bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Nonconvergence of Factals: A nonmetric Common Factor Analysis
Authors: Mooijaart Ab 
Published: January 2006

FACTALS is a nonmetric common factor analysis model for multivariate data whose variables may be nominal, ordinal or interval. In FACTALS an Alternating Least Squares algorithm is utilized which is claimed to be monotonically convergent.In this paper it is shown that this algorithm is based upon an erroneous assumption, namely that the least squares loss function (which is in this case a nonscale free loss function) can be transformed into a scalefree loss function. A consequence of this is that monotonical convergence of the algorithm can not be guaranteed.
Conditional Covariance Structure of Generalized Compensatory Multidimensional Items
Authors: Zhang Jinming , Stout William 
Published: January 2006

Some nonparametric dimensionality assessment procedures, such as DIMTEST and DETECT, use nonparametric estimates of item pair conditional covariances given an appropriately chosen subtest score as their basic building blocks. Such conditional covariances given some subtest score can be regarded as an approximation to the conditional covariances given an appropriately chosen unidimensional latent composite, where the composite is oriented in the multidimensional test space direction in which the subtest score measures best. In this paper, the structure and properties of such item pair conditional covariances given a unidimensional latent composite are thoroughly investigated, assuming a semiparametric IRT modeling framework called a generalized compensatory model. It is shown that such conditional covariances are highly informative about the multidimensionality structure of a test. The theory developed here is very useful in establishing properties of dimensionality assessment procedures, current and yet to be developed, that are based upon estimating such conditional covariances.In particular, the new theory is used to justify the DIMTEST procedure. Because of the importance of conditional covariance estimation, a new bias reducing approach is presented. A byproduct of likely independent importance beyond the study of conditional covariances is a rigorous score information based definition of an item's and a score's direction of best measurement in the multidimensional test space.
Glycerol kinase deficiency presenting with hypodipsia, osmotic diuresis and severe hypernatraemia
Authors: Mak T. W. L. , Wong L. M. , Wong S. N. , Tse K. , Lai J. P. S. 
Published: January 2006

SummaryA Chinese boy with glycerol kinase deficiency is reported. His presentation with severe hypernatraemia secondary to hypodipsia and glycerol‐induced osmotic diuresis is unusual and not previously described in the literature.
Decreased plasma concentration of von Willebrand factor antigen (VWF:Ag) in patients with glycogen storage disease type Ia
Authors: MÜHlhausen C. , Schneppenheim R. , Budde U. , Merkel M. , Muschol N. , Ullrich K. , Santer R. 
Published: January 2006

SummaryDespite highly increased blood lipids, patients with glycogen storage disease type Ia (GSD Ia) do not develop premature vascular complications. Since this could be due to changes of coagulation factors, coagulation tests (including von Willebrand factor (VWF) antigen (VWF:Ag) ELISA, VWF:collagen binding activity (VWF:CB) and VWF multimer analysis) were performed in 10 GSD Ia patients, single cases of other GSD types, and in both healthy and hyperlipidaemic controls. In 60% of GSD Ia patients we found abnormal results, with a decrease of VWF:Ag and multimer analysis showing reduced intensity of individual oligomers in the presence of all multimers with a normal triplet structure. We interpret these findings as an aquired ‘von Willebrand syndrome type I’ in GSD Ia. The underlying metabolic mechanism and a potential role in the protection from vascular complication still needs to be evaluated.
S‐Adenosylhomocysteine hydrolase deficiency: A second patient, the younger brother of the index patient, and outcomes during therapy
Authors: Barić I. , Ćuk M. , Fumić K. , Vugrek O. , Allen R. H. , Glenn B. , Maradin M. , Pažanin L. , Pogribny I. , Radoš M. , Sarnavka V. , Schulze A. , Stabler S. , Wagner C. , Zeisel S. H. , Mudd S. H. 
Published: January 2006

