bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mast cells dysregulate apoptotic and cell cycle genes in mucosal squamous cell carcinoma
Authors: Ch'ng Sydney , Sullivan Michael , Yuan Lan , Davis Paul , Tan Swee T 
Published: December 2006

Abstract

Background
Mucosal squamous cell carcinoma of the head and neck is a disease of high mortality and morbidity. Interactions between the squamous cell carcinoma and the host's local immunity, and how the latter contributes to the biological behavior of the tumor are unclear. In vivo studies have demonstrated sequential mast cell infiltration and degranulation during squamous cell carcinogenesis. The degree of mast cell activation correlates closely with distinct phases of hyperkeratosis, dysplasia, carcinoma in-situ and invasive carcinoma. However, the role of mast cells in carcinogenesis is unclear.

Aim
This study explores the effects of mast cells on the proliferation and gene expression profile of mucosal squamous cell carcinoma using human mast cell line (HMC-1) and human glossal squamous cell carcinoma cell line (SCC25).

Methods
HMC-1 and SCC25 were co-cultured in a two-compartment chamber, separated by a polycarbonate membrane. HMC-1 was stimulated to degranulate with calcium ionophore A23187. The experiments were done in quadruplicate. Negative controls were established where SCC25 were cultured alone without HMC-1. At 12, 24, 48 and 72 hours, proliferation and viability of SCC25 were assessed with MTT colorimetric assay. cDNA microarray was employed to study differential gene expression between co-cultured and control SCC25.

Results
HMC-1/SCC25 co-culture resulted in suppression of growth rate for SCC-25 (34% compared with 110% for the control by 72 hours, p < 0.001), and dysregulation of genes TRAIL, BIRC4, CDK6, Cyclin G2 and CDC6 in SCC25.

Conclusion
We show that mast cells have a direct inhibitory effect on the proliferation of mucosal squamous cell carcinoma in vitro by dysregulating key genes in apoptosis and cell cycle control.
IMP PCR primers detect single nucleotide polymorphisms for Anopheles gambiae species identification, Mopti and Savanna rDNA types, and resistance to dieldrin in Anopheles arabiensis
Authors: Wilkins Elien E , Howell Paul I , Benedict Mark Q 
Published: December 2006

Abstract

Background
Polymerase chain reactions to distinguish single-nucleotide polymorphisms are commonly used for mosquito identification and identifying insecticide resistance alleles. However, the existing methods used for primer design often result in analyses that are not robust or require additional steps.

Methods
Utilizing oligonucleotides that are unique in having an intentional mismatch to both templates three bases from the SNP at the 3-prime end, three new PCR assays that distinguish SNP targets using standard gel electrophoresis of undigested DNA fragments were developed and tested. These were applied to: (1) an alternative ribosomal DNA PCR assay to distinguish five members of the Anopheles gambiae complex; (2) detection of the Mopti and Savanna rDNA types; and (3) an assay to distinguish resistance to dieldrin (Rdl) alleles in Anopheles arabiensis.

Results
Reproducible specific amplification of the target alleles was observed in all three assays. The results were consistent with existing analyses but proved simpler and the results more distinct in our hands.

Conclusion
The simplicity and effectiveness of the method should be utilized in these and other PCR analyses to increase their specificity and simplicity. These results have the potential to be extended not only to mosquito analyses but also to parasite and human polymorphisms.
Race-specific geography of prostate cancer incidence
Authors: DeChello Laurie M , Gregorio David I , Samociuk Holly 
Published: December 2006

Abstract

Background
This study evaluated geographic distribution of race-specific prostate cancer incidence in Connecticut and Massachusetts. This cross-sectional analysis of census and cancer registry data included records of 29,040 Whites and 1,647 African Americans diagnosed with incident prostate cancer between 1994 and 1998. A spatial scan statistic was used to detect and test significance of the geographic variation in race-specific incidence rates within the two-state area.

