bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of consistent novel submegabase deletions in low‐grade oligodendrogliomas using array‐based comparative genomic hybridization
Authors: Rossi Michael R. , Gaile Daniel , LaDuca Jeffrey , Matsui Sei‐Ichi , Conroy Jeffrey , McQuaid Devin , Chervinsky David , Eddy Roger , Chen Hai‐Shen , Barnett Gene H. , Nowak Norma J. , Cowell John K. 
Published: June 2005

AbstractWe have analyzed 18 low‐grade gliomas using array comparative genomic hybridization (aCGH) with an average resolution of <500 kb. Because the majority of these tumors showed loss of chromosome arms 1p and 19q, we used custom statistical approaches to define submegabase hemizygous losses throughout the genome that correlated with 19q loss. As a result of this analysis, we have identified a ∼550‐kb region in 11q13 and a ∼300‐kb region in 13q12 that showed hemizygous deletion in virtually all the tumors analyzed regardless of their 1p/19q status. FISH analyses of interphase nuclei from the same tumors used for aCGH analysis confirmed the hemizygous loss. The identification of such specific changes provides a potentially very useful diagnostic marker for this subgroup of low‐grade tumors. These regions of the genome define small numbers of candidate genes that are within the deletions. The aCGH analysis also defined the spectrum of gain and loss of genomic regions in low‐grade oligodendrogliomas. © 2005 Wiley‐Liss, Inc.
Interstitial telomeric DNA sequences of Chinese hamster cells are hypersensitive to nitric oxide damage, and DNA‐PKcs has a specific local role in its repair
Authors: Mosquera Alejandro , Gosálvez Jaime , Sabatier Laure , Fernández José Luis 
Published: June 2005

AbstractThe DNA breakage detection–fluorescence in situ hybridization (DBD‐FISH) procedure was used to analyze DNA single‐strand breaks (SSBs) and alkali‐labile sites induced by exposure to the nitric oxide (NO) donors sodium nitroprusside (SNP) and 3‐morpholinosydnomine hydrochloride (SIN‐1) in the whole genome and in long interstitial telomeric repeat sequence (ITRS) blocks from Chinese hamster cells. The relative density of DNA damage generated in the ITRS by X‐rays was similar to that induced in the genome overall, whereas it was 1.7 times higher when the alkylating agent MNNG was assayed. Nevertheless, after SNP or SIN‐1 treatment, ITRSs proved to be 2.8 and 2.7 times relatively more damaged, respectively, than the whole genome. When the DNA‐dependent protein kinase catalytic subunit (DNA‐PKcs) was not active, as in XR‐C1 mutant cells, the repair kinetics in the whole genome did not differ from that in the parental cell line with X‐ray or SNP exposure. However, whereas the SSBs and alkali‐labile sites induced in the ITRS by X‐rays exhibited rejoining kinetics similar to that of the parental cell line, the damage induced by SNP was more slowly rejoined. This implies a role for DNA‐PKcs in the repair of DNA damage induced by NO, especially in ITRSs. The results demonstrated intragenomic heterogeneity of NO‐induced DNA damage and repair; there was a higher density of DNA damage in the ITRS blocks, possibly because of their guanine richness. This suggests that a parallel process may occur in the terminal telomeres, which has implications for premature aging and neoplastic development by chronic NO exposure in vivo. © 2005 Wiley‐Liss, Inc.
Somatic genetic changes accompanying lung tumor development
Authors: Foster Nicola A. , Banerjee Anindo K. , Xian Jian , Roberts Ian , Pezzella Francesco , Coleman Nicholas , Nicholson Andrew G. , Goldstraw Peter , George Jeremy P. , Rabbitts Pamela H. 
Published: June 2005