SummaryS‐Adenosylhomocysteine (AdoHcy) hydrolase deficiency has been proven in a human only once, in a recently described Croatian boy. Here we report the clinical course and biochemical abnormalities of the younger brother of this proband. This younger brother has the same two mutations in the gene encoding AdoHcy hydrolase, and has been monitored since birth. We report, as well, outcomes during therapy for both patients. The information obtained suggests that the disease starts in utero and is characterized primarily by neuromuscular symptomatology (hypotonia, sluggishness, psychomotor delay, absent tendon reflexes, delayed myelination). The laboratory abnormalities are markedly increased creatine kinase and elevated aminotransferases, as well as specific amino acid aberrations that pinpoint the aetiology. The latter include, most importantly, markedly elevated plasma AdoHcy. Plasma S‐adenosylmethionine (AdoMet) is also elevated, as is methionine (although the hypermethioninaemia may be absent or nonsignificant in the first weeks of life). The disease seems to be at least to some extent treatable, as shown by improved myelination and psychomotor development during dietary methionine restriction and supplementation with creatine and phosphatidylcholine.
Mucopolysaccharidosis I: α‐L‐Iduronidase mutations in three Tunisian families
Authors: Laradi S. , Tukel T. , Erazo M. , Shabbeer J. , Chkioua L. , Khedhiri S. , Ferchichi S. , Chaabouni M. , Miled A. , Desnick R. J. 
Published: January 2006

AbstractMucopolysaccharidosis type I (MPS I) is a lysosomal storage disease resulting from the defective activity of the enzyme α‐L‐iduronidase (IDUA). The disease has severe and milder phenotypic subtypes. The IDUA mutations in five MPS I patients from three unrelated families from central and southern Tunisia were determined by amplifying and sequencing each of the IDUA exons and intron–exon junctions. Two novel IDUA mutations, c.1805delTinsGAACA in exon 13 and I270S in exon 7, and two previously reported mutations, P533R and R628X, were detected. The two patients in family 1 who had the Hurler phenotype were homoallelic for the novel deletion‐insertion mutation. The patient in family 2 who also had the Hurler phenotype was heteroallelic for the novel missense mutation I270S and the previously reported nonsense mutation R628X. The two patients in family 3 who had the Hurler–Scheie phenotype were homoallelic for P533R. In addition, six known IDUA polymorphisms were identified. These are the first Tunisian MPS I patients to be genotyped. The identification of these mutations and their genotype–phenotype correlations should facilitate prenatal diagnosis and counselling for MPS I in Tunisia, where a very high rate of consanguinity exists.
Incorporating gene functions as priors in model-based clustering of microarray gene expression data
Authors: Pan Wei 
Published: January 2006

AbstractMotivation: Cluster analysis of gene expression profiles has been widely applied to clustering genes for gene function discovery. Many approaches have been proposed. The rationale is that the genes with the same biological function or involved in the same biological process are more likely to co-express, hence they are more likely to form a cluster with similar gene expression patterns. However, most existing methods, including model-based clustering, ignore known gene functions in clustering.Results: To take advantage of accumulating gene functional annotations, we propose incorporating known gene functions as prior probabilities in model-based clustering. In contrast to a global mixture model applicable to all the genes in the standard model-based clustering, we use a stratified mixture model: one stratum corresponds to the genes of unknown function while each of the other ones corresponding to the genes sharing the same biological function or pathway; the genes from the same stratum are assumed to have the same prior probability of coming from a cluster while those from different strata are allowed to have different prior probabilities of coming from the same cluster. We derive a simple EM algorithm that can be used to fit the stratified model. A simulation study and an application to gene function prediction demonstrate the advantage of our proposal over the standard method.Contact: weip@biostat.umn.edu
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)
Authors: Zhou Fengfeng , Xue Yu , Yao Xuebiao , Xu Ying 
Published: January 2006

