bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of malignant pediatric renal tumors by gene expression
Authors: Huang Chiang‐Ching , Cutcliffe Colleen , Coffin Cheryl , Sorensen Poul H. B. , Beckwith J. Bruce , Perlman Elizabeth J. 
Published: January 2006

AbstractBackgroundThe most common malignant renal tumors of childhood are Wilms tumor (WT), clear cell sarcoma of the kidney (CCSK), cellular mesoblastic nephroma (CMN), and rhabdoid tumor of the kidney (RTK). Because these tumors present significant diagnostic difficulties, the goal was to define diagnostically useful signatures based on gene expression.ProceduresGene expression analysis using oligonucleotide arrays was performed on a training set of 47 tumors (10 CCSKs, 9 CMNs, 8 RTKs, and 20 WTs). Classifiers were developed for each tumor type using variations of compound covariate class predictor. The classifiers were applied to an independent test set of 72 tumors (3 CMN, 7 CCSK, 4 RTK, and 58 WT). Central review diagnosis was utilized as the gold standard. Correlation with the institutional diagnosis and qualitative estimation of confidence levels at the time of central review were noted.ResultsWithin the training set, classifiers resulted in no errors when >10 genes were utilized. Top genes in each classifier were verified using quantitative reverse transcription‐polymerase chain reaction (RT‐PCR). Applying the classifiers to the test set, 71 of 72 tumors were correctly classified with a confidence level of >99%. The exception was incorrectly classified by the gold standard. In comparison, by histopathology 31% of the non‐WT were not accurately classified by the local institution, and 29% were classified with <95% confidence on central review.ConclusionsClassifiers based on gene expression provide diagnostic confidence and accuracy greater than that of pathologic analysis alone. Tumors that show ambiguous gene expression profiles are those that are also pathologically and molecularly ambiguous and merit further analysis. Pediatr Blood Cancer © 2006 Wiley‐Liss, Inc.
Characterization of plasma gelsolin as a substrate for matrix metalloproteinases
Authors: Park Sung‐Min , Hwang In Kwan , Kim Se Yeon , Lee Seo‐Jin , Park Kang‐Sik , Lee Seung‐Taek 
Published: January 2006

AbstractWe previously showed that plasma gelsolin, a major component of the extracellular actin scavenging system, is an matrix metalloproteinase (MMP)‐14 substrate. Here we confirmed that plasma gelsolin is cleaved by MMP‐14 at the plasma level, and found that it was most efficiently digested by MMP‐3 followed by MMP‐2, MMP‐1, MMP‐14, and MMP‐9, in that order. Plasma gelsolin (90 kDa) was cut into several fragments of 43–48 kDa by MMP‐3. The MMP‐3 cleavage sites in plasma gelsolin were determined by labeling the C termini generated by in‐gel digestion with 50% H218O combined with peptide mass mapping, and sequencing of the N‐terminal amino acids. Plasma gelsolin was cleaved at Asn416‐Val417, Ser51‐Met52, and Ala435‐Gln436.Proteolytic cleavage by MMP‐3 resulted in considerable loss of its actin filament‐depolymerizing activity. This suggests that MMPs weaken the extracellular actin‐scavenging system by cleaving plasma gelsolin and may, therefore, be involved in pathological conditions induced by extracellular actin, such as endothelial injury, respiratory distress syndrome, hepatic necrosis, and septic shock.
Identification of an anti‐aldolase autoantibody as a diagnostic marker for diabetic retinopathy by immunoproteomic analysis
Authors: Ahn Bo‐Young , Song Eun‐Sun , Cho Yang Je , Kwon Oh Woong , Kim Jin Kook , Lee Na Gyong 
Published: January 2006

