bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative evolution history of SINEs in <i>Arabidopsis thaliana</i> and <i>Brassica oleracea:</i> evidence for a high rate of SINE loss
Authors: Lenoir A. , Pélissier T. , Bousquet-Antonelli C. , Deragon J.M. 
Published: July 2005

<i>Brassica oleracea</i> and <i>Arabidopsis thaliana</i> belong to the <i>Brassicaceae</i><i>(Cruciferae)</i> family and diverged 16 to 19 million years ago. Although the genome size of <i>B. oleracea</i> (∼600 million base pairs) is more than four times that of <i>A. thaliana</i> (∼130 million base pairs), their gene content is believed to be very similar with more than 85% sequence identity in the coding region. Therefore, this important difference in genome size is likely to reflect a different rate of non-coding DNA accumulation. Transposable elements (TEs) constitute a major fraction of non-coding DNA in plant species. A different rate in TE accumulation between two closely related species can result in significant genome size variations in a short evolutionary period. Short interspersed elements (SINEs) are non-autonomous retroposons that have invaded the genome of most eukaryote species. Several SINE families are present in <i>B. oleracea</i> and <i>A. thaliana</i> and we found that two of them (called RathE1 and RathE2) are present in both species. In this study, the tempo of evolution of RathE1 and RathE2 SINE families in both species was compared. We observed that most <i>B. oleracea</i> RathE2 SINEs are “young” (close to the consensus sequence) and abundant while elements from this family are more degenerated and much less abundant in <i>A. thaliana</i>. However, the situation is different for the RathE1 SINE family for which the youngest elements are found in <i>A. thaliana</i>. Surprisingly, no SINE was found to occupy the same (orthologous) genomic locus in both species suggesting that either these SINE families were not amplified at a significant rate in the common ancestor of the two species or that older elements were lost and only the recent (lineage-specific) insertions remain. To test this latter hypothesis, loci containing a recently inserted SINE in the <i>A. thaliana</i> col-0 ecotype were selected and characterized in several other <i>A. thaliana</i> ecotypes. In addition to the expected SINE containing allele and the pre-integrative allele (i.e. the “empty” allele), we observed in the different ecotypes, alleles with truncated portions of the SINE (up to the complete loss of the element) and of the immediate genomic flanking sequences. The absence of SINEs in orthologous positions between <i>B. oleracea</i> and <i>A. thaliana</i> and the presence in recently diverged <i>A. thaliana</i> ecotypes of alleles containing severely truncated SINEs suggest a very high rate of SINE loss in these species.
Gender, Aging, and Subjective Well-Being
Authors: Inglehart Ronald 
Published: July 2005

Previous research has consistently found that men and women have similar levels of happiness, life satisfaction, and other global measures of subjective well-being. This article demonstrates that significant gender-related differences in subjective well-being exist— but tend to be concealed by an interaction effect between age, gender and well-being. Women under 45 tend to be happier than men; but older women are less happy. Thus, in a pooled sample of 146,000 respondents from 65 societies, among the youngest group, 24 percent of the men and 28 percent of the women describe themselves as very happy; but among the oldest group, only 20 percent of the women describe themselves as very happy, while 25 percent of the men do so. The relationship between gender and well-being reverses itself, moving from a female advantage of 4 points to a deficit of 5 points. Given the huge sample size, these differences are highly significant. The aspiration-adjustment model implies that, despite their continuing disadvantages in income, status, and power, women of today should show higher levels of subjective well-being than men. A global women’s movement has been pushing for gender equality throughout the world, with some success, so that currently, women’s achievement tends to be above traditional aspiration levels. But this is offset by a systematic tendency to devalue older women. This tendency is particularly strong in advanced industrial societies where women have made the most progress—but where the mass media and advertising convey the message that only young women are beautiful and devalue the social worth of older women (Bluhm 2000). This produces an interaction between gender, age, and well-being that conceals statistically significant and theoretically interesting gender differences in subjective well-being.
World music and the search for difference
Authors: Haynes Jo 
Published: July 2005

