bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situ analysis of FOXP3+ regulatory T cells in human colorectal cancer
Authors: Loddenkemper Christoph , Schernus Martin , Noutsias Michel , Stein Harald , Thiel Eckhard , Nagorsen Dirk 
Published: December 2006

AbstractThe immune system spontaneously responds to tumor-associated antigens in peripheral blood of colorectal cancer (CRC) patients. Regulatory T cells (Treg) are suspected of influencing the interaction between the tumor and immune system and thus the course of malignant diseases. However, the function of Tregs in the development of T cell responses and on the clinical course of CRC is not clear. We analyzed Treg infiltration (FOXP3 staining)in situin 40 CRC patients and investigated whether there is a correlation to disease stage, systemic T cell response, and survival. Treg infiltration was significantly higher in CRC than in healthy colon. Stromal Treg infiltration was significantly higher than epithelial infiltration in CRC. Furthermore, Treg infiltration in the tumor was significantly higher in limited disease than in metastatic CRC. The average Treg infiltration rate in the tumor was non-significantly higher in patients without systemic TAA-specific T cell response. Survival did not differ between patients with high Treg infiltration and those with low Treg infiltration. In conclusion, a direct link between Treg infiltration in the tumor and the development of a systemic T cell response in CRC cannot be proven. However, local Treg infiltration was significantly higher in limited disease, in which a systemic TAA-directed T cell responses is less frequently observed.
Effect of extracorporeal liver support by MARS and Prometheus on serum cytokines in acute-on-chronic liver failure
Authors: Stadlbauer Vanessa , Krisper Peter , Aigner Reingard , Haditsch Bernd , Jung Aleksandra , Lackner Carolin , Stauber Rudolf E 
Published: December 2006

Abstract
Introduction
Cytokines are believed to play an important role in acute-on-chronic liver failure (ACLF). Extracorporeal liver support systems may exert beneficial effects in ACLF via removal of cytokines. At present, two systems are commercially available, the Molecular Adsorbent Recirculating System (MARS™) and Fractionated Plasma Separation, Adsorption and Dialysis (Prometheus™). The aim of this study was to compare the effects of MARS and Prometheus treatments on serum cytokine levels and their clearances.

Methods
Eight patients with ACLF underwent alternating treatments with either MARS or Prometheus in a randomized cross-over design. Thirty-four treatments (17 MARS, 17 Prometheus) were available for analysis. Serum cytokines were measured before and after each treatment, and cytokine clearance was calculated from paired arterial and venous samples and effective plasma flow one hour after the start of treatment.

Results
Baseline serum levels of interleukin (IL)-6, IL-8, IL-10, tumor necrosis factor-alpha (TNF-α), and soluble TNF-α receptor 1 were significantly elevated in patients with ACLF. Measurable plasma clearances were detected for all cytokines tested, but no significant changes in serum levels of any cytokine were found after treatments with MARS or Prometheus. In MARS treatments, IL-10 was cleared from plasma more efficiently than IL-6. Clearance of IL-10 was higher in Prometheus than in MARS treatments.

Conclusion
Cytokines are cleared from plasma by both MARS and Prometheus, but neither system is able to change serum cytokine levels. This discrepancy is probably due to a high rate of cytokine production in patients with ACLF.
An environmental signature for 323 microbial genomes based on codon adaptation indices
Authors: Willenbrock Hanni , Friis Carsten , Juncker Agnieszka S , Ussery David W 
Published: December 2006

Abstract
Background
Codon adaptation indices (CAIs) represent an evolutionary strategy to modulate gene expression and have widely been used to predict potentially highly expressed genes within microbial genomes. Here, we evaluate and compare two very different methods for estimating CAI values, one corresponding to translational codon usage bias and the second obtained mathematically by searching for the most dominant codon bias.

Results
The level of correlation between these two CAI methods is a simple and intuitive measure of the degree of translational bias in an organism, and from this we confirm that fast replicating bacteria are more likely to have a dominant translational codon usage bias than are slow replicating bacteria, and that this translational codon usage bias may be used for prediction of highly expressed genes. By analyzing more than 300 bacterial genomes, as well as five fungal genomes, we show that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle, for instance soil bacteria and soil symbionts, spore formers, enteric bacteria, aquatic bacteria, and intercellular and extracellular pathogens.

