bluuebunny/crossref_metadata_2025_split huggingface dataset:
GROUND STATE SOLUTIONS FOR -SUPERLINEAR -LAPLACIAN EQUATIONS
Authors: CHEN YI , TANG X. H. 
Published: May 2014

AbstractIn this paper, we deduce new conditions for the existence of ground state solutions for the$p$-Laplacian equation$$\begin{equation*} \left \{ \begin{array}{@{}ll} -\mathrm {div}(|\nabla u|^{p-2}\nabla u)+V(x)|u|^{p-2}u=f(x, u), \quad x\in {\mathbb {R}}^{N},\\[5pt] u\in W^{1, p}({\mathbb {R}}^{N}), \end{array} \right . \end{equation*}$$which weaken the Ambrosetti–Rabinowitz type condition and the monotonicity condition for the function$t\mapsto f(x, t)/|t|^{p-1}$. In particular, both$tf(x, t)$and$tf(x, t)-pF(x, t)$are allowed to be sign-changing in our assumptions.
Archaeal MBF1 binds to 30S and 70S ribosomes via its helix–turn–helix domain
Authors: Blombach Fabian , Launay Helene , Snijders Ambrosius P. L. , Zorraquino Violeta , Wu Hao , de Koning Bart , Brouns Stan J. J. , Ettema Thijs J. G. , Camilloni Carlo , Cavalli Andrea , Vendruscolo Michele , Dickman Mark J. , Cabrita Lisa D. , La Teana Anna , Benelli Dario , Londei Paola , Christodoulou John , van der Oost John 
Published: May 2014

MBF1 (multi-protein bridging factor 1) is a protein containing a conserved HTH (helix–turn–helix) domain in both eukaryotes and archaea. Eukaryotic MBF1 has been reported to function as a transcriptional co-activator that physically bridges transcription regulators with the core transcription initiation machinery of RNA polymerase II. In addition, MBF1 has been found to be associated with polyadenylated mRNA in yeast as well as in mammalian cells. aMBF1 (archaeal MBF1) is very well conserved among most archaeal lineages; however, its function has so far remained elusive. To address this, we have conducted a molecular characterization of this aMBF1. Affinity purification of interacting proteins indicates that aMBF1 binds to ribosomal subunits. On sucrose density gradients, aMBF1 co-fractionates with free 30S ribosomal subunits as well as with 70S ribosomes engaged in translation. Binding of aMBF1 to ribosomes does not inhibit translation. Using NMR spectroscopy, we show that aMBF1 contains a long intrinsically disordered linker connecting the predicted N-terminal zinc-ribbon domain with the C-terminal HTH domain. The HTH domain, which is conserved in all archaeal and eukaryotic MBF1 homologues, is directly involved in the association of aMBF1 with ribosomes. The disordered linker of the ribosome-bound aMBF1 provides the N-terminal domain with high flexibility in the aMBF1–ribosome complex. Overall, our findings suggest a role for aMBF1 in the archaeal translation process.
Protein kinase D1 is essential for Ras-induced senescence and tumor suppression by regulating senescence-associated inflammation
Authors: Wang Pan , Han Limin , Shen Hong , Wang Pengfeng , Lv Cuicui , Zhao Ganye , Niu Jing , Xue Lixiang , Wang Qiming Jane , Tong Tanjun , Chen Jun 
Published: May 2014

Significance
Oncogene-induced senescence (OIS) is an initial barrier for cancer development. Reactive oxygen species (ROS) play critical roles in oncogenic Ras OIS. Senescent cells develop a senescence-associated secretory phenotype (SASP), which has important role in tumor suppression and tissue repair. However, the mechanisms underlying the SASP regulation are not clear. In this paper, we show that ROS-protein kinase Cδ (PKCδ)-protein kinase D1 (PKD1) axis is essential for SASP induction and maintenance via modulation of NF-κB activity. Considering the pivotal role of both SASP and ROS in systemic aging and age-related diseases, the link between ROS-PKCδ-PKD1 pathway and SASP regulation elucidated here may provide a new target to intervene in age-related inflammation and diseases.
Dimer recognition and secretion by the ESX secretion system inBacillus subtilis
Authors: Sysoeva Tatyana A. , Zepeda-Rivera Martha A. , Huppert Laura A. , Burton Briana M. 
Published: May 2014

