bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-proteome interaction mining
Authors: Bock Joel R. , Gough David A. 
Published: December 2002

Abstract
Motivation: A major post-genomic scientific and technological pursuit is to describe the functions performed by the proteins encoded by the genome. One strategy is to first identify the protein–protein interactions in a proteome, then determine pathways and overall structure relating these interactions, and finally to statistically infer functional roles of individual proteins. Although huge amounts of genomic data are at hand, current experimental protein interaction assays must overcome technical problems to scale-up for high-throughput analysis. In the meantime, bioinformatics approaches may help bridge the information gap required for inference of protein function. In this paper, a previously described data mining approach to prediction of protein–protein interactions (Bock and Gough, 2001, Bioinformatics, 17, 455–460) is extended to interaction mining on a proteome-wide scale. An algorithm (the phylogenetic bootstrap) is introduced, which suggests traversal of a phenogram, interleaving rounds of computation and experiment, to develop a knowledge base of protein interactions in genetically-similar organisms.
Results: The interaction mining approach was demonstrated by building a learning system based on 1,039 experimentally validated protein–protein interactions in the human gastric bacterium Helicobacter pylori. An estimate of the generalization performance of the classifier was derived from 10-fold cross-validation, which indicated expected upper bounds on precision of 80% and sensitivity of 69% when applied to related organisms. One such organism is the enteric pathogen Campylobacter jejuni, in which comprehensive machine learning prediction of all possible pairwise protein–protein interactions was performed. The resulting network of interactions shares an average protein connectivity characteristic in common with previous investigations reported in the literature, offering strong evidence supporting the biological feasibility of the hypothesized map. For inferences about complete proteomes in which the number of pairwise non-interactions is expected to be much larger than the number of actual interactions, we anticipate that the sensitivity will remain the same but precision may decrease. We present specific biological examples of two subnetworks of protein–protein interactions in C. jejuni resulting from the application of this approach, including elements of a two-component signal transduction systems for thermoregulation, and a ferritin uptake network.
Contact: dgough@bioeng.ucsd.edu
* To whom correspondence should be addressed.
ConSurf: Identification of Functional Regions in Proteins
by Surface-Mapping of Phylogenetic Information
Authors: Glaser Fabian , Pupko Tal , Paz Inbal , Bell Rachel E. , Bechor-Shental Dalit , Martz Eric , Ben-Tal Nir 
Published: December 2002

Abstract
Summary: We recently developed algorithmic tools for the identification of functionally important regions in proteins of known three dimensional structure by estimating the degree of conservation of the amino-acid sites among their close sequence homologues. Projecting the conservation grades onto the molecular surface of these proteins reveals patches of highly conserved (or occasionally highly variable) residues that are often of important biological function. We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins.
Availability: The ConSurf web server is available at:http://consurf.tau.ac.il.
Contact: fabian@ashtoret.tau.ac.iltal@ism.ac.jpinbalp@ashtoret.tau.ac.ilrebell@ashtoret.tau.ac.ildalit@ashtoret.tau.ac.ilemartz@microbio.umass.edubental@ashtoret.tau.ac.il
Supplementary Information: A set of examples is available at http://consurf.tau.ac.il under ‘GALLERY’.
* To whom correspondence should be addressed.
Genetic algorithms applied to multi-class prediction for
the analysis of gene expression data
Authors: Ooi C. H. , Tan Patrick 
Published: December 2002

