bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mining gene expression databases for association rules
Authors: Creighton Chad , Hanash Samir 
Published: December 2002

Abstract
Motivation: Global gene expression profiling, both at the transcript level and at the protein level, can be a valuable tool in the understanding of genes, biological networks, and cellular states. As larger and larger gene expression data sets become available, data mining techniques can be applied to identify patterns of interest in the data. Association rules, used widely in the area of market basket analysis, can be applied to the analysis of expression data as well. Association rules can reveal biologically relevant associations between different genes or between environmental effects and gene expression. An association rule has the form LHS ⇒ RHS, where LHS and RHS are disjoint sets of items, the RHS set being likely to occur whenever the LHS set occurs. Items in gene expression data can include genes that are highly expressed or repressed, as well as relevant facts describing the cellular environment of the genes (e.g. the diagnosis of a tumor sample from which a profile was obtained).
Results: We demonstrate an algorithm for efficiently mining association rules from gene expression data, using the data set from Hughes et al. (2000, Cell, 102, 109–126) of 300 expression profiles for yeast. Using the algorithm, we find numerous rules in the data. A cursory analysis of some of these rules reveals numerous associations between certain genes, many of which make sense biologically, others suggesting new hypotheses that may warrant further investigation. In a data set derived from the yeast data set, but with the expression values for each transcript randomly shifted with respect to the experiments, no rules were found, indicating that most all of the rules mined from the actual data set are not likely to have occurred by chance.
Availability: An implementation of the algorithm using Microsoft SQL Server with Access 2000 is available at http://dot.ped.med.umich.edu:2000/pub/assoc_rules/assoc_rules.zip. Our results from mining the yeast data set are available at http://dot.ped.med.umich.edu:2000/pub/assoc_rules/yeast_results.zip.
Contact: ccreight@umich.edu
* To whom correspondence should be addressed.
Numerical study of the effectivity index for an anisotropic error indicator based on Zienkiewicz–Zhu error estimator
Authors: Picasso M. 
Published: December 2002

AbstractThe framework of Formaggia and Perotto (Numerische Mathematik 2001; 89: 641–667) is considered to derive a new anisotropic error indicator for a Laplace problem in the energy norm. The matrix containing the error gradient is approached using a Zienkiewicz–Zhu error estimator. A numerical study of the effectivity index is proposed for anisotropic unstructured meshes, showing that our indicator is sharp. An anisotropic adaptive algorithm is implemented, aiming at controlling the estimated relative error. Copyright © 2003 John Wiley & Sons, Ltd.
A simple solution for lateral buckling of thin‐walled symmetric members
Authors: Wang Quanfeng 
Published: December 2002

AbstractThe lateral buckling of a simply supported symmetric thin‐walled member is investigated. An energy equation for the lateral buckling of thin‐walled member has been presented in which the effects of torsion and assumed warping are taken into account. Using variation method helps to derive the governing differential equation together with appropriated boundary conditions. The lateral buckling loads are obtained by solving the differential equation numerically using Galerkin's method of weighted residuals. The method presented in this paper yields the formula for computing the lateral buckling load that is very simple and straightforward. By the study, a very complex practical eigenvalue problem can be transformed into a very simple one. The results predicted with the analytical method are in good agreement with the ones obtained by experimental, finite integral, non‐linear finite element methods and optimal analysis. The fast convergence of the method makes it possible to write the resulting formulae in a likely closed form which is very simple and very convenient to use. Copyright © 2003 John Wiley & Sons, Ltd.
Neuropathological evidence for ischemia in the white matter of the dorsolateral prefrontal cortex in late‐life depression
Authors: Thomas Alan J. , Perry Robert , Kalaria Rajesh N. , Oakley Arthur , McMeekin William , O'Brien John T. 
Published: December 2002

