julilili42/papers huggingface dataset:
Object Presence Modulates Activity within the Somatosensory Component of the Action Observation Network
2011-06-20

In the present study, we used functional magnetic resonance imaging to investigate the influence that the presence of an object, intended as the target for an action, might have on the neural circuit underlying the observation of the movement of others (action observation network [AON]). This system entails a simulation process of the observed movement occurring via the recruitment of the motor and somatosensory cortices involved in the execution of such movement. Here, participants were requested to observe grasping actions ending behind a partition knowing in advance whether a target-object would be present (i.e., object-directed action) or absent (i.e., non object-directed action). These "action" conditions were compared with "control" conditions in which a stationary hand was presented either alone or together with the target-object hidden behind the partition. Activation within most regions of the AON was similar for observing partially occluded object-related and non object-related actions. However, within one of the regions belonging to the AON, namely in the somatosensory cortices, blood oxygen level-dependent activity was modulated by the presence of a target-object. We interpreted such modulation as demonstration of the differential involvement of the somatosensory component of the AON for the coding of these 2 types of actions.
RA–RAR-β counteracts myelin-dependent inhibition of neurite outgrowth via Lingo-1 repression
2011-06-20

After an acute central nervous system injury, axonal regeneration is limited as the result of a lack of neuronal intrinsic competence and the presence of extrinsic inhibitory signals. The injury fragments the myelin neuronal insulating layer, releasing extrinsic inhibitory molecules to signal through the neuronal membrane–bound Nogo receptor (NgR) complex. In this paper, we show that a neuronal transcriptional pathway can interfere with extrinsic inhibitory myelin-dependent signaling, thereby promoting neurite outgrowth. Specifically, retinoic acid (RA), acting through the RA receptor β (RAR-β), inhibited myelin-activated NgR signaling through the transcriptional repression of the NgR complex member Lingo-1. We show that suppression of Lingo-1 was required for RA–RAR-β to counteract extrinsic inhibition of neurite outgrowth. Furthermore, we confirm in vivo that RA treatment after a dorsal column overhemisection injury inhibited Lingo-1 expression, specifically through RAR-β. Our findings identify a novel link between RA–RAR-β–dependent proaxonal outgrowth and inhibitory NgR complex–dependent signaling, potentially allowing for the development of molecular strategies to enhance axonal regeneration after a central nervous system injury.
Lessons from Nature for the Construction of Ceramic Cellular Materials for Superior Energy Absorption
2011-06-20

Abstract Sea urchin spines combine extreme lightweight construction with impact resistance and improved mechanical strength although being made of presumably brittle calcium carbonate (calcite). Lance and pencil sea urchins (Phyllacanthus imperialis and Heterocentrotus mammillatus) are of particular interest as they exhibit large and mechanical very stable spines and the constructional concepts of these spines was translated into graded porous alumina ceramics derived from starch‐blended slip casting. A high level of porosity (&gt;30 vol%) is identified as the important element for graceful failure in polycrystalline alumina and graded porosity, i.e., layers of higher and lower density, can significantly improve the impact resistance of the material giving raise to what we refer to as cascading graceful failure: a mechanical response of porous materials with curved layers of graded porosity that maintains a high level of compressive strength even after the linear elastic threshold is surpassed and local structural collapse occurs.
The Polymorphic HCMV Glycoprotein UL20 Is Targeted for Lysosomal Degradation by Multiple Cytoplasmic Dileucine Motifs
2011-06-20