Abstract
Summary: Palmitoylation is an important post-translational lipid modification of proteins. Unlike prenylation and myristoylation, palmitoylation is a reversible covalent modification, allowing for dynamic regulation of multiple complex cellular systems. However, in vivo or in vitro identification of palmitoylation sites is usually time-consuming and labor-intensive. So in silico predictions could help to narrow down the possible palmitoylation sites, which can be used to guide further experimental design. Previous studies suggested that there is no unique canonical motif for palmitoylation sites, so we hypothesize that the bona fide pattern might be compromised by heterogeneity of multiple structural determinants with different features. Based on this hypothesis, we partition the known palmitoylation sites into three clusters and score the similarity between the query peptide and the training ones based on BLOSUM62 matrix. We have implemented a computer program for palmitoylation site prediction, Clustering and Scoring Strategy for Palmitoylation Sites Prediction (CSS-Palm) system, and found that the program's prediction performance is encouraging with highly positive Jack-Knife validation results (sensitivity 82.16% and specificity 83.17% for cut-off score 2.6). Our analyses indicate that CSS-Palm could provide a powerful and effective tool to studies of palmitoylation sites.
Availability: CSS-Palm is implemented in PHP/PERL+MySQL and can be freely accessed at
Contact: yaoxb@ustc.edu.cn; xuyn@bmb.uga.edu
Supplementary information: Supplementary data are available at Bionformatics online.
VISSA: a program to visualize structural features from structure sequence alignment
Authors: Li Weizhong , Godzik Adam 
Published: January 2006

Abstract
Motivation: Multiple sequence alignment is an important tool to understand and analyze functions of homologous proteins. However, the logic of residue conservation/variation is usually apparent only in three-dimensional (3D) space, not on a primary sequence level. Thus, in a traditional multiple alignment it is often difficult to directly visualize and analyze key residues because they are masked by other residues along the alignment. Here we present an integrated multiple alignment and 3D structure visualization program that can (1) map and highlight residues from a 1D alignment onto a 3D structure and vice versa and (2) display only the alignment of preselected, key residues. This program, called Visualize Structure Sequence Alignment, also has many other built-in tools that can help analyze multiple sequence alignments.
Availability:
Contact: liwz@burnham.org
Prevention of amyloid fibril formation of amyloidogenic chicken cystatin by site‐specific glycosylation in yeast
Authors: He Jianwei , Song Youtao , Ueyama Nobuhiro , Saito Akira , Azakami Hiroyuki , Kato Akio 
Published: January 2006

AbstractTo address the role of glycosylation on fibrillogenicity of amyloidogenic chicken cystatin, the consensus sequence for N‐linked glycosylation (Asn106‐Ile108 → Asn106‐Thr108) was introduced by site‐directed mutagenesis into the wild‐type and amyloidogenic chicken cystatins to construct the glycosylated form of chicken cystatins. Both the glycosylated and unglycosylated forms of wild‐type and amyloidogenic mutant I66Q cystatin were expressed and secreted in a culture medium of yeast Pichia pastoris transformants. Comparison of the amount of insoluble aggregate, the secondary structure, and fibrillogenicity has shown that the N‐linked glycosylation could prevent amyloid fibril formation of amyloidogenic chicken cystatin secreted in yeast cells without affecting its inhibitory activities. Further study showed this glycosylation could inhibit the formation of cystatin dimers. Therefore, our data strongly suggested that the mechanism causing the prevention of amyloidogenic cystation fibril formation may be realized through suppression of the formation of three‐dimensional domain‐swapped dimers and oligomers of amyloidogenic cystatin by the glycosylated chains at position 106.
Photonic activation of disulfide bridges achieves oriented protein immobilization on biosensor surfaces
Authors: Neves‐Petersen Maria Teresa , Snabe Torben , Klitgaard Søren , Duroux Meg , Petersen Steffen B. 
Published: January 2006

