bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does childbirth alter the reflex pelvic floor response to coughing?
Authors: Dietz H. P. , Bond V. , Shek K. L. 
Published: September 2011

AbstractObjectiveTo determine the prevalence of and to quantify the effect of reflex pelvic floor activation on coughing in nulliparous pregnant women, and to assess peripartal changes and any association with stress urinary incontinence.MethodsBetween April 2008 and March 2010, 131 nulliparous pregnant women were recruited from an antenatal clinic. All participants were interviewed and underwent four‐dimensional translabial ultrasound examination at antepartum (35.8 (mean) weeks' gestation) and postpartum (4.6 (mean) months) visits. Four‐dimensional ultrasound volume datasets of the pelvic floor during coughs were obtained at a minimum frame rate of 16 Hz, using a 10° volume acquisition angle. To quantify a reflex levator contraction we measured the midsagittal hiatal diameter at multiple time points. Levator integrity was determined using tomographic ultrasound imaging.ResultsFrom 131 women recruited, 47 datasets were technically suboptimal, leaving 84. There was a visible pelvic floor reflex in 82 (98%) cases. At the postpartum visit this was reduced to 63/84, i.e. 75% (P < 0.001). The magnitude of a reflex contraction was markedly reduced postpartum, from 4.8 mm to 2.0 mm (P < 0.001), and this effect was associated with delivery mode (P = 0.042). There was a trend towards an association between lower reflex contraction magnitude and stress incontinence (0.87 ± 3.18 mm vs. 2.36 ± 3.5 mm; P = 0.08) at the postpartum follow‐up visit.ConclusionsPelvic floor reflexes are altered by childbirth. This alteration may be associated with vaginal delivery. Reflex magnitude may be associated with postpartum stress urinary incontinence. The clinical significance of this finding is uncertain. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Symmetry‐adapted perturbation theory of intermolecular forces
Authors: Szalewicz Krzysztof 
Published: September 2011

AbstractBasic concepts and most recent developments of symmetry‐adapted perturbation theory (SAPT) are described. In particular, the methods that combine SAPT with density‐functional theory are discussed. It is explained how SAPT allows one to predict and understand the structure and properties of clusters and condensed phase. The broadest range of such predictions can be achieved by constructing potential energy surfaces from a set of SAPT interaction energies and using these surfaces in nuclear dynamics calculations. © 2011 John Wiley & Sons, Ltd.This article is categorized under:Electronic Structure Theory > Ab Initio Electronic Structure Methods
Marital Shopping and Epidemic AIDS
Authors: Magruder Jeremy R. 
Published: September 2011

Abstract
HIV risks decline sharply at age 30 for women in South Africa, long before coital frequencies or pregnancies decrease. I evaluate several prominent behavioral models of HIV, and find that these do not suggest sharply decreasing risks with age. I formulate a model of spousal search and find that “marital shopping” can generate epidemic HIV prevalence despite low transmission rates because search behavior interacts with dynamics of HIV infectiousness. The implied age-infection profile closely mimics that in South Africa, and the suggested behavior matches that reported by South Africans. Condom use in new relationships and transmission rate reductions are both found to be effective policies and, when used together, eliminate the potential of spousal search to spread HIV. In contrast, antiretroviral treatment is found to have only a minimal effect on the epidemic.
Oligogalacturonide-Auxin Antagonism Does Not Require Posttranscriptional Gene Silencing or Stabilization of Auxin Response Repressors in Arabidopsis
Authors: Savatin Daniel V. , Ferrari Simone , Sicilia Francesca , De Lorenzo Giulia 
Published: September 2011