Abstract
Motivation: An important challenge in the use of large-scale gene expression data for biological classification occurs when the expression dataset being analyzed involves multiple classes. Key issues that need to be addressed under such circumstances are the efficient selection of good predictive gene groups from datasets that are inherently ‘noisy’, and the development of new methodologies that can enhance the successful classification of these complex datasets.
Methods: We have applied genetic algorithms (GAs) to the problem of multi-class prediction. A GA-based gene selection scheme is described that automatically determines the members of a predictive gene group, as well as the optimal group size, that maximizes classification success using a maximum likelihood (MLHD) classification method.
Results: The GA/MLHD-based approach achieves higher classification accuracies than other published predictive methods on the same multi-class test dataset. It also permits substantial feature reduction in classifier genesets without compromising predictive accuracy. We propose that GA-based algorithms may represent a powerful new tool in the analysis and exploration of complex multi-class gene expression data.
Availability: Supplementary information, data sets and source codes are available at http://www.omniarray.com/bioinformatics/GA
Contact: cmrtan@nccs.com.sg
* To whom correspondence should be addressed.
MADGE: scalable distributed data management software for
cDNA microarrays
Authors: McIndoe Richard A. , Lanzen Aaron , Hurtz Kimberly 
Published: December 2002

Abstract
Motivation: The human genome project and the development of new high-throughput technologies have created unparalleled opportunities to study the mechanism of diseases, monitor the disease progression and evaluate effective therapies. Gene expression profiling is a critical tool to accomplish these goals. The use of nucleic acid microarrays to assess the gene expression of thousands of genes simultaneously has seen phenomenal growth over the past five years. Although commercial sources of microarrays exist, investigators wanting more flexibility in the genes represented on the array will turn to in-house production. The creation and use of cDNA microarrays is a complicated process that generates an enormous amount of information. Effective data management of this information is essential to efficiently access, analyze, troubleshoot and evaluate the microarray experiments.
Results: We have developed a distributable software package designed to track and store the various pieces of data generated by a cDNA microarray facility. This includes the clone collection storage data, annotation data, workflow queues, microarray data, data repositories, sample submission information, and project/investigator information. This application was designed using a 3-tier client server model. The data access layer (1st tier) contains the relational database system tuned to support a large number of transactions. The data services layer (2nd tier) is a distributed COM server with full database transaction support. The application layer (3rd tier) is an internet based user interface that contains both client and server side code for dynamic interactions with the user.
Availability: This software is freely available to academic institutions and non-profit organizations athttp://www.genomics.mcg.edu/niddkbtc
Contact: rmcindoe@mail.mcg.edu
* To whom correspondence should be addressed.
Caregivers of people with Alzheimer's disease: a qualitative study from the Indian 10/66 Dementia Research Network
Authors: Shaji K. S. , Smitha K. , Lal K. Praveen , Prince M. J. 
Published: December 2002

AbstractBackgroundDementia is a rapidly growing problem in all parts of the developing world. Such societies are characterised by low levels of awareness regarding dementia as a chronic degenerative brain syndrome, and by an absence of supportive health and welfare services. There is reliance upon families as the cornerstone of support and care. However, surprisingly little is known of the care arrangements for people with dementia and the strain experienced by their family caregivers.MethodIn a qualitative study of 17 caregivers of people with Alzheimer's disease identified through an innovative case‐finding program in Thrissur, South India, we obtained information on the range of care arrangements, attitudes towards care giving roles and sources of strain.ResultsThe majority of caregivers were young women, often daughters‐in‐law of women with dementia. The principal sources of caregiver strain were behavioural problems associated with the dementia syndrome, and incontinence. Strain was exacerbated by the lack of supportive response by local health services, and by lack of support and, sometimes, criticism from other family members. Family conflict was commonly encountered. The majority of caregivers experienced significant deterioration in their mental health. One caregiver unfortunately committed suicide after the death of her husband.ConclusionsThere is a clear need for more education, advice and support for families affected by dementia. Community services in developing countries should consider training existing domiciliary outreach services, the community‐based multi‐purpose health workers, to identify and support family caregivers. Copyright © 2002 John Wiley & Sons, Ltd.
A three‐factor analytic model of the MADRS in geriatric depression
Authors: Parker R. D. , Flint Elizabeth P. , Bosworth Hayden B. , Pieper Carl F. , Steffens David C. 
Published: December 2002