Human cytomegalovirus (HCMV) is a widespread and persistent beta‐herpesvirus. The large DNA genome of HCMV encodes many proteins that are non‐essential for viral replication including numerous proteins subverting host immunosurveillance. One of them is the barely characterized UL20, which is encoded adjacent to the well‐defined immunoevasins UL16 and UL18. UL20 is a type I transmembrane glycoprotein with an immunoglobulin‐like ectodomain that is highly polymorphic among HCMV strains. Here, we show that the homodimeric UL20, by virtue of its cytoplasmic domain, does not reach the cell surface but is targeted to endosomes and lysosomes. Accordingly, UL20 exhibits a short half‐life because of rapid lysosomal degradation. Trafficking of UL20 to lysosomes is determined by several, independently functioning dileucine‐based sorting motifs in the cytoplasmic domain of UL20 and involves the adaptor protein (AP) complex AP‐1. Combined substitution of three dileucine motifs allowed strong cell surface expression of UL20 comparable to UL20 mutants lacking the cytoplasmic tail. Finally, we show that the intracellularly located UL20 also is subject to lysosomal degradation in the context of viral infection. Altogether, from these data, we hypothesize that UL20 is destined to efficiently sequester yet‐to‐be defined cellular proteins for degradation in lysosomes.
Transfection of Short-Interfering RNA Silences Adhesion Molecule Expression on Cardiac Microvascular Cells
2011-06-20

This investigation demonstrates that liposomal transfection of HCMEC with specific siRNA sequences is capable of both repressing adhesion molecule expression and of reducing subsequent leukocyte-endothelial actions.
Quantity implicatures, exhaustive interpretation, and rational conversation
2011-06-21

Quantity implicatures are inferences triggered by an utterance based on what other utterances a speaker could have made instead. Using ideas and formalisms from game theory, I demonstrate that these inferences can be explained in a strictly Gricean sense as *rational behavior*. To this end, I offer a procedure for constructing the context of utterance insofar as it is relevant for quantity reasoning as a game between speaker and hearer. I then give a new solution concept that improves on classical equilibrium approaches in that it uniquely selects the desired "empirically correct" play in these interpretation games by a chain of back-and-forth reasoning about players' behavior. To make this formal approach more accessible to a wider audience, I give a simple algorithm with the help of which the model's solution can be computed without having to do heavy calculations of probabilities, expected utilities and the like. This rationalistic approach subsumes and improves on recent exhaustivity-based approaches. It makes correct and uniform predictions for quantity implicatures of various epistemic varieties, free choice readings of disjunctions, as well as a phenomenon tightly related to the latter, namely so-called "simplification of disjunctive antecedents". doi:10.3765/sp.4.1 <a href="http://semantics-online.org/sp-bib/franke-2011.bib">BibTeX info</a>
A Metal-Free Amination of Benzoxazoles – The First Example of an Iodide-Catalyzed Oxidative Amination of Heteroarenes
2011-06-21

An efficient transition-metal-free amination of benzoxazoles has been developed. With catalytic amounts of tetrabutylammoniumiodide (TBAI), aqueous solutions of H(2)O(2) or TBHP as co-oxidant and under mild reaction conditions, highly desirable 2-aminobenzoxazoles were isolated in excellent yields of up to 93%. First mechanistic experiments indicate the in situ iodination of the secondary amine as the putative mode of activation.
Spatial Resolution and Perception of Patterns Mediated by a Subretinal 16-Electrode Array in Patients Blinded by Hereditary Retinal Dystrophies
2011-06-21

Subretinal electric stimulation can yield reliable, predictable percepts. Patterned perception is feasible, enabling blind persons to recognize shapes and discriminate different letters. Stimulation paradigms must be optimized, to further increase spatial resolution, demanding a better understanding of physical and biological effects of single versus repetitive stimulation (ClinicalTrials.gov number, NCT00515814).
Inhibition of DNA gyrase and DNA topoisomerase IV of Staphylococcus aureus and Escherichia coli by aminocoumarin antibiotics
2011-06-21

The study provides insights about the substituents that are important for the inhibitory activity of aminocoumarins against the target enzymes, which will facilitate the rational design of improved antibiotics.
Testosterone suppresses phospholipase D, causing sex differences in leukotriene biosynthesis in human monocytes
2011-06-21

