bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Secondary Covariates when Estimating latent Trait Population Distributions
Authors: Thomas Neal 
Published: January 2006

The U.S. National Assessment of Educational Progress (NAEP), the Third International Mathematics and Science Study (TIMSS), and the U.S. Adult Literacy Survey collect probability samples of students (or adults) who are administered brief examinations in subject areas such as mathematics and reading (cognitive variables), along with background demographic (primary) and educational environment (secondary) questions. The demographic questions are used in the primary reporting, while the numerous “explanatory” secondary variables, or “covariates”, are only directly utilized in subsequent secondary analyses. The covariates are also used indirectly to create the plausible values (multiple imputations) that are an integral part of analyses because of the use of sparse matrix sampling of cognitive items. The improvement in the precision of the primary reporting due to the inclusion of the covariates is assessed here and contrasted with the precision of reporting using plausible values created using only the primary demographic variables.The results demonstrate that the improvement in precision depends on the matrix sampling designs for the cognitive assessments. The improvements range from essentially none for the most common designs, to moderate for some less common designs. Consequently, two potential changes in the reporting procedures that could improve the statistical and operational efficiency of primary reporting are (a) eliminate or reduce the collection of covariates and increase the number of cognitive items, (b) to avoid delays, eliminate the covariates from the creation of plausible values used for the primary reports, but include them later when creating public-use files for secondary analyses. The potential improvements in statistical and operational efficiency must be weighed against the intrinsic interest in the covariates, and the potential for small discrepancies in the primary and secondary reporting.
A Person-Fit Index for Polytomous Rasch Models, Latent Class Models, and Their Mixture Generalizations
Authors: von Davier Matthias , Molenaar Ivo W. 
Published: January 2006

A normally distributed person-fit index is proposed for detecting aberrant response patterns in latent class models and mixture distribution IRT models for dichotomous and polytomous data.This article extends previous work on the null distribution of person-fit indices for the dichotomous Rasch model to a number of models for categorical data. A comparison of two different approaches to handle the skewness of the person-fit index distribution is included.
Testing methods for X-machines: a review
Authors: Bogdanov K. , Holcombe M. , Ipate F. , Seed L. , Vanak S. 
Published: January 2006

Abstract
The X-machine testing method has been developed as an application of the W-method to testing the control structure of an implementation, against a specification. The method was proven to demonstrate the equivalence of the behaviour of the two, subject to a number of conditions both a specification and an implementation are expected to satisfy, such as (1) determinism of the two and (2) that functions labelling arcs on a transition diagram of a specification control structure have been tested in advance. Since the original publication of the testing method, a number of extensions have been published, removing the restrictions mentioned above. This paper surveys the extensions of the X-machine testing method, for (1) testing of functions together with testing of a transition diagram, (2) equivalence testing of a non-deterministic implementation against a non-deterministic specification, (3) conformance testing of a deterministic implementation against a non-deterministic specification and (4) equivalence testing of a system of concurrently executing and communicating X-machines, against a specification.
Nonviral in vivo gene transfer in the mucopolysaccharidosis I murine model
Authors: Camassola M. , Braga L. M. , Delgado‐Cañedo A. , Dalberto T. P. , Matte U. , Burin M. , Giugliani R. , Nardi N. B. 
Published: January 2006

SummaryMucopolysaccharidosis I (MPS I) is a lysosomal disorder characterized by a deficiency of the enzyme α‐L‐iduronidase (IDUA), which is responsible for the degradation of glycosaminoglycans (GAGs). This deficiency leads to the accumulation of dermatan and heparan sulphate in lysosomes. Presently available treatments include bone marrow transplantation and enzyme replacement therapies, both of which are limited in their effects. In this work, knockout (KO) MPS I mice were treated with a nonviral vector containing the human IDUA cDNA. KO mice were transfected by hydrodynamic injection of pRIDUA in the caudal vein (i.v., n = 3) or by intraperitoneal injection of pRIDUA/Superfect complexes (i.p., n = 3). GAG concentration and IDUA activity were analysed in the kidneys, spleen, lungs, brain and liver. The expression of IDUA in the organs of i.v.‐ and i.p.‐treated mice was also analysed by real‐time reverse‐transcription (RT) PCR and compared by relative quantification. The concentration of GAGs in the organs differed between KO and wild‐type mice. In the spleen and liver, GAG levels were lower in i.v.‐ and i.p.‐treated KO mice than in control nontreated animals. Real‐time RT‐PCR showed that the transgene is expressed in all the analysed organs of i.p.‐ and i.v.‐treated KO mice. Enzyme activity was similarly observed in all the organs analysed. Our data suggest that this kind of transfection may be a useful tool for studies of nonviral protocols for gene therapy of MPS.
Influence of D‐arabitol and ribitol on neuronal network activity
Authors: Klusmann A. , Fleischer W. , Waldhaus A. , Siebler M. , Mayatepek E. 
Published: January 2006