Abstract
α-1-4-Linked oligogalacturonides (OGs) derived from plant cell walls are a class of damage-associated molecular patterns and well-known elicitors of the plant immune response. Early transcript changes induced by OGs largely overlap those induced by flg22, a peptide derived from bacterial flagellin, a well-characterized microbe-associated molecular pattern, although responses diverge over time. OGs also regulate growth and development of plant cells and organs, due to an auxin-antagonistic activity. The molecular basis of this antagonism is still unknown. Here we show that, in Arabidopsis (Arabidopsis thaliana), OGs inhibit adventitious root formation induced by auxin in leaf explants as well as the expression of several auxin-responsive genes. Genetic, biochemical, and pharmacological experiments indicate that inhibition of auxin responses by OGs does not require ethylene, jasmonic acid, and salicylic acid signaling and is independent of RESPIRATORY BURST OXIDASE HOMOLOGUE D-mediated reactive oxygen species production. Free indole-3-acetic acid levels are not noticeably altered by OGs. Notably, OG- as well as flg22-auxin antagonism does not involve any of the following mechanisms: (1) stabilization of auxin-response repressors; (2) decreased levels of auxin receptor transcripts through the action of microRNAs. Our results suggest that OGs and flg22 antagonize auxin responses independently of Aux/Indole-3-Acetic Acid repressor stabilization and of posttranscriptional gene silencing.
Estimation of geological dip and curvature from time‐migrated zero‐offset reflections in heterogeneous anisotropic media
Authors: Tygel Martin , Ursin Bjørn , Iversen Einar , de Hoop Maarten V. 
Published: September 2011

ABSTRACTStarting from a given time‐migrated zero‐offset data volume and time‐migration velocity, recent literature has shown that it is possible to simultaneously trace image rays in depth and reconstruct the depth‐velocity model along them. This, in turn, allows image‐ray migration, namely to map time‐migrated reflections into depth by tracing the image ray until half of the reflection time is consumed. As known since the 1980s, image‐ray migration can be made more complete if, besides reflection time, also estimates of its first and second derivatives with respect to the time‐migration datum coordinates are available. Such information provides, in addition to the location and dip of the reflectors in depth, also an estimation of their curvature. The expressions explicitly relate geological dip and curvature to first and second derivatives of reflection time with respect to time‐migration datum coordinates. Such quantitative relationships can provide useful constraints for improved construction of reflectors at depth in the presence of uncertainty. Furthermore, the results of image‐ray migration can be used to verify and improve time‐migration algorithms and can therefore be considered complementary to those of normal‐ray migration. So far, image‐ray migration algorithms have been restricted to layered models with isotropic smooth velocities within the layers. Using the methodology of surface‐to‐surface paraxial matrices, we obtain a natural extension to smooth or layered anisotropic media.
New developments of the magnetic tilt‐depth method to improve structural mapping of sedimentary basins
Authors: Fairhead J. Derek , Salem Ahmed , Cascone Lorenzo , Hammill M. , Masterton Sheona , Samson Esuene 
Published: September 2011

ABSTRACTThis paper interprets aeromagnetic data for a deep basin section of the Karroo rift in south‐east Tanzania. We use a novel integrated approach involving the application of advanced derivatives to define structure and the tilt‐depth method to determine and map the depth to basement. In the latter case we use the result of both reduced to pole and reduced to equator data to help constrain the shape and depth of the basin. We show that for a reduced to pole aeromagnetic data set, the generalized form of the local phase, called the tilt derivative, is an effective means of providing an initial (first pass) mapping of a sedimentary basin in terms of its fault structure, dip direction of faults and depth to basement. Since the amplitude of the tilt derivative does not contain information on the strength of the geomagnetic field nor magnetization (other than inclination) of the causative body, the susceptibility contrast across faults/contacts is derived from the analytic signal derivative. We also investigate how effective the tilt derivative and tilt‐depth method are for structural and depth to basement mapping in regions close to the magnetic equator, where the reduction to pole transform is often unstable; this is done using the same Tanzania data set transformed to the pole and the equator. We find that the tilt derivative applied to the reduction to equator data cannot be used to map the structure because of the effects of magnetic anisotropy, which results in the magnetic response of structures varying with strike azimuth. To overcome this anisotropy problem the analytic signal and/or local wavenumber derivatives, which are for all practical purposes independent of inclination, provide the best means of defining the major structural trends. We also find that the tilt‐depth method provides coherent depth to basement estimates for both reduced to pole and reduced to equator data. For the deep basin sections of the Karroo rift, there is a sparsity of tilt‐depth results from both the reduced to pole and reduced to equator data sets. However, each set of results has a different spatial coverage, so when combined they provide a better spatial sampling of the long wavelength magnetic character of the basin and thus improve the constraints on the minimum curvature gridding method to map the shape and depth of the basin.
ABGD, Automatic Barcode Gap Discovery for primary species delimitation
Authors: PUILLANDRE N. , LAMBERT A. , BROUILLET S. , ACHAZ G. 
Published: September 2011