Results
Significant geographic variation in age-adjusted incidence rates among both White and African American men was observed, with little overlap noted between distributions. Identified locations reflected patterns of residential segregation and socio-economic conditions. Among Whites, places with higher than expected incidence had higher socioeconomic status than places with lower than expected incidence. No discernable relationship between social indicators and rate variation among African Americans was evident.

Conclusion
Differences in race-specific geographic distribution of prostate cancer incidence do not suggest a shared environmental etiology. Furtherstudyof genetic, behavioral and health carefactors affecting the occurrence and/or reporting of the disease is warranted. This study highlights the need for race- and geographic-specific interventions to better control disease within at-risk communities and for on-going analysis into social and contextual factors that contribute to observed disparities between African Americans and Whites in the occurrence of cancer.
Analytical and preparative applications of magnetic split-flow thin fractionation on several ion-labeled red blood cells
Authors: Tsai Hweiyan , Fang Ying S , Fuh C Bor 
Published: December 2006

Abstract

Background
Magnetic Split-flow thin (SPLITT) fractionation is a newly developed technique for separating magnetically susceptible particles. Particles with different field-induced velocities can be separated into two fractions by adjusting applied magnetic forces and flow-rates at inlets and outlets.

Methods
Magnetic particles, Dynabeads, were used to test this new approach of field-induced velocity for susceptibility determination using magnetic SF at different magnetic field intensities. Reference measurements of magnetic susceptibility were made using a superconducting quantum interference device (SQUID) magnetometer. Various ion-labeled red blood cells (RBC) were used to study susceptibility determination and throughput parameters for analytical and preparative applications of magnetic SPLITT fractionation (SF), respectively. Throughputs were studied at different sample concentrations, magnetic field intensities, and channel flow-rates.

Results
The susceptibilities of Dynabeads determined by SPLITT fractionation (SF) were consistent with those of reference measurement using a superconducting quantum interference device (SQUID) magnetometer. Determined susceptibilities of ion-labeled RBC were consistent within 9.6% variations at two magnetic intensities and different flow-rates. The determined susceptibilities differed by 10% from referenced measurements. The minimum difference in magnetic susceptibility required for complete separation was about 5.0 × 10-6 [cgs]. Sample recoveries were higher than 92%. The throughput of magnetic SF was approximately 1.8 g/h using our experimental setup.

Conclusion
Magnetic SF can provide simple and economical determination of particle susceptibility. This technique also has great potential for cell separation and related analysis. Continuous separations of ion-labeled RBC using magnetic SF were successful over 4 hours. The throughput was increased by 18 folds versus early study. Sample recoveries were 93.1 ± 1.8% in triplicate experiments.
Psychogenic or neurogenic origin of agrammatism and foreign accent syndrome in a bipolar patient: a case report
Authors: Poulin Stéphane , Macoir Joël , Paquet Nancy , Fossard Marion , Gagnon Louis 
Published: January 2007

Abstract

Background
Foreign accent syndrome (FAS) is a rare speech disorder characterized by the appearance of a new accent, different from the speaker's native language and perceived as foreign by the speaker and the listener. In most of the reported cases, FAS follows stroke but has also been found following traumatic brain injury, cerebral haemorrhage and multiple sclerosis. In very few cases, FAS was reported in patients presenting with psychiatric disorders but the link between this condition and FAS was confirmed in only one case.

Case presentation
In this report, we present the case of FG, a bipolar patient presenting with language disorders characterized by a foreign accent and agrammatism, initially categorized as being of psychogenic origin. The patient had an extensive neuropsychological and language evaluation as well as brain imaging exams. In addition to FAS and agrammatism, FG also showed a working memory deficit and executive dysfunction. Moreover, these clinical signs were related to altered cerebral activity on an FDG-PET scan that showed diffuse hypometabolism in the frontal, parietal and temporal lobes bilaterally as well as a focal deficit in the area of the anterior left temporal lobe. When compared to the MRI, these deficits were related to asymmetric atrophy, which was retrospectively seen in the left temporal and frontal opercular/insular region without a focal lesion.

