bluuebunny/crossref_metadata_2025_split huggingface dataset:
FcγRIIB signals inhibit BLyS signaling and BCR-mediated BLyS receptor up-regulation
Authors: Crowley Jenni E. , Stadanlick Jason E. , Cambier John C. , Cancro Michael P. 
Published: September 2008

AbstractThese studies investigate how interactions between the BCR and FcγRIIB affect B lymphocyte stimulator (BLyS) recep-tor expression and signaling. Previous studies showed that BCR ligation up-regulates BLyS binding capacity in mature B cells, reflecting increased BLyS receptor levels. Here we show that FcγRIIB coaggregation dampens BCR-induced BLyS receptor up-regulation. This cross-regulation requires BCR and FcγRIIB coligation, and optimal action relies on the Src-homology-2 (SH2)–containing inositol 5 phosphase-1 (SHIP1). Subsequent to FcγRIIB/BCR coaggregation, the survival promoting actions of BLyS are attenuated, reflecting reduced BLyS receptor signaling capacity in terms of Pim 2 maintenance, noncanonical NF-κB activation, and Bcl-xL levels. These findings link the negative regulatory functions of FcγRIIB with BLyS-mediated B-cell survival.
Management of anticoagulation in patients with subacute heparin-induced thrombocytopenia scheduled for heart transplantation
Authors: Selleng Sixten , Haneya Assad , Hirt Stephan , Selleng Kathleen , Schmid Christof , Greinacher Andreas 
Published: September 2008

AbstractAnticoagulation management of patients with recent heparin-induced thrombocytopenia (HIT) requiring cardiopulmonary bypass (CPB) surgery is a serious challenge, and especially difficult in patients requiring urgent heart transplantation. As nonheparin anticoagulants during CPB bear a high risk of major bleeding, these patients are at risk of being taken off the transplant list. Short-term use of unfractionated heparin (UFH) for CPB, with restriction of UFH to the surgery itself, is safe and effective in patients with a history of HIT who test negative for antiplatelet factor 4 (PF4)/heparin antibodies. We present evidence that it is safe to expand the concept of UFH reexposure to patients with subacute HIT (ie, those patients with recent HIT in whom the platelet count has recovered but in whom anti-PF4/heparin IgG antibodies remain detectable) requiring heart transplantation, if they test negative by a sensitive functional assay using washed platelets. This can be lifesaving in patients with end-stage heart failure.
Investigation of hydrogen abstraction from methyl glucoside by active oxygen species under oxygen delignification conditions. Part 1: Study on the anomeric position
Authors: Konishi Fumiko , Yokoyama Tomoya , Matsumoto Yuji 
Published: September 2008

Abstract
We investigated whether active oxygen species (AOS) abstract the anomeric hydrogen from a carbohydrate model compound, methyl β-d-glucopyranoside (MGPβ) under conditions simulating oxygen delignification in pulp and paper mills (0.5 mol l-1 NaOH, 0.36 mmol l-1 Fe3+, 1.1 MPa O2, 95°C). The simulation involved in situ AOS generation by reaction of 2,4,6-trimethylphenol with O2, so that various types of AOS were operative in the system. MGPβ was degraded slightly more than methyl α-d-glucopyranoside (MGPα) when they were jointly reacted with AOS. Thus, we suggest that the configurational difference in their anomeric positions has some effects on their reactions with AOS. When MGPβ and methyl β-d-(1-2
H)glucopyranoside (MGPβ-1D) were jointly reacted with AOS, MGPβ was degraded slightly more than MGPβ-1D. This difference results from the kinetic isotope effect, indicating that the anomeric hydrogen of MGPβ is undoubtedly abstracted by AOS, although the contribution of this abstraction to the overall degradation of MGPβ has not been clarified yet. MGPβ and MGPβ-1D were also jointly subjected to alkaline hydrogen peroxide treatment (0.5 mol l-1 NaOH, 0.36 mmol l-1 Fe3+, 95°C) in which the oxyl anion radical (O-·), the conjugate base of hydroxyl radical (HO·), is likely only one of the AOS to degrade these compounds. Since no difference in degradation was observed, some AOS other than O-· must participate in anomeric hydrogen abstraction from MGPβ in these oxygen-alkali treatments. When MGPα and methyl α-d-(1-2
H)glucopyranoside were jointly reacted with AOS, almost no difference in degradation was observed. This result suggests that abstraction of the anomeric hydrogen from MGPα by AOS is no more than a very minor reaction. It was confirmed that the anomeric hydrogen of MGPβ is activated towards AOS reaction owing to the anomeric effect, which is in fact a stereoelectronic effect.
Hydrolytic stability of water-soluble spruce O-acetyl galactoglucomannans
Authors: Xu Chunlin , Pranovich Andrey , Hemming Jarl , Holmbom Bjarne , Albrecht Simone , Schols Henk A. , Willför Stefan 
Published: September 2008