AbstractBackgroundSignal hyperintensities on magnetic resonance imaging in late‐life depression are associated with treatment resistance and poor outcome. These lesions are probably vascular in origin and proposed sites for vascular damage include the dorsolateral prefrontal cortex (DLPFC) and anterior cingulate cortex (ACC).MethodsWe therefore examined white matter in these areas for microvascular disease and evidence of ischemia using intercellular adhesion molecule‐1 (ICAM‐1) and vascular adhesion molecule‐1 (VCAM‐1). We obtained postmortem tissue from elderly depressed (n = 20) and control (n = 20) subjects and blindly rated microvascular disease and ICAM‐1 and VCAM‐1 amount using quantitative image analysis in sections of the DLPFC, ACC and occipital cortex (OC; control area).ResultsWe found a significant increase in ICAM‐1 in the deep white matter of the DLPFC in the depressed group (p = 0.01) and a trend towards an increase for VCAM‐1 (p = 0.10). In the gyral white matter there was a trend towards significance for both molecules (p = 0.07 and 0.10). No differences were found in the ACC or OC or for microvascular disease in any area.ConclusionsThese findings are consistent with white matter ischemia in the DLPFC and lend support to the ‘vascular depression’ hypothesis. They implicate the DLPFC as an important site in the pathogenesis of late‐life depression and have major implications for the understanding and management of late‐life depression and raise the possibility of novel treatments being introduced in the future. Copyright © 2002 John Wiley & Sons, Ltd.
On morphometric properties of basins, scale effects and hydrological response
Authors: Moussa Roger 
Published: December 2002

AbstractOne of the important problems in hydrology is the quantitative description of river system structure and the identification of relationships between geomorphological properties and hydrological response. Digital elevation models (DEMs) generally are used to delineate the basin's limits and to extract the channel network considering pixels draining an area greater than a threshold area S. In this paper, new catchment shape descriptors, the geometric characteristics of an equivalent ellipse that has the same centre of gravity, the same principal inertia axes, the same area and the same ratio of minimal inertia moment to maximal inertia moment as the basin, are proposed. They are applied in order to compare and classify the structure of seven basins located in southern France. These descriptors were correlated to hydrological properties of the basins' responses such as the lag time and the maximum amplitude of a geomorphological unit hydrograph calculated at the basin outlet by routing an impulse function through the channel network using the diffusive wave model. Then, we analysed the effects of the threshold area S on the topological structure of the channel network and on the evolution of the source catchment's shape. Simple models based on empirical relationships between the threshold S and the morphometric properties were established and new catchment shape indexes, independent of the observation scale S, were defined. This methodology is useful for geomorphologists dealing with the shape of source basins and for hydrologists dealing with the problem of scale effects on basin topology and on relationships between the basin morphometric properties and the hydrological response. Copyright © 2002 John Wiley & Sons, Ltd.
Effective crystal potential from electronegativity viewpoint
Authors: Koleżyński Andrzej , Ptak Wiesław S. , Tkacz‐Śmiech Katarzyna 
Published: December 2002

AbstractThe model based on the assumption of the existence of an interatomic distance dependent, local, effective crystal field applied to the alkaline metals and diamondlike structure crystals (C, Si, Ge, Sn) is presented. We applied the modified model to the calculation of the binding energy and the bulk modulus for the diamondlike crystals. The results of the calculation of the binding energy and the bulk modulus show that well‐chosen parameters allows reproduction of the proper values of the binding energy at the equilibrium position. The values of the effective charges and, based on them, electronegativity values show very good correlation with electronegativity values due to Görlich, Gordy, and Phillips, giving a method for comparison of the different a priori and a posteriori electronegativity scales. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Density functional theory application to double quantum dots: Influence of mismatch on the addition energy spectra of vertical diatomic artificial molecules
Authors: Austing D. G. , Sasaki S. , Muraki K. , Ono K. , Tarucha S. , Barranco M. , Emperador A. , Pi M. , Garcias F. 
Published: December 2002

AbstractLocal spin density functional theory calculations for double quantum dots are compared with experimental data to explain the evolution of addition energy spectra with the interdot distance. Realistic features such as finite thickness and nonidentical constituent dots are included in the calculation. We can thus evaluate the heteronuclear character of the diatomic artificial quantum molecules due to a small unavoidable mismatch introduced in their fabrication. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Import of proteins into mitochondria: A novel pathomechanism for progressive neurodegeneration
Authors: Bauer M. F. , Neupert W. 
Published: December 2002