Discussion
To our knowledge, FG is the first case of FAS imaged with an 18F-FDG-PET scan. The nature and type of neuropsychological and linguistic deficits, supported by neuroimaging data, exclude a neurotoxic or neurodegenerative origin for this patient's clinical manifestations. For similar reasons, a psychogenic etiology is also highly improbable.

Conclusion
To account for the FAS and agrammatism in FG, various explanations have been ruled out. Because of the focal deficit seen on the brain imaging, involving the left insular and anterior temporal cortex, two brain regions frequently involved in aphasic syndrome but also in FAS, a cerebrovascular origin must be considered the best explanation to account for FG's language deficits.
Variations in cyclin D1 levels through the cell cycle determine the proliferative fate of a cell
Authors: Yang Ke , Hitomi Masahiro , Stacey Dennis W 
Published: December 2006

Abstract
We present evidence that variations in cyclin D1 levels through the cell cycle are essential for continuing proliferation. Cyclin D1 levels must be high during G1 phase for a cell to initiate DNA synthesis, but then must be suppressed to low levels during S phase to allow for efficient DNA synthesis. This suppression during S phase is apparently regulated by cell cycle position alone and occurs automatically during each cell cycle. If the cell is to continue proliferating, cyclin D1 levels must be induced once again during G2 phase. This induction depends upon the activity of proliferative signaling molecules, and ensures that the extracellular environment continues to be conducive for growth. We propose that the suppression of cyclin D1 levels during each S phase ensures that the subsequent induction during G2 phase, and the resulting commitment to continuing proliferation, is closely linked to the cellular growth environment.
Evidence of a linkage between matrilin-1 gene (MATN1) and idiopathic scoliosis
Authors: Montanaro Lucio , Parisini Patrizio , Greggi Tiziana , Di Silvestre Mario , Campoccia Davide , Rizzi Simona , Arciola Carla Renata 
Published: December 2006

Abstract

Background
In a previous study, a number of genes, associated with spine musculoskeletal deformity phenotypes in mouse and in synteny between mouse and man, were identified as candidate genes for IS. Among these genes, MATN 1, which carries a polymorphic microsatellite marker within its sequence, was selected for a linkage analysis. MATN1 is localised at 1p35 and is mainly expressed in cartilage. The objective of this study was to assess a linkage disequilibrium between the matrilin-1 (MATN 1) gene and the idiopathic scoliosis (IS).

Methods
The genetic study was conducted on a population of 81 trios, each consistent of a daughter/son affected by idiopathic scoliosis (IS) and both parents. In all trios components, the region of MATN1 gene containing the microsatellite marker was amplified by a polymerase chain reaction. The amplicons were analysed by a DNA sequencer-genotyper. The statistical linkage analysis was performed using the extended transmission/disequilibrium test.

Results
Three microsatellite polymorphisms, respectively consisting of 103 bp, 101 bp and 99 bp, were identified. ETDT evidenced a significant preferential transmission for the 103 bp allele (Chi-square = 5.058, df = 1, P = 0.024)

Conclusion
The results suggest that the familial idiopathic scoliosis is associated to the MATN1 gene.
Dofequidar Fumarate (MS-209) in Combination With Cyclophosphamide, Doxorubicin, and Fluorouracil for Patients With Advanced or Recurrent Breast Cancer
Authors: Saeki Toshiaki , Nomizu Tadashi , Toi Masakazu , Ito Yoshinori , Noguchi Shinzaburo , Kobayashi Tadashi , Asaga Taro , Minami Hironobu , Yamamoto Naohito , Aogi Kenjiro , Ikeda Tadashi , Ohashi Yasuo , Sato Wakao , Tsuruo Takashi 
Published: December 2006