Abstract
Water-soluble native O-acetyl galactoglucomannan (GGM) from spruce is a polysaccharide that can be produced in an industrial scale. To develop GGM applications, information is needed on its stability, particularly under acidic conditions. Therefore, acid hydrolysis of spruce GGM was investigated at various pH levels and temperatures. The results allow an estimation of the stability of GGM under food processing conditions and in biological systems. Determination of the average molar mass demonstrated that spruce GGM was stable at pH 1 and 37°C, as well as at pH 3 and 70°C. GGM was hydrolysed at pH 1 and 90°C. GGM oligomers and monomers were detected after degradation. Some of the oligomers contained O-acetyl groups. Monosaccharides were the predominant products in the hydrolysates after treatment at pH 1 and 90°C for 48 h. Pentoses, present in GGM samples as impurities, were released more easily than GGM hexoses. Glucose was more difficult to release than mannose. Traces of 6-deoxy-mannose and levoglucosan were found in the hydrolysates, indicating further degradation of hydrolysed monosaccharides.
Staatliche Institution und innergemeindlicher Diskurs: Politische Entscheidungsfindung in Sparta? (State Institutions and Discourse within the Community: Political Decision Making in Sparta?)
Authors: Link Stefan 
Published: September 2008

Zusammenfassung
Die Studie fragt nach den Möglichkeiten und Grenzen politischer Entscheidungsfindung in Sparta. Anhand verschiedener Beispiele arbeitet sie heraus, daß die Spartaner Prozesse einer gemeinschaftlichen Willensbildung nach Möglichkeit umgingen und folglich dazu neigten, politische Entscheidungen zu verzögern oder überhaupt zu vermeiden; war das nicht möglich, argumentierten sie gerne auf irgendeiner nicht-politischen Ebene und beschlossen daher nach sachfremden Erwägungen.
Als Grund für diesen Charakterzug spartanischer Politik wird auf den Zuschnitt der wichtigsten spartanischen Institutionen (und zwar insbesondere den des Doppelkönigtums und den des Ephorats) verwiesen: Offensichtlich war nicht ein einziges dieser Verfassungsorgane mit Blick auf die Frage ins Leben gerufen oder ausgestaltet worden, ob und wie es zu einer geordneten politischen Willensbildung im öffentlichen Raum beitragen könnte. Diesem Befund entspricht, daß auch die Frage, wie die verschiedenen staatlichen Institutionen untereinander interagieren sollten, bis zum Ende der spartanischen Geschichte ungelöst blieb.
Die schon in der Antike sehr bewunderte Stabilität des spartanischen Staates erscheint aus diesem Blickwinkel eher als das Ergebnis von Agonie denn als das Resultat eines bewußten und gewollten Konservatismus.
Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution
Authors: Durrett Rick , Schmidt Deena 
Published: September 2008

AbstractResults of Nowak and collaborators concerning the onset of cancer due to the inactivation of tumor suppressor genes give the distribution of the time until some individual in a population has experienced two prespecified mutations and the time until this mutant phenotype becomes fixed in the population. In this article we apply these results to obtain insights into regulatory sequence evolution in Drosophila and humans. In particular, we examine the waiting time for a pair of mutations, the first of which inactivates an existing transcription factor binding site and the second of which creates a new one. Consistent with recent experimental observations for Drosophila, we find that a few million years is sufficient, but for humans with a much smaller effective population size, this type of change would take &gt;100 million years. In addition, we use these results to expose flaws in some of Michael Behe's arguments concerning mathematical limits to Darwinian evolution.
Distributions of Hardy–Weinberg Equilibrium Test Statistics
Authors: Rohlfs R V , Weir B S 
Published: September 2008

