bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of protein lysate microarrays to molecular marker verification and quantification
Authors: Ramaswamy Anitha , Lin E , Chen Iou , Mitra Rahul , Morrisett Joel , Coombes Kevin , Ju Zhenlin , Kapoor Mini 
Published: November 2005

AbstractThis study presents the development and application of protein lysate microarray (LMA) technology for verification of presence and quantification of human tissue samples for protein biomarkers. Sub-picogram range sensitivity has been achieved on LMA using a non-enzymatic protein detection methodology. Results from a set of quality control experiments are presented and demonstrate the high sensitivity and reproducibility of the LMA methodology. The optimized LMA methodology has been applied for verification of the presence and quantification of disease markers for atherosclerosis. LMA were used to measure lipoprotein [a] and apolipoprotein B100 in 52 carotid endarterectomy samples. The data generated by LMA were validated by ELISA using the same protein lysates. The correlations of protein amounts estimated by LMA and ELISA were highly significant, with r2≥ 0.98 (p ≤ 0.001) for lipoprotein [a] and with r2≥ 0.94 (p ≤ 0.001) for apolipoprotein B100. This is the first report to compare data generated using proteins microarrays with ELISA, a standard technology for the verification of the presence of protein biomarkers. The sensitivity, reproducibility, and high-throughput quality of LMA technology make it a potentially powerful technology for profiling disease specific protein markers in clinical samples.
Prevalence and correlates of abscesses among a cohort of injection drug users
Authors: Lloyd-Smith Elisa , Kerr Thomas , Hogg Robert S , Li Kathy , Montaner Julio SG , Wood Evan 
Published: November 2005

Abstract
Recent studies have indicated that injection-related infections such as abscesses and cellulitis account for the majority of emergency room visits and acute hospitalizations accrued by local injection drug users. The objective of this analysis was to examine the prevalence and correlates of developing an abscess among a cohort of injection drug users in Vancouver and to identify socio-demographic and drug use variables associated with abscesses at baseline. We examined abscesses among participants enrolled in a prospective cohort of injection drug users. Categorical variables were analyzed using the Pearson's chi-square test and continuous variables were analyzed using the Wilcoxon signed rank test. Among 1 585 baseline participants, 341 (21.5%) reported having an abscess in the last six months. In a logistic regression model that adjusted for all variables that were associated with having an abscess at p < 0.1 in univariate analyses, female gender [odds ratio (OR) = 1.7, [95%CI: 1.2 – 2.4]; p = 0.002), recent incarceration (OR = 1.7, [95%CI: 1.3 – 2.2]; p < 0.001), sex trade involvement (OR = 1.4 [95% CI: 1.0 – 2.0]; p = 0.03), frequent cocaine use (OR = 1.5 [95%CI: 1.2 – 2.0]; p = 0.002) and HIV serostatus (OR = 1.5, [95%CI: 1.2 – 2.0]; p = 0.003) were positively associated with having an abscess. Explanations for these associations require further study, and interventions are needed to address this highly prevalent concern.
Retroperitoneal myolipoma
Authors: Behranwala Kasim A , Chettiar Krissen , El-Bahrawy Mona , Stamp Gordon , Kakkar Ajay K 
Published: November 2005

Abstract

Background
Myolipoma is a benign tumour in which smooth muscle cells are mixed with adipocytes.

Case presentation
A 34-year old lady presented with a mass in the right iliac fossa detected on computerised tomographic (CT) scan. Wide excision of the retroperitoneal mass was done. Histopathology showed features of myolipoma. There was no recurrence or metastasis at three years.

Conclusion
Myolipoma is a rare benign entity; hence a benign course and good prognosis are expected.
Zebrafish sex determination and differentiation: Involvement of FTZ-F1 genes
Authors: von Hofsten Jonas , Olsson Per-Erik 
Published: November 2005

Abstract
Sex determination is the process deciding the sex of a developing embryo. This is usually determined genetically; however it is a delicate process, which in many cases can be influenced by environmental factors. The mechanisms controlling zebrafish sex determination and differentiation are not known. To date no sex linked genes have been identified in zebrafish and no sex chromosomes have been identified. However, a number of genes, as presented here, have been linked to the process of sex determination or differentiation in zebrafish. The zebrafish FTZ-F1 genes are of central interest as they are involved in regulating interrenal development and thereby steroid biosynthesis, as well as that they show expression patterns congruent with reproductive tissue differentiation and function. Zebrafish can be sex reversed by exposure to estrogens, suggesting that the estrogen levels are crucial during sex differentiation. The Cyp19 gene product aromatase converts testosterone into 17 beta-estradiol, and when inhibited leads to male to female sex reversal. FTZ-F1 genes are strongly linked to steroid biosynthesis and the regulatory region of Cyp19 contains binding sites for FTZ-F1 genes, further linking FTZ-F1 to this process. The role of FTZ-F1 and other candidates for zebrafish sex determination and differentiation is in focus of this review.
Trading people versus trading time: What is the difference?
Authors: Damschroder Laura J , Roberts Todd R , Goldstein Christine C , Miklosovic Molly E , Ubel Peter A 
Published: November 2005

