bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helicobacter pylori in colorectal neoplasms: is there an aetiological relationship?
Authors: Jones Mary , Helliwell Peter , Pritchard Colin , Tharakan Joseph , Mathew Joseph 
Published: May 2007

Abstract

Background
This pilot study was carried out to determine whether Helicobacter pylori can be detected in normal colon or in association with colorectal neoplasia.

Methods
Paraffin processed colonic tissue blocks of normal colonic mucosa (n = 60), and patients diagnosed as adenoma (n = 60), and adenocarcinoma (n = 60) were retrieved from our archive; the adenoma group included tubular (n = 20), tubulovillous (n = 20) and villous adenomas (n = 20). 4 μm sections were stained by immunohistochemical methods using anti-Helicobacter pylori antibodies (polyclonal NCL-HPp and monoclonal NCL-C-jejuni).

Results
Significant numbers of Helicobacter pylori were identified in tubular adenomas (OR = 11.13; 95%CI = 1.62–76.70), tubulovillous adenomas (OR = 10.45; 95%CI = 1.52–71.52) and adenocarcinomas (OR = 8.13; 95%CI = 1.40–46.99) compared to controls: there was no association in numbers of Helicobacter pylori and villous adenomas (OR = 2.95; 95%CI = 0.29–9.96).

Conclusion
We conclude that although, in this pilot study, there appears to be an association in the prevalence of Helicobacter pylori with some, but not all, colorectal neoplasms, we can not infer causality from these results. These findings need to be further substantiated with a prospective study and the use of molecular biological techniques to determine a causal association.
Worksite environment physical activity and healthy food choices: measurement of the worksite food and physical activity environment at four metropolitan bus garages
Authors: Shimotsu Scott T , French Simone A , Gerlach Anne F , Hannan Peter J 
Published: May 2007

AbstractBackgroundThe present research describes a measure of the worksite environment for food, physical activity and weight management. The worksite environment measure (WEM instrument) was developed for the Route H Study, a worksite environmental intervention for weight gain prevention in four metro transit bus garages in Minneapolis-St. Paul.MethodsTwo trained raters visited each of the four bus garages and independently completed the WEM. Food, physical activity and weight management-related items were observed and recorded on a structured form. Inter-rater reliability was computed at the item level using a simple percentage agreement.ResultsThe WEM showed high inter-rater reliability for the number and presence of food-related items. All garages had vending machines, microwaves and refrigerators. Assessment of the physical activity environment yielded similar reliability for the number and presence/absence of fitness items. Each garage had a fitness room (average of 4.3 items of fitness equipment). All garages had at least one stationary bike and treadmill. Three garages had at least one weighing scale available. There were no designated walking areas inside or outside. There were on average < 1 food stores or restaurants within sight of each garage. Few vending machine food and beverage items met criteria for healthful choices (15% of the vending machine foods; 26% of the vending machine beverages). The garage environment was perceived to be not supportive of healthy food choices, physical activity and weight management; 52% reported that it was hard to get fruits and vegetables in the garages, and 62% agreed that it was hard to be physically active in the garages.ConclusionThe WEM is a reliable measure of the worksite nutrition, physical activity, and weight management environment that can be used to assess changes in the work environment.
Differential affinity of mammalian histone H1 somatic subtypes for DNA and chromatin
Authors: Orrego Mary , Ponte Imma , Roque Alicia , Buschati Natascha , Mora Xavier , Suau Pedro 
Published: May 2007

