bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smoking, quitting and mortality in an elderly cohort of 56 000 Hong Kong Chinese
Authors: Lam Tai Hing , Li Zhi Bin , Ho Sai Yin , Chan Wai Man , Ho Kin Sang , Tham May Ked , Cowling Benjamin J , Schooling C Mary , Leung Gabriel M 
Published: June 2007

Background:Although the harms of smoking are well established, it is unclear how they extend into old age in the Chinese.Aim:To examine the relationship of smoking with all-cause and major cause-specific mortality in elderly Chinese men and women, respectively, in Hong Kong.Methods:Mortality by smoking status was examined in a prospective cohort study of 56 167 (18 749 men, 37 416 women) Chinese aged ⩾65 years enrolled from 1998 to 2000 at all the 18 elderly health centres of the Hong Kong Government Department of Health.Results:After a mean follow-up of 4.1 years, 1848 male and 2035 female deaths occured among 54 214 subjects (96.5% successful follow-up). At baseline, more men than women were current smokers (20.3% vs 4.0%) and former smokers (40.8% vs 7.9%). The adjusted RRs (95% CI) for all-cause mortality in former and current smokers, compared with never smokers, were 1.39 (1.23 to 1.56) and 1.75 (1.53 to 2.00) in men and 1.43 (1.25 to 1.64) and 1.38 (1.14 to 1.68) in women, respectively. For current smokers, the RRs (95% CI) for all-cause mortality were 1.59 (1.39 to 1.82), 1.72 (1.48 to 2.00) and 1.84 (1.43 to 2.35) for daily consumption of 1–9, 10–20 and >21 cigarettes, respectively (p for trend <0.001). RRs (95% CI) were 1.49 (1.30 to 1.72) and 2.20 (1.88 to 2.57) in former and current smokers for all deaths from cancer, and 1.24 (1.04 to 1.47) and 1.57 (1.28 to 1.94) for all cardiovascular deaths, respectively. Quitters had significantly lower risks of death than current smokers from all causes, lung cancer, all cancers, stroke and all cardiovascular diseases.Conclusions:In old age, smoking continues to be a major cause of death, and quitting is beneficial. Smoking cessation is urgently needed in rapidly ageing populations in the East.
Changes in smoking prevalence in Ukraine in 2001–5
Authors: Andreeva Tatiana I , Krasovsky Konstantin S 
Published: June 2007

Objectives:To analyse trends in smoking prevalence in Ukraine from three surveys conducted in 2001–5, and to explore correlates of observed changes, in order to estimate the stage of tobacco epidemic in Ukraine.Design:Repeated national interview surveys in Ukraine in 2001, 2002 and 2005.Main outcome measure:Prevalence of current smoking among the population aged ⩾15 years.Results:The age-standardised prevalence of current smoking in Ukrainian men was 54.8% in 2001 and 66.8% in 2005. Among Ukrainian women, prevalence increased from 11.5% in 2001 to 20.0% in 2005. ORs for yearly increase in prevalence were estimated as 1.164 (95% CI 1.111 to 1.220) for men and 1.187 (1.124 to 1.253) for women, which implies that, on average, 3–4% of men and 1.5–2% of women living in Ukraine join the smoking population each year.Conclusions:In Ukraine, smoking prevalence is increasing in most population groups. Among men, the medium deprivation group with secondary education has the highest smoking prevalence. Among women, while the most educated, young and those living in larger cities are the leading group for tobacco use, other groups are also increasing their tobacco use. Tobacco promotion efforts appear to have been significantly more effective in Ukraine than smoking control efforts. The decrease in real cigarette prices in Ukraine in 2001–5 could be the main factor explaining the recent growth in smoking prevalence.
A GALLERY OF CHUA ATTRACTORS: PART IV
Authors: BILOTTA ELEONORA , DI BLASI GIANPIERO , STRANGES FAUSTO , PANTANO PIETRO 
Published: June 2007