AbstractObjectiveMajor depression is a heterogeneous disorder, perhaps comprising several clinical subtypes or subgroups of symptoms. This study examined whether items on the Montgomery‐Åsberg Depression Rating Scale (MADRS) form distinct symptom subgroups among geriatric depressive patients that might form the basis of new outcome measures for tracking treatment effects.MethodThe study examined a sample of 225 adults age 59 and older diagnosed with major depression. Factor analysis with oblique rotation was used to analyze baseline MADRS item scores.ResultsThree distinct interpretable factors were obtained; all ten items loaded <0.60 on a domain. The first factor, dysphoric apathy/retardation, comprised five items: apparent sadness, reported sadness, lassitude, reduced concentration, and inability to feel. Psychic anxiety, the second factor, included three items: inner tension, pessimistic thoughts, and suicidal thoughts. The third factor, vegetative symptoms, resulted from items involving sleep and appetite.ConclusionsThe study produced three interpretable MADRS factors reflecting geriatric depression dimensions that may be useable to monitor focused treatment outcomes. Copyright © 2002 John Wiley & Sons, Ltd.
A methodology to study rain splash and wash processes under natural rainfall
Authors: Van Dijk A. I. J. M. , Bruijnzeel L. A. , Eisma E. H. 
Published: December 2002

AbstractThe complex interactions between rainfall‐driven erosion processes and rainfall characteristics, slope gradient, soil treatment and soil surface processes are not very well understood. A combination of experiments under natural rainfall and a consistent physical theory for their interpretation is needed to shed more light on the underlying processes. The present study demonstrates such a methodology. An experimental device employed earlier in laboratory studies was used to measure downslope rain splash and ‘splash‐creep’, lateral splash, upslope splash and rainfall‐driven runoff transport (wash) from a highly aggregated clay‐rich oxisol exposed to natural rainfall in West Java, Indonesia. Two series of measurements were made: the first with the soil surface at angles of 0°, 5°, 15° and 40°; and the second all at an angle of 5° but with different tillage and mulching treatments. A number of rainfall erosivity indices were calculated from rainfall intensity measurements and compared with measured transport components. Overall storm kinetic energy correlated reasonably well with sediment transport, but much better agreement was obtained when a threshold rainfall intensity (20 mm h−1) was introduced. Rain splash transport measurements were interpreted using a recently developed theory relating detachment to sediment transport. Furthermore, a conceptually sound yet simple wash transport model is advanced that satisfactorily predicted observed washed sediment concentrations. The lack of replication precluded rigorous assessment of the effect of slope and soil treatment on erosion processes, but some general conclusions could still be drawn. The results stress the importance of experiments under conditions of natural rainfall. Copyright © 2002 John Wiley & Sons, Ltd.
Evaluation of the snow‐covered area data product from MODIS
Authors: Maurer Edwin P. , Rhoads Joshua D. , Dubayah Ralph O. , Lettenmaier Dennis P. 
Published: December 2002