SummaryTo date, two new defects in the pentose phosphate pathway have been identified in patients with abnormalities in their polyol profiles. Some of them presented with neurological symptoms of so far unknown aetiology. The pathophysiological role of polyols, e.g. in the brain, is relatively unknown. We tested the neurotoxicity of polyols using a ‘neurochip’ model. After exposure of cortical rat neurons to D‐arabitol and ribitol in increasing concentrations up to 10 mmol/L, the electrophysiological activity was measured. No acute effect on the spontaneous network activity of cortical neurons was observed. We speculate that polyols have only secondary effects on brain dysfunction.
A comparative study of cytoplasmic granules imaged by the real‐time microscope, Nile Red and Filipin in fibroblasts from patients with lipid storage diseases
Authors: Pham N.‐A. , Gal M. R. , Bagshaw R. D. , Mohr A. J. , Chue B. , Richardson T. , Callahan J. W. 
Published: January 2006

SummaryCytoplasmic granules in fibroblasts, visualized without stains, or labelled with Nile red, Filipin, or anti‐LAMP‐1 (lysosome‐associated membrane protein 1), were imaged using the real‐time microscope (RTM). New advances in light microscope technology were applied to detect cytoplasmic granules (RTM‐visible granules) and characterize them by imaging contrast, size, shape, cellular distribution, composition, motion dynamics and quantity. Appearing as solid spheroids or ring structures, the majority of the RTM‐visible granules contained Nile‐red labelled neutral lipids. A smaller subpopulation, appearing dimmer, with less imaging contrast, contained Filipin‐labelled free cholesterol. Most lipid storage granules have a diameter ranging from 0.3 μm to 0.6 μm, with a small population measuring up to 1 μm. They typically clustered in the perinuclear region and displayed relatively small oscillatory motion. Immunofluorescence based on LAMP‐1 labelling highlighted granular structures that were distinct and separate from RTM‐visible granules and other structures in the light modality of the microscope. RTM‐visible granules were associated with disease phenotypes that have increased cellular neutral lipid stores corresponding to the Nile red‐labelled droplets (e.g. triacylglycerides, cholesterol esters). As predicted, the fibroblast strains with a defect resulting in Wolman disease, when compared to control samples, consistently had RTM‐visible granules, higher in imaging contrast and with larger diameters, that were labelled with Nile red, and also an increased frequency of Filipin–cholesterol complexes. By comparison, in fibroblasts where the lipid storage is less evident (Gaucher and Farber diseases) or from GM1 gangliosidosis, where the primary storage substances are oligosaccharides, fewer and smaller RTM‐visible granules were observed. In some cases, changes in contrast and morphology in the unstained cytoplasmic compartments were more evident than in the labelled structures. In summary, applying the RTM imaging system to fibroblasts enables differences between the various disease types to be seen and, in specific examples, a unique phenotype can be readily discerned.
Comprehensive analysis of pyrimidine metabolism in 450 children with unspecific neurological symptoms using high–pressure liquid chromatography–electrospray ionization tandem mass spectrometry
Authors: Schmidt C. , Hofmann U. , Kohlmüller D. , Mürdter T. , Zanger U. M. , Schwab M. , Hoffmann G. F. 
Published: January 2006

SummaryTo evaluate the significance of inborn metabolic disorders of the pyrimidine degradation pathway, 450 children with unspecific neurological symptoms were comprehensively studied; 200 healthy children were recruited as controls. Uracil and thymine as well as their degradation products in urine were determined with an improved method based on reversed‐phase HPLC coupled with electrospray ionization tandem mass spectrometry and detection by multiple‐reaction monitoring using stable‐isotope‐labelled reference compounds as internal standards.From the results of the control group we established age‐related reference ranges of all pyrimidine degradation products. In the patient group, two children with dihydropyrimidine dehydrogenase (DPYD) deficiency were identified; one of these was homozygous for the exon 14‐skipping mutation of the DPYD gene. In addition, two patients with high uracil, dihydrouracil and β‐ureidopropionate were found to have ornithine transcarbamylase deficiency. In the urine of 9 patients, β‐alanine was markedly elevated owing to treatment with vigabatrin, an irreversible inhibitor of GABA transaminase, which interferes with β‐alanine breakdown. Four patients had exclusively high levels of β‐aminoisobutyrate (β‐AIB) due to a low activity of the D‐β‐AIB‐pyruvate aminotransferase, probably without clinical significance.In conclusion, quantitative investigation of pyrimidine metabolites in children with unexplained neurological symptoms, particularly epileptic seizures with or without psychomotor retardation, can be recommended as a helpful tool for diagnosis in clinical practice. Sensitive methods and age‐related reference ranges enable the detection of partial enzyme deficiencies.
Gordon syndrome and succinylcholine
Authors: Puura A. , Schultz R. 
Published: January 2006

