Contact: mccon012@mc.duke.edu
Supplementary information: For more information on TreeMapClusterView (see http://mendel.mc.duke.edu/bioinformatics/software/boxclusterview/), and http://mendel.mc.duke.edu/bioinformatics/software/geneplacer/).
* To whom correspondence should be addressed.
An ontology driven architecture for derived representations of macromolecular structure
Authors: Greer Douglas S. , Westbrook John D. , Bourne Philip E. 
Published: September 2002

Abstract
Summary: An object metamodel based on a standard scientific ontology has been developed and used to generate a CORBA interface, an SQL schema and an XML representation for macromolecular structure (MMS) data. In addition to the interface and schema definitions, the metamodel was also used to generate the core elements of a CORBA reference server and a JDBC database loader. The Java source code which implements this metamodel, the CORBA server, database loader and XML converter along with detailed documentation and code examples are available as part of the OpenMMS toolkit.
Availability: http://openmms.sdsc.edu
Contact: dsg@sdsc.edu
* To whom correspondence should be addressed.
The uses of colour vision: behavioural and physiological distinctiveness of colour stimuli
Authors: Derrington Andrew M. , Parker Amanda , Barraclough Nick E. , Easton Alexander , Goodson G. R. , Parker Kris S. , Tinsley Chris J. , Webb Ben S. 
Published: September 2002

Colour and greyscale (black and white) pictures look different to us, but it is not clear whether the difference in appearance is a consequence of the way our visual system uses colour signals or a by–product of our experience. In principle, colour images are qualitatively different from greyscale images because they make it possible to use different processing strategies. Colour signals provide important cues for segmenting the image into areas that represent different objects and for linking together areas that represent the same object. If this property of colour signals is exploited in visual processing we would expect colour stimuli to look different, as a class, from greyscale stimuli. We would also expect that adding colour signals to greyscale signals should change the way that those signals are processed. We have investigated these questions in behavioural and in physiological experiments.We find that male marmosets (all of which are dichromats) rapidly learn to distinguish between colour and greyscale copies of the same images. The discrimination transfers to new image pairs, to new colours and to image pairs in which the colour and greyscale images are spatially different.We find that, in a proportion of neurons recorded in the marmoset visual cortex, colour–shifts in opposite directions produce similar enhancements of the response to a luminance stimulus.We conclude that colour is, both behaviourally and physiologically, a distinctive property of images.
Association of Plasma Viral RNA Load with Prognosis in Cats Naturally Infected with Feline Immunodeficiency Virus
Authors: Goto Yuko , Nishimura Yoshiaki , Baba Kenji , Mizuno Takuya , Endo Yasuyuki , Masuda Kenichi , Ohno Koichi , Tsujimoto Hajime 
Published: September 2002

ABSTRACT
We measured the quantity of plasma feline immunodeficiency virus (FIV) RNA using a real-time sequence detecting system. Plasma viral RNA load was shown to correlate with the clinical stage, survival time, and disease progression in naturally FIV-infected cats. The present study indicates that the plasma viral RNA load can be used as a clinical marker representing the impairment of the immune system and predicting the clinical outcome in FIV-infected cats.
The Upstream Regulatory Region of Human Papillomavirus Type 31 Is Insensitive to Glucocorticoid Induction
Authors: Bromberg-White Jennifer L. , Meyers Craig 
Published: September 2002

ABSTRACT
The upstream regulatory region (URR) of various types of human papillomaviruses (HPVs) has been shown to contain functional glucocorticoid response elements (GREs), including HPV type 11 (HPV11), HPV16, and HPV18. Glucocorticoids have been demonstrated to induce the transcriptional activity of the early promoters of these HPV types. Although it has been assumed that the URR of HPV31 contains at least one GRE, no functionality has been demonstrated. We attempt to show here inducibility of the URR of HPV31 by the synthetic glucocorticoid dexamethasone (dex). By sequence analysis we identified three potential GREs in the URR of HPV31. Gel shift analysis indicated that each of these three sites has the potential to be a functional GRE. However, constructs containing the full-length URR, 5′ deletions of the URR, and an internal fragment of the URR containing all three putative GREs were only weakly inducible by dex. Linker scanning mutants, whereby each potential GRE was replaced individually, in double combination, or in triple combination by a unique polylinker, had no effect on dex inducibility. Replacement of each of the three HPV31 GREs with the GRE of HPV18 failed to induce a response to dex. Placement of the HPV18 GRE into the URR of HPV31 in a region similar to its location in the HPV18 URR was also unable to result in a strong dex induction of the HPV31 URR. These data suggest that the lack of dex inducibility is due to the overall context of the HPV31 URR and may be dependent on the requirements of the major early promoter for transcriptional activation. Finally, replacement of the HPV18 GRE with each of the HPV31 GREs in HPV18 only showed weak inducibility, indicating that the three GREs of HPV31 are in fact only weak inducers of dex. Overall, these data suggest that dex responsiveness, along with oncogenic potential, may provide a possible explanation for the classification of HPV31 as an intermediate-risk virus and demonstrate the complexity of transcriptional regulation of the URR of HPV.
In Rat Dorsal Root Ganglion Neurons, Herpes Simplex Virus Type 1 Tegument Forms in the Cytoplasm of the Cell Body
Authors: Miranda-Saksena Monica , Boadle Ross A. , Armati Patricia , Cunningham Anthony L. 
Published: September 2002