ABSTRACT Sex disparities in inflammation have been reported, but the cellular and molecular basis for these discrepancies is unknown. Monocytes are central effector cells in immunity and possess high capacities to produce proinflammatory leukotrienes (LTs). Here, we investigated sex differences in the activation of 5‐lipoxygenase (5‐LO), the key enzyme in LT biosynthesis, in human peripheral monocytes. In cells from females, 5‐LO product formation was 1.8‐fold higher than in cells from males, as evaluated by HPLC. When female monocytes were resuspended in plasma from males, 5‐LO products were significantly lower than in female plasma. Interestingly, 5α‐dihydrotestosterone (5α‐DHT, 10 nM) repressed LT synthesis in female cells down to the levels observed in males, while estradiol (100 nM) was without effect, and progesterone (100 nM) caused only a slight inhibition. 5α‐DHT (10 nM) caused ERK phosphorylation and inhibition of phospholipase D (PLD), as evaluated by Western blot and measurement of PLD activity via radioenzymatic diacylglyceride (DAG) and nonradioactive choline assays. Accordingly, PLD activity and DAG formation were 1.4‐ to 1.8‐fold lower in male vs. female monocytes connected to increased ERK phosphorylation. Our data indicate that ERK activation by androgens in monocytes represses PLD activity, resulting in impaired 5‐LO product formation due to lack of activating DAGs.—Pergola, C., Rogge, A., Dodt, G., Northoff, H., Weinigel, C., Barz, D., Rådmark, O., Sautebin, L., Werz, O. Testosterone suppresses phospholipase D, causing sex differences in leukotriene biosynthesis in human monocytes. FASEB J. 25, 3377–3387 (2011). www.fasebj.org
Self-Resistance and Cell Wall Composition in the Glycopeptide Producer Amycolatopsis balhimycina
2011-06-21

ABSTRACT The prevailing resistance mechanism against glycopeptides in Gram-positive pathogens involves reprogramming the biosynthesis of peptidoglycan precursors, resulting in d -alanyl- d -lactate depsipeptide termini. Amycolatopsis balhimycina produces the vancomycin-like glycopeptide balhimycin and therefore has to protect itself from the action of the glycopeptide. We studied the roles of the accessory resistance gene orthologs vanY b , vnlR b , and vnlS b , which are part of the balhimycin biosynthetic gene cluster (represented by the subscript “b”). The VanY b carboxypeptidase cleaved the terminal d -Ala from peptidoglycan precursors, and its heterologous expression enhanced glycopeptide resistance in Streptomyces coelicolor . The VanRS-like two component system VnlRS b was not involved in glycopeptide resistance or in the expression of the vanHAX glycopeptide resistance genes. Mature A. balhimycina peptidoglycan contained mainly tri- and tetrapeptides, with only traces of the d -Ala- d -Ala-ending pentapeptides that are binding sites for the antibiotic produced. The structure of the peptidoglycan precursor is consistent with the presence of vanHAX genes, which were identified outside the balhimycin synthesis cluster. Both wild-type and non-antibiotic-producing mutant strains synthesized peptidoglycan precursors ending mainly with d -Lac, indicating constitutive synthesis of a resistant cell wall. A. balhimycina could provide a model for an ancestral glycopeptide producer with constitutively expressed resistance genes.
Learning How to Identify Speciesin a Situated Learning Scenario:Using Dynamic-StaticVisualizations to Prepare Studentsfor Their Visit to The Aquarium
2011-06-21

This study investigated whether studying dynamic-static visualizations prepared first-year Biology students better for an out-of-classroom experience in an aquarium than learning how to identify species with more traditional instructional materials. During an initial classroom phase, learners either watched underwater videos of 15 freshwater fish species (video-group, n=46) or they were asked to identify preserved specimens of the same fish with the help of a dichotomous identification key (key-group, n=43). Subsequently, all students were asked to identify the taught species during their visit to the aquarium. Our results indicate that the video-group was able to identify more species correctly than the key-group directly after the classroom instruction, whereas both groups performed equally well after the aquarium visit.
High-Level Fluorescence Labeling of Gram-Positive Pathogens
2011-06-22