SignificanceBacteria use a wide range of secretion mechanisms to export proteins from the cytoplasm. These secretion pathways differ in the nature of substrate recognition signal and the mode of substrate translocation. This work elucidates fundamental properties of substrate secretion by the early secretory antigen 6 kDa (ESX) system. We use systematic mutagenesis and targeted crosslinking of an ESX substrate fromBacillus subtilisto provide, to our knowledge, the first experimental evidence for secretion of an intact dimeric complex requiring a composite recognition signal formed by both members of the complex.
Anti-aging and anti-microbial effects of melleolide on various types of yeast
Authors: Nakaya Shigeru , Kobori Hajime , Sekiya Atsushi , Kawagishi Hirokazu , Ushimaru Takashi 
Published: May 2014

Abstract
The chronological lifespan (CLS) of the budding yeast Saccharomyces cerevisiae is a model for the aging of post-mitotic cells in higher eukaryotes. In this study, we found that the sesquiterpene aryl ester melleolide expands the CLS of budding yeast. In contrast, melleolide compromised the CLS of the fission yeast Schizosaccharomyces pombe. This indicates that melleolide might have a potential anti-aging activity against some types of cell, and that it might be useful as a selective anti-fungal drug.
Improved ethanol production from cheese whey, whey powder, and sugar beet molasses by “Vitreoscilla hemoglobin expressing” Escherichia coli
Authors: Akbas Meltem Yesilcimen , Sar Taner , Ozcelik Busra 
Published: May 2014

Abstract
This work investigated the improvement of ethanol production by engineered ethanologenic Escherichia coli to express the hemoglobin from the bacterium Vitreoscilla (VHb). Ethanologenic E. coli strain FBR5 and FBR5 transformed with the VHb gene in two constructs (strains TS3 and TS4) were grown in cheese whey (CW) medium at small and large scales, at both high and low aeration, or with whey powder (WP) or sugar beet molasses hydrolysate (SBMH) media at large scale and low aeration. Culture pH, cell growth, VHb levels, and ethanol production were evaluated after 48 h. VHb expression in TS3 and TS4 enhanced their ethanol production in CW (21–419%), in WP (17–362%), or in SBMH (48–118%) media. This work extends the findings that “VHb technology” may be useful for improving the production of ethanol from waste and byproducts of various sources.
Structural alteration of cell surface heparan sulfate through the stimulation of the signaling pathway for heparan sulfate 6-O-sulfotransferase-1 in mouse fibroblast cells
Authors: Nishida Mitsutaka , Kozakai Takeru , Nagami Keitaro , Kanamaru Yoshihiro , Yabe Tomio 
Published: May 2014

Abstract
Heparan sulfate (HS) is a randomly sulfated polysaccharide that is present on the cell surface and in the extracellular matrix. The sulfated structures of HS were synthesized by multiple HS sulfotransferases, thereby regulating various activities such as growth factor signaling, cell differentiation, and tumor metastasis. Therefore, if the sulfated structures of HS could be artificially controlled, those manipulations would help to understand the various functions depending on HS. However, little knowledge is currently available to realize the mechanisms controlling the expression of such enzymes. In this study, we found that the ratio of 6-O-sulfated disaccharides increased at 3 h after adrenaline stimulation in mouse fibroblast cells. Furthermore, adrenaline-induced up-regulation of HS 6-O-sulfotransferase-1 (6-OST-1) was controlled by Src-ERK1/2 signaling pathway. Finally, inhibiting the signaling pathways for 6-OST-1 intentionally suppressed the adrenaline-induced structural alteration of HS. These observations provide fundamental insights into the understanding of structural alterations in HS by extracellular cues.
1-Kestose consumption during pregnancy and lactation increases the levels of IgA in the milk of lactating mice
Authors: Jinno Shinji , Nakamura Yoshitaka , Nagata Masashi , Takahashi Takeshi 
Published: May 2014

Abstract
To examine the effect of dietary supplementation with 1-kestose on the IgA levels in milk, BALB/c mice were fed diets with or without 5% 1-kestose during pregnancy and lactation. The total and specific IgA levels in the milk were measured at 7 and 14 days after delivery. A two-way ANOVA with repeated measures resulted in a significant effect of 1-kestose-supplementation on total IgA concentrations (p &lt; 0.05) and the level of anti-Bacteroides IgA (p &lt; 0.05). A significant positive correlation was found between the mean count of Bacteroides spp. in maternal feces and the total IgA concentration in maternal milk (r = 0.55, p &lt; 0.05), suggesting a potential link between the gut and mammary gland immune system. In conclusion, this study demonstrated the effects of dietary prebiotics on milk IgA production.
Enantiospecific synthesis and filed evaluation of four stereoisomers of 10,14-dimethyloctadec-1-ene, a sex pheromone component secreted by female moths of the apple leafminer
Authors: Taguri Tomonori , Yaginuma Katuhiko , Yamamoto Masanobu , Fujii Toru , Ando Tetsu 
Published: May 2014