Purpose To evaluate the efficacy and tolerability of dofequidar plus cyclophosphamide, doxorubicin, and fluorouracil (CAF) therapy in comparison with CAF alone, in patients with advanced or recurrent breast cancer. Dofequidar is a novel, orally active quinoline derivative that reverses multidrug resistance. Patients and Methods In this randomized, double-blind, placebo-controlled trial, patients were treated with six cycles of CAF therapy: 28 days/cycle, with doxorubicin (25 mg/m2) and fluorouracil (500 mg/m2) administered on days 1 and 8 and cyclophosphamide (100 mg orally [PO]) administered on day 1 through 14. Patients received dofequidar (900 mg PO) 30 minutes before each dose of doxorubicin. Primary end point was overall response rate (ORR; partial or complete response). In total, 221 patients were assessable. Results ORR was 42.6% for CAF compared with 53.1% for dofequidar + CAF, a 24.6% relative improvement and 10.5% absolute increase (P = .077). There was a trend for prolonged progression-free survival (PFS; median 241 days for CAF v 366 days for dofequidar + CAF; P = .145). In retrospectively defined subgroups, significant improvement in PFS in favor of dofequidar was observed in patients who were premenopausal, had no prior therapy, and were stage IV at diagnosis with an intact primary tumor. Except for neutropenia and leukopenia, there was no statistically significant excess of grade 3/4 adverse events compared with CAF. Treatment with dofequidar did not affect the plasma concentration of doxorubicin. Conclusion Dofequidar + CAF was well tolerated and is suggested to have efficacy in patients who had not received prior therapy.
Rapid purification of RNAs using fast performance liquid chromatography (FPLC)
Authors: Kim Insil , McKenna Sean A. , Viani Puglisi Elisabetta , Puglisi Joseph D. 
Published: December 2006

We present here an improved RNA purification method using fast performance liquid chromatography (FPLC) size-exclusion chromatography in place of denaturing polyacrylamide gel electrophoresis (PAGE). The method allows preparation of milligram quantities of pure RNA in a single day. As RNA oligonucleotides behave differently from globular proteins in the size-exclusion column, we present standard curves for RNA oligonucleotides of different lengths on both the Superdex 75 column and the Superdex 200 size-exclusion column. Using this approach, we can separate monomer from multimeric RNA species, purify the desired RNA product from hammerhead ribozyme reactions, and isolate refolded RNA that has aggregated after long-term storage. This methodology allows simple and rapid purification of RNA oligonucleotides for structural and biophysical studies.
G72/G30 Genes and Schizophrenia: A Systematic Meta-analysis of Association Studies
Authors: Li Dawei , He Lin 
Published: December 2006

Abstract
Schizophrenia may result from a neurotransmission hypofunction of glutamatergic and N-methyl-d-aspartate (NMDA) receptors. Linkage disequilibrium mapping has identified several promising and novel positional candidates, including the G72/G30 and d-amino-acid oxidase (DAAO) genes. Since the first positive association report, many subsequent studies have attempted to replicate the association but the results have been mixed. To try to resolve this inconsistency and to elucidate the relationship between the important glutamate-related genes and schizophrenia, the current meta-analysis has combined samples involving 16 polymorphisms covering all published case-control and family-based association studies up to October 2005. The results suggest that there is weak evidence of association between the G72/G30 genes and schizophrenia.
Identifying Quantitative Trait Locus by Genetic Background Interactions in Association Studies
Authors: Jannink Jean-Luc 
Published: December 2006

Abstract
Association studies are designed to identify main effects of alleles across a potentially wide range of genetic backgrounds. To control for spurious associations, effects of the genetic background itself are often incorporated into the linear model, either in the form of subpopulation effects in the case of structure or in the form of genetic relationship matrices in the case of complex pedigrees. In this context epistatic interactions between loci can be captured as an interaction effect between the associated locus and the genetic background. In this study I developed genetic and statistical models to tie the locus by genetic background interaction idea back to more standard concepts of epistasis when genetic background is modeled using an additive relationship matrix. I also simulated epistatic interactions in four-generation randomly mating pedigrees and evaluated the ability of the statistical models to identify when a biallelic associated locus was epistatic to other loci. Under additive-by-additive epistasis, when interaction effects of the associated locus were quite large (explaining 20% of the phenotypic variance), epistasis was detected in 79% of pedigrees containing 320 individuals. The epistatic model also predicted the genotypic value of progeny better than a standard additive model in 78% of simulations. When interaction effects were smaller (although still fairly large, explaining 5% of the phenotypic variance), epistasis was detected in only 9% of pedigrees containing 320 individuals and the epistatic and additive models were equally effective at predicting the genotypic values of progeny. Epistasis was detected with the same power whether the overall epistatic effect was the result of a single pairwise interaction or the sum of nine pairwise interactions, each generating one ninth of the epistatic variance. The power to detect epistasis was highest (94%) at low QTL minor allele frequency, fell to a minimum (60%) at minor allele frequency of about 0.2, and then plateaued at about 80% as alleles reached intermediate frequencies. The power to detect epistasis declined when the linkage disequilibrium between the DNA marker and the functional polymorphism was not complete.
Estimation of Population Heterozygosity and Library Construction-Induced Mutation Rate From Expressed Sequence Tag Collections
Authors: Long A D , Beldade P , Macdonald S J 
Published: December 2006