AbstractThe Moderate Resolution Imaging Spectroradiometer (MODIS), flown on board the Terra Earth Observing System (EOS) platform launched in December 1999, produces a snow‐covered area (SCA) product. This product is expected to be of better quality than SCA products based on operational satellites (notably GOES and AVHRR), due both to improved spectral resolution and higher spatial resolution of the MODIS instrument. The gridded MODIS SCA product was compared with the SCA product produced and distributed by the National Weather Service National Operational Hydrologic Remote Sensing Center (NOHRSC) for 46 selected days over the Columbia River basin and 32 days over the Missouri River basin during winter and spring of 2000–01. Snow presence or absence was inferred from ground observations of snow depth at 1330 stations in the Missouri River basin and 762 stations in the Columbia River basin, and was compared with the presence/absence classification for the corresponding pixels in the MODIS and NOHRSC SCA products. On average, the MODIS SCA images classified fewer pixels as cloud than NOHRSC, the effect of which was that 15% more of the Columbia basin area could be classified as to presence–absence of snow, while overall there was a statistically insignificant difference over the Missouri basin. Of the pixels classified as cloud free, MODIS misclassified 4% and 5% fewer overall (for the Columbia and Missouri basins respectively) than did the NOHRSC product. When segregated by vegetation cover, forested areas had the greatest differences in fraction of cloud cover reported by the two SCA products, with MODIS classifying 13% and 17% less of the images as cloud for the Missouri and Columbia basins respectively. These differences are particularly important in the Columbia River basin, 39% of which is forested. The ability of MODIS to classify significantly greater amounts of snow in the presence of cloud in more topographically complex, forested, and snow‐dominated areas of these two basins provides valuable information for hydrologic prediction. Copyright © 2003 John Wiley & Sons, Ltd.
Optimized structures of Si28 and Ba@Si28 clusters: Ab initio study
Authors: Tsumuraya Kazuo , Nagano Takatoshi , Eguchi Haruki , Takenaka Hiroyuki 
Published: December 2002

AbstractFirst‐principle electronic structure calculations are carried out for the Si28 and endohedral Ba@Si28 clusters, which are components of the clusters in the silicon clathrate II. We obtain the structurally optimized cage structures of the clusters and the exohedral binding nature of Si atom on the Ba@Si28 clusters. The hollow Si28 cluster relaxes into the Si24‐like cluster in the clathrate I, having four exohedral Si atoms outside the hexagon. The hexagons on the Ba@Si28 cluster deforms into chair‐type with relaxation. The exohedral Si atom is the most stable at the edge center near the top that forms three pentagons. We propose a mechanism of the growth of the clathrates. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
DFT study of the electronic structure and Jahn–Teller effect of tetrabromomethane cation
Authors: Miguel Beatriz , García de la Vega José Manuel 
Published: December 2002

AbstractA density functional theory study of the cation obtained by ionization of tetrabromomethane is reported. C2v is the only one of the possible structures of subgroups of Td group, which presents energies below the first vertical ionization. A slight minimum corresponding to a C3v structure in a complex of CBrBr, similar to CF, has been found. A detailed study of the reaction path for producing CBr + Br is considered. Different possible outcomes of the experiments are discussed in light of the theoretical results. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
NQR parameters: Electric field gradient tensor and asymmetry parameter studied in terms of density functional theory
Authors: Latosińska J. N. 
Published: December 2002

AbstractThe calculations of the electric field gradients were performed in the different basis sets at the selected ab initio, density functional theory (DFT), and ECP levels of the theory. The most reliable QCC and η values were obtained within the DFT and with the use of B3LYP functional and middle 6‐31G* or extended 6‐311G* basis sets. The universality of the B3LYP/6‐31G* method was checked by comparing the experimental and calculated Up values as only such a comparison enables assessment of the quality of the results obtained for different (heavy and light) nuclei. The NQR parameters obtained with the use of all‐electrons (AE) and pseudopotential (ECP) methods for a group of halogens or nitrogen‐containing compounds were compared and the former were found to be close to the experimental values. The explanation of so extremely small values of EFG calculated with the use of pseudopotential was proposed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Intelligent control of DC motor driven mechanical systems: a robust learning control approach
Authors: Kuc Tae‐Yong , Baek Seung‐Min , Sohn Kyung‐Oh , Kim Jin‐Oh 
Published: December 2002

AbstractA robust learning controller is presented for DC motor driven mechanical systems with friction. The proposed controller takes advantage of both robust and learning control approaches to learn and compensate periodic and non‐periodic uncertain dynamics. In the learning controller, a set of learning rules is implemented in which three types of learnings occur: one is direct learning of desired inverse dynamics input and the other two learning of unknown linear parameters and nonlinear bounding functions in the models of system dynamics and friction. The global asymptotic stability of learning control system is shown by using the Lyapunov stability theory. Experimental data demonstrate the effectiveness of developed learning approach to tracking of DC motor driven mechanical systems. Copyright © 2002 John Wiley & Sons, Ltd.
Clinical, biochemical and genetic aspects and neuronal migration in peroxisome biogenesis disorders
Authors: Suzuki Y. , Shimozawa N. , Imamura A. , Fukuda S. , Zhang Z. , Orii T. , Kondo N. 
Published: December 2002