AbstractThe vast majority of mitochondrial proteins are encoded as precursors by the nuclear genome. A major aspect of mitochondrial biogenesis is therefore the transfer of nuclear‐encoded, cytosplasmically synthesized precursor proteins across and into the mitochondrial membranes. During the past years the use of simple model organisms such as the yeasts S. cerevisiae and N. crassa has helped considerably to identify and unravel the structure and function of a substantial number of components involved in targeting of nuclear‐encoded preproteins to mitochondria. Several pathways and a number of components were characterized that are involved in guiding mitochondrial preproteins to their specific sites of function. In particular, import of nuclear‐ encoded precursor proteins into and across the mitochondrial inner membrane is mediated by two distinct translocases, the TIM23 complex and the TIM22 complex. Both TIM complexes cooperate with the general preprotein translocase of the outer membrane, TOM complex. The TIM complexes differ in the their substrate specificity. While the TIM23 complex mediates import of preproteins with a positively charged matrix targeting signal, the TIM22 complex facilitates the insertion of a class of hydrophobic proteins with internal targeting signals into the inner membrane. Most recently the rapid progress of research has allowed elucidation of a new mitochondrial disease on the molecular level. This rare X‐linked progressive neurodegenerative disorder, named Mohr–Tranebjaerg (MT syndrome), is caused by mutations in the DDP1 gene and includes sensorineural deafness, blindness, mental retardation and a complex movement disorder. The analysis of the novel pathomechanism is based on the homology of the affected DDP1 protein to a family of conserved yeast components acting along the TIM22 pathway. This contribution briefly summarizes the current knowledge of the pathways of protein import and proposes a mechanism to explain how defective import leads to neurodegeneration.
Enzyme replacement and beyond
Authors: Desnick R. J. 
Published: December 2002

AbstractDuring the last decade, enzyme replacement therapy for lysosomal storage diseases became a reality with the demonstration of its safety and effectiveness in type 1 Gaucher disease. Currently, enzyme replacement and several other potential therapeutic strategies are being developed for selected lysosomal storage diseases, including Fabry disease due to the deficient activity of α‐galactosidase A (α‐Gal A). The development and clinical evaluation of these new therapies require a stepwise process, each step being rigorously reviewed and approved by national or international regulatory agencies. For lethal disorders that affect small populations, such as many inherited metabolic diseases, this process can be accelerated by ‘orphan drug’ and ‘fast track’ regulations. As an example of the drug development process, the development of recombinant human α‐Gal A (r‐hαGal A) replacement for Fabry disease is presented, including the preclinical studies in the ‘Fabry mouse’ model, and the clinical phase 1/2, phase 3, and phase 3 extension studies, which demonstrate the safety and efficacy of this new therapy.
Amino acids: Analytical aspects
Authors: Mayne P. D. , Roche G. , Deverell D. 
Published: December 2002

AbstractThis workshop was organized as a direct response to concerns and queries raised by laboratory personnel, both in Europe and in the United States, about the imminent withdrawal of Beckman Coulter from the amino acid analysis market. The topics covered included external quality control schemes, standard operating procedures for amino acid analysis and instrumentation, both from a user's perspective and that of the company representatives. There was a discussion panel of all speakers following the presentations.
Changes in clinical practice with the unravelling of diseases: Connective‐tissue disorders
Authors: Spranger J. 
Published: December 2002

AbstractUnravelling of diseases is achieved in steps by sequentially describing their phenotype, natural course, aetiology and pathogenesis. Through succinct clinical observation, conglomerates of heterogeneous connective‐tissue disorders, such as various forms of disproportionate dwarfism, have been split into well‐defined entities. They have often been confirmed by biochemical and molecular analysis. On the other hand, seemingly disparate disorders have been shown to be pathogenetically related and to be variable expressions of common defects. Examples are the mucopolysaccharidoses and type II collagenopathies. Disease recognition through splitting and lumping has improved prevention and prognostication. It is the basic requirement for future therapeutic attempts on a pathogenetic or molecular level.
Liver repopulation for the treatment of metabolic diseases
Authors: Grompe M. 
Published: December 2002