AbstractCarcinomas are believed to develop by incremental steps of increasingly abnormal morphology driven by accumulating somatic genetic changes. This process is often difficult to study, as the early stages are undetectable. We used fluorescence bronchoscopy, which enhances detection of preinvasive bronchial lesions, and have obtained sequential biopsies of carcinoma in situ (CIS) from a patient with no detectable tumor and from a squamous cell carcinoma that developed 19 months after presentation at the site of one of the previous CIS lesions. Biopsies of preinvasive CIS, which follow‐up showed had different pathologic outcomes, and tumor were microdissected to obtain enriched cell populations and DNA prepared from them. Molecular characteristics of these biopsies were compared by loss of heterozygosity analysis, TP53 mutation analysis, and comparative genomic hybridization. Although all lesions examined had the same TP53 mutation and almost identical allelotypes, differences were observed. Loss in 5q21 and amplification of 3q25–26 were associated with the lesion that progressed and the subsequent carcinoma. Allele loss at 4p16 was detected in the tumor but not in any of the CIS lesions, suggesting it was a late event associated with tumor invasion. Amplification at 4q12 was specifically observed in the tumor and in the CIS at the site of eventual tumor formation. Although these findings may be unique to this one patient, the successful demonstration of sequential genetic changes raises the possibility that this approach, unencumbered by interpatient variability between lesions, will greatly facilitate the identification of molecular events driving the invasive process © 2005 Wiley‐Liss, Inc.
Possible linkage of a breast cancer‐susceptibility locus to the ABO locus: Sensitivity of LOD scores to a single new recombinant observation
Authors: Skolnick M. H. , Thompson E. A. , Bishop D. T. , Cannon L. A. , Rao D. C. 
Published: June 2005

AbstractWe present evidence of a pedigree in which a major gene for breast cancer‐susceptibility appears to segregate in a dominant fashion. Linkage analysis suggests that the breast cancer‐susceptibility locus in this family may be linked to the ABO locus, which is located on band q34 of chromosome 9. At an early stage in the analysis, a LOD score of 3.0 for zero recombination was obtained for linkage between ABO and the susceptibility locus, but a single recombinant reduced the LOD score to 1.72 at a recombination fraction of 0.06. A final observation of a nonrecombinant brings the LOD score for this pedigree to 1.99 at \documentclass{article}\pagestyle{empty}\begin{document}$\documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm{\theta }} $\end{document}$\end{document} = 0.05. We attempt to put these results in perspective by discussing the sensitivity of the LOD score to the next observation. Examples of the volatility of LOD scores are given. These simple calculations show that tight linkage represents the worst case for the interpretation of a LOD score of 3.0. Finally, we discuss the linkage between the breast cancer‐susceptibility locus and the ABO blood group and approaches to confirming or denying this result.
Genetics of the Lp lipoprotein in Japanese‐Americans
Authors: Morton Newton E. , Berg Kåre , Dahlen Gösta , Ferrell Robert E. , Rhoads George G. , Rao D. C. 
Published: June 2005

AbstractSegregation analysis of four Lp assays on 557 children in 227 families reveals a dominant major gene and a residual heritable component that may reflect one or more alleles of weaker effect. Close or moderate linkage to esterase‐D (ESD) is excluded.
Regional assignments of three polymorphic DNA segments on human chromosome 15
Authors: Brissenden J. E. , Page D. C. , de Martinville B. , Trowsdale J. , Botstein D. , Francke U. , Lalouel J. M. 
Published: June 2005

AbstractHybridization of probe pDP151 (locus D15S2) to genomic human DNAs digested with EcoRI revealed allelic restriction fragments 9 and 11 kilobase‐pairs (kb) in length. Hybridization of pDP151 to EcoRI‐digested DNAs from 21 Chinese hamster × human hybrid cell clones containing different subsets of human chromosomes demonstrated cosegregation of the 9 and 11 kb EcoRI fragments with human chromosome 15. D15S2 and two other polymorphic loci previously mapped to chromosome 15–D15S1 and D15S6—were localized to specific regions on human chromosome 15. Eight Chinese hamster × human somatic cell hybrid clones derived from a human donor heterozygous for a balanced translocation between chromosomes 15 and 22 [t(15;22)(q14;q13.3); Oliver et al, Cytogenet Cell Genet 22:503–510, 1978] were studied. After digestion of human and hybrid DNAs with HindIII and Southern blotting, pDP151 (D15S2) and pMS1‐14 (D15S1) hybridized to fragments of 4 and 4.5 kb, respectively. Further, pMS1‐14 (D15S1) and p9‐1a (D15S6) hybridized to EcoRI fragments of 3.5 and 3.2 kb. All fragments cosegregated with the der(22) derivative chromosome containing region 15q14→15qter. In situ hybridization of these probes to normal human chromosomes mapped the corresponding loci with greater precision: D15S1 to 15q15→15q21, D15S2 to 15q15→15q22, and D15S6 to 15q22→15q24.
A resolution of the ascertainment sampling problem: IV. Continuous phenotypes
Authors: Ewens WJ , Green RM , Vogler G. P. , Rao D. C. 
Published: June 2005