AbstractIt is well established that test statistics and P-values derived from discrete data, such as genetic markers, are also discrete. In most genetic applications, the null distribution for a discrete test statistic is approximated with a continuous distribution, but this approximation may not be reasonable. In some cases using the continuous approximation for the expected null distribution may cause truly null test statistics to appear nonnull. We explore the implications of using continuous distributions to approximate the discrete distributions of Hardy–Weinberg equilibrium test statistics and P-values. We derive exact P-value distributions under the null and alternative hypotheses, enabling a more accurate analysis than is possible with continuous approximations. We apply these methods to biological data and find that using continuous distribution theory with exact tests may underestimate the extent of Hardy–Weinberg disequilibrium in a sample. The implications may be most important for the widespread use of whole-genome case–control association studies and Hardy–Weinberg equilibrium (HWE) testing for data quality control.
The Genetic Architecture of Complex Traits in Teosinte (Zea maysssp.parviglumis): New Evidence From Association Mapping
Authors: Weber Allison L , Briggs William H , Rucker Jesse , Baltazar Baltazar M , de Jesús Sánchez-Gonzalez José , Feng Ping , Buckler Edward S , Doebley John 
Published: September 2008

AbstractPrevious association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for association with 31 traits in a population of 817 individuals. Thirty-three significant associations for markers from 15 candidate genes and 10 traits survive correction for multiple testing. Our analyses suggest several new putative causative relationships between specific genes and trait variation in teosinte. For example, two ramosa genes (ra1 and ra2) associate with ear structure, and the MADS-box gene, zagl1, associates with ear shattering. Since zagl1 was previously shown to be a target of selection during maize domestication, we suggest that this gene was under selection for its effect on the loss of ear shattering, a key domestication trait. All observed effects were relatively small in terms of the percentage of phenotypic variation explained (&lt;10%). We also detected several epistatic interactions between markers in the same gene that associate with the same trait. Candidate-gene-based association mapping appears to be a promising method for investigating the inheritance of complex traits in teosinte.
Optimal Design of Genetic Studies of Gene Expression With Two-Color Microarrays in Outbred Crosses
Authors: Lam Alex C , Fu Jingyuan , Jansen Ritsert C , Haley Chris S , de Koning Dirk-Jan 
Published: September 2008

Abstract
Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes. Efficient use of microarrays is paramount in experimental design as the cost of conducting this type of study is high. For those organisms where recombinant inbred lines are available for mapping, the “distant pair design” maximizes the number of informative contrasts over all marker loci. Here, we describe an extension of this design, named the “optimal pair design,” for use with F2 crosses between outbred lines. The performance of this design is investigated by simulation and compared to several other two-color microarray designs. We show that, for a given number of microarrays, the optimal pair design outperforms all other designs considered for detection of expression quantitative trait loci (eQTL) with additive effects by linkage analysis. We also discuss the suitability of this design for outbred crosses in organisms with large genomes and for detection of dominance.
Identification of Single-Nucleotide Polymorphism in the Progesterone Receptor Gene and Its Association With Reproductive Traits in Rabbits
Authors: Peiró R , Merchán M , Santacreu M A , Argente M J , García M L , Folch J M , Blasco A 
Published: September 2008