AbstractBackgroundHistone H1 is involved in the formation and maintenance of chromatin higher order structure. H1 has multiple isoforms; the subtypes differ in timing of expression, extent of phosphorylation and turnover rate. In vertebrates, the amino acid substitution rates differ among subtypes by almost one order of magnitude, suggesting that each subtype might have acquired a unique function. We have devised a competitive assay to estimate the relative binding affinities of histone H1 mammalian somatic subtypes H1a-e and H1° for long chromatin fragments (30–35 nucleosomes) in physiological salt (0.14 M NaCl) at constant stoichiometry.ResultsThe H1 complement of native chromatin was perturbed by adding an additional amount of one of the subtypes. A certain amount of SAR (scaffold-associated region) DNA was present in the mixture to avoid precipitation of chromatin by excess H1. SAR DNA also provided a set of reference relative affinities, which were needed to estimate the relative affinities of the subtypes for chromatin from the distribution of the subtypes between the SAR and the chromatin. The amounts of chromatin, SAR and additional H1 were adjusted so as to keep the stoichiometry of perturbed chromatin similar to that of native chromatin. H1 molecules freely exchanged between the chromatin and SAR binding sites. In conditions of free exchange, H1a was the subtype of lowest affinity, H1b and H1c had intermediate affinities and H1d, H1e and H1° the highest affinities. Subtype affinities for chromatin differed by up to 19-fold. The relative affinities of the subtypes for chromatin were equivalent to those estimated for a SAR DNA fragment and a pUC19 fragment of similar length. Avian H5 had an affinity ~12-fold higher than H1e for both DNA and chromatin.ConclusionH1 subtypes freely exchangein vitrobetween chromatin binding sites in physiological salt (0.14 M NaCl). The large differences in relative affinity of the H1 subtypes for chromatin suggest that differential affinity could be functionally relevant and thus contribute to the functional differentiation of the subtypes. The conservation of the relative affinities for SAR and non-SAR DNA, in spite of a strong preference for SAR sequences, indicates that differential affinity alone cannot be responsible for the heterogeneous distribution of some subtypes in cell nuclei.
Media and education play a tremendous role in mounting AIDS awareness among married couples in Bangladesh
Authors: Rahman Mohammad Shafiqur , Rahman Mohammad Lutfor 
Published: May 2007

AbstractBackgroundTo quarantine the spreading possibility of HIV virus to general population boosting public awareness is must. But the proper awareness level is substantially low in Bangladesh. This paper aims to identify the factors associated with the awareness regarding HIV/AIDS through a bivariate and multivariate analysis using the data extracted from Bangladesh Demography and Health Survey (BDHS) 1999–2000.ResultsThe findings of both techniques show that education, occupation, socioeconomic status, status of household food consumption, area of residence and media exposure have significant (p < 0.001) contribution in determining HIV/AIDS awareness level. It also reveals that media, particularly TV, and education play the leading role regarding this issue while the others have an indirect relationship. The odds of awareness among higher educated women and men were 4.69 and 77.73 times of no educated women and men respectively. In addition, both women and men those who regularly watch TV were 8.6 times more likely to be aware about AIDS compared to those who never watch TV. This phenomenon holds true for both women and men.ConclusionAt this instant it is urgent to give emphasis on education, alleviation of poverty, ensuring electronic media exposure, head to head communication program, institutional based sex education and necessary information to learn about HIV/AIDS for the young, adult and adolescents all over the country.
Early efforts in modeling the incubation period of infectious diseases with an acute course of illness
Authors: Nishiura Hiroshi 
Published: May 2007

AbstractThe incubation period of infectious diseases, the time from infection with a microorganism to onset of disease, is directly relevant to prevention and control. Since explicit models of the incubation period enhance our understanding of the spread of disease, previous classic studies were revisited, focusing on the modeling methods employed and paying particular attention to relatively unknown historical efforts. The earliest study on the incubation period of pandemic influenza was published in 1919, providing estimates of the incubation period of Spanish flu using the daily incidence on ships departing from several ports in Australia. Although the study explicitly dealt with an unknown time of exposure, the assumed periods of exposure, which had an equal probability of infection, were too long, and thus, likely resulted in slight underestimates of the incubation period.After the suggestion that the incubation period follows lognormal distribution, Japanese epidemiologists extended this assumption to estimates of the time of exposure during a point source outbreak. Although the reason why the incubation period of acute infectious diseases tends to reveal a right-skewed distribution has been explored several times, the validity of the lognormal assumption is yet to be fully clarified. At present, various different distributions are assumed, and the lack of validity in assuming lognormal distribution is particularly apparent in the case of slowly progressing diseases. The present paper indicates that (1) analysis using well-defined short periods of exposure with appropriate statistical methods is critical when the exact time of exposure is unknown, and (2) when assuming a specific distribution for the incubation period, comparisons using different distributions are needed in addition to estimations using different datasets, analyses of the determinants of incubation period, and an understanding of the underlying disease mechanisms.
First introduction of highly pathogenic H5N1 avian influenza A viruses in wild and domestic birds in Denmark, Northern Europe
Authors: Bragstad Karoline , Jørgensen Poul H , Handberg Kurt , Hammer Anne S , Kabell Susanne , Fomsgaard Anders 
Published: May 2007