Fluorescence labeling of bacterial pathogens has a broad range of interesting applications including the observation of living bacteria within host cells. We constructed a novel vector based on the E. coli streptococcal shuttle plasmid pAT28 that can propagate in numerous bacterial species from different genera. The plasmid harbors a promoterless copy of the green fluorescent variant gene egfp under the control of the CAMP-factor gene (cfb) promoter of Streptococcus agalactiae and was designated pBSU101. Upon transfer of the plasmid into streptococci, the bacteria show a distinct and easily detectable fluorescence using a standard fluorescence microscope and quantification by FACS-analysis demonstrated values that were 10-50 times increased over the respective controls. To assess the suitability of the construct for high efficiency fluorescence labeling in different gram-positive pathogens, numerous species were transformed. We successfully labeled Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus dysgalactiae subsp. equisimilis, Enterococcus faecalis, Enterococcus faecium, Streptococcus mutans, Streptococcus anginosus and Staphylococcus aureus strains utilizing the EGFP reporter plasmid pBSU101. In all of these species the presence of the cfb promoter construct resulted in high-level EGFP expression that could be further increased by growing the streptococcal and enterococcal cultures under high oxygen conditions through continuous aeration.
OCCUPATIONAL MOBILITY AND DEVELOPMENTS OF INEQUALITY ALONG THE LIFE COURSE
2011-06-22

ABSTRACT On the basis of inter-cohort comparisons, this paper describes patterns of intra-generational occupational mobility in Germany and their long-term trends since World War II. It also presents conceptual links between individual mobility and developments of inequality along the life course, with a special focus on the question of the extent to which employment careers are characterised by specific forms of cumulative advantage and disadvantage. Finally, it is asked how intra-generational developments are related to inter-generational social mobility. The paper also discusses how mobility patterns can be linked to specific institutions which – together with labour market conditions – are crucial determinants of the development of inequality within a cohort. In its empirical part, the paper presents evidence from cohort-specific analyses based on life-course data from a broad range of West German birth cohorts.
Flower visitors ofAechmea nudicaulis(Bromeliaceae): species richness, visitation frequency, and interactions in different habitats of southern Brazil
2011-06-22

The present study aimed to record all flower visitors of Aechmea nudicaulis (Bromeliaceae) and their foraging behavior as well as their role in animal–plant and animal–animal relationships, and to assess temporal pattern of visitation on flowers. In order to estimate the influence of habitat on species richness and abundance, we compared the diversity and visitation frequency of flower visitors to Ae. nudicaulis in three different habitat types – secondary forest, low and high vegetation restinga – in Paraná and Santa Catarina. We recorded 40 taxa of flower visitors. The secondary forest sites showed highest, the restinga habitats lowest species richness and visitation frequency. Main visitor groups were birds, bees and butterflies. The species spectrum differed considerably among habitats and similarity was lowest between the two secondary forests in Paraná and Santa Catarina. We recorded mainly hummingbirds (54.6% of all visits) as flower visitors in Paraná, whereas flowers in Santa Catarina were dominated by bees (44.5–59.7% of all visits). The temporal pattern of visits was similar at all sites; visits occurred mainly in the morning hours. However, there was no significant correlation between number of visits and hour of day. In contrast to the expectation that Ae. nudicaulis flowers, due to their morphology, attract mainly hummingbirds, they were visited by a much wider spectrum of animal species, mainly insects and arachnids, varying according to habitat. Our findings answer the question of what attracts animals to the inflorescences and elucidate the nature of some of the manifold interactions between Ae. nudicaulis and its associated flower visitors.
The termination region of high-mass microquasar jets(corrigendum)
2011-06-22

1 Dublin Institute for Advanced Studies, 31 Fitzwilliam Place, Dublin 2, Ireland e-mail: valenti@cp.dias.ie 2 Dept. d’Astronomia i Astrofisica, Universitat de Valencia, C/ Dr. Moliner 50, 46100, Burjassot (Valencia), Spain e-mail: Manel.Perucho@uv.es 3 Institut fur Astronomie und Astrophysik, Universitat Tubingen, Sand 1, 72076 Tubingen, Germany 4 INTEGRAL Science Data Centre, Universite de Geneve, Chemin d’Ecogia 16, 1290 Versoix, Switzerland e-mail: pol.bordas@uni-tuebingen.de
The histone acetyltransferase p300 promotes intrinsic axonal regeneration
2011-06-23