AbstractPhotonic induced immobilization is a novel technology that results in spatially oriented and spatially localized covalent coupling of biomolecules onto thiol‐reactive surfaces. Immobilization using this technology has been achieved for a wide selection of proteins, such as hydrolytic enzymes (lipases/esterases, lysozyme), proteases (human plasminogen), alkaline phosphatase, immunoglobulins' Fab fragment (e.g., antibody against PSA [prostate specific antigen]), Major Histocompability Complex class I protein, pepsin, and trypsin. The reaction mechanism behind the reported new technology involves “photonic activation of disulfide bridges,” i.e., light‐induced breakage of disulfide bridges in proteins upon UV illumination of nearby aromatic amino acids, resulting in the formation of free, reactive thiol groups that will form covalent bonds with thiol‐reactive surfaces (see Fig. 1). Interestingly, the spatial proximity of aromatic residues and disulfide bridges in proteins has been preserved throughout molecular evolution. The new photonic‐induced method for immobilization of proteins preserves the native structural and functional properties of the immobilized protein, avoiding the use of one or more chemical/thermal steps. This technology allows for the creation of spatially oriented as well as spatially defined multiprotein/DNA high‐density sensor arrays with spot size of 1 μm or less, and has clear potential for biomedical, bioelectronic, nanotechnology, and therapeutic applications.
Phenotypic characterization of endometrial stromal sarcoma of the uterus
Authors: Yamada Kazumi , Kano Junko , Tsunoda Hajime , Yoshikawa Hiroyuki , Okubo Chigusa , Ishiyama Tadashi , Noguchi Masayuki 
Published: January 2006

Endometrial stromal sarcoma (ESS) of the uterus is a rare uterine malignancy that has not been characterized in detail. To characterize the phenotype of ESS of the uterus, we extracted RNA from ESS and the stroma of normal endometrium using a tissue microdissection system and compared the expression profiles in the two tissues. After suppression subtractive hybridization and differential screening, we detected the metastasis‐associated lung adenocarcinoma transcript 1 (MALAT‐1) gene as one of the major genes upregulated in ESS, and a full‐length placental cDNA clone (CS0DI066YJ10) as one of the major genes downregulated. The results were confirmed by in situ hybridization in four resected specimens of ESS and 36 biopsy specimens of normal endometrial tissue. All ESS (4/4) and all cases of endometrial stromal cells in the proliferative phase (13/13) were positive for MALAT‐1, but samples of normal stroma in the secretory phase and menopausal state included some that were negative or weakly positive for MALAT‐1 (5/13 and 3/10, respectively). In contrast, all ESS and 12 of 13 cases of stromal cells in the proliferative phase were negative for the full‐length placental cDNA clone but 10 of 13 cases of endometrial stromal cells in the secretory phase were positive for transcripts of the gene (P < 0.05). These results indicated that endometrial stromal cells have different phenotypic characteristics between proliferative and secretory phases and the tumor cells of ESS have the phenotypic character of endometrial stromal cells in the proliferative phase. (Cancer Sci 2006; 97: 106  – 112)
Epstein–Barr virus involvement is a predictive factor for the resistance to chemoradiotherapy of gastric diffuse large B‐cell lymphoma
Authors: Yoshino Tadashi , Nakamura Shigeo , Matsuno Yoshihiro , Ochiai Atsushi , Yokoi Takio , Kitadai Yasuhiko , Suzumiya Junji , Tobinai Kensei , Kobayashi Yukio , Oda Ichiro , Mera Kiyomi , Ohtsu Atsushi , Ishikura Satoshi 
Published: January 2006

Primary gastric diffuse large B‐cell lymphomas are generally well controlled by non‐surgical treatment with combination chemotherapy followed by radiotherapy. We have previously reported that over 90% of patients achieved complete response (CR) with this therapeutic strategy: three cycles of cyclophosphamide, adriamycin, vincristine and prednisone followed by radiotherapy (40.5 Gy). Although the CR rate was very high, some patients still showed resistance to this combination therapy. In order to clarify the factors related to therapy resistance, we examined the relationship between Epstein–Barr virus (EBV), which was examined using an in situ hybridization technique, and the patients’ clinical courses. Out of the 50 patients, four were EBV positive; over half of lymphoma cells were positive for EBV by in situ hybridization. Of the three EBV‐positive patients, two showed progressive disease and one achieved partial response (PR). Two of the patients died of disease progression. The other patient achieved CR, but the lymphoma recurred with distant metastasis in the cerebellum 3 months after remission. In the present study, eight patients did not achieve CR or they relapsed, four patients showed progressive disease, one patient achieved PR, and three patients achieved CR with recurrence. Therefore, half of these unfavorable patients were EBV positive. This finding strongly indicated that EBV‐associated gastric diffuse large B‐cell lymphomas frequently show resistance to standard chemoradiotherapy, although some other adverse factors remain unclear. (Cancer Sci 2006; 97: 163 –166)
What are children's trusts? Early findings from a national survey
Authors: Bachmann M.O. , Reading R. , Husbands C. , O'Brien M. , Thoburn J. , Shemilt I. , Watson J. , Jones N. , Haynes R. , Mugford M. ,   the NECT team
Published: January 2006