SummaryWe present a case of 6‐year‐old boy who developed severe hyperkalaemia and ventricular tachycardia after administration of succinylcholine. Ventricular tachycardia was defibrillated and Gordon syndrome, which was diagnosed subsequently, was treated successfully. Paediatric patients with underlying metabolic disorders such as Gordon syndrome are at high risk of developing severe hyperkalaemia after succinylcholine administration.
Mutation spectrum of type I glycogen storage disease in Hungary
Authors: Miltenberger‐Miltenyi G. , Szonyi L. , Balogh L. , Utermann G. , Janecke A. R. 
Published: January 2006

SummaryWe performed mutation analysis in 12 Hungarian type I glycogen storage disease (GSD I) patients in order to determine the mutation spectrum. All patients were clinically classified as GSD Ia. Nine patients carried biallelic G6PC mutations (p.Q27fsX35, p.D38V, p.W70X, p.K76N, p.W77R, p.R83C, p.E110Q, p.G222R), with E110Q reported only in Hungary. However, three patients displayed two common G6PT1 (SLC37A4) mutations (p.L348fsX400, p.C183R) which were originally described in association with GSD Inon‐a. Review of the literature and our data show that G6PT1 mutations are not associated with neutropenia and related clinical findings in approximately 10% of these cases. Homozygosity for the truncating G6PT1 mutation p.L348fsX400 can be observed with and without neutropenia, indicating that one or more modifiers of the action of G6PT1 exist. Our data are suitable to provide DNA‐based and thus noninvasive confirmation of diagnosis in Hungarian patients with this disorder.
Mutational spectrum in ten Italian patients affected by methylmalonyl‐CoA mutase deficiency
Authors: Cavicchi C. , Donati M. A. , Pasquini E. , Poggi G. M. , Dionisi‐Vici C. , Parini R. , Zammarchi E. , Morrone A. 
Published: January 2006

SummaryWe report seven novel mutations, including three amino acids substitutions (p.Glu286Lys, p.Cys560Tyr, p.Pro615Leu), two nonsense mutations (p.Arg31X, p.Glu 451X), one splicing defect (c.2125−1G >A), one small deletion (c.1758–1759delA) and nine previously described mutations identified in 10 unrelated Italian patients affected by mut MMA.
Hyperammonaemic encephalopathy induced by a commercial very‐low‐energy diet in a neglected ornithine‐carbamoyltransferase‐deficient woman
Authors: Vinzio S. , Perrin A. E. , Forestier E. , Schlienger J. L. , Goichot B. 
Published: January 2006

SummaryThis case report describes a 31‐year‐old woman with a neglected ornithine carbamoyltransferase deficiency, admitted for a hyperammonaemic encephalopathy induced by a commercial very low‐energy diet. To our knowledge, this is the first reported case and it underlines the potential risk of such a diet in patients with undiagnosed or neglected ornithine carbamoyltransferase deficiency.
Mucopolysaccharidosis I under enzyme replacement therapy with laronidase—A mortality case with autopsy report
Authors: Lin H.‐Y. , Lin S.‐P. , Chuang C.‐K. , Chen M.‐R. , Chen B.‐F. , Wraith J. E. 
Published: January 2006

AbstractThere is little information about MPS I‐related complications during laronidase therapy. We describe the first autopsy report of a young male MPS I patient who died of infection‐induced cardiopulmonary failure following 2 years of weekly treatment with laronidase.
Methionine adenosyltransferase (MAT) I/III deficiency with concurrent hyperhomocysteinaemia: Two novel cases
Authors: Linnebank M. , Lagler F. , Muntau A. C. , Röschinger W. , Olgemöller B. , Fowler B. , Koch H. G. 
Published: January 2006