World music has been immersed in a series of complex ethical, political and aesthetic debates since its emergence as a new musical category in the 1980s. These debates have been fuelled by competing perspectives that portray world music as either an exemplar of progressive cosmopolitan politics that foster cultural hybridity or as reinforcing fixed and unitary conceptions of difference through an essentializing representation of cultures. By utilizing interviews with key people involved in the organization of world music in Britain, this article centralizes this tension by examining the role of difference in world music. Bourdieu’s concept of cultural intermediary is used here as a descriptive label for the work of those involved in this research and as an explanatory tool to highlight how difference defines the interaction between the substantive and symbolic processes within the British world music scene. This article argues that the work of cultural intermediaries demonstrates the ambivalent cultural processes within the performance, management and consumption of world music. This is evident in the series of recursive shifts within world music that employ a model of difference that draws on both the binary logic of traditional meanings of race/ethnicity and hybridity. In so doing, this article also examines how world music affinity and consumption, which takes people across arbitrarily ascribed boundaries, challenges the idea that normative racialized identities are meant to provide a fixed set of cultural values, musical tastes and social attitudes.
CD8+ T lymphocytes in lung tissue from patients with idiopathic pulmonary fibrosis
Authors: Daniil Zoe , Kitsanta Panagiota , Kapotsis George , Mathioudaki Maria , Kollintza Androniki , Karatza Marilena , Milic-Emili Joseph , Roussos Charis , Papiris Spyros A 
Published: July 2005

AbstractBackgroundSeveral studies have implicated a role of inflammation in the pathogenesis of lung damage in idiopathic pulmonary fibrosis (IPF). Parenchymal lung damage leads to defects in mechanics and gas exchange and clinically manifests with exertional dyspnea. Investigations of inflammatory cells in IPF have shown that eosinophils, neutrophils and CD8+TLs may be associated with worse prognosis. We wished to investigate by quantitative immunohistochemistry infiltrating macrophages, neutrophils and T lymphocytes (TLs) subpopulations (CD3+, CD4+and CD8+) in lung tissue of patients with IPF and their correlation with lung function indices and grade of dyspnoea.MethodsSurgical biopsies of 12 patients with IPF were immunohistochemically stained with mouse monoclonal antibodies (anti-CD68for macrophages, anti-elastase for neutrophils, and anti-CD3, anti-CD4, anti-CD8for CD3+TLs, CD4+TLs, and CD8+TLs respectively). The number of positively stained cells was determined by observer-interactive computerized image analysis (SAMBA microscopic image processor). Cell numbers were expressed in percentage of immunopositive nuclear surface in relation to the total nuclear surface of infiltrative cells within the tissue (labeling Index). Correlations were performed between cell numbers and physiological indices [FEV1, FVC, TLC,DLCO, PaO2, PaCO2and P(A-a)O2)] as well as dyspnoea scores assessed by the Medical Research Council (MRC) scale.ResultsElastase positive cells accounted for the 7.04% ± 1.1 of total cells, CD68+cells for the 16.6% ± 2, CD3+TLs for the 28.8% ± 7, CD4+TLs for the 14.5 ± 4 and CD8+TLs for the 13.8 ± 4. CD8+TLs correlated inversely with FVC % predicted (rs= -0.67, p = 0.01), TLC % predicted (rs= -0.68, p = 0.01), DLCO % predicted (rs= -0.61, p = 0.04), and PaO2(rs= -0.60, p = 0.04). Positive correlations were found between CD8+TLs and P(A-a)O2(rs= 0.65, p = 0.02) and CD8+TLs and MRC score (rs= 0.63, p = 0.02). Additionally, CD68+cells presented negative correlations with both FVC % predicted (rs= -0.80, p = 0.002) and FEV1% predicted (rs= -0.68, p = 0.01).ConclusionIn UIP/IPF tissue infiltrating mononuclear cells and especially CD8+TLs are associated with the grade of dyspnoea and functional parameters of disease severity implicating that they might play a role in its pathogenesis.
The effect of prior statin use on 30-day mortality for patients hospitalized with community-acquired pneumonia
Authors: Mortensen Eric M , Restrepo Marcos I , Anzueto Antonio , Pugh Jacqueline 
Published: July 2005

Abstract

Background
Recent studies suggest that HMG-CoA reductase inhibitors ("statins") may have beneficial effects for patients at risk for some types of infections. We examined the effect of prior outpatient use of statins on mortality for patients hospitalized with community-acquired pneumonia.