ABSTRACT

The herpes simplex virus type 1 (HSV-1) tegument is the least understood component of the virion, and the mechanism of tegument assembly and incorporation into virions during viral egress has not yet been elucidated. In the present study, the addition of tegument proteins (VP13/14, VP16, VP22, and US9) and envelope glycoproteins (gD and gH) to herpes simplex virions in the cell body of rat dorsal root ganglion neurons was examined by immunoelectron microscopy. All tegument proteins were detected diffusely spread in the nucleus within 10 to 12 h and, at these times, nucleocapsids were observed budding from the nucleus. The majority (96%) of these nucleocapsids had no detectable label for tegument and glycoproteins despite the presence of tegument proteins in the nucleus and glycoproteins adjacent to the nuclear membrane. Immunolabeling for tegument proteins and glycoproteins was found abundantly in the cytoplasm of the cell body in multiple discrete vesicular areas: on unenveloped, enveloped, or partially enveloped capsids adjacent to these vesicles and in extracellular virions. These vesicles and intracytoplasmic and extracellular virions also labeled with Golgi markers, giantin, mannosidase II, and TGN38. Treatment with brefeldin A from 2 to 24 h postinfection markedly inhibited incorporation into virions of VP22 and US9 but to a lesser degree with VP16 and VP13/14. These results suggest that, in the cell body of neurons, most tegument proteins are incorporated into unenveloped nucleocapsids prior to envelopment in the Golgi and the
trans
-Golgi network. These findings give further support to the deenvelopment-reenvelopment hypothesis for viral egress. Finally, the addition of tegument proteins to unenveloped nucleocapsids in the cell body allows access to these unenveloped nucleocapsids to one of two pathways: egress through the cell body or transport into the axon.
INCONSISTENT REQUIREMENTS: AN ARGUMENTATION VIEW
Authors: PERRUSSEL LAURENT , CHARREL PIERRE-JEAN 
Published: September 2002

In this article, we present a logical framework for reasoning about inconsistent requirements in the context of multi-viewpoint requirements engineering process. In order to analyse the sources of inconsistencies and to reason with inconsistent requirements, we present an argumentation view of the requirements. Intuitively, argumentation is a tool for reasoning with inconsistent knowledge: requirements are defined in terms of arguments (a conclusion with its support); then, a class of acceptable arguments is built (arguments with no counter arguments). We suggest to characterize different classes of requirements ordered in the following way: from weakly confident to strongly confident (i.e. consistent). In the paper, we present inference rules to build intra and inter-viewpoint reasoning. Inference rules stem from the classes of requirements. We show how this work is useful for the requirements engineers in analysing inconsistent fragments of requirements.
Limit theorems for solutions of stochastic differential equation problems
Authors: Scheidt J. Vom , Purkert W. 
Published: September 2002

In this paper linear differential equations with random processes as coefficients and as inhomogeneous term are regarded. Limit theorems are proved for the solutions of these equations if the random processes are weakly correlated processes.Limit theorems are proved for the eigenvalues and the eigenfunctions of eigenvalue problems and for the solutions of boundary value problems and initial value problems.
Translation planes of even order in which the dimension has only one odd factor
Authors: Ostrom T. G. 
Published: September 2002

Let G be an irreducible subgroup of the linear translation complement of a finite translation plane of order qd where q is a power of 2. GF(q) is in the kernel and d = 2sr where r is an odd prime. A prime factor of |G| must divide .One possibility (there are no known examples) is that G has a normal subgroup W which is a W‐group for some prime W.The maximal normal subgroup 0(G) satisfies one of the following:1. Cyclic. 2. Normal cyclic subgroup of index r and the nonfixed‐point‐free elements in 0(G) have order r. 3. 0(G) contains a group W as above.
LNC points for m‐convex sets
Authors: Breen Marilyn 
Published: September 2002