Abstract
A total of 598 F2 does from a cross between the high and low lines selected divergently for uterine capacity during 10 generations were used in a candidate gene analysis. The presence of major genes affecting the number of implanted embryos and uterine capacity has been suggested in lines divergently selected for uterine capacity. Uterine capacity is a main component of litter size. The progesterone receptor gene was tested as a candidate gene to determine whether polymorphisms explain differences in litter size and its components. Fragments of the promoter region and exons 1–8 were amplified and sequenced. One SNP was found in the promoter region, 2464G&gt;A, three SNPs in the 5′-UTR exon 1, and a silence SNP in exon 7. The first four SNPs were segregated in two haplotypes. The allele G found in the promoter region was found in 75% of the high-line parental animals and in 29% of the low-line parental animals. The GG genotype had 0.5 kits and 0.5 implanted embryos more than the AA genotype. At 48 hr of gestation, the difference in early embryo survival and embryonic stage of development was small. However, at 72 hr of gestation, the GG genotype had 0.36 embryos more than the AA genotype and also had a more advanced embryonic stage of development, showing a lower percentage of compacted morulae and a higher percentage of blastocysts. The difference in litter size between the GG and GA genotypes was similar to the difference found between homozygote genotypes; however, differences in implanted embryos, early embryo survival, and embryo development were not detected between the GG and GA genotypes.
Identification of Selective Sweeps in Closely Related Populations of the House Mouse Based on Microsatellite Scans
Authors: Teschke Meike , Mukabayire Odette , Wiehe Thomas , Tautz Diethard 
Published: September 2008

AbstractGenome scans of polymorphisms promise to provide insights into the patterns and frequencies of positive selection under natural conditions. The use of microsatellites as markers has the potential to focus on very recent events, since in contrast to SNPs, their high mutation rates should remove signatures of older events. We assess this concept here in a large-scale study. We have analyzed two population pairs of the house mouse, one pair of the subspecies Mus musculus domesticus and the other of M. m. musculus. A total of 915 microsatellite loci chosen to cover the whole genome were assessed in a prescreening procedure, followed by individual typing of candidate loci. Schlötterer's ratio statistics (lnRH) were applied to detect loci with significant deviations from patterns of neutral expectation. For eight loci from each population pair we have determined the size of the potential sweep window and applied a second statistical procedure (linked locus statistics). For the two population pairs, we find five and four significant sweep loci, respectively, with an average estimated window size of 120 kb. On the basis of the analysis of individual allele frequencies, it is possible to identify the most recent sweep, for which we estimate an onset of 400–600 years ago. Given the known population history for the French–German population pair, we infer that the average frequency of selective sweeps in these populations is higher than 1 in 100 generations across the whole genome. We discuss the implications for adaptation processes in natural populations.
unc-44 Ankyrin and stn-2 γ-Syntrophin Regulate sax-7 L1CAM Function in Maintaining Neuronal Positioning in Caenorhabditis elegans
Authors: Zhou Shan , Opperman Karla , Wang Xuelin , Chen Lihsia 
Published: September 2008

Abstract
The L1 family of single-pass transmembrane cell adhesion molecules (L1CAMs) is conserved from Caenorhabditis elegans and Drosophila to vertebrates and is required for axon guidance, neurite outgrowth, and maintenance of neuronal positions. The extracellular region of L1CAMs mediates cell adhesion via interactions with diverse cell-surface and extracellular matrix proteins. In contrast, less is known regarding the function of the intracellular domains in the L1CAM cytoplasmic tail. Previously, we identified a role of the C. elegans L1CAM homolog, SAX-7, in maintaining neuronal and axonal positioning. Here, we demonstrate that this function is dependent on three conserved motifs that reside in the SAX-7 cytoplasmic tail: (1) the FERM-binding motif, (2) the ankyrin-binding domain, and (3) the PDZ-binding motif. Furthermore, we provide molecular and genetic evidence that UNC-44 ankyrin and STN-2 γ-syntrophin bind SAX-7 via the respective ankyrin-binding and PDZ-binding motifs to regulate SAX-7 function in maintaining neuronal positioning.
Proteasomal Regulation of the Proliferation vs. Meiotic Entry Decision in the Caenorhabditis elegans Germ Line
Authors: MacDonald Lindsay D , Knox Aaron , Hansen Dave 
Published: September 2008