The literature on Chua Oscillator includes more than a thousand papers, describing an astonishing variety of chaotic behavior. Gallery of Chua attractors, Part IV presents a collection of 101, previously unknown attractors, generated by a generalization of Chua circuit with a smooth nonlinear function. The gallery is the result of an extensive exploration of the parameter space for Chua cubic system, in which we used PCA and Hausdorf Distances to guide us. During this exploration we sensed the beauty of the chaotic patterns and recorded this beauty for the nonlinear community. The attractors we describe here represent only a small proportion of those we discovered during our exploration of phase space: much intensive research remains to be done. However, the very number of attractors we found suggests it might be possible not only to detect the morphogenetic processes which determine the points in phase space ("catastrophe points") where a family of attractors disappears and another one comes to life, but to identify more general "laws of morphogenesis" governing the behavior of these systems. In this paper, we outline five such rules.
BIPHASIC OPTICAL SIGNAL OF AN OSCILLATING NONSTATIONARY BELOUSOV–ZHABOTINSKY BULK REACTION AND ITS SIMILARITY TO SOME NEUROPHYSIOLOGICAL EVENTS
Authors: DOLZMANN K. , KALTENBACH S. , HANKE W. , FERNANDES DE LIMA V. M. 
Published: June 2007

Oscillating chemical bulk reactions of the Belousov–Zhabotinsky (BZ) type usually show a well-defined periodical color change representing the underlying chemical reactions. Models including up to more than 50 coupled reactions have been developed to describe the BZ-reaction in detail, however, typically a much simpler set of equations is used (i.e. the Brüsselator, the FKN, or the FitzHugh–Nagumo model). There are various types of oscillating reactions with color changes, for example, from transparent to yellow ( Ce catalyzed), or from blue to red (Ferroin catalyzed). In equilibrium systems and in models each color-change is usually a simple curve with one maximum, and the oscillation is stable in time. We have investigated the detailed structure of the intrinsic optical signal (IOS) of a BZ-reaction in-depth andfound, in a nonstationary ferroin catalyzed BZ-reaction, a much more complex optical behavior. Amazingly, this IOS with its detailed time dependence very much resembles electrical and optical signals from important neuronal processes. These are especially the sodium current during action potentials (AP) and the retinal spreading depression (SD). The time-scale of all these processes can be different by decades. This principal similarity, however, points to a deeper common theoretical basis of all these processes as assumed up to now, and makes the presented type of BZ-reaction an ideal model for a variety of neurophysiological signals, although the mechanisms are strictly different.
Neutrophils efficiently cross-prime naive T cells in vivo
Authors: Beauvillain Céline , Delneste Yves , Scotet Mari , Peres Audrey , Gascan Hugues , Guermonprez Pierre , Barnaba Vincenzo , Jeannin Pascale 
Published: June 2007

Abstract
Neutrophils are professional phagocytes that migrate early, in high number, to the infection sites. Our study has analyzed how neutrophils cross-present antigens and influence CD8+ T-cell responses. By using highly purified neutrophils from peritoneal exudates and bone marrow, we have shown that neutrophils cross-present ovalbumin to a CD8+ T-cell hybridoma and to naive CD8+ T cells from OT1 transgenic mice. Cross-presentation by neutrophils was TAP and proteasome dependent and was as efficient as in macrophages. Moreover, it actually occurred earlier than in professional antigen-presenting cells. Peritoneal exudate neutrophils from mice injected intraperitoneally with ovalbumin also cross-presented ovalbumin, proving that neutrophils take up and present exogenous antigens into major histocompatibility complex I (MHC I) molecules in vivo. We then evaluated the in vivo influence of antigen cross-presentation by neutrophils on CD8+ T-cell response using β2-microglobulin-deficient mice transferred with OT1 CD8+ T cells and injected with ovalbumin-pulsed neutrophils. Four days after neutrophil injection, OT1 cells proliferated and expressed effector functions (IFN-γ production and cytolysis). They also responded efficiently to a rechallenge with ovalbumin-pulsed dendritic cells in CFA. These data are the first demonstration that neutrophils cross-prime CD8+ T cells in vivo and suggest that they may constitute, together with professional antigen-presenting cells, an attractive target to induce cytotoxic T cells in vaccines.
A phase 1 clinical-laboratory study of clofarabine followed by cyclophosphamide for adults with refractory acute leukemias
Authors: Karp Judith E. , Ricklis Rebecca M. , Balakrishnan Kumudha , Briel Janet , Greer Jacqueline , Gore Steven D. , Smith B. Douglas , McDevitt Michael A. , Carraway Hetty , Levis Mark J. , Gandhi Varsha 
Published: June 2007