Abstract
Unigene alignments obtained from cDNA libraries made using multiple individuals are not currently used to estimate population heterozygosity, as they are known to harbor mutations created during library construction. We describe an estimator of population heterozygosity that utilizes only SNPs unlikely to be library construction artifacts.
Evaluation of the Genomic Extent of Effects of Fixed Inversion Differences on Intraspecific Variation and Interspecific Gene Flow in Drosophila pseudoobscura and D. persimilis
Authors: Machado Carlos A , Haselkorn Tamara S , Noor Mohamed A F 
Published: December 2006

Abstract
There is increasing evidence that chromosomal inversions may facilitate the formation or persistence of new species by allowing genetic factors conferring species-specific adaptations or reproductive isolation to be inherited together and by reducing or eliminating introgression. However, the genomic domain of influence of the inverted regions on introgression has not been carefully studied. Here, we present a detailed study on the consequences that distance from inversion breakpoints has had on the inferred level of gene flow and divergence between Drosophila pseudoobscura and D. persimilis. We identified the locations of the inversion breakpoints distinguishing D. pseudoobscura and D. persimilis in chromosomes 2, XR, and XL. Population genetic data were collected at specific distances from the inversion breakpoints of the second chromosome and at two loci inside the XR and XL inverted regions. For loci outside the inverted regions, we found that distance from the nearest inversion breakpoint had a significant effect on several measures of divergence and gene flow between D. pseudoobscura and D. persimilis. The data fitted a logarithmic relationship, showing that the suppression of crossovers in inversion heterozygotes also extends to loci located outside the inversion but close to it (within 1–2 Mb). Further, we detected a significant reduction in nucleotide variation inside the inverted second chromosome region of D. persimilis and near one breakpoint, consistent with a scenario in which this inversion arose and was fixed in this species by natural selection.
Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis
Authors: West Marilyn A L , Kim Kyunga , Kliebenstein Daniel J , van Leeuwen Hans , Michelmore Richard W , Doerge R W , St. Clair Dina A 
Published: December 2006

Abstract
The genetic architecture of transcript-level variation is largely unknown. The genetic determinants of transcript-level variation were characterized in a recombinant inbred line (RIL) population (n = 211) of Arabidopsis thaliana using whole-genome microarray analysis and expression quantitative trait loci (eQTL) mapping of transcript levels as expression traits (e-traits). Genetic control of transcription was highly complex: one-third of the quantitatively controlled transcripts/e-traits were regulated by cis-eQTL, and many trans-eQTL mapped to hotspots that regulated hundreds to thousands of e-traits. Several thousand eQTL of large phenotypic effect were detected, but almost all (93%) of the 36,871 eQTL were associated with small phenotypic effects (R2 &lt; 0.3). Many transcripts/e-traits were controlled by multiple eQTL with opposite allelic effects and exhibited higher heritability in the RILs than their parents, suggesting nonadditive genetic variation. To our knowledge, this is the first large-scale global eQTL study in a relatively large plant mapping population. It reveals that the genetic control of transcript level is highly variable and multifaceted and that this complexity may be a general characteristic of eukaryotes.