Conclusion
The results and the approach described here may be used to acquire new knowledge regarding species lifestyle and to elucidate relationships between organisms that are far apart evolutionarily.
At Play on the Borders of the Diegetic: Story Boundaries and Narrative Interpretation
Authors: Mackey Margaret 
Published: December 2006

Working with young readers, aged 10 to 14, as they responded to narrative texts in a variety of media (Mackey, 2002), I observed a recurring phenomenon: In a variety of ways they repeatedly stepped in and out of the fictional universe of their different stories. Some examples will perhaps give the flavor of this experience:Two 14-year-old girls playing Starship Titanic alternate between lively engagement in the narrative world of the story and stepping outside the fiction to console themselves, “Oh well, if we die, we can just start again.” A 10-year-old girl speaks of alternating between the novel and the computer game of My Teacher is an Alien, using the novel as a source of game-playing repertoire. Two 10-year-old boys look at the DVD of the film Contact, learning how the special effects of an explosion scene were composed, and commenting on how their new awareness of scene construction would affect how they view the film in the future.As I recorded and analyzed numerous examples of such behaviors, I was struck by a common element of interpretive activity on the boundaries of the fictional universe. Sensitized to the topic, I began to notice, and then to collect, examples of contemporary texts that foster various forms of such border crossing, in and out of the diegesis, the framework of events as narrated in the text. This article explores how an awareness of this aspect of contemporary texts may enhance our understanding of interpretive processes and expand what happens in literature classes.
Universality and Specificity of Polymer Gels Viewed by Scattering Methods
Authors: Shibayama Mitsuhiro 
Published: December 2006

Abstract
Concentration fluctuations in polymer gels are composed of dynamic thermal fluctuations and frozen inhomogeneities. Particularly, the latter is a characteristic of gels and is due to cross-linking. The frozen inhomogeneities manifest unique properties in polymer gels. Speckle patterns are commonly observed in gels. The time-correlation function of the scattering intensity entails a power-law behavior at the sol–gel transition. The appearance of speckle patterns is related to the nonergodicity of gels, and the power-law behavior corresponds to the self-similarity of clusters at the gelation threshold. In this review, it will be demonstrated that light scattering is one of the most powerful tools for structure characterization of polymer gels. Then, the universality and specificity of polymer gels will be examined for various types of gels, including physical gels, composite gels, and gelators.
Briaexcavatins G and H, Two New Briaranes from the Octocoral Briareum excavatum
Authors: Chen Yu-Pei , Wu Shwu-Li , Su Jui-Hsin , Lin Mei-Ru , Hu Wan-Ping , Hwang Tsong-Long , Sheu Jyh-Horng , Fan Tung-Yung , Fang Lee-Shing , Sung Ping-Jyun 
Published: December 2006

Abstract
Two new briarane-related diterpenoids, designated as briaexcavatins G (1) and H (2), were isolated from the octocoral Briareum excavatum, collected off southern Taiwan coast. The structures, including the absolute stereochemistry of these two new metabolites, were established by spectroscopy and chemical conversion. The configuration of briarane 2 was further supported by molecular mechanics calculations. Briarane 1 showed weak inhibitory effects on human neutrophil elastase release.
Mutual Responses in the Midst of an Era: Aaron Copland's The Tender Land and Leonard Bernstein's Candide
Authors: CRIST ELIZABETH B. 
Published: December 2006