AbstractClofarabine has shown impressive response rates in patients with acute leukemias. In vitro investigations with clofarabine in combination with cyclophosphamide in primary cells have demonstrated synergistic cytotoxicity and inhibition of DNA repair. Based on these clinical and laboratory observations, we designed a mechanism-based combination protocol with clofarabine and cyclophosphamide for patients with relapsed acute leukemias. Eighteen patients were treated with cyclophosphamide (200 mg/m2) alone on day 0 and with clofarabine plus cyclophosphamide on day 1. Clinical responses, toxicity, DNA damage measured as H2AX phosphorylation, and accumulation of clofarabine triphosphate (TP) were analyzed. At dose level 1 (20 mg/m2 clofarabine + cyclophosphamide, 6 patients) and dose level 0 (10 mg/m2 clofarabine + cyclophosphamide, 12 patients) overall response rates were 50% and 30%, respectively, with responses in 4 (67%) of 6 patients with refractory acute lymphoblastic leukemia. Dose-limiting toxicity occurred at dose level 1 with prolonged marrow aplasia. Four (22%) patients died from prolonged aplasia (1), fungal pneumonia (1), or multiorgan failure (2). In 12 of 13 patient samples, increased DNA damage (γH2AX) was observed with clofarabine and cyclophosphamide compared with cyclophosphamide alone. In conclusion, pharmacodynamic end points along with clinical results suggest usefulness of this combination strategy, whereas toxicity data suggest reduction in chemotherapeutic intensity. This clinical trial is registered with the National Cancer Institute's PDQ at www.clinicaltrials.gov as no. JHOC-J0561.
Transcriptome changes and cAMP oscillations in an archaeal cell cycle
Authors: Baumann Anke , Lange Christian , Soppa Jörg 
Published: June 2007

Abstract

Background
The cell cycle of all organisms includes mass increase by a factor of two, replication of the genetic material, segregation of the genome to different parts of the cell, and cell division into two daughter cells. It is tightly regulated and typically includes cell cycle-specific oscillations of the levels of transcripts, proteins, protein modifications, and signaling molecules. Until now cell cycle-specific transcriptome changes have been described for four eukaryotic species ranging from yeast to human, but only for two prokaryotic species. Similarly, oscillations of small signaling molecules have been identified in very few eukaryotic species, but not in any prokaryote.

Results
A synchronization procedure for the archaeon Halobacterium salinarum was optimized, so that nearly 100% of all cells divide in a time interval that is 1/4th of the generation time of exponentially growing cells. The method was used to characterize cell cycle-dependent transcriptome changes using a genome-wide DNA microarray. The transcript levels of 87 genes were found to be cell cycle-regulated, corresponding to 3% of all genes. They could be clustered into seven groups with different transcript level profiles. Cluster-specific sequence motifs were detected around the start of the genes that are predicted to be involved in cell cycle-specific transcriptional regulation. Notably, many cell cycle genes that have oscillating transcript levels in eukaryotes are not regulated on the transcriptional level in H. salinarum.
Synchronized cultures were also used to identify putative small signaling molecules. H. salinarum was found to contain a basal cAMP concentration of 200 μM, considerably higher than that of yeast. The cAMP concentration is shortly induced directly prior to and after cell division, and thus cAMP probably is an important signal for cell cycle progression.

Conclusion
The analysis of cell cycle-specific transcriptome changes of H. salinarum allowed to identify a strategy of transcript level regulation that is different from all previously characterized species. The transcript levels of only 3% of all genes are regulated, a fraction that is considerably lower than has been reported for four eukaryotic species (6% – 28%) and for the bacterium C. crescentus (19%).
It was shown that cAMP is present in significant concentrations in an archaeon, and the phylogenetic profile of the adenylate cyclase indicates that this signaling molecule is widely distributed in archaea. The occurrence of cell cycle-dependent oscillations of the cAMP concentration in an archaeon and in several eukaryotic species indicates that cAMP level changes might be a phylogenetically old signal for cell cycle progression.
Glycosylation, transport, and complex formation of palmitoyl protein thioesterase 1 (PPT1) – distinct characteristics in neurons
Authors: Lyly Annina , von Schantz Carina , Salonen Tarja , Kopra Outi , Saarela Jani , Jauhiainen Matti , Kyttälä Aija , Jalanko Anu 
Published: June 2007