AbstractWithin uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model‐based one‐sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.
Cretaceous black shale: a window into microbial life adaptation
Authors: Pacton Muriel , Schmid Thomas , Gorin Georges , Massault Marc , Stadler Johannes 
Published: September 2011

Terra Nova, 23, 362–368, 2011AbstractAs bacteria are usually incompletely preserved in the geological record, their recognition can only be based on their degradation‐resistant cell walls. However, the latter provide no indication about conditions occurring before the death of the bacteria. In this article, we attempt to demonstrate the syngenecity of bacteria found in the Albian oceanic anoxic event (OAE1b) from the Urbino level and highlight their physiology from their possible intracellular components. Dark storage inclusions have been identified as inorganic polyphosphate, in addition to carotenoids which have been encountered in the cell. Before death, stress and deprivation resulted in drastic changes in physiology generating properties such as regulatory functions of polyphosphates and the ability of carotenoids to rigidify membranes. Therefore, this starvation strategy induced a more resistant state possibly enhancing the preservation of these bacteria. These results demonstrate the potential for exploring indications of past microbial life in other black shales.
The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis are both bifunctional and interact with the catalytic and nucleotide‐binding domains of pyruvate, orthophosphate dikinase
Authors: Astley Holly M. , Parsley Kate , Aubry Sylvain , Chastain Chris J. , Burnell Jim N. , Webb Michael E. , Hibberd Julian M. 
Published: September 2011

SummaryPyruvate orthophosphate dikinase (PPDK) is a key enzyme in C4 photosynthesis and is also found in C3 plants. It is post‐translationally modified by the PPDK regulatory protein (RP) that possesses both kinase and phosphotransferase activities. Phosphorylation and dephosphorylation of PPDK lead to inactivation and activation respectively. Arabidopsis thaliana contains two genes that encode chloroplastic (RP1) and cytosolic (RP2) isoforms of RP, and although RP1 has both kinase and phosphotransferase activities, to date RP2 has only been shown to act as a kinase. Here we demonstrate that RP2 is able to catalyse the dephosphorylation of PPDK, although at a slower rate than RP1 under the conditions of our assay. From yeast two‐hybrid analysis we propose that RP1 binds to the central catalytic domain of PPDK, and that additional regions towards the carboxy and amino termini are required for a stable interaction between RP2 and PPDK. For 21 highly conserved amino acids in RP1, mutation of 15 of these reduced kinase and phosphotransferase activity, while mutation of six residues had no impact on either activity. We found no mutant in which only one activity was abolished. However, in some chimaeric fusions that comprised the amino and carboxy termini of RP1 and RP2 respectively, the kinase reaction was severely compromised but phosphotransferase activity remained unaffected. These findings are consistent with the findings that both RP1 and RP2 modulate reversibly the activity of PPDK, and possess one bifunctional active site or two separate sites in close proximity.
A rice calcium‐dependent protein kinase OsCPK12 oppositely modulates salt‐stress tolerance and blast disease resistance
Authors: Asano Takayuki , Hayashi Nagao , Kobayashi Michie , Aoki Naohiro , Miyao Akio , Mitsuhara Ichiro , Ichikawa Hiroaki , Komatsu Setsuko , Hirochika Hirohiko , Kikuchi Shoshi , Ohsugi Ryu 
Published: September 2011