ABSTRACT
Aaron Copland's The Tender Land (1954) and Leonard Bernstein's Candide (1956) both comment sharply on McCarthyism, but their broader political implications are less clear. While the story of each may be read in terms of postwar liberalism, a position itself informed by anticommunist ideology, two crucial ensembles reflect a decidedly leftist perspective. “The Promise of Living,” which ends act 1 of The Tender Land, and “Make Our Garden Grow,” the finale of Candide, celebrate a grand, utopian ideal—the politically outmoded, progessive ideal of community as a collective forged through common experience and shared labor—in musical terms that evoke the era of the Popular Front.
Despite their similarities, however, “The Promise of Living” and “Make Our Garden Grow” arrive at structurally distinct points in their perspective works and announce different dramatic as well as political ends. Ultimately one community comes together while the other falls apart, and these divergent trajectories speak to the experiences of the composers themselves as representatives of separate political generations. Using achival research, cultural history, and music analysis, I argue that at these moments The Tender Land and Candide reject the conservative and liberal anticommunism of their mutual Cold War context to remember or imagine the possibilities of a vital Left.
Homeologous Recombination Plays a Major Role in Chromosome Rearrangements That Occur During Meiosis of Brassica napus Haploids
Authors: Nicolas Stéphane D , Mignon Guillaume Le , Eber Frédérique , Coriton Olivier , Monod Hervé , Clouet Vanessa , Huteau Virginie , Lostanlen Antoine , Delourme Régine , Chalhoub Boulos , Ryder Carol D , Chèvre Anne Marie , Jenczewski Eric 
Published: December 2006

Abstract
Chromosomal rearrangements can be triggered by recombination between distinct but related regions. Brassica napus (AACC; 2n = 38) is a recent allopolyploid species whose progenitor genomes are widely replicated. In this article, we analyze the extent to which chromosomal rearrangements originate from homeologous recombination during meiosis of haploid B. napus (n = 19) by genotyping progenies of haploid × euploid B. napus with molecular markers. Our study focuses on three pairs of homeologous regions selected for their differing levels of divergence (N1/N11, N3/N13, and N9/N18). We show that a high number of chromosomal rearrangements occur during meiosis of B. napus haploid and are transmitted by first division restitution (FDR)-like unreduced gametes to their progeny; half of the progeny of Darmor-bzh haploids display duplications and/or losses in the chromosomal regions being studied. We demonstrate that half of these rearrangements are due to recombination between regions of primary homeology, which represents a 10- to 100-fold increase compared to the frequency of homeologous recombination measured in euploid lines. Some of the other rearrangements certainly result from recombination between paralogous regions because we observed an average of one to two autosyndetic A–A and/or C–C bivalents at metaphase I of the B. napus haploid. These results are discussed in the context of genome evolution of B. napus.
Mitochondrial Genome Sequence Evolution in Chlamydomonas
Authors: Popescu Cristina E , Lee Robert W 
Published: December 2006

Abstract
The mitochondrial genomes of the Chlorophyta exhibit significant diversity with respect to gene content and genome compactness; however, quantitative data on the rates of nucleotide substitution in mitochondrial DNA, which might help explain the origin of this diversity, are lacking. To gain insight into the evolutionary forces responsible for mitochondrial genome diversification, we sequenced to near completion the mitochondrial genome of the chlorophyte Chlamydomonas incerta, estimated the evolutionary divergence between Chlamydomonas reinhardtii and C. incerta mitochondrial protein-coding genes and rRNA-coding regions, and compared the relative evolutionary rates in mitochondrial and nuclear genes. Synonymous and nonsynonymous substitution rates do not differ significantly between the mitochondrial and nuclear protein-coding genes. The mitochondrial rRNA-coding regions, however, are evolving much faster than their nuclear counterparts, and this difference might be explained by relaxed functional constraints on the mitochondrial translational apparatus due to the small number of proteins synthesized in Chlamydomonas mitochondria. Substitution rates at synonymous sites in a nonstandard mitochondrial gene (rtl) and at intronic and synonymous sites in nuclear genes expressed at low levels suggest that the mutation rate is similar in these two genetic compartments. Potential evolutionary forces shaping mitochondrial genome evolution in Chlamydomonas are discussed.
Haplotype Probabilities for Multiple-Strain Recombinant Inbred Lines
Authors: Teuscher Friedrich , Broman Karl W 
Published: December 2006