AbstractThis paper considers ascertainment corrections for continuous phenotypes. Two main points are considered. The first is a discussion of what ascertainment corrections can be devised to ensure asymptotically unbiased parameter estimates when the nature of the ascertainment procedure is not known. The second is an analysis of the properties of various forms of ascertainment correction possible when the nature of the ascertainment procedure is known. Some ascertainment corrections are thus shown to be valid and others invalid.
Alternative genetic models for the inheritance of the phenylthiocarbamide taste deficiency
Authors: Olson Jane M. , Boehnke Michael , Neiswanger Katherine , Roche Alex F. , Siervogel Roger M. , MacCluer Jean W. 
Published: June 2005

AbstractPedigree segregation analysis was used to examine several one‐ and two‐locus models of the inheritance of phenylthiocarbamide (PTC) taste deficiency that extend the traditional one‐locus recessive model by the addition of either another allele or another locus, and in some cases predict two types of nontasters. These models allow nontaster by nontaster matings to produce taster offspring, consistent with our data and several previous studies which use the Harris and Kalmus [Annals of Eugenics 15:24–32, 1949] dilution method. The models fit our data set of 1,152 individuals from 120 families significantly better than the one‐locus recessive model. The best fit was obtained with a two‐locus model in which one locus controls PTC tasting and the other locus controls a more general taste ability. This model is consistent with research on the physiology of PTC tasting and with results from genetic linkage studies. Further study is suggested to evaluate better the accuracy of the proposed model.
Blood pressure and other cardiovascular disease risk factors in black adults with sickle cell trait or glucose‐6‐phosphate dehydrogenase deficiency
Authors: Nwankwo Martin U. , Bunker Clareann H. , Ukoli Flora A. , Omene Jackson A. , Freeman Donald T. , Vergis Emanuel N. , Yeh Lan Lan , Kuller Lewis H. , Rao D. C. 
Published: June 2005

AbstractIn this study, we examined the relationship of two common genetic markers in black populations, sickle cell trait and glucose‐6‐phosphate dehydrogenase (G‐6‐PD) deficiency, to cardiovascular risk factors. The subjects were Nigerian civil servants in Benin City, Nigeria. We measured blood pressure, height, weight, sickle cell hemoglobin, G‐6‐PD, proteinuria, microalbuminuria and fasting serum cholesterol, high‐density lipoprotein cholesterol (HDL), triglycerides, apoprotein (APO) AI, and APO B. Data were collected on age, alcohol consumption, cigarette smoking, job status, and years lived in an urban area. There were 257 males (3 SS hemoglobin, 73 AS, 181 AA) and 69 females (23 AS, 46 AA). In comparing cardiovascular risk factors, males differed only in percent of smokers (31.5 in AS vs. 17.8 in AA, P < 0.01). Among females, only high‐density lipoprotein (HDL) cholesterol differed (61.5 mg/dl in AS vs. 52.4 in AA, P < 0.01). We hypothesize that females with sickle cell trait are more likely to use oral contraceptives than nontrait females. If so, the high‐estrogen oral contraceptives available in Nigeria could elevate HDL. G‐6‐PD deficiency status among males (52 deficient, 207 nondeficient) and females (1 deficient, 5 carriers, 65 nondeficient) was not related to any of the cardiovascular risk factors. We conclude that sickle cell hemoglobin trait and G‐6‐PD deficiency are not useful genetic markers for risk factors for cardiovascular disease.
Genetic markers associated with high density lipoprotein cholesterol levels in a biracial population sample
Authors: Anderson Richard A. , Burns Trudy L. , Wallace Robert B. , Folsom Aaron R. , Sprafka J. Michael , Vogler G. P. 
Published: June 2005

AbstractAn explanation for the consistently documented finding of higher levels of high density lipoprotein‐cholesterol in black men relative to white men was sought by comparing the frequency of restriction fragment length polymorphism markers present in blacks and in whites at the gene loci coding for the two major apolipoprotein constituents of high density lipoprotein, apolipoproteins AI and AII. The measurements were made in population‐based samples of 45 to 54‐year‐old black (n = 190) and white (n = 370) subjects from the Minnesota Heart Survey for whom lipoprotein levels were available. The mean high density lipoprotein‐cholesterol level for black men in the sample (47 ± 1.5 mg/dl) was higher (P < 0.05) than that for white men (42 ± 0.9 mg/dl), while levels in women were not different between races. While the SacI and MspI markers at the apolipoprotein AI‐CIII‐AIV gene locus showed similar frequencies in blacks compared to whites, the degree of the linkage disequilibrium previously noted between these markers in white subjects was altered in blacks and the minor allele of the PstI marker at this locus was virtually absent in the black subjects (P < 0.005 vs whites). For black men, there were significant associations of the M2 allele and the S2M2 haplotype at the apolipoprotein AI locus with lower high density lipoprotein‐cholesterol levels. The results are consistent with the hypothesis that DNA sequence variations in the vicinity of the apolipoprotein AI‐CIII‐AIV gene locus are associated with the difference in high density lipoprotein‐cholesterol levels between blacks and whites. © 1992 Wiley‐Liss, Inc.
Genetic analysis combining path analysis with regressive models: The beta path model of polygenic and familial environmental transmission
Authors: Li Zhaohai , Bonney George E. , Rao D. C. 
Published: June 2005