Methods
A retrospective cohort study conducted at two tertiary teaching hospitals. Eligible subjects were admitted with a diagnosis of, had a chest x-ray consistent with, and had a discharge ICD-9 diagnosis of pneumonia. Subjects were excluded if they were "comfort measures only" or transferred from another acute care hospital. Subjects were considered to be on a medication if they were taking it at the time of presentation.

Results
Data was abstracted on 787 subjects at the two hospitals. Mortality was 9.2% at 30-days and 13.6% at 90-days. At presentation 52% of subjects were low risk, 34% were moderate risk, and 14% were high risk based on the pneumonia severity index. In the multivariable regression analysis, after adjusting for potential confounders including a propensity score, the use of statins at presentation (odds ratio 0.36, 95% confidence interval 0.14–0.92) was associated with decreased 30-day mortality.

Discussion
Prior outpatient statin use was associated with decreased mortality in patients hospitalized with community-acquired pneumonia despite their use being associated with comorbid illnesses likely to contribute to increased mortality. Confirmatory studies are needed, as well as research to determine the mechanism(s) of this protective effect.
Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes
Authors: Callebaut Isabelle , Prat Karine , Meurice Edwige , Mornon Jean-Paul , Tomavo Stanislas 
Published: July 2005

AbstractBackgroundTo date, only a few transcription factors have been identified in the genome of the parasitePlasmodium falciparum, the causative agent of malaria. Moreover, no detailed molecular analysis of its basal transcription machinery, which is otherwise well-conserved in the crown group of eukaryotes, has yet been reported. In this study, we have used a combination of sensitive sequence analysis methods to predict the existence of several parasite encoded general transcription factors associated with RNA polymerase II.ResultsSeveral orthologs of general transcription factors associated with RNA polymerase II can be predicted among the hypothetical proteins of theP. falciparumgenome using the two-dimensional Hydrophobic Cluster Analysis (HCA) together with profile-based search methods (PSI-BLAST). These predicted orthologous genes encoding putative transcription factors include the large subunit of TFIIA and two candidates for its small subunit, the TFIIE β-subunit, which would associate with the previously known TFIIE α-subunit, the TFIIF β-subunit, as well as the p62/TFB1 subunit of the TFIIH core. Within TFIID, the putative orthologs of TAF1, TAF2, TAF7 and TAF10 were also predicted. However, no candidates for TAFs with classical histone fold domain (HFD) were found, suggesting an unusual architecture of TFIID complex of RNA polymerase II in the parasite.ConclusionTaken together, these results suggest that more general transcription factors may be present in theP. falciparumproteome than initially thought. The prediction of these orthologous general transcription factors opens the way for further studies dealing with transcriptional regulation inP. falciparum. These alternative and sensitive sequence analysis methods can help to identify candidates for other transcriptional regulatory factors inP. falciparum. They will also facilitate the prediction of biological functions for several orphan proteins from other apicomplexan parasites such asToxoplasma gondii,Cryptosporidium parvumandEimeria.
Application of four dyes in gene expression analyses by microarrays
Authors: Staal Yvonne CM , van Herwijnen Marcel HM , van Schooten Frederik J , van Delft Joost HM 
Published: July 2005

Abstract

Background
DNA microarrays are widely used in gene expression analyses. To increase throughput and minimize costs without reducing gene expression data obtained, we investigated whether four mRNA samples can be analyzed simultaneously by applying four different fluorescent dyes.

Results
Following tests for cross-talk of fluorescence signals, Alexa 488, Alexa 594, Cyanine 3 and Cyanine 5 were selected for hybridizations. For self-hybridizations, a single RNA sample was labelled with all dyes and hybridized on commercial cDNA arrays or on in-house spotted oligonucleotide arrays. Correlation coefficients for all combinations of dyes were above 0.9 on the cDNA array. On the oligonucleotide array they were above 0.8, except combinations with Alexa 488, which were approximately 0.5. Standard deviation of expression differences for replicate spots were similar on the cDNA array for all dye combinations, but on the oligonucleotide array combinations with Alexa 488 showed a higher variation.