Abstract
All four stereoisomers of 10,14-dimethyloctadec-1-ene, a sex pheromone component of the apple leafminer (Lyonetia prunifoliella: Lepidoptera), were synthesized starting from (R)- and (S)-propylene oxide by applying stereospecific inversion of chiral secondary tosylates as a key step. Field evaluation showed that male moths of the Japanese population were selectively attracted by the (10S,14S)-isomer and that the activity was not inhibited by the enantiomer.
Enzymatic fragmentation of carbohydrate moieties of radish arabinogalactan-protein and elucidation of the structures
Authors: Shimoda Ryohei , Okabe Kohei , Kotake Toshihisa , Matsuoka Koji , Koyama Tetsuo , Tryfona Theodora , Liang Hui-Chung , Dupree Paul , Tsumuraya Yoichi 
Published: May 2014

Abstract
We investigated the structures of L-arabino-galactooligosaccharides released from the sugar moieties of a radish arabinogalactan-protein (AGP) by the action of exo-β-(1→3)-galactanase. We detected a series of neutral β-(1→6)-linked galactooligosaccharides forming branches of one to up to at least 19 consecutive Gal groups, together with corresponding acidic derivatives terminating in 4-O-methyl-glucuronic acid (4-Me-GlcA) at the non-reducing end. Some oligosaccharide chains of degree of polymerization (dp) higher than 3 for neutral, and 4 for acidic oligomers were modified with L-Araf residues. The acidic tetrasaccharide 4-Me-β-GlcA-(1→6)[α-L-Araf-(1→3)]-β-Gal-(1→6)-Gal was detected as an abundant L-Araf-containing oligosaccharide among these neutral and acidic oligomers. A pentasaccharide containing an additional L-Araf group attached to the L-Ara in the tetrasaccharide through an α-(1→5)-linkage was also found. We observed L-arabino-galactooligosaccharides substituted with single or disaccharide L-Araf units at different Gal residues along these neutral and acidic β-(1→6)-galactooligosaccharide chains, indicating that these side chains are highly variable in length and substituted variously with L-Araf residues.
Detection of choline and phosphatidic acid (PA) catalyzed by phospholipase D (PLD) using MALDI-QIT-TOF/MS with 9-aminoacridine matrix
Authors: Park Kyung-eui , Kim Jun-dal , Nagashima Yusuke , Kako Koichiro , Daitoku Hiroaki , Matsui Motoki , Park Gwi Gun , Fukamizu Akiyoshi 
Published: May 2014

Abstract
Phospholipase D (PLD) catalyzes the hydrolysis of phosphatidylcholine (PC), the most abundant phospholipids of plasma membrane, resulting in the production of choline and phosphatidic acid (PA). Choline is a precursor of the neurotransmitter acetylcholine, whereas PA functions as an intracellular lipid mediator of diverse biological functions. For assessing PLD activity in vitro, PLD-derived choline has been often analyzed with radioactive or non-radioactive methods. In this study, we have developed a new method for detecting choline and PA with MALDI-QIT-TOF/MS by using 9-aminoacridine as a matrix. The standard calibration curves showed that choline and PA could be detected with linearity over the range from 0.05 and 1 pmol, respectively. Importantly, this method enables the concomitant detection of choline and PA as a reaction product of PC hydrolysis by PLD2 proteins. Thus, our simple and direct method would be useful to characterize the enzymatic properties of PLD, thereby providing insight into mechanisms of PLD activation.
What Is the Best Method? Recovery of Methicillin-Resistant Staphylococcus aureus and Extended-Spectrum β-Lactamase–Producing Escherichia coli from Inanimate Hospital Surfaces
Authors: Claro Tânia , Galvin Sandra , Cahill Orla , Fitzgerald-Hughes Deirdre , Daniels Stephen , Humphreys Hilary 
Published: May 2014

Environmental sampling in hospitals, when required, needs to be reliable. We evaluated different methods of sampling methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamase–producing Escherichia coli on 5 materials of the hospital setting. Petrifilms and contact plates were superior to swabs for all of the surfaces studied.Infect Control Hosp Epidemiol 2014;35(7):869–871
High-frequency Ventilation Does Not Provide Mortality Benefit in Comparison with Conventional Lung-protective Ventilation in Acute Respiratory Distress Syndrome
Authors: Maitra Souvik , Bhattacharjee Sulagna , Khanna Puneet , Baidya Dalim K. 
Published: May 2014

AbstractAbstract
A meta-analysis of 1,759 patients from seven randomized controlled trials documents that the use of HFOV does not offer a mortality benefit and appears to prolong the duration of mechanical ventilation.