Axonal regeneration and related functional recovery following axonal injury in the adult central nervous system are extremely limited, due to a lack of neuronal intrinsic competence and the presence of extrinsic inhibitory signals. As opposed to what occurs during nervous system development, a weak proregenerative gene expression programme contributes to the limited intrinsic capacity of adult injured central nervous system axons to regenerate. Here we show, in an optic nerve crush model of axonal injury, that adenoviral (cytomegalovirus promoter) overexpression of the acetyltransferase p300, which is regulated during retinal ganglion cell maturation and repressed in the adult, can promote axonal regeneration of the optic nerve beyond 0.5 mm. p300 acetylates histone H3 and the proregenerative transcription factors p53 and CCAAT-enhancer binding proteins in retinal ganglia cells. In addition, it directly occupies and acetylates the promoters of the growth-associated protein-43, coronin 1 b and Sprr1a and drives the gene expression programme of several regeneration-associated genes. On the contrary, overall increase in cellular acetylation using the histone deacetylase inhibitor trichostatin A, enhances retinal ganglion cell survival but not axonal regeneration after optic nerve crush. Therefore, p300 targets both the epigenome and transcription to unlock a post-injury silent gene expression programme that would support axonal regeneration.
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
2011-06-23

Abstract Summary: The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. Availability: KEGGtranslator is freely available as a JavaTM Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application. Contact: clemens.wrzodek@uni-tuebingen.de Supplementary information: Supplementary data are available at Bioinformatics online.
Gender-Specific Interplay of Signaling through β-Catenin and CAR in the Regulation of Xenobiotic-Induced Hepatocyte Proliferation
2011-06-24

Aberrant signaling through the Wnt/β-catenin pathway is a critical determinant in human and rodent liver carcinogenesis and generally accepted to be a potent driver of proliferation. Xenobiotic agonists of the constitutive androstane receptor (CAR) induce massive acute hyperplasia of mouse liver and facilitate the outgrowth of hepatocellular carcinomas with activated β-catenin. In the present study, the interplay of β-catenin-dependent and CAR-dependent signaling in the liver and its effect on hepatocyte proliferation were analyzed in transgenic mice with hepatocyte-specific knockout of Ctnnb1 (encoding β-catenin) following treatment with two CAR agonists, 1,4-bis[2-(3,5-dichloropyridyloxy)]-benzene (TCPOBOP) and phenobarbital. Hepatocyte-specific knockout of β-catenin inhibited CAR agonists-induced hepatocyte proliferation in male mice. By contrast, the proliferative effect of CAR agonists was strongly augmented in female β-catenin knockout animals. This was due to prolonged proliferation of the knockout hepatocytes. CAR-mediated hepatocyte proliferation was, at least in part, dependent on estrogen signaling and was associated with enhanced expression of FoxM1 and elevated activity of the PDK1/p90RSK pathway. In conclusion, our study shows that gender-specific factors determine whether β-catenin signaling plays a pro- or an antiproliferative role in the regulation of mouse hepatocyte proliferation induced by CAR agonists.
Automatic Sentiment Classification of Product Reviews Using Maximal Phrases Based Analysis
2011-06-24

In this paper we explore the use of phrases occurring maximally in text as features for sentiment classification of product reviews. The goal is to find in a statistical way representative words and phrases used typically in positive and negative reviews. The approach does not rely on predefined sentiment lexicons, and the motivation for this is that potentially every word could be considered as expressing something positive and/or negative in different situations, and that the context and the personal attitude of the opinion holder should be taken into account when determining the polarity of the phrase, instead of doing this out of particular context.
Evidence for direct binding of glycerol to photosystem I
2011-06-25

The interaction between glycerol and photosystem I (PSI) was investigated using low temperature single‐molecule spectroscopy. PSI complexes were dissolved in three different solutions: in buffer solution, in 66% glycerol/buffer solution, and in 66% glycerol/buffer solution that was afterwards diluted by buffer; the final glycerol concentration was &lt;1‰. Mean fluorescence spectra and intercomplex heterogeneity of PSI complexes in 66% glycerol/buffer solution and in the re‐diluted solution show high similarity, but differ from complexes in buffer solution indicating that the glycerol concentration is not the determining factor modifying the spectral properties. However, the exposure of PSI to a high glycerol concentration during sample preparation affects PSI and the effect is maintained if glycerol is removed from the solution.