AbstractWe have extended the class D regressive model for the purpose of combined path and segregation analyses by incorporating the BETA path model. We have done this by expressing correlations among residuals from major genotype (RMGs) of family members under the class D regressive model as functions of path coefficients under the BETA path model. The likelihood function under the combined model was factorized into a product of conditional densities, which is dominated by bivariate normal densities. Statistical inferences under the combined model are analogous to those under the class D regressive model.
Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo‐β‐lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry
Authors: Antony Jens , Piquemal Jean‐Philip , Gresh Nohad 
Published: June 2005

AbstractUsing the polarizable molecular mechanics method SIBFA, we have performed a search for the most stable binding modes of D‐ and L‐thiomandelate to a 104‐residue model of the metallo‐β‐lactamase from B. fragilis, an enzyme involved in the acquired resistance of bacteria to antibiotics. Energy balances taking into account solvation effects computed with a continuum reaction field procedure indicated the D‐isomer to be more stably bound than the L‐one, conform to the experimental result. The most stably bound complex has the S− ligand bridging monodentately the two Zn(II) cations and one carboxylate O− H‐bonded to the Asn193 side chain. We have validated the SIBFA energy results by performing additional SIBFA as well as quantum chemical (QC) calculations on small (88 atoms) model complexes extracted from the 104‐residue complexes, which include the residues involved in inhibitor binding. Computations were done in parallel using uncorrelated (HF) as well as correlated (DFT, LMP2, MP2) computations, and the comparisons extended to corresponding captopril complexes (Antony et al., J Comput Chem 2002, 23, 1281). The magnitudes of the SIBFA intermolecular interaction energies were found to correctly reproduce their QC counterparts and their trends for a total of twenty complexes. © 2005 Wiley Periodicals, Inc. J Comput Chem 11: 1131–1147, 2005
On perfect nonlinear functions
Authors: Xiyong Zhang , Wenbao Han , Shuqin Fan 
Published: June 2005

AbstractAn Erratum has been published for this article in Journal of Combinatorial Designs 14: 82–82, 2006.We give the equivalence between perfect nonlinear functions and appropriate splitting semi‐regular relative difference sets, construct a class of splitting relative difference sets by using Galois rings and bent functions, and prove that there exists a 4‐phase perfect nonlinear function if and only if the number of input variables is at least twice the number of output variables. © 2005 Wiley Periodicals, Inc.
Preparation of cells cultured on silicon wafers for mass spectrometry analysis
Authors: Wittig Andrea , Wiemann Martin , Fartmann Michael , Kriegeskotte Christian , Arlinghaus Heinrich F. , Zierold Karl , Sauerwein Wolfgang 
Published: June 2005

AbstractThe distribution of specific atoms and molecules within living cells is of high interest in bio‐medical research. Laser secondary neutral mass spectrometry (laser‐SNMS) and time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) detect atoms with high sensitivity and spatial resolution. The application of these methods to cultured cells requires special preparation techniques preserving morphological and chemical integrity of the living cells. The cells should, therefore, be grown on a conducting material preventing charging of the sample during ion bombardment. Silicon is currently used as the preferred support material for non‐biological samples in mass spectrometry. This study investigates (1) the influence of silicon surfaces on cell growth and (2) the suitability of a sandwiched, rapid freezing method to analyse transmembrane ion gradients. Human melanoma cells were grown on silicon with polished or etched surfaces. Growth kinetics were studied using the Sulforhodamine‐B assay. Number, shape, and morphology of the cells were assessed by epifluorescence microscopy of calcein AM‐ and DAPI‐stained cells. Cells were subjected to rapid freezing, freeze‐fracturing, and freeze‐drying prior to analysis by TOF‐SIMS and laser‐SNMS. While cell numbers and morphology on the rough silicon wafers were impaired, morphology and growth kinetics of cells on polished silicon were identical to control cells on cell culture tested polystyrene. TOF‐SIMS and laser‐SNMS resulted in high‐resolution elemental images and mass spectra. Measurement of the intracellular Na+ and K+ concentrations revealed a ratio as observed in living cells. In conclusion, culturing cells on polished silicon wafers followed by sandwiched, rapid freezing is an adequate preparation method to study intracellular ion distribution with mass spectrometry. Microsc. Res. Tech. 66:248–258, 2005. © 2005 Wiley‐Liss, Inc.
Elemental changes in the brain, muscle, and gut cells of the housefly, Musca domestica, exposed to heavy metals
Authors: Tylko Grzegorz , Banach Zuzanna , Borowska Joanna , Niklińska Maria , Pyza Elżbieta 
Published: June 2005