AbstractRecombinant inbred lines (RIL) derived from multiple inbred strains can serve as a powerful resource for the genetic dissection of complex traits. The use of such multiple-strain RIL requires a detailed knowledge of the haplotype structure in such lines. Broman (2005) derived the two- and three-point haplotype probabilities for 2n-way RIL; the former required hefty computation to infer the symbolic results, and the latter were strictly numerical. We describe a simpler approach for the calculation of these probabilities, which allowed us to derive the symbolic form of the three-point haplotype probabilities. We also extend the two-point results for the case of additional generations of intermating, including the case of 2n-way intermated recombinant inbred populations (IRIP).
Functional Analysis of Gene Duplications in Saccharomyces cerevisiae
Authors: Guan Yuanfang , Dunham Maitreya J , Troyanskaya Olga G 
Published: December 2006

Abstract
Gene duplication can occur on two scales: whole-genome duplications (WGD) and smaller-scale duplications (SSD) involving individual genes or genomic segments. Duplication may result in functionally redundant genes or diverge in function through neofunctionalization or subfunctionalization. The effect of duplication scale on functional evolution has not yet been explored, probably due to the lack of global knowledge of protein function and different times of duplication events. To address this question, we used integrated Bayesian analysis of diverse functional genomic data to accurately evaluate the extent of functional similarity and divergence between paralogs on a global scale. We found that paralogs resulting from the whole-genome duplication are more likely to share interaction partners and biological functions than smaller-scale duplicates, independent of sequence similarity. In addition, WGD paralogs show lower frequency of essential genes and higher synthetic lethality rate, but instead diverge more in expression pattern and upstream regulatory region. Thus, our analysis demonstrates that WGD paralogs generally have similar compensatory functions but diverging expression patterns, suggesting a potential of distinct evolutionary scenarios for paralogs that arose through different duplication mechanisms. Furthermore, by identifying these functional disparities between the two types of duplicates, we reconcile previous disputes on the relationship between sequence divergence and expression divergence or essentiality.
The Evolutionary History of Drosophila buzzatii. XXXVI. Molecular Structural Analysis of Osvaldo Retrotransposon Insertions in Colonizing Populations Unveils Drift Effects in Founder Events
Authors: García Guerreiro María Pilar , Fontdevila Antonio 
Published: December 2006

Abstract
Previous work on transposable element distribution in colonizing populations of Drosophila buzzatii revealed a high frequency of occupancy in several chromosomal sites. Two explanatory hypotheses were advanced: the founder hypothesis, by which founder genetic drift was responsible, and the unstable hypothesis that assigns this unusual distribution to bursts of transposition toward some chromosomal sites. Here, we study the molecular structure of three euchromatic Osvaldo clones isolated from sites occupied at high (A4 and B9) and low frequency (B4) in colonizing populations, to test these hypotheses. Large insertions, duplications, and indels in the Osvaldo coding region and LTR were detected in the A4 clone and a truncated Osvaldo with many substitutions was found in the B9 clone. These altered sequences indicate that the two copies of this retroelement are precolonization insertions. Interestingly, the LTR of the A4 clone and the reverse transcriptase region of B9 show identical sequences in all colonizing populations indicating, most probably, that they are identical by descent. Moreover, Osvaldo is inserted at the same nucleotide site in all colonizing populations. On the other hand an almost identical LTR sequence, except by 1 base deletion, was found in the B4 clone compared to the canonical active Osvaldo element. These results suggest that Osvaldo copies in highly occupied sites are, most probably, identical by descent and strongly favor the founder hypothesis. On the other hand, low-insertion-frequency sites could represent recent transposition events. This work emphasizes the importance of molecular population studies to disentangle the effects of genetic drift and transposition in colonization.
The Overexpression of aSaccharomyces cerevisiaeCentromeric Histone H3 Variant Mutant Protein Leads to a Defect in Kinetochore Biorientation
Authors: Collins Kimberly A , Camahort Raymond , Seidel Chris , Gerton Jennifer L , Biggins Sue 
Published: December 2006