AbstractCirculating autoantibodies specific for retinal proteins are associated with retinal destruction in patients with diabetic retinopathy (DR). In this study, we screened diabetic sera for the presence of anti‐retinal autoantibodies with an aim of developing diagnostic markers for DR. Immunoblot analysis of DR patients' sera with human retinal cytosolic proteins revealed a higher incidence of anti‐retinal autoantibodies, compared to normal blood donors or diabetic patients without DR. Anti‐retinal protein autoantibody profiles of DR patient sera were obtained by 2‐DE immunoblot analysis. Specifically, 20 protein spots reactive with DR patient sera were identified by ESI‐MS/MS. Of these spots, 14 were specific for DR patients, and 4 reacted with both non‐proliferative DR (non‐PDR) and PDR sera. The anti‐aldolase autoantibody was selected as a DR marker candidate, and specific reactivity of DR patient sera was confirmed by immunoblot analysis with rabbit aldolase. The serum anti‐aldolase autoantibody level was measured by ELISA. DR patients showed significantly higher autoantibody levels than normal donors or diabetic patients without retinopathy. However, no significant differences were observed between non‐PDR and PDR patients, suggesting that the level of anti‐aldolase autoantibody is not determined by the severity of retinopathy in diabetic patients. Our data collectively demonstrate that the anti‐aldolase autoantibody serves as a useful marker for DR diagnosis.
Linker chains of the gigantic hemoglobin of the earthworm Lumbricus terrestris: Primary structures of linkers L2, L3, and L4 and analysis of the connectivity of the disulfide bonds in linker L1
Authors: Kao Wen‐Yen , Qin Jun , Fushitani Kenzo , Smith Sandra S. , Gorr Thomas A. , Riggs Claire K. , Knapp James E. , Chait Brian T. , Riggs Austen F. 
Published: January 2006

AbstractThe extracellular hemoglobin (Hb) of the earthworm, Lumbricus terrestris, has four major kinds of globin chains: a, b, c, and d, present in equimolar proportions, and additional non‐heme, non‐globin scaffolding chains called linkers that are required for the calcium‐dependent assembly of the full‐sized molecule. The amino acid sequences of all four of the globin chains and one of the linkers (L1) have previously been determined. The amino acid sequences via cDNA of each of the three remaining linkers, L2, L3, and L4, have been determined so that the sequences of all constituent polypeptides of the hemoglobin are now known. Each linker has a highly conserved cysteine‐rich segment of ∼ 40 residues that is homologous with the seven ligand‐binding repeats of the human low‐density lipoprotein receptor (LDLR). Analysis of linker L1 shows that the connectivity of the three disulfide bonds is exactly the same as in the LDLR ligand‐binding repeats. The presence of a calcium‐binding site comprising one glutamyl and three aspartyl residues in both the LDLR repeats and in the linkers supports the suggestion that calcium is required for the folding and disulfide connectivity of the linkers as in the LDLR repeats. Linker L2 is markedly heterogeneous and contains unusual glycine‐rich sequences near the NH2‐terminus and a polar zipper‐like sequence with imperfect repeats of Asp‐Asp‐His at the carboxyl terminus. Similar Asp‐Asp‐His repeats have been found in a protein homologous to superoxide dismutase in the hemolymph of certain mussels. These repeats may function as metal‐binding sites. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Wind lidar evaluation at the Danish wind test site in Høvsøre
Authors: Smith David A. , Harris Michael , Coffey Adrian S. , Mikkelsen Torben , Jørgensen Hans E. , Mann Jakob , Danielian Régis 
Published: January 2006

AbstractInitial assessments of a wind lidar have shown the technology to have significant potential for wind field measurements in the wind energy industry. A more extended evaluation is now reported using a scanning lidar next to a meteorological mast with calibrated anemometers at the Risø wind test site in Høvsøre on the windy northwest coast of Denmark. Results are presented of wind speed comparisons at heights up to 100 m above ground level showing excellent correlation between the lidar and the cup anemometers. Copyright © 2006 John Wiley & Sons, Ltd.
Effects of selective excitation of x‐ray fluorescence of light elements: fluorine, oxygen, nitrogen and carbon
Authors: Dukhanin A. Y. , Pavlinsky G. V. 
Published: January 2006