AbstractThe toxic effects of heavy metals on organisms are well established. However, their specific action at the cellular level in different tissues is mostly unknown. We have used the housefly, Musca domestica, as a model organism to study the toxicity of four heavy metals: copper (Cu), zinc (Zn), cadmium (Cd), and lead (Pb). These have been fed to larvae at low and high, semi‐lethal concentrations, and their accumulation in the head, thorax, and abdomen was subsequently measured in adult flies. In addition, their impact on the cellular concentration of several elements important for cell metabolism—sodium (Na+), magnesium (Mg++), phosphorous (P), sulphur (S), chloride (Cl−) and potassium (K+)—were measured in neural cells, muscle fibers, and midgut epithelial cells. Our study showed that the heavy metals accumulate mainly in the abdomen, in which the concentrations of two of the xenobiotic metals, Cd and Pb, were 213 and 23 times more concentrated, respectively, than in controls. All the heavy metals affected the cellular concentration of light elements in all cell types, but the changes observed were dependent on tissue type and were specific for each heavy metal, and its concentration. Microsc. Res. Tech. 66:239–247, 2005. © 2005 Wiley‐Liss, Inc.
Cadmium distribution and effects on ultrastructureand chlorophyll status in photobionts and mycobionts of Xanthoria parietina
Authors: Sanità Di Toppi Luigi , Musetti Rita , Vattuone Zulema , Pawlik‐Skowrońska Barbara , Fossati Fabrizia , Bertoli Lorenzo , Badiani Maurizio , Favali Maria Augusta 
Published: June 2005

AbstractIn this work, we tried to go deeper inside distribution and toxicity of cadmium (Cd) in the macrolichen Xanthoria parietina (L.) Th. Fr. Thalli of this species were treated with 0 (control), 4.5, 9, 18, or 36 μM Cd for 24 or 48 hours. Transmission electron microscopy, X‐ray microanalysis, and electron energy loss spectroscopy were exploited to study distribution and ultrastructural effects of Cd in thalli; spectrophotometric techniques were utilized for measuring Cd effects on chlorophyll (Chl) content; light fluorescence microscopy was used to evaluate Chl autofluorescence. The highest Cd concentration caused ultrastructural alterations both in the mycobiont and in the photobiont, more severe in the latter, decreased total Chl content and progressively quenched Chl autofluorescence. Cell wall immobilization was observed in both bionts, and evidence pointing to a Cd‐binding ability by the concentric bodies in the mycobiont was also obtained. Lower Cd concentrations led to slight or even no effects on thallus structures and on Chl content and autofluorescence. The results obtained suggest that: (1) among the two bionts, the algal partner appears to be more susceptible to Cd stress, probably because of the presence of delicate and sensitive components such as the chloroplast and photosynthetic pigments; (2) a concentration threshold exists for the occurrence of evident structural and functional damage in X. parietina thalli exposed to Cd. Microsc. Res. Tech. 66:229–238, 2005. © 2005 Wiley‐Liss, Inc.
The revolution of counting “tops”: Two decades of the disector principle in morphological research
Authors: Geuna Stefano 
Published: June 2005

AbstractTwenty years have passed since the publication of the seminal paper enunciating the disector principle by an author using the pseudonym D.C. Sterio. During this time, methods based on the revolutionary principle of counting “tops” have become progressively better known and have been included in several commercially available systems for quantitative morphology. Analysis of the number of published studies citing Sterio's paper on the ISI Web of Knowledge® database showed that its scientific “impact factor” has almost continuously risen since its publication, indicating the growing knowledge about disector‐based methods in the various scientific fields where morphological quantification is required. This report briefly reviews the first two decades of disector use, pointing to its advantages as well as to shortcomings that have recently been addressed in critical papers and have given rise to a lively debate on the role of counting tops in quantitative morphology today. Microsc. Res. Tech. 66:270–274, 2005. © 2005 Wiley‐Liss, Inc.