AbstractPeroxisome biogenesis disorders (PBDs) are severe autosomal recessive neurological diseases caused by a defect of peroxisomal assembly factors. Zellweger syndrome, the most severe phenotype, is characterized by hypotonia, psychomotor retardation and neuronal migration disorder. Neonatal adrenoleukodystrophy and infantile Refsum disease are milder phenotypes of this disease. Thirteen complementation groups have been established since the genetic heterogeneity of PBDs was elucidated in 1988. Eleven genes for PBDs have been identified either by a functional complementation cloning or by EST homology searches. In 1992, the first gene for PBDs, PEX2, was identified. It encodes peroxisomal integral membrane protein with a RING finger domain. PEX5 and PEX7 are the genes for peroxisomal targeting signal (PTS)‐1 and ‐2 receptors, respectively. PEX3, PEX16 and PEX19 are considered to be required for the early stage of peroxisome biogenesis. PEX13 protein has an SH3 docking site that binds to the PTS‐1 receptor. PEX1 and PEX6 encode ABC protein, and PEX10 and PEX12 also encode integral membrane protein, with RING finger. Temperature‐sensitivity, whereby peroxisomal biogenesis and metabolic dysfunctions are restored at 30°C in cells from mild phenotypes, is a useful event for predicting the clinical severity and for elucidation of peroxisome biogenesis. Investigations using knockout mice are expected to facilitate understanding of migration disorders.
The Paradoxes and Promise of Community Coalitions
Authors: Chavis David M. 
Published: December 2002

AbstractCommunity coalitions, as they are currently applied, are unique organizations whose ability to promote community change is different from other types of community organizations. This article explores those differences and elaborates how community coalitions can use those differences to transform conflict into greater capacity, equity, and justice. Concerns are also raised in this article about how community coalitions can intentionally and unintentionally protect the status quo and contain the empowerment of grassroots leadership and those of marginalized groups. There is a need for more theory, research, and discourse on how community coalitions can transform conflict into social change and how they can increase the power of grassroots and other citizen‐lead organizations.
Enzyme replacement therapy in mucopolysaccharidosis type I: Progress and emerging difficulties
Authors: Wraith J. E. 
Published: December 2002

AbstractMucopolysaccharidosis type I is due to a deficiency of the lysosomal enzyme α‐L‐iduronidase (EC 3.2.1.76) and is associated with a defect in the catabolism of the glycosaminoglycans heparan and dermatan sulphate. The clinical picture produced by this abnormal storage is diverse and ranges from a disorder that is fatal in the early months of life, due to cardiomyopathy, to a condition compatible with a normal life‐span. It has become usual to describe the phenotypes associated with this spectrum of disorders after their eponymous names, Hurler (MPS IH, severe), Scheie (MPS IS, mild) and Hurler/Scheie (MPS IH/S, intermediate). Severely affected patients have progressive learning difficulties, facial and skeletal deformities, cardiac disease, corneal clouding, respiratory compromise and joint stiffness. Patients with MPS IH typically die in the first decade of life. MPS IH/S usually have normal intelligence and die in their twenties of cardiorespiratory disease. Patients with MPS IS may have joint stiffness, aortic valve disease and corneal clouding, but are often able to live a normal life‐span. Enzyme replacement therapy has been developed as a potential therapy for some patients with MPS I. This process has been helped by the study of a naturally occurring canine model of the disease, which produces a phenotype similar to MPS IH/S in the human. This review details the progress that has been made in this area and also highlights some potential problems with the introduction of therapy.