Background:
Despite implementation of lung-protective ventilation strategy, acute respiratory distress syndrome is associated with significant mortality, which necessitates the evaluation of ventilatory modes other than conventional lung-protective strategy. This meta-analysis of the randomized controlled trials has been undertaken to know whether high-frequency oscillatory ventilation (HFOV) provides any mortality benefit over conventional ventilation in adult patients with acute respiratory distress syndrome.

Methods:
Published randomized controlled trials comparing HFOV with conventional lung-protective ventilation in adult patients with acute respiratory distress syndrome were included in this meta-analysis.

Results:
A total 1,759 patient data from seven randomized controlled trials have been analyzed here. Primary outcome of the review is in-hospital/30-day mortality and secondary outcomes are duration of intensive care unit stay, duration of mechanical ventilation, requirement of additional treatment, and complications associated with the interventions. HFOV does not offer any in-hospital/30-day mortality benefit (386 of 886 in HFOV vs. 368 of 873 in conventional ventilation; risk ratio, 0.96; 95% CI, 0.77 to 1.19; P = 0.70) over conventional ventilation. It may also prolong the duration of mechanical ventilation (mean difference, 1.18 days; 95% CI, 0.00 to 2.35 days; P = 0.05). Duration of intensive care unit stay (mean difference, 1.24 days; 95% CI, −0.08 to 2.56 days; P = 0.06) and requirement of neuromuscular blocker is similar between two treatment arm. Incidence of refractory hypoxemia is significantly less (risk ratio, 0.60; 95% CI, 0.39 to 0.93; P = 0.02) with the use of HFOV. HFOV is not associated with increased incidence of barotrauma and refractory hypotension.

Conclusion:
HFOV should not be used routinely in all adult patients with acute respiratory distress syndrome as primary ventilation strategy in place of conventional lung-protective ventilation.
Cosi2: An efficient simulator of exact and approximate coalescent with selection
Authors: Shlyakhter Ilya , Sabeti Pardis C. , Schaffner Stephen F. 
Published: May 2014

AbstractMotivationEfficient simulation of population genetic samples under a given demographic model is a prerequisite for many analyses. Coalescent theory provides an efficient framework for such simulations, but simulating longer regions and higher recombination rates remains challenging. Simulators based on a Markovian approximation to the coalescent scale well, but do not support simulation of selection. Gene conversion is not supported by any published coalescent simulators that support selection.ResultsWe describecosi2, an efficient simulator that supports both exact and approximate coalescent simulation with positive selection.cosi2improves on the speed of existing exact simulators, and permits further speedup in approximate mode while retaining support for selection.cosi2supports a wide range of demographic scenarios including recombination hot spots, gene conversion, population size changes, population structure and migration.cosi2implements coalescent machinery efficiently by tracking only a small subset of the Ancestral Recombination Graph, sampling only relevant recombination events, and using augmented skip lists to represent tracked genetic segments. To preserve support for selection in approximate mode, the Markov approximation is implemented not by moving along the chromosome but by performing a standard backwards-in-time coalescent simulation while restricting coalescence to node pairs with overlapping or near-overlapping genetic material. We describe the algorithms used bycosi2and present comparisons with existing selection simulators.AvailabilityA free C++ implementation ofcosi2is available athttp://broadinstitute.org/∼ilya/cosi2.Contactilya@broadinstitute.org
Locus architecture affects mRNA expression levels in Drosophila embryos
Authors: Lydiard-Martin Tara , Bragdon Meghan , Eckenrode Kelly B. , Wunderlich Zeba , DePace Angela H. 
Published: May 2014

AbstractStructural variation in the genome is common due to insertions, deletions, duplications and rearrangements. However, little is known about the ways structural variants impact gene expression. Developmental genes are controlled by multiple regulatory sequence elements scattered over thousands of bases; developmental loci are therefore a good model to test the functional impact of structural variation on gene expression. Here, we measured the effect of rearranging two developmental enhancers from theeven-skipped (eve)locus inDrosophila melanogasterblastoderm embryos. We systematically varied orientation, order, and spacing of the enhancers in transgenic reporter constructs and measured expression quantitatively at single cell resolution in whole embryos to detect changes in both level and position of expression. We found that the position of expression was robust to changes in locus organization, but levels of expression were highly sensitive to the spacing between enhancers and order relative to the promoter. Our data demonstrate that changes in locus architecture can dramatically impact levels of gene expression. To quantitatively predict gene expression from sequence, we must therefore consider how information is integrated both within enhancers and across gene loci.
RNA-seq gene profiling - a systematic empirical comparison
Authors: Fonseca Nuno A. , Marioni John , Brazma Alvis 
Published: May 2014