AbstractBackgroundPerson trade-off (PTO) elicitations yield different values than standard utility measures, such as time trade-off (TTO) elicitations. Some people believe this difference arises because the PTO captures the importance of distributive principles other than maximizing treatment benefits. We conducted a qualitative study to determine whether people mention considerations related to distributive principles other than QALY-maximization more often in PTO elicitations than in TTO elicitations and whether this could account for the empirical differences.Methods64 members of the general public were randomized to one of three different face-to-face interviews, thinking aloud as they responded to TTO and PTO elicitations. Participants responded to a TTO followed by a PTO elicitation within contexts that compared either: 1) two life-saving treatments; 2) two cure treatments; or 3) a life-saving treatment versus a cure treatment.ResultsWhen people were asked to choose between life-saving treatments, non-maximizing principles were more common with the PTO than the TTO task. Only 5% of participants considered non-maximizing principles as they responded to the TTO elicitation compared to 68% of participants who did so when responding to the PTO elicitation. Non-maximizing principles that emerged included importance of equality of life and a desire to avoid discrimination. However, these principles were less common in the other two contexts. Regardless of context, though, participants were significantly more likely to respond from a societal perspective with the PTO compared to the TTO elicitation.ConclusionWhen lives are at stake, within the context of a PTO elicitation, people are more likely to consider non-maximizing principles, including the importance of equal access to a life-saving treatment, avoiding prejudice or discrimination, and in rare cases giving treatment priority based purely on the position of being worse-off.
CD8+, HLA-unrestricted, cytotoxic T-lymphocyte line against malignant melanoma
Authors: Somasundaram Rajasekharan , Caputo Laura , Guerry DuPont , Herlyn Dorothee 
Published: November 2005

AbstractA CD8+cytotoxic T lymphocyte (CTL) line was derived from the peripheral blood mononuclear cells of a patient with primary melanoma. The CD8+CTL line specifically lysed the autologous primary melanoma cells and not the natural killer cell-sensitive K562 cells or lymphokine activated killer cell-sensitive DAUDI cells. When a large panel of human leukocyte antigen (HLA)-matched and -unmatched allogeneic melanoma, glioma, breast and colorectal carcinoma cells was tested as targets in cytolysis assays, 4 HLA-matched and two HLA-unmatched allogeneic metastatic melanoma lines were lysed by the CD8+CTL. Lysis of autologous and allogeneic melanoma cells was dependent on the effector-to-target cell ratio. Lysis of autologous melanoma cells was not blocked by anti-HLA class I or class II antibodies, confirming that the cytolytic activity of the CD8+CTL was HLA-unrestricted. CTL lysis of autologous melanoma cells was CD3 (T cell receptor) dependent and FAS-FAS-L, and CD1 independent. Identification of the melanoma-associated antigen recognized by the HLA-unrestricted CTL may provide a vaccine for a broad population of melanoma patients.
Autoantibody profiles in the sera of patients with Q fever: characterization of antigens by immunofluorescence, immunoblot and sequence analysis
Authors: Camacho MT , Outschoorn I , Tellez A , Sequí J 
Published: November 2005

AbstractRecent reports have shown that some of the immunological aspects of Q fever, a rickettsiosis caused byCoxiella burnetii, could be related to self-antigen responses. The aim of this study was to determine the specificity of the autoantibody response of patients with acute and chronic Coxiella infections. Smooth muscle and cardiac muscle-specific autoantibodies were observed in significant percentages in acutely or chronically affected Q fever patients when compared to healthy volunteers. Moreover, the incidence of cardiac muscle-specific autoantibody was significantly higher among chronically ill patients compared to acutely ill patients. Moreover, a band of 50 kD of a HeLa extract was detected in most of the sera of individuals with chronic infections and previous sequence analysis suggests that this antigen presents a high degree of homology with the human actin elongation factor 1 alpha. Further research would be necessary to confirm if antibodies to human cytoskeletal proteins could be of clinical importance in chronically infected Q fever patients.
Co-occurrence of autoimmune thyroid disease in a multiple sclerosis cohort
Authors: Sloka JS , Phillips Pryse-WEM , Stefanelli M , Joyce C 
Published: November 2005

Abstract

Background
Multiple sclerosis (MS), Hashimoto's disease and Graves' disease are autoimmune diseases that may share similar pathogenic mechanisms. The co-occurrence rates and demographic characteristics of Graves' disease and Hashimoto's disease (HT) in our MS population are compared with the general population.