AbstractChromosomes segregate using their kinetochores, the specialized protein structures that are assembled on centromeric DNA and mediate attachment to the mitotic spindle. Because centromeric sequences are not conserved, centromere identity is propagated by an epigenetic mechanism. All eukaryotes contain an essential histone H3 variant (CenH3) that localizes exclusively to centromeres. Because CenH3 is required for kinetochore assembly and is likely to be the epigenetic mark that specifies centromere identity, it is critical to elucidate the mechanisms that assemble and maintain CenH3 exclusively at centromeres. To learn more about the functions and regulation of CenH3, we isolated mutants in the budding yeast CenH3 that are lethal when overexpressed. These CenH3 mutants fall into three unique classes: (I) those that localize to euchromatin but do not alter kinetochore function, (II) those that localize to the centromere and disrupt kinetochore function, and (III) those that no longer target to the centromere but still disrupt chromosome segregation. We found that a class III mutant is specifically defective in the ability of sister kinetochores to biorient and attach to microtubules from opposite spindle poles, indicating that CenH3 mutants defective in kinetochore biorientation can be obtained.
Sap1 Promotes the Association of the Replication Fork Protection Complex With Chromatin and Is Involved in the Replication Checkpoint in Schizosaccharomyces pombe
Authors: Noguchi Chiaki , Noguchi Eishi 
Published: December 2006

Abstract
Sap1 is involved in replication fork pausing at rDNA repeats and functions during mating-type switching in Schizosaccharomyces pombe. These two roles are dependent on the ability of Sap1 to bind specific DNA sequences at the rDNA and mating-type loci, respectively. In S. pombe, Swi1 and Swi3 form the replication fork protection complex (FPC) and play important roles in the activation of the replication checkpoint and the stabilization of stalled replication forks. Here we describe the roles of Sap1 in the replication checkpoint. We show that Sap1 is involved in the activation of the replication checkpoint kinase Cds1 and that sap1 mutant cells accumulate spontaneous DNA damage during the S- and G2-phases, which is indicative of fork damage. We also show that sap1 mutants have a defect in the resumption of DNA replication after fork arrest. Sap1 is localized at the replication origin ori2004 and this localization is required for the association of the FPC with chromatin. We propose that Sap1 is required to recruit the FPC to chromatin, thereby contributing to the activation of the replication checkpoint and the stabilization of replication forks.
Xlf1 Is Required for DNA Repair by Nonhomologous End Joining in Schizosaccharomyces pombe
Authors: Cavero Santiago , Chahwan Charly , Russell Paul 
Published: December 2006

Abstract
The accurate repair of DNA double-strand breaks is essential for cell survival and maintenance of genome integrity. Here we describe xlf1+, a gene in the fission yeast Schizosaccharomyces pombe that is required for repair of double-strand breaks by nonhomologous end joining during G1 phase of the cell cycle. Xlf1 is the ortholog of budding yeast Nej1 and human XLF/Cernunnos proteins.
Exploratory Activity in Drosophila Requires thekurtzNonvisual Arrestin
Authors: Liu Lingzhi , Davis Ronald L , Roman Gregg 
Published: December 2006

AbstractWhen Drosophila adults are placed into an open field arena, they initially exhibit an elevated level of activity followed by a reduced stable level of spontaneous activity. We have found that the initial elevated component arises from the fly's interaction with the novel arena since: (1) the increased activity is independent of handling prior to placement within the arena, (2) the fly's elevated activity is proportional to the size of the arena, and (3) the decay in activity to spontaneous levels requires both visual and olfactory input. These data indicate that active exploration is the major component of elevated initial activity. There is a specific requirement for the kurtz nonvisual arrestin in the nervous system for both the exploration stimulated by the novel arena and the mechanically stimulated activity. kurtz is not required for spontaneous activity; kurtz mutants display normal levels of spontaneous activity and average the same velocities as wild-type controls. Inhibition of dopamine signaling has no effect on the elevated initial activity phase in either wild-type or krz1 mutants. Therefore, the exploratory phase of open field activity requires kurtz in the nervous system, but is independent of dopamine's stimulation of activity.