SummaryThis study reports three novel mutations of the methionine adenosyltransferase (MAT) lA gene and confirms that hyperhomocysteinaemia may be a characteristic finding in MAT I/III deficiency. Thus, MAT I/III deficiency is important in the differential diagnoses of hyperhomocysteinaemia, which may lead to clinical complications of MAT I/III deficiency.
Polynomial model approach for resynchronization analysis of cell-cycle gene expression data
Authors: Qiu Peng , Wang Z. Jane , Liu K. J. Ray 
Published: January 2006

Abstract
Motivation: Identification of genes expressed in a cell-cycle-specific periodical manner is of great interest to understand cyclic systems which play a critical role in many biological processes. However, identification of cell-cycle regulated genes by raw microarray gene expression data directly is complicated by the factor of synchronization loss, thus remains a challenging problem. Decomposing the expression measurements and extracting synchronized expression will allow to better represent the single-cell behavior and improve the accuracy in identifying periodically expressed genes.
Results: In this paper, we propose a resynchronization-based algorithm for identifying cell-cycle-related genes. We introduce a synchronization loss model by modeling the gene expression measurements as a superposition of different cell populations growing at different rates. The underlying expression profile is then reconstructed through resynchronization and is further fitted to the measurements in order to identify periodically expressed genes. Results from both simulations and real mircorarray data show that the proposed scheme is promising for identifying cyclic genes and revealing underlying gene expression profiles.
Availability: Contact the authors.
Contact: qiupeng@umd.edu
Supplementary information: Supplementary data are available at:
Structural disorder of a new zeolite-like lithosilicate, K2.6Li5.4[Li4Si16O38]·4.3H2O
Authors: Park So-Hyun , Boysen Hans , Parise John B. 
Published: January 2006

The framework structure of the synthetic microporous lithosilicate RUB-30 (K2.6Li5.4[Li4Si16O38]·4.3H2O) is similar to that of the fibrous zeolites such as natrolite, edingtonite and thomsonite, since all their frameworks include the same secondary structural building unit, the so-called 4–1 T
5O10 cluster of tetrahedra. Unique to the structure of RUB-30, each 4–1 unit consists of a LiSi4O10 moiety within which the single [LiO4] tetrahedron is strictly segregated from the other four [SiO4] tetrahedra. The connection of neighboring 4–1 units through edge-sharing [LiO4] tetrahedra results in a new framework topology. The present work reports an `average' structure of RUB-30 solved by synchrotron X-ray single-crystal diffraction data collected at a second-generation source. A superstructure with a × 2b × c (relative to the subcell quoted above) could be seen in X-ray diffraction data collected with better resolution and higher brightness at a third generation source. Diffuse streaks along k with l = odd and unusual superstructure hkl reflections, with k = odd and l = odd only, indicate a more complicated real structure of the material. To explain this observation we propose two different structure types which are statistically, but coherently, intergrown in RUB-30.
Variation of loop sequence alters stability of cytolethal distending toxin (CDT): Crystal structure of CDT from Actinobacillus actinomycetemcomitans
Authors: Yamada Taro , Komoto Junichi , Saiki Keitarou , Konishi Kiyoshi , Takusagawa Fusao 
Published: January 2006

AbstractCytolethal distending toxin (CDT) secreted by Actinobacillus actinomycetemcomitans induces cell cycle arrest of cultured cells in the G2 phase. The crystal structure of the natural form of A. actinomycetemcomitans DCT (aCDT) has been determined at 2.4 Å resolution. aCDT is a heterotrimer consisting of the three subunits, aCdtA, aCdtB, and aCdtC. Two crystallographically independent aCDTs form a dimer through interactions of the aCdtB subunits. The primary structure of aCDT has 94.3% identity with that of Haemophilus ducreyi CDT (hCDT), and the structure of aCDT is quite similar to that of hCDT reconstituted from the three subunits determined recently. However, the molecular packings in the crystal structures of aCDT and hCDT are quite different. A careful analysis of molecular packing suggests that variation of the amino acid residues in a nonconserved loop (181TSSPSSPERRGY192 of aCdtB and 181NSSSSPPERRVY192 of hCdtB) is responsible for the different oligomerization of very similar CDTs. The loop of aCdtB has a conformation to form a dimer, while the loop conformation of hCdtB prevents hCDT from forming a dimer. Although dimerization of aCDT does not affect toxic activity, it changes the stability of protein. aCDT rapidly aggregates and loses toxic activity in the absence of sucrose in a buffered solution, while hCDT is stable and retains toxic activity. Another analysis of crystal structures of aCDT and hCDT suggests that the receptor contact area is in the deep groove between CdtA and CdtC, and the characteristic “aromatic patch” on CdtA.
Crystal structural analysis and metal‐dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+
Authors: Doudeva Lyudmila G. , Huang Hsinchin , Hsia Kuo‐Chiang , Shi Zhonghao , Li Chia‐Lung , Shen Yongliang , Cheng Yi‐Sheng , Yuan Hanna S. 
Published: January 2006