Abstract

Background
Neuronal ceroid lipofuscinoses (NCLs) are collectively the most common type of recessively inherited childhood encephalopathies. The most severe form of NCL, infantile neuronal ceroid lipofuscinosis (INCL), is caused by mutations in the CLN1 gene, resulting in a deficiency of the lysosomal enzyme, palmitoyl protein thioesterase 1 (PPT1). The deficiency of PPT1 causes a specific death of neocortical neurons by a mechanism, which is currently unclear. To understand the function of PPT1 in more detail, we have further analyzed the basic properties of the protein, especially focusing on possible differences in non-neuronal and neuronal cells.

Results
Our study shows that the N-glycosylation of N197 and N232, but not N212, is essential for PPT1's activity and intracellular transport. Deglycosylation of overexpressed PPT1 produced in neurons and fibroblasts demonstrates differentially modified PPT1 in different cell types. Furthermore, antibody internalization assays showed differences in PPT1 transport when compared with a thoroughly characterized lysosomal enzyme aspartylglucosaminidase (AGA), an important observation potentially influencing therapeutic strategies. PPT1 was also demonstrated to form oligomers by size-exclusion chromatography and co-immunoprecipitation assays. Finally, the consequences of disease mutations were analyzed in the perspective of our new results, suggesting that the mutations increase both the degree of glycosylation of PPT1 and its ability to form complexes.

Conclusion
Our current study describes novel properties for PPT1. We observe differences in PPT1 processing and trafficking in neuronal and non-neuronal cells, and describe for the first time the ability of PPT1 to form complexes. Understanding the basic characteristics of PPT1 is fundamental in order to clarify the molecular pathogenesis behind neurodegeneration in INCL.
A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer
Authors: Rogers Matthew B , Watkins Russell F , Harper James T , Durnford Dion G , Gray Michael W , Keeling Patrick J 
Published: June 2007

Abstract

Background
Lateral gene transfer is increasingly invoked to explain phylogenetic results that conflict with our understanding of organismal relationships. In eukaryotes, the most common observation interpreted in this way is the appearance of a bacterial gene (one that is not clearly derived from the mitochondrion or plastid) in a eukaryotic nuclear genome. Ideally such an observation would involve a single eukaryote or a small group of related eukaryotes encoding a gene from a specific bacterial lineage.

Results
Here we show that several apparently simple cases of lateral transfer are actually more complex than they originally appeared: in these instances we find that two or more distantly related eukaryotic groups share the same bacterial gene, resulting in a punctate distribution. Specifically, we describe phylogenies of three core carbon metabolic enzymes: transketolase, glyceraldehyde-3-phosphate dehydrogenase and ribulose-5-phosphate-3-epimerase. Phylogenetic trees of each of these enzymes includes a strongly-supported clade consisting of several eukaryotes that are distantly related at the organismal level, but whose enzymes are apparently all derived from the same lateral transfer. With less sampling any one of these examples would appear to be a simple case of bacterium-to-eukaryote lateral transfer; taken together, their evolutionary histories cannot be so simple. The distributions of these genes may represent ancient paralogy events or genes that have been transferred from bacteria to an ancient ancestor of the eukaryotes that retain them. They may alternatively have been transferred laterally from a bacterium to a single eukaryotic lineage and subsequently transferred between distantly related eukaryotes.

Conclusion
Determining how complex the distribution of a transferred gene is depends on the sampling available. These results show that seemingly simple cases may be revealed to be more complex with greater sampling, suggesting many bacterial genes found in eukaryotic genomes may have a punctate distribution.
Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation
Authors: Mägi Reedik , Pfeufer Arne , Nelis Mari , Montpetit Alexandre , Metspalu Andres , Remm Maido 
Published: June 2007

Abstract

Background
New technologies have enabled genome-wide association studies to be conducted with hundreds of thousands of genotyped SNPs. Several different first-generation genome-wide panels of SNPs have been commercialized. The total amount of common genetic variation is still unknown; however, the coverage of commercial panels can be evaluated against reference population samples genotyped by the International HapMap project. Less information is available about coverage in samples from other populations.