Abstract

Background
Since 2005 highly pathogenic (HP) avian influenza A H5N1 viruses have spread from Asia to Africa and Europe infecting poultry, humans and wild birds. HP H5N1 virus was isolated in Denmark for the first time in March 2006. A total of 44 wild birds were found positive for the HP H5N1 infection. In addition, one case was reported in a backyard poultry flock.

Results
Full-genome characterisation of nine isolates revealed that the Danish H5N1 viruses were highly similar to German H5N1 isolates in all genes from the same time period. The haemagglutinin gene grouped phylogenetically in H5 clade 2 subclade 2 and closest relatives besides the German isolates were isolates from Croatia in 2005, Nigeria and Niger in 2006 and isolates from Astrakhan in Russia 2006. The German and Danish isolates shared unique substitutions in the NA, PB1 and NS2 proteins.

Conclusion
The first case of HP H5N1 infection of wild and domestic birds in Denmark was experienced in March 2006. This is the first full genome characterisation of HP H5N1 avian influenza A virus in the Nordic countries. The Danish viruses from this time period have their origin from the wild bird strains from Qinghai in 2005. These viruses may have been introduced to the Northern Europe through unusual migration due to the cold weather in Eastern Europe at that time.
A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells
Authors: Li Zheng , Srivastava Shireesh , Yang Xuerui , Mittal Sheenu , Norton Paul , Resau James , Haab Brian , Chan Christina 
Published: May 2007

Abstract

Background
Free fatty acids (FFA) and tumor necrosis factor alpha (TNF-α) have been implicated in the pathogenesis of many obesity-related metabolic disorders. When human hepatoblastoma cells (HepG2) were exposed to different types of FFA and TNF-α, saturated fatty acid was found to be cytotoxic and its toxicity was exacerbated by TNF-α. In order to identify the processes associated with the toxicity of saturated FFA and TNF-α, the metabolic and gene expression profiles were measured to characterize the cellular states. A computational model was developed to integrate these disparate data to reveal the underlying pathways and mechanisms involved in saturated fatty acid toxicity.

Results
A hierarchical framework consisting of three stages was developed to identify the processes and genes that regulate the toxicity. First, discriminant analysis identified that fatty acid oxidation and intracellular triglyceride accumulation were the most relevant in differentiating the cytotoxic phenotype. Second, gene set enrichment analysis (GSEA) was applied to the cDNA microarray data to identify the transcriptionally altered pathways and processes. Finally, the genes and gene sets that regulate the metabolic responses identified in step 1 were identified by integrating the expression of the enriched gene sets and the metabolic profiles with a multi-block partial least squares (MBPLS) regression model.

Conclusion
The hierarchical approach suggested potential mechanisms involved in mediating the cytotoxic and cytoprotective pathways, as well as identified novel targets, such as NADH dehydrogenases, aldehyde dehydrogenases 1A1 (ALDH1A1) and endothelial membrane protein 3 (EMP3) as modulator of the toxic phenotypes. These predictions, as well as, some specific targets that were suggested by the analysis were experimentally validated.
Accelerated cellular senescence in degenerate intervertebral discs: a possible role in the pathogenesis of intervertebral disc degeneration
Authors: Le Maitre Christine Lyn , Freemont Anthony John , Hoyland Judith Alison 
Published: May 2007