AbstractThis paper describes three variants of the selective excitation of elements with low atomic number, i.e. fluorine, oxygen, nitrogen and carbon. One of the variants considers intra‐atomic cascade transitions in the elements of the enclosing matrix. Selective excitation effect values were calculated with consideration of atom excitation by photo‐ and Auger electrons, originating in the material irradiated. It is shown that in some cases the total input of the effects of selective excitation amounts to a few tens of percent of the analytical signal intensity. This study also examines x‐ray fluorescence excitation by irradiating x‐ray tubes with different anodes and varying beryllium window thickness. Copyright © 2006 John Wiley & Sons, Ltd.
The antecedents and consequences of autonomous self‐regulation for college: A self‐determination theory perspective on socialization
Authors: Niemiec Christopher P. , Lynch Martin F. , Vansteenkiste Maarten , Bernstein Jessey , Deci Edward L. , Ryan Richard M. 
Published: January 2006

ABSTRACTUsing self‐determination theory, two studies investigated the relations among perceived need support from parents, their adolescents’ autonomous self‐regulation for academics, and the adolescents’ well‐being. Study 1 indicated that perceived need support from parents independently predicted adolescents’ well‐being, although when mothers’ and fathers’ data were examined separately, the relation was stronger for mothers than for fathers. In Study 2, autonomous self‐regulation for planning to attend college was a significant partial mediator of the relation of adolescents’ perceived need support to well‐being. Thus, perceived need support from parents does seem important for the development of adolescents’ autonomous self‐regulation and well‐being.
Antipsychotic type and correlates of antipsychotic treatment discontinuation in the outpatient treatment of schizophrenia
Authors: Haro Josep Maria , Novick Diego , Belger Mark , Jones Peter B. 
Published: January 2006

AbstractAntipsychotic medication maintenance and the factors influencing it were analyzed using data from the SOHO study, a large observational study of the outcomes of antipsychotic treatment for schizophrenia in Europe. A total of 7186 adult patients in the outpatient setting who were initiating or changing their antipsychotic medication and who were prescribed only one antipsychotic after the baseline visit were analyzed. Medication maintenance at 12 months varied with the type of antipsychotic prescribed, being highest with clozapine (79.5%) and olanzapine (77.0%), and lowest with quetiapine (51.4%) and amisulpride (58.2%). Multiple logistic regression analysis demonstrated that the type of antipsychotic prescribed at baseline was the most important predictor of medication maintenance. Alcohol dependency, taking mood stabilizers, compulsory admission or arrest in the previous 6 months, greater clinical severity, and changing antipsychotic medication due to lack of effectiveness at baseline predicted a higher frequency of medication discontinuation in the subsequent 12 months. In contrast, medication maintenance was higher among patients who were treatment naïve at baseline, socially active or who had loss of libido at baseline. The findings from this study should be interpreted conservatively because of its non-randomized observational design.
Mechanism of toxicity of the branched‐chain fatty acid phytanic acid, a marker of Refsum disease, in astrocytes involves mitochondrial impairment
Authors: Reiser Georg , Schönfeld Peter , Kahlert Stefan 
Published: January 2006

AbstractPhytanic acid is a saturated branched‐chain fatty acid, which is formed by bacterial degradation of chlorophyll in the intestinal tract of ruminants. The methyl group in β‐position prevents degradation of phytanic acid by the β‐oxidation pathway. Therefore, degradation of phytanic acid is initiated by α‐oxidation in peroxisomes. The inherited peroxisomal disorder Refsum disease is characterised by accumulation of phytanic acid. Unusually high concentrations of phytanic acid can be found in the plasma of Refsum disease patients, who suffer from neurodegeneration and muscle dystrophy. Phytanic acid has been suggested to be causally involved in the clinical symptoms. To elucidate the pathogenic mechanism, we investigated the influence of phytanic acid in rat hippocampal astrocytes by monitoring the cytosolic Ca2+ concentration, the mitochondrial membrane potential (Δψm), the generation of reactive oxygen species as well as the cellular ATP level. In response to phytanic acid (100 μM) cytosolic Ca2+ was quickly increased. The phytanic acid‐evoked Ca2+ response was transient and involved activation of intracellular Ca2+ stores. In isolated rat brain mitochondria, phytanic acid dissipated Δψm in a reversible and dose‐dependent manner. Moreover, phytanic acid released cytochrome c from mitochondria. Depending on the mitochondrial activity state, phytanic acid either stimulated or inhibited the electron flux within the respiratory chain. In addition, phytanic acid induced substantial generation of reactive oxygen species in isolated mitochondria as well as in intact cells. Phytanic acid caused cell death of astrocytes within a few hours of exposure. In conclusion, we suggest that phytanic acid initiates astrocyte cell death by activating the mitochondrial route of apoptosis.
Using replication research for just‐in‐time purchasing construct development
Authors: Kaynak Hale , Hartley Janet L. 
Published: January 2006