AbstractBackground  The Children Act 2004 and National Service Framework for Children, Young People and Maternity Services require fuller integration of health, education and social services for children and young people in England and Wales. The UK government supported the establishment of 35 experimental children's trust pathfinders (henceforth called children's trusts) in England.Methods  A questionnaire was completed by managers in all 35 children's trusts a year after their start. Children's trust documents were examined. Census and performance indicators were compared between children's trust areas and the rest of England.Results  Children's trust areas had demographic and social characteristics typical of England. All children's trusts aimed to improve health, education and social services by greater managerial and service integration. All had boards representing the three sectors; other agencies’ representation varied. Two‐thirds of children's trusts had moved towards pooling budgets in at least some service areas. At this stage in their development, some had prioritized joint procurement or provision of services, with formal managerial structures, while others favoured an informal strategic planning, co‐ordination and information sharing approach. The commonest priorities for services development were for disabled children (16 children's trusts), followed by early intervention (11) and mental health services (8).Conclusions  The diverse strategies adopted by these 35 children's trusts during their first year is due to their own characteristics and to the way government strategy developed during this period. Whilst some prioritized organizational development, joint financing and commissioning, and information sharing, others laid more emphasis on mechanisms for bringing front‐line professionals closer together. Their experiences are of value to others deciding how best to integrate children's services.
The marriage‐related risk factors during maternal pregnancy in children with attention‐deficit hyperactivity disorder
Authors: Lee C.‐Y. , Chang Y.‐Y. , Lung F.‐W. 
Published: January 2006

AbstractBackground  The purpose of this research was to investigate the relationship between marriage‐related risk factors during maternal pregnancy and subsequent development of attention‐deficit hyperactivity disorder (ADHD).Methods  The research design was a retrospective case–control study. The case group included 60 patients that fulfilled the ADHD criteria of Fourth Edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM‐IV). The controls were normal children randomly selected and matched for their sex and age. Their biological mothers completed a questionnaire about marital adaptation, marital satisfaction and the incidence of stressful life events during pregnancy.Results  The results showed that the incidence of positive life events, marital adaptation and marital satisfaction during maternal pregnancy was significantly lower in the case group, and conditional logistic regression analysis showed that marital adaptation during pregnancy and pregnancy before marriage were important risk factors for ADHD.Conclusion  Negative emotion during maternal pregnancy may be an important risk factor for ADHD.
Authoritative parenting and parental stress in parents of pre‐school and older children with developmental disabilities
Authors: Woolfson L. , Grant E. 
Published: January 2006

AbstractBackground  Rearing a child with a developmental disability is associated with increased parental stress. Theories of stress and adjustment and bi‐directional theories of child development suggest that parenting could influence these negative outcomes.Methods  Relationships between parenting approaches and stress in parents of children with developmental disabilities (DD) (N = 53) were examined across two age groups, 3–5 years and 9–11 years and compared with a contrast group of typically developing children (TD) (N = 60). Measures used were the Parenting Stress Index‐Short Form and Rickel and Biasatti's modification of Block's Child Rearing Practices Report, classified into Baumrind's parenting styles using Reitman and Gross's method.Results  Parents in the older DD group used Authoritative parenting less than parents in the younger DD group, while the opposite developmental pattern was seen in the TD group. Multivariate analysis of variance showed a significant group × parenting style interaction for Parental Distress, Parent–Child Dysfunctional Interaction and Difficult Child. Stress measures were higher for the DD group and seemed to be associated with Authoritative parenting approaches, an effect that was not observed in the TD group.Conclusions  Findings suggest that the well‐established effect of group on stress may be moderated by parenting style. Authoritative parenting may be highly stressful for parents of children with DD to implement, resulting in a decrease in its use across the two age groups.