Results
In this study we compare four commercial panels: the HumanHap 300 and HumanHap 550 Array Sets from the Illumina Infinium series and the Mapping 100 K and Mapping 500 K Array Sets from the Affymetrix GeneChip series. Tagging performance is compared among HapMap CEPH (CEU), Asian (JPT, CHB) and Yoruba (YRI) population samples. It is also evaluated in an Estonian population sample with more than 1000 individuals genotyped in two 500-kbp ENCODE regions of chromosome 2: ENr112 on 2p16.3 and ENr131 on 2p37.1.

Conclusion
We found that in a non-reference Caucasian population, commercial SNP panels provide levels of coverage similar to those in the HapMap CEPH population sample. We present the proportions of universal and population-specific SNPs in all the commercial platforms studied.
Evolutionary implications of inversions that have caused intra-strand parity in DNA
Authors: Okamura Kohji , Wei John , Scherer Stephen W 
Published: June 2007

Abstract

Background
Chargaff's rule of DNA base composition, stating that DNA comprises equal amounts of adenine and thymine (%A = %T) and of guanine and cytosine (%C = %G), is well known because it was fundamental to the conception of the Watson-Crick model of DNA structure. His second parity rule stating that the base proportions of double-stranded DNA are also reflected in single-stranded DNA (%A = %T, %C = %G) is more obscure, likely because its biological basis and significance are still unresolved. Within each strand, the symmetry of single nucleotide composition extends even further, being demonstrated in the balance of di-, tri-, and multi-nucleotides with their respective complementary oligonucleotides.

Results
Here, we propose that inversions are sufficient to account for the symmetry within each single-stranded DNA. Human mitochondrial DNA does not demonstrate such intra-strand parity, and we consider how its different functional drivers may relate to our theory. This concept is supported by the recent observation that inversions occur frequently.

Conclusion
Along with chromosomal duplications, inversions must have been shaping the architecture of genomes since the origin of life.
Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence
Authors: Gundogdu Ozan , Bentley Stephen D , Holden Matt T , Parkhill Julian , Dorrell Nick , Wren Brendan W 
Published: June 2007

Abstract

Background

Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. The original annotation was a milestone in Campylobacter research, but is outdated. We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation.

Results
Re-annotation was carried out using sequence database searches such as FASTA, along with programs such as TMHMM for additional support. The re-annotation also utilises sequence data from additional Campylobacter strains and species not available during the original annotation. Re-annotation was accompanied by a full literature search that was incorporated into the updated EMBL file [EMBL: AL111168]. The C. jejuni NCTC11168 re-annotation reduced the total number of coding sequences from 1654 to 1643, of which 90.0% have additional information regarding the identification of new motifs and/or relevant literature. Re-annotation has led to 18.2% of coding sequence product functions being revised.

Conclusions
Major updates were made to genes involved in the biosynthesis of important surface structures such as lipooligosaccharide, capsule and both O- and N-linked glycosylation. This re-annotation will be a key resource for Campylobacter research and will also provide a prototype for the re-annotation and re-interpretation of other bacterial genomes.
Autocorrelation analysis reveals widespread spatial biases in microarray experiments
Authors: Koren Amnon , Tirosh Itay , Barkai Naama 
Published: June 2007

AbstractBackgroundDNA microarrays provide the ability to interrogate multiple genes in a single experiment and have revolutionized genomic research. However, the microarray technology suffers from various forms of biases and relatively low reproducibility. A particular source of false data has been described, in which non-random placement of gene probes on the microarray surface is associated with spurious correlations between genes.ResultsIn order to assess the prevalence of this effect and better understand its origins, we applied an autocorrelation analysis of the relationship between chromosomal position and expression level to a database of over 2000 individual yeast microarray experiments. We show that at least 60% of these experiments exhibit spurious chromosomal position-dependent gene correlations, which nonetheless appear in a stochastic manner within each experimental dataset. Using computer simulations, we show that large spatial biases caused in the microarray hybridization step and independently of printing procedures can exclusively account for the observed spurious correlations, in contrast to previous suggestions. Our data suggest that such biases may generate more than 15% false data per experiment. Importantly, spatial biases are expected to occur regardless of microarray design and over a wide range of microarray platforms, organisms and experimental procedures.ConclusionsSpatial biases comprise a major source of noise in microarray studies; revision of routine experimental practices and normalizations to account for these biases may significantly and comprehensively improve the quality of new as well as existing DNA microarray data.