Conclusion
In conclusion, the four dyes can be used simultaneously for gene expression experiments on the tested cDNA array, but only three dyes can be used on the tested oligonucleotide array. This was confirmed by hybridizations of control with test samples, as all combinations returned similar numbers of differentially expressed genes with comparable effects on gene expression.
A role for the Tec family kinase ITK in regulating SEB induced Interleukin-2 production in vivo via c-jun phosphorylation
Authors: Ragin Melanie J , Hu Jianfang , Henderson Andrew J , August Avery 
Published: July 2005

Abstract
Background
Exposure to Staphylococcal Enterotoxin B (SEB), a bacterial superantigen secreted by the Gram-positive bacteria Staphyloccocus aureus, results in the expansion and eventual clonal deletion and anergy of Vβ8+ T cells, as well as massive cytokine release, including Interleukin-2 (IL-2). This IL-2 is rapidly secreted following exposure to SEB and may contribute to the symptoms seen following exposure to this bacterial toxin. The Tec family kinase ITK has been shown to be important for the production of IL-2 by T cells stimulated in vitro and may represent a good target for blocking the production of this cytokine in vivo. In order to determine if ITK represents such a target, mice lacking ITK were analyzed for their response to SEB exposure.

Results
It was found that T cells from mice lacking ITK exhibited significantly reduced proliferative responses to SEB exposure in vitro, as well as in vivo. Examination of IL-2 production revealed that ITK null mice produced reduced levels of this cytokine in vitro, and more dramatically, in vivo. In vivo analysis of c-jun phosphorylation, previously shown to be critical for regulating IL-2 production, revealed that this pathway was specifically activated in SEB reactive Vβ8+ (but not non-reactive Vβ6+) T cells from WT mice, but not in Vβ8+ T cells from ITK null mice. However, toxicity analysis indicated that both WT and ITK null animals were similarly affected by SEB exposure.

Conclusion
These data show that ITK is required for IL-2 production induced by SEB in vivo, and may regulate signals leading IL-2 production, in part by regulating phosphorylation of c-jun. The data also suggest that perturbing T cell activation pathways leading to IL-2 does not necessarily lead to improved responses to SEB toxicity.
Psychophysiological effects of a web-based stress management system: A prospective, randomized controlled intervention study of IT and media workers [ISRCTN54254861]
Authors: Hasson Dan , Anderberg Ulla Maria , Theorell Töres , Arnetz Bengt B 
Published: July 2005

Abstract

Background
The aim of the present study was to assess possible effects on mental and physical well-being and stress-related biological markers of a web-based health promotion tool.

Methods
A randomized, prospectively controlled study was conducted with before and after measurements, involving 303 employees (187 men and 116 women, age 23–64) from four information technology and two media companies. Half of the participants were offered web-based health promotion and stress management training (intervention) lasting for six months. All other participants constituted the reference group. Different biological markers were measured to detect possible physiological changes.

Results
After six months the intervention group had improved statistically significantly compared to the reference group on ratings of ability to manage stress, sleep quality, mental energy, concentration ability and social support. The anabolic hormone dehydroepiandosterone sulphate (DHEA-S) decreased significantly in the reference group as compared to unchanged levels in the intervention group. Neuropeptide Y (NPY) increased significantly in the intervention group compared to the reference group. Chromogranin A (CgA) decreased significantly in the intervention group as compared to the reference group. Tumour necrosis factor α (TNFα) decreased significantly in the reference group compared to the intervention group. Logistic regression analysis revealed that group (intervention vs. reference) remained a significant factor in five out of nine predictive models.

Conclusion
The results indicate that an automatic web-based system might have short-term beneficial physiological and psychological effects and thus might be an opportunity in counteracting some clinically relevant and common stress and health issues of today.
Socioeconomic factors and adolescent pregnancy outcomes: distinctions between neonatal and post-neonatal deaths?
Authors: Markovitz Barry P , Cook Rebeka , Flick Louise H , Leet Terry L 
Published: July 2005

Abstract
Background
Young maternal age has long been associated with higher infant mortality rates, but the role of socioeconomic factors in this association has been controversial. We sought to investigate the relationships between infant mortality (distinguishing neonatal from post-neonatal deaths), socioeconomic status and maternal age in a large, retrospective cohort study.

Methods
We conducted a population-based cohort study using linked birth-death certificate data for Missouri residents during 1997–1999. Infant mortality rates for all singleton births to adolescent women (12–17 years, n = 10,131; 18–19 years, n = 18,954) were compared to those for older women (20–35 years, n = 28,899). Logistic regression was used to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI) for all potential associations.