SummaryCalcium‐dependent protein kinases (CDPKs) regulate the downstream components in calcium signaling pathways. We investigated the effects of overexpression and disruption of an Oryza sativa (rice) CDPK (OsCPK12) on the plant’s response to abiotic and biotic stresses. OsCPK12‐overexpressing (OsCPK12‐OX) plants exhibited increased tolerance to salt stress. The accumulation of hydrogen peroxide (H2O2) in the leaves was less in OsCPK12‐OX plants than in wild‐type (WT) plants. Genes encoding reactive oxygen species (ROS) scavenging enzymes (OsAPx2 and OsAPx8) were more highly expressed in OsCPK12‐OX plants than in WT plants, whereas the expression of the NADPH oxidase gene, OsrbohI, was decreased in OsCPK12‐OX plants compared with WT plants. Conversely, a retrotransposon (Tos17) insertion mutant, oscpk12, and plants transformed with an OsCPK12 RNA interference (RNAi) construct were more sensitive to high salinity than were WT plants. The level of H2O2 accumulation was greater in oscpk12 and OsCPK12 RNAi plants than in the WT. These results suggest that OsCPK12 promotes tolerance to salt stress by reducing the accumulation of ROS. We also observed that OsCPK12‐OX seedlings had increased sensitivity to abscisic acid (ABA) and increased susceptibility to blast fungus, probably resulting from the repression of ROS production and/or the involvement of OsCPK12 in the ABA signaling pathway. Collectively, our results suggest that OsCPK12 functions in multiple signaling pathways, positively regulating salt tolerance and negatively modulating blast resistance.
Dynamic evolution of herbivore‐induced sesquiterpene biosynthesis in sorghum and related grass crops
Authors: Zhuang Xiaofeng , Köllner Tobias G. , Zhao Nan , Li Guanglin , Jiang Yifan , Zhu Liucun , Ma Jianxin , Degenhardt Jörg , Chen Feng 
Published: September 2011

SummarySorghum (Sorghum bicolor) plants damaged by insects emit a blend of volatiles, predominantly sesquiterpenes, that are implicated in attracting natural enemies of the attacking insects. To characterize sesquiterpene biosynthesis in sorghum, seven terpene synthase (TPS) genes, SbTPS1 through SbTPS7, were identified based on their evolutionary relatedness to known sesquiterpene synthase genes from maize and rice. While SbTPS6 and SbTPS7 encode truncated proteins, all other TPS genes were determined to encode functional sesquiterpene synthases. Both SbTPS1 and SbTPS2 produced the major products zingiberene, β‐bisabolene and β‐sesquiphellandrene, but with opposite ratios of zingiberene to β‐sesquiphellandrene. SbTPS3 produced (E)‐α‐bergamotene and (E)‐β‐farnesene. SbTPS4 formed (E)‐β‐caryophyllene as the major product. SbTPS5 produced mostly (E)‐α‐bergamotene and (Z)‐γ‐bisabolene. Based on the genome sequences of sorghum, maize and rice and the sesquiterpene synthase genes they contain, collinearity analysis identified the orthologs of sorghum sesquiterpene synthase genes, except for SbTPS4, in maize and rice. Phylogenetic analysis implied that SbTPS1, SbTPS2 and SbTPS3, which exist as tandem repeats, evolved as a consequence of local gene duplication in a lineage‐specific manner. Structural modeling and site‐directed mutagenesis experiments revealed that three amino acids in the active site play critical roles in defining product specificity of SbTPS1, SbTPS2, SbTPS3 and their orthologs in maize and rice. The naturally occurring functional variations of sesquiterpene synthases within and between species suggest that multiple mechanisms, including lineage‐specific gene duplication, subfunctionalization, neofunctionalization and pseudogenization of duplicated genes, have all played a role in the dynamic evolution of insect‐induced sesquiterpene biosynthesis in grasses.
A tomato LysM receptor‐like kinase promotes immunity and its kinase activity is inhibited by AvrPtoB
Authors: Zeng Lirong , Velásquez André C. , Munkvold Kathy R. , Zhang Jingwei , Martin Gregory B. 
Published: September 2011