Abstract
Reproductive fitness in many animals relies upon a tight balance between the number of cells that proliferate in the germ line and the number of cells that enter meiosis and differentiate as gametes. In the Caenorhabditis elegans germ line, the GLP-1/Notch signaling pathway controls this balance between proliferation and meiotic entry. Here we describe the identification of the proteasome as an additional regulator of this balance. We show that a decrease in proteasome activity, through either genetic mutation or RNAi to core components of the proteasome, shifts this balance toward excess germ-line proliferation. We further demonstrate that there are likely two or more proteasome targets that contribute to excess germ-line proliferation when proteasome activity is reduced. One of these targets is likely a component or regulator of the Notch-signaling pathway, while the other functions on one of the two major redundant genetic pathways downstream of GLP-1/Notch signaling. We propose a model in which the proteasome degrades proteins that are necessary for proliferation as cells switch from proliferation to meiotic entry.
Controlling Type-I Error of the McDonald–Kreitman Test in Genomewide Scans for Selection on Noncoding DNA
Authors: Andolfatto Peter 
Published: September 2008

Abstract
Departures from the assumption of homogenously interdigitated neutral and putatively selected sites in the McDonald–Kreitman test can lead to false rejections of the neutral model in the presence of intermediate levels of recombination. This problem is exacerbated by small sample sizes, nonequilibrium demography, recombination rate variation, and in comparisons involving more recently diverged species. I propose that establishing significance levels by coalescent simulation with recombination can improve the fidelity of the test in genomewide scans for selection on noncoding DNA.
Dominance, Overdominance and Epistasis Condition the Heterosis in Two Heterotic Rice Hybrids
Authors: Li Lanzhi , Lu Kaiyang , Chen Zhaoming , Mu Tongmin , Hu Zhongli , Li Xinqi 
Published: September 2008

Abstract
Two recombinant inbred (RI) populations having 194 and 222 lines each, derived, respectively, from a highly heterotic inter- (IJ) and intrasubspecific (II) hybrid, were backcrossed to their respective parents. The RI and two backcross populations along with F1 and its two parents of each hybrid were evaluated for nine important traits, including grain yield and eight other yield-related traits. A total of 76 quantitative trait loci (QTL) for the IJ hybrid and 41 QTL for the II hybrid were detected in the RI population, midparent heterosis of two backcross populations, and two independent sets of data by summation (L1 + L2) and by subtraction (L1 − L2) of two backcross populations (L1 and L2). The variance explained by each QTL ranged from 2.6 to 58.3%. In the IJ hybrid, 42% (32) of the QTL showed an additive effect, 32% (24) a partial-to-complete dominant effect, and 26% (20) an overdominant effect. In the II hybrid, 32% (13) of the QTL demonstrated an additive effect, 29% (12) a partial-to-complete dominant effect, and 39% (16) an overdominant effect. There were 195 digenic interactions detected in the IJ hybrid and 328 in the II hybrid. The variance explained by each digenic interaction ranged from 2.0 to 14.9%. These results suggest that the heterosis in these two hybrids is attributable to the orchestrated outcome of partial-to-complete dominance, overdominance, and epistasis.
The Different Sources of Variation in Inbreeding Depression, Heterosis and Outbreeding Depression in a Metapopulation ofPhysa acuta
Authors: Escobar Juan Sebastián , Nicot Antoine , David Patrice 
Published: September 2008

AbstractUnderstanding how parental distance affects offspring fitness, i.e., the effects of inbreeding and outbreeding in natural populations, is a major goal in evolutionary biology. While inbreeding is often associated with fitness reduction (inbreeding depression), interpopulation outcrossing may have either positive (heterosis) or negative (outbreeding depression) effects. Within a metapopulation, all phenomena may occur with various intensities depending on the focal population (especially its effective size) and the trait studied. However, little is known about interpopulation variation at this scale. We here examine variation in inbreeding depression, heterosis, and outbreeding depression on life-history traits across a full-life cycle, within a metapopulation of the hermaphroditic snail Physa acuta. We show that all three phenomena can co-occur at this scale, although they are not always expressed on the same traits. A large variation in inbreeding depression, heterosis, and outbreeding depression is observed among local populations. We provide evidence that, as expected from theory, small and isolated populations enjoy higher heterosis upon outcrossing than do large, open populations. These results emphasize the need for an integrated theory accounting for the effects of both deleterious mutations and genetic incompatibilities within metapopulations and to take into account the variability of the focal population to understand the genetic consequences of inbreeding and outbreeding at this scale.