Results
The risk of infant (OR 1.95, CI 1.54–2.48), neonatal (1.69, 1.24–2.31) and post-neonatal mortality (2.47, 1.70–3.59) were significantly higher for younger adolescent (12–17 years) than older (20–34 years) mothers. After adjusting for race, marital status, age-appropriate education level, parity, smoking status, prenatal care utilization, and poverty status (indicated by participation in WIC, food stamps or Medicaid), the risk of post-neonatal mortality (1.73, 1.14–2.64) but not neonatal mortality (1.43, 0.98–2.08) remained significant for younger adolescent mothers. There were no differences in neonatal or post-neonatal mortality risks for older adolescent (18–19 years) mothers.

Conclusion
Socioeconomic factors may largely explain the increased neonatal mortality risk among younger adolescent mothers but not the increase in post-neonatal mortality risk.
Children's acceptance of milk with xylitol or sorbitol for dental caries prevention
Authors: Castillo Jorge L , Milgrom Peter , Coldwell Susan E , Castillo Ramon , Lazo Rocio 
Published: July 2005

AbstractBackgroundXylitol, a polyol sugar, has been shown to reduce dental caries when mixed with food or chewing gum. This study examines the taste acceptability of xylitol in milk as a first step toward measuring the effectiveness of xylitol in milk for the reduction of dental caries in a public health program.MethodsThree different types of milk (Ultra High Temperature (UHT), powder and evaporated) were tested for acceptability by 75 Peruvian children (25 per milk group, ages 4 to 7 years). Each group evaluated xylitol and sorbitol in one type of milk. In the first phase, each child was presented with a tray of four plastic cups containing 50 ml of milk with 0.021 g/ml xylitol, 0.042 g/ml xylitol, 0.042 g/ml sorbitol or no sugar. Each child was asked to taste the samples in a self-selected order. After tasting each sample, the child placed the milk cup in front of one of three cartoon faces (smile, frown or neutral) representing the child's response to the taste of each sample. In the second phase, the child was asked to rank order the milk samples within each category (smile, frown or neutral). Ranks within categories were then combined to obtain a rank ordering for all the test samples.ResultsThe ranking from best to worst for the samples across categories (UHT, powder, evaporated) was xylitol (0.0.042 g/ml), sorbitol (0.042 g/ml), xylitol (0.021 g/ml) and milk alone (Friedman's ANOVA). Xylitol and sorbitol were preferred over milk alone, and xylitol (0.042 g/ml) was preferred to sorbitol (0.042 g/ml)(p < .05 sign test).ConclusionMilk sweetened with xylitol is well accepted by Peruvian children ages 4–7 years.
Multidrug Resistance-Associated Protein 1 (MRP1) mediated vincristine resistance: effects of N-acetylcysteine and Buthionine Sulfoximine
Authors: Akan Ilhan , Akan Selma , Akca Hakan , Savas Burhan , Ozben Tomris 
Published: July 2005

AbstractBackgroundMultidrug resistance mediated by the multidrug resistance-associated protein 1 (MRP1) decreases cellular drug accumulation. The exact mechanism of MRP1 involved multidrug resistance has not been clarified yet, though glutathione (GSH) is likely to have a role for the resistance to occur. N-acetylcysteine (NAC) is a pro-glutathione drug. DL-Buthionine (S,R)-sulfoximine (BSO) is an inhibitor of GSH synthesis. The aim of our study was to investigate the effect of NAC and BSO on MRP1-mediated vincristine resistance in Human Embryonic Kidney (HEK293) and its MRP1 transfected 293MRP cells. Human Embryonic Kidney (HEK293) cells were transfected with a plasmid encoding whole MRP1 gene. Both cells were incubated with vincristine in the presence or absence of NAC and/or BSO. The viability of both cells was determined under different incubation conditions. GSH, Glutathione S-Transferase (GST) and glutathione peroxidase (GPx) levels were measured in the cell extracts obtained from both cells incubated with different drugs.ResultsN-acetylcysteine increased the resistance of both cells against vincristine and BSO decreased NAC-enhanced MRP1-mediated vincristine resistance, indicating that induction of MRP1-mediated vincristine resistance depends on GSH. Vincristine decreased cellular GSH concentration and increased GPx activity. Glutathione S-Transferase activity was decreased by NAC.ConclusionOur results demonstrate that NAC and BSO have opposite effects in MRP1 mediated vincristine resistance and BSO seems a promising chemotherapy improving agent in MRP1 overexpressing tumor cells.