SummaryResistance in tomato (Solanum lycopersicum) to infection by Pseudomonas syringae involves both detection of pathogen‐associated molecular patterns (PAMPs) and recognition by the host Pto kinase of pathogen effector AvrPtoB which is translocated into the host cell and interferes with PAMP‐triggered immunity (PTI). The N‐terminal portion of AvrPtoB is sufficient for its virulence activity and for recognition by Pto. An amino acid substitution in AvrPtoB, F173A, abolishes these activities. To investigate the mechanisms of AvrPtoB virulence, we screened for tomato proteins that interact with AvrPtoB and identified Bti9, a LysM receptor‐like kinase. Bti9 has the highest amino acid similarity to Arabidopsis CERK1 among the tomato LysM receptor‐like kinases (RLKs) and belongs to a clade containing three other tomato proteins, SlLyk11, SlLyk12, and SlLyk13, all of which interact with AvrPtoB. The F173A substitution disrupts the interaction of AvrPtoB with Bti9 and SlLyk13, suggesting that these LysM‐RLKs are its virulence targets. Two independent tomato lines with RNAi‐mediated reduced expression of Bti9 and SlLyk13 were more susceptible to P. syringae. Bti9 kinase activity was inhibited in vitro by the N‐terminal domain of AvrPtoB in an F173‐dependent manner. These results indicate Bti9 and/or SlLyk13 play a role in plant immunity and the N‐terminal domain of AvrPtoB may have evolved to interfere with their kinase activity. Finally, we found that Bti9 and Pto interact with AvrPtoB in a structurally similar although not identical fashion, suggesting that Pto may have evolved as a molecular mimic of LysM‐RLK kinase domains.
Humoral immunomodulatory effect of influenza vaccine in potential blood donors: implications for transfusion safety
Authors: Delaney M. , Warner P. , Nelson K. , Gleckler C. , Price T. , Madeleine M. 
Published: September 2011

Background: Generalised immune stimulation may follow vaccination causing increased antibody titres of nonvaccine‐related antibodies or bystander antibodies, including those to human leukocyte antigens (HLA) and ABO blood group antigens. HLA antibodies may lead to transfusion‐related acute lung injury. High‐titre ABO antibodies may cause acute haemolytic transfusion reactions after plasma‐incompatible platelet transfusion. It is unknown if these antibodies can be stimulated by vaccination in otherwise normal subjects.Methods: Blood samples of healthy volunteers who received the 2009 influenza vaccine were analysed for HLA and ABO antibodies before and 14 days after vaccination (n = 86). Age, gender and history of exposure to foreign tissue, through pregnancy, blood transfusion or tissue transplant were collected. Results were analysed with descriptive statistics, paired t‐test and χ2 test.Results: There was no increase in HLA or ABO antibody levels after vaccination (P = not significant). Forty per cent of subjects (n = 35) had previously formed HLA antibody and 16% (7 males and 7 females) had HLA sensitisation but did not report foreign tissue exposure. The average panel reactive antibody of the HLA sensitised but nonexposed subjects was lower in males than females (3·4 and 28·6%, respectively, P = 0·015, t‐test), suggesting that some females may have had unrecognised pregnancy.Conclusions: HLA or ABO antibodies did not appear to be stimulated by the 2009 influenza vaccine. Female blood donors with putatively unrecognised pregnancies may have higher risk for HLA sensitisation than previously thought. Further study using different vaccine formulations may lead to better understanding of the risks of bystander antibodies in the blood donor population.