AbstractCurrent evidence implicates intervertebral disc degeneration as a major cause of low back pain, although its pathogenesis is poorly understood. Numerous characteristic features of disc degeneration mimic those seen during ageing but appear to occur at an accelerated rate. We hypothesised that this is due to accelerated cellular senescence, which causes fundamental changes in the ability of disc cells to maintain the intervertebral disc (IVD) matrix, thus leading to IVD degeneration. Cells isolated from non-degenerate and degenerate human tissue were assessed for mean telomere length, senescence-associated β-galactosidase (SA-β-gal), and replicative potential. Expression of P16
INK4A
(increased in cellular senescence) was also investigated in IVD tissue by means of immunohistochemistry. RNA from tissue and cultured cells was used for real-time polymerase chain reaction analysis for matrix metalloproteinase-13, ADAMTS 5 (a disintegrin and metalloprotease with thrombospondin motifs 5), and P16
INK4A
. Mean telomere length decreased with age in cells from non-degenerate tissue and also decreased with progressive stages of degeneration. In non-degenerate discs, there was an age-related increase in cellular expression of P16
INK4A
. Cells from degenerate discs (even from young patients) exhibited increased expression of P16
INK4A
, increased SA-β-gal staining, and a decrease in replicative potential. Importantly, there was a positive correlation between P16
INK4A
and matrix-degrading enzyme gene expression. Our findings indicate that disc cell senescence occurs in vivo and is accelerated in IVD degeneration. Furthermore, the senescent phenotype is associated with increased catabolism, implicating cellular senescence in the pathogenesis of IVD degeneration.
Cooling and hemodynamic management in heatstroke: practical recommendations
Authors: Bouchama Abderrezak , Dehbi Mohammed , Chaves-Carballo Enrique 
Published: May 2007

Abstract
Introduction
Although rapid cooling and management of circulatory failure are crucial to the prevention of irreversible tissue damage and death in heatstroke, the evidence supporting the optimal cooling method and hemodynamic management has yet to be established.

Methods
A systematic review of all clinical studies published in Medline (1966 to 2006), CINAHL (Cumulative Index to Nursing & Allied Health Literature) (1982 to 2006), and Cochrane Database was performed using the OVID interface without language restriction. Search terms included heatstroke, sunstroke, and heat stress disorders.

Results
Fourteen articles reported populations subjected to cooling treatment for classic or exertional heatstroke and included data on cooling time, neurologic morbidity, or mortality. Five additional articles described invasive monitoring with central venous or pulmonary artery catheters. The four clinical trials and 15 observational studies covered a total of 556 patients. A careful analysis of the results obtained indicated that the cooling method based on conduction, namely immersion in iced water, was effective among young people, military personnel, and athletes with exertional heatstroke. There was no evidence to support the superiority of any one cooling technique in classic heatstroke. The effects of non-invasive, evaporative, or conductive-based cooling techniques, singly or combined, appeared to be comparable. No evidence of a specific endpoint temperature for safe cessation of cooling was found. The circulatory alterations in heatstroke were due mostly to a form of distributive shock associated with relative or absolute hypovolemia. Myocardial failure was found to be rare.

Conclusion
A systematic review of the literature failed to identify reliable clinical data on the optimum treatment of heatstroke. Nonetheless, the findings of this study could serve as a framework for preliminary recommendations in cooling and hemodynamic management of heatstroke until more evidence-based data are generated.
Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, nuclear factor-κB and other signal transcription factors in head and neck squamous cell carcinoma
Authors: Yan Bin , Yang Xinping , Lee Tin-Lap , Friedman Jay , Tang Jun , Van Waes Carter , Chen Zhong 
Published: May 2007

Abstract
Background
Differentially expressed gene profiles have previously been observed among pathologically defined cancers by microarray technologies, including head and neck squamous cell carcinomas (HNSCCs). However, the molecular expression signatures and transcriptional regulatory controls that underlie the heterogeneity in HNSCCs are not well defined.