AbstractOrthotopic liver transplantation is the treatment of choice for several inborn errors of metabolism. Unfortunately, the supply of donor organs is limiting and therefore many patients cannot benefit from this therapy. In contrast, hepatocyte transplantation could potentially overcome the shortage in donor livers by use of cells from a single donor for multiple recipients. In classic hepatocyte transplantation, however, only 1% of the liver mass or less can be replaced by donor cells. Recently, though, it has been shown in animal models that >90% of host hepatocytes can be replaced by a small number of transplanted donor cells in a process we term ‘therapeutic liver repopulation’. This phenomenon is analogous to repopulation of the haematopoietic system after bone marrow transplantation. Liver repopulation occurs when transplanted cells have a growth advantage in the setting of damage to recipient liver cells. It has been discovered that transplanted cells from extrahepatic sources such as the adult pancreas or bone marrow can also be used for liver repopulation. Because bone marrow donors are widely available, this finding raises the hope of therapeutic application of these cells in the future. Here, the current knowledge regarding therapeutic liver repopulation and the hopeful implications for treatment of liver diseases will be discussed.
Polyunsaturated fatty acid deficiency during dietary treatment of very long‐chain acyl‐CoA dehydrogenase deficiency. Rescue with soybean oil
Authors: Ruiz‐Sanz J. I. , Aldamiz‐Echevarria L. , Arrizabalaga J. , Aquino L. , Jimeno P. , Pérez‐Nanclares G. , Sanjurjo P. 
Published: December 2002

AbstractNutritional management of very long‐chain acyl‐CoA dehydro‐genase (VLCAD) deficiency is based on the avoidance of fasting and substitution of medium‐chain triglycerides for long‐ and very long‐chain triglycerides. We report two cases of this disease, which developed ω‐6 essential fatty acid deficiency after three and five months from the beginning of nutritional therapy (SHS product: Monogen). This alteration could be especially dangerous in these patients owing to their possible susceptibility to the development of pigmentary retinopathy. The incorporation of linoleic acid as 3–4% of total caloric intake supported as soybean oil ameliorates this deficiency. We wish to remark on this early complication in the nutritional management of VLCAD deficiency and the possibility of rescue by the incorporation of soybean oil into the diet.
Frontal lobe dementia with abnormal cholesterol metabolism and heterozygous mutation in sterol 27‐hydroxylase gene (CYP27)
Authors: Sugama S. , Kimura A. , Chen W. , Kubota S. , Seyama Y. , Taira N. , Eto Y. 
Published: December 2002

AbstractOf the primary dementing disorders that cause frontotemporal dementia, the best‐known is Pick disease. We report on a 44‐year‐old woman with progressive frontal lobe dementia and spastic paraplegia. Examination revealed increased serum levels of cholestanol with abnormal cholesterol metabolism and a heterozygous mutation of the sterol 27‐hydroxylase gene (CYP27). Biochemical findings were compatible with cerebrotendinous xanthomatosis (CTX); however, the clinical manifestations were very dissimilar. To our knowledge, a symptomatic carrier of this mutation among CTX patients has not been reported. We speculate that the present patient has a previously undescribed neurodegenerative disease related to abnormal cholesterol metabolism with this heterozygous mutation.
Fluvoxamine and sleep disturbances in posttraumatic stress disorder
Authors: Neylan Thomas C. , Metzler Thomas J. , Schoenfeld Frank B. , Weiss Daniel S. , Lenoci Maryann , Best Suzanne R. , Lipsey Tami L. , Marmar Charles R. 
Published: December 2002

AbstractThis study assesses the efficacy of fluvoxamine treatment on different domains of subjective sleep quality in Vietnam combat veterans with chronic posttraumatic stress disorder (PTSD). Medically healthy male Vietnam theater combat veterans (N = 21) completed a 10‐week open label trial. Fluvoxamine treatment led to improvements in PTSD symptoms and all domains of subjective sleep quality. The largest effect was for dreams linked to the traumatic experience in combat. In contrast, generic unpleasant dreams showed only a modest response to treatment. Sleep maintenance insomnia and the item “troubled sleep” showed a large treatment response, whereas sleep onset insomnia improved less substantially. These therapeutic benefits contrast with published reports that have found activating effects of Selective Serotonin Reuptake Inhibitors on the sleep electroencephalogram.
Reconstructing trauma memories: A prospective study of “Amnesic” trauma survivors
Authors: Harvey Allison G. , Bryant Richard A. 
Published: December 2002