AbstractAccurately quantifying gene expression levels is a key goal of experiments using RNA-sequencing to assay the transcriptome. This typically requires aligning the short reads generated to the genome or transcriptome before quantifying expression of pre-defined sets of genes. Differences in the alignment/quantification tools can have a major effect upon the expression levels found with important consequences for biological interpretation. Here we address two main issues: do different analysis pipelines affect the gene expression levels inferred from RNA-seq data? And, how close are the expression levels inferred to the “true” expression levels?We evaluate fifty gene profiling pipelines in experimental and simulated data sets with different characteristics (e.g, read length and sequencing depth). In the absence of knowledge of the ‘ground truth’ in real RNAseq data sets, we used simulated data to assess the differences between the “true” expression and those reconstructed by the analysis pipelines. Even though this approach does not take into account all known biases present in RNAseq data, it still allows to estimate the accuracy of the gene expression values inferred by different analysis pipelines. The results show that i) overall there is a high correlation between the expression levels inferred by the best pipelines and the true quantification values; ii) the error in the estimated gene expression values can vary considerably across genes; and iii) a small set of genes have expression estimates with consistently high error (across data sets and methods). Finally, although the mapping software is important, the quantification method makes a greater difference to the results.
Gender orientation and retail atmosphere: effects on value perception
Authors: Borges Adilson , Babin Barry J. , Spielmann Nathalie 
Published: May 2014

PurposeEvaluative processes made in retail environments have been shown to vary between groups, particularly between men and women. The purpose of this paper is to demonstrate that a hedonic or utilitarian store atmosphere leads to different evaluations depending on the consumer's gender orientation.Design/methodology/approachA pre‐test identifies hedonic and utilitarian store atmospheres. A main study uses an experimental design to compare the impact of these atmospheres on overall store quality, price perceptions and willingness to pay for products in these stores in function of the consumers' gender orientation.FindingsThe results show that hedonic atmospheres lead to higher quality perception, higher price perception and higher purchase intention among female‐oriented consumers. Moreover, female‐oriented consumers are willing to pay 32 per cent more for the same product when this product is offered in a hedonic store atmosphere. Retailers should consider carefully how store design affects evaluations among male versus female‐oriented consumers.Research limitation/implicationsThe use of students reduces the generalisability of the results. Future research can test the propositions further.Originality/valueThe results suggest that perceptions of store atmospheres are moderated by gender orientation, which is a segmentation variable that may be more relevant in today's gender‐blurring retail environments. Furthermore, the results show how value can be perceived from store atmospheres and transferred to products.
Is There a Role for Ivabradine Beyond its Conventional Use?
Authors: Bonadei Ivano , Vizzardi Enrico , Sciatti Edoardo , Carubelli Valentina , Lombardi Carlo Mario , D'Aloia Antonio , Metra Marco 
Published: May 2014

SummaryResults of recent clinical trials in patients with stable angina and chronic heart failure have successfully demonstrated a beneficial role of use of ivabradine in addition to the conventional therapy. Based on the results of these trials, the aim of our review was to give an overview of the literature about the use of ivabradine in clinical settings outside its usual purpose.
Phagocytic ability declines with age in adult Drosophila hemocytes
Authors: Horn Lucas , Leips Jeff , Starz‐Gaiano Michelle 
Published: May 2014

SummaryMost multicellular organisms show a physiological decline in immune function with age. However, little is known about the mechanisms underlying these changes. We examined Drosophila melanogaster, an important model for identifying genes affecting innate immunity and senescence, to explore the role of phagocytosis in age‐related immune dysfunction. We characterized the localized response of immune cells at the dorsal vessel to bacterial infection in 1‐week‐ and 5‐week‐old flies. We developed a quantitative phagocytosis assay for adult Drosophila and utilized this to characterize the effect of age on phagocytosis in transgenic and natural variant lines. We showed that genes necessary for bacterial engulfment in other contexts are also required in adult flies. We found that blood cells from young and old flies initially engulf bacteria equally well, while cells from older flies accumulate phagocytic vesicles and thus are less capable of destroying pathogens. Our results have broad implications for understanding how the breakdown in cellular processes influences immune function with age.