Results
Genome-wide cDNA microarray profiling of ten HNSCC cell lines revealed novel gene expression signatures that distinguished cancer cell subsets associated with p53 status. Three major clusters of over-expressed genes (A to C) were defined through hierarchical clustering, Gene Ontology, and statistical modeling. The promoters of genes in these clusters exhibited different patterns and prevalence of transcription factor binding sites for p53, nuclear factor-κB (NF-κB), activator protein (AP)-1, signal transducer and activator of transcription (STAT)3 and early growth response (EGR)1, as compared with the frequency in vertebrate promoters. Cluster A genes involved in chromatin structure and function exhibited enrichment for p53 and decreased AP-1 binding sites, whereas clusters B and C, containing cytokine and antiapoptotic genes, exhibited a significant increase in prevalence of NF-κB binding sites. An increase in STAT3 and EGR1 binding sites was distributed among the over-expressed clusters. Novel regulatory modules containing p53 or NF-κB concomitant with other transcription factor binding motifs were identified, and experimental data supported the predicted transcriptional regulation and binding activity.

Conclusion
The transcription factors p53, NF-κB, and AP-1 may be important determinants of the heterogeneous pattern of gene expression, whereas STAT3 and EGR1 may broadly enhance gene expression in HNSCCs. Defining these novel gene signatures and regulatory mechanisms will be important for establishing new molecular classifications and subtyping, which in turn will promote development of targeted therapeutics for HNSCC.
An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
Authors: Okoniewski Michał J , Yates Tim , Dibben Siân , Miller Crispin J 
Published: May 2007

AbstractAffymetrix exon arrays contain probesets intended to target every known and predicted exon in the entire genome, posing significant challenges for high-throughput genome-wide data analysis. X:MAP http://xmap.picr.man.ac.uk, an annotation database, and exonmap http://www.bioconductor.org/packages/2.0/bioc/html/exonmap.html, a BioConductor/R package, are designed to support fine-grained analysis of exon array data. The system supports the application of standard statistical techniques, prior to the use of genome scale annotation to provide gene-, transcript- and exon-level summaries and visualization tools.
Tin-Free Radical Carbon–Carbon Bond-Forming Reactions Based on α-Scission of Alkylsulfonyl Radicals
Authors: Kim Sunggak , Kim Sangmo 
Published: May 2007

Abstract
Tin-free radical reactions based on α-scission of alkylsulfonyl radicals are very useful for the formation of carbon–carbon bonds and include allylation, acylation, cyanation, vinylation, and carbonylation. For secondary, tertiary, and benzylic radicals, it is possible to use the corresponding iodides as precursors but the primary radicals still require the use of phenyl tellurides or alkyl allyl sulfones. Especially, alkyl allyl sulfones are highly efficient and most reliable primary alkyl radical precursors for the further formation of carbon–carbon bonds. The present approach is very useful for introducing various functional groups such as carbonyl and alkenyl groups under tin-free conditions.
Radiation-Induced Cross-Linking of Gelatin by Using γ-Rays: Insoluble Gelatin Hydrogel Formation
Authors: Bessho Masahiko , Kojima Takao , Okuda Shuichi , Hara Masayuki 
Published: May 2007

Abstract
Gelatin hydrogels with various concentrations were cross-linked by the irradiation with 60Co γ-rays, and we investigated the radiation-induced cross-linking of gelatin hydrogels by estimating the physical properties of irradiated hydrogels. In case of the 1, 5, and 10% (w/v) gelatin solutions, the specific water content of the irradiated hydrogels, the index showing the extent of cross-linking depended on the absorbed dose, and that of the irradiated gelatin hydrogels with the lower concentration decreased drastically. The breaking strength correlated to the absorbed dose, irrespective of the initial gelatin concentration. More than 8 kGy irradiation induced insolubility due to the cross-linking of the gelatin hydrogels. Besides, γ-ray irradiation to gelatin with free amino acids revealed that amino acids, which have side chains of hydrocarbon groups that are more than two carbon atoms, obstructed the cross-linking of gelatin hydrogels. It is thought that the hydrocarbon groups, such as an alkyl or a phenyl group of the side chains, are the cross-linking sites of gelatin hydrogels.