Let S be closed, m‐convex subset of Rd, S locally a full d‐dimensional, with Q the corresponding set of lnc points of S. If q is an essential lnc point of order k then for some neighborhood U of q, Q ⋂ U is expressible as a union of k or fewer (d − 2)‐dimensional manifolds, each containing q For S compact, if to every q ∈ Q there corresponds a k > 0 such that q is an essential lnc point of order k then Q may be written as a finite union of (d − 2)‐manifolds.For q any lnc point of S and N a convex neighborhood of q, N ⋂ bdry  S⊈Q That is, Q is nowhere dense in bdry S. Moreover, if conv(Q ⋂ N)⫅S then Q ⋂ N is not homeomorphic to a (d − 1)‐dimensional manifold.
Functions in the space R2(E) at boundary points of the interior
Authors: Wolf Edwin 
Published: September 2002

Let E be a compact subset of the complex plane ℂ. We denote by R(E) the algebra consisting of (the restrictions to E of) rational functions with poles off E. Let m denote 2‐dimensional Lebesgue measure. For p ≥ 1, let Rp(E) be the closure of R(E) in Lp(E, dm).In this paper we consider the case p = 2. Let x ϵ ∂E be a bounded point evaluation for R2(E). Suppose there is a C > 0 such that x is a limit point of the set s = {y | y ϵ Int E, Dist(y, ∂E) ≥ C|y − x|}. For those y ϵ S sufficiently near x we prove statements about |f(y) − f(x)| for all f ϵ R(E).
Modified Gauss‐Legendre, Lobatto and Radau cubature formulas for the numerical evaluation of 2‐D singular integrals
Authors: Theocaris P. S. 
Published: September 2002

A numerical technique, first reported in 1979 in refs.[1] and [2], for the numerical evaluation of two‐dimensional Cauchy-type principal‐value integrals, is
extended in this paper to include several cubature formlas of the Radau and Lobatto types. For the construction of such a cubature formula the 2‐D singular integral is considered as an iterated one, and the second‐order pole involved in this integral analyzed into a pair of complex poles. Based on this procedure, the methods of numerical integration, valid for one‐dimensional singular integrals, are extanded to the case of two‐dimensional singular integrals. The cubature formulas of the Lobatto‐ and Radau‐type are now formulated to include the cases where some of the desired abscissas may be chosen accordins to any appropriate criterion.Moreover, the theory developed is enlarged to include the case of a 2‐D principal‐value integral, containing a logarithmic singularity. The validity of the results is illustrated by considering certain numerical examples. Furthermore, a complete analysis of the convergence and the construction of error estimates is also presented.
Coefficient estimates for some classes of p‐valent functions
Authors: Aouf M. K. 
Published: September 2002

Let Ap, where p is a positive integer, denote the class of functions which are analytic in U = {z : |z| < 1}.For 0 < λ ≤ 1, , 0 ≤ β < p, let Fλ(α, β, p) denote the class of functions f(z) ∈ Ap which satisfy the condition

urn:x-wiley:01611712:media:ijmm136791:ijmm136791-math-0003

where .Also let Cλ(b, p), where p is a positive integer, 0 < λ < 1, and b ≠ 0 is any complex number, denote the class of functions g(z) ∈ Ap which satisfy the condition

urn:x-wiley:01611712:media:ijmm136791:ijmm136791-math-0005

urn:x-wiley:01611712:media:ijmm136791:ijmm136791-math-0006

In this paper we obtain sharp coefficient estimates for the above mentioned classes.
A quasitopos containing CONV and MET as full subcategories
Authors: Lowen E. , Lowen R. 
Published: September 2002

We show that convergence spaces with continuous maps and metric spaces with
contractions, can be viewed as entities of the same kind. Both can be characterized by a limit function λ which with each filter ℱ associates a map λℱ from the underlying set to the extended positive real line. Continuous maps and contractions can both be characterized as limit function preserving maps.The properties common to both the convergence and metric case serve as a basis for
the definition of the category, CAP. We show that CAP is a quasitopos and that, apart from the categories CONV, of convergence spaces, and MET, of metric spaces, it also contains the category AP of approach spaces as nicely embedded subcategories.