AbstractThe nuclease domain of ColE7 (N‐ColE7) contains an H‐N‐H motif that folds in a ββα‐metal topology. Here we report the crystal structures of a Zn2+‐bound N‐ColE7 (H545E mutant) in complex with a 12‐bp duplex DNA and a Ni2+‐bound N‐ColE7 in complex with the inhibitor Im7 at a resolution of 2.5 Å and 2.0 Å, respectively. Metal‐dependent cleavage assays showed that N‐ColE7 cleaves double‐stranded DNA with a single metal ion cofactor, Ni2+, Mg2+, Mn2+, and Zn2+. ColE7 purified from Escherichia coli contains an endogenous zinc ion that was not replaced by Mg2+ atconcentrations of <25mM, indicating thatzincisthe physiologically relevant metal ion in N‐ColE7 in host E. coli. In the crystal structure of N‐ColE7/DNA complex, the zinc ion is directly coordinated to three histidines and the DNA scissile phosphate in a tetrahedral geometry. In contrast, Ni2+ is bound in N‐ColE7 in two different modes, to four ligands (three histidines and one phosphate ion), or to five ligands with an additional water molecule. These data suggest that the divalent metal ion in the His‐metal finger motif can be coordinated to six ligands, such as Mg2+ in I‐PpoI, Serratia nuclease and Vvn, five ligands or four ligands, such as Ni2+ or Zn2+ in ColE7. Universally, the metal ion in the His‐metal finger motif is bound to the DNA scissile phosphate and serves three roles during hydrolysis: polarization of the P–O bond for nucleophilic attack, stabilization of the phosphoanion transition state and stabilization of the cleaved product.
1α,25‐Dihydroxyvitamin D3 downmodulates the functional differentiation of Th1 cytokine‐conditioned bone marrow‐derived dendritic cells beneficial for cytotoxic T lymphocyte generation
Authors: Matsuzaki Junko , Tsuji Takemasa , Zhang Yue , Wakita Daiko , Imazeki Ikuo , Sakai Tomoaki , Ikeda Hiroaki , Nishimura Takashi 
Published: January 2006

Various dendritic cell subsets are induced from bone marrow cells under different cytokine conditions. We have demonstrated previously that the Th1‐cytokine‐conditioned bone marrow‐derived dendritic cell (BMDC) subset BMDC1 (generated in the presence of granulocyte‐macrophage colony‐stimulating factor [GM‐CSF] + interleukin [IL]‐3 + interferon [IFN]‐γ+ IL‐12) induces a much stronger type 1 immune response than BMDC0 (GM‐CSF + IL‐3). In the present study, we investigated the effect of 1α,25‐dihydroxyvitamine D3 (VitD3), which is a known immunomodulating drug, on the differentiation of BMDC subsets. The addition of VitD3 significantly influenced the functional differentiation of BMDC1 compared with BMDC0. Specifically, the addition of VitD3 greatly decreased the expression levels of MHC class I, CD80, CD40 and leukocyte function‐associated antigen (LFA)‐1 molecules on BMDC1. In addition, VitD3‐treated BMDC1 (VD3‐BMDC1) almost completely lost their immunostimulating activity for inducing type 1 immunity and cytotoxic T lymphocyte generation. A failure in the induction of type 1 immunity by VD3‐BMDC1 appeared to be due to the following: (i) the expression of co‐stimulatory molecules on VD3‐BMDC1 was strongly downmodulated compared with BMDC1 generated without VitD3; and (ii) VD3‐BMDC1 showed significantly lower mRNA expression of IFN‐γ and IFN‐β, factors that are essential for cytotoxic T lymphocyte induction. VitD3 inhibited the differentiation of functionally competent BMDC1 during the early phase of differentiation but not during the late differentiation period. A possible reason for the inhibition of BMDC1 differentiation by VitD3 is reduced phosphorylation of STAT1 during early differentiation. Taken together, VitD3 strongly suppressed T‐cell responses by inhibiting functional differentiation of precursor dendritic cells into functional BMDC1 that are feasible for inducing Th1‐dependent cellular immunity. (Cancer Sci 2006; 97: 139 –147)