AbstractThe purpose of this study was to investigate memory for trauma in patients who were initially amnesic of the trauma as a result of mild traumatic brain injury (MTBI). Motor vehicle accident survivors who sustained a MTBI were assessed for their memory within 1‐month posttrauma (n = 79) and again at 2‐years post‐trauma (n = 50). Consistent with their brain injury, all patients reported significant amnesia of their accident at initial assessment. At 2‐years posttrauma, 40% were able to remember their accident. Reporting memory for the trauma was associated with shorter duration of posttraumatic amnesia. These findings suggest that people reconstruct memories of trauma in the absence of complete encoding of the experience. Possible mechanisms for memory reconstruction are considered.
Treatment of combat‐related nightmares using imagery rehearsal: A pilot study
Authors: Forbes David , Phelps Andrea , McHugh Tony 
Published: December 2002

AbstractPosttraumatic nightmares are a hallmark of PTSD and distinct from general nightmares as they are often repetitive and faithful representations of the traumatic event. This paper presents data from a pilot study that examined the use of Imagery Rehearsal in treating combat‐related nightmares of 12 Vietnam veterans with PTSD. Three treatment groups, comprising 4 veterans in each, completed standardised treatment across 6 sessions. Treatment effects were investigated using nightmare diaries and established instruments, including the IES‐R, BDI, BAI, and SCL‐90‐R. The data demonstrate significant reductions in nightmares targeted, and improvements in PTSD and comorbid symptomatology. The paper recommends that, on the basis of the promising preliminary data, a randomised control trial be established to assess imagery ability and attidude toward nightmares.
Variable clinical presentation in lysosomal storage disorders
Authors: Beck M. 
Published: December 2002

AbstractSummary: Extensive clinical heterogeneity is seen in lysosomal storage disorders, regarding the age of onset and severity of symptoms, the organs involved, and effects on the central nervous system. A broad phenotypic spectrum is seen, for example, in mucopolysaccharidosis type I (Hurler/Scheie disease), Gaucher disease, the severalforms of GM2‐gangliosidosis and the different manifestations of β‐galactosidasedeficiency (GM1‐gangliosidosis and Morquio disease type B). Variable clinical expression of the same enzyme defect is not well understood. The presence of different mutations is only part of the explanation, as intrafamilial variability is observed in many cases. Other mechanisms, for example the effect of specific activators, may also have an influence on phenotype.
A case of PDH‐E1α mosaicism in a male patient with severe metabolic lactic acidosis
Authors: Seyda A. , Chun K. , Packman S. , Robinson B. H. 
Published: December 2002

AbstractWe have characterized a novel mutation in a male patient that affects the coding sequence of PDH‐E1α gene and changes arginine‐141 to a leucine. This nucleotide substitution was found in about 75% of the studied DNA (fibroblasts, liver and muscle), a scenario that would indicate a case of E1α mosaicism in a male patient. When the mutant E1α protein was expressed in human skin fibroblasts with zero endogenous pyruvate dehydrogenase complex activity and E1α protein expression, no significant restoration of activity was recorded, in contrast to the wild‐type cDNA, even though both wild‐type and mutant protein levels were comparable. We concluded that the R141L mutation is a severe one and that it must have occurred in one of the E1α alleles during early embryogenesis.
Neuroleptic malignant syndrome during zuclopenthixol therapy in X‐linked cerebral adrenoleukodystrophy
Authors: Rubio‐Gozalbo M. E. , van Waardenburg D. A. , Forget P. P. , Spaapen L. J. M. , Verrips A. , Vroomen P. C. A. J. 
Published: December 2002

AbstractAn 8 year‐old boy with X‐ALD under treatment with simvastatin developed a severe adverse reaction when the dose of his other medication, zuclopenthixol was increased. Both drugs were withdrawn after a diagnosis of neuroleptic malignant syndrome was made.