AbstractUsing replication research, the validity of the just‐in‐time purchasing (JITP) construct is established. Although empirical researchers have examined JITP over the last two decades, a consistent set of valid, reliable factors has not been used. The lack of valid construct is a barrier to hypotheses testing and meta‐analyses on JITP. This study confirmed the validity of six JITP factors: top management commitment, employee relations, training, supplier quality management, transportation, and quantities delivered using two different data sets and testing the first‐ and second‐order structure of the JITP construct. Content validity, reliability, unidimensionality, convergent validity, discriminant validity, criterion‐related validity, and an invariant factorial structure of the JITP construct were empirically established.
“Binary Synthesis”: Goethe's Aesthetic Intuition in Literature and Science
Authors: Stephenson Roger H. 
Published: January 2006

ArgumentThis essay seeks to identify the cultural significance of Goethe's scientific writings. He reformulates, in the light of his own concrete experience, “crucial turning-points” (Hauptmomente) in the history of science – key ideas, the historical understanding of which is vital to present understanding – thus situating his own scientific work at the bi-polar center of the Western scientific tradition, conceived as the dramatic interplay over centuries of two opposing modes of thought. For in his experimentation he recaptures the glimpse of living form gained in aesthetic perception (Anschauung), from which such inherited theoretical positions are ultimately derived. At each stage of this process, imagination, in its aesthetic modality, is essential, for it alone reveals the world as it truly is. The literary quality of his writings on nature, as on culture, reveals Goethe's stylistic achievement in devising a medium in which the insights gained in contemplation may be so transmitted as to make a similar, imaginative, appeal to his reader – re-enacting the abstract-concrete equilibrium characterizing all aesthetic experience. Matching his style to the subtle, delicate, connectedness of Nature, Goethe recreates the delights of participating in natural creativity. His Janus-faced, scientific-literary, style illustrates “binary synthesis,” the principle that unites Goethe's science with his art.Beauty is the normal state.(Ralph Waldo Emerson, The Conduct of Life)There can be no such thing as an eclectic philosophy, but there can be eclectic philosophers. But an eclectic is anyone who, from whatever exists and is happening round about, appropriates the things he or she finds congenial to her or his nature; and this context validly includes all that can be called culture and progress in a theoretical and practical sense. It follows that two eclectic philosophers could turn into the greatest opponents if they are antagonistic to one another, each picking out whatever suits him or her in every traditional system of philosophy.(Goethe, Wilhelm Meister's Journeyman Years)
Genetic Code, Text, and Scripture: Metaphors and Narration in German Molecular Biology
Authors: Brandt Christina 
Published: January 2006