Methods
The prevalence of thyroid disease in our MS patients was determined by chart review and survey. Previous diagnosis of thyroid disease, age at diagnosis, treatment used, and about the use of disease modifying medications used to treat their MS were asked. Chart reviews were used to estimate the population prevalence of Graves' disease and Hashimoto's disease and to estimate the demographics of patients with thyroid disease.

Results
A significant co-occurrence of Graves' disease with MS (p = 0.002), and a non-significant co-occurrence of Hashimoto's disease were noted (p = 0.097). No difference in the age of onset or gender of thyroid disease in MS patients compared to the general population was found.

Conclusion
There is a significant co-occurrence in patients with MS and Graves' disease, and a trend to co-occurrence in patients with MS and Hashimoto's disease. There are no differences in the demographics of patients with thyroid disease in our MS patients compared to the general population.
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome
Authors: Lipatov Mikhail , Lenkov Kapa , Petrov Dmitri A , Bergman Casey M 
Published: November 2005

AbstractBackgroundRecent analysis of the human and mouse genomes has shown that a substantial proportion of protein coding genes andcis-regulatory elements contain transposable element (TE) sequences, implicating TE domestication as a mechanism for the origin of genetic novelty. To understand the general role of TE domestication in eukaryotic genome evolution, it is important to assess the acquisition of functional TE sequences by host genomes in a variety of different species, and to understand in greater depth the population dynamics of these mutational events.ResultsUsing anin silicoscreen for host genes that contain TE sequences, we identified a set of 63 mature "chimeric" transcripts supported by expressed sequence tag (EST) evidence in theDrosophila melanogastergenome. We found a paucity of chimeric TEs relative to expectations derived from non-chimeric TEs, indicating that the majority (~80%) of TEs that generate chimeric transcripts are deleterious and are not observed in the genome sequence. Using a pooled-PCR strategy to assay the presence of gene-TE chimeras in wild strains, we found that over half of the observed chimeric TE insertions are restricted to the sequenced strain, and ~15% are found at high frequencies in North AmericanD. melanogasterpopulations. Estimated population frequencies of chimeric TEs did not differ significantly from non-chimeric TEs, suggesting that the distribution of fitness effects for the observed subset of chimeric TEs is indistinguishable from the general set of TEs in the genome sequence.ConclusionIn contrast to mammalian genomes, we found that fewer than 1% ofDrosophilagenes produce mRNAs that includebona fideTE sequences. This observation can be explained by the results of our population genomic analysis, which indicates that most potential chimeric TEs inD. melanogasterare deleterious but that a small proportion may contribute to the evolution of novel gene sequences such as nested or intercalated gene structures. Our results highlight the need to establish the fixity of putative cases of TE domestication identified using genome sequences in order to demonstrate their functional importance, and reveal that the contribution of TE domestication to genome evolution may vary drastically among animal taxa.
Dynamic regulation of integrin activation by intracellular and extracellular signals controls oligodendrocyte morphology
Authors: Olsen Inger Marie , ffrench-Constant Charles 
Published: November 2005

Abstract

Background

Myelination requires precise control of oligodendrocyte morphology and myelin generation at each of the axons contacted by an individual cell. This control must involve the integration of extracellular cues, such as those on the axon surface, with intrinsic developmental programmes. We asked whether integrins represent one class of oligodendrocyte cell-surface receptors able to provide this integration.

Results

Integrins signal via a process of activation, a conformational change that can be induced either by "outside-in" signals comprising physiological extracellular matrix ligands (mimicked by the pharmacological use of the divalent cation manganese) or "inside-out" signalling molecules such as R-Ras. Increasing levels of outside-in signalling via the laminin receptor α6β1 integrin were found to promote oligodendrocyte processing and myelin sheet formation in culture. Similar results were obtained when inside-out signalling was increased by the expression of a constitutively-active R-Ras. Inhibiting inside-out signalling by using dominant-negative R-Ras reduces processes and myelin sheets; importantly, this can be partially rescued by the co-stimulation of outside-in signalling using manganese.

Conclusion

The balance of the equilibrium between active and inactive integrins regulates oligodendrocyte morphology, which is itself regulated by extrinsic and intrinsic cues so providing a mechanism of signal integration. As laminins capable of providing outside-in signals are present on axons at the time of myelination, a mechanism exists by which morphology and myelin generation might be regulated independently in each oligodendrocyte process.
Analysis of variation of amplitudes in cell cycle gene expression
Authors: Liu Delong , Gaido Kevin W , Wolfinger Russ 
Published: November 2005

Abstract

Background
Variation in gene expression among cells in a population is often considered as noise produced from gene transcription and post-transcription processes and experimental artifacts. Most studies on noise in gene expression have emphasized a few well-characterized genes and proteins. We investigated whether different cell-arresting methods have impacts on the maximum expression levels (amplitudes) of a cell cycle related gene.

Results
By introducing random noise, modeled by a von Mises distribution, to the phase angle in a sinusoidal model in a cell population, we derived a relationship between amplitude and the distribution of noise in maximum transcription time (phase). We applied our analysis to Whitfield's HeLa cell cycle data. Our analysis suggests that among 47 cell cycle related genes common to the 2nd experiment (thymidine-thymidine method) and the 4th experiment (thymidine-nocodazole method): (i) the amplitudes of CDC6 and PCNA, which are expressed during G1/S phase, are smaller in the 2nd experiment than in the 4th, while the amplitude of CDC20, which is expressed during G2/M phase, is smaller in the 4th experiment; and (ii) the two cell-arresting methods had little impact on the amplitudes of the other 43 genes in the 2nd and 4th experiments.

Conclusion
Our analysis suggests that procedures that arrest cells in different stages of the cell cycle differentially affect expression of some cell cycle related genes once the cells are released from arrest. The impact of the cell-arresting method on expression of a cell cycle related gene can be quantitatively estimated from the ratio of two estimated amplitudes in two experiments. The ratio can be used to gauge the variation in the phase/peak expression time distribution involved in stochastic transcription and post-transcriptional processes for the gene. Further investigations are needed using normal, unperturbed and synchronized HeLa cells as a reference to compare how many cell cycle related genes are directly and indirectly affected by various cell-arresting methods.
Development of an improved microneutralization assay for respiratory syncytial virus by automated plaque counting using imaging analysis
Authors: Zielinska Edyta , Liu Daiqing , Wu Hong-Yin , Quiroz Jorge , Rappaport Ruth , Yang Da-Ping 
Published: November 2005

Abstract

Background
Respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infection in infants and young children. Although several experimental RSV vaccines are under investigation, immuno therapy is the only treatment currently available. In assessing the immunogenicity of various vaccine formulations, a plaque reduction neutralization assay for the evaluation of RSV neutralizing antibody has been widely used. The method produces reliable results, but it is tedious and labor intensive as it relies on manual counting by laboratory personnel. To facilitate evaluation of phase II and phase III vaccine clinical trials, a more rapid, reliable and efficient neutralization assay is needed.

Results
An improved microneutralization assay for quantifying RSV neutralizing antibodies was developed using an ImmunoSpot® Series I Analyzer (Cellular Technology Ltd., Cleveland, OH) for automated plaque counting. The method is an improvement of the established classical microneutralization assay in which immunostained plaques on transparent tissue culture plates are counted manually under a dissecting microscope. Image analyzer technology allows for fully automated counting of plaques distributed throughout an entire well. Adjustments, such as the use of opaque tissue culture plates and the TMB substrate, True Blue™ (KPL, Gaithersburg, MD), were required to adapt the assay for optimal detection of plaques by the image analyzer. The suitability and the accuracy of the method for counting RSV plaques were determined by comparative testing of a reference serum and two control sera by manual and automated counting methods. The results showed that the two methods were highly correlated (R = 0.9580) and the titers generated by them were within two-fold.

Conclusion
Our results demonstrate that the semi-automated assay is rapid and reliable. It provides results within two fold to the classical plaque microneutralization assay and is readily applied to the evaluation of neutralizing antibody titers in sera obtained from epidemiology or vaccine clinical trials.
Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species
Authors: Hammond John P , Broadley Martin R , Craigon David J , Higgins Janet , Emmerson Zoe F , Townsend Henrik J , White Philip J , May Sean T 
Published: November 2005

Abstract
High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L.) Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM) probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P) stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ and may be used to facilitate transcriptomic analyses of a wide range of plant and animal species in the absence of custom arrays.