ArgumentThis paper examines the role of metaphors in science on the basis of a historical case study. The study explores how metaphors of “genetic information,” “genetic code,” and scripture representations of heredity (i.e. the metaphorical comparison of DNA with text and alphabet) entered molecular biology and reshaped experimentation during the 1950s and 1960s. Following the approach of the philosopher Hans Blumenberg, I will argue that metaphors are not merely a means of popularization or a specific kind of modeling (by building analogies) but rather are representations that can unfold an operational force of their own.While the influence of cybernetics and information theory on molecular biology is well documented in historical analysis throughout recent years, this paper offers new insights into the metaphysical and religious resonances of textual metaphors in the life sciences. The main focus will be on developments in Germany, in particular on the work of the German biochemist Gerhard Schramm. In this historical case study the interaction between metaphors and experimental practices will be discussed. The paper analyzes different phases in the use of metaphors during the 1950s and 1960s: it will explore how the metaphors of a “genetic alphabet” or of “genetic code” (which were used with an illustrative purpose in the 1950s) developed into a new research program and eventually attained ontological status in the early 1960s. At that time Schramm's use of textual metaphors was reminiscent of nineteenth-century German natural philosophy. In this case, the metaphorical shift shows how the metaphor of a “genetic text” or a “genetic code,” which were central for the emerging molecular biology, drew on older cultural traditions with all of their metaphysical and religious preoccupations.
Empirical evidence for a nonlinear effect of galactic cosmic rays on clouds
Authors: Harrison R.Giles , Stephenson David B 
Published: January 2006

Galactic cosmic ray (GCR) changes have been suggested to affect weather and climate, and new evidence is presented here directly linking GCRs with clouds. Clouds increase the diffuse solar radiation, measured continuously at UK surface meteorological sites since 1947. The ratio of diffuse to total solar radiation—the
diffuse fraction
(DF)—is used to infer cloud, and is compared with the daily mean neutron count rate measured at Climax, Colorado from 1951–2000, which provides a globally representative indicator of cosmic rays. Across the UK, on days of high cosmic ray flux (above 3600×10
2
neutron counts h
−1
, which occur 87% of the time on average) compared with low cosmic ray flux, (i) the chance of an overcast day increases by (19±4) %, and (ii) the diffuse fraction increases by (2±0.3) %. During sudden transient reductions in cosmic rays (e.g. Forbush events), simultaneous decreases occur in the diffuse fraction. The diffuse radiation changes are, therefore, unambiguously due to cosmic rays. Although the statistically significant nonlinear cosmic ray effect is small, it will have a considerably larger aggregate effect on longer timescale (e.g. centennial) climate variations when day-to-day variability averages out.
Environmental and management determinants of vegetation state on protected areas in the eastern Lowveld of South Africa
Authors: Peel M. J. S. , Kruger J. M. , Zacharias P. J. K. 
Published: January 2006

AbstractPrincipal driving determinants (rainfall, geology, soil, tree density and canopy cover, animal numbers and feeding classes, and fire) of vegetation structure and function in the Lowveld savanna in South Africa were grouped for a 7‐year period to establish their influence on the limiting herbaceous layer. Grass type, abundance and cover were examined (450 sites; approximately 4000 km2). Using ordination, the variation and differences in the herbaceous‐response variables viz. perennial composition and cover allowed for the broad environmental grouping of areas of similar ecological potential. We demonstrate that areas of higher ecological potential carried higher densities of large herbivores without detrimentally affecting herbaceous composition and cover. The results have implications for land users and policy makers in terms of setting animal stocking density guidelines.
Virological analysis and phenotypic characterization of peripheral blood lymphocytes of hepatitis C virus-infected patients with and without mixed cryoglobulinaemia
Authors: Sansonno D , Lauletta G , Montrone M , Tucci F A , Nisi L , Dammacco F 
Published: January 2006

SummaryIn clinical and pathological terms hepatitis C virus (HCV)-infected patients can be subdivided into two main groups with and without mixed cryoglobulinaemia (MC). Involvement of blood mononuclear cells by HCV has potentially important implications. To this end, HCV-RNA levels in peripheral blood lymphocytes (PBL) preparations of 20 chronically HCV-infected patients with MC were measured and compared with those found in a group of 20 patients without MC matched for age, serum HCV-RNA, infectious genotype, source and presumable duration of infection. Phenotypic abnormalities of PBL subsets in each group of patients were determined by cell surface marker expression and compared. Results showed a significant enrichment of HCV-RNA in PBL of MC patients compared with a non-MC group (P = 0·01). Different distribution of HCV-RNA was accompanied by evidence of an increased frequency of circulating B cells. These data indicate that MC patients are characterized distinctly